Genetics biweekly vol.35, 10th August — 24th August
TL;DR
- A team has uncovered surprising mechanical behaviors of the nucleus. For years, the nucleus within a cell was thought to be elastic like a rubber ball, deforming and snapping back into shape as the cell navigated through pores and between fibers inside the human body. Researchers have now discovered that the nucleus is more complex than originally believed, behaving more like a liquid drop than a rubber ball.
- The flash of lightning and the dance of auroras contain a fourth state of matter known as plasma, which researchers have harnessed to produce a gas that may activate plant immunity against wide-spread diseases.
- With super-resolution imaging, researchers discovered that cells change the physical structure of their genome when they’re affected by disease.
- T cells are our immune system’s customised tools for fighting infectious diseases and tumor cells. On their surface, these special white blood cells carry a receptor that recognizes antigens. With the help of cryo-electron microscopy, biochemists and structural biologists were able to visualize the whole T-cell receptor complex with bound antigen at atomic resolution.
- Researchers have used a novel algorithm called PeakMatch to reconstruct actual-time gene expression patterns from single-cell RNAseq datasets and demonstrate that circadian clock genes regulate plant cell differentiation. The study not only sheds new light on the regulation of cell fate determination, but also provides a powerful new algorithm that can be applied to a wide range of single-cell transcriptomes.
- Nearly all vital functions in the human body are regulated by so-called G protein-coupled receptors on the cell surface. These receptors thus serve as attractive drug targets to treat various diseases. Researchers have now discovered that empty spaces inside these receptors are important for their activation and thus for relaying messages to the inner cell. Their approach to locate these voids may help to direct the search for novel drugs.
- Scientists have developed improved methods for generating micro-organospheres (MOS) and have shown that they can be used as patient avatars for studies involving direct viral infection, immune cell penetration and high-throughput therapeutic drug screening — something that is not obtainable with conventional patient-derived models.
- With antibiotic-resistant bacteria on the rise, scientists have been searching for ways to shut down the Type IV secretion system (T4SS), a protein complex on the outer envelope of bacterial cells that helps them to exchange DNA with neighboring bacteria and resist antibiotics.
- Two novel hypotheses have been proposed that address the ‘two-fold cost of sex’: one of the biggest enigmas in the evolution of sexual reproduction.
- Likely in order to survive in the oral cavity, bacteria evolved to divide along their longitudinal axis without parting from one another. Environmental cell biologists and microbial geneticists have just published their new insights. In their work, they described the division mode of these caterpillar-like bacteria and their evolution from a rod-shaped ancestor. They propose to establish Neisseriaceae oral bacteria as new model organisms that could help pinpoint new antimicrobial targets.
- And more!
Overview
Genetic technology is defined as the term which includes a range of activities concerned with the understanding of gene expression, advantages of natural genetic variation, modifying genes and transferring genes to new hosts. Genes are found in all living organisms and are transferred from one generation to the next. Gene technology encompasses several techniques including marker-assisted breeding, RNAi and genetic modification. Only some gene technologies produce genetically modified organisms.
Modern genetic technologies like genome editing would not be possible without all the previous generations of genetic technologies that have enabled scientists to discover what genes are, what they do and how DNA can be modified to add, remove or replace genes. You can find major genetic technologies development milestones via the link.
Gene Technology Market
- The valuation of the genetic engineering market is projected to escalate to USD 6.90 MN by the end of 2027.
- Global Genetic Engineering Market is projected to grow at 12.48% CAGR during the assessment period (2017–2027).
- North America holds the largest share in the global genetic engineering market, followed by Europe and the Asia Pacific, respectively.
- Another research provider, MarketsandMarkets, forecasts the genome editing, genome engineering market to grow from USD 3.19 billion in 2017 to USD 6.28 billion by 2022, at a compounded annual growth rate (CAGR) of 14.5% during the forecast period. The key factors propelling market growth are rising government funding and growth in the number of genomics projects, high prevalence of infectious diseases (like COVID-19) and cancer, technological advancements, increasing production of genetically modified (GM) crops, and growing application areas of genomics.
