Category Archives: Biology

Biology

Feathers from deceased birds help scientists understand new threat to avian populations – EurekAlert

image:

A working turbine at a wind energy facility in Northern California

Credit: Todd Katzner

As concernsover the worlds declining bird population mount, animal ecologists developed an analytical approach to better understand one of the latest threats to feathered creatures: the rise of wind and solar energy facilities.

Bird mortality has become an unintended consequence of renewable energy development, said Hannah Vander Zanden, an assistant professor of biology at the University of Florida. If we want to minimize or even offset these fatalities, especially for vulnerable populations, we need to identify the geographic origin of affected birds. In other words, are the dead birds local or are they coming from other parts of North America?

Birds can be killed when they collide with wind turbines, fly into solar panels they mistake for bodies of water or become singed by the intense heat from concentrating solar power plants. While the death rate of birds due to these energy facilities is far less than deaths due to domestic cats and collisions with building, efforts to mitigate this problem is important, scientists say.

Vander Zanden and colleagues performed geospatial analyses of stable hydrogen isotope data obtained from feathers of 871 individual birds found dead at solar and wind energy facilities in California, representing 24 species.

Their analysis of natural-occurring markers in the feathers provided information about where the feathers were grown based on the water the birds consumed.

With these markers, we could determine whether the bird was local or if it was migrating from somewhere else, said Vander Zanden, who is the principal investigator of UFs Animal Migration and Ecology Lab.

Results from the study, which were published Friday in the journal Conservation Biology, show that the birds killed at the facilities were from a broad area across the continent. Their geographical origins varied among species and included a mix of local and nonlocal birds.

Researchers found most birds killed at solar facilities were nonlocal and peaked during the migratory periods of April and September through October. The percentage of migratory birds found at wind facilities nearly matched that of local birds, at 51%, Vander Zanden said.

This kind of data can help inform us about best strategies to use to minimize or mitigate the fatalities, she said. For example, facilities management could work with conservationists to improve the local habitat to help protect local birds or improve other parts of the species range where the migratory birds originate.

The results also illustrate the power of stable isotope data to assess future population growth or decline patterns for birds due to a variety of reasons.

Studying the remains of animals is a noninvasive approach to get information that is otherwise hard to track and apply to conservation, Vander Zanden said. Its a great way to understand the mysteries about animals.

Conservation Biology

The geographic extent of bird populations affected by renewable-energy development

5-Jan-2024

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.

Continue reading here:

Feathers from deceased birds help scientists understand new threat to avian populations - EurekAlert

Biology

Lighting the circuits to risky decision-making – EurekAlert

image:

Bananas represent the reward and the crocodile represents the risk. The blue path is a low risk-low return decision, while the pink path is a high risk-high return decision.

Credit: Trais/WPI-ASHBi

Life consists of infinite possibilities appearing in the real world as multiple choices, that then require decision-making in order to determine the best course of action. However, with every choice there also exists a certain amount of uncertainty or risk. Therefore, behind every decision, lies an intricate evaluation process that balances the risks and rewards associated with taking such actions. This can, in extreme cases, manifest itself as a pathological behavioral state of high risk-high return (HH) and low risk-low return (LL) decision processing that has been associated with gambling disorders.

Although these higher cognitive processes occur seamlessly within the cerebral cortex of our brains dozens to hundreds of times daily the exact underlying neural circuits have remained elusive due to the technical difficulties of specifically targeting and manipulating these neural circuits.

A new study published Science, from a team of researchers led by Dr. Tadashi Isa at the Institute for the Advanced Study of Human Biology (WPI-ASHBi) and Graduate School of Medicine/Kyoto University, have identified and selectively manipulated using optogenetics a method that can modulate the activity of specific neurons with light the distinct neural circuits responsible for balancing risk vs. reward-return decision-making in primates. They show the behavioral changes resulting from stimulating these circuits accumulate over time and have long-term consequences independent of any stimulus providing insights into potential mechanisms underlying pathological risk-taking behaviors such as gambling disorders.

Various experimental paradigms have been developed to evaluate decision-making behavior, with the Iowa Gambling Task being arguably the most famous. However, such neuropsychological tasks are often limited by their design, as they cannot sufficiently uncouple higher-order cognitive processes.

To determine the pure choice bias between HH and LL decisions, Isa and colleagues first designed their own decision paradigm to uncouple risk-dependent choice behavior from other higher-order cognitive processes. Using eye movement to indicate their choice, macaque monkeys were trained to perform a cue/target choice task with water as their reward, consisting of 5 different HH-LL choices across 5 different sets of equivalent expected value (volume of reward awarded multiplied by probability), making a total of 25 potential options. Consistent with other primate studies that looked at risk-behavior, the authors found that primates had an inherent bias for HH over LL choices.

In the early 20th century, the cerebral cortex was mapped into 52 regions, known as Brodmann areas, based on their distinct cellular morphology and organization. The deeper, or ventral, parts of Brodmann area 6 (area 6V), were long thought to only function as a motor area in humans and primates. But more recently, regions overlapping area 6V have also been associated with decision-making processes, though direct evidence supporting such a function has been lacking.

By pharmacologically inactivating several candidate frontal brain regions, using the selective GABAA receptor agonist muscimol, the authors found that the ventral part of area 6V (area 6VV) to be responsible for the HH choice behavior. Interestingly, despite the orbitofrontal cortex (OFC) and the dorsal anterior cingulate cortex (aACC) being considered to play central roles in reward-based decision-making in monkeys, inactivating these regions had little effect on preference for HH choice.

Indeed, we were really surprised that neither the OFC nor the aACC were important for risk-dependent decision-making comments Dr. Ryo Sasaki, the first author of the study.

The ventral tegmental area (VTA) of the brain is essential for reward-associated processes, which is integral to risk-related decision-making. A subpopulation of dopaminergic neurons residing in the VTA are connected to the prefrontal cortex, including area 6V, also known as the mesofrontal (or the mesocortical) pathway.

To dissect the specific role of the mesofrontal pathway in risk-dependent decision-making, Isa and collaborators used an elegant optogenetic strategy, whereby an array consisting of 29 LED lights coupled to electrocorticogram (ECoG) electrodes was engineered (dimensions: 19mm x 12mm) and implanted into area 6V of primate brains expressing photoactivatable proteins in VTA neurons. During the narrow time window of decision-making, the authors precisely manipulated the neural activity of defined VTA terminals in area 6V by turning ON specific LEDs in their array, while simultaneously recording the activity within area 6V, that also included more superficial, or dorsal regions (area 6VD; approximately 2-3mm above area 6VV). The authors uncovered two subcircuits within the mesofrontal pathway with distinct roles in risk-dependent decision-making. They found HH-preference was dependent on the VTA-6VV pathway, whereas LL preference was dependent on the VTA-6VD pathway.

The spatiotemporal resolution of our LED/ECoG array was essential in distinguishing the VTA-6VV and VTA-6VD pathways and deciphering their distinct functional roles in risk-dependent decision-making claims Sasaki.

These findings were further validated by computational decoding, which recapitulated the choice preference behavior induced by photostimulation in primates in silico.

Interestingly, upon repetitive stimulation of either the VTA-6VV or the VTA-6VD pathways, Isa and coauthors observed cumulative effects that persisted over time, leading to long-term changes in preference for HH and LL choice in primates, respectively independent of any photostimulation. Isa comments, ...such long-term changes in choice behavior were rather unexpected and he adds, ... but this may now also offer a mechanistic explanation for how gambling disorders arise.

Exactly how these distinct circuits contribute to balancing our day-to-day decision-making remains unclear, but the authors believe other brain regions are likely to also contribute to this process.

Considering the similarities (in structure and function) between human and non-human primate brains, our findings may have potential therapeutic implications, and even applications in the future, for the treatment of pathological forms of risk-taking such as gambling disorders, he says.

These findings were published in Science on January 5th 2024.

By

Spyros Goulas, Ph.D.

Scientific Advisor

Institute for the Advanced Study of Human Biology (WPI-ASHBi) / Kyoto University

Email: goulas.spyros.3n@kyoto-u.ac.jp

First/Corresponding Author of Study

Ryo Sasaki, Ph.D.

Assistant Professor

Department of Neuroscience, Graduate School of Medicine / Kyoto University

Email: sasaki.ryo.3r@kyoto-u.ac.jp

Lead Principal Investigator/Corresponding Author of Study

Tadashi Isa, M.D., Ph.D.

Professor

Department of Neuroscience, Graduate School of Medicine

Institute for the Advanced Study of Human Biology (WPI-ASHBi) / Kyoto University

Email: isa.tadashi.7u@kyoto-u.ac.jp

###

About Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University

What key biological traits make us human, and how can knowing these lead us to better cures for disease? ASHBi investigates the core concepts of human biology with a particular focus on genome regulation and disease modeling, creating a foundation of knowledge for developing innovative and unique human-centric therapies.

