Biology Research News

For any organism to survive and thrive, its cells must tightly regulate when and where specific genes are active. New research by EMBL Heidelberg’s Noh Group, in collaboration with EMBL Australia, reveals key control sites that govern this process, particularly in relation to the activity of ancient viral sequences embedded in the genome to know how cells suppress genomic traces of ancient viruses.

Date	September 18, 2024
Source	European Molecular Biology Laboratory
Summary	Researchers have discovered key cellular control sites that regulate gene expression and prevent the activation of hidden genomic regions, including ancient viral sequences.

If you want to know recent biology news like How Cells Suppress Genomic Traces of Ancient Viruses: Smell Prepares Nematodes and the human gut to combat infections, Mantis Shrimp-Clam Relationship Challenges a Biological Principle, Injury Dressings in First-Aid Kits Can Identify Shark Species After Bite Incidents, Harnessing big data helps scientists home in on new antimicrobials, New geological datings place the first European hominids in the south of the Iberian Peninsula, A New Rule of Biology Focusing on Evolution and Aging.

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How Cells Suppress Genomic Traces of Ancient Viruses

For organisms, it’s essential to regulate when and where specific genes are expressed. Naturally occurring chemical modifications to histone proteins, which bind to DNA, are thought to play a significant role in this process. However, their direct influence on gene expression was uncertain. Through experimentation, researchers have demonstrated that certain histone sites serve as crucial control points, helping to prevent the accidental activation of genomic regions, including remnants of ancient viral sequences.

Our genomes are vast — a typical human cell contains over 6 billion units of DNA, or ‘base pairs.’ However, accessing the right information at the right time to perform specific functions presents a challenge. This is where epigenetic signatures come into play. Think of the genome as a book; epigenetic marks are like highlights on the pages or notes in the margins. But it’s unclear whether these marks direct the cell, telling it to “read this” or “ignore this,” or if they are simply remnants of past activity.

They focused on H3.3, a histone protein that binds to DNA and helps maintain its structure. H3.3 has sites on its tail, K9 and K27, that are often chemically modified. These modifications are believed to be epigenetic markers that regulate gene expression, but it has not been proven that they act as control sites.

The researchers experimentally altered these sites, creating a version of H3.3 that couldn’t be chemically modified. In terms of the book analogy, this created a page that couldn’t be marked, allowing the team to explore the consequences of losing these marks. By comparing the effects of losing modifications at each control site, they gained insights into their roles in gene regulation.

The scientists found that mutating these sites in mouse stem cells caused defects in differentiation, growth, and survival. It also led to the improper activation of genes across the genome, including immune-specific genes that shouldn’t be expressed in stem cells. This indicates that these sites normally help repress certain genes, preserving the stem cell state. The effects varied between the two control sites, highlighting their distinct roles in gene regulation.

Further analysis revealed that some activated regions are ancient viral remnants integrated into the genome, known as endogenous retroviruses (ERVs).

By mutating the K9 site in stem cells, the team found that many ‘cryptic’ enhancers, normally silenced, became active. “Repression of these unique genomic regions is essential for maintaining the cell’s gene expression balance,” Noh said. Activating these enhancers disrupts the gene regulatory network, impacting stem cell identity and function.

This study, conducted in collaboration with researchers from EMBL Australia, Washington University in St. Louis, and EMBL Heidelberg, was published in Nature Communications.

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Using CRISPR/Cas9 genome editing, researchers have successfully engineered stable Euglena. CRISPR/Cas9 alters Euglena to develop possible biofuel source mutants capable of producing wax esters with improved cold flow properties, making them ideal for biofuel feedstock.

Date	September 13, 2024
Source	Osaka Metropolitan University
Summary	Mutant microalgae generate wax esters for biofuel feedstock with enhanced cold flow.

