It’s possible that I shall make an ass of myself. But in that case one can always get out of it with a little dialectic. I have, of course, so worded my proposition as to be right either way (K.Marx, Letter to F.Engels on the Indian Mutiny)
Exploratory behavior is one of the fundamental personality traits of animals – and these traits influence their probability of survival, among other things. For example, curious individuals can inhabit different areas in their habitats compared to more cautious conspecifics. At the same time, however, they expose themselves to a greater risk of being discovered and eaten.
Exploratory behavior as a factor in evolution
The cichlids of Africa’s Lake Tanganyika exhibit extraordinary diversity in terms of shape, diet, habitat and coloration. This allows them to inhabit various ecological niches and therefore to engage in less competition with one another. Researchers have long suspected that also curiosity acts as a driver in the formation of new species and therefore biodiversity. Now, a research team led by Professor Walter Salzburger from the University of Basel has used the example of the extremely diverse cichlid fishes of Lake Tanganyika to investigate the role of behavioral differences in adaptation to different ecological niches.
For a total of nine months, first author Dr. Carolin Sommer-Trembo recorded the “exploratory behavior” of 57 different cichlid species at the Southern shore of Lake Tanganyika in Zambia. To this end, the zoologist made video recordings of how the approximately 700 cichlids caught in the lake behaved in a new environment in form of large experimental ponds. She then released the animals back into the wild.
Back in Basel, Sommer-Trembo used these videos to determine which areas of the experimental pond each fish explored within a 15-minute period. “On the whole, large differences in exploratory behavior were observed between the cichlid species, and these differences were also confirmed under laboratory conditions,” says the evolutionary biologist. Detailed analyses of the data revealed a strong correlation between exploratory behavior and the habitat – and body shape – of the respective cichlid species. For example, species that live near the shores, with a bulkybody shape, are more curious than elongated species living in open water. “This puts the focus back on animal behavior as driving force behind key evolutionary processes,” says Sommer-Trembo.
Specific mutations make the fish more curious
In order to investigate the genetic basis of the observed behavioral differences in cichlids, the research team worked together with Dr. Milan Malinsky from the University of Bern to develop a new method for analyzing the existing genomes that allowed them to compare data across different species.
Using their new method, the researchers identified a genetic variant in the genome of cichlids that showed a near perfect correlation with exploratory behavior: species with a “T” at this specific position in the DNA are curious, whereas species with a “C” are less exploratory.
When the researchers used the “genetic scissors” CRISPR-Cas9 to induce targeted mutations in the corresponding region of the genome, the exploratory behavior of the fish changed – they became more curious. Moreover, the team was able to use artificial intelligence and information about the genetic variant, body structure and habitat to predict the exploratory behavior of cichlid species that, initially, had not been examined for their exploratory behavior.
Implications for human behavior?
The genetic variant identified by the researchers is located in the immediate vicinity of the gene cacng5b, which shows activity in the brain. This is the “fishy” version of a gene that is also found in other vertebrates. For example, the human variant is associated with psychiatric diseases such as schizophrenia and bipolar disorders, which may in turn be correlated with personality disorders.
“We’re interested in how personality traits can affect mechanisms of biodiversity in the animal kingdom,” says Sommer-Trembo. “But who knows: ultimately, we might also learn something about the foundations of our own personality.”
Individuals of the species Cyprichromis coloratus have a medium curiosity.
The exploration behavior of Eretmodus cyanostictus is medium
CAPTION
The species Ophthalmotilapia ventralis is a particularly reserved cichlid and does not like to explore.
The genetics of niche-specific behavioral tendencies in an adaptive radiation of cichlid fishes
CRISPR is promising to tackle antimicrobial resistance, but remember bacteria can fight back
Experts looking to use the Nobel winning technology to target resistance genes and make bacteria sensitive to first line antibiotics again; but the bacteria have ways to fight back
EUROPEAN SOCIETY OF CLINICAL MICROBIOLOGY AND INFECTIOUS DISEASES
In the second new research review on this subject, Assistant Prof. Ibrahim Bitar,Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University in Prague, Plzen, Czech Republic, will give an overview of the molecular biology of CRISPR technology in explaining how it can used to tackle antimicrobial resistance.
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR associated genes (cas) are widespread in the genome of many bacteria and are a defence mechanism against foreign invaders such as plasmids and viruses. The CRISPR arrays are composed of a repeated array of short sequences, each originating from and exactly matching a nucleic acid sequence that once invaded the host.
Accompanying CRISPR sequences, there are 4-10 CRISPR-associated genes (cas), which are highly conserved and encode the Cas proteins. Cas proteins conduct adaptive immunity in prokaryotes (bacteria) based on immunological memories stored in the CRISPR array. The CRISPR/Cas system integrates a small piece of foreign DNA from invaders such as plasmids and viruses into their direct repeat sequences and will recognise and degrade the same external DNA elements during future invasions.
As the CRISPR/Cas systems integrate DNA from invading pathogens in chronical order, genotyping can be used to trace the clonality and the origin of the isolates and define them as a population of strains that were subjected to the same environmental conditions including geographic location (region) and community/hospital settings and eventually further extended to track pathogenic bacteria around human society.
CRISPR/Cas systems can also be employed for developing antimicrobial agents: introduction of self-targeting crRNAs will effectively and selectively kill target bacterial populations. Due to the shortage of available effective antimicrobial agents in treating multidrug-resistant (MDR) infections, researchers started to search for alternative methods to fight MDR infections rather than going through the process of developing new antimicrobial agents which can go on for decades. As a result, the concept of CRISPR/Cas-based selective antimicrobials was first developed and demonstrated in 2014. Vectors coding Cas9 and guide RNAs targeting genomic loci of a specific bacterial strain/species can be delivered to the target strain via bacteriophages or conjugative bacterial strains. In theory, delivery of the engineered CRISPR/Cas systems specifically eliminates target strains from the bacterial population, yet it is not that simple.
