Much of cell behavior is governed by the actions of biomolecular condensates: building block molecules that glom together and scatter apart as needed. Biomolecular condensates constantly shift their phase, sometimes becoming solid, sometimes like little droplets of oil in vinegar, and other phases in between.

Understanding the electrochemical properties of such slippery molecules has been a recent focus for researchers at Washington University in St. Louis.

In research published in Nature Chemistry, Yifan Dai, assistant professor of biomedical engineering at the McKelvey School of Engineering, shares the rules involving the intracellular electrochemical properties that affect movement and chemical activities inside the cell and how that might impact cell processes as a condensate ages. The research can inform the development of treatments for diseases like amyotrophic lateral sclerosis (ALS) or cancer.

Extracellular flow—the movement of ions between cell membrane channels—is well studied, but little was known about those same electrochemical fields at play inside the cell.

“In the past century, people have learned a lot regarding electrochemical effects caused by extracellular environmental perturbances. However, in the intracellular world, we do not know much yet,” said Dai.

This work is one of the very first steps to writing those rules. Dai and collaborators from Stanford University, including Professors Guosong Hong and Richard N. Zare, show that condensation and the non-equilibrium process after condensation is itself a way to regulate the electrochemical dynamics of the environments.

By  Leah Shaffer, Washington University in St. Louis

Article can be accessed on: phys.org

Gut microbiota may be the key factor explaining why certain individuals do not respond well to the pneumococcal vaccine, a bacterium that can cause various diseases, such as pneumonia. This conclusion is drawn from a recent study led by the B Cell Biology Research Group at the Hospital del Mar Research Institute, published in Science Advances.

Researchers analyzed vaccine responses using genetically modified mouse models to study two types of pneumococcal vaccines-one commonly used in children and another in adults. Although these vaccines function through different mechanisms, both provide broad coverage.

However, in individuals with a specific type of immunodeficiency, immunoglobulin A (IgA) deficiency, the immune system does not always mount an adequate response, leaving them vulnerable to respiratory infections that can lead to severe complications. The reason: poor regulation of gut microbiota.

IgA plays a crucial role in controlling gut microbiota. It regulates its function and ensures that its presence remains beneficial to the body. However, in the absence of IgA, the bacteria that make up the microbiota can overgrow and spread beyond the intestines.

This overgrowth triggers an immune system response to keep the bacteria in check, but this response remains persistently active over time, leading to immune cell exhaustion.

 

By Hospital del Mar Medical Research Institute

Article can be accessed on: phys.org

Plants like Arabidoposis thaliana use a protein called decrease in DNA methylation 1 (DDM1) to methylate DNA to compact it, while human cells use a homologous protein. Loss of this protein in humans leads to a genetic syndrome, but A. thaliana plants that lacked DDM1 due to gene mutation continued to segregate chromosomes with no apparent impact on their phenotype. However, researchers previously found that these mutants activated a specific family of transposable elements (TEs) in their genome which produced short interfering RNAs that are involved in the RNA interference (RNAi) process that silence gene expression.

“We wondered whether this RNAi might be somehow making up the loss of centromere function,” said Rob Martienssen, a plant geneticist at Cold Spring Harbor Laboratory. In a study published in Nature Plants, Martienssen and his team showed that one family of TEs enriched in the centromere of chromosome 5 in A. thaliana produced short hairpin RNAs that were integral to the proper structure and function of that centromere.

In mutants that lacked DDM1 and RNAi machinery, the researchers found that chromosome 5 failed to segregate properly, causing infertility and other defects. They mapped the DNA region responsible for these effects to the centromere of chromosome 5 and determined that this region was enriched in their previously-identified TE family using long-read sequencing.

In the absence of DDM1 and RNAi, this TE doesn’t produce small RNAs, so the centromere is not methylated. These mutants also had few epigenetic tags on their histones, which contribute to the structure of the centromere.

When researchers supplied short RNA hairpins derived from this TE to the DDM1 and RNAi mutants, the hairpins promoted the proper epigenetic markers on the centromeric histones and reversed the chromosomal segregation defect.

 

By Shelby Bradford, PhD

Article can be accessed on: The Scientist

Bacteria in the human gut microbiome maintain a delicate balance, where beneficial bacteria keep potentially harmful microbes in check. Antibiotic treatment can disrupt this harmony, allowing pathogens like Clostridium difficile to wreak havoc, causing diarrhea, stomach cramps, and colon inflammation. Antibiotics also deplete the healthy microbiome, which paves the way for reinfection. Infection recurrences are difficult to treat, with one recurrence increasing the risk of repeated reinfections.