About the World Premier International Research Center Initiative (WPI)

The WPI program was launched in 2007 by Japan's Ministry of Education, Culture, Sports, Science and Technology (MEXT) to foster globally visible research centers boasting the highest standards and outstanding research environments. Numbering more than a dozen and operating at institutions throughout the country, these centers are given a high degree of autonomy, allowing them to engage in innovative modes of management and research. The program is administered by the Japan Society for the Promotion of Science (JSPS).

Experimental study

Animals

Balancing risk-return decisions by manipulating the mesofrontal circuits in primates

5-Jan-2024

Continue reading here:

Lighting the circuits to risky decision-making - EurekAlert

Biology

Inside Science: Revolution in Biology and Its Impact, by Benjamin Lewin – Shepherd Express

WithInside Science, veteran science writer-editor Benjamin Lewin wonders about the changes coming to research methods from the application of AI, which can sort through massive amounts of raw data. And yet, who will have the final interpretation of that data, if there ever is a final interpretation?

Lewin is concerned about the increasing specialization within science, whose researchers know absolutely everything about one thing, but often at the price of being unable to see the broad picture. Coauthors of a single research paper are often unable to understanding the papers meaning beyond their own contributions. Lewin has no patience with the postmodern idea of science as culturally constructed, yet acknowledges how the rise and fall of dogmas illustrate the role of fashion in science. He focuses on biology inInside Science, his own area of specialty as editor ofCell, a leading journal in that field.

Get Inside Science on Amazon here.

Paid link

David Luhrssen lectured at UWM and the MIAD. He is author of The Vietnam War on Film, Encyclopedia of Classic Rock, and Hammer of the Gods: Thule Society and the Birth of Nazism.

Jan. 05, 2024

8:36 a.m.

See original here:

Inside Science: Revolution in Biology and Its Impact, by Benjamin Lewin - Shepherd Express

Biology

Spain to launch an atlas of all living beings cell by cell – EL PAS USA

Some of the worlds top scientists met on May 15 in Barcelona to discuss the crazy idea of studying each species of living being, cell by cell, in order to complete an atlas capable of shedding light on the evolution of life on Earth and the origin of human thought and disease. Seemingly over-ambitious, the idea came to Arnau Seb Pedrs, 37, a biologist from the village of La Fuliola in Lleida, in Catalonia, Spain. Seb Pedrs studies cells, but his real passion is ornithology. He travels to exotic places and makes a point of catching sight of absolutely all bird species in the region, even if he has to spend a week chasing a nondescript brown bird. This all-encompassing ambition may explain his determination to compile what he has called the Cellular Atlas of Biodiversity.

Seb Pedrs works at the Center for Genomic Regulation, close to Barcelonas Somorrostro beach, once a district of shantytowns and now home to half a dozen cutting-edge scientific institutes. The biologists office is small and simple. Three jellyfish, named Gary, Gerry and Cherry, swim around a circular fish tank. From his desk, the researcher proclaims that his project is no longer a pipe dream. The Gordon and Betty Moore Foundation, established in California by the co-founder of Intel and his wife, has just put up 3.6 million to launch the initiative.

Seb Pedrs already made global headlines in September. His team analyzed the four known species of placozoans cell by cell strange creatures shaped like tiny pancakes. They are marine organisms barely a millimeter in size, which diverged from the human group 800 million years ago and consist of 50,000 cells each. The meticulous work of Seb Pedrs and his colleagues has revealed that these tiny beings, lacking a brain or any other organ, possess something similar to neurons, the cells responsible for thought.

The biologist argues that the Cellular Atlas of Biodiversity would reveal a multitude of natures secrets. We have to be prepared to come across unexpected findings, he says. Our study of placozoans was not undertaken with a view to understanding the evolution of neurons and the nervous system. That naturalistic motivation is what I like the most. We are explorers.

Every living being has a unique DNA, present in each of its cells. In the case of human beings, DNA is like a piano with 20,000 keys, which are the genes. All cells have the same piano, but each of them plays a different tune, which is why some are neurons in the brain and others are part of the muscle or the fat around our middle. According to Seb Pedrs, a couple of years ago, his group created the first cell-by-cell atlas of the cauliflower coral, an organism that forms reefs in the shallow waters of the Indian and Pacific oceans. The analysis revealed 40 different cell types. One of them, in charge of making the coral cling to the rock, constantly touches a key that triggers the production of an antimicrobial compound, as if it wanted to clean up its surroundings. The study of the corals cells brought to light a new substance with antibiotic potential during a global alert about the threat of superbugs resistant to all known drugs. It was a surprise, says Seb Pedrs. The potential for finding new genes with new functions is very high.

The May 15 meeting in Barcelona was a success, marking the first time that a scientific alliance of this size has been launched in Spain. It was attended by the leaders of the main international organizations in the field, such as the American biologist Harris Lewin, coordinator of the Earth BioGenome Project, which aims to read the DNA of all species of animals, plants, fungi and protists. Also participating were Stein Aerts, the Belgian bioengineer behind the Fly Cell Atlas, and British researcher Mark Blaxter, who studies 70,000 U.K. species in Darwins Tree of Life project. The heads of the Human Cell Atlas, the Israeli scientist Aviv Regev and the German Sarah Teichmann, joined via videoconference.

The 3.6 million from the Moore Foundation will be used to launch phase 0 of the project, according to Seb Pedrs. The biologist and his colleagues will fine-tune the methods for analyzing each species and prepare the infrastructure of the vast database, in collaboration with Irene Papatheodorou of the European Bioinformatics Institute in Hinxton, England. We want to have a home for the data we will start producing on a large scale already set up, he says.

There are a lot of people working on this in the world, but there is a lack of coordination, adds Seb Pedrs. When you want to access the results for a species, its absolute chaos. There are no standards of any kind. Nor is there a coordinated effort to see who does what. Its the Wild West.

Seb Pedrs is currently putting the finishing touches to an article on the initiative for a leading scientific journal. I know of many people who have done many experiments that have not worked out, wasting thousands and thousands of euros, but there is no culture of publishing your methods and explaining what has not worked for you, Seb Pedrs. The next person who tries it is back at square one. We want to open up the field and let no one keep their magic tricks to themselves.

Phase 0 of the project will investigate eight species that have already been analyzed cell by cell in order to test the protocols. This group will consist of the fruit fly, the worm Caenorhabditis elegans, an annelid (also from the worm group), a plant of the genus Marchantia, an anemone, a fungus, a brown algae, and possibly a sea urchin or a starfish. We want to study organisms that are difficult to handle, with hard casing, to test six cell-by-cell analysis methods, says Seb Pedrs. The usual techniques involve breaking the subject into pieces and obtaining a suspension of single cells using force, sound waves and enzymes. This is followed by examining which keys of the DNA piano each cell plays. We want to obtain a universal method, says Seb Pedrs.

The project will open up a new world for science. Cell atlases not only tell you about the biology of the organism you are analyzing, says Seb Pedrs. You can also study its interactions with what else is inside its cells. His team has investigated microalgal blooms in the ocean, linked to giant viruses that hijack cellular machinery. Scientists can analyze what type of cells the invaders are in and how they usurp the piano keys.

Seb Pedrs is already calculating what phase 1 of the project might look like. We could start with about 100 species spanning the entire tree of life, he says. We will need another 10 to 15 million. Ideally, we would like to sample organisms that are on both sides of major transitions, such as the emergence of multicellular beings and the origin of the nervous system.

Seb Pedrs grew up among the steppe birds typical of the drylands of Lleida. He has made expeditions to study bird life in North Africa, Turkey, Thailand, Chile and Israel, with more than 2,000 species observed. He recently saw his first Tengmalms owl in Spain. In the eastern jungles of Australia, he encountered the mythical cassowary, a bird measuring up to two meters that has been known to kill humans. In his small office in Barcelona there is no decoration, just a drawing of a tapaculo a brown bird from Chile and a postcard with the face of Charles Darwin, the father of the theory of evolution by natural selection. We are interested in studying the evolution of cell types, he says. But first there are a lot of technical questions that are dense and boring, but which we need to solve.

Sign up for our weekly newsletter to get more English-language news coverage from EL PAS USA Edition

See the original post:

Spain to launch an atlas of all living beings cell by cell - EL PAS USA

Biology

Physics, Chemistry Couldnt Give Rise to Biology – Discovery Institute

Photo credit: Rmi Walle, via Unsplash.

The laws of nature provide stable conditions and physical boundaries within which biological outcomes are possible. Laws are, in effect, a chessboard. They provide a stable platform and non-negotiable boundaries. But they do not determine the movement of pieces or the outcome of the game.

Or do they? Rope Kojonen, a theologian at the University of Helsinki, argues for the compatibility of design and evolution. My colleagues Steve Dilley, Brian Miller, Casey Luskin, and Ipublished a reviewof Kojonens thoughtful book,The Compatibility of Evolution and Design, in the journalReligions.In a series atEvolution News, we have been expanding on our response to Dr. Kojonen. Here, I will shift gears to analyze his claims about the laws of nature and their role in the origin of biological complexity and diversity.