Latest News & Research
The Nucleus Bypasses Obstacles by Deforming Like a Drop with Surface Tension Mediated by Lamin A/C
by Aditya Katiyar, Jian Zhang, Jyot D. Antani, Yifan Yu, Kelsey L. Scott, Pushkar P. Lele, Cynthia A. Reinhart‐King, Nathan J. Sniadecki, Kyle J. Roux, Richard B. Dickinson, Tanmay P. Lele in Advanced Science
For years, the nucleus within a cell was thought to be elastic like a rubber ball, deforming and snapping back into shape as the cell navigated through pores and between fibers inside the human body. Researchers at Texas A&M University and the University of Florida have discovered that the nucleus is more complex than originally believed, behaving more like a liquid drop than a rubber ball.
“The discovery that the nucleus deforms like a liquid drop calls for a fresh look at how the nuclear shape becomes abnormal in diseases like cancer,” said Dr. Tanmay Lele, Unocal Professor in the Department of Biomedical Engineering. Lele, a Cancer Prevention & Research Institute of Texas (CPRIT) Scholar, is co-leading the team that uncovered the surprising mechanical behaviors of the nucleus.
The genetic material governing a cell’s function and behavior, called the genome, is safely stored in the nucleus. Nearly 150 years of looking through microscopes has taught pathologists and researchers that misshapen nuclei are warning signs of diseases like cancer. Cancer cells with such abnormal nuclei are able to migrate to other parts of the body in a process called cancer metastasis, a spreading that can be lethal.
Nuclear shape observations are used in cancer diagnosis even today. But why nuclei become abnormal has remained unclear. Understanding how nuclei become misshapen may help uncover a way to aid cell nuclei in regaining their normal shapes, leading to new approaches for treating cancer.
The findings from this study are critical to understanding how a protective layer surrounding the nucleus, called the lamina, helps preserve nuclear shape while cells crawl through the tortuous paths through pores and around tissue fibers. Lele and his fellow researchers began their exploration of nuclear behaviors by placing fibroblasts, the most common type of connective-tissue cells in animals, into a miniature obstacle course of tiny, flexible pillars 1/100th of the width of a human hair. In order for the cells to crawl through this obstacle course, their nuclei had to squeeze in between the pillars. The researchers observed the movements with an advanced high-resolution microscope that could image the 3D shapes of the nuclei.
Imaging revealed that the pillars created deep indentations into the nuclear surface. Yet the overall nuclear shape was preserved, allowing the nucleus to successfully pass like a liquid drop, and unlike a springy elastic rubber ball, through the obstacles. The research also revealed that a depletion of lamin A/C, one of the normal protein components of lamina, caused the nuclei to get entangled in the obstacles. The discovery suggests that lamin A/C helps maintain the surface tension of the “nuclear drop.”
“Our work points to a fundamental mechanism by which the nucleus preserves its shape and protects its genome,” Lele said. “Our discovery also helps us better understand how misshapen nuclei arise in cancer and how to potentially make them normal again. We are now studying the implications of the drop model for the abnormal nuclear shapes commonly observed in cancer.”
Evolution of longitudinal division in multicellular bacteria of the Neisseriaceae family
by Sammy Nyongesa, Philipp M. Weber, Ève Bernet, Francisco Pulido, et al in Nature Communications
Likely in order to survive in the oral cavity, bacteria evolved to divide along their longitudinal axis without parting from one another. A research team co-led by environmental cell biologist Silvia Bulgheresi from the University of Vienna and microbial geneticist Frédéric Veyrier from the Institut national de la recherche scientifique (INRS) just published their new insights. In their work, they described the division mode of these caterpillar-like bacteria and their evolution from a rod-shaped ancestor. They propose to establish Neisseriaceae oral bacteria as new model organisms that could help pinpoint new antimicrobial targets.
Although our mouth houses over 700 species of bacteria and its microbiota is, therefore, as diverse as that of our gut, not much is known about how oral bacteria grow and divide. The mouth is a tough place to live in for bacteria. The epithelial cells lining the inner surface of the oral cavity are constantly shed and, together with salivary flow, organisms that inhabit this surface will therefore struggle for attachment. It is perhaps to better stick to our mouth that bacteria of the family Neisseriaceae have evolved a new way to multiply. Whereas typical rods split transversally and then detach from each other, some commensal Neisseriaceae that live in our mouths, however, attach to the substrate with their tips and divide longitudinally — along their long axis. In addition to that, once cell division is completed, they remain attached to one another forming caterpillar-like filaments. Some cells in the resulting filament also adopt different shapes, possibly to perform specific functions to the benefit of the whole filament.