In the past decade, researchers have shown that transplanting fecal material from healthy donors can prevent recurrent C. difficile infections. However, this procedure is not without risks.

“To a certain extent, a fecal transplant is almost like going to the pharmacist where they take a little bit of everything off the shelf and put it into one pill, assuming that something will probably help,” said Jordan Bisanz, a biochemist and molecular biologist at The Pennsylvania State University, in a press release. “But we don’t know 100 percent what’s in there.”

Now, in research published in Cell Host & Microbe, Bisanz and his colleagues have identified which gut bacteria can suppress C. difficile infections, laying the foundation for probiotic-based strategies as an alternative to antibiotics and fecal microbiota transplants.

Bisanz and his team started out by investigating C. difficile’s “friends,” microbes that coexist with it, and its “enemies,” those that may suppress the bacterium. They performed a meta-analysis of previously published studies containing information about C. difficile load in people alongside gut microbiome sequencing data. With the help of machine learning, they identified 25 bacterial strains that cooccurred with C. difficile, and 37 strains that were negatively correlated with its presence.

The researchers then created a community of bacteria by coculturing the 37 strains negatively linked to C. difficile. Treating a C. difficile culture with this synthetic version of a fecal microbiota transplant (sFMT) reduced its growth. When the researchers exposed sFMT-colonized mice to C. difficile, the animals had significantly less weight loss and toxin abundance compared to control mice that received bacteria-free media.

To investigate whether a sFMT protected mice from antibiotic-induced C. difficile reinfection, the researchers treated mice with an antibiotic, infected them with C. difficile, and then treated them with another antibiotic before subjecting them to a sFMT. Compared to controls, sFMT-treated mice showed delayed infection relapse and reduced disease severity.

 

By Sneha Khedkar

Article can be accessed on: The Scientist

Using an approach called DNA origami, scientists at Caltech have developed a technique that could lead to cheaper, reusable biomarker sensors for quickly detecting proteins in bodily fluids, eliminating the need to send samples out to lab centers for testing.

“Our work provides a proof-of-concept showing a path to a single-step method that could be used to identify and measure nucleic acids and proteins,” says Paul Rothemund (BS ’94), a visiting associate at Caltech in computing and mathematical sciences, and computation and neural systems.

A paper describing the work recently appeared in the journal Proceedings of the National Academy of Sciences. The lead authors of the paper are former Caltech postdoctoral scholar Byoung-jin Jeon and current graduate student Matteo M. Guareschi, who completed the work in Rothemund’s lab.

“Our work provides a proof-of-concept showing a path to a single-step method that could be used to identify and measure nucleic acids and proteins,” says Paul Rothemund (BS ’94), a visiting associate at Caltech in computing and mathematical sciences, and computation and neural systems.

A paper describing the work recently appeared in the journal Proceedings of the National Academy of Sciences. The lead authors of the paper are former Caltech postdoctoral scholar Byoung-jin Jeon and current graduate student Matteo M. Guareschi, who completed the work in Rothemund’s lab.

 

By Kimm Fesenmaier, California Institute of Technology

Article can be accessed on: phys.org

 

Stanford University researchers developed a machine learning-based method capable of diagnosing multiple diseases using B cell and T cell receptor sequences. The model, called Machine learning for Immunological Diagnosis (Mal-ID), distinguished between COVID-19, HIV, lupus, type 1 diabetes, influenza vaccination response, and healthy states, achieving near-perfect classification.

Conventional diagnostics rely on patient history, physical examinations, and laboratory tests, often requiring multiple rounds to diagnose complex diseases like autoimmune conditions.

B cell receptors (BCRs) and T cell receptors (TCRs) are generated through random recombination processes and change after infections, vaccinations, or in autoimmune diseases, offering potential as biomarkers for immune activity. Leveraging receptor sequence data could allow simultaneous assessment of various diseases.

In the study, “Disease diagnostics using machine learning of B cell and T cell receptor sequences,” published in Science, researchers analyzed BCR heavy chain and TCR beta chain sequences from 593 individuals.

Participants included 63 with COVID-19, 95 with HIV, 86 with lupus, 92 with type 1 diabetes, 37 who received influenza vaccination, and 220 healthy controls. Paired BCR and TCR data were available for 542 individuals.

Mal-ID correctly classified immune status from blood samples of 542 individuals with both BCR and TCR data. High classification performance was achieved with BCR data alone with an area under the receiver operating characteristic curve (AUROC) of 0.959 in the full 593 cohort.