While these systems can seem a target for manipulation/intervention, all bacteria are regulated by multiple pathways to ensure the bacteria retains control over the process. Therefore, there remain several major challenges in using this system as an antimicrobial agent.
Most methods require delivery of the re-sensitised system by conjugation; the vector is carried by a non-virulent lab strain bacteria that is supposed to go and share the vector/plasmid through conjugation. The conjugation process is a natural process that the bacteria do which results in sharing plasmids among each other (even with other species). The percentage of conjugated (successfully delivered) bacteria in the total bacterial population is critical to the re-sensitised efficiency. This process is governed by several complicated pathways.
Bacteria also possess built-in anti-CRISPR systems, that can repair any damage caused by CRISPR-Cas systems. Defence systems that the bacteria uses to protect itself from foreign DNA often co-localise within defence islands (genomic segments that contain genes with similar function in protecting the host from invaders) in bacterial genomes; for example: acr (a gene that acts, with other similar variants, as a repressor of plasmid conjugative systems) often cluster with antagonists of other host defence functions (e.g., anti-restriction modification systems) and experts hypothesise that MGEs (mobile genetic elements) organise their counter defence strategies in “anti-defence” islands.
Assistant Professor Bitar concludes: “In summary, this method seems very promising as an alternative way of fighting antimicrobial resistance. The method uses the concept of re-sensitising the bacteria in order to make use of already available antibiotics – in other words, removing their resistance and making them vulnerable again to first-line antibiotics. Nevertheless, the bacterial pathways are always complicated and such systems are always heavily regulated by multiple pathways. These regulated pathways must be studied in depth in order to avoid selective pressure favoring anti-CRISPR systems activation, hence prevalence of resistance in a more aggressive manner.”
Experts developing way to harness Nobel Prize winning CRISPR technology to deal with antimicrobial resistance (AMR)
EUROPEAN SOCIETY OF CLINICAL MICROBIOLOGY AND INFECTIOUS DISEASES
Antimicrobial resistance (AMR) is continuing to increase globally, with rates of AMR in most pathogens increasing and threatening a future in which every day medical procedures may no longer be possible and infections thought long dealt with could kill regularly again. As such, new tools to battle AMR are vitally needed.
In a new research review at this year’s ESCMID Global Congress (formerly ECCMID – Barcelona 27-30 April) shows how the latest CRISPR-Cas gene editing technology can be used to help modify and attack AMR bacteria. The presentation is by Dr Rodrigo Ibarra-Chávez, Department of Biology, University of Copenhagen, Denmark.
CRISPR-Cas gene editing technology is a groundbreaking method in molecular biology that allows for precise alterations to the genomes of living organisms. This revolutionary technique, which brought its inventors, Jennifer Doudna and Emmanuelle Charpentier, the Nobel Prize in Chemistry in 2020, enables scientists to accurately target and modify specific segments of an organism's DNA (genetic code). Functioning like molecular ‘scissors’ with the guidance of guide RNA (gRNA), CRISPR-Cas can cut the DNA at designated spots. This action facilitates either the deletion of unwanted genes or the introduction of new genetic material into an organism's cells, paving the way for advanced therapies.
Dr Ibarra-Chávez says: “Fighting fire with fire, we are using CRISPR-Cas systems (a bacterial immunity system) as an innovative strategy to induce bacterial cell-death or interfere with antibiotic resistance expression – both hold promise as novel sequence-specific targeted ‘antimicrobials’.”
One line of their work involves creating guided systems against antimicrobial resistance genes could treat infections and prevent dissemination of resistance genes.
Mobile genetic elements (MGEs) are parts of the bacterial genome that can move about to other host cells or also transfer to another species. These elements drive bacterial evolution via horizontal gene transfer. Dr Ibarra-Chávez explains how repurposing mobile genetic elements (MGEs) and choosing the delivery mechanism involved in the antimicrobial strategy is important for reaching the target bacterium.
A phage is a virus that infects bacteria, and it is also considered MGE, as some can remain dormant in the host cell and transfer vertically. The MGEs his team is using are phage satellites, which are parasites of phages. He says: “These ‘phage satellites’ hijack parts of the viral particles of phages to ensure their transfer to host cells. In contrast to phages, satellites can infect bacteria without destroying them, offering a step-change over existing methods involving phages and thus developing an arsenal of viral particles that are safe to use for applications such as detection and modification via gene delivery. Phage particles are very stable and easy to transport and apply in medical settings. It is our task to develop safe guidelines for their application and understand the resistance mechanisms that bacteria can develop.”
Bacteria can evolve mechanisms to evade the action of the CRISPR-Cas system and delivery vectors can be vulnerable to anti-MGE defences. Thus Dr Ibarra-Chávez’s team and others are developing the use of anti-CRISPRs and defence inhibitors in the delivery payloads to counter these defences, to enable the CRISPR to arrive and attack the AMR genes in the cell.
Dr Ibarra-Chávez will also discuss how combination strategies employing CRISPR-Cas systems could promote antibiotic susceptibility in a target bacterial population. Phages have a particular selective pressure on AMR cells, which can improve the effect of some antibiotics. Similarly, using CRISPR-Cas in combination with phages and/or antibiotics, it is possible to suppress the mechanisms of resistance that infectious bacteria may develop by targeting such virulence/resistance genes, making these therapies safer.
He explains: “Bacteria are particularly good at adapting and becoming resistance. I believe we need to be cautious and try using combinatorial strategies to avoid the development of resistance, while monitoring and creating guidelines of new technologies.”
Dr Ibarra-Chávez has primarily focused on tackling resistance in Staphylococcus aureus and Escherichia coli. Now, in collaboration with Prof. Martha Clokie and Prof. Thomas Sicheritz-Pontén, his team will treat group A Streptococci necrotising soft tissue infection (flesh eating bacteria) using the combination approaches described above.
