Parallel single B cell transcriptomics to elucidate pig B cell repertoire.

Pork is the most widely consumed meat on the planet, placing swine health as a critical factor for both the world economy and the food industry. Infectious diseases in pigs not only threaten these sectors but also raise zoonotic concerns, as pigs can act as "mixing vessels" for several animals and human viruses and can lead to the emergence of new viruses that are capable of infecting humans. Several efforts are ongoing to develop pig vaccines, albeit with limited success.

Phylogenetic assessment within a species complex of a subterranean rodent (Geomys bursarius) with conservation implications for isolated subspecies.

Range contraction and expansion from glaciation have led to genetic divergence that may be particularly pronounced in fossorial species with low dispersal. The plains pocket gopher (Geomys bursarius) is a fossorial species that ranges widely across North America but has a poorly understood phylogeny. We used mitogenomes (14,996 base pairs) from 56 individuals across seven subspecies, plus two outgroup species, to assess genetic divergence from minimum spanning trees, measure genetic distances, and infer phylogenetic trees using BEAST.

Invited review: Genomic modifications of lactic acid bacteria and their applications in dairy fermentation.

Lactic acid bacteria (LAB) have a long history of safe use in milk fermentation and are generally recognized as health-promoting microorganisms when present in fermented foods. Lactic acid bacteria are also important components of the human intestinal microbiota and are widely used as probiotics. Considering their safe and health-beneficial properties, LAB are considered appropriate vehicles that can be genetically modified for food, industrial and pharmaceutical applications.

Young apple polyphenols confer excellent physical and oxidative stabilities to soy protein emulsions for effective β-carotene encapsulation and delivery.

Protein emulsions' poor physical and oxidative stabilities restrict their use in functional foods. Soy protein isolate (SPI) emulsions' physical stability was enhanced by adding young apple polyphenols (YAP) in this study, but decreased when YAP was 0.12%.

Universal Fragility of Spin Glass Ground States under Single Bond Changes.

We consider the effect of perturbing a single bond on ground states of nearest-neighbor Ising spin glasses, with a Gaussian distribution of the coupling constants, across various two- and three-dimensional lattices and regular random graphs. Our results reveal that the ground states are strikingly fragile with respect to such changes. Altering the strength of only a single bond beyond a critical threshold value leads to a new ground state that differs from the original one by a droplet of flipped spins whose boundary and volume diverge with the system size-an effect that is reminiscent of the more familiar phenomenon of disorder chaos.

Label-Free Monitoring of Coculture System Dynamics: Probing Probiotic and Cancer Cell Interactions via Infrared Spectroscopic Imaging.

Evaluating the dynamic interaction of microorganisms and mammalian cells is challenging due to the lack of suitable platforms for examining interspecies interactions in biologically relevant coculture conditions. In this work, we demonstrate the interaction between probiotic bacteria ( and ) and A498 human cancer cells , utilizing a hydrogel-based platform in a label-free manner by infrared spectroscopy. The strain recapitulated in the compartment system secretes polypeptide molecules such as nisin, which has been reported to trigger cell apoptosis.

A library-on-library screen reveals the breadth expansion landscape of a broadly neutralizing betacoronavirus antibody.

Broadly neutralizing antibodies (bnAbs) typically evolve cross-reactivity breadth through acquiring somatic hypermutations. While evolution of breadth requires improvement of binding to multiple antigenic variants, most experimental evolution platforms select against only one antigenic variant at a time. In this study, a yeast display library-on-library approach was applied to delineate the affinity maturation of a betacoronavirus bnAb, S2P6, against 27 spike stem helix peptides in a single experiment.

PTBP1 mediates Sertoli cell actin cytoskeleton organization by regulating alternative splicing of actin regulators.

Spermatogenesis is a biological process within the testis that produces haploid spermatozoa for the continuity of species. Sertoli cells are somatic cells in the seminiferous epithelium that orchestrate spermatogenesis. Cyclic reorganization of Sertoli cell actin cytoskeleton is vital for spermatogenesis, but the underlying mechanism remains largely unclear.

NR0B2 re-educates myeloid immune cells to reduce regulatory T cell expansion and progression of breast and other solid tumors.

Although survival from breast cancer has dramatically increased, many will develop recurrent, metastatic disease. Unfortunately, survival for this stage of disease remains very low. Activating the immune system has incredible promise since it has the potential to be curative.