Lupus was accurately distinguished from other conditions with 93% sensitivity and 90% specificity. External datasets validated the model’s generalizability, achieving up to 1.0 AUROC on independent BCR cohorts and 0.99 AUROC on TCR cohorts after threshold adjustments.

 

 

By Justin Jackson, Medical Xpress

Article can be accessed on: MedicalXpress

Lymphatic filariasis, a devastating parasitic disease transmitted by mosquitoes, affects more than 110 million people worldwide. People who suffer from the infection experience extremely painful edema with thickening of skin and underlying tissue, which can lead to permanent disability. There is no rapid cure for the infection, and most of the current treatments do not effectively target adult worms. Furthermore, these treatments are not suitable for children and pregnant women.

To develop new treatments for the microscopic roundworms that cause this debilitating disease, chemist Andrés Palencia knew he needed to get creative. Palencia, whose work at the Institute for Advanced Biosciences focuses on the structural biology of novel therapeutic targets, explored a relatively underutilized approach. Instead of targeting the parasitic worms themselves, Palencia turned his attention to the worm microbiome. “There is a lot of research going on in human microbiota,” said Palencia. “But the microbiota is [also] really important for some pathogens.”

Back in the 1970s, researchers first discovered that filariasis-causing parasitic worms housed Gram-negative bacteria within their cells; further studies showed that most filarial worms that infect people depend on this bacterium, called Wolbachia, for their growth and survival.² Leveraging this, Palencia’s team developed a therapy to inhibit Wolbachia’s growth disrupting its symbiosis with its worm host. The results, published in Science Advances, highlight the potential of targeting key elements of the microbiome in disease-causing organisms as a promising approach to controlling parasitic infections in humans.

Researchers have previously demonstrated that broad-spectrum antibiotics can deplete Wolbachia bacteria, subsequently reducing the burden of filarial worms in mouse models. However, these drugs can also disrupt the human microbiome by killing beneficial bacteria, so researchers are searching for therapeutics that selectively inhibit Wolbachia growth.

However, it is difficult to identify new and specific targets in Wolbachia, said Palencia, mainly because it is challenging to grow the bacterium in the lab. “It’s symbiosis with the host is so strong, that you will have to grow the host along with Wolbachia,” Palencia explained. This makes it more difficult to use genetic tools to manipulate the bacterial genome.

To circumvent this challenge, Palencia’s team turned to a previously-described in vitro model that uses Wolbachia-infected insect cells for high-throughput screening of drug molecules. Using this system, the researchers could observe Wolbachia within insect cells through fluorescence and easily track the effects of various drugs. They tested a library of more than 200 boron-based compounds that have previously shown antimicrobial properties and identified a handful of these compounds that were active against Wolbachia.

The team then performed further experiments to characterize the activity and efficacy of these candidates, and determined that two compounds, Cmpd6 and Cmpd9, most effectively reduced Wolbachia numbers in the cells.

Since the development of a safe and effective drug requires understanding its mechanism of action, the researchers sought to decipher how these compounds work. Palencia’s team, along with other research groups, had previously shown that boron-based compounds target bacterial Leucyl-tRNA synthetase (LeuRS), an enzyme involved in protein synthesis. To test whether the candidate compounds were also binding to LeuRS, the researchers purified a part of the Wolbachia protein that contained the potential drug-binding site.

 

 

 

By Sneha Khedkar

Article can be accessed on: The Scientist

During translation, multiple ribosomes travel along the nucleic acid chain to build polypeptides that become functional proteins. Occasionally, these molecular decoders pause on the mRNA, either because they are instructed to do so or they have difficulty traversing the sequence. Previous studies that investigated these events looked at isolated ribosomal proteins as opposed to the multiple ribosomes typically involved in translation, leaving questions about how these pauses affect translation and how they are overcome.

To elucidate this process, a team led by Marvin Tanenbaum, a molecular biologist studying single-molecule dynamics at Hubrecht Institute, developed a novel imaging method to study ribosome dynamics. In a study published in Cell, Tanenbaum and his team demonstrated that ribosomes use collisions to move past pause sites and other complicated segments of mRNA to increase translation efficiency. These findings introduce a new mechanism in translation and polypeptide formation.

First, the researchers generated stopless-ORF circular RNAs (socRNAs) that promoted continuous translation for extended periods of time. The researchers visualized translation, including ribosome pauses, by using the intensity of GFP-tagged antibodies on the polypeptide to measure polypeptide elongation.