The researchers explain: “Multicellularity makes cooperation between cells possible, for example in the form of division of labor, and may therefore help bacteria to survive nutritional stress.”
The team of researchers first employed electron microscopy to survey bacterial cell shape across the Neisseriaceae family that include the two standard cell shapes (rod and coccus) in addition to the caterpillar-like filaments. By comparing their cell shapes and genomes throughout the Neisseriaceae family, they could infer that the multicellular, longitudinally dividing bacteria evolved out of rod-shaped, transversally dividing bacteria. Moreover, they could pinpoint which genes were likely responsible for the unusual multiplication strategy. They then used fluorescence labelling techniques to visualize the progression of cell growth in the multicellular bacteria and finally compared the genetic make-up of these with ‘classic’, rod-shaped species. Finally, they tried to recreate that evolution by introducing the genetic changes into rod-shaped Neisseriaceae. Although they could not force rod-shaped bacteria to become multicellular, genetic manipulation resulted into longer and thinner cells.
“We speculate that in the course of evolution, through a reworking of the elongation and division processes, the cell shape changed, perhaps to better thrive in the oral cavity”, Frédéric Veyrier (INRS).
“Apart from helping us to understand how cell shape evolved, multicellular Neisseriaceae may be useful to study how bacteria learned to live attached to the surface of animals, the only place they have been found to occur so far. Half of us is carrying them in our mouths, by the way”, explains Silvia Bulgheresi from the Department of Functional and Evolutionary Ecology at the University of Vienna.
However, Philipp Weber from the University of Vienna, PhD student in Bulgheresi’s team, who also worked on the study, highlights that “expanding the cell biology field to additional morphologies and symbiotic species is also crucial to increase the pool of protein targets (e.g., antibiotic targets) for biopharmaceutical applications.” Sammy Nyongesa, PhD student in Veyrier’s team from INRS, adds: “An evolutionary approach, such as that undertaken here for the Neisseriaceae, can shed light on new, unforeseen protein targets”.
Activation of plant immunity by exposure to dinitrogen pentoxide gas generated from air using plasma technology
by Daiki Tsukidate, Keisuke Takashima, Shota Sasaki, Shuhei Miyashita, Toshiro Kaneko, Hideki Takahashi, Sugihiro Ando in PLOS ONE
The flash of lightning and the dance of auroras contain a fourth state of matter known as plasma, which researchers have harnessed to produce a gas that may activate plant immunity against wide-spread diseases.
“Currently, chemical pesticides are the mainstay of disease control in agriculture, but they can contaminate the soil and harm the ecosystem,” said paper author Sugihiro Ando, associate professor in the Graduate School of Agricultural Science at Tohoku University. “We need to develop plant disease control technologies that can help establish a sustainable agricultural system. The use of plant immunity is one of the most effective disease control methods because it utilizes the innate resistance of plants and has a low environmental impact.”
Using their previously developed device that derives plasma from the air, the researchers produced dinitrogen pentoxide, a reactive nitrogen species (RNS). This molecule is related to reactive oxygen species (ROS), in that both damage cells and trigger specific stress responses in organisms.
“It is well known that reactive species are important signaling factors in the immune response of plants, but the specific physiological function of dinitrogen pentoxide is poorly understood,” Ando said. “Plants produce reactive species as a defense response when they perceive an infectious stimulus from a pathogen. The generated reactive species function as signaling molecules that contribute to the activation of plant immunity.”
According to Ando, reactive species are linked to plant hormones such as salicylic acid, jasmonic acid and ethylene, which help regulate plant immunity, but the physiological function of dinitrogen pentoxide is poorly understand.
“Since reactive species are known to have important functions in plant immunity, we analyzed weather exposure of plants to dinitrogen pentoxide gas could enhance disease resistance,” Ando said.
The researchers exposed thale cress, a small plant commonly used as a model system for scientific research, to dinitrogen pentoxide gas for 20 seconds a day for three days. The plants were then infected with one of three common plant pathogens: a fungus, a bacterium or a virus. The plants with the fungus or the virus showed suppressed progression of the pathogen, while those with the bacterium had a similar proliferation as the control plants.