If you want to know recent biology news like CRISPR/Cas9 alters Euglena to develop a possible biofuel source: Smell Prepares Nematodes and the human gut to combat infections, Mantis Shrimp-Clam Relationship Challenges a Biological Principle, Injury Dressings in First-Aid Kits Can Identify Shark Species After Bite Incidents, Harnessing big data helps scientists home in on new antimicrobials, New geological datings place the first European hominids in the south of the Iberian Peninsula, A New Rule of Biology Focusing on Evolution and Aging.

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How CRISPR/Cas9 alters Euglena to develop a possible biofuel source

• News about biofuels often mentions used cooking oil as a feedstock, but if it contains animal fat, it can solidify in cold temperatures. This occurs because the fatty acids in these and other saturated fats have long carbon chains with single bonds. That’s where Euglena comes in.
• A team from Osaka Metropolitan University has discovered a way for one species of this microalgae to produce wax esters with shorter carbon chains.
• Using CRISPR/Cas9 genome editing, Dr. Masami Nakazawa and her team from the Graduate School of Agriculture’s Department of Applied Biochemistry successfully engineered stable mutants of Euglena gracilis.
• These mutants produced wax esters with carbon chains two atoms shorter than the wild-type species, improving the cold flow properties of the esters, and making them more suitable for biofuel feedstock.
• Euglena gracilis is particularly favorable for biofuel production due to its ease of growth via photosynthesis and its anaerobic production of wax esters.
• This achievement is expected to be a foundational technology to replace some petroleum-based wax ester production with biological alternatives.

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A recent study from the University of Ottawa has revealed that certain fish use their tastebuds to monitor oxygen levels in water. Zebrafish Sense Oxygen, its larvae, a freshwater species from the minnow family, can “taste” oxygen using the same cells they use for detecting food. These taste bud cells also act as oxygen sensors, playing a vital role in regulating the fish’s breathing response when oxygen levels are low. This dual function of taste cells was previously unknown and challenges our current understanding of sensory systems in aquatic animals.

Date	September 12, 2024
Source	University of Ottawa
Summary	Researchers have uncovered a connection between taste and respiration in fish. This finding could enhance our understanding of how fish sense and adapt to environmental changes.

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Emeritus Professor in the biology department at the University of Ottawa have uncovered a fascinating link between taste and respiration in fish. Their research offers the first direct evidence of oxygen-sensing cells involved in controlling breathing, surprisingly located within the fish’s taste buds.

How Zebrafish Sense Oxygen

The research team employed advanced techniques, such as intracellular calcium imaging in live fish, to reach these findings.

“We observed that these sensory cells activate when exposed to low oxygen, or hypoxia,” explained co-author Yihang Kevin Pan, a postdoctoral fellow in Professor Perry’s lab. “When we removed these cells, the fish’s breathing patterns under hypoxic conditions were disrupted. On the other hand, stimulating the nerves from the taste buds triggered breathing.”

This discovery has significant implications for understanding how fish adapt to environmental changes. It suggests that the ability to “taste” oxygen in water may be a critical survival mechanism, helping fish quickly detect and respond to low-oxygen conditions.

The study also highlights the extraordinary adaptability of sensory systems in nature. “It’s a perfect example of how one biological structure can serve multiple functions,” Pan noted. “In this case, taste buds not only detect taste but also play a crucial respiratory role.”

As climate change continues to impact aquatic ecosystems, understanding how fish perceive and react to environmental shifts becomes increasingly important. Beyond its scientific implications, this discovery could have practical benefits for the protection and management of aquatic life.

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A recent groundbreaking research reveals the hidden impact of stress on sperm. It highlights that stress-related changes in sperm motility occur after the stress has subsided, not during it, leading to enhanced sperm performance. This finding is crucial for understanding how stress influences reproduction and can lead to improved fetal development outcomes.

Date	September 11, 2024
Source	University of Colorado Anschutz Medical Campus
Summary	Researchers discover that stress-induced events, such as the pandemic, trigger improvements in the male reproductive system after the stressful period has passed.