The laws of nature are at the heart of Kojonens model. They are the mechanisms of design, the linchpin of Kojonens project to wed design and evolution. To evaluate his model, however, we need to be clear about what exactly his position is. Kojonen is not entirely clear about how the laws of nature (and initial conditions) are said to bring about the origin of life, the diversification of life, and human cognition. However, there seem to be at least three possible ways to interpret Kojonens model:

Lets discuss point one, namely, that the laws of nature (and the like) have causal power or limit the possibility space enough that the diversity of plant and animal species observed today emerged from unicellular organisms. While I am personally convinced that design is evident in the very fabric of the universe and yes, in the laws of physics and chemistry, these material mechanisms do not have sufficient causal power or limit the possibilities sufficiently to explain how the diversity of organisms came to be (if these laws have stayed the same over time). To support this point, Ill talk about the capabilities of the laws of physics and chemistry and give examples of how they currently interact with biology.

In Kojonens model, the laws of nature do the heavy lifting in terms of creating biological complexity. While Kojonen cites an array of other factors e.g., environmental conditions, structuralism, convergence, and evolutionary algorithms its also clear that these factors are undergirded by the laws of nature themselves. But there are limits to the creative power of the laws of nature. If it turns out that the laws have limited ability to produce biological complexity, then other factors (such as the environment, convergence, etc.) thatdependupon the laws of nature likewise have limits. If Kojonen thinks that these other factors have creative powers thattranscendthe limits of the laws of nature, then the burden is on him to show that.Is it possible for the laws of nature to be a causal force or sufficiently constrain the possibility space?

According to one definition, a mechanism is a process that acts on objects to produce an outcome. Here I will define a material mechanism as a process by which a physical object is acted upon by one of the physical laws. Material objects are built from the elements of the periodic table, and the laws of physics and chemistry are the constant processes that constrain how material objects behave. To understand materialistic mechanisms, lets look at a few illustrations.

Definition:The law of universal gravitation says an object will attract another object proportionally to the product of their masses and inversely related to the square of their distance from each other.

This law tells us how objects behave toward one another. Gravity constrains motion, whether that motion is human, planetary, or light. A complex system may also be able to detect gravity and use it as a cue. Lets look at an example of plant growth. Leaves grow in the opposite direction of gravitational pull, but roots grow downward in the direction of gravitational pull. What causes this? Is it gravity? Definitely not. Root growth occurs through the division of stem cells in the root meristem, located at the tip of the root. Thus, root stem cells rely on gravity as a cue to be detected by their sensors, so that they know where to direct their growth. But gravity is not the mechanism that creates plant morphology. Rather, plants work within the constraints of gravity and exploit it via sensors to scaffold their architecture.

Definition:The electrostatic laws state that charges attract or repel with a force that is proportional to the product of their charges and inversely proportional to the square of the distance between them, depending on whether they are alike or different.

Electrostatic laws describe the attraction of positively charged ions to negatively charged ions. These laws constrain (but do not cause) the way an electrochemical gradient can be formed and work across a membrane. The charge and concentration differential across a membrane creates an electrical field. The cell then uses the potential energy of the electrical field to generate energy, convey electrical signals, and power the delivery of nutrients into the cell. The crucial point here is that electrochemical gradients are not an emergent property of the electrostatic laws. Instead, they are caused by molecular machinery. As Elbert Branscomb and Michael J. Russell say in a recent BioEssays paper, to function, life has to take its transformations out of the hands of chemistry and operate them itself, using macromolecular mechano-chemical machines, requiring one machine (roughly) for each transformation; life must, in Nick Lanes evocative phrasing, transcend chemistry.(Branscomb and Russell 2018)

How do electrostatic laws interface with organisms body plans? Organism body patterning is formed in part by bioelectrical networks, which operate across cell fields to integrate information and mediate morphological decision-making. (Djamgoz and Levin 2022) The bioelectrical networks play critical roles by regulating gene expression, organ morphogenesis, and organ patterning. This is, of course, exactly what would be necessary as an emergent property from electrostatic laws for them to have generative capacity. But these bioelectric networks no more emerge from the electrostatic laws than do cellular networks; rather, these bioelectric networks are information rich networks which carry information in a bioelectric code which can be understood by the sender and receiver.(Levin 2014)

Now the electrostatic laws, in conjunction with the design of the periodic table of elements, constrain the possible chemical space of molecule bonding arrangements. For example, based on the chemical characteristics of hydrogen and oxygen as well as the electrostatic laws, H2O has a specific bonding configuration. These mechanisms can thus explain the origin and ready formation of some simple molecules. But what about more complex molecules like those used in life? According to a paper in the journalNature, Chemical space and biology, The chemical compounds used by biological systems represent a staggeringly small fraction of the total possible number of small carbon-based compounds with molecular masses in the same range as those of living systems (that is, less than about 500 daltons). Some estimates of this number are in excess of 1060.(Dobson 2004)This statement is consistent with our observation that complex molecules like glucose and nucleic acids result from enzymes. If one thinks that electrostatic laws and the periodic table limit the search space so that molecules like nucleic acids form on their own, then nucleic acids should form spontaneously from phosphate, nitrogen, carbon, hydrogen, and oxygen, just like water does. But this is not something that is observed. Instead, complex molecules in an appreciable quantity can only be built using enzymes (which are built using information in DNA) or in highly controlled laboratory synthesis environments. Not to mention the fact that there must be something in the natural laws that forces the chemistry of life to use only left-handed molecules. And if that is true, then why arent all molecules left-handed as this would seem to require a rule in the laws.

If one grants the first cell (supposing the origin of life is a miraculous event), there remain thousands of unique molecular compounds essential for the diversity of life to be selected from the chemical space. We know that many of these molecular structures are multipurpose, recyclable, and essential to other ecosystem members. The design of these molecules and the enzymes that make and break them down appears to have required foresight for the needs and functions of the ecosystem as well as an in-depth understanding of chemistry and biochemistry. Is this type of information and causal power available in the electrostatic laws or the other laws of nature?

Definition:The first law of thermodynamics says that matter and energy cannot be created or destroyed but can only change form. The second law of thermodynamics says that closed systems always move toward states of greater disorder. Open systems move toward equilibrium, where the disorder (aka entropy) of the universe is at its maximum.

The laws of thermodynamics place constraints on what biological organisms must do to remain alive. That is, organisms must capture, harness, and expend energy to maintain a state far from equilibrium. To do this, organisms must/do have incredibly designed architectures that reflect a highly advanced understanding and exploitation of the laws of nature. For example, in central carbon metabolism, energy is extracted from the molecule glucose in the most efficient way possible. But just because this biochemical pathway exhibits an architecture that is amazingly designed to leverage the constraints imposed by thermodynamics does not mean that the laws provide a mechanism by which these complex systems arose in the first place. In other words, simply because a vehicle is highly efficient does not imply that the laws of thermodynamics designed it. More likely, it means whoever designed the vehicle had a thorough understanding of thermodynamics.

Definition:Quantum physics describes the physical properties at the level of atoms and subatomic particles using the wave function, which is determined by the Schrdinger equation. The Schrdinger equation is the quantum counterpart of Newtons second law, describing what happens in the quantum realm to systems of subatomic particles.

Schrdinger equations are linear equations, so when added, the outcome is also linear. This is very different from what is observed in the real world. For biology and complex systems, conditional branching occurs, as in the example:

If {antibiotic is detected} then (express antibiotic efflux pump). If {antibiotic decreases} then (decrease expression of antibiotic efflux pump).

This type of branching found in complex systems cannot be boiled down to a wave function. Thus, as George Ellis, a leading theorist in cosmology and complex systems, says [T]here is no single wave function for a living cell or macroscopic objects such as a cat or a brain. In short, the complex nonlinear world is unable to arise from a single wavefunction.

Definition:The behavior that an organism programmatically/cognitively undertakes to avoid death.

The laws of physics and chemistry do NOT include natural selection. Natural selection is an outcome of the programming of a specific goal:desire to survive. As such, I define natural selection as the change in populations that depends upon their programmed and, in some cases, cognitive capacity to survive and the environmental factors they face. Please note that this definition is different from how most people might think of natural selection, but one hopes it is more accurately aligned with how it actually works. To support this goal, the desire to survive, organisms have a variety of mechanisms that may include both voluntary and involuntary responses. For example, in humans, the immune system would be an example of an involuntary response (programmatically compiled) where the defenses of the body fight off invaders. An example of a voluntary response (a cognitive response) in humans might be when someone runs for their life from a bear or kills a poisonous snake. Another example of an involuntary mechanism is natural genetic engineering. In case you arent familiar with natural genetic engineering, it just means that cells have the capability to actively reorganize and modify their own genomes to enable survival. This involves mechanisms like transposition (movements of genetic elements within the genome), gene duplication, horizontal gene transfer (transfer of genetic material between different organisms), and other forms of genetic rearrangement. Another important example is phenotypic plasticity, which has frequently been confused for natural selection but is the ability of an individual organism to exhibit different phenotypes (observable characteristics or traits), for example, in response to changes it senses in the environment. Phenotypic plasticity occurs too rapidly to be driven by mutation and selection; thus, it is recognized as an innate adaptation algorithm embedded within an organism.