“These results suggest that the dinitrogen pentoxide gas exposure could control plant disease depending on the type of pathogen,” Ando said.
A genetic analysis revealed that the gas specifically activated the jasmonic acid and ethylene signaling pathways and appeared to lead to the synthesis of antimicrobial molecules, which Ando said may have contributed to the observed disease resistance.
“Dinitrogen pentoxide gas can be used to activate plant immunity and control plant diseases,” Ando said. “Through plasma technology, the gas can be produced from air and electricity, without special materials. The gas can also be converted to nitric acid, when dissolved in water, and used as a fertilizer for plants. This technology can contribute to the construction of a sustainable agricultural system as a clean technology with minimal environmental impact.”
Next, the researchers plan to study how their technology works with crops and in greenhouse cultivation.
Filling of a water-free void explains the allosteric regulation of the β1-adrenergic receptor by cholesterol
by Layara Akemi Abiko, Raphael Dias Teixeira, Sylvain Engilberge, Anne Grahl, Tobias Mühlethaler, Timothy Sharpe, Stephan Grzesiek in Nature Chemistry
Nearly all vital functions in the human body are regulated by so-called G protein-coupled receptors on the cell surface. These receptors thus serve as attractive drug targets to treat various diseases. Researchers have now discovered that empty spaces inside these receptors are important for their activation and thus for relaying messages to the inner cell. Their approach to locate these voids may help to direct the search for novel drugs.
The G protein-coupled receptors (GPCRs) enable us to see, taste food, feel cold or warm, or respond to stress, among other things. Located on the cell surface, GPCRs sense a large variety of signals such as nutrients, light, odors or hormones. By changing their conformation, they transmit this information from the outside to the inside of the cell. The accumulated knowledge about GPCRs has tremendously affected modern medicine: about one-third of all marketed drugs target GPCRs.
Using cutting-edge technology, the research team led by Prof. Stephan Grzesiek, together with collaborators at the Biozentrum of the University of Basel and the Paul Scherrer Institute, has now discovered that GPCRs contain completely empty cavities which are important for their activation. Their recent, experimental approach, may direct and speed up the search for new and more specific drug candidates with fewer side effects. Although the 826 GPCRs within the human body respond to many different stimuli, they all share a common architecture.
“Our aim is to understand at the atomic level how GPCRs transmit signals,” says Dr. Layara Abiko, who co-directed the study. “For many years, we have therefore been studying the β1-adrenergic receptor, a GPCR that prepares the body for fight or flight.” The hormone adrenaline binds to and activates the receptor which triggers a stress response, for example, causing an increase in heart rate and blood pressure.”
Beta-blockers inhibit this receptor and thus are effective drugs to treat hypertension or cardiovascular diseases.
“Thanks to high-pressure NMR and our experimental approach using X-ray scattering on receptor crystals that incorporated the noble gas xenon, we could further complete the picture of this highly dynamic receptor,” says Abiko. “Previously, it was assumed that the cavities inside the receptor are filled with water. We have now revealed that some of them are empty.”
During activation, the conformation of the receptor changes in such a way that these dry voids get compressed and disappear. Consequently, the receptor shrinks just like when you squeeze a sponge. In case of the β1-adrenergic receptor, this conformational change is key for initiating the body’s fight-or-flight response.
The researchers have now been able to exactly localize two of such empty cavities and revealed that cholesterol — an important cell membrane component — can fill one of these. Like a wedge, cholesterol impedes the receptor from squeezing and changing to its fully active state.
“Blocking this void obstructs the subtle, but essential movements required to activate the GPCR,” explains Abiko. “We think, this wedge effect could be another layer of receptor regulation.”
But why can scouting for dry voids be important? Classical drug binding sites are often similar among GPCR subclasses. A drug directed to such a site may bind to more than one receptor and therefore cause unwanted side effects. In contrast, the dry cavities differ considerably between GPCRs, even when they are from the same subclass. This makes them highly selective drug targets.
“In this way, you may design drugs that are highly specific for one receptor,” explains Abiko. The developed new approach may locate such unconventional drug binding sites which differ strongly between the receptors. This can help the screening process for new therapeutics, save time and reduce costs.