If you want to know recent biology news like Groundbreaking research reveals the hidden impact of stress on sperm: Smell prepares nematodes and the human gut to combat infections, Mantis Shrimp-Clam Relationship Challenges a Biological Principle, Injury Dressings in First-Aid Kits Can Identify Shark Species After Bite Incidents, Harnessing big data helps scientists home in on new antimicrobials, New geological datings place the first European hominids in the south of the Iberian Peninsula, A New Rule of Biology Focusing on Evolution and Aging.

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How new research reveals the hidden impact of stress on sperm

• A pioneering study led by researchers at the University of Colorado Anschutz Medical Campus has uncovered that stress-induced changes in sperm motility occur after a stressful event, rather than during it, resulting in enhanced sperm performance. This discovery is critical for understanding how stress influences the reproductive process and may improve fetal development outcomes.
• Published today in Nature Communications, the research addresses a five-decade decline in semen quality linked to environmental stressors. The study reveals that stress affects sperm motility—the ability of sperm to travel through the female reproductive system to fertilize an egg.
• Researchers observed alterations in extracellular vesicles (EVs), tiny particles released from the male reproductive tract that play a role in sperm development and maturation. These changes were noted only after the stressor had passed.
• The research demonstrates a significant, time-dependent boost in sperm motility after perceived stress, aligning with prior findings on changes in microRNA in human sperm.
• This post-stress improvement in sperm function could have evolutionary benefits, potentially enhancing birth rates, particularly after challenging events like the COVID-19 pandemic.
• The research was conducted in both human and animal models, showing that stress-induced EVs improved sperm motility and mitochondrial respiration—the energy production needed to power cellular activities.
• Because the results were consistent in humans and animals, the findings suggest a universal biological response across species, providing insights into reproductive health.
• Though the study focused on males, researchers emphasize the importance of exploring how stress affects both partners in the fertility process. They are particularly interested in how stress impacts fetal development, especially the brain.
• Since stress is a common aspect of daily life, learning how it affects reproduction and development is vital for improving fertility and addressing ecological challenges, particularly for endangered species.
• The team is expanding their research to investigate how stress information is encoded into EVs, its effects on fertilization, and its impact on brain development.
• Additionally, they are launching a trial to further explore the relationship between EVs and sperm in seminal fluid. So new research reveals the hidden impact of stress on sperm, has a great future.

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Farmed in Okinawa for their nutritional value, these large meso-predators have had their entire genome sequenced, yielding unexpected findings. Because Unexpected hormone-related gene activity is found in the early larval stage of the Malabar grouper, these genes are activated twice during larval development—once in the early larval stage and again during metamorphosis. This early activation has not been observed in other fish species, making the grouper’s case exceptional.

Date	September 10, 2024
Source	Okinawa Institute of Science and Technology (OIST) Graduate University
Summary	Researchers have uncovered distinct gene activation patterns during Malabar grouper larval development, identifying a surprising early peak in thyroid and corticoid gene activation.

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Why unexpected hormone-related gene activity is found in the early larval stage of the Malabar grouper

Researchers from the Marine Climate Change Unit and Marine Eco-Evo-Devo Unit at the Okinawa Institute of Science and Technology (OIST) have uncovered unique gene activation patterns during Malabar grouper larval development. Their study, published in eLife, is the first to demonstrate that thyroid and corticoid genes are activated twice during larval development—once in the early larval stage and again during metamorphosis. This early activation is unprecedented in any fish species, making the Malabar grouper case exceptional.

As meso-predators, groupers play a vital role in maintaining the health and balance of marine ecosystems. The Malabar grouper (Epinephelus malabaricus), known as Yaito-hata in Japan, can grow up to two meters long. However, overexploitation due to their popularity and high market value has endangered many grouper species. To address this threat and meet demand, grouper aquaculture farms have been established in Okinawa and other regions.