So, the desire to survive, coupled with environmental conditions and random mutations that favor some individuals over others, is natural selection. As natural selection relies on the agent- or life-specific mechanism of a desire to survive, it cannot account for anything related to the origin of life, only the diversification of life. The degree to which natural selection can account for the diversification of life is an active area of research, but ID proponents Douglas Axe and Brian Miller have discovered some important limits. Miller summarized decades of research on the topic of protein evolution, which relies on natural selection, in our response to Rope Kojonen. In short, they have shown that natural selection is not capable of creating a high-complexity enzyme from a random sequence of amino acids or of transforming one protein fold into a different fold without guidance. This is effectively an upper bound for what natural selection can accomplish, which bears not only on origin-of-life scenarios but also on the ability of life to diversify from a single organism into the diversity we see today.

The emergent properties of physics and chemistry are necessary, but not sufficient to explain the origin or diversification of biological organisms. Gravity can be used as a cue by biology to determine directionality, but gravity doesnt make a leaf grow up or a root grow down that happens only because a complex system is sensing, interpreting, and acting on the gravitational cue. The design of the periodic table of elements constrains the bonding pattern between hydrogen and oxygen and bestows upon water its life-giving properties, but these constraints on chemical bonding do not cause the formation of DNA or other complex molecules. Enzymes are necessary for more complex molecules to be formed at the rate required for life. The electrostatic laws describe how positive and negative charges attract one another, but these laws do not cause the formation of an electrochemical gradient across a membrane that only happens because molecular machines harness energy to push a system away from equilibrium. In quantum physics, the linear wave function describes the wave-particle duality of matter, but it cannot account for the conditional branching observed in complex systems.

In short, the best way to summarize the capacity of all these material mechanisms is in George Elliss words from his recent article, Quantum physics and biology: the local wavefunction approach: The laws of physics do not determine any specific outcomes whatsoever. Rather they determine the possibility space within which such outcomes can be designed.(Ellis 2023)

Tomorrow we will look at the second interpretation of Kojonens model for how the laws of nature and initial conditions could bring about life and its diversification.

Continue reading here:

Physics, Chemistry Couldnt Give Rise to Biology - Discovery Institute

Biology

Multiple reaction monitoring assays for large-scale quantitation of proteins from 20 mouse organs and tissues … – Nature.com

Justice, M. J. & Dhillon, P. Using the mouse to model human disease: increasing validity and reproducibility. Dis. Model. Mech. 9, 101103 (2016).

Article CAS PubMed PubMed Central Google Scholar

Perlman, R. L. Mouse models of human disease: an evolutionary perspective. Evol. Med. Public Health 2016, 170176 (2016).

PubMed PubMed Central Google Scholar

Ben-David, U., Beroukhim, R. & Golub, T. R. Genomic evolution of cancer models: perils and opportunities. Nat. Rev. Cancer 19, 97109 (2019).

Article CAS PubMed PubMed Central Google Scholar

Kersten, K., de Visser, K. E., van Miltenburg, M. H. & Jonkers, J. Genetically engineered mouse models in oncology research and cancer medicine. EMBO Mol. Med. 9, 137153 (2017).

Article CAS PubMed Google Scholar

Nadeau, J. H. & Auwerx, J. The virtuous cycle of human genetics and mouse models in drug discovery. Nat. Rev. Drug Discov. 18, 255272 (2019).

Article CAS PubMed Google Scholar

Meehan, T. F. et al. Disease model discovery from 3,328 gene knockouts by the International Mouse Phenotyping Consortium. Nat. Genet. 49, 12311238 (2017).

Article CAS PubMed PubMed Central Google Scholar

Gamazon, E. R., Zwinderman, A. H., Cox, N. J., Denys, D. & Derks, E. M. Multi-tissue transcriptome analyses identify genetic mechanisms underlying neuropsychiatric traits. Nat. Genet. 51, 933940 (2019).

Article CAS PubMed PubMed Central Google Scholar

Mardinoglu, A., Uhlen, M. & Born, J. Broad views of non-alcoholic fatty liver disease. Cell Syst. 6, 79 (2018).

Article CAS PubMed Google Scholar

Neidlin, M., Dimitrakopoulou, S. & Alexopoulos, L. G. Multi-tissue network analysis for drug prioritization in knee osteoarthritis. Sci. Rep. 9, 112 (2019).

Article CAS Google Scholar

Zhuang, J. et al. Comparison of multi-tissue aging between human and mouse. Sci. Rep. 9, 19 (2019).

Article Google Scholar

Drawnel, F. M. et al. Molecular phenotyping combines molecular information, biological relevance, and patient data to improve productivity of early drug discovery. Cell Chem. Biol. 24, 624634.e3 (2017).

Article CAS PubMed Google Scholar

Karczewski, K. J. & Snyder, M. P. Integrative omics for health and disease. Nat. Rev. Genet. 19, 299310 (2018).

Article CAS PubMed PubMed Central Google Scholar

Baker, E. S. et al. Mass spectrometry for translational proteomics: progress and clinical implications. Genome Med. 4, 63 (2012).

Article CAS PubMed PubMed Central Google Scholar

Schubert O. T., et al. Quantitative proteomics: challenges and opportunities in basic and applied research | Kopernio. https://kopernio.com/viewer?doi=10.1038%2Fnprot.2017.040&token=WzIwMzcwMDUsIjEwLjEwMzgvbnByb3QuMjAxNy4wNDAiXQ.CjCfIPEraaJ57uSrmk6-FV12Ifw.

Vidova, V. & Spacil, Z. A review on mass spectrometry-based quantitative proteomics: targeted and data independent acquisition. Anal. Chim. Acta 964, 723 (2017).

Article CAS PubMed Google Scholar

Mendes, M. L. & Dittmar, G. Targeted proteomics on its way to discovery. Proteomics 22, 2100330 (2022).

Article CAS Google Scholar

Sobsey, C. A. et al. Targeted and untargeted proteomics approaches in biomarker development. Proteomics 20, 1900029 (2020).

Article CAS Google Scholar

Ebhardt, H. A., Root, A., Sander, C. & Aebersold, R. Applications of targeted proteomics in systems biology and translational medicine. Proteomics 15, 31933208 (2015).

Article CAS PubMed PubMed Central Google Scholar

Meyer, J. G. & Schilling, B. Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques. Expert Rev. Proteom. 14, 419429 (2017).

Article CAS Google Scholar

Zhu, Y., Aebersold, R., Mann, M. & Guo, T. SnapShot: clinical proteomics. Cell 184, 48404840.e1 (2021).

Article CAS PubMed Google Scholar

Do, M. et al. Clinical application of multiple reaction monitoring-mass spectrometry to human epidermal growth factor receptor 2 measurements as a potential diagnostic tool for breast cancer therapy. Clin. Chem. 66, 13391348 (2020).

Article PubMed Google Scholar

Son, M. et al. A clinically applicable 24-protein model for classifying risk subgroups in pancreatic ductal adenocarcinomas using multiple reaction monitoring-mass spectrometry. Clin. Cancer Res. 27, 33703382 (2021).

Article CAS PubMed Google Scholar

Illiano, A. et al. Multiple reaction monitoring tandem mass spectrometry approach for the identification of biological fluids at crime scene investigations. Anal. Chem. 90, 56275636 (2018).

Article CAS PubMed Google Scholar

Huang, J. et al. Quantitation of human milk proteins and their glycoforms using multiple reaction monitoring (MRM). Anal. Bioanal. Chem. 409, 589606 (2017).

Article CAS PubMed Google Scholar

Albrecht, S. et al. Multiple reaction monitoring targeted LC-MS analysis of potential cell death marker proteins for increased bioprocess control. Anal. Bioanal. Chem. 410, 31973207 (2018).

Article CAS PubMed Google Scholar

Wang, Z. et al. A multiplex protein panel assay for severity prediction and outcome prognosis in patients with COVID-19: an observational multi-cohort study. eClinicalMedicine 49, 101495 (2022).

Ciccimaro, E. & Blair, I. A. Stable-isotope dilution LCMS for quantitative biomarker analysis. Bioanalysis 2, 311341 (2010).

Article CAS PubMed Google Scholar

Abbatiello, S. E. et al. Large-scale interlaboratory study to develop, analytically validate and apply highly multiplexed, quantitative peptide assays to measure cancer-relevant proteins in plasma. Mol. Cell. Proteom. 14, 23572374 (2015).

Article CAS Google Scholar

Arnold, S. L., Stevison, F. & Isoherranen, N. Impact of sample matrix on accuracy of peptide quantification: assessment of calibrator and internal standard selection and method validation. Anal. Chem. 88, 746753 (2016).

Article CAS PubMed Google Scholar

Hoofnagle, A. N. et al. Recommendations for the generation, quantification, storage and handling of peptides used for mass spectrometry-based assays. Clin. Chem. 62, 4869 (2016).

Article CAS PubMed PubMed Central Google Scholar

Chiva, C. & Sabid, E. Peptide selection for targeted protein quantitation. J. Proteome Res. 16, 13761380 (2017).

Article CAS PubMed Google Scholar

Mohammed, Y. et al. PeptidePicker: a scientific workflow with web interface for selecting appropriate peptides for targeted proteomics experiments. J. Proteom. 106, 151161 (2014).