Aberrant chromatin reorganization in cells from diseased fibrous connective tissue in response to altered chemomechanical cues
by Su-Jin Heo, Shreyasi Thakur, Xingyu Chen, Claudia Loebel, Boao Xia, Rowena McBeath, Jason A. Burdick, Vivek B. Shenoy, Robert L. Mauck, Melike Lakadamyali in Nature Biomedical Engineering
Imagine you’re trying to do a job and all of the information you need to do it is in a few books at the library. Except, those books are randomly arranged along with all the other books on shelves across the whole building. Without that vital information from the books you were looking for, you wouldn’t perform your job very well.
This is the situation that researchers at the Perelman School of Medicine at the University of Pennsylvania found when they studied the nucleus of cells inside connective tissues deteriorating as a result of tendinosis. Disease-related disruptions in the environments that cells exist in caused the re-organization of the genome — which is the sum of an organism’s DNA sequences — inside the cell’s nucleus, changing the way cells functioned and making them unable to reorder their DNA information in the right way again. These findings point to the possibility of new treatments — such as small-molecule therapies — to bring in a sort of librarian that could restore order to the affected cells.
“This is really important because the research tells us, for the first time, that diseased connective tissue cells change the physical structure of their genomes and stop responding to normal physical cues from their environment,” said the study’s lead author, Su Chin Heo, PhD,an assistant professor of Orthopaedic Surgery. “If we can figure out exactly why this happens, we might be able to ‘unlock’ the diseased state of these cells, and bring them back toward a healthy state.”
“Microscale” changes in the environments that cells exist in have macro-level effects because of the way they change cell behaviors and how a body functions. But this dynamic is not well understood. So Heo and colleagues set out to examine how cells in degenerating connective tissue respond to changes in their physical environment and, particularly, how the spatial organization of chromatin — the material that DNA is made out of, which has been shown to differ based on cell type — might be affected by changes brought on by disease. To do this, the team used the latest super-resolution imaging techniques to observe human cell models, specifically tenocytes (tendon cells involved in maintaining the tissue’s structure) and mesenchymal stromal cells (similar to stem cells, they can become a variety of cells needed to build or maintain tissue).
In these models, the researchers observed that chemical and mechanical changes within environments mimicking degenerating tendons resulted in tenocytes improperly re-ordering their chromatin. And even when the researchers presented these cells with the proper mechanical environment, they saw that the cells had lost their ability to properly re-organize their genome back to a normal state — the cells could no longer respond correctly. Cells that were healthy responded well to the same chemical and mechanical prompts, so it seems that the diseased cells forgot what they were doing, or couldn’t access the right information in their crisis response.
“While we discovered that cells in diseased microenvironments lose their epigenetic memory, these results also suggest that epigenetic treatments — like small molecule medications — could restore healthy genome organization and may prove effective treatments in conditions affecting dense tissues,” said the study’s senior author, Melike Lakadamyali, PhD, an associate professor of Physiology. “That’s something that we plan to follow up on and test.”
The researchers already have secured grants studying whether cartilage cells and meniscus cells are affected similarly by disease-disrupted genomes. They’re also studying whether the aging process has a similar effect.
“Once we understand these and the specific cellular processes that makes them happen — what locks the library door — we can use small molecule drugs as skeleton keys to either try to stop it from happening or reverse the process,” said study co-senior-author Robert Mauck, PhD, a professor of Orthopaedic Surgery and director of Penn’s McKay Orthopaedic Research Laboratory.
Structure of a fully assembled tumor-specific T cell receptor ligated by pMHC
by Lukas Sušac, Mai T. Vuong, Christoph Thomas, Sören von Bülow, Caitlin O’Brien-Ball, Ana Mafalda Santos, Ricardo A. Fernandes, Gerhard Hummer, Robert Tampé, Simon J. Davis in Cell
T cells are our immune system’s customised tools for fighting infectious diseases and tumour cells. On their surface, these special white blood cells carry a receptor that recognises antigens. With the help of cryo-electron microscopy, biochemists and structural biologists from Goethe University Frankfurt, in collaboration the University of Oxford and the Max Planck Institute of Biophysics, were able to visualise the whole T-cell receptor complex with bound antigen at atomic resolution for the first time. Thereby they have helped us understand a fundamental process which may pave the way for novel therapeutic approaches targeting severe diseases.
