Category Archives: Cell Biology

Enduring research: The constant threat of influenza virus outbreaks – Open Access Government

In light of the on-going global SARS-CoV-2 outbreak, that is keeping world health hostage, severely paralysing the world economy and strongly restricting social life, we are now experiencing the impact of a pandemic and how much the life as we know it depends on the options we have to stand up against such threats. This becomes even more relevant when one considers that this virus is just one of a multitude of viral foes with highly devastating potential.

The SARS-CoV-2 belongs to the large group of viruses that possess an RNA genome and has made its way from the animal kingdom into humans causing a zoonosis, which has spread around the world. The vast majority of newly emerging and re-emerging infectious diseases are caused by RNA viruses, with West Nile-, Ebola-, influenza-, and SARS viruses being prominent examples. RNA viruses have an enormous genetic plasticity, facilitating rapid adaptation of animal RNA viruses to new hosts including humans and rapid development of resistance against (directly acting) antiviral drugs. Such zoonotic RNA viruses may cause major outbreaks and severe disease in humans, especially in cases where there is no pre-existing immunity in the human population, exemplified by the current pandemic.

As such, the influenza A viruses (IAVs) stand out among these potential enemies. Their natural reservoir are aquatic birds and IAVs possess a great zoonotic potential as they can infect different avian and mammalian animal hosts, from which they can be transmitted to humans. This is based on their ability to gradually change their genome by mutation or even reassemble their genome segments during co-infection of the host cell with different IAV strains, resulting in a high genetic diversity1.

The devastating Spanish Flu led to the most dramatic pandemic of the last century, globally killing more than 25 million people within 25 weeks between 1918/1919. Subsequently, a new pandemic strain the Asian Flu emerged in 1957 leading to at least one million fatalities. In 1968, the pandemic Hong Kong Flu emerged, resulting in about one million deaths. In 1977, Russian Flu spread worldwide, causing severe infections in humans with a 50% fatality rate among school-aged children. In 2009, a reassortant IAV with a unique genome constellation most likely generated in pigs led to the first pandemic of the current century, known as Swine Flu [1 and references therein].

Among the available options for control and prevention of IAV infections, vaccination is still the primary option and the most effective method to combat IAV infection. As seen with the efforts undertaken to develop a vaccine against SARS-CoV-2 this takes time and a potential vaccine will not be available at the start of an outbreak caused by a yet unknown virus. To establish the first line of defence against newly emerging IAV, for which vaccines are generally not available, potent and broadly acting antivirals are urgently needed. Ideally, these compounds should be widely available, have broad-spectrum activity against a range of IAV and be unlikely to cause viral resistance.

Currently, all approved and most of the antivirals in development act directly against the virus [1 and references therein]. As IAVs can quickly adapt to these directly acting selective pressures, such therapeutic approaches lose their effectiveness over time. Nevertheless, all viruses absolutely depend on services provided by the infected host cell. To address the problem of viral resistance in antiviral drug development, the work of the authors pioneered in the identification and inhibition of specific cellular (rather than viral) functions/factors that are essential for IAV. The highly specific inhibition of cellular functions is expected to fulfil most, if not all, of the above requirements, preventing efficient viral replication when the respective cellular factor is impaired. The combined and long-lasting collaboration between the three laboratories of the authors has successfully demonstrated that this approach possesses a great potential to define novel and effective antivirals by in-depth basic molecular virological research.

In 2001, we demonstrated for the first time that a specific virus-induced intracellular signalling event the Raf/MEK/ERK cascade is essential for efficient production of infectious IAV progeny. IAV replicate their genomes by their own polymerases within the nucleus of the infected cell and thus need to export their genome from nucleus to the cell membrane where virus particles form to be released. Inhibition of the cascade by specific inhibitors, which block this pathway at the level of the kinase MEK results in nuclear retention of viral genome complexes (RNPs) and concomitantly inhibits virus production2. The relevance of this cascade for IAV was then further demonstrated in vivo in mice3 and moreover also for influenza B viruses (IBV), which together with IAV cause seasonal epidemics. Importantly, neither IAV nor IBV develops resistance under treatment4.

Analysis of the functional role of the cascade within the viral replication cycle established that cell membrane accumulation of the viral HA-protein triggers activation of the cascade and induces nuclear RNP export. This represents an auto-regulative spatial-temporal coordination of nuclear RNP export to a point when all viral components are ready for virus budding5. More recent results indicate that the cascade does not affect nuclear export in general, for example, by interfering with the cellular nuclear export machinery, but rather specifically acts on the export of viral vRNPs by controlling specific modifications of viral proteins.

Interestingly, among human IAVs, those possessing a higher polymerase activity lead to more HA production and enhanced activation of the HA-induced Raf/MEK/ERK signal cascade6. Apart from tissue damage caused by the virus lytic replication, an imbalanced overproduction of antiviral cytokines can cause severe lung damage as observed in human infections with highly pathogenic avian influenza viruses (HPAIV). We showed that inhibition of the signalling cascade decreased both, virus titres and cytokine expression. This was not only true in vitro, but also in infected mice. Hereby we could demonstrate for the first time that IAV titres and pro-inflammatory cytokine expression can be modulated simultaneously7.

We continued our investigations with the experimental MEK inhibitor U0126, validating its ability to suppress propagation of the 2009 pandemic IAV (H1N1pdm09), as well as HPAIV in cell culture and also in vivo in the mouse lung. Notably, U0126 impaired all tested IAV strains, including oseltamivir (Tamiflu) resistant variants. Furthermore, treatment of mice with U0126 via the aerosol route led to the protection of IAV-infected mice against a 100x lethal viral challenge. Moreover, no adverse effects were detected in cell culture or in the mouse8.

As U0126 is an experimental substance, we aimed to elucidate the efficacy of a compound that was tested in clinical investigations aiming to translate our research into the development of a therapeutic approach. In consequence, we studied the antiviral potential of the clinically tested MEK inhibitor Cl-1040 against various IAV. CI-1040 was originally developed as an anti-tumour drug where it showed low toxicity. We found that Cl-1040 significantly reduces virus titres in vitro and is effective against a broad range of IAV strains, including HPAIV, as well as against a Tamiflu-resistant IAV strain and, that it reduces IAV lung titres in vivo a mouse model. Importantly, the treatment window for Cl-1040 expands up to 48 h post-infection when Tamiflu treatment has lost its effectiveness9.

Most recently we compared the antiviral potency of CI-1040 versus its major active metabolite ATR-002, in vitro as well as in the mouse model. In cell culture assays, approximately 10-fold more ATR-002 is needed for the same antiviral activity as CI-1040. Interestingly, considerably lower concentrations of ATR-002 were required to reduce the viral load in vivo. Pharmacokinetic studies showed a far higher bioavailability for ATR-002 than for CI-1040 demonstrating the in vivo superiority of ATR-002 as an antiviral agent, despite its weaker cell membrane permeability10.

Since the Raf/MEK/ERK pathway is activated by many RNA viruses11, it was a valid assumption that also other viruses may exploit this signalling pathway and may be sensitive to MEK inhibition. This was confirmed in studies on the replication of Borna Disease viruses12 or Respiratory Syncytial viruses13, which was efficiently blocked by MEK inhibition, albeit by mechanisms different of that found for IAV.

The enormous potential of inhibiting cellular MEK in the fight against RNA viruses becomes particularly relevant in the face of the COVID-19 crisis. Previous work by others has shown that the membrane-located S-protein of the 2003 SARS-CoV is involved in the induction of the Raf/MEK/ERK pathway. Furthermore, infection of cultured cells with mouse hepatitis virus (MHV) a murine coronavirus also activated the signal cascade, and the investigative MEK inhibitor U0126 significantly impaired MHV replication. The inhibitory effect of U0126 on MHV appeared to be a general phenomenon observed in all six different MHV strains and in three different cell types tested [11 and references within]. This tempts us to speculate that MEK inhibitors, such as ATR-002, could possibly be effective against SARS-CoV-2.

Meanwhile, our work is being actively translated into a therapeutic approach in collaboration with Atriva Therapeutics, Germany, and ATR-002 has by now undergone pharmacokinetic studies, as well as a very successful Phase I clinical study. This randomised, double-blind, placebo-controlled dose escalation study demonstrated the safety and tolerability of ATR-002 and the observed pharmacokinetic profile supports the intended once-daily regime for the further Phase II clinical development. Potential advantages of this host-targeting approach are the prolonged treatment window and the reduced potential of viral resistance, both compared to therapies that directly target viral structures.

Our brief summary recapitulating 19 years of collaborative work in basic virological research clearly shows that continuing funding of such efforts has a great potential to provide a health benefit to European societies.

Stephan Pleschka1*, Oliver Planz 2, Stephan Ludwig 3

1 Institute for Medical Virology, Justus Liebig University, Giessen, GermanyGerman Center for Infectious Research (DZIF), Partner site Giessen, Germany.

2 Institute of Cell Biology and Immunology, Eberhard Karls University Tuebingen, Germany.

3 Institute of Virology, Westfaelische-Wilhelms-University Muenster, Germany.

References

1 Mostafa A, Abdelwhab EM, Mettenleiter TC, Pleschka S. 2018. Zoonotic Potential of Influenza A Viruses: A Comprehensive Overview. Viruses 10.

2 Pleschka S, Wolff T, Ehrhardt C, Hobom G, Planz O, Rapp UR, Ludwig S. 2001. Influenza virus propagation is impaired by

inhibition of the Raf/MEK/ERK signalling cascade. Nat Cell Biol 3:301-305.

3 Olschlager V, Pleschka S, Fischer T, Rziha HJ, Wurzer W, Stitz L, Rapp UR, Ludwig S, Planz O. 2004. Lung-specific expression of active Raf kinase results in increased mortality of influenza A virus-infected mice. Oncogene 23:6639-6646.

4 Ludwig S, Wolff T, Ehrhardt C, Wurzer WJ, Reinhardt J, Planz O, Pleschka S. 2004. MEK inhibition impairs influenza B virus propagation without emergence of resistant variants. FEBS Lett 561:37-43.

5 Marjuki H, Alam MI, Ehrhardt C, Wagner R, Planz O, Klenk HD, Ludwig S, Pleschka S. 2006. Membrane accumulation of

influenza A virus hemagglutinin triggers nuclear export of the viral genome via protein kinase Calpha-mediated activation of ERK signaling. J Biol Chem 281:16707-16715.

6 Marjuki H, Yen HL, Franks J, Webster RG, Pleschka S, Hoffmann E. 2007. Higher polymerase activity of a human influenza virus enhances activation of the hemagglutinin-induced Raf/MEK/ERK signal cascade. Virol J 4:134.

7 Pinto R, Herold S, Cakarova L, Hoegner K, Lohmeyer J, Planz O, Pleschka S. 2011. Inhibition of influenza virus-induced NF-kappaB and Raf/MEK/ERK activation can reduce both virus titers and cytokine expression simultaneously in vitro and in vivo. Antiviral Res 92:45-56.

8 Droebner K, Pleschka S, Ludwig S, Planz O. 2011. Antiviral activity of the MEK-inhibitor U0126 against pandemic H1N1v and highly pathogenic avian influenza virus in vitro and in vivo. Antiviral Res 92:195-203.

9 Haasbach E, Muller C, Ehrhardt C, Schreiber A, Pleschka S, Ludwig S, Planz O. 2017. The MEK-inhibitor CI-1040 displays a broad anti-influenza virus activity in vitro and provides a prolonged treatment window compared to standard of care in vivo. Antiviral Res 142:178-184.

10 Laure M, Hamza H, Koch-Heier J, Quernheim M, Muller C, Schreiber A, Muller G, Pleschka S, Ludwig S, Planz O. 2020.

Antiviral efficacy against influenza virus and pharmacokinetic analysis of a novel MEK-inhibitor, ATR-002, in cell culture and in the mouse model. Antiviral Res 178:104806.

11 Pleschka S. 2008. RNA viruses and the mitogenic Raf/MEK/ERK signal transduction cascade. Biol Chem 389:1273-1282.

12 Planz O, Pleschka S, Oesterle K, Berberich-Siebelt F, Ehrhardt C, Stitz L, Ludwig S. 2003. Borna disease virus nucleoprotein

interacts with the CDC2-cyclin B1 complex. J Virol 77:11186-11192.

13 Preugschas HF, Hrincius ER, Mewis C, Tran GVQ, Ludwig S, Ehrhardt C. 2019. Late activation of the Raf/MEK/ERK pathway is required for translocation of the respiratory syncytial virus F protein to the plasma membrane and efficient viral replication. Cell Microbiol 21:e12955.

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Enduring research: The constant threat of influenza virus outbreaks - Open Access Government

Magenta Therapeutics and Beam Therapeutics Announce Collaboration to Evaluate Targeted Antibody-Drug Conjugate (ADC) MGTA-117 as Conditioning Regimen…

CAMBRIDGE, Mass.--(BUSINESS WIRE)--Magenta Therapeutics (Nasdaq: MGTA) and Beam Therapeutics (Nasdaq: BEAM) today announced a non-exclusive research and clinical collaboration agreement to evaluate the potential utility of MGTA-117, Magentas novel targeted ADC for conditioning of patients with sickle cell disease and beta-thalassemia receiving Beams base editing therapies. Beam is pursuing two differentiated base editing approaches to treat hemoglobinopathies: its hereditary persistence of fetal hemoglobin (HPFH) program to precisely and robustly elevate fetal hemoglobin, which could be used in treatments for both sickle cell disease and beta-thalassemia, as well as a novel approach to directly correct the sickle causing point mutation (Makassar).