Article CAS Google Scholar

Chiva, C. et al. Isotopologue multipoint calibration for proteomics biomarker quantification in clinical practice. Anal. Chem. 91, 49344938 (2019).

Article CAS PubMed Google Scholar

LeBlanc, A. et al. Multiplexed MRM-based protein quantitation using two different stable isotope-labeled peptide isotopologues for calibration. J. Proteome Res. 16, 25272536 (2017).

Article CAS PubMed Google Scholar

Mohammed, Y., Pan, J., Zhang, S., Han, J. & Borchers, C. H. ExSTA: external standard addition method for accurate high-throughput quantitation in targeted proteomics experiments. Proteomics Clin. Appl. 12, 1600180 (2018).

Article PubMed Google Scholar

Pino, L. K. et al. Calibration using a single-point external reference material harmonizes quantitative mass spectrometry proteomics data between platforms and laboratories. Anal. Chem. 90, 1311213117 (2018).

Article CAS PubMed PubMed Central Google Scholar

Whiteaker, J. R. et al. Using the CPTAC Assay Portal to identify and implement highly characterized targeted proteomics assays. Methods Mol. Biol. Clifton NJ 1410, 223236 (2016).

Article CAS Google Scholar

Parker, C. E. & Borchers, C. H. Mass spectrometry based biomarker discovery, verification, and validationquality assurance and control of protein biomarker assays. Mol. Oncol. 8, 840858 (2014).

Article CAS PubMed PubMed Central Google Scholar

Kennedy, J. J. et al. Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins. Nat. Methods 11, 149155 (2014).

Article CAS PubMed Google Scholar

Michaud, S. A. et al. Molecular phenotyping of laboratory mouse strains using 500 multiple reaction monitoring mass spectrometry plasma assays. Commun. Biol. 1, 19 (2018).

Article CAS Google Scholar

Whiteaker, J. R. et al. CPTAC Assay Portal: a repository of targeted proteomic assays. Nat. Methods 11, 703704 (2014).

Article CAS PubMed PubMed Central Google Scholar

Geiger, T. et al. Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse. Mol. Cell. Proteom. 12, 17091722 (2013).

Article CAS Google Scholar

Viode, A. et al. A simple, time- and cost-effective, high-throughput depletion strategy for deep plasma proteomics. Sci. Adv. 9, eadf9717 (2023).

Article CAS PubMed PubMed Central Google Scholar

Batth, T. S., Francavilla, C. & Olsen, J. V. Off-line high-pH reversed-phase fractionation for in-depth phosphoproteomics. J. Proteome Res. 13, 61766186 (2014).

Article CAS PubMed Google Scholar

Faca, V. et al. Contribution of protein fractionation to depth of analysis of the serum and plasma proteomes. J. Proteome Res. 6, 35583565 (2007).

Article CAS PubMed Google Scholar

Taoufiq, Z. et al. Hidden proteome of synaptic vesicles in the mammalian brain. Proc. Natl Acad. Sci. 117, 3358633596 (2020).

Article CAS PubMed PubMed Central Google Scholar

Kaur, G. et al. Extending the depth of human plasma proteome coverage using simple fractionation techniques. J. Proteome Res. 20, 12611279 (2021).

Article CAS PubMed Google Scholar

Jankovska, E., Svitek, M., Holada, K. & Petrak, J. Affinity depletion versus relative protein enrichment: a side-by-side comparison of two major strategies for increasing human cerebrospinal fluid proteome coverage. Clin. Proteom. 16, 9 (2019).

Article Google Scholar

Wang, D. et al. A deep proteome and transcriptome abundance atlas of 29 healthy human tissues. Mol. Syst. Biol. 15, e8503 (2019).

Article PubMed PubMed Central Google Scholar

Castillo, E. et al. Comparative profiling of cortical gene expression in Alzheimers disease patients and mouse models demonstrates a link between amyloidosis and neuroinflammation. Sci. Rep. 7, 17762 (2017).

Patir, A., Shih, B., McColl, B. W. & Freeman, T. C. A core transcriptional signature of human microglia: derivation and utility in describing region-dependent alterations associated with Alzheimers disease. Glia 67, 12401253 (2019).

Article PubMed Google Scholar

Anderson, N. L. & Anderson, N. G. The human plasma proteome: history, character, and diagnostic prospects *. Mol. Cell. Proteom. 1, 845867 (2002).

See the original post:

Multiple reaction monitoring assays for large-scale quantitation of proteins from 20 mouse organs and tissues ... - Nature.com

Biology

Calendar of events, awards and opportunities – ASBMB Today

Every week, we update this list with new meetings, awards, scholarships and events to help you advance your career.If youd like us to feature something that youre offering to the bioscience community, email us with the subject line For calendar. ASBMB members offerings take priority, and we do not promote products/services. Learn how to advertise in ASBMB Today.

The Art of Science Communication is an eight-week online course designed to provide you with fundamental training in science communication. Whether you're a professional scientist, educator or a scientist in training, the ASC course will equip you with the knowledge to effectively and confidently present your science to nonexpert audiences in formal and informal settings. The course delves into the essential elements of crafting a compelling presentation through instructional videos, background material, live online discussions and peer-to-peer mentoring. The course starts Jan. 22 and concludes on March 15. Space is limited. You now have until Jan. 7 to reserve your spot.

The Air Force Research LaboratoryScholars Program is administered by Universities Space Research Associationwith the goal of "strengthening the science, technology, engineeringand mathematics workforce pipeline." Undergraduate- and graduate-level university students pursuing STEM degrees and upper-level high school students are invited to apply for the AFRL Scholars Program. Selected students will participate in paid internship opportunities and "gain valuable hands-on experiences working with full-time AFRL scientists and engineers on cutting-edge research and technology and are able to contribute to unique, research-based projects." Learn more.

The Opentrons Flex Nucleic Acid Extraction Workstation is a "benchtop liquid handler with up to 96-sample throughput." At 12 p.m. Eastern on Jan. 10, Opentrons Labworks, Inc. is hosting a webinar about automating nucleic acid extraction, the workstation, and "how to change deck layout, swap a pipette and perform autocalibration." Learn more.

Discover BMB is the annual meeting of the American Society for Biochemistry and Molecular Biology. The 2025 meeting will be held in Chicago, and we're calling on ASBMB members to help shape the programming. Self-nominate yourself today for a speaking slot! This is your chance to let the organizing committee know about your research. Applicants must be regular, industry or early-career members of the ASBMB. To apply, briefly describe (2,000 characters or fewer) your recent work as it relates to one of the 2025 themes. See the themes and apply.Learn more about the call for self-nominations.

The American Society of Gene and Cell Therapy is partnering with the American Association for the Advancement of Scienceto host a one-yearpolicy fellowship on Capitol Hill. "Fellows will provide high-quality, science-based, independent guidance to federal policy makers and elevate awareness of the society among policymaking circles." Learn more.

At 12 p.m. Eastern on Jan. 16, the International Union of Biochemistry and Molecular Biology Trainee Initiative is hosting webinar titled "Addressing mental health in research from scientists for scientists." The online event and panel discussion will feature mental health experts and scientists sharing their experiences. It will cover strategies to manage mental health crises and offer inspiration through personal stories of triumph over adversity. Speakers include Madeline McGhee, a laboratory techician at Massachusetts Institute of Technology, and Alexander Tsai, a psychiatrist and associate professor of psychiatry at Harvard Medical School. Follow the IUBMB Trainee Initiative on Instagram, @iubmb_trainee, for more speaker announcements. Learn more and register.

Genetic Engineering & Biotechnology Newsis hosting a webinar titled "Improved AAV capsid purification via high-resolution chromatography" at 11 a.m. Eastern on Jan. 16. During the webinar, Ale trancar of Sartorius BIA Separations will "discuss various chromatographic methods to consistently separate empty, partial, and full capsids in large-scale AAV manufacturing." Learn more.

Negotiations occur every day in the scientific laboratory and workplace and often involve issues that are key to research success and career advancement. This workshop, co-sponsored by the ASBMB Women in Biochemistry and Molecular Biology Committee and the Committee on the Advancement of Women Chemists, teaches the fundamentals of negotiation relevant to a variety of one-on-one conversations and group settings. Topics include:

At 1 p.m. Eastern on Jan. 17, the Federation of American Societies for Experimental Biology is hosting a webinar about how to create a quality data-management plan for your next National Institutes of Health grant. The webinar will review policy requirements for plans and provide step-by-step guidance. Learn more.

Discover BMB is the annual meeting of the American Society for Biochemistry and Molecular Biology. The 2024 meeting will be held in San Antonio, and we're now accepting late-breaking abstracts for poster presentations. When you present your research at #DiscoverBMB, you get the recognition and constructive feedback that you need to make your work even better. The meeting will be held March 2326 in San Antonio, Texas. See the abstract categories and submit your late-breaking abstract.