The immune system of vertebrates is a powerful weapon against external pathogens and cancerous cells. T cells play a curcial role in this context. They carry a special receptor called the T-cell receptor on their surface that recognises antigens — small protein fragments of bacteria, viruses and infected or cancerous body cells — which are presented by specialised immune complexes. The T-cell receptor is thus largely responsible for distinguishing between “self” and “foreign.” After binding of a suitable antigen to the receptor, a signalling pathway is triggered inside the T cell that “arms” the cell for the respective task. However, how this signalling pathway is activated has remained a mystery until now — despite the fact that the T-cell receptor is one of the most extensively studied receptor protein complexes.
For the structural analysis, the researchers chose a T-cell receptor used in immunotherapy to treat melanoma and which had been optimised for this purpose in several steps in such a way that it binds its antigen as tightly as possible. A particular challenge on the way to structure determination was to isolate the whole antigen receptor assembly consisting of eleven different subunits from the cell membrane. “Until recently, nobody believed that it would be possible at all to extract such a large membrane protein complex in a stable form from the membrane,” says Tampé.
Once they had successfully achieved this, the researchers used a trick to fish those receptors out of the preparation that had survived the process and were still functional: due to the strong interaction between the receptor complex and the antigen, they were able to “fish” one of the most medically important immune receptor complexes. The subsequent images collected at the cryo-electron microscope delivered groundbreaking insights into how the T-cell receptor works, as Tampé summarises: “On the basis of our structural analysis, we were able to show how the T-cell receptor assembles and recognises antigens and hypothesise how signal transduction is triggered after antigen binding.” According to their results, the big surprise is that there is evidently no significant change in the receptor’s spatial structure after antigen binding, as this was practically the same both with and without an antigen.
The remaining question is how antigen binding could instead lead to T-cell activation. The co-receptor CD8 is known to approach the T-cell receptor after antigen binding and to stimulate the transfer of phosphate groups to its intracellular part. The researchers assume that this leads to the formation of structures which exclude enzymes that cleave off phosphate groups (phosphatases). If these phosphatases are missing, the phosphate groups remain stable at the T-cell receptor and can trigger the next step of the signalling cascade.
“Our structure is a blueprint for future studies on T-cell activation,” Tampé is convinced. “In addition, it’s an important stimulus for employing the T-cell receptor in a therapeutic context for treating infections, cancer, and autoimmune diseases.”
The origination events of gametic sexual reproduction and anisogamy
by Yukio Yasui, Eisuke Hasegawa in Journal of Ethology
Two novel hypotheses have been proposed that address the “two-fold cost of sex”: one of the biggest enigmas in the evolution of sexual reproduction.
The evolution of sexual reproduction in living beings is one of the biggest mysteries in biology. There are two known modes of reproduction: asexual, where the organism creates clones of itself, and sexual, where gametes from two individuals fuse to give rise to progeny. There are many hypotheses that address various aspects of the evolution of sexual reproduction; nonetheless, there are also many questions that are still unanswered. The biggest question in the study of the evolution of sexual reproduction is the question of cost. Sexual reproduction requires exponentially more energy than asexual reproduction. Nevertheless, sexual reproduction has two major advantages over asexual reproduction: it results in genetic diversity in offspring, and it eliminates harmful mutations.
Associate Professor Eisuke Hasegawa of Hokkaido University and Associate Professor Yukio Yasui of Kagawa University have proposed and modeled two novel hypotheses which address two open questions in the study of the evolution of sexual reproduction. The researchers proposed hypotheses to address the “two-fold cost of sex”: the cost of meiosis and the cost of producing large numbers of male gametes. Sexual reproduction can be isogamous, where the gametes are all of the same size, or it can be anisogamous, where the female gametes are large, while the male gametes are small and numerous. The hypotheses were tested by computer modelling.
The first hypothesis they proposed is the “seesaw effect” by which a large number of harmful mutations are eliminated. The first individual to have a sex-controlling gene — that allowed for meiosis to occur — produced four gametes. Only gametes with the sex-controlling gene could fuse, fixing it in the population and erasing the cost of meiosis. In addition, any harmful mutations were diluted or discarded depending on whether they were associated with the sex-controlling gene.