ARTICLE PUBLICATION DATE
26-Apr-2024
Thursday, April 25, 2024
Unveiling the mysteries of cell division in embryos with timelapse photography
With the help of medaka fish, CRISPR and new imaging techniques, researchers have set a new standard for studying cell division at the very earliest stages of life
OKINAWA INSTITUTE OF SCIENCE AND TECHNOLOGY (OIST) GRADUATE UNIVERSITY
VIDEO:
TIMELAPSE OF A GENE-EDITED MEDAKA FISH EMBRYO UNDERGOING MITOSIS. THE MITOTIC SPINDLE – THE GREEN STRANDS IN THE MIDDLE OF THE CELLS – CAN BE SEEN ALIGNING AND SEGREGATING DUPLICATED CHROMOSOMES, SHOWN IN MAGENTA.
CREDIT: AI KIYOMITSU, CELL DIVISION DYNAMICS UNIT AT THE OKINAWA INSTITUTE OF SCIENCE AND TECHNOLOGY (OIST).
The beginning of life is shrouded in mystery. While the intricate dynamics of mitosis is well-studied in the so-called somatic cells – the cells that have a specialized function, like skin and muscle cells – they remain elusive in the first cells of our bodies, the embryonic cells. Embryonic mitosis is notoriously difficult to study in vertebrates, as live functional analyses and -imaging of experimental embryos are technically limited, which makes it hard to track cells during embryogenesis.
However, researchers from the Cell Division Dynamics Unit at the Okinawa Institute of Science and Technology (OIST) have recently published a paper in Nature Communications, together with Professors Toshiya Nishimura from Hokkaido University (previously at Nagoya University), Minoru Tanaka from Nagoya University, Satoshi Ansai from Tohoku University (currently at Kyoto University), and Masato T. Kanemaki from the National Institute of Genetics. The study takes the first major steps towards answering questions about embryonic mitosis, thanks to a combination of novel imaging techniques, CRISPR/Cas9 genome editing technology, a modern protein-knockdown system, and medaka, or Japanese rice fish (Oryzias latipes). The timelapses that they have produced help answer fundamental questions about the intricate process of equally dividing chromosomes during embryonic mitosis, and simultaneously chart the next frontier of scientific exploration. As Professor Tomomi Kiyomitsu, senior author of the study, describes the timelapses: “they are beautiful, both on their own and because they lay a new foundation for elucidating embryonic mitosis.”
Central to the mystery of embryonic mitosis is the crucial step when the chromosomes, which contain all the genetic information of the cell, are aligned and segregated equally into daughter cells. A key player in this process is the mitotic spindle, which is made of microtubules – long protein fibers used for intra-cellular structure and transport – that radiates from opposite poles of the spindle and attaches to the chromosomes in the middle. The spindle captures duplicated chromosomes properly and segregates them equally into the daughter cells during division. There are many factors determining spindle formation, and one of these is the protein Ran-GTP, which plays an essential role in cell division of female reproductive cells, which lack centrosomes – cell organelles responsible for assembling microtubules – but not in small somatic cells, which do have centrosomes. However, it has long been unclear whether Ran-GTP is required for spindle assembly in vertebrate early embryos, which contain centrosomes but have unique features, like a larger cell size.
In contrast to mammalian early embryos, embryonic cells in fish are transparent and develop synchronously in a uniform, single-cell layer sheet, which makes them significantly easier to track. The medaka turned out to be particularly well-suited for the researchers, as these fish tolerate a wide range of temperatures, produce eggs daily, and have a relatively small genome. Being temperature-tolerant means that the medaka embryonic cells could survive at room temperature, making them particularly suited for long, live timelapse photography.
The fact that medaka produce eggs frequently and have a relatively small genome size makes them good candidates for CRISPR/Cas9-mediated genome editing. With this technology, the researchers have created genetically modified, or transgenic, medaka whose embryonic cells literally highlight the dynamics of certain proteins involved in mitosis.
In studying the timelapses of the developing mitotic spindle in live, transgenic medaka embryos, the researchers discovered that large early embryos assemble unique spindles different from somatic spindles. In addition, Ran-GTP plays a decisive role in spindle formation in early embryonic divisions, but the importance diminishes in later stage embryos. This is possibly because the spindle structure is remodeled as cells get smaller during development, though the exact reason is a subject for future research.
The researchers also discovered that the early embryonic cells do not have a dedicated spindle assembly checkpoint, which characterizes most somatic cells, and which serves to ensure that the chromosomes are properly aligned before segregation. As Professor Kiyomitsu surmises, “the checkpoint is not active, and yet the chromosome segregations are still very accurate. This could be explained by the fact that embryonic cells need to divide very quickly, but it is something that we want to study further.”
While genetically modifying the medaka fish and studying the early embryos have led to new key insights into embryonic mitosis, this is just the beginning for Professor Kiyomitsu and the team. In addition to questions related to the diminishing role of Ran-GTP in later stages and the missing spindle assembly checkpoint, he points to the satisfying symmetry of cell divisions in the timelapses: “The spindle formation is characterized by a high degree of symmetry, as the cells appear to be dividing in the sizes and defined directions, and the spindle is consistently in the center of the cells. How can the spindle orient itself so regularly across the cells, and how is it able to find the center every time?”
Moving beyond the timelapses, the team also hopes to further solidify this new foundation with additional medaka gene-lines to serve as models for research in embryonic cells, and at the same time optimize the genome editing process. Eventually, the team wants to test for generalizability of their findings by studying embryonic mitosis in other organisms, and at a later stage, they want to explore the evolution of spindle assembly and embryonic divisions, which would also contribute to a better understanding of human embryogenesis and to developing diagnosis and treatment of human infertility.