As Tanenbaum and his team watched translation unfold, they found that at any given time, each socRNA was bound by one to four ribosomes and that these molecular machines exhibited varied translation speeds. With the help of computational models, the researchers demonstrated how faster incoming ribosomes “bump into” the stalled-out ribosomes. These collisions occurred rapidly even when there were as few as two ribosomes on the socRNA.

Previous studies showed that when the leading protein stalls, the ribosome collisions that occur trigger the removal of the affected ribosomes. However, Tanenbaum’s team didn’t see this occurring in their experiments. They estimated that the collisions that they observed lasted between a few milliseconds to seconds, so they set out to determine whether the length of time a collision lasts influences its outcome.

 

By Shelby Bradford, PhD

Article can be accessed on: The Scientist

 

The epigenetic state of chromatin, gene activity, and chromosomal positions are interrelated. A research team from the IPK Leibniz Institute (IPK) and the Karlsruhe Institute of Technology (KIT) has investigated how the chromosomal location affects epigenetic stability and gene expression through chromosome engineering. The results are published in the journal New Phytologist.

Chromosomal rearrangements, such as chromosome segment inversions, may affect the epigenetic landscape as well as gene expression. Indeed, different kinds of chromosome segment inversions have been found in many prominent crops like rice, maize, and barley.

Until now, it has only been possible to study historical chromosome rearrangements that have occurred naturally. With the recent establishment of the CRISPR/Cas-based chromosome engineering technique, pre-defined chromosome rearrangements can now be induced, and their genetic and epigenetic consequences can be analyzed immediately after they occur.

To elucidate the effect of chromosomal inversions on the epigenetic state of chromatin and the activity of genes, the research team used CRISPR/Cas-based chromosome engineering to generate chromosomal inversions of different sizes in the model plant Arabidopsis thaliana. The epigenetic state of these lines was compared to wild-type plants. Finally, the effect of the chromosomal rearrangements on the activity of genes was analyzed.

“Our results indicated that none of the studied inverted chromosome segments and their neighboring regions changed in epigenetic marks and gene expression besides minor genome-wide effects,” explains Dr. Solmaz Khosravi, first author of the study. Gene expression analysis showed that genome-wide, only 0.50–1% of genes were differentially expressed following the induction of the inversions.

 

By Leibniz Institute of Plant Genetics and Crop Plant Research

Article can be accessed on: phys.org

Cellular communication is vital for passing information to neighboring cells. One key messenger in this process is an exosome, a nanosized particle that buds off from a progenitor cell, carrying molecular cargo. Because these small, cellular vehicles carry contents from their parent cells, exosomes can serve as snapshots for a given population of cells, including tumors.

“If you can sample a vesicle, or any entity, from blood, it gives you a huge advantage, being a low or minimally invasive strategy to monitor cancer or detect cancer,” said David Greening, a biologist who studies extracellular vesicles like exosomes at La Trobe University.

One strategy to improve the use of exosomes as cancer biomarkers is to identify surface proteins on these vesicles that reflect their originating tumor. L-type amino acid transporter 1 (LAT1), a surface protein that shuttles large amino acids into the cell, is predominantly associated with cancerous cells and correlates with tumor severity. These characteristics made the protein an attractive target for therapeutic intervention, with one LAT1 inhibitor currently undergoing clinical trials.

In a study published in Scientific Reports, researchers demonstrated the potential of LAT1 on exosomes from pancreatic and other cancer cell lines as a biomarker. “[Now] we can detect and treat cancer using the same target,” said Ryuichi Ohgaki, a pharmacologist at Osaka University and study coauthor.

Ohgaki and his team studied the role of LAT1 in driving cancer progression for years. Inspired by previous work that measured cancer-associated proteins on exosomes, the group set out to investigate the correlation between LAT1 expression on exosomes and their originating cancer cells.

To explore this relationship, the team used ultracentrifugation to isolate these particles from human pancreatic, cervical, and bile duct tumor cell lines. In most of the tested cell lines, LAT1 expression on exosomes correlated with LAT1 expression on cell membranes.

To study exosomes in vivo, the team introduced pancreatic cancer cells into the peritoneal cavity of mice. One month later, they used immunohistochemistry to measure LAT1 expression in tumor tissue and adjacent nontumor cells, finding the protein exclusively in the tumor tissue. When they isolated exosomes from the peritoneal cavities of tumor-bearing and control mice, they detected greater LAT1 expression on the vesicles from the mice with tumors.

 

 

By Shelby Bradford, PhD

Article can be accessed on: The Scientist