The second hypothesis, the development of anisogamy via “inflated isogamy,” was developed from the first hypothesis. They suggest that, originally, multicellular organisms with higher energy generation evolved; then, the gamete size increased (“inflated isogamy”) as the increased resources in larger gametes increased the survival rate of offspring. Then, the male gametes reduced in size to fertilize more female gametes — depending on the inflated female gametes to provide the resources for survival. This strategy does not involve any extra cost on the part of the female; in fact, it may have triggered their counteradaptation to the current-day meiosis in females that results in just one female gamete (the oocyte) per gametocyte.
With these hypotheses, the authors have addressed the question of “two-fold cost of sex,” and have also hypothesized that the first sexual reproduction required only one individual, and was a self-fertilizing event. However, the two hypotheses are still in their initial stages, and further work is required to address specific assumptions and conclusions underlying them.
A guiding role of the Arabidopsis circadian clock in cell differentiation revealed by time-series single-cell RNA sequencing
by Kotaro Torii, Keisuke Inoue, Keita Bekki, Kazuya Haraguchi, Minoru Kubo, Yuki Kondo, Takamasa Suzuki, Akane Kubota, Kyohei Uemoto, Hanako Shimizu, Masato Saito, Hiroo Fukuda, Takashi Araki, Motomu Endo in Cell Reports
They say timing is everything, and that couldn’t be more true for cell cycle progression and differentiation. Now, researchers from Japan have found that the circadian clock is crucial for proper plant development.
In a study, researchers at Nara Institute of Science and Technology (NAIST) have revealed that the circadian clock plays a guiding role in plant cell differentiation. The circadian clock is involved in both cell-cycle progression and cell fate transitions. The involvement of circadian clocks in the process of differentiation has been shown in many multicellular organisms; however, how plant circadian clocks regulate cell differentiation remains unclear.
“Elucidating how the circadian clock is involved in cell differentiation is important to understand the basis of cell fate determination,” explains Motomu Endo, senior author of the study. “However, this has been difficult to investigate in plants because it is challenging to isolate single plants’ cells, and existing analytical methods rely on “pseudo-time” analysis that does not accurately reflect normal circadian rhythms.”
To address these challenges, the researchers used tiny glass tubes to isolate individual cells from developing plants and analyzed the expression of various genes related to circadian rhythms and cell differentiation in each cell. They then developed a new algorithm called PeakMatch to reconstruct actual-time gene expression patterns from the single-cell datasets.
“Using this powerful approach, we were able to show that the expression profile of clock genes is changed prior to cell differentiation,” states Endo. “Specifically, in early differentiating cells, the induction of the clock gene LUX ARRYTHMO directly targets genes involved in cell-cycle progression to regulate cell differentiation.”
Further investigation showed that large-scale changes in the circadian clock profile in undifferentiated cells induce the expression of the clock gene LUX, which directly triggers cell differentiation.
“Taken together, our results show that the plant circadian clock plays a guiding role in cell differentiation,” says Endo. “Importantly, our study also provides an approach for time-series analysis at single-cell resolution.”
Because the development of circadian rhythms during cell differentiation is observed in animals as well as in plants, the finding that clock genes directly regulate cell fate determination and cell division may help understand how cell differentiation is controlled in multicellular organisms. The newly developed PeakMatch algorithm can also be applied to all kinds of single-cell transcriptomes in other organisms.
Rapid tissue prototyping with micro-organospheres
by Zhaohui Wang, Matteo Boretto, Rosemary Millen, et al in Stem Cell Reports
A team of scientists, led by Xiling Shen, Ph.D., Chief Scientific Officer, and Professor at the Terasaki Institute for Biomedical Innovation (TIBI), has reached new levels in patient model development. They have developed improved methods for generating micro-organospheres (MOS) and have shown that these MOS have superior capabilities for a variety of clinical uses. As documented, their MOS can be used as patient avatars for studies involving direct viral infection, immune cell penetration and high-throughput therapeutic drug screening, something that is not obtainable with conventional patient-derived models.
Dr. Shen’s team has developed emulsion microfluidic technology for creating MOS, tiny, nanoliter-sized basal membrane extract (BME) droplets composed of tissue cell mixtures which can be generated at a rapid pace from an automated device. After the droplets are created, excess oil is removed by an innovative membrane demulsification process, leaving behind thousands of viscous, uniformly sized droplets which contain tiny 3D tissue structures.