“With this paper, we have created a solid foundation,” summarizes Professor Kiyomitsu, “but we have also opened a new frontier. Embryonic mitosis is beautiful, mysterious, and challenging to study, and we hope that with our work, we can eventually get a little closer to understanding the intricate processes at the beginning of life.”
Timelapse of a gene-edited medaka fish embryo undergoing mitosis. This slightly later stage footage shows how the cells rapidly duplicate, align, and segregate the chromosomes (magenta) using the mitotic spindle (green), which is composed of microtubules.
Slowed down and zoomed-in footage of the mechanisms for copying, aligning, and segregating chromosomes (magenta) into two daughter cells in an gene-edited medaka embryo. The microtubules making up the mitotic spindle are shown in green.
Injecting RNA into a medaka embryo (IMAGE)
OKINAWA INSTITUTE OF SCIENCE AND TECHNOLOGY (OIST) GRADUATE UNIVERSITY
Dr. Ai Kiyomitsu from the Cell Division Dynamics Unit, first author of the paper, injecting RNA into a medaka embryo as part of the CRISPR/Cas9-mediated genome editing process.
CREDIT
Tomomi Kiyomitsu, Okinawa Institute of Science and Technology (OIST).
Ran-GTP assembles a specialized spindle structure for accurate chromosome segregation in medaka early embryos
Monday, April 15, 2024
Pea plants that flower for longer
A team from the IBMCP (CSIC-UPV) has identified a gene that controls the production of flowers and fruits in legumes, considered to be the crop of the future
UNIVERSITAT POLITÈCNICA DE VALÈNCIA
IMAGE:
IBMCP RESEARCHERS: CRISTINA FERRÁNDIZ, PACO MADUEÑO, IRENE MARTÍNEZ, ANA BERBEL Y VICENTE BALANZÀ.
The end of the reproductive period, when flowers and fruits are produced, is a crucial moment in the life cycle of plants. However, the factors that control this process still need to be better understood. A research team led by the Research Institute for Plant Molecular and Cellular Biology (IBMCP), a joint centre of the Consejo Superior de Investigaciones Científicas ( Spanish National Research Council) (CSIC) and the Universitat Politècnica de València (UPV), has found that a gene called FUL controls the duration of the reproductive phase in crops such as peas. This gene would be used as a biotechnological tool to prolong this phase, thus increasing the production of fruits and seeds in peas and other legumes such as chickpeas, lentils or beans. The work has been published in the Proceedings of the National Academy of Sciences (PNAS).
Annual plants have only one reproductive season, producing flowers and fruits. Scientists are looking for genetic factors that cause plants to stop flowering to control the length of their reproductive phase. A few years ago, the group led by Cristina Ferrándiz, a CSIC research professor at the IBMCP, identified a gene called FUL (FRUITFULL) as a very important regulator of the flowering stops.
"The first studies were conducted only in Arabidopsis, a laboratory plant of no agronomic interest," Ferrándiz recalls. "We wanted to know if this function of FUL was the same in other species, especially crop species, and if we could use this knowledge to generate plants that produce flowers and fruits for longer, and therefore have a higher yield," she summarises. To this end, the team led by CSIC researcher Francisco Madueño at the IBMCP and other French and Canadian scientists studied the role of the FUL gene in pea plants, a legume with high nutritional value.
"We have seen that mutations that lead to a loss of function of the FUL genes in peas cause the plants to produce flowers, and consequently fruits, for much longer. This tells us that FUL controls the duration of the reproductive phase not only in the laboratory plant Arabidopsis but also in other species, including crop plants," explains Ferrándiz. "The prolonged flower and fruit production means that in certain pea varieties, mutations in the FUL genes can double the seed production, with identical nutritional characteristics to non-mutant plants, both in the greenhouse and the field," he says.
Mutants generated by classical methods
The research's authors, published in the latest issue of PNAS, emphasise that to obtain the mutations in the FUL genes analysed, they used mutant banks obtained by classical methods without generating transgenic plants. As a result, "the method for obtaining new plant varieties can be based on traditional mutagenesis, as used today and in this study, or on gene editing using CRISPR, the most promising and powerful tool for precision agriculture in the near future," says Francisco Madueño.
The potential application of these results is to use the FRUITFULL genes as a biotechnological tool to improve the yield of leguminous crops. The most significant increase in seed yield has been observed in medium-yielding pea varieties. In contrast, in high-yielding varieties, which already have a very high yield, the effect of mutations in the FUL genes is small," says Ferrándiz.
For the IBMCP researchers, the FRUITFULL genes could be beneficial to quickly and directly improve legume varieties. They are very valuable because they have interesting characteristics, such as high resistance to pathogens or drought, but are currently not used because of their low yields. "Mutating the FUL genes in these varieties would most likely also make them high-yielding and useful for agriculture. This could be very important given the challenges we face in the context of the climate crisis and the need to develop varieties that can better withstand it," they argue.
nalysis of pea mutants reveals the conserved role of FRUITFULL controlling the end of flowering and its potential to boost yield.
Study reveals potential to reverse lung fibrosis using the body’s own healing technique
MICHIGAN MEDICINE - UNIVERSITY OF MICHIGAN
The most common type of lung fibrosis — scarring of the lungs -- is idiopathic, meaning of unknown cause.
Researchers are urgently trying to find ways to prevent or slow idiopathic pulmonary fibrosis (IPF) and related lung conditions, which can cause worsening shortness of breath, dry cough, and extreme fatigue. Average survival following diagnosis of IPF is just three to five years, and the disease has no cure.
A recent U-M study from a team led by Sean Fortier, M.D. and Marc Peters-Golden, M.D. of the Division of Pulmonary and Critical Care Medicine at U-M Medical School uncovers a pathway used during normal wound healing that has the potential to reverse IPF.