RNA Analysis Unveils Unusual Hormone Activation

The genome is the complete set of genetic material in an organism, and scientists can study how it functions through transcriptomic analysis, which reveals which genes are activated at specific times. The researchers examined the gene expression of thyroid and corticoid hormones during the grouper’s larval development, including the critical phase of metamorphosis.

Malabar grouper larvae drift in the open ocean for around 60 days before returning to coastal areas. During this period, they undergo a dramatic, hormone-driven metamorphosis, marked by spine regression and the appearance of adult-like pigmentation.

Genomic analysis clearly shows heightened thyroid and corticoid gene activation during metamorphosis, coinciding with the emergence of adult pigmentation and the loss of spines on the larvae’s dorsal and pectoral fins. What’s particularly interesting is the surge in these genes early in the larval stage, which we haven’t observed in other fish species.

Dr. Natacha Roux, a researcher also measured thyroid hormone and corticoid levels in the larvae and saw a spike at the beginning of development, confirming the genomic results. While the cause of this early activation is unclear, they suspect it may be linked to the development of larval spines, aiding buoyancy and deterring predators.

FAQ on unexpected hormone-related gene activity is found in the early larval stage of the Malabar grouper

Date	September 4, 2024
Source	Southern Methodist University
Summary	Biologists are employing a new method called SMIRC to collect samples from the world’s oceans. This technique has the potential to identify novel compounds that could pave the way for the development of next-generation antibiotics.

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How Innovative Method Developed for Studying Oceanic Microbes

When SMU researcher Alexander Chase was a child, he was captivated by the diverse plant life in tropical rainforests and wondered about undiscovered species. This curiosity now drives him to collect oceanic samples using a novel method called Small Molecule In situ Resin Capture (SMIRC), which may help identify compounds for next-generation antibiotics.

Microbial natural products, derived from microorganisms, are crucial for many modern medicines, including antibiotics. Microbes produce various chemical compounds during their lifespans, some of which are valuable for pharmaceuticals. Traditionally, new compounds have been found by culturing microbes from wild samples in the lab, a method that has become less effective over time due to the similarity of newly discovered chemical “scaffolds” to known ones. These scaffolds are essential for drug development.

Chase, an assistant professor at the Roy M. Huffington Department of Earth Sciences, explains that the traditional method limits discovery to familiar bacterial strains and their compounds, missing out on the vast chemical diversity in the ocean. SMIRC addresses this by capturing microbial products directly in their natural environment, bypassing the need for lab cultivation.

A recent study published in Nature Communications details how SMIRC, using an absorbent resin called HP-20, successfully collected microbial compounds from wild samples. Initial tests in seagrass areas near San Diego yielded an antibiotic compound and chrysoeriol, a plant-derived antibacterial agent. A modified SMIRC method, combining HP-20 with agar to promote microbial growth, identified a new compound, aplysiopsene A.

Further tests in a protected marine reserve at Cabrillo National Monument collected complex chemical mixtures, possibly due to the area’s low human impact. Although none of the new compounds led to antibiotics, cabrillostatin, one of the discovered compounds, shows potential for cancer and heart disease treatment.

Chase emphasizes that the ocean remains largely unexplored, especially the deep ocean, and SMIRC provides a new tool to study marine microorganisms and their compounds. This advancement is crucial in addressing antibiotic resistance and other health challenges.

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How fish intestines could influence the future of skincare products? Cosmetics and skincare products often feature unusual ingredients, like snail mucin, valued for its moisturizing and antioxidant benefits. However, researchers have discovered something even more unconventional: molecules produced by bacteria found in fish intestines. In cell studies, these compounds demonstrated skin-brightening and anti-wrinkle effects, suggesting they could become key ingredients in future skincare formulations.

Date	September 5, 2024
Source	American Chemical Society
Summary	Researchers reported in ACS Omega may have discovered an even more unconventional ingredient: molecules produced by bacteria found in fish intestines.