The team went on to demonstrate unique MOS capabilities and features in several first-of-its-kind experiments. They were able to show that the MOS could be created from a variety of different tissue sources and the resultant MOS had retention of histopathological morphology, capacity for differentiation and genetic expression, and the ability to be frozen and sub-cultured, as in conventional organoids.
Experiments were conducted to test the ability to infect MOS with viruses. Unlike with conventional organoids, MOS can be directly infected with viruses without the removal and suspension of cells from its surrounding BME scaffold, hence recapitulating the process of viral infection of the host tissue. Dr. Shen’s team was able to create a MOS atlas of human respiratory and digestive tissues from patient autopsies and infect them with SARS-COV-2 viruses, followed by drug screening to identify drugs that block viral infection and replication within those tissues.
MOS also provide a unique platform for studying and developing immune cell therapy. Within natural diffusion limit of vascularized tissue, tumor-derived MOS allowed sufficient penetration by therapeutic immune T-cells such as CAR-T, enabling a novel T cell potency assay to assess tumor killing by the engineered T-cells. Such a model would be highly useful in investigating tumor responsiveness and in developing anti-tumor immune cell therapies.
MOS could be further integrated with deep-learning imaging analysis for rapid drug testing of small and heterogeneous clinical tumor biopsies. Moreover, the algorithm was able to distinguish cytotoxic vs. cytostatic drug effects and drug-resistant clones that will give rise to later relapse. This groundbreaking capability will pave the way for MOS to be used in the clinic to inform therapeutic decisions.
“Dr. Shen and his team continue to refine and improve upon the MOS technology and to spotlight its versatility, not only as a physiological model for screening potential personalized treatments, but for disease studies and a variety of other applications as well,” said Ali Khademhosseini, Ph.D., TIBI’s Director and CEO. “It looks to be the wave of the future for precision medicine.”
Cryo-EM structure of a type IV secretion system
by Kévin Macé, Abhinav K. Vadakkepat, Adam Redzej, Natalya Lukoyanova, Clasien Oomen, Nathalie Braun, Marta Ukleja, Fang Lu, Tiago R. D. Costa, Elena V. Orlova, David Baker, Qian Cong, Gabriel Waksman in Nature
With antibiotic-resistant bacteria on the rise, scientists have been searching for ways to shut down the Type IV secretion system (T4SS), a protein complex on the outer envelope of bacterial cells that helps them to exchange DNA with neighboring bacteria and resist antibiotics.
Now a collaboration between UT Southwestern computational biologist Qian Cong, Ph.D., and molecular biologists at the University of London has elucidated the structure of the T4SS complex, providing a blueprint that could help researchers design drugs that slow development of antibiotic resistance.
“For the first time, we determined the 3D structure of the entire T4SS complex,” said Dr. Cong, Assistant Professor of Biophysics and in the Eugene McDermott Center for Human Growth and Development at UTSW.
The team in London was led by Gabriel Waksman, Ph.D., whose lab has been working for more than two decades to understand T4SS, especially how it forms a thin, hollow structure called a pilus, which connects to nearby bacteria to share genes. For this project, his team used cryo-electron microscopy (cryo-EM) — a process that freezes proteins and uses beams of electrons to obtain high-resolution microscopic images — to elucidate the structure of T4SS. This was no small feat since the T4SS complex is larger than 99.6% of all those included to date in the worldwide library of protein structures.
Dr. Cong then used her background in statistics and machine learning to analyze T4SS protein sequences from several bacteria to generate structural predictions, which were compared to the cryo-EM data. Her computational analysis supported the cryo-EM data and suggested a hypothesis about the function of T4SS. While it was already known that T4SS is involved in pilus assembly, she predicted how it occurs. With that prediction in hand, Dr. Waksman’s team was able to make specific mutations within the relevant pieces of the complex and validate Dr. Cong’s hypothesis in live bacteria.
“In addition to the contribution we have made toward the development of drugs to slow the spread of antibiotic resistance genes, this study showcases the power of modern computational methods to validate experimental results and suggest functional insights beyond available experimental data,” said Dr. Cong, a Southwestern Medical Foundation Scholar in Biomedical Research.
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