Using a mouse model, they simulated IPF by administering bleomycin, a chemotherapy agent that causes cell injury and confirmed that the resulting lung scarring resolved itself over the span of about six weeks.
Because of this, “studying fibrosis is kind of tough,” said Fortier. “If we’re going to give experimental drugs to try and resolve fibrosis, we have to do it before it resolves on its own.
Otherwise, we will not be able to tell if the resolution was the action of the drug or natural repair mechanisms of the body.”
However, he said, “there’s actually a lot to learn about how the mouse gets better on its own. If we can learn the molecular mechanisms by which this occurs, we may uncover new targets for IPF.”
The process by which lung injury either leads to healing or fibrosis relies in part on what happens to a cell called a fibroblast, which forms connective tissue.
During injury or illness, fibroblasts are activated, becoming myofibroblasts that form scar tissue by secreting collagen. When the job is done, these fibroblasts must be deactivated, or de-differentiated, to go back to their quiet state or undergo programmed cell death and be cleared.
“This is the major distinction between normal wound healing and fibrosis – the persistence of activated myofibroblasts,” explained Fortier. That deactivation is controlled by molecular brakes. The study examined one of these brakes, called MKP1 – which the team found was expressed at lower levels in fibroblasts from patients with IPF.
By genetically eliminating MKP1 in fibroblasts of mice after establishing lung injury, the team saw that fibrosis continued uncontrolled.
“Instead of at day 63, seeing that nice resolution, you still see fibrosis,” said Fortier.
“We argued by contradiction: when you knock out this brake, fibrosis that would otherwise naturally disappear, persists and therefore MKP1 is necessary for spontaneous resolution of fibrosis.”
They performed several additional studies using CRISPR techniques to demonstrate how MKP1 applies the brakes, mainly by deactivating the enzyme p38α, which is implicated in a cell’s reaction to stress.
Furthermore, they demonstrated that neither of the two current FDA approved drugs for lung fibrosis, pirfenidone and nintedanib, are able to turn off myofibroblasts.
“That’s totally in keeping with the fact that they do slow the progression, but they don’t halt or reverse disease,” said Fortier.
Fortier hopes the discovery that this pathway reverses fibrosis leads to exploration of additional brakes on fibrosis.
“So much work on fibrosis has focused on how we can prevent it, but when a patient presents to my clinic with a dry cough, shortness of breath, and low oxygen as a result of underlying IPF, the scarring is already present. Of course, we’d love a way to prevent the scarring from getting worse, but the Holy Grail is to reverse it.”
Additional authors: Natalie Walker, Loka R. Penke, Jared Baas, Qinxue Shen, Jennifer Speth, Steven K. Huang, Rachel L. Zemans, and Anton M. Bennett
Citation: “MAP kinase phosphatase-1 inhibition of p38α within lung myofibroblasts is essential for spontaneous fibrosis resolution,” Journal of Clinical Investigation. DOI: 10.1172/JCI172826
MAP kinase phosphatase-1 inhibition of p38α within lung myofibroblasts is essential for spontaneous fibrosis resolution
Thursday, April 04, 2024
FLORA
New sunflower family tree reveals multiple origins of flower symmetry
PENN STATE
IMAGE:
A NEW SUNFLOWER FAMILY TREE REVEALS THAT FLOWER SYMMETRY EVOLVED MULTIPLE TIMES INDEPENDENTLY. SPECIES OF THE SUNFLOWER FAMILY WITH OR WITHOUT BILATERAL FLOWER SYMMETRY. CHRYSANTHEMUM LAVANDULIFOLIUM (UPPER LEFT) AND ARTEMISIA ANNUA (UPPER RIGHT) ARE CLOSELY RELATED SPECIES FROM THE SAME TRIBE; THE FORMER HAS BILATERALLY SYMMETRIC FLOWERS (THE RAYS) AND THE LATTER DOES NOT. RUDBECKIA HIRTA (LOWER LEFT) FROM THE SUNFLOWER TRIBE HAS BILATERALLY SYMMETRIC FLOWERS, AND EUPATORIUM CHINENSE (LOWER RIGHT) FROM THE EUPATORIEAE TRIBE DOES NOT; THESE TWO TRIBES ARE CLOSELY RELATED GROUPS. A SUNFLOWER (CENTER) SHOWS FLOWERS WITH BILATERAL SYMMETRY (THE LARGE PETAL-LIKE FLOWERS IN THE OUTER ROW) AND WITHOUT (THE SMALL FLOWERS IN THE INNER ROWS).
UNIVERSITY PARK, Pa. — The sunflower family tree revealed that flower symmetry evolved multiple times independently, a process called convergent evolution, among the members of this large plant family, according to a new analysis. The research team, led by a Penn State biologist, resolved more of the finer branches of the family tree, providing insight into how the sunflower family — which includes asters, daisies and food crops like lettuce and artichoke — evolved.
A paper describing the analysis and findings, which researchers said may help identify useful traits to selectively breed plants with more desirable characteristics, appeared online in the journal Plant Communication.
“Convergent evolution describes the independent evolution of what appears to be the same trait in different species, like wings in birds and bats,” said Hong Ma, Huck Chair in Plant Reproductive Development and Evolution, professor of biology in the Eberly College of Science at Penn State and the leader of the research team. “This can make it difficult to determine how closely related two species are by comparing their traits, so having a detailed family tree based on DNA sequence is crucial to understanding how and when these traits evolved.”
The sunflower head, for example, is actually a composite composed of multiple much smaller flowers. While the head is generally radially symmetric — it can be divided into two equal halves in multiple directions like a starfish or a pie — the individual flowers can have different forms of symmetry. According to the new study, bilateral symmetry — where there is only one line that divides the flower into two equal halves — has evolved and been lost multiple times independently in sunflowers over evolutionary history. The researchers found that this convergent evolution is likely related to changes in the number of copies and the expression patterns of the floral regulatory gene, CYC2.