Conditioning is a critical component necessary to prepare a patients body to receive the edited cells, which carry the corrected gene and must engraft in the patients bone marrow in order to be effective. Todays conditioning regimens rely on nonspecific chemotherapy or radiation, which are associated with significant toxicities. MGTA-117 precisely targets only hematopoietic stem and progenitor cells, sparing immune cells, and has shown high selectivity, potent efficacy, wide safety margins and broad tolerability in non-human primate models. MGTA-117 may be capable of clearing space in bone marrow to support long-term engraftment and rapid recovery in patients.

Beam has demonstrated the ability to edit individual DNA bases in hematopoietic stem cells at high efficiency and with little impact on the viability of edited cells relative to unedited cells using its novel base editing technology. Combining MGTA-117 with Beams HPFH and Makassar base editors could meaningfully advance the treatment of patients with sickle cell disease or beta-thalassemia.

We believe patients will benefit from a more precise process to remove hematopoietic stem cells and prepare them to receive genetic medicines. Magenta has developed targeted ADCs as the preferred modality for our conditioning programs, and we have designed MGTA-117 specifically to optimize it for use with a genetically-modified cell product delivered in a transplant setting, said Jason Gardner, D.Phil., president and chief executive officer, Magenta Therapeutics. Beams next-generation base editing technology complements our next-generation conditioning approach very well, and we are excited to combine these strengths to address the still-significant unmet medical needs of the sickle cell and beta-thalassemia patient communities.

Base editing has the potential to offer lifelong treatment for patients with many diseases, including sickle cell disease and beta-thalassemia. Our novel base editors create precise single base changes in genes without cutting the DNA, enabling durable correction of hematopoietic stem cells with minimal effects on cell viability or genomic integrity, said John Evans, chief executive officer of Beam. Combining the precision of our base editing technology with the more targeted conditioning regimen enabled by MGTA-117 could further improve therapeutic outcomes for patients suffering from these severe diseases. We look forward to partnering with the Magenta team to explore these novel technologies together.

Beam will be responsible for clinical trial costs related to development of Beams base editors when combined with MGTA-117, while Magenta will continue to be responsible for all other development costs of MGTA-117. Magenta will also continue to develop MGTA-117 in other diseases, including blood cancers and genetic diseases. Each company will retain all commercial rights to their respective technologies.

About MGTA-117

MGTA-117, Magentas most advanced conditioning program, is a CD117-targeted antibody engineered for the transplant setting and conjugated to amanitin, a toxin in-licensed from Heidelberg Pharma. It is designed to precisely deplete only hematopoietic stem and progenitor cells and has shown high selectivity, potent efficacy, wide safety margins and broad tolerability in non-human primate models, suggesting that it may be capable of clearing space in bone marrow to support long-term engraftment and rapid recovery in patients. Magenta plans to complete IND-enabling studies this year and initiate clinical studies in 2021. Magenta will continue to develop MGTA-117 in other diseases, including blood cancers and genetic diseases.

About Magenta Therapeutics

Magenta Therapeutics is a clinical-stage biotechnology company developing medicines to bring the curative power of immune system reset through stem cell transplant to more patients with autoimmune diseases, genetic diseases and blood cancers. Magenta is combining leadership in stem cell biology and biotherapeutics development with clinical and regulatory expertise, a unique business model and broad networks in the stem cell transplant world to revolutionize immune reset for more patients. Magenta is based in Cambridge, Mass. For more information, please visit http://www.magentatx.com. Follow Magenta on Twitter: @magentatx.

About Base Editing and Beam TherapeuticsBeam Therapeutics (Nasdaq: BEAM) is a biotechnology company developing precision genetic medicines through the use of base editing. Beams proprietary base editors create precise, predictable and efficient single base changes, at targeted genomic sequences, without making double-stranded breaks in the DNA. This enables a wide range of potential therapeutic editing strategies that Beam is using to advance a diversified portfolio of base editing programs. Beam is a values-driven organization focused on its people, cutting-edge science, and a vision of providing life-long cures to patients suffering from serious diseases. For more information, visit http://www.Beamtx.com.

Magenta Therapeutics Forward-Looking StatementsThis press release may contain forward-looking statements and information within the meaning of The Private Securities Litigation Reform Act of 1995 and other federal securities laws, including, without limitation, statements regarding the research and clinical collaboration agreement between Magenta and Beam, including the timing, progress and success of the collaboration contemplated under the agreement, the successful evaluation of MGTA-117 in conjunction with Beams base-editing therapies under the agreement, the anticipated cost allocation and other commercial terms under the agreement, Magentas strategy and business plan, the future development, manufacture and commercialization between Beam and Magenta as well as statements regarding expectations and plans for the anticipated timing of Magentas clinical trials and regulatory filings and the development of Magentas product candidates and advancement of Magentas preclinical programs. The use of words such as may, will, could, should, expects, intends, plans, anticipates, believes, estimates, predicts, projects, seeks, endeavor, potential, continue or the negative of such words or other similar expressions can be used to identify forward-looking statements. The express or implied forward-looking statements included in this press release are only predictions and are subject to a number of risks, uncertainties and assumptions, including, without limitation, risks set forth under the caption Risk Factors in Magentas most recent Annual Report on Form 10-K filed on March 3, 2020, as updated by Magentas most recent Quarterly Report on Form 10-Q and its other filings with the Securities and Exchange Commission, risks, uncertainties and assumptions regarding the impact of the COVID-19 pandemic to Magentas business, operations, strategy, goals and anticipated timelines, and risks, uncertainties and assumptions inherent in preclinical and clinical studies, including, without limitation, whether results from preclinical studies or earlier clinical studies will be predictive of the results of future trials and the expected timing of submissions for regulatory approval or review by governmental authorities. In light of these risks, uncertainties and assumptions, the forward-looking events and circumstances discussed in this press release may not occur and actual results could differ materially and adversely from those anticipated or implied in the forward-looking statements. You should not rely upon forward-looking statements as predictions of future events. Although Magenta believes that the expectations reflected in the forward-looking statements are reasonable, it cannot guarantee that the future results, levels of activity, performance or events and circumstances reflected in the forward-looking statements will be achieved or occur. Moreover, except as required by law, neither Magenta nor any other person assumes responsibility for the accuracy and completeness of the forward-looking statements included in this press release. Any forward-looking statement included in this press release speaks only as of the date on which it was made. We undertake no obligation to publicly update or revise any forward-looking statement, whether as a result of new information, future events or otherwise, except as required by law.

Beam Forward-Looking Statements

This press release contains forward-looking statements. Investors are cautioned not to place undue reliance on these forward-looking statements, including statements about the timing, progress and success of the collaboration contemplated under the agreement between Beam and Magenta, the successful evaluation of MGTA-117 in conjunction with Beams base-editing therapies under the agreement, the expected timing of filing INDs applications and the therapeutic applications of Beams technology. Each forward-looking statement is subject to risks and uncertainties that could cause actual results to differ materially from those expressed or implied in such statement. Applicable risks and uncertainties include the risks and uncertainties, among other things, regarding: the success in development and potential commercialization of our product candidates; Beams ability to obtain, maintain and enforce patent and other intellectual property protection for our product candidates; whether preclinical testing of our product candidates and preliminary or interim data from preclinical and clinical trials will be predictive of the results or success of ongoing or later clinical trials; that enrollment of clinical trials may take longer than expected; that Beams product candidates will experience manufacturing or supply interruptions or failures; that Beam will be unable to successfully initiate or complete the preclinical and clinical development and eventual commercialization of product candidates; that the development and commercialization of Beams product candidates will take longer or cost more than planned; the impact of COVID-19 on Beams business and the other risks and uncertainties identified under the heading Risk Factors and in Beams Annual Reports on Form 10-K for the year ended December 31, 2019 and in Beams Quarterly Report on Form 10-Q for the quarter ended March 31, 2020, and in any subsequent filings with the Securities and Exchange Commission. These forward-looking statements (except as otherwise noted) speak only as of the date of this press release. Factors or events that could cause Beams actual results to differ may emerge from time to time, and it is not possible for Beam to predict all of them. Beam undertakes no obligation to update any forward-looking statement, whether as a result of new information, future developments or otherwise, except as may be required by applicable law.

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Magenta Therapeutics and Beam Therapeutics Announce Collaboration to Evaluate Targeted Antibody-Drug Conjugate (ADC) MGTA-117 as Conditioning Regimen...

Novel DNA analysis will help to identify food origin and counterfeit food in the future – Baltic Times

Estonian scientists are developing a DNA-based method of analysis that enables them to identify food components and specify the origin of a foodstuff.

Bioinformatics specialists at the University of Tartu, in cooperation with the Competence Centre on Health Technologies, have published a research paper in the journal Frontiers in Plant Science in which they indicated the possibility to identify components in thermally processed food using DNA analysis even if the quantities were very small. The scientists analysed thermally processed cookies that contained a small amount of lupin flour. The DNA analysis provided reliable identification of lupin even when the lupin flour content in the dough was just 0.02%.

Food always contains the DNA traces of the plants, animals and microorganisms that have been used or that the food or its raw materials have come into contact with in the production process. DNA analysis can provide valuable information on the content, origin, safety and health benefits of food and will make the identification of counterfeit foods and non-compliances in the ingredients specified on the packaging more reliable in the future. For example, certain cases gained attention last year in which the origin of honey and the authenticity of Estonian honey needed verification. The novel DNA analysis would make it possible to solve such issues.

According to Kairi Raime, the lead author of the article, Research Fellow of Bioinformatics at the Institute of Molecular and Cell Biology and a doctoral student at the University of Tartu, their method is a major step forward in the development of DNA-based methods for food analysis. Our method helps to identify the actual biological contents and origins of food via DNA information and thus ensures the safety and authenticity of the food, she explained. Raime is planning to defend her PhD dissertation on the topic.

The DNA may be significantly degraded in processed food. Scientists extracted DNA from the cookies and analysed it using DNA sequencing technology. For the analysis of a single biscuit, approximately 20 million DNA sequences were obtained. Based on these, and by using bioinformatic analysis, it was possible to specify the DNA of the species found in the sample analysed. The main issue was the preparation of the DNA for sequencing, as the DNA is often degraded in food and even minute amounts of DNA molecules must be identified.

Kaarel Krjutkov, Head of the Precision Medicine Laboratory of the Competence Centre on Health Technologies and Senior Research Fellow of Molecular Medicine at the University of Tartu, whose laboratory was used to prepare the sequencing of the DNA extracted from the biscuits, noted that faking the DNA fingerprint of a food is complicated and expensive, and it is therefore cheaper to offer authentic food. People can see that in medicine, precise DNA analysis is already a reality, but in food industry and in the field of food safety, the golden age of DNA-based analysis is yet to come, Krjutkov remarked.

The research used a method based on short, unique DNA sequences (k-mers) for analysing genomic DNA data, which enables the scientists to quickly identify plant or bacterial DNA present in a food or an environmental sample. The Chair of Bioinformatics at the Institute of Molecular and Cell Biology at the University of Tartu has been developing competence in the bioinformatics of k-mers and DNA analysis over the last five years. The software developed in the Chair of Bioinformatics has been used both in medicine and for providing food safety.

The article authors earlier cooperation resulted in the NIPTIFY foetal chromosomal disorder test, which helps to detect, with almost 100% accuracy, the DNA sequences causing foetal Down syndrome in the mothers blood sample as early as the tenth week of pregnancy. The genome analysis method developed in the Chair of Bioinformatics is used to identify pathogenic bacteria, specify their disease-causing capabilities and predict antibiotic resistance. This enabled Maido Remm, Professor of Bioinformatics at the University of Tartu, and his working group to advise the management board of a production company contaminated with a dangerous strain and to help determine the spread of type ST1247 in the company during the listeria outbreak in autumn 2019.

According to Remm, the research article proves that DNA sequencing can also be used for identifying allergenic ingredients in processed food. DNA sequencing is a promising diagnostic method which makes it possible to quickly obtain precise information about food and the microbes around us, he said. The use of sequencing and k-mers makes it possible in a very short time to implement a diverse range of diagnostic tests that meet the needs of researchers and companies.

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Novel DNA analysis will help to identify food origin and counterfeit food in the future - Baltic Times

Hyderabads CCMB develops Covid test that can handle up to 50,000 times more samples – ThePrint

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Hyderabad: A new Covid-19 test developed by the Centre for Cellular and Molecular Biology (CCMB) can test 20,000-50,000 Covid-19 samples daily a breakthrough that could significantly enhance Indias testing capacity, according to the institutes director Rakesh Mishra.

In an interview to ThePrint, Mishra said if all goes well, the new Next Generation Sequencing (NGS) kit will be operational in about four weeks. It will change the game, he said.

Presently, cities like Hyderabad and Bengaluru are conducting about 1,000-2,000 tests every day, he said. In the last 24 hours, India conducted tests on 1.08 lakh samples.

According to Mishra, the new kit will offer diagnosis through sequencing of several pieces of the virus genetic material, and lessen the chances of inaccurate testing.