Are you a scientist curious about how your expertise can contribute to the greater good? This webinar will help you understand the broad range of government roles beyond what you might ordinarily think of as public sector. From research and innovation to policy development and implementation, the government offers a vast array of avenues for scientists to apply their skills and knowledge. Unlock the door to a world of possibilities as we discuss government careers in the sciences and explore the diverse opportunities available for scientists looking to make a meaningful impact on society. This event is sponsored by the ASBMB Education and Professional Development Committee Graduate/Postdoctoral Subcommittee. Learn more and register for free.

Join the ASBMB public affairs department for its monthly "Finding the funds" webinar connectingASBMB members with the unique funding opportunities that are available to them as BMB scientists. In this edition, Gail McLean of the Department of Energy Office of Science will present on DOE funding priorities, award opportunities and training grants. Learn more.

Genetic Engineering & Biotechnology Newsis hosting a virtual event on Jan. 24 about the state of cell and gene therapy. Speakers from industry and academia will "discuss the latest research developments, innovations, and disruptive technologies that are impacting patients lives today and will spur cell and gene therapies to bigger and better things tomorrow." Learn more.

Science's "Dance Your Ph.D. Contest" is now accepting entries! In this competition, scientists are invited to explain their research through dance. Here are the steps to enter, from Science Magazine's LinkedIn:

There are three prizes. The first two categories come with $750 prizes and are"physics, biology, chemistryand social science" and "AI/quantum." The top prize, for "Dance Champ," is $2,000. Learn more.

This webinarhosted by Brukerwill "overview the versatile roles of NMR spectroscopy in RNA drug discovery for providing the structural basis for the rational drug design. Advanced techniques for simplifying crowded spectra of large RNAs will be discussed." Learn more.

FASEB's Catalyst Conferences are "short, virtual meetings that are intended to help foster communities in emerging areas of biology." This is the first Catalyst Conference of 2024, and it "will bring together scientists to discuss on the many unresolved and still debated issues on TDP-43 structure, biology, misbehaviorand involvement in diseases." Learn more.

The Centre for Predictive Human Model Systems (CPHMS) is hosting a webinar on how single-cell transcriptomics can help researchers untangle the intricacies of oral cancer. At 4 p.m. Indian Standard Time (5:30 a.m. Eastern Time) on Feb. 2, Arindam Maitra at the National Institute of Biomedical Genomics, West Bengal will share about his research on gingiva-buccal oral cancer. Learn more.

The Lasker Foundation is accepting nominations for the 2024 Lasker Awards in biomedical research and advocacy. Prize categories include: Basic Medical Research, Clinical Medical Researchand Public Service. Winners will receive a $250,000 honorarium. "Since 1945, the Lasker Foundation has conferred more than 410 awards, which recognize the contributions of scientists, physicians, and public citizens who have made major advances in the understanding, diagnosis, treatment, cure, and prevention of human disease." Learn more.

At 1 p.m. Eastern on Feb. 14, FASEBis hosting a webinar titled"5 reasons we can't publish your dataset." This virtual conversation will cover "best practices for preparing datasets and how to avoid common mistakes," plus "some of the most common reasons data is sent back to authors" to help attendees ensure their dataset is published rapidly and smoothly. Learn more.

The NIH's Summer Internship Program is "an opportunity for students in college, graduate, and professional school to perform a summer research internship in the Intramural Research Program at the NIH." Interns work with a principal investigator and research opportunities include: "biomedical, behavioral, and social sciences with opportunities to explore basic, translationaland clinical research." There will be a Q&A webinar at 3 p.m. Eastern on Jan. 4. Learn more.

In observance of Rare Disease Week, the Food & Drug Administration will host a virtual public meeting on March 1 from 9 a.m.4:30 p.m. Eastern. Topics that will be covered during panel discussionsinclude "the legal framework for approving studies and medical products at FDA, what FDA does during review processes to approve medical products, decentralized clinical trials and digital health technologies" and more. As stated in the event description, "stakeholders are invited to provide their perspectives on the discussion questions through the public docket." Learn more.

The 2024 National Postdoctoral Conference will be held in Seattle. It is "the largest national conference and networking event dedicated to the postdoctoral community " during which attendees will have the "opportunity to gather and enhance their professional development and leadership skills." Learn more.

#DiscoverBMB is the annual meeting of the American Society for Biochemistry and Molecular Biology. With a mission to share the latest, most impactful research findings in the molecular life sciences, #DiscoverBMB offers an exciting agenda that includes talks by the field's foremost experts, interactive workshops on the latest trends, technologies and techniques, and an invigorating exhibition of posters, services and products. The meeting attracts researchers in academia and industry, educators, trainees and students from across the globe. It offers unparalleled opportunities for collaborating, networking and recruiting. See the symposia themes and organizers.Learn more.

The Scientist Mentoring & Diversity Program is a one-year career mentoring program that pairs ethnically diverse students (undergraduate juniors and seniors, baccalaureate, master's or Ph.D.), postdocs and early-career researchers with industry mentors "who work at companies in the medical technology, biotechnology and consumer healthcare industries." Scholars will attend a five-day training session "to learn about career opportunities in industry and receive career development coaching. They also attend a major industry conference." Learn more.

The fields of transcription biochemistry and molecular biology have become one with chromatin biology and epigenetics with extensive cross-talk. RNA polymerase II and its transcription machinery play an essential role in the modification and remodeling of chromatin,and chromatin regulates gene expression in both normal and pathological conditions. With recent innovations and technological advances in clinical and preclinical research, personalized medicine is becoming a reality, in part because of advances in our understanding of RNA polymerase II. Many established and new investigators have taken on the challenge of elucidating the molecular mechanisms of gene expression by RNA polymerase II in the context of chromatin. The community is highly dynamic and multi-disciplinary, with an ever-changing set of focal areas that establish new paradigms and new ways of thinking about the topic. Even after decades of study, this research area continues to advance, reveal new concepts, and bolsters almost every other area of biology. Learn more.

The 2025 Deuel conference will be hosted at the Hyatt Regency in Long Beach, Calif. It is a must-attend event for leading lipids investigators and for scientists whove just begun to explore the role of lipids in their research programs. This event will bring together a diverse array of people including those who have not attended Deuel or perhaps any lipid meeting before. The conference is a forum for the presentation of new and unpublished data, and attendees enjoy the informal atmosphere that encourages free and open discussion. Interested scientists are invited to attend and encourage trainees to submit abstracts. Learn more.

This five-day symposium, held at the Broad Institute of MIT and Harvard in Cambridge, Mass., will be an international forum for discussion of the remarkable advances in cell and human protein biology revealed by ever-more-innovative and powerful proteomics technologies. Formerly known as the "International symposium on mass spectrometry in the health and life sciences," the meeting has been renamed to reflect the growing number of partial and non-mass spectrometrybased methods under discussion.

The symposium will juxtapose sessions about methodological advances with sessions about the roles those advances play in solving problems and seizing opportunities to understand the composition, dynamics and function of cellular machinery in numerous biological contexts. In addition to celebrating these successes, we also intend to articulate urgent, unmet needs and unsolved problems that will drive the field in the future. In addition to talks by invited plenary and session speakers, short talks will be selected from submitted abstracts. See the program of our previous meeting.

Themes:

We are now accepting proposals for scientific events to be held in 2024 and 2025. You pick the topic, the sessions and the speakers, and well do the rest.

Thats right! Well manage registration, market the event to tens of thousands of scientists, and handle all the logistics so that you can focus on the science.

The top areas of research interest among ASBMB members include the following, but well consider all proposals:

What molecule, method or research question needs more attention? Were here to help you realize your vision and deliver cutting-edge science to the BMB community.

Propose an event.

Van Andel Institute offers sernior graduate studentswho are exploring postdoc optionsthe opportunity to visit VAI to learn about its postdoctoral training positions. Applications are accepted year-round, and participants will meet one-on-one with faculty and explore VAI's scientific resources.There is no cost to attend for selected applicants. Learn more.

Graduate students, postdoctoral fellows and established senior investigators are all invited to participate in Janelia's Visiting Scientist Program. Janelia accepts visitor proposals on a continuous basis. Since 2007, more than 410 visiting scientists from 23 countries have participated in the program. Learn more.

See original here:

Calendar of events, awards and opportunities - ASBMB Today

Biology

Cell type evolution reconstruction across species through cell phylogenies of single-cell RNA sequencing data – Nature.com

Sulston, J. E., Schierenberg, E., White, J. G. & Thomson, J. N. The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev. Biol. 100, 64119 (1983).

Article PubMed CAS Google Scholar

Martindale, M. Q. & Henry, J. Q. Intracellular fate mapping in a basal metazoan, the ctenophore Mnemiopsis leidyi, reveals the origins of mesoderm and the existence of indeterminate cell lineages. Dev. Biol. 214, 243257 (1999).

Article PubMed CAS Google Scholar

Spencer Chapman, M. et al. Lineage tracing of human development through somatic mutations. Nature 595, 8590 (2021).

Article PubMed CAS Google Scholar

Tanay, A. & Seb-Pedrs, A. Evolutionary cell type mapping with single-cell genomics. Trends Genet. 37, 919932 (2021).