In recent years, many family trees for a group of related species have been built by extensively using transcriptomes, which are the genetic sequences of essentially all of the genes expressed by a species, the researchers explained. Transcriptomes are easier to acquire than high-quality whole-genome sequences for a species but are still difficult and costly to prepare and require fresh plant samples. To increase the number of species available for comparison the team turned to low-coverage genome sequences, which are produced through a process called genome skimming and are relatively inexpensive and easy to prepare, even from dried plant samples.
“To get an accurate whole-genome sequence for a species, each letter of its DNA alphabet must be read — or covered — multiple times to minimize errors,” Ma said. “For the purposes of building a family tree, we show in this paper that we can get away with lower coverage genome sequences. This allowed us to increase the number of species in our analysis, which, in turn, allowed us to resolve more of the finer branches on the sunflower family tree.”
The team used a combination of publicly available and newly generated transcriptomes, along with a large number of newly obtained skimmed genomes, for a total of 706 species with representatives from 16 subfamilies, 41 tribes and 144 subtribe-level groups in the sunflower family. The subfamilies are major subdivisions of the family, while the tribes and subtribe can contain one or more of genera, which is the classification level just above the species.
“Previous versions of the sunflower family tree had established the relationships among most of the subfamilies and many tribes, which are equivalent to the main branches of a tree,” Ma said. “With our increased sample size, we were able to resolve more of the smaller branches and twigs at the subtribe and genus level. This higher-resolution tree allowed us to reconstruct where and when traits like flower symmetry evolved, demonstrating that bilateral symmetry must have evolved many times independently.”
The team also studied the molecular evolution of genes involved in flower development among sunflowers. They found that one of these genes, CYC2, which is found in multiple copies in the genomes of each species, was activated in species with bilaterally symmetric flowers, suggesting that it might be part of the molecular basis for the convergent evolution of this trait. To further test this, the team performed experiments to quantify CYC2 gene expression in the flowers of species with different types of symmetry.
“Our analysis showed a clear relationship between CYC2 expression and flower symmetry, suggesting that changes in how these genes are used in various sunflower species is likely involved in the convergent evolution observed in the family,” Ma said. “The sunflower family is one of the two largest families of flowering plants containing over 28,000 species, including many economically important agricultural and horticultural species. Understanding how these species are related to one another allows us to determine how and when their traits evolved. This knowledge could also be used to identify useful traits that could be bred into domesticated species from closely related wild ones.”
In addition to Ma, the research team includes Guojin Zhang at Penn State; Junbo Yang, Jie Cai, Zhi-Rong Zhang and Lian-Ming Gao at the Kunming Institute of Botany in Kunming, China; Caifei Zhang at the Wuhan Botanical Garden and Sino-Africa Joint Research Centre in Wuhan, China; Bohan Jiao and Tiangang Gao at the State Key Laboratory of Plant Diversity and Specialty Crops in Beijing, China; and Jose L. Panero at the University of Texas, Austin.
Funding from the Eberly College of Science and the Huck Institutes of the Life Sciences at Penn State, the Strategic Priority Research Program of the Chinese Academy of Sciences, the Large-scale Scientific Facilities of the Chinese Academy of Sciences, and the National Natural Science Foundation of China supported this research.
Passion fruit (Passiflora edulis), renowned for its nutritional richness and aromatic fruits, is widely cultivated in tropical and subtropical regions. Passion fruit can not only be harvested year-round, but also can be used as a horticultural plant, which contributes significantly to its economic value. In addition, its special floral structure makes it an excellent and unique plant model for investigating floral organ morphology. The MADS-box gene family, essential in plant growth and development, plays a pivotal role in various biological processes including floral organ morphology. Although extensive research has been carried out on members of the MADS-box gene family in various plants, a comprehensive investigation of MADS-box gene family members in passion fruit has not yet been reported.
In this study, researchers combined hidden Markov model (HMM) and BLAST search to identify 52 members of the MADS-box gene family, designated as PeMADS1-PeMADS51 based on their sequential positions on the chromosomes, while a single member mapped to a contig was named PeMADS52. These genes displayed variable protein lengths and molecular weights, with isoelectric points ranging from acidic to basic. The stability, aliphatic index, and hydropathicity analyses suggested varied thermal stability and hydrophobicity among the proteins. The prediction of subcellular localization reveals that PeMADS proteins were mainly localized in the nucleus, chloroplasts, and mitochondria. Sequence alignment and 3D structural modeling revealed a highly conserved MADS-domain from 52 PeMADS proteins.
Phylogenetic analysis further classified 52 MADS-box genes into two types with five subgroups (type I: Mα, Mβ, Mγ; type II: MIKCC, MIKC*). The structural analysis illustrated that PeMADS proteins within the same subfamily are relatively conserved. The examination of cis-regulatory elements revealed insights into the genes' responses to light, hormones, and stress, emphasizing their regulatory versatility. Chromosomal mapping and synteny analyses highlighted the gene family's evolutionary trajectory, with evidence of duplication events contributing to its expansion and diversification.
Notably, researchers proposed an ABC(D)E model to elucidate the regulation of the unique floral structure (sepal-petal-corona-stamen-carpel) in passion fruit. Expression pattern analyses in floral tissues suggested the involvement of specific PeMADS genes in implementing the ABC(D)E model of floral organ identity. The distinct coronas were predominately controlled by B-, C(D)- and E-class genes, supporting the speculation that the corona might have originated from stamens. Many PeMADS genes were also involved in the development regulation of non-floral organ development and stress responses. The study's findings on temperature and phytohormone responsiveness underscore the gene family's adaptability to environmental stimuli.
Overall, this work establishes a foundational understanding of the MADS-box gene family in passion fruit, offering insights into their evolutionary history, structural characteristics, and functional roles in both floral and non-floral organ development, paving the way for future functional characterizations.