India is currently testing for Covid-19 through real-time polymerase chain reaction (RT-PCR) technique. In the current method, nasal swabs are taken from a person in VTM (viral transport medium). The liquid is taken from this, RNA (ribonucleic acid) is extracted and RT-PCR test is conducted, said Mishra.

The isolation of RNA makes RT-PCR expensive and more time-consuming. The NGS technique will do away with that, he said.

A collection centre can collect thousand samples in one go, as more than that can be a logistical problem, and we will collect samples from 20 to 50 centres, said the CCMB chief. The test results would come in two days and at one-third the cost but with the same amount of efficiency, he added.

The new testing module will also help in surveillance of Covid-19 suspects, he said. The Next Generation Sequencing will help in diagnosis and surveying the disease at a much faster rate, Mishra told ThePrint.

The RT-PCR test works by sequencing and then testing with a fluorescent dye just one sample at a time. The NGS tests are done under a similar mechanism, but the difference between it and single DNA sequencing (called Sanger sequencing) is the volume. The NGS method allows for virologists and technicians to sequence hundreds of thousands of samples in parallel due to the improved design of sequencing machines, which can hold multiple samples instead of just one.

This is a high-throughput process that saves both time and cost. Additionally, the improved machines also come with improved sensitivity and are capable of detecting the virus RNA with fewer chances of a false negative.

The project is in collaboration with Syngene, a Bengaluru-based company. The process for the kits approval from the Indian Council of Medical Research (ICMR), Indias nodal Covid-19 testing body, is underway, said the CCMB director.

The effort has come from the Hyderabad-based primary research institute, Council of Scientific and Industrial Research (CSIR) centre, which has been working on enhancing Covid-19 testing in India.

Also read: Cases, fatality rate or deaths per million, India in control of Covid: Niti Aayog expert

In response to ICMRs latest guidelines that focus on testing only symptomatic patients, Rakesh Mishra said, Testing is like seeing whats around us. If you see more, you will be more informed.

If you give me a choice, I will test everybody as it helps understand where to do a lockdown or where to resume business, he said.

Noting concerns about resources among governments, he said, If we test more, we will be in a better position. He added that healthcare workers, in particular, must be tested at least every two weeks.

With worlds eyes set on developing a Covid-19 vaccine as soon as possible, Mishra said the CCMB was also working on one. In an ideal scenario, the vaccine the institute is developing will be ready for use by the first half of next year, he added.

The research institute has established stable virus cultures using coronavirus from patients samples. This will help us in vaccine development and drug testing to fight Covid-19. Now we can confidently say that were done with a major chunk of the work as for isolating the infectious viruses from other isolates, said Mishra.

The CCMB, which cultures the virus in its labs, uses vero cells (from the kidney of monkeys) to establish cell lines to grow the virus for developing a vaccine.

We have a special Bio Safety level 3 lab where we culture the live virus, he said. CCMB is also using a version of the vero cell called E6. It is also getting human epithelial cells from the lungs from I-Step, another company in Bengaluru, in a joint collaboration. This is exactly from where the virus spreads so these cells help us study it properly, he said.

Out of a team of 60 people working on the vaccine, 45 are students of the institute who volunteered to be part of the process.

Also read:Covid patients with high blood pressure face double risk of death, says Chinese study

The novel coronavirus originated in mid-November to December in China, the CCMB director told ThePrint. The institute was able to calculate this based on the timing of the mutation rate.

The scientists working at the institute discovered that after the infection originated from Wuhan in China, it came to Southeast Asia in mid-February when a new clade emerged A3i, which is unique to India and Southeast Asia, and is the second most dominant in the country.

It contributes to 41 per cent of the infection among patients in the country, he said.

The two clades in India are A3i and A2a, which is known across the world. A clade is a cluster of SARS CoV-2 (novel coronavirus) that are similar in evolution and grouped together due to certain characteristic mutations.

Mishra said the virus reached Hyderabad first from where it spread in India. Although some isolated cases did come to Kerala from Wuhan, the major cases first arrived in Hyderabad and across Telangana followed by Tamil Nadu and some parts of Delhi before the lockdown was enforced on 25 March, he said.

From the mutation, it theoretically appears that it could affect it (the virus) by slowing down the spread and showing up in patients in a less symptomatic manner The virus will be less efficient. It may spread less efficiently, it may be less symptomatic. Either of the two can happen, he said, adding that its too early to tell but there is sufficient evidence to investigate this further.

The CSIR institute director also highlighted that CCMB is working on an alternative to plasma therapy, in partnership with a Hyderabad-based company and the University of Hyderabad.

Since we have an immense amount of inactivated virus to work on the vaccine, one can also inject that in large animals, say a horse, and make an antibody in the horse and collect it and use it as an antidote in patients to test it, he said.

A Hyderabad-based company is taking the virus from CCMB and using it to test in horses. It will be like replacing plasma therapy as one of the options to treat patients, so were hoping to get beneficial results from there too, he said, adding that horse antibodies have been used since 1890.

Talking about how scientific solutions have been overlooked in India, Rakesh Mishra said, We spend very little money on research, science and technology, but we need to realise solutions to problems lie in science.

Referring to how the economy world over has been hit due to coronavirus, he said the solutions will come from a lab. The government and big industrial houses have perhaps realised this amid the spread of Covid-19 a positive side-effect of the disease.

Also read:AstraZenecas cancer drug shows early signs of promise in treating severe Covid cases

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Hyderabads CCMB develops Covid test that can handle up to 50,000 times more samples - ThePrint

COVID-19 in India may have originated from Europe and Middle East: Study – Northeast Now

Researchers have claimed that the novel coronavirus in India may have originated from Europe, South Asia, Middle East and Oceania.

According to a study conducted by experts from the Indian Institute of Science (IISc), there is a close connection between source of virus and the countries that are most travelled by Indians.

The study which was conducted by MainakMondal, AnkitaLawarde and KumaravelSomasundaram from the Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, was published in the scientific journal Current Science.

The researchers carried out systematic analysis of genome sequences of Indian SARS-CoV-2 isolates and inferred the possible source of origin and important genetic variants of Indian viruses.

The analysis revealed that most Indian SARS-CoV-2 viruses (129 out of 137) show more similarity to that of specific countries, the study said.

In cluster A, Indian samples show more similarity to the viruses found in Oceania, Kuwait and South Asian samples, while in the cluster B, Indian samples show more similarity to mainly European and few numbers of Middle East/South Asian samples, it added.

The study stated that these results indicate that majority of Indian SARS-CoV-2 viruses have originated from Europe, Middle East, South Asia and Oceania regions.

The remaining Indian isolates have grouped with other clusters which contained most samples from China and East Asia.

This indicates that these viruses might have been introduced by Indian travellers from China and its neighbouring countries as they show close resemblance to ancestral Chinese virus, it added.

The possible spread of the SARS-CoV-2 virus to India through Middle East countries from Europe and Oceania regions cannot be ruled out, the study said.

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COVID-19 in India may have originated from Europe and Middle East: Study - Northeast Now

Developmental biology of Helicoforamina reveals holozoan affinity, cryptic diversity, and adaptation to heterogeneous environments in the early…

Abstract

The exceptional fossil preservation of the early Ediacaran Wengan biota provides a unique window on the interval of Earth history in which animal lineages emerged. It preserves a diversity of similarly ornamented encysted developmental stages previously interpreted as different developmental stages of one taxon. Although Helicoforamina wenganica is distinguished from other forms by a helical groove or canal, it has been interpreted as a developmental stage of cooccurring metazoan, nonmetazoan holozoan, or green algal taxa. Using x-ray microtomography, we show that Helicoforamina developed through one-, four-, and eight-cell stages, to hundreds and thousands of cells. Putative hatchlings are artifacts of incompletely preserved cyst walls. Our results preclude inclusion of Helicoforamina into life cycles assembled from other components of the Wengan biota but support a holozoan affinity. The similarly ornamented encysted forms shared among the diverse Wengan biota represent parallel adaptations to the temporally and spatially heterogeneous Ediacaran shallow marine environments.

The early Ediacaran Wengan biota of the Doushantuo Formation (609 million years old, Wengan County, Guizhou Province, Southwest China) is one of the few windows of exceptional preservation at the time in Earth history in which molecular clock analyses estimate the fundamental clades and body plans of animal to have emerged (1, 2). The biota is dominated by a diversity of developmental stages of microscopic organisms preserved with high fidelity, including not only component cells but also subcellular organelles and cytoplasmic structures (3). Hence, the Wengan biota affords a uniquely direct insight into the developmental evolution of early body plans. However, interpretation of the fossils has proven challenging because the component developmental stages lack the systematically distinctive features of body plans and because of the difficulty of disambiguating developmental stages of the same organism from developmental stages of disparate organisms (46). This is no more obvious than for the enigmatic Helicoforamina, which has variously been interpreted to represent nonmetazoan holozoans [holozoans include ichthyosporeans, filastereans, choanoflagellates, and metazoans (4)], green algae (7), or, most commonly, as the long-sought late embryonic stages of metazoans otherwise represented by Megasphaera (8).

Helicoforamina is part of a broader complex of embryo-like fossils that includes Tianzhushania, Megasphaera, Caveasphaera, and Spiralicellula (Fig. 1). Megasphaera is known from developmental stages representative of successive rounds of equal palintomy (9, 10), generally considered a senior synonym of Parapandorina (several to tens of cell stages) and Megaclonophycus (hundreds of cell stages) (11). Megasphaera ornata is distinguished in preserving an outer envelope with a cerebral, fractal, or dimpled surface ornamentation (Fig. 1, A to C) (10), but its distinction from other genera has been considered taphonomic rather than taxonomic (12). A similar envelope is encountered in co-occurring Spiralicellula (7) and Caveasphaera (13), but Spiralicellula is distinguished by its spiral cell morphology (Fig. 1, D and E) and Caveasphaera exhibits a different embryology of branching cell masses (Fig. 1, F to H) and shows no evidence of binary reductive palintomy (13). Co-occurring Helicoforamina wengica (Fig. 1, I to M) is of comparable size (500- to 900-m diameter, mean = 748.7 m, n = 314, SD = 94.3) to Megasphaera and has an envelope that is effectively indistinguishable from that of Megasphaera except for the presence of a dextrally coiled helical canal, groove, and/or sequence of pores that have been interpreted as a developing excystment structure, sites of cilia, or gas exchange (8). This helical structure is limited to the multilayered surface envelope (Fig. 1, I to T), completing three dextral loops in its course from one pole of the envelope to the other. However, the morphology of some specimens has been interpreted as evidence of uncoiling and invagination, such that the helical structure is imposed on natural internal molds of the envelope (8).

(A to C) Megasphaera, scanning electron microscopy (SEM) images (43). (A) NIGP127672. (B) NIGP127673. (C) NIGP127674. (D and E) Spiralicellula, SEM images. (D) NIGP127675. (E) NIGP127676. (F to H) Caveasphaera (13). (F) SEM image, NIGP171728. (G and H) Surface renderings. (G) NIGP171725. (H) NIGP171726. (I to M) Helicoforamina, surface renderings. (I) NIGP173059. (J) NIGP173060. (K) NIGP173061. (L) NIGP173062. (M) NIGP173063. (N to Q) Virtual sections of (I) to (L), respectively. (R) Transparent models of (L), showing shrunken internal body. (S and T) Magnifications of (N) and (P), respectively, showing the detail of the histology of the envelopes at the spots where the helical canals and pores developed. (U) Magnification of (Q), showing putative subcellular structures within the internal body. Scale bars, (A) 154 m, (B) 134 m, (C) 150 m, (D) 190 m, (E) 210 m, (F) 87 m, (G) 118 m, (H) 168 m, (I) 137 m, (J and O) 140 m, (K) 132 m, (M) 150 m, (L, Q, and R) 114 m, (N) 135 m, (P) 147 m, (S) 45 m, (T) 33 m, and (U) 30 m.

In its first detailed description, Xiao et al. (8) entertained two interpretations; one, which was later adopted by Huldtgren et al. (4), posited that Helicoforamina represented a one-cell egg that developed into the multicelled Spiralicellula (Fig. 2A), which is composed of cells that are similarly dextrally spiraled. This was effectively dismissed on the observation that the spirals in Spiralicellula complete only two loops of the cell (Fig. 1, D and E), do not always extend between poles, and there is no evidence for the transformation of the inner body of Helicoforamina and the multiple helical cells of Spiralicellula. In their preferred hypothesis, Xiao et al. (8) interpreted Helicoforamina as the postblastula developmental product of Megasphaera that, in turn, developed into Sinocyclocyclicus, a co-occurring tubular body fossil interpreted as a cnidarian (Fig. 2B) (14, 15). If correct, they argued that intermediate forms would be discovered demonstrating the reorganization of Megaclonophycus-stage blastomeres into a Helicoforamina helical inner body (8). Tang et al. (16) suggested that Helicoforamina and Spiralicellula represent embryos of Eoandromeda, which they compared to adult octocorals and ctenophores (Fig. 2C). Wang et al. (17) rejected linking Helicoforamina and Sinocyclocyclicus on the basis of the autapomorphic helical structure, preferring to interpret Helicoforamina as a foraminifer, with the helically arranged pores representing sites for extrusion of pseudopodia. Zhang and Pratt (7) interpreted Helicoforamina and Spiralicellula as stages in alternating sexual and asexual life cycles of a chlorophyceaean alga (Fig. 2D), based principally on the inferred ecology of the environment in which they lived, their comparable abundance, and the resemblance of their thick ornamented cyst wall to the zygospores of Chlorophyceae.