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How fish intestines could influence the future of skincare products

Although fish intestines might seem an unlikely source for cosmetic ingredients, it’s not unprecedented. Many significant drugs have been discovered in unexpected places—penicillin’s antibiotic properties were found after a moldy experiment, and the brain cancer drug Marizomib was derived from microbes in deep-sea sediments.

The gut microbes of the red seabream and blackhead seabream, found in the western Pacific Ocean, could be promising sources for new compounds. While these microbes were identified in 1992 and 2016, respectively, their compounds had not been studied until now.

Researchers Hyo-Jong Lee and Chung Sub Kim explored whether these bacteria produce any metabolites with cosmetic benefits. They identified 22 molecules from the gut bacteria of these fish and tested their ability to inhibit tyrosinase and collagenase enzymes in lab-grown mouse cells. Tyrosinase is linked to melanin production, which can cause hyperpigmentation, while collagenase breaks down collagen, leading to wrinkles. Three molecules from the red seabream bacteria effectively inhibited both enzymes without harming the cells, showing potential as anti-wrinkle and skin-brightening agents for future cosmetic use.

The research was supported by various organizations including the Marine Biotechnology Program, the National Research Foundation of Korea, and the Technology Development Program, among others.

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Scientists render living animal tissue transparent because making living tissue transparent allows researchers to observe biological processes, blood vessels, and organs in real-time without invasive surgery. This could greatly enhance medical imaging, biological research, and our understanding of how the body functions.

Date	September 5, 2024
Source	University of Texas at Dallas
Summary	In a groundbreaking study, researchers have successfully made the skin on the skulls and abdomens of live mice transparent by applying a solution containing water and a common yellow food dye known as tartrazine.

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How scientists render living animal tissue transparent

Dr. Zihao Ou, assistant professor of physics at The University of Texas at Dallas, led the study, which was published in the September 6 issue of Science. While conducting the research as a postdoctoral fellow at Stanford University, Ou and his colleagues explored the properties of living skin, which typically scatters light, making it opaque. ‘We combined tartrazine, a light-absorbing molecule, with skin, which scatters light. Together, they created transparency,’ explained Ou, who joined UT Dallas in August.

The effect occurs because dissolving the dye in water changes the solution’s refractive index to match that of skin components, reducing light scattering similar to how fog dissipates. In their experiments, the solution was rubbed onto the mice’s skin, and after the dye diffused, the skin became transparent. The process is reversible, with the dye eventually metabolized and excreted naturally.

Within minutes, researchers were able to observe blood vessels on the brain’s surface and internal organs through the transparent skin. The treated areas took on an orange hue due to the use of FD&C Yellow #5, a food-grade dye found in common snacks. ‘The dye is safe, inexpensive, and highly efficient,’ said Ou.

Although the method has not been tested on humans, whose skin is thicker than that of mice, Ou sees potential applications in medicine. ‘Ultrasound is the current go-to for viewing inside the body, but this technique could offer a more accessible alternative,’ he noted.

One immediate benefit of the technology could be its impact on optical imaging research, where it could revolutionize how live tissue is studied. Ou plans to continue this work at his Dynamic Bio-imaging Lab at UT Dallas, exploring dosages for human tissue and testing other materials that may outperform tartrazine.

The study, co-authored by Stanford researchers and funded by grants from federal agencies, has led to a patent application for the technology.”

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Much like ecosystems depend on the structure provided by termites, termite research also needs a strong foundation. So the terminology of termites has been revised. Now, a new classification system for termites has been developed, the result of collaboration among 46 researchers from across the globe.

Date	September 5, 2024
Source	Okinawa Institute of Science and Technology (OIST) Graduate University
Summary	A comprehensive classification system for termites has been established through expert consensus and advanced modeling

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Why the terminology of termites has been revised

Just as ecosystems depend on termites for their structure, termite research also needs a solid foundation. Now, a new, globally-developed classification system for termites has emerged, thanks to the collaboration of 46 researchers. This system, based on expert consensus and extensive data analysis, was recently published in Nature Communications. According to Dr. Simon Hellemans, lead author and member of the Evolutionary Genomics Unit at the Okinawa Institute of Science and Technology (OIST), ‘We’ve addressed previous ambiguities with a robust, modular system for classifying termites. This new framework provides a stable platform for future research into termite diversification and their ecological roles, as well as potential discoveries.