# These authors contributed equally: Chang An, Jingyi Liao, Lin Lu
Affiliations
1.Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
2.BGI-Shenzhen, University of Chinese Academy of Sciences, Beijing 100049, China
3.Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning Investigation Station of South Subtropical Fruit Trees, Ministry of Agriculture, Nanning 530004, China
4.Pingtan Science and Technology Research Institute, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
About Yuan Qin
She is the Dean of the College of Life Sciences at Fujian Agriculture and Forestry University. Her research areas include molecular mechanisms of plant female gametophyte development and molecular regulation of plant adversity development.
Carnation (Dianthus caryophyllus L.) is a flower widely cultivated for its appealing apperance and frangance. However, it faces postharvest challenges that can affect its ornamental quality, primarily due to water stress and microbial growth. Research has highlighted the significant role of ethylene in the flower's lifespan, with variations in sensitivity and production across different varieties. Key genes involved in ethylene biosynthesis, such as ACS and ACO, have been identified, and genetic manipulation to alter ethylene production has shown promise in extending the vase life of carnations. However, there is a lack of comprehensive research on the postharvest physiological changes across different carnation species, indicating a critical area for future investigation to improve cut flower preservation techniques further.
In this study, 14 commercially carnation varieties were exposed to ethylene gas at a concentration of 10 μL/L for 4 hours to explore the effect of ethylene on the vase life of various varieties. The results showed that the varieties responded differently to ethylene, with 'Master' exhibiting the most significant reduction in vase life post-treatment. Conversely, 'Snow White' showed no change in vase life, indicating minimal ethylene sensitivity. Furthermore, water content analysis across different senescence stages in selected varieties revealed that ethylene treatment accelerated water loss, particularly noticeable in the complete wilting stage.
Ethylene release measurements provided insights into the varieties' ethylene production patterns, revealing varied responses, with 'Master' displaying a unique peak in ethylene release at 24 hours, contrasting with 'Snow White's' lower ethylene sensitivity. Gene expression analysis focused on DcACS1, DcACO1, DcEBF1/2, and DcERF-1, crucial for ethylene biosynthesis and signaling. Notably, 'Master' showed a dramatic increase in DcACS1 and DcACO1 expression after ethylene treatment, while 'Snow White' had the lowest increase, which correlates with their ethylene sensitivity.
To further understand ethylene's role in senescence, transient silencing and overexpression experiments were conducted targeting DcACS1 and DcACO1 genes. As a result, silencing DcACS1 in 'Master' delayed senescence and maintained flower disc whiteness, whereas overexpressing DcACS1 accelerated senescence. Similar trends were observed with DcACO1, where its silencing delayed senescence, and overexpression promotedit, confirming the pivotal role of these genes in carnation senescence.
In conclusion, this study underscores the intricate relationship between ethylene sensitivity, water content regulation, and genetic factors in determining the postharvest lifespan of carnation flowers. It also highlights the potential for genetic manipulation to extend vase life, providing insights for breeding and selecting long-lived carnation varieties, paving the way for future research on the molecular mechanisms governing ethylene-induced senescence in cut flowers.
Min Wang1,2,3,#, Man Wang1,2,3,#, Chenyu Ni1,2,3,#, Shan Feng1,2,3, Yan Wang1,2,3, Linlin Zhong1,3, Yunjiang Cheng1,2,3, Manzhu Bao1,5,6 & Fan Zhang1,2,3,4,5,6,*
# These authors contributed equally: Min Wang, Man Wang, Chenyu Ni
Affiliations
1. National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
2. Hubei Hongshan Laboratory, Wuhan 430070, China
3. National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan 430070, China
4. Yunnan Seed Laboratory, Kunming 650200, China
5. The Institute of Flowers Research, Huazhong Agricultural University, Wuhan 430070, China
6. Key Laboratory of Huazhong Urban Agriculture, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
About Fan Zhang
Professor, Huazhong Agricultural University. His main research interests include the molecular mechanisms of plant floral organ senescence and post-harvest senescence of important ornamental flowers and fresh cut flowers.
In China, a country hosting over 1,700 of the world’s roughly 30,000 orchid species, the orchid industry has witnessed substantial growth fueled by advancements in science and technology. Ornamental Plant Research published online a review article entitled “The China orchid industry: past and future perspectives” on 12 January 2024.
This review explores China's orchid industry, tracing its deep cultural connections to orchids back to ancient times and highlighting the significant evolution and modern advancements that position China as a global leader in orchid cultivation. With a history enriched by figures like Confucius and Qu Yuan, and a preference for fragrant Cymbidium species. As one of the global leaders in orchid diversity, China attaches great importance to the protection of orchid diversity. With the emergence of high-throughput sequencing, many SNP markers have been discovered in orchids. These markers contribute to the study of the origin, evolution, and genetic diversity of orchids. The genomes of 26 orchids have been subjected to high-throughput sequencing, and a large number of sequencing results have driven the exploration of key genes in orchids. Significant progress has been made in research on flower patterns, flowering time, color of flowers and leaves, aroma, and disease resistance.
Furthermore, the review discusses the challenges and advancements in orchid resistance research, breeding technologies, and rapid propagation methods that leverage tissue culture for enhancing orchid cultivation. It emphasizes the potential of molecular marker-assisted breeding, transgenic breeding, and gene editing to revolutionize orchid breeding. In addition, this article also presents the challenges posed by diseases and pests to the orchid industry, and cultivating stem tip culture of virus-free seedlings is the main method for controlling viral diseases. Endophytic fungi are an important component of the orchid microbiota and have a positive impact on orchid reproduction, growth, development, and resistance.
In summary, the prospects of the orchid industry are vast, with untapped ornamental and medicinal orchid species offering new avenues for commercial development. As China continues to influence global orchid trends and markets, its role as a major center for orchid research, development, production, and consumption is undeniably pivotal for the future growth and diversification of the global orchid industry.