(A to D) Various life cycles for Helicoforamina proposed previously. (A) Helicoformina as one-cell egg of multicellular Spiralicellula (4). (B) Helicoforamina as an embryo of tubular microfossils Sinocyclocyclicus at postblastula stage (8). (C) Helicoforamina as an embryo of Eoandromeda (16). (D) Helicoforamina and Spiralicellula as stages in alternating sexual (yin) and asexual (yang) phases of the life cycle of a chlorophyceaean alga (7). (E) A simplified phylogenetic tree of Holozoa, with fungi as the outgroup. The potential placements for Helicoforamina in the holozoan tree are indicated in cyan.

In large part, this phylogenetic controversy arises because so little is known about the biology of Helicoforamina. Tomographic analyses of Megasphaera and of Spiralicellula have yielded further insights into their developmental biology, demonstrating unequivocally that, like Megasphaera, cells in Spiralicellula were nucleated and underwent binary and equal reductive palintomy (3, 4). However, there have been no further insights into the biology of Helicoforamina and, thus, no data to marshal in tests of a developmental link to co-occurring taxa. To remedy this deficit, we undertook tomographic analysis of a collection of 327 specimens of Helicoforamina, revealing specimens that harbor cells (Figs. 3 and 4) arranged either into a tight tetrad (Fig. 3, D to H), an octad (Fig. 3, I to K), or hundreds of rounded and dispersed cells (Fig. 4, A to D). These are equivalent to the early palintomic stages of Megasphaera and Spiralicellula; hence, we reject the hypothesis of a developmental link between Helicoforamina, Megasphaera, and Spiralicellula, which must, rather, represent equivalent developmental stages of disparate taxa. Furthermore, our results provide conclusive evidence that the similar nature of the envelope ornament, which inspired synonymy of Megasphaera and Helicoforamina, belies a diversity of taxa. Thus, the diversity of taxa represented by the Wengan assemblage must be much greater than previously thought.

(A to C) NIGP173064, single-cell stage. (D to F) NIGP173065, four-cell stage. (G and H) NIGP173066, four-cell stage. (I to K) NIGP173067, eight-cell stage. (A, D, G, and I) Surface renderings. (B, E, H, and J) Virtual sections showing internal structures. (C, F, and K) Transparent models showing nucleus and cells. (J) A sketch of (J), showing the cell boundaries. The arrow in (B) indicates the nucleus. Scale bars, (A to C) 174 m, (D to F) 120 m, and (G to K) 145 m.

(A to C) NIGP173068; (E to G) NIGP173069; (I to K) NIGP173070. (A, E, G, and I) Surface renderings. (B, F, and J) Virtual sections. (C and K) Transparent models showing internal cells or shrunk inner bodies. (D, H, and L) Close-up views of (B), (F), and (J), respectively, showing multicellular structures. Scale bars, (A and C) 150 m, (B) 142 m, (D) 50 m, (E and G) 140 m, (F) 170 m, (H) 42 m, (I to K) 165 m, and (L) 45 m.

We obtained submicrometer-scale tomographic data for more than 300 specimens of Helicoforamina wenganica representative of known morphological and taphonomic range, based on a rich fossil assemblage from 54 Quarry in the Baiyan-Gaoping anticline of Wengan County, Guizhou Province, South China (18). Specimens vary in terms of the extent of the helically arranged pits, canal, or groove, but also in terms of the preserved thickness of the outer wall (Figs. 1 and 3 to 6) and the degree of postmortem shrinkage (e.g., Fig. 5A). In the best-preserved specimens, the outer wall is thick (12 to 31 m) and multilayered (e.g., Fig. 1, I to L and N to Q), but in others, the outer wall is incomplete (e.g., Fig. 1M) or delaminated with intervening voids (e.g., Fig. 1N, Q, and S) or void-filling diagenetic cements (e.g., Fig. 5, B and J). Consequently, the characteristic helically arranged channel, canal, or pores of Helicoforamina vary in the extent to which they penetrate the outer wall, incompletely in well-preserved specimens and completely in specimens where the inner layers are absent. In the best-preserved specimens, the inner surface of the outer wall is unaffected by the helical channel, canal, or pores (Fig. 1, N, O, and S), or the inner surface exhibits a broad convexity to accommodate an associated increase in the thickness of the outer wall (e.g., Fig. 1, P and T). Where the outer wall has delaminated (e.g., Fig. 1, N and S), it can exhibit much greater variation in thickness, and this has a concomitant impact on the morphology of natural endocasts, which vary from spherical to a more approximately helical (Fig. 6). The helical endocasts are an artifact of differential compaction of a delaminated outer wall; the outer wall retains its thickness around the helical canals but is otherwise compacted, resulting in convex bulges into the central lumen associated with the helical canal (Fig. 6, I to L). In many specimens, the outer wall is entirely absent, or there is a pseudowall composed of a late diagenetic crust in a more highly x-ray attenuating mineral phase (e.g., Fig. 5, C and K). The helical channel or canal can be preserved; nevertheless (Fig. 5, C to G and K to O), given that no aspects of internal biology are preserved in these specimens, we presume that the histology of the outer wall is absent because it is not preserved rather than because it has not developed.

(A) NIGP173071. (B) NIGP173072. (C) NIGP173073. (D) NIGP173074. (E) NIGP173075. (F) NIGP173076. (G) NIGP173077. (H) NIGP173078. (A to H) Surface renderings. (I to P) Virtual sections of (A) to (H), respectively, showing internal structures. Scale bars, (A, B, I, and J) 200 m, (C and K) 175 m, (D and L) 187 m, (E and M) 170 m, (F and N) 185 m, and (G, O, H, and P) 165 m.

(A) NIGP173079. (E) NIGP173080. (I) NIGP173081. (A, E, and I) Surface renderings. (B, F, and J) Virtual sections of (A), (E), and (I), respectively. (C and G) Sketches of (B) and (F), respectively, showing the relationship between the inner wall of the envelopes and the inner bodies. The arrows indicate the positions of the groove. (D and H) Close-up views of (B) and (F), respectively, showing the boundaries between the inner wall and inner bodies. (K) Transparent model of (I), showing internal cells. (L) Transparent model of internal cells. Scale bars, 50 m for (D) and (H), 150 m for the others.

Beneath the outer wall, the specimens are invariably solid and almost always show evidence of multiple phases of void-filling cement, manifest as mineral phases with different x-ray attenuation profiles. These vary from fine-grained and largely homogenous (Fig. 5, E and M) to clotted fabrics (Fig. 6, E to H), to layered anatomosing geode-like void-filling patterns of calcium phosphate mineralization (Fig. 5, F and N). Some specimens retain open voids (e.g., Fig. 5, G and O), while in others, such spaces are filled with macroscopic crystals of calcite or dolomite (e.g., Fig. 5, B and J); intermediates (e.g., Fig. 5, C, K, H, and P) demonstrate that this difference reflects the degree of dissolution of the carbonate matrix during the acetic acid recovery of the specimens. A small number of specimens also include large pyrite crystals within the natural endocast, distinguished by crystal habit and high x-ray attenuation.

Some specimens show evidence of inner bodies smaller than the inner volume of the outer wall, but which trace its shape, reflecting postmortem shrinkage [e.g., Figs. 1 (K, L, P to R) and 4 (I to K)]; the intervening volume is occupied by coarse void-filling cement, while the inner body is more finely crystalline, characteristic of mineralization of an original biological substrate (Fig. 1, P, Q, and U) (19). In some specimens, centrifugal lining of the void beneath the inner surface of the outer wall can create the impression of a thickened outer wall, but this is a diagenetic void-filling mineral artifact (e.g., Fig. 1, N and S). Sometimes, the shrunken inner body is surrounded by a delaminated and incomplete outer wall, the matrix between which has subsequently been void filled (Figs. 1, L and Q, and 4, I to K).

Sixteen specimens preserve biological structures inside the outer envelope (Figs. 3, 4, and 6). These include two specimens in which a membrane-bound, large intracellular structure is centrally located (Fig. 3B) and shows similar preservation and size akin to the nuclei of Megasphaera and Spiralicellula, indicating that they are preserved at a single-cell stage of development (Fig. 3, A to C). Four specimens preserve the walls of four large cells, arranged tetrahedrally (Fig. 3, D to H), and two additional specimens preserve eight large cells in a coordinated arrangement (Fig. 3, I to K). These large cells are of equal size within each specimen and fill more or less fully the space enclosed by the outer wall. A couple of specimens preserve small spheroids in a manner akin to the cells in specimens of Megaclonophycus-stage Megasphaera (e.g., Fig. 4, A to D), where the cell membrane exhibits evidence of centripetal and/or centrifugal mineralization (19). The spheroidal morphology of the cells and their discrete distribution suggest that if they were once associated, they have been disaggregated. Last, four specimens preserve polygonal celllike structures, circa 10 to 20 m in diameter, around the periphery of the inner body (e.g., Fig. 4, E to H) or completely fill the shrunken inner body (e.g., Fig. 4, I to L). Normally, only the cell membranes are preserved and the cells themselves are empty or filled by homogeneous mineralization.

Our data allow us to constrain existing interpretations of the biology of Helicoforamina and assess the hypotheses on its relationship to co-occurring Megasphaera, Sinocyclocyclicus, and Spiralicellula. The available evidence indicates that the known forms of Helicoforamina do not represent late developmental stages. The presence of one-, four-, and eight-celled developmental stages reflects an early stage of development, compatible with successive rounds of binary reductive palintomy from a single mother cell. Additional specimens that preserve evidence of hundreds to thousands of cells indicate successive rounds of cell division and, therefore, a protracted period of development within the helical envelope; by comparison, metazoan embryos have ordinarily undergone differentiation and epithelialization at comparable cell stages (20). The partially uncoiled morphology of the early cleaving specimens (e.g., Fig. 6, I to L) suggests that the putative prehatchling is a taphonomic artifact, resulting from the distortion of the inner surface of the outer wall, which gives rise to natural endocasts with broad and deeply excavated helical grooves that reflect the position of the relatively uncompacted helical canal. The differential preservation of the helical groove, canal, and pores indicates that, for the known developmental stages, these structures were limited to the wall of the envelope. Hence, they could not have served a role in gas exchange between the interior and exterior (8), nor could they represent sites of pseudopodial extension (17).

It is tempting to interpret the different states of the helical structure, viz as a groove, canal, and series of pores, as a pattern of development. There are specimens in our collection in which a helical groove is only very weakly developed (e.g., Fig. 1J). However, there is insufficient independent evidence of developmental polarity from the cells preserved inside to justify such an interpretation.

Despite their similarity, we can reject the hypothesis of a developmental link between Helicoforamina and Megasphaera (4, 8, 12). This is because the tetrahedral and octahedral arrangement of cells in Helicoforamina (Fig. 3) and the Parapandorina stage of Megasphaera (9, 20) demonstrates that they represent equivalent developmental stages and, hence, the morphological distinctiveness of their envelope morphology precludes the possibility that they are derived from the same organism.

Similarly, we reject the hypothesis of homology between Helicoforamina and Spiralicellula (4, 7, 8, 16) because the material basis for this hypothesis, that the spiral internal bodies of Helicoforamina resemble the component cells of Spiralicellula, is a taphonomic artifact of preservation in Helicoforamina. Hence, anticipated intermediate stages (8, 12) between Helicoforamina and Spiralicellula have not been recovered despite extensive sampling by us and others. No helical structures develop on the surface of the large dividing cells of Helicoforamina, which is distinct from the morphology of the dividing cells of Spiralicellula, neither is there evidence of helical canals or a sequence of pores on the envelopes of Spiralicellula. Last, the (taphonomically derived) inner bodies of Helicoforamina differ in scale from the co-occurring microtubular fossils, such as Sinocyclocyclicus (21). The resemblance of Helicoforamina to these fossils is superficial and cannot be interpreted as indicative of affinity.

Previous attempts to resolve the affinity of Helicoforamina have relied upon a developmental association of Helicoforamina with other embryo-like taxa in the Wengan biota. With these links rejected, we must also reject the associated interpretations of affinity. Instead, we attempt to resolve the affinity of Helicoformina based only on its preserved anatomy and development. The characteristics of binary reductive palintomy of cells with flexible walls and Y-shaped cell interfaces, enclosed within a complex multilaminate cyst wall, allow us to conclude minimally that these specimens of Helicoforamina reflect coordinately dividing multicelled stages in a broader life cycle. The similarity between Helicoforamina and Megasphaera in the ornament and complex histological structure of the outer wall of, as well as the well-preserved nuclei in some specimens, also allows us to conclude that Helicoforamina is a eukaryote, at the very least.