Article PubMed CAS Google Scholar

Shekhar, K. et al. Comprehensive classification of retinal bipolar neurons by single-cell transcriptomics. Cell 166, 13081323 (2016).

Gilbert, E. et al. Molecular and cellular architecture of the larval sensory organ in the cnidarian Nematostella vectensis. Development 149, dev200833 (2022).

Article PubMed PubMed Central CAS Google Scholar

Kin, K., Nnamani, M. C., Lynch, V. J., Michaelides, E. & Wagner, G. P. Cell-type phylogenetics and the origin of endometrial stromal cells. Cell Rep. 10, 13981409 (2015).

Article PubMed CAS Google Scholar

Liang, C., Forrest, A. R. R. & Wagner, G. P. The statistical geometry of transcriptome divergence in cell-type evolution and cancer. Nat. Commun. 6, 6066 (2015).

Article PubMed CAS Google Scholar

Musser, J. M. et al. Profiling cellular diversity in sponges informs animal cell type and nervous system evolution. Science 374, 717723 (2021).

Article PubMed PubMed Central CAS Google Scholar

Hughes, A. L. & Friedman, R. A phylogenetic approach to gene expression data: evidence for the evolutionary origin of mammalian leukocyte phenotypes. Evol. Dev. 11, 382390 (2009).

Article PubMed PubMed Central CAS Google Scholar

Wagner, G. P. Homology, Genes, and Evolutionary Innovation (Princeton Univ. Press, 2014).

Arendt, D. et al. The origin and evolution of cell types. Nat. Rev. Genet. 17, 744757 (2016).

Article PubMed CAS Google Scholar

Arendt, D. The evolution of cell types in animals: emerging principles from molecular studies. Nat. Rev. Genet. 9, 868882 (2008).

Article PubMed CAS Google Scholar

Arendt, D. Evolution of eyes and photoreceptor cell types. Int. J. Dev. Biol. 47, 563571 (2003).

PubMed Google Scholar

Arendt, D., Bertucci, P. Y., Achim, K. & Musser, J. M. Evolution of neuronal types and families. Curr. Opin. Neurobiol. 56, 144152 (2019).

Article PubMed PubMed Central CAS Google Scholar

Serb, J. M. & Oakley, T. H. Hierarchical phylogenetics as a quantitative analytical framework for evolutionary developmental biology. Bioessays 27, 11581166 (2005).

Article PubMed CAS Google Scholar

Packer, J. S. et al. A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution. Science 365, eaax1971 (2019).

Article PubMed PubMed Central CAS Google Scholar

Wagner, D. E. & Klein, A. M. Lineage tracing meets single-cell omics: opportunities and challenges. Nat. Rev. Genet. 21, 410427 (2020).

Article PubMed PubMed Central CAS Google Scholar

Whitman, C. O. The embryology of Clepsine. J. Cell Sci. s2-18, 215315 (1878).

Article Google Scholar

Raj, B. et al. Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain. Nat. Biotechnol. 36, 442450 (2018).

Article PubMed PubMed Central CAS Google Scholar

Nowell, P. C. The clonal evolution of tumor cell populations. Science 194, 2328 (1976).

Article PubMed CAS Google Scholar

Navin, N. et al. Tumour evolution inferred by single-cell sequencing. Nature 472, 9094 (2011).

Article PubMed PubMed Central CAS Google Scholar

Yang, D. et al. Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution. Cell 185, 19051923 (2022).

Levy, S. et al. A stony coral cell atlas illuminates the molecular and cellular basis of coral symbiosis, calcification, and immunity. Cell 184, 29732987 (2021).

Seidel, S. & Stadler, T. TiDeTree: a Bayesian phylogenetic framework to estimate single-cell trees and population dynamic parameters from genetic lineage tracing data. Proc. R. Soc. B 289, 20221844 (2022).

Article PubMed PubMed Central Google Scholar

Zhao, Z.-M. et al. Early and multiple origins of metastatic lineages within primary tumors. Proc. Natl Acad. Sci. USA 113, 21402145 (2016).

Article PubMed PubMed Central CAS Google Scholar

Moravec, J. C., Lanfear, R., Spector, D. L., Diermeier, S. D. & Gavryushkin, A. Testing for phylogenetic signal in single-cell RNA-seq data. J. Comput. Biol. 30, 518537 (2023).

Article PubMed PubMed Central CAS Google Scholar

Saitou, N. & Nei, M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406425 (1987).

PubMed CAS Google Scholar

Paganos, P., Voronov, D., Musser, J. M., Arendt, D. & Arnone, M. I. Single-cell RNA sequencing of the Strongylocentrotus purpuratus larva reveals the blueprint of major cell types and nervous system of a non-chordate deuterostome. Elife 10, e70416 (2021).

Article PubMed PubMed Central CAS Google Scholar

Wang, Y. et al. Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature 512, 155160 (2014).

Article PubMed PubMed Central CAS Google Scholar

Frumkin, D., Wasserstrom, A., Kaplan, S., Feige, U. & Shapiro, E. Genomic variability within an organism exposes its cell lineage tree. PLoS Comput. Biol. 1, e50 (2005).

Article PubMed PubMed Central Google Scholar

Tarashansky, A. J. et al. Mapping single-cell atlases throughout Metazoa unravels cell type evolution. Elife 10, e66747 (2021).

Article PubMed PubMed Central CAS Google Scholar

van Zyl, T. et al. Cell atlas of aqueous humor outflow pathways in eyes of humans and four model species provides insight into glaucoma pathogenesis. Proc. Natl Acad. Sci. USA 117, 1033910349 (2020).

Article PubMed PubMed Central Google Scholar

Seb-Pedrs, A. et al. Early metazoan cell type diversity and the evolution of multicellular gene regulation. Nat. Ecol. Evol. 2, 11761188 (2018).

Article PubMed PubMed Central Google Scholar

Wang, R. et al. Construction of a cross-species cell landscape at single-cell level. Nucleic Acids Res. 51, 501516 (2023).

Article PubMed CAS Google Scholar

Chen, D. et al. Single cell atlas for 11 non-model mammals, reptiles and birds. Nat. Commun. 12, 7083 (2021).

Article PubMed PubMed Central CAS Google Scholar

Dunn, C. W., Zapata, F., Munro, C., Siebert, S. & Hejnol, A. Pairwise comparisons across species are problematic when analyzing functional genomic data. Proc. Natl Acad. Sci. USA 115, E409E417 (2018).

Article PubMed PubMed Central CAS Google Scholar

Felsenstein, J. Phylogenies and the comparative method. Am. Nat. 125, 115 (1985).

Article Google Scholar

Grafen, A. The phylogenetic regression. Phil. Trans. R. Soc. Lond. B 326, 119157 (1997).

Google Scholar

Seb-Pedrs, A., Degnan, B. M. & Ruiz-Trillo, I. The origin of Metazoa: a unicellular perspective. Nat. Rev. Genet. 18, 498512 (2017).

Article PubMed Google Scholar

Mah, J. L., Christensen-Dalsgaard, K. K. & Leys, S. P. Choanoflagellate and choanocyte collar-flagellar systems and the assumption of homology. Evol. Dev. 16, 2537 (2014).

Article PubMed CAS Google Scholar

Laundon, D., Larson, B. T., McDonald, K., King, N. & Burkhardt, P. The architecture of cell differentiation in choanoflagellates and sponge choanocytes. PLoS Biol. 17, e3000226 (2019).

Article PubMed PubMed Central Google Scholar

Hafemeister, C. & Satija, R. Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. Genome Biol. 20, 296 (2019).

Article PubMed PubMed Central CAS Google Scholar

Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 35733587 (2021).

Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 18881902 (2019).

McInnes, L., Healy, J. & Melville, J. UMAP: Uniform Manifold Approximation and Projection for dimension reduction. Preprint at http://arxiv.org/abs/1802.03426 (2020).

Felsenstein, J. Maximum-likelihood estimation of evolutionary trees from continuous characters. Am. J. Hum. Genet. 25, 471492 (1973).

PubMed PubMed Central CAS Google Scholar

Felsenstein, J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783791 (1985).

Article PubMed Google Scholar

Lemoine, F. et al. Renewing Felsensteins phylogenetic bootstrap in the era of big data. Nature 556, 452456 (2018).

Article PubMed PubMed Central CAS Google Scholar

Thorley, J. L. & Wilkinson, M. Testing the phylogenetic stability of early tetrapods. J. Theor. Biol. 200, 343344 (1999).

Article PubMed CAS Google Scholar

Levy, C., Khaled, M. & Fisher, D. E. MITF: master regulator of melanocyte development and melanoma oncogene. Trends Mol. Med. 12, 406414 (2006).

Article PubMed CAS Google Scholar

van Zyl, T. et al. Cell atlas of the human ocular anterior segment: tissue-specific and shared cell types. Proc. Natl Acad. Sci. USA 119, e2200914119 (2022).

Article PubMed PubMed Central Google Scholar

Sokal, R. R. et al. Principles of Numerical Taxonomy (WH Freeman & Co, 1963).

Sokal, R. R. & Michener, C. D. A statistical method for evaluating systematic relationships. Univ. Kans. Sci. Bull. 38, 14091438 (1958).