1.Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China
2.Department of Biological Sciences, National University of Singapore, Singapore 119543, Singapore
About Genfa Zhu
He is currently the director of the Environmental Horticulture Research Institute, Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization. He is mainly engaged in research on identification and evaluation of orchid germplasm resources, genetic breeding, molecular biology, cytology, tissue culture and rapid propagation technology.
Chrysanthemum, celebrated for its ornamental, medicinal, and beverage value, faces significant threats from bacterial and fungal infections, particularly black spot disease caused by Alternaria alternate, which leads to severe economic losses. Current research has focused on developing resistant germplasm as an eco-friendly alternative to pesticides. Despite these efforts, the search for germplasm with exceptional disease resistance is ongoing, and the integration of physical and chemical plant defenses and secondary metabolites into breeding strategies remains underexplored. Therefore, further investigation into how these defenses contribute to resistance against black spot disease in chrysanthemum is of great importance to enhance breeding efforts for disease-resistant cultivars.
In this study, researchers employed simplified detached leaf inoculation assay and whole plant inoculation assay to assess the resistance of 14 chrysanthemum-related genera (CRG) to black spot disease. After artificial inoculation and identification based on disease indices, two disease-resistant germplasm resources (R), 11 moderately resistant materials (MR), and one sensitive (S) material were obtained. The results showed good reproducibility and correlation between methods, highlighting C. japonese and A. parviflora as resistant, and revealing significant physical and chemical defense mechanisms contributing to disease resistance.
Further analysis focused on the leaf epidermis structure of resistant and susceptible germplasms, revealing notable differences in trichome morphology and density, stomatal characteristics, and wax content, which correlated with resistance levels. For instance, R1 had significantly higher trichome density and wax content, contributing to its resistance. Additionally, volatile organic compounds (VOCs) analysis indicated that resistant germplasms produced higher terpenoid content, with Germacrene D significantly inhibiting A. alternata growth, suggesting its role in chemical defense.
In conclusion, the study not only identified C. japonese and A. parviflora as resistant through a combination of physical (trichome density, stomatal closure, wax content) and chemical defenses (high VOCs and terpenoid content) but also demonstrated the importance of both types of defenses in disease resistance. These findings enhance our understanding of CRG resistance to black spot disease, offering insights into breeding strategies and the potential use of physical and chemical traits as markers for disease resistance.
State Key Laboratory of Crop Genetics and Germplasm Enhancement / Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs / Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration / College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
About Zhiyong Guan
Professor, Nanjing Agricultural University. His main research interests include: ornamental plant germplasm resources and utilization, Chrysanthemum germplasm resources, high yield and quality control of Chrysanthemum, Chrysanthemum cultivation and adversity physiology.
Leaf aging is a complex biological phenomenon influenced by growth stages, plant hormones, and various environmental conditions. In the context of forage and turf grasses, managing leaf aging can significantly enhance the quality of forage, improve the aesthetic and functional value of lawns and turfs, and increase the resistance of grasses to stress. Leaf senescence is a process characterized by extensive changes in gene regulation and metabolism, including shifts in chlorophyll breakdown. Thoroughly studying the molecular mechanisms involved in leaf aging is of great significance for improving the comfort of lawns, grass yield, and raw material quality.
Grass Research published online a review article entitled “Leaf senescence in forage and turf grass: progress and prospects” on 28 February 2024. This paper highlights recent advancements in research on leaf aging across key forage and turf grass varieties, aiming to shed light on developing effective strategies to slow down leaf aging in these grass species.
In this review, authors explore the crucial role of regulating leaf senescence in enhancing biomass yield and quality for forage and turf grass species, along with improving the aesthetics and functionality of lawns and turfs. Leaf senescence, the final stage of leaf development, is characterized by the breakdown of chlorophyll, carbohydrates, proteins, and nucleic acids, facilitating the reallocation of nutrients to new growth. This process is significantly influenced by both internal and environmental factors, including plant age, hormones, light, and stress from drought, salinity, pathogens, and herbivory. The dynamic and complex nature of leaf senescence, highlighted by changes in leaf color and cellular structure, underscores its importance in plant life cycles and agricultural productivity.
The review then delves into the molecular genetics underpinning leaf senescence, focusing on chromatin remodeling, DNA transcription, and various post-transcriptional modifications that govern the expression of senescence-associated genes (SAGs). Special emphasis was placed on external factors that affect the aging of grass leaves, such as light conditions, atmospheric pollution, elevated CO2 levels, temperature, soil water content, saline-alkali and toxic metals, fungi, bacteria, and management practices like fertilization and mowing. These factors collectively impact the progression of leaf senescence, ultimately affecting plant growth, yield, and quality.
Highlighted studies on key grass species such as Medicago truncatula, alfalfa, perennial ryegrass, switchgrass, and creeping bentgrass reveal significant genetic insights and potential strategies to delay leaf senescence. Multiple stay-green genotypes have been identified and incorporated into breeding plans to minimize yield loss in plants grown under adverse environmental conditions.
The review also highlights the importance of further research to elucidate the specific mechanisms of leaf senescence in forage and turf grasses and to develop effective methods for its delay. The application of CRISPR gene-editing technology and the identification of key regulatory genes offer promising prospects for breeding programs aimed at achieving higher quality, yield, and stress tolerance in these grass species. Overall, this review underscores the complexity of leaf senescence, its impact on plant productivity and aesthetics, and the potential of genetic research to enhance the sustainability and performance of forage and turf grasses.
1.Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
2.Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 74078-1010, USA
3.College of Agro-grassland Science, Nanjing Agricultural University, Nanjing 210095, China
About Maofeng Chai
Professor, College of Grassland Science, Qingdao Agricultural University. His research interests include plant molecular biology, genetic improvement of forage and turfgrass.