In the history of interpretations of the Wengan biota, Y-shaped cell interfaces are seen also in Megasphaera, where they have been commonly interpreted to indicate animal affinity (5, 12, 22); however, Y-shaped cell interfaces are encountered in embryo-like conformations of cells in diverse eukaryotes including ciliates, rhodophytes, and nonmetazoan holozoans (18). Yin et al. (13) reviewed the diversity of embryo-like developmental stages that occur in eukaryotes. Among these, the known developmental stages of Helicoforamina bear a strong resemblance to the early binary reductive palintomic stages of rhodophyte embryos (23, 24). However, the resemblance is limited to the early stages of palintomy in Helicoforamina, since rhodophytes undergo morphogenesis after just four or five rounds of palintomy (2325), which is inconsistent with the fact that Helicoforamina stages can have hundreds of cells. Furthermore, while Helicoforamina begins palintomy within its multilaminate ornate cyst, rhodophyte embryos are initially naked, only later developing an irregular mucilaginous sheath (26). Given such simple clusters of cells, it is conceivable that the grade of organization exhibited by Helicoforamina could have evolved as a multicellular stage in any, or even many, lineages of eukaryote. However, all of the eukaryote lineages that have evolved embryo-like stages in their life cycle are generally more similar to each other than any one of them is to Helicoforamina, with the exception of holozoans [see (13) for Caveasphaera]. It is the combination of recurrent rounds of coordinated cell division exhibited by (and inferred in) Helicoforamina, developing within a relatively complex multilaminate cyst, that sets it apart, since all other nonholozoan multicellular eukaryote life history stages undergo rapid morphogenesis after just one or a handful of rounds of reductive division (13). Certainly, nonmetazoan holozoans such as ichthyosporeans and filastereans generate multicelled stages within their respective life cycles (2729), some with a degree of coordination that goes beyond that currently known in Helicoforamina (30). However, the structure of the enveloping cyst in Helicoforamina is itself more complex than is seen in nonmetazoan holozoans.

This same debate has played out over phylogenetic interpretations of Megasphaera and Spiralicellula. Like Helicoforamina, they exhibit patterns of development compatible with early cleavage stages of animal embryos, but these may be shared primitive characteristics of holozoan life cycles (4). Chen et al. (5) attempted to identify definitive metazoan characteristics, including cell differentiation, germ-soma separation, and apoptosis. Evidence of cell differentiation manifests as diad cells among monads, but this is more likely a consequence of asynchronous cell division (20), and elongate peripheral cells, which can also be interpreted as a consequence of postmortem loss of cell adhesion, inflation, and the constraints of an enclosing envelope (31). Germ-soma separation is evidenced by local clusters of distinctly smaller cells that are envisaged as product of the diad cells, but there is no evidence of this developmental relationship, and identical cell clusters occur in co-occurring multicellular algae, suggesting an exogenous origin (32). Conversely, Huldtgren et al. (4) attempted to reject a metazoan affinity in demonstrating that the early palintomically dividing cells of Megasphaera and Spiralicellula result ultimately in a peanut-shaped multicellular body composed of hundreds of thousands of cells that are shed to the environment. However, although a convincing case can be made for a developmental link between the Parapandorina stage (with tens of cells) and the Megaclonophycus stage (composed of hundreds to thousands of cells), the search for intermediates that might bridge the developmental gap to the peanut-shaped stages, or peanut-shaped stages retaining the Megasphaera-grade envelope, has not been fruitful (12, 33). Hence, it is difficult to rationalize whether Megasphaera and Spiralicellula preserve only holozoan symplesiomorphies because developmental stages exhibiting metazoan synapomorphies have not been preserved [a stemward slippage (34) filter of developmental stages] or whether it is because they represent nonmetazoan holozoans. The same holds true for Helicoforamina, which, like Megasphaera and Spiralicellula, might most safely be interpreted as total-group holozoans, i.e., on the available evidence, it is not possible to discriminate definitively between a nonmetazoan holozoan and metazoan interpretation (Fig. 2E). A similar conclusion was reached for co-occurring Caveasphaera, which is known from a much more extensive series of developmental stages and which exhibits a more complex pattern of embryology (13).

The similarity in the envelope ornament and histology of Helicoforamina and Megasphaera, as well as Spiralicellula and Caveasphaera, provides conclusive evidence that this character is not in and of itself informative, either of affinity to living clades or as a basis for grouping the disparate developmental stages preserved in the Wengan biota. This is important because this character has been used to rationalize most of such fossils as representing developmental stages of a single organism (e.g., 4, 7, 8, 12), diminishing perception of the diversity of organisms preserved in this unique window on early Ediacaran marine life. It also exposes to scrutiny why such a diversity of developmental stages of disparate organisms are preserved at all and belies the view that developmental stages of a single organism could be so abundantly fossilized (7, 35). The convergent evolution of an encysted developmental stage probably explains the preservation of this same developmental stage across diverse taxa because experiments have shown that encysted embryos have elevated fossilization potential compared with other developmental stages (36). Further sampling is required to establish the extent of the diversity and developmental biology of Ediacaran marine life in the Wengan biota that has been obscured hitherto by a common envelope morphology and structure.

In the interim, it is pertinent to consider why such diverse organisms should have converged on such similar cyst walls of comparable size, multilaminate structure, and surface ornamentation. The comparatively large size of these and other early developmental stages [e.g., Sporosphaera (37)] implies maternal investment of energy stores to facilitate long gestation and direct development, and preserved intracellular lipid vesicles have been described from Spiralicellula and Megasphaera (20). Comparable cyst walls have been interpreted as diapause stages in the embryology of early metazoans (38, 39). Regardless of their affinity, these factors suggest an adaptation to the spatially and temporally heterogeneous conditions that occurred in shallow marine environments through much of the Ediacaran (40). Although the Wengan biota is interpreted to have been deposited under oxygenated conditions, conditions would have been especially challenging for benthic organisms or life stages given the strong and fluctuating redox conditions associated with the attendant sedimentary phosphogenesis (12).

Our analysis of the developmental biology of Helicoforamina also highlights the challenge of reconstructing the embryology and life cycle of fossil organisms, distinguishing whether disparate specimens represent different developmental stages of a single organism, or comparable versus different developmental stages of different organisms. In this instance, it has been possible to rationalize these competing interpretations because the Ediacaran Wengan biota is so abundantly preserved. Fossilized embryonic stages are much rarer in the other deposits in which they are known (41), rendering the developmental relationships among specimens less open to testing and, therefore, less secure, limiting our ability to test hypotheses of developmental evolution otherwise based solely on phylogenetic inference of the life histories of living organisms.

We studied a rich collection of specimens of Helicoforamina wenganica from the early Ediacaran Wengan biota to test established hypotheses on the biological affinity and developmental relationship of this taxon to other, better known taxa from the deposit. We describe its taphonomy and demonstrate that putative prehatchling stages are taphonomic artifacts. Further, rare specimens of Helicoforamina preserve cells inside, indicative of coordinated and equal palintomy. These data allow us to reject all established hypotheses that propose a developmental relationship of this taxon to other taxa (Fig. 2, A to D); Helicoforamina is a distinct taxon, not merely a distinct developmental stage. This evidences a much richer diversity of taxa and developmental stages preserved in this unique window on early Ediacaran marine life than has been perceived hitherto. We constrain the affinity of Helicoforamina to Holozoa; we cannot discriminate between nonmetazoan and metazoan holozoan affinities (Fig. 2E). The diverse Wengan biota shares similarly ornamented encysted developmental stages as an adaptation to the temporally and spatially heterogeneous nature of Ediacaran shallow marine environments.

We obtained an abundant collection of Helicoforamina wenganica through acetic acid dissolution of phosphoritic dolomite from the Upper Grey Facies (Units 4b; 18) of the Doushantuo Formation at 54 Quarry, in the Baiyan-Gaoping anticline of Wengan County, Guizhou Province, Southwest China. For further information on the geographic location, stratigraphy, and environmental interpretation, see Cunningham et al. (18) and references therein. The Wengan assemblage is dominated by embryo-like fossils with a cerebral, fractal, or dimpled surface ornamentation that have been variably attributed to Megasphaera, Tianzhushania, and Yintianzhushania. Given the implications of our study that there is a cryptic diversity of taxa that cannot be discriminated on the basis of their surface ornamentation, in the text, we refer to them all to Megasphaera, pending establishment of criteria on which they may be consistently discriminated.

The best preserved of these were subjected to tomographic analysis using a Carl Zeiss Xradia 520 Versa x-ray tomographic microscope at Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences (NIGPAS), and synchrotron radiation x-ray tomographic microscopy (srXTM) at the X02DA TOMCAT beamline of the Swiss Light Source (SLS; Paul Scherrer Institute, Villigen, Switzerland) and BM5 beamline of the European Synchrotron Radiation Facility (ESRF; Grenoble, France). Measurements on the Xradia instrument were obtained with an operating voltage of 50 kV, LE1 filter, and 4 objective yielding isotropic voxel dimensions of 0.82 to 1.1 m, collecting 3001 projections through a rotation of 360. srXTM data were obtained using 10 and 20 objective lenses at SLS (yielding reconstructed tomographic data with voxel dimensions of 0.65 and 0.325 m, respectively) or 10 objective lens at ESRF (voxel dimension of 0.75 m) at energy levels of 15 to 20 keV and exposure times of 50 to 400 ms. Projections (1501) were taken equianglularly through 180o of rotation within the beam. Projections were postprocessed and rearranged into flat- and dark-fieldcorrected sinograms, and reconstruction was performed on a 60-core Linux PC farm, using a highly optimized routine based on the Fourier transform method and a regridding procedure (42). Slice data were analyzed and manipulated using VGStudioMax (www.volumegraphics.com). Given that the x-rays from the synchrotron sources are monochromatic, differences in contrast in the resulting tomographic slices reflect the densities of the fossil materials they pass through.

This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

V. Krishnamurthy, in Reproductive Biology of Plants, B. M. Johri, P. S. Srivastava, Eds. (Springer, Heidelberg, Berlin, 2001), pp. 5795.

H. Suga, I. Ruiz-Trillo, in Evolutionary Transitions to Multicellular Life: Principles and Mechanisms, I. Ruiz-Trillo, A. M. Nedelcu, Eds. (Springer, 2015), vol. 2, pp. 117128.

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Developmental biology of Helicoforamina reveals holozoan affinity, cryptic diversity, and adaptation to heterogeneous environments in the early...

Protein Assay Market Next Big Thing | Major Giants Bio-Rad Laboratories, Thermo Fisher Scientific, Merck – Personal Injury Bureau UK

Global Protein Assay Market Report from AMA Researchhighlights deep analysis on market characteristics, sizing, estimates and growth by segmentation, regional breakdowns& country along with competitive landscape, players market shares, and strategies that are key in the market. The exploration provides a 360 view and insights, highlighting major outcomes of the industry. These insights help the business decision-makers to formulate better business plans and make informed decisions to improved profitability. In addition, the study helps venture or private players in understanding the companies in more detail to make better informed decisions.

Major Players in This Report Include,

Bio-Rad Laboratories, Inc. (United States), Thermo Fisher Scientific (United States), Merck & Co., Inc., (United States), Promega Corporation (United States), GE Healthcare (United States), PerkinElmer, Inc., (United States), Geno Technology Inc (United States), Cell Signaling Technology, Inc. (United States), Abcam (United Kingdom), Novus Biologicals (United States), NanoString Technologies, Inc. (United States) and Soltec Bioscience Inc. (United States)

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The protein assays are necessary for the processing of protein samples for isolation, separation, and analysis by various methods. The protein quantification is an integral part of any laboratory research including the protein processing procedure. The assay quantifies the total protein content in a sample or in a formulated product, as it is necessary to quantify the accurate protein as a range of other critical assays requires total protein content results in order to generate data for results. The advancements in molecular biology techniques have widely influenced the adoption of protein research along with the government initiatives for technological advancements in research that are leading the market.This growth is primarily driven by Growing demand for the accurate spectroscopic analytical procedure in disease diagnosis as well as scientific research to measure the concentration of protein in a solution or any research to derive results. Its results or reactions are dependent on the amino acid composition of the measured proteins. the estimation of protein concentration is necessary for protein purification, cell biology, etc..

Market Drivers

Market Trend

Restraints

Opportunities

Increasing Government Initiatives in Protein Assay will Boost the Market and Surging Demand for Protein Assay in Lifesciences Research

Challenges

Problems with Equipment Used in Protein Assay

Global Protein Assay Market Report offers a detailed overview of this market and discusses the dominant factors affecting the growth of the market. The impact of Porters five armies on the market over the next few years has been discussed for a long time in this study. We will also forecast global market size and market outlook over the next few years.

Types of Products,Applications and Global Protein Assay Market Report Geographical Scope taken as the Main Parameter for Market Analysis. This Research Report Conducts an assessment of the industry chain supporting this market. It also provides accurate information on various aspects of this market, such as production capacity, available production capacity utilization, industrial policies affecting the manufacturing chain and market growth.

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In this research study, the prime factors that are impelling the growth of the Global Protein Assaymarket report have been studied thoroughly in a bid to estimate the overall value and the size of this market by the end of the forecast period. The impact of the driving forces, limitations, challenges, and opportunities has been examined extensively. The key trends that manage the interest of the customers have also been interpreted accurately for the benefit of the readers.

The Global Protein Assaymarket study is being classified by Type, Applicationsand major geographies with country level break-up that includes South America (Brazil, Argentina, Rest of South America), Asia Pacific (China, Japan, India, South Korea, Taiwan, Australia, Rest of Asia-Pacific), Europe (Germany, France, Italy, United Kingdom, Netherlands, Rest of Europe), MEA (Middle East, Africa), North America (United States, Canada, Mexico).