Google Scholar

Read more:

Cell type evolution reconstruction across species through cell phylogenies of single-cell RNA sequencing data - Nature.com

Biology

Glycoscience Explained: The Sugar Coating of Life – SciTechDaily

Glycobiology, evolving beyond its roots in carbohydrate chemistry, is now a key field in understanding lifes molecular mechanisms. Glycans, essential in various biological functions, are the focus of groundbreaking research and technological innovations, revealing their critical roles in health and disease. Credit: SciTechDaily.com

Researchers are working to advance the field of glycoscience, illuminating the essential role of carbohydrates for human health and disease.

In the narrowest sense, glycobiology is the study of the structure, biology, and evolution of glycans, the carbohydrates and sugar-coated molecules found in every living organism. As a recent symposium at MIT made clear, the field is in the midst of a renaissance that could reshape scientists understanding of the building blocks of life.

Originally coined in the 1980s to describe the merging of traditional research in carbohydrate chemistry and biochemistry, glycobiology has come to encompass a much broader and multidisciplinary set of ideas. Glycoscience may actually be a more appropriate name for the rapidly growing field, reflecting its broad application not just to biology and chemistry but also to bioengineering, medicine, materials science, and more.

Its becoming increasingly clear that these glycans have a very important role to play in health and disease, says Laura Kiessling, the Novartis Professor of Chemistry. It may seem daunting initially, but devising new tools and identifying new kinds of interactions requires exactly the sort of creative problem-solving skills that people have at MIT.

Glycans include a diverse set of molecules with linear and branched structures that are critical for basic biological functions. With no known exception, all cells in nature are coated with these sugar molecules from the intricate chains of sugars surrounding most cellular surfaces to the conjugated molecules formed when sugars attach like scaffolding to lipids and proteins. Theyre absolutely fundamental to life. For example, Kiessling points out that the most abundant organic molecule on the planet is the carbohydrate cellulose.

Sperm-egg binding is mediated by an interaction between a protein and a carbohydrate, she says. None of us would exist without these interactions.

Though talking about carbs and sugars might leave some people focused on their diet, glycans are actually among the most important biomolecules out there. They store energy and, in some cases like cellulose, provide the structural framework for multicellular organisms. They mediate communication between cells; influence interactions like that between a host and parasite; and shape immune responses, disease progression, development, and physiology.

In Professor Laura Kiesslings lab, researchers are working to understand the protein-carbohydrate interactions at a molecular level, such as the protein human intelectin-1 (hiTLN-1) shown here. Understanding the proteins glycobiology could facilitate the development of new antibiotics and antimicrobial therapeutics. Credit: Kiessling Lab

It turns out that some of these structures, which we didnt even know existed in the body in such abundance until recently, have so many different biological functions, says Andrew and Erna Viterbi Professor of Biological Engineering Katharina Ribbeck. With this rapid expansion of knowledge, it feels like were just beginning to understand how diverse and important those functions are to biology.

With a better understanding of how ubiquitous and critical these molecules are, researchers in applied fields like biotechnology and medicine have turned their attention to glycoscience as a tool to pinpoint the drivers of disease.

Many conditions have been linked to defects in how glycans are produced in the body or issues with glycosylation, the process by which carbohydrates attach to proteins and other molecules. That includes certain forms of cancer. Cancer cells have even been shown to cloak themselves in certain glycoproteins to evade an immune response.

On the flip side, glycans may be a repository of potential therapeutics. The blood thinner Heparin, one of the worlds best-selling prescription drugs, for example, is a carbohydrate-based drug.

Glycans and sugar-binding proteins like lectins even help influence the exchange of microbes across mucus layers in the human body, from the brain to the gut. Glycans dangling off mucus interact with microbes, letting good ones in and reducing the virulence of problematic ones by interrupting cell signaling or stopping pathogens from releasing toxins.

Despite how crucial this sugar coat is, for a long time, molecular biologists focused on nucleic acids and proteins, paying relatively little attention to the sugars that coated them.

The tools we have to examine the functions of other molecules are largely absent for glycans, says Kiessling, who is also an institute member of the Broad Institute of MIT and Harvard.

For example, the DNA and RNA sequences of a cell predict what proteins that cell makes, so scientists can track where a protein is and what its doing using a genetically-encoded tag. But the structure of glycans isnt so obviously encoded in a cells DNA, and a single protein can be decorated with many different chains of carbohydrates.

In addition, the immense diversity of forms carbohydrates can take, and the fact that they break down quickly in the bloodstream, has made it challenging to synthesize glycans or target them for drug development. So, creative new methods are needed to track them.

Its a classic chicken-and-egg situation. As scientists better understand the importance of glycans for so many biological processes, it has incentivized them to develop better tools for studying glycans, in turn, producing even more data on just what these molecules can do. In 2022, in fact, the Nobel Prize was awarded to Carolyn Bertozzi at Stanford University, a pioneer in glycobiology, for her work on tracking molecules in cells, which she and others have applied to glycans.

But artificial intelligence could facilitate an evolutionary leap in the field.

I think glycobiology is, more than almost any other field, ripe and ready for an AI interpretation, Ribbeck says, explaining how AI might enable scientists to read the glycan code in the same way they have with the human genome. That would allow researchers to predict the actual function of a glycan based on data about its structure. From there, they could identify what changes lead to disease or increase disease susceptibility and, most importantly, come up with ways to repair those defects.

The increasing interest in computation reflects the inherent interdisciplinarity that has defined glycoscience from the beginning.

Just at MIT, for example, related research is happening across the Institute. Kiessling describes MIT as a playground for interdisciplinary research, which has enabled significant advances in the field with applications to biotechnology, cancer research, brain science, immunology, and more.

In the Department of Chemistry, Kiessling is studying carbohydrate-binding proteins, and how their interactions with glycans affect the immune system. Shes also working with Bryan Bryson, an associate professor in the Department of Biological Engineering, and Deborah Hung, a core faculty member at The Broad Institute of MIT and Harvard, using carbohydrate analogs to test differences in strains of tuberculosis in South Africa. Meanwhile, assistant professor of biological engineering Jessica Stark is pioneering approaches to better understand the roles of glycans in the immune system. Tobi Oni, a fellow at the Whitehead Institute for Biomedical Research, is looking to glycans to help detect and target tumors in pancreatic cancer. Barbara Imperiali, the Class of 1922 Professor of Biology and Chemistry, is studying the carbohydrates that envelop the cells of microbes like bacteria, and Professor Matthew Shoulders in the Department of Chemistry is studying the role of glycans in synthesizing and folding proteins.

Were at a very exciting and unique position combining disciplines to address and answer entirely new questions relevant for disease and health, says Ribbeck.The field in and of itself is not new, but what is new is the contribution that MIT, in particular, could make with a creative combination of science, engineering, and computation.

See the original post here:

Glycoscience Explained: The Sugar Coating of Life - SciTechDaily

Biology

Charleroi biology students team up online with scientists for research projects – The Mon Valley Independent

Submitted Shown, from left, are Charleroi Advanced Placement biology students Bailey Gillen, Addacie Durka, Angela Mathers, Suki Yu, Lairah Dipietrantonio and McKenna Shields. They recently had their work on two separate projects featured on planting science.org. Missing from the photo is Aiden Iadanza, who also participated on one of the teams.

By TAYLOR BROWN Senior Reporter [emailprotected] Charleroi High School Advanced Placement biology students will have their work recognized as model projects for other learners. The project got its start after CAHS science teacher Michele Piatt participated in a research study funded by the National Science Foundation to determine if in-person teacher professional development is more effective than virtual teacher training based on student outcomes. As part of the project, her AP biology students completed several lab activities on the bioenergetic processes of photosynthesis and cell respiration using the plantingscience.org website investigation theme, Power of Sunlight. Students were divided into small groups and each group was assigned to their own scientist mentor that they communicated with on the plantingscience.org platform throughout their investigations. The scientist mentors were volunteers who work in the plant science field all over the world. The project ended with the students designing their own experiment and sharing their results with their scientist mentor. Two of the groups in Piatts AP biology class had their projects nominated, judged and were awarded recognition as Star Projects, which will now be used as models for other learners and researchers. The group Lets Take a Cellfie comprised students Lairah Dipietrantonio, Angela Mathers, McKenna Shields and Suki Yu. Their mentor, Nora Gavin-Smyth, works at the Chicago Botanic Garden and Northwestern University. The goal of their project was to see if the pH of a solution would increase/decrease with the presence of either oxygen or cellular respiration. This group really worked together to communicate with their scientist mentor at every step of the investigation, Piatt said. They were vary thorough in their discussions and asked intriguing questions. The design of their experiment was innovative as they used additional materials beyond the Planting Science investigations. The second group, Plants vs. AP Bio comprised Addacie Durka, Bailey Gillen and Aiden Iadanza.

To read the rest of the story, please see a copy of Thursdays Mon Valley Independent, call 724-314-0035 to subscribe or subscribe to our online edition at http://monvalleyindependent.com.

Go here to read the rest:

Charleroi biology students team up online with scientists for research projects - The Mon Valley Independent