A Reunified Termite Family Through Refined Classification

Taxonomy, the classification of organisms, is essential to all biological research. As Dr. Hellemans explains, ‘To study anything in nature, you need to define your units of observation.’ While species don’t care whether we call them Heterotermitidae or Rhinotermitidae, clear classification is critical for researchers to focus their work and communicate effectively. In the past, these classifications were often based on an organism’s physical traits and behaviors, which led to some ambiguities—especially in species like termites, where visual distinctions are subtle.

Over time, this led to a confusing termite family tree, particularly as some species evolved quickly. Despite their diversity, termites were historically grouped into only ten families, often mixing species with unclear evolutionary connections. In taxonomy, monophyly refers to species sharing a common ancestor, while polyphyly groups species by shared traits rather than ancestry, and paraphyly includes some, but not all, descendants of a common ancestor. Termites, while a monophyletic group within cockroaches, have long been classified in ways that involve much polyphyly and paraphyly.

Dr. Hellemans and his team solved this by using extensive data analysis and new morphological surveys, splitting up large subfamilies to eliminate paraphyly and polyphyly in the termite family tree. ‘This allows us to accommodate new species while preserving historical names,’ says Dr. Hellemans, emphasizing the importance of maintaining a stable termite nomenclature.

The new classification is entirely monophyletic, clarifying evolutionary relationships and making it easier to categorize new species. This precision benefits both research and pest control efforts. For instance, the destructive Coptotermes gestroi termite was once grouped with non-pest species like Dolichorhinotermes longilabius due to their physical similarities. Recent phylogenetic studies, however, have confirmed their divergence, reclassifying C. gestroi into the Heterotermitidae family.

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Butterflies at risk have a better chance of survival with human intervention. For years, scientists have warned about the rapid global decline of insect populations due to factors like climate change, habitat destruction, and pesticide use. The study examined data from 114 populations of 31 butterfly species across 10 U.S. states. Researchers discovered that these vulnerable butterflies are experiencing population declines at an average rate of 8% annually, leading to a 50% decrease over a decade. However, the findings suggest that proper habitat management may slow or even reverse these dramatic declines, offering a glimmer of hope for their survival.

Date	September 4, 2024
Source	Washington State University
Summary	A recent study has found that some of the most endangered butterflies are more likely to survive when humans actively manage their habitats.

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Why Butterflies at risk have a better chance of survival with human intervention

• Some of the most endangered butterfly species show improved survival rates when their habitats are actively managed by humans, according to a recent study.
• The research of butterflies at risk have a better chance of survival with human intervention is led by Washington State University researchers Cheryl Schultz and Collin Edwards, the team analyzed data from 114 populations of 31 butterfly species across 10 U.S. states.
• The study published in the Journal of Applied Ecology, the study offers hope that human-managed habitats may slow or even reverse these declines.
• The clearest finding is that butterflies thrive where people actively manage habitats. That’s exciting because it shows habitat management can have a positive impact, even in the face of climate change.
• Due to climate change, many butterflies have shifted the timing of their seasonal activities, often emerging earlier. The ecological impact of such timing shifts remains unclear, but the study found that for these species, large shifts were generally harmful.
• The study included species like the Oregon silverspot, Taylor’s checkerspot, Karner blue, and frosted elfin. It also featured Fender’s blue, a butterfly that has rebounded from near extinction in the 1990s to over 30,000 today.
• Researchers found that habitat interventions such as prescribed burns, mowing, weeding, and planting nectar or “host” plants were tailored to each area’s needs. Volunteers can assist with habitat management through planting and invasive species removal, while homeowners can contribute by creating butterfly-friendly gardens.

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