The Global Protein Assayis segmented by following Product Types:

Type (BCA Protein Assay, Bradford Protein Assay, Biuret Protein Assay, Lowry Protein Assay, Test Strip-Based Assays, Others), Application (Life Science Research, Molecular Biology, Pharmaceuticals, Disease Diagnosis, Others), Equipment (Spectrophotometer (Tecan), Whatman 1 paper (Whatman)), Assay Standards (Bovine Serum Albumin (BSA) Standard, Bovine Gamma Globulin (BGG) Standard)

The report concludes with in-depth details on the business operations and financial structure of leading vendors in the Global Protein Assay market report, Overview of Key trends in the past and present are in reports that are reported to be beneficial for companies looking for venture businesses in this market. Information about the various marketing channels and well-known distributors in this market was also provided here. This study serves as a rich guide for established players and new players in this market.

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Current Scenario Analysis for Decision Framework

Key Strategic Developments in Global Protein Assay Market:

The research includes the key strategic activities such as Research & Development (R&D) initiatives, Merger & Acquisition (M&A) completed, agreements, new launches, collaborations, partnerships & (JV) Joint ventures, and regional growth of the key competitors operating in the market at global and regional scale to overcome current slowdown due to COVID-19.

Key Market Features in Global Protein Assay Market

The report highlights Global Protein Assay market features, including revenue size, weighted average regional price, capacity utilization rate, production rate, gross margins, consumption, import & export, demand & supply, cost bench-marking in Global Protein Assay, market share and annualized growth rate (Y-o-Y) and Periodic CAGR.

Extracts from Table of Contents

Global Protein AssayMarket Research Report

Chapter 1 Global Protein AssayMarket Overview

Chapter 2 Global Economic Impact on Industry

Chapter 3 Global Market Competition by Manufacturers

Chapter 4 Global Revenue (Value, Volume*) by Region

Chapter 5 Global Supplies (Production), Consumption, Export, Import by Regions

Chapter 6 Global Revenue (Value, Volume*), Price* Trend by Type

Chapter 7 Global Market Analysis by Application

.continued

This report also analyzes the regulatory framework of the Global Markets Global Protein AssayMarket Report to inform stakeholders about the various norms, regulations, this can have an impact. It also collects in-depth information from the detailed primary and secondary research techniques analyzed using the most efficient analysis tools. Based on the statistics gained from this systematic study, market research provides estimates for market participants and readers.

About Author:

Advance Market Analytics is Global leaders of Market Research Industry provides the quantified B2B research to Fortune 500 companies on high growth emerging opportunities which will impact more than 80% of worldwide companies revenues.

Our Analyst is tracking high growth study with detailed statistical and in-depth analysis of market trends & dynamics that provide a complete overview of the industry. We follow an extensive research methodology coupled with critical insights related industry factors and market forces to generate the best value for our clients. We Provides reliable primary and secondary data sources, our analysts and consultants derive informative and usable data suited for our clients business needs. The research study enable clients to meet varied market objectives a from global footprint expansion to supply chain optimization and from competitor profiling to M&As.

Contact US:

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Protein Assay Market Next Big Thing | Major Giants Bio-Rad Laboratories, Thermo Fisher Scientific, Merck - Personal Injury Bureau UK

Laser Microdisection Market Highly Favourable with new Demand to the Growth Rate by 2025 | Danaher, 3DHISTECH, Fluidigm, Epistem – Medic Insider

AMA Research have added latest edition of survey study on Global Laser Microdisection Market with 100+ market data Tables, Pie Chat, Graphs & Figures spread through Pages and easy to understand detailed analysis. At present, the market is developing its presence. The Research report presents a complete assessment of the Market and contains a future trend, current growth factors, attentive opinions, facts, and industry validated market data. The research study provides estimates for Global Laser Microdisection Forecast till 2025*. Some are the key players taken under coverage for this study is Thermo Fisher Scientific Inc. (United States), ZEISS International (Germany), Danaher (United States), 3DHISTECH (Hungary), Molecular Machines and Industries GmbH (Germany), Fluidigm Corporation (United States), VitroVivo Biotech (United States), Epistem Ltd. (Germany) and CaresBio Laboratory LLC (United States).

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Tissue microdissection is defined as a process of isolating a morphologically distinct population of cells from a tissue section or cytological preparation composed of a mixture of heterogeneous cell types. Laser capture microdissection (LCM) is mainly used to isolate specific cells from microscopic regions of tissue, cells, or organisms. Various tissue microdissection techniques have been used to isolate pure cell populations. It is the contamination-free procedure for obtaining subpopulations of tissue cells under direct microscopic visualization. This isolates specific cells by dissecting unwanted cells and harvests the cells of interest directly to give pure enriched cells.

Important Features that are under offering & key highlights of the report:

1) How Study Have Considered the Impact of COVID-19 / Economic Slowdown of 2020?

Analyst at AMA are constantly gathering and conducting survey with opinion leaders and Industry experts from various region to minutely understand impact on growth as well as local reforms to evaluate study and market estimates. Due to lockdown different online medium and procedures are followed like Survey Monkey, LinkedIn Connections, and Email reach and industry forum to established industry viewpoint to garner rich insights for study. A special chapter in the study presents Impact Analysis of COVID-19 on Global Laser Microdisection Market along with tables and graphs related to various country and segments showcasing impact on growth trends.

2) Can list of players be customizing according to targeted regional geographies to match business objective?

Considering heat map analysis and based on market buzz or voice the profiled list of companies in the report are Thermo Fisher Scientific Inc. (United States), ZEISS International (Germany), Danaher (United States), 3DHISTECH (Hungary), Molecular Machines and Industries GmbH (Germany), Fluidigm Corporation (United States), VitroVivo Biotech (United States), Epistem Ltd. (Germany) and CaresBio Laboratory LLC (United States). Yes, further list of players can also be customized as per your requirement keeping in mind your areas of interest and adding local emerging players and leaders from targeted geography.

** List of companies covered may vary in the final report subject to Name Change / Merger & Acquisition Activity etc. based on the difficulty of survey since data availability needs to be confirmed by research team especially in case of privately held company. Up to 2 players can be added at no additional cost.

3) Can Market be broken down by different set of application and types?

Additional segmentation / Market breakdown is possible subject to data availability, feasibility and depending upon timeline and toughness of survey. However a detailed requirement needs to be prepared before making any final confirmation.

** 3+ Additional country of your interest can be included at no added cost feasibility test would be conducted by Analyst team of AMA based on the requirement shared and accordingly deliverable time will also be disclosed.

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To comprehend Laser Microdisection market dynamics in the world mainly, the worldwide Laser Microdisection market is analyzed across major global regions. AMA also provides customized specific regional and country-level reports for the following areas.

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Major Highlights of TOC:

Chapter One: Market Overview

Chapter Two: Executive Summary - Free of Cost

Chapter Three: Market Dynamics USD1000

Market Drivers, Market Challenges, Market Trends, Restraints & Opportunities, Post Covid Scenario

Chapter Four: Market Factor Analysis USD400

Supply/Value Chain, Porters Five Forces, PESTEL analysis, Market Entropy, Patent & Trademark Analysis, Bargain Power

Chapter Five: Global Loan Origination Software, by Market Segmentation and Geography (value, volume**) (2014-2019) USD1400

by Application (Molecular Biology, Cell Biology, Forensic Science), End-user (Academic and Government Research Institutes, Hospitals, Pharmaceutical and Biotechnology Companies, Contract Research Organizations), Offering (Reagents & Media, Assay Kits, Others), Systems (Infrared LCM, Ultraviolet and Infrared LCM, Immunofluorescence LCM)

.

.

Global Laser Microdisection Region

North America (United States, Canada and Mexico)

Europe (Germany, France, United Kingdom, Spain, Italy, Netherlands, Switzerland, Nordic, Others)

Asia-Pacific (Japan, China, Australia, India, Taiwan, South Korea, Middle East & Africa, Others)

Chapter Six: Global Laser Microdisection Manufacturers/Players Analysis USD1200

Competitive Landscape, Comparative Market Share Analysis (2018-2019), Peer Group Analysis (2019), BCG Matrix, Company Profile, Product/Service Offering Matrix

Chapter Seven: Global Loan Origination Software, by Market Segmentation and Region (value, volume**) (2020-2025) USD1400

Sections same as Chapter Five

Chapter Eight:Company profiles / Competitive Landscape [12 Players] USD1250

Chapter Nine: Methodology/Research Approach, Data Source, Disclaimer

** If applicableActual Numbers & In-Depth Analysis, Business opportunities, Market Size Estimation Available in Full Report.

AMA also offers Custom Research services providing focused, comprehensive and tailored research according to clientele objectives. Thanks for reading this article; you can also get individual chapter wise section or region wise report like North America, Europe or Asia.

About Author:

Advance Market Analytics is Global leaders of Market Research Industry provides the quantified B2B research to Fortune 500 companies on high growth emerging opportunities which will impact more than 80% of worldwide companies revenues.

Our Analyst is tracking high growth study with detailed statistical and in-depth analysis of market trends & dynamics that provide a complete overview of the industry. We follow an extensive research methodology coupled with critical insights related industry factors and market forces to generate the best value for our clients. We Provides reliable primary and secondary data sources, our analysts and consultants derive informative and usable data suited for our clients business needs. The research study enable clients to meet varied market objectives a from global footprint expansion to supply chain optimization and from competitor profiling to M&As.

Contact Us:

Craig Francis (PR & Marketing Manager)

AMA Research & Media LLP

Unit No. 429, Parsonage Road Edison, NJ

New Jersey USA 08837

Phone: +1 (206) 317 1218

[emailprotected]

Connect with us atLinkedIn|Facebook|Twitter

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Laser Microdisection Market Highly Favourable with new Demand to the Growth Rate by 2025 | Danaher, 3DHISTECH, Fluidigm, Epistem - Medic Insider

Study shows how combining two drugs may be an effective treatment for HLH – News-Medical.Net

Reviewed by Emily Henderson, B.Sc.Jun 12 2020

Scientists at St. Jude Children's Research Hospital, UCSF Benioff Children's Hospitals and Baylor College of Medicine are investigating how to best treat hemophagocytic lymphohistiocytosis (HLH), a rare immune disorder. Their work, appearing as an advance online publication today in Blood, details how combining two drugs may be a good treatment for HLH.

For the last 20 years, treatment for HLH has remained a combination of the drugs dexamethasone and etoposide. But we know that many patients either do not respond to this regimen or later relapse, so we dug into the biology to come up with a different treatment strategy."

Kim Nichols, M.D., co-senior author of St. Jude Oncology

In HLH, the immune system becomes over-activated and immune cells produce cytokines, which are chemicals released into the bloodstream to try to recruit and activate additional immune cells. Patients with HLH can experience a cytokine storm syndrome where so many cytokines start circulating that they feed upon themselves to further drive immune activation.

There are several cytokines elevated in HLH patients. Some of these cytokines bind to receptors on the cell's surface. When that happens, those receptors recruit and activate Janus kinases (JAKs), which are signaling molecules.

Previous research by Nichols revealed that the JAK1/2 inhibitor ruxolitinib had a positive effect in mouse models of HLH. By inhibiting the JAK/STAT pathway, ruxolitinib interferes with cytokine communication. Nichols and her team wanted to better understand the mechanism behind this and investigate whether any particular cytokine was more important to inhibit.

"We wanted to know whether any of the cytokines that are elevated in HLH contribute to dexamethasone resistance, and if so, whether blocking the signaling of these cytokines might reverse treatment resistance," said co-first author Katherine Verbist, Ph.D., of St. Jude Oncology.

The researchers' work in cell lines and mouse models determined that of all the cytokines elevated in HLH, interleukin-2 is critically important to driving resistance to dexamethasone. Interleukin-2 is produced by activated T cells and promotes their survival. The researchers showed that by blocking the effect of interleukin-2, the T cells can be re-sensitized to and destroyed by dexamethasone.

The researchers found that the combination of dexamethasone and ruxolitinib was significantly more effective in quelling the signs of HLH in animal models compared to treatment with either drug alone. The study provides additional evidence to support testing the combination through a clinical trial.

"We were able to take lessons learned from our studies of pediatric leukemia, which is also often treated with dexamethasone, and apply them to our study of cytokines in HLH," said co-senior author Michelle Hermiston, M.D., Ph.D., of UCSF Benioff Children's Hospitals. "Like in leukemia, we were able to show that a specific cytokine signaling through the JAK pathway could promote resistance to treatment."

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Study shows how combining two drugs may be an effective treatment for HLH - News-Medical.Net

Multiplexed whole-animal imaging with reversibly switchable optoacoustic proteins – Science Advances

INTRODUCTION

Photo- or optoacoustic (OA) imaging combines optical contrast with ultrasound resolution, enabling high-resolution, real-time in vivo imaging well beyond the 1-mm penetration depth typical of microscopy methods (1, 2). OA has already provided intriguing insights into tumor heterogeneity (3), neuronal dynamics (4), psoriasis (5), and brown fat metabolism (6) based on endogenous contrast from hemoglobin and lipids (7, 8). This is complemented by theranostic research (9, 10) and clinical application (11), e.g., imaging of Crohns disease (12). However, OA imaging has not yet become a routine tool in life sciences because of the lack of strong OA contrast agents that can be expressed in desired cell types (13). The few transgenic labels used in OA so far (8) give weak signals that cannot rise above the strong background due to hemoglobin. Photochromic proteins that can be reversibly switched between two states by light can overcome this limitation by entirely separating the label signal, which modulates in accordance with the illumination, from the background, which remains constant (14). This concept, despite being validated in several studies (1520), has not been implemented widely because it requires complex instrumentation and data analysis tools. Here, we introduce two reversibly switchable OA proteins (rsOAPs) and demonstrate their use with widely accessible off-the-shelf commercial imaging systems as well as our open-access machine learning (ML)based software code for analysis. One of our new rsOAPs shows high switching speeds and dynamic range of photomodulation that allow us to resolve the signals of different cell populations labeled with differentiable rsOAPs in close proximity in the same animal, demonstrating the potential for simultaneous tracking of different cellular processes through temporal multiplexing.

(A) Homology model (iTasser, based on 6g1y) of ReBphP-PCM. Truncation sides indicated. (B) Schematic representation of truncations. (C) Photoinduced differential spectra for truncations. (D and E) Similar representations for RpBphP1. (F) Stabilization of the BV D-ring in RpBphP1 and DrBphP. (G) Similar representation for PaBphP, which shows an arginine similar to ReBphP, presumably abstracting D194 and destabilizing the Pfr state, yielding a faster photoswitching.

Bacterial photoreceptors called bacteriophytochromes (BphPs) (21) have emerged as most suitable for rsOAP development due to their strong absorption in the near-infrared range and low photofatigue (22). To identify the most promising candidate for further development, we screened eight native BphPs (table S1) and selected the one from Rhizobium etli. A set of truncations enabled us to minimize its size and optimize its photoswitching characteristics. In brief, on the basis of existing structural data as well as homology models, we created truncations containing the minimum PAS-GAF-PHY photosensory core domains [photosensory core module (PCM)] together with extra amino acids from the annotated linkers between PHY and histidine kinase domains and tested their characteristics in regard to signal generation and photoswitching (Fig. 1, A to E, and note S1). The final variant ReBphP-PCM shows twofold larger change in OA signal (Fig. 2G), more than fivefold faster switching (Fig. 2, C and D), and greater resistance to photofatigue than other rsOAPs (Fig. 2E), while its high molar absorbance is on par with the recently described Deinococcus radiodurans DrBphP-PCM (92,000 M1 cm1; Fig. 2, B and G) (19). Those characteristics enable higher numbers of switching cycles per second, which improves sensitivity and allows imaging over longer timeframes. On the molecular level, this acceleration of switching speed is the result of a less stabilized Pfr state favoring the photoinduced transition to Pr. The destabilization is likely caused by an arginine present in ReBphP but not in RpBphP1 and DrBphP. This arginine, by interacting with a conserved aspartate, which, in turn, interacts with the D-ring of the Pfr state chromophore, weakens Pfr stabilization (Fig. 1, F and G, and note S1).

(A) Principle of photoswitching in BphPs (top) and concept of temporal unmixing of two labels (green ball and blue star; bottom). Illumination shown in dark red (780 nm) and red (630 nm). Pr refers to the red state, while Pfr refers to the far-red state. The bottom part of the panel was adapted with permission from (14). (B) Absorbance spectra of Pr and Pfr states of the three rsOAPs in comparison to hemoglobin (HbO2 and Hb, 1999, S. Prahl, omlc.org). (C) Switching cycles of the rsOAPs. Only OA signal at 770 nm is shown. a.u., arbitrary units. (D) Single switching cycle from (C), shown with an exponential fit. (E) Photofatigue of the proteins per cycle. (F) Absorbance ratio between the Pfr and Pr state for different wavelengths. (G) Absorbance (filled bars) and OA signal intensity (hollow) ratio between the Pfr and Pr state for the three rsOAPs at 770 nm. (H) Matthews coefficient shown as a function of number of cycles and pulses. Shown is the analysis of a 4T1 tumor expressing ReBphP-PCM; histology was used as ground truth. All proteins have been adjusted to equal Soret peak absorption.

Our truncation strategy also proved successful in obtaining a switchable RpBphP1-PCM from Rhodopseudomonas palustris, in contrast to a previous report that truncated forms of this protein do not undergo reversible switching (19). Our engineered RpBphP1-PCM maintains the far-red state (Pfr) extinction coefficient and photochromic behavior of the parental RpBphP1 (Figs. 1E and 2B and fig. S1), and the change in its OA signal following illumination at 770 nm is similar to that of the previously described DrBphP-PCM (Fig. 2G). (Plasmid for expressing ReBphP-PCM in bacteria and eukaryotic cells or for introduction into viral vectors can be obtained from Addgene.) Both new rsOAPs are monomeric (fig. S2) and show higher expression in mammalian cells than the full-length parental proteins (fig. S3). The two developed rsOAPs and DrBphP-PCM show distinctive switching speeds, which is the reason for our ability to discriminate the proteins in vivo successfully. As a result, probes expressed in different cells in close proximity in the animal can be distinguished during high-resolution OA imaging.

We performed all OA imaging using an off-the-shelf, commercially available multispectral OA tomography device with a 10-Hz pulsed tunable laser and a 256-element transducer array (MSOT, iThera Medical). Off-switching of rsOAPs was achieved with light at 770 nm, which gave the highest difference in OA signal intensity between the on and off states (fig. S5A), while on switching was achieved using light at 680 nm. Lower wavelengths did not substantially improve the transition to the on state (fig. S5B). The number of laser pulses per wavelength was chosen to cover the full switching kinetics, but it can be significantly reduced using information-content analysis, which allows an estimate of the minimal number of cycles and pulses per cycle required to discern the labeled structure, thus effectively limiting imaging dwell time, which is essential for, e.g., time-resolved studies (Fig. 2H, fig. S6, and note S2). All temporal unmixing was conducted with in-house code developed to analyze time-varying patterns in the reconstructed data in the frequency and time domains using classic ML approaches (Fig. 3, Materials and Methods, and notes S3 and S4). In brief, after running fluence and motion correction on the data, a range of distinctive features was extracted from the photomodulated signal for each voxel of the tomography images. On the basis of a set of these data and corresponding histology as ground truth, a bagged random forest algorithm (23) was trained and validated on independent datasets of a different type to prevent overfitting. The ensuing model was then used to analyze all data in this study. The code for data preparation, for analysis with the model used in this work, and for generation of new models is available to the community along with graphical user interfaces.

The time-varying patterns in the OA raw data are extracted in the Feature calculation (blue) and analyzed using a classification model in the Data analysis step (yellow). In Model building (green), a classification model is trained based on imaging data with associated histology ground truth. In the script, two algorithms can be selected: bagged tree or support vector machine. For uniformity, the images shown in this work exclusively use the bagged tree approach, although the support vector machine has some virtues (note S4).

The OA imaging scheme is shown in Fig. 4A. First, we used rsOAPs for superficial in vivo imaging. We imaged the development of 4T1 mouse mammary gland tumors coexpressing ReBphP-PCM and green fluorescent protein (GFP) after they were grafted onto the backs of FoxN1 nude mice (n = 3). The initial population of 0.8 106 injected cells was readily visualized separate from all background absorbers (Fig. 4B), as was the growing tumor mass at all days after injection (fig. S7, A to D). To test whether this imaging is also possible in brain tissue after light passes through the skull, we implanted 0.7 106 4T1 cells coexpressing ReBphP-PCM and GFP at a depth of 3.6 mm and imaged them immediately thereafter. Comparison of the OA images with fluorescence images obtained after sacrificing mice revealed perfect overlap of the labeling, confirming background-free identification of 1.4 105 cells deep in the mouse brain (Fig. 4C). Next, we used the same rsOAP to image deep-seated tumors of HCT116 human colon carcinoma cells implanted intraperitoneally (n = 2). From day 3 onward, we were able to visualize the growth of several individual tumor sites to a depth of ~1 cm (fig. S7, E and F). Comparison of OA images and histology obtained after sacrifice confirmed identification of all malignant tissue (Fig. 4, D to F, and fig. S7, E and G), including small tumors or metastatic patches containing less than 10,000 cells (fig. S7, I and J).

In certain experiments, GFP was coexpressed to allow fluorescence imaging of histology slices. (A) Schematic of OA tomography used in this work. (B) 4T1 cells (0.8 106 injected subcutaneously) stably expressing ReBphP-PCM and imaged on day 9. (C) 4T1 cells (0.7 106 injected intracranially) stably expressing ReBphP-PCM imaged at a depth of 3.6 mm in the brain (arrow I) immediately after injection. (D) Volume representation of HCT116 cells (1.5 106 injected intraperitoneally) stably expressing ReBphP-PCM at consecutive time points. (E) Histology of the same mouse at day 14. (D and E) Arrows indicate distinctive tumor masses. (F) Certainty of prediction (weighted sum of tree scores) indicating quality of discerning label signal or background of regions of interest shown in (E) (right). (G) Imaging of the indicated concentrations of Jurkat T cells in Matrigel expressing ReBphP-PCM immediately after subcutaneous implantation; because of the polymerization process, no homogeneity is expected. (H) Imaging of the indicated concentrations of E. coli expressing ReBphP-PCM in Matrigel immediately after subcutaneous implantation. In (B), (C), (G), and (H), color maps refer to R2 (detection quality). All slices are single representative slices. All scale bars, 1 mm. Earlier time points and data from additional mice can be found in fig. S7.

To assess the sensitivity of imaging with our rsOAPs, we imaged dorsal implants of Matrigel containing different numbers of Jurkat T lymphocytes stably coexpressing ReBphP-PCM and GFP in mice (Fig. 4G). We detected populations as small as 500 cells/l, suggesting the potential for sensitive tracking of immune processes. Similarly, imaging of dorsal implants of Matrigel containing bacteria expressing ReBphP-PCM detected populations as small as 14,000 bacteria/l (Fig. 4H). This sensitivity may be useful for studying and optimizing bacteria-based tumor therapies (24).

A strong advantage of photocontrollable labels is the possibility to delineate multiple labels based on their individual switching kinetics. To demonstrate this, we imaged 1-mm alginate beads filled with Escherichia coli expressing ReBphP-PCM, RpBphP1-PCM, or DrBphP-PCM. All beads were unambiguously identified on the basis of their switching kinetics (Fig. 5A). The same differentiation was achieved in vivo after implanting Jurkat T lymphocytes expressing ReBphP-PCM or DrBphP1-PCM and E. coli expressing RpBphP1-PCM into the back of mice (Fig. 5B).

(A) Imaging of an alginate bead phantom containing E. coli expressing rsOAPs ReBphP-PCM, RpBphP1-PCM, and DrBphP-PCM. (B) Imaging of Jurkat T cells and E. coli (1.4 106) expressing each of the three rsOAPs imaged immediately after implantation into a 4T1 tumor. (C) Imaging of a 4T1 tumor with implants of two Jurkat T cells expressing rsOAPs. Zones of mixture of the two populations with distinct kinetics are colored yellow. In (A) to (E), color maps indicate clusters showing distinguishable kinetics. (D) Imaging of a 4T1 tumor stably expressing ReBphP-PCM at day 9 (arrows II and III) imaged immediately after E. coli (108 cells) expressing DrBphP-PCM have been injected into the tumor (arrow I). Histology confirmation is inferred from fluorescence in DrBphP-PCM (Cy5 only) and ReBphP-PCM (GFP primarily). (E) Volume representation of k. All slices are single representative slices. All scale bars, 1 mm.

Because the kinetics of photoswitching are energy dependent, fluence changes due to light attenuation by surrounding absorbersphotochromic or staticcomplicates temporal multiplexing (note S5). Thus, one aim of our development of the fast-switching ReBphP-PCM was to achieve a switching time constant clearly separate from other rsOAPs. We show that 4T1 tumor expressing ReBphP-PCM and GFP are readily distinguished from infiltrating DrBphP-PCMexpressing E. coli cells (intratumorally injected 108 bacteria; Fig. 5, D and E). This means that multiplexing is possible for co-registration studies and that the concentrations of the labels can be estimated based on the convoluted kinetics (fig. S8). Similarly, we show this for two populations of rsOAP labeled Jurkat T lymphocytes in a 4T1 tumor (intratumorally injected 5 105 cells; Fig. 5C). Hence, temporally unmixed multiplexed OA imaging of cells of the immune system enables following their function and involvement in disease mechanism in vivo, longitudinal on the organism level.

The combination of OA and transgenic rsOAP labels allows the tracking of specific cell populations in vivo, which can open up possibilities for longitudinal studies of intact animals in diverse fields such as immunology, developmental biology, neurology, and cancer research. To support these studies, we describe next-generation rsOAPs that provide faster switching and greater resistance to photofatigue than existing rsOAPs, allowing highly sensitive detection, and importantly true multiplexing, without interference from hemoglobin or other abundant absorbers in vivo. These rsOAPs can be used with off-the-shelf equipment and our ML-based open-access image processing code to detect populations of fewer than 500 cells in vivo. The approach relies entirely on a time series of images, thus making the concept translatable between different OA imaging devices. These tools will facilitate the wider use of OA imaging in life sciences, particularly for the study of cellular dynamics and interactions on the level of whole organisms.

RpBphP1 (16) was obtained from Addgene (V. Verkhusha, plasmid no. 79845). Mammalian optimized ReBphP was synthesized as gene strings (GeneArt, Life Technologies, Regensburg, Germany). All other BphPs used in the study have been a gift from A. Mglich (University of Bayreuth, Germany).

For bacterial protein expression, the coding sequences of all BphPs used in the study except RpBphP1 were polymerase chain reaction (PCR)amplified as a Nde I/Xho I fragment and cloned into the second multiple cloning site of the pET-Duet1 vector (Novagen, Merck Millipore). RpBphP1 was PCR-amplified as a Nde I/Pac I fragment and cloned into the second multiple cloning site of the pET-Duet1 vector. In addition, for biliverdin synthesis, the heme oxygenase (HO) of Nostoc sp. was cloned using Nco I/Hind III into the first multiple cloning site of pET-Duet1.

For equimolar mammalian expression, first, ReBphP_P2A and mCherry were PCR-amplified and then stitched using overlap PCR as an Eco RI/Xba I fragment and cloned in a pcDNA3.0 vector (Thermo Fisher Scientific). Later similar constructs for other BphPs were made by amplifying them as Eco RI/Not I fragment and inserted in place of ReBphP1-PCM in the above construct. The resulting plasmids allowed the equimolar coexpression of RpBphP1, RpBphP1-PCM, ReBphP-PCM, ReBphP-PCM, or DrBphP-PCM and mCherry proteins.

Proteins have been expressed in E. coli strain BL21 (DE3) (New England Biolabs, #C2527). In brief, plasmids expressing BphPs and HO were transformed into the BL21 host cells. Bacterial cells were grown in LB media supplemented with ampicillin at 37C until the culture reached OD (optical density) 0.6, followed by induction of protein expression by addition of IPTG (isopropyl--d-thiogalactopyranoside) and further incubation for 16 to 18 hours at 22C. The next day, the bacterial pellet was collected by centrifugation and pellet was resuspended in phosphate-buffered saline (PBS). After cell lysis, proteins were purified by immobilized metal affinity chromatography in PBS, followed by gel filtration on a HiLoad 26/600 Superdex 75 pg (GE Healthcare Life Sciences, Freiburg, Germany).

For absorption spectra, the purification buffer was exchanged against PBS and the proteins were measured with a Shimadzu UV-1800 spectrophotometer (Shimadzu Inc., Kyoto, Japan) using a 100-l quartz cuvette. To measure the ON (Pfr) and OFF (Pr) spectra of respective proteins, photoswitching was carried out using 650/20-nm or 780/20-nm light-emitting diodes (Thorlabs) placed above the quartz cuvette in the spectrophotometer.

Fluorescence measurements for all BphPs were performed with a Cary Eclipse Fluorescence spectrophotometer (Varian Inc., Australia). Photoswitching was carried out as above. Fluorescence measurement was done by fixing excitation wavelength at 700 nm and emission wavelength at 720 nm. Excitation wavelength and emission slit were set to 5 nm, and the absorbance at the excitation wavelength was always equal to 0.1 to avoid inner filter effects.

4T1 and Jurkat cells were maintained in RPMI 1640. HeLa and HCT116 cells were maintained in Dulbeccos modified Eagles medium (DMEM) and McCoy 5A medium, respectively. All media were supplemented with 10% fetal bovine serum (Invitrogen) and antibiotics [penicillin (100 U/ml) and streptomycin (100 mg/ml)]. Cells were cultivated at 37C and 5% CO2.

Tissue culture. The Platinum-E and RD114 packaging cell lines were cultivated in cDMEM (Complete Dulbeccos modified Eagle medium), HCT116 cell line was grown in McCoy 5A medium (Life Technologies), and 4T1 and Jurkat cells were cultured in cRPMI (Complete Roswell Park Memorial Institute)1640 Medium. All media were supplemented with 10% fetal calf serum, 0.025% l-glutamine, 0.1% Hepes, 0.001% gentamicin, and 0.002% streptomycin.

Generation of constructs. ReBphP-PCM-IRES-GFP was amplified using specific primers (5-ATTAGCGGCCGCGCCACCATGAGCGGCACCAGAG-3 and 5-ATTAGAATTCTCACTTGTACAGCTCGTCCATGCCGTGAGTG-3) and cloned into the mP71 using Not I and Eco RI restriction sites. The mP71 vector was a gift from W. Uckert.

Generation of cell lines. For retrovirus production, Platinum-E or RD114 packaging cells were transfected with the retroviral vector mP71-ReBphP-PCM-IRES-GFP using calcium phosphate precipitation. The supernatant of the packing cells was collected at 48 and 72 hours after transfection and purified from the remaining cells by centrifugation at 1500 rpm at 4C for 7 min. One day before transduction, nontissue culturetreated 48-well plates were coated with RetroNectin (Clontech) according to the manufacturers recommendations overnight at 4C. After washing once with PBS, virus supernatant was added and centrifuged at 3000g and 32C for 2 hours. Virus supernatant was removed, and cell lines (4T1, HCT116, and Jurkat) were added in 400 l of the respective medium supplemented with 1:100 LentiBOOST Solution A and 1:100 LentiBOOST Solution B (Sirion Biotech). Cells were then spinoculated at 800g at 32C for 1.5 hours. After 5 days of culture, cells were sorted for high expression of GFP using flow cytometry.

All animal experiments were approved by the government of Upper Bavaria and were carried out in accordance with the approved guidelines. For 4T1 xenografts of stably expressing ReBphp-PCM and GFP, 0.8 106 cells in PBS have been implanted in the back of FoxN1 nude mice (Charles River Laboratories, Boston, USA) and maintained for 9 days. For HCT116 cells expressing ReBphP-PCM and GFP, 1.5 106 cells in 200 l PBS have been injected intraperitoneally in FoxN1 nude mice and were maintained for 14 days. For intracranial injections of stably expressing ReBphP-PCM and GFP 4T1 cells, mice were first anesthetized according to the animal protocol. The head of the mouse was fixed in a Stereotaxic frame (David Kopf Instruments, model 940), an incision in the skin was made using a scalpel, and a small hole was drilled into the skull. Later, 5-l cells (0.14 106 cells/l) were injected slowly with a 10-l Hamilton syringe (26Gs). The incision in the skin was closed using Histoacryl (B. Braun Melsungen AG). The mice were scanned in MSOT and sacrificed immediately after scanning. For Matrigel implants of Jurkat cells expressing ReBphP-PCM, different concentrations of cells ranging from 6400 to 500 cells/l were implanted subcutaneously in the back of the mice. Similarly, bacterial cells expressing ReBphP-PCM in different concentrations (1.4 105 to 1.4 104 cells/l) were also implanted in the back of the mice. For multiplexing experiment, bacterial cells expressing rsOAPs individually with the concentration of 1.4 106 cells/l were implanted on the back of the mice in the same plane. For multiplexing experiment in vivo, intratumoral injections, bacterial cells expressing DrBphP-PCM resuspended in PBS have been injected into the 4T1 tumor expressing ReBphP-PCM and GFP using an insulin syringe with a 30-gauge needle.

For all MSOT imaging, mice have been anesthetized using 2% isoflurane in O2. Anesthetized mice were placed in the MSOT holder using ultrasound gel and water as coupling media. After termination of the experiments, all mice have been sacrificed and stored at 80C for cryosectioning.

Phantom and mice data were acquired using a commercially available MSOT scanner (MSOT In Vision 256-TF, iThera Medical GmbH, Munich, Germany). In brief, nanosecond pulsed light was generated from a tunable optical parametric oscillator (OPO) laser and delivered to the sample through a ring-type fiber bundle. The wavelengths, 680 and 770 nm, were used for photoswitching and imaging in phantoms and in mice. Light absorbed by the sample generates an acoustic signal that propagates through the sample and is detected outside the sample by a cylindrically focused 256-element transducer. The transducer array had a central frequency of 5 MHz (6 dB was approximately 90%) with a radius of curvature of 40 mm and an angular coverage of 270. Acoustic signals were detected as time series pressure readouts at 2030 discrete time points at 40 MS/s (Mega-samples per second). The acquired acoustic data were reconstructed using the ViewMSOT version 3.8.1.04 (iThera Medical GmbH, Munich, Germany) software with the following settings: 50 kHz to 6.5 MHz; trim speed of 7.

All data analysis was conducted using MATLAB2018b. The data reconstructed with ViewMSOT were loaded into MATLAB by iThera MATLAB code (iThera MATLAB, version: msotlib_beta_rev75). All analyses were carried out with the code provided along with this manuscript (note S3). In brief, movement correction was done by phase correlation preliminary to optimization-based image co-registration with the intensity and nonrigid co-registration of frames of the first cycle being used as reference. For further processing, different features of the time series have been computed and are used for classification/switching label detection using an ML model. For fast Fourier transform, repetitive frequency of the whole concatenated signal for each image point is computed to identify signals corresponding to the illumination schedule. For exponential fitting, the normalized mean kinetic of all cycles is used. Then, the coefficients compared to an expected exponential kinetic are calculated and used as a quality measure. Here, positive and negative exponential are considered. Using fit coefficients and quality of fit (R2) as measures, only 77% accuracy compared to a ground truth is achieved. Thus, additional features are invoked. Overall, all analyzed features are (i and ii) the coefficient for the exponential fit (exp(b(x + 1)) and exp(b(x 1) + 1) of the mean kinetic (mean of all cycles); (iii) R2 of the fit; (iv) the mean intensity over the concatenated signal; (v) max-min of all the data at the pixel; (vi to ix) median maximums and minimums of cycles along with SD; (x) number of cycles with positive or negative trend; (xi) the length of the part of the cycle that shows a trend, i.e., at what point the signal vanishes in the noise; and (xii) Fourier coefficient for the expected frequency defined by the photocontrol schedule. All those are used as predictor values for an unmixing model based on random forest approaches (23, 25)for overall model, trained on 4T1 day 9 as well as highest concentration of Jurkat T lymphocytes. We used 50 trees in the ensemble, as further increase of number did not lead to out-of-bag error decrease. This approach resulted in model performance increase up to 96% of positive predictive value for ground truth (see note S4 for more details on the use of ML in this work).

For visualization, data were not further processed and are shown against the respective slice at 680 nm as anatomy information, except in the case of 4T1 injected in brain where the anatomy is shown at 900 nm. Representative slices are shown. For clustering, appropriate ranges of the kinetic parameter were chosen on the unmixed data to distinguish different labels.

After sacrificing, the mice were cryopreserved at 80C. To detect the fluorescence in tumors, the respective part of the mouse was embedded in Tissue-Tek O.C.T. (Sakura Finetek Europe B.V., Zoeterwonde, The Netherlands). Sections (10 m) were cut (Leica CM1950, Leica Microsystems, Wetzlar, Germany) for brain, 4T1, and HCT116 mice at the interval of 150, 250, and 500 m, respectively, and imaged using a 482/35-nm bandpass for excitation and 535/38-nm bandpass filter for detection of GFP fluorescence. Images were taken using an Andor LucaR charge-coupled device camera (DL-604M, Andor Technology, Belfast, UK) with 10-s exposure and a gain of 10. On the basis of the histology, ground truth on co-registered images was created using a semiautomatic procedure based on anatomical markers and intensity-based multimodal co-registration together with a nonrigid spline-based method and human (two independent)based selection of signals in the fluorescence images.

A 2 to 4% (w/v) aqueous solution of sodium alginate was prepared in PBS. E. coli strain BL21 cells expressing rsOAPs were harvested by centrifugation (4000 rpm, 20 min) and resuspended in PBS. The cell suspensions were then mixed with sterile alginate. Beads were formed by filling the alginate cell mixtures in the syringe with 30-gauge needle, followed by centrifugation at 300 rpm, which allowed the addition of the mixtures into sterile CaCl2 (200 mM). The cell-containing beads, 1 mm in diameter, were allowed to solidify for 10 min before CaCl2 was replaced by fresh distilled water. The cell beads were then randomly distributed in the agar phantom with 1.5% (w/w) agar and 3.5% (v/v) intralipid emulsion and imaged in MSOT as described elsewhere.

For OA characterization of rsOAPs, custom-made experimental setup was used as described earlier (22). Briefly, nanosecond excitation pulses were generated by an OPO laser (SpitLight DPSS 250 ZHGOPO, InnoLas) running at a repetition rate of 50 Hz. Constant pulse energy was ensured using a half-wave plate in a motorized rotation stage (PRM1Z8, Thorlabs) and a polarizing beam splitter; using a lookup table and adapting the polarization with the half-wave plate, we kept the power constant at 1.3 mJ (otherwise mentioned) over the whole illumination schedule. Samples were injected into an acoustically coupled flow chip (-Slide I 0.2 Luer, hydrophobic, uncoated, ibidi) and illuminated from one side using a fiber bundle (CeramOptec) at a constant pulse energy of 1.3 mJ at the fiber output. Photoswitching was carried out by illuminating the sample alternatively with 650- and 780-nm light. OA signals were detected with a cylindrically focused single-element transducer (V382-SU, 3.5 MHz, Olympus) followed by signal amplification by 60 dB with a wide-band voltage amplifier (DHPVA-100, Femto) and digitized at 100 MS/s with a data acquisition card (RZE-002 400, GaGe). Dependency of Pfr Pr conversion on 770-nm pulse energy was measured with different pulse energies (0.4, 0.7, 1.0, and 1.3 mJ). Dependency of Pfr Pr conversion on repetition rate of laser was measured with three different laser repetition rates (10, 25, and 50 Hz). Effect of different switching ON wavelength and resulting dynamic range at 770 nm was measured using different switching ON wavelength ranging from 630 to 680 nm.

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