Determinants of raffinose family oligosaccharide use in species.

species are successful colonizers of the human gut and can utilize a wide variety of complex polysaccharides and oligosaccharides that are indigestible by the host. To do this, they use enzymes encoded in Polysaccharide Utilization Loci (PULs). While recent work has uncovered the PULs required for use of some polysaccharides, how utilize smaller oligosaccharides is less well studied.

Gelatin maleimide microgels for hematopoietic progenitor cell encapsulation.

Hematopoietic stem cells (HSCs) are the apical cells of the hematopoietic system, giving rise to cells of the blood and lymph lineages. HSCs reside primarily within bone marrow niches that contain matrix and cell-derived signals that help inform stem cell fate. Aspects of the bone marrow microenvironment have been captured in vitro by encapsulating cells within hydrogel matrices that mimic native mechanical and biochemical properties.

Epistasis mediates the evolution of the receptor binding mode in recent human H3N2 hemagglutinin.

The receptor-binding site of influenza A virus hemagglutinin partially overlaps with major antigenic sites and constantly evolves. In this study, we observe that mutations G186D and D190N in the hemagglutinin receptor-binding site have coevolved in two recent human H3N2 clades. X-ray crystallography results show that these mutations coordinately drive the evolution of the hemagglutinin receptor binding mode.

The Lreu_1276 protein from represents a third family of dihydroneopterin triphosphate pyrophosphohydrolases in bacteria.

Unlabelled: Tetrahydrofolate is a cofactor involved in C metabolism including biosynthesis pathways for adenine and serine. In the classical tetrahydrofolate biosynthesis pathway, the steps removing three phosphate groups from the precursor 7,8-dihydroneopterin triphosphate (DHNTP) remain unclear in many bacteria. DHNTP pyrophosphohydrolase hydrolyzes pyrophosphate from DHNTP and produces 7,8-dihydroneopterin monophosphate.

A metabolomics pipeline highlights microbial metabolism in bloodstream infections.

The growth of antimicrobial resistance (AMR) highlights an urgent need to identify bacterial pathogenic functions that may be targets for clinical intervention. Although severe infections profoundly alter host metabolism, prior studies have largely ignored microbial metabolism in this context. Here, we describe an iterative, comparative metabolomics pipeline to uncover microbial metabolic features in the complex setting of a host and apply it to investigate gram-negative bloodstream infection (BSI) in patients.

Organoborane Se and Te Precursors for Controlled Modulation of Reactivity in Nanomaterial Synthesis.

To exploit the distinctive optoelectrical properties of nanomaterials, precise control over the size, morphology, and interface structure is essential. Achieving a controlled synthesis demands precursors with tailored reactivity and optimal reaction temperatures. Here, we introduce organoborane-based selenium and tellurium precursors borabicyclononane-selenol (BBN-SeH) and tellurol (BBN-TeH).

Perception of motion salience shapes the emergence of collective motions.

Despite the profound implications of self-organization in animal groups for collective behaviors, understanding the fundamental principles and applying them to swarm robotics remains incomplete. Here we propose a heuristic measure of perception of motion salience (MS) to quantify relative motion changes of neighbors from first-person view. Leveraging three large bird-flocking datasets, we explore how this perception of MS relates to the structure of leader-follower (LF) relations, and further perform an individual-level correlation analysis between past perception of MS and future change rate of velocity consensus.

How much could improving photosynthesis increase crop yields? A call for systems-level perspectives to guide engineering strategies.

Global yield gaps can be reduced through breeding and improved agronomy. However, signs of yield plateaus from wheat and rice grown in intensively farmed systems indicate a need for new strategies if output is to continue to increase. Approaches to improve photosynthesis are suggested as a solution.

Quantum Dot-Fab' Conjugates as Compact Immunolabels for Microtubule Imaging and Cell Classification.

Antibodies and their conjugates of fluorescent labels are widely applied in life sciences research and clinical pathology. Among diverse label types, compact quantum dots (QDs) provide advantages of multispectral multiplexing, bright signals in the deep red and infrared, and low steric hindrance. However, QD-antibody conjugates have random orientation of the antigen-binding domain which may interfere with labeling and are large (20-30 nm) and heterogeneous, which limits penetration into biospecimens.

A Gram-negative-selective antibiotic that spares the gut microbiome.

Infections caused by Gram-negative pathogens are increasingly prevalent and are typically treated with broad-spectrum antibiotics, resulting in disruption of the gut microbiome and susceptibility to secondary infections. There is a critical need for antibiotics that are selective both for Gram-negative bacteria over Gram-positive bacteria, as well as for pathogenic bacteria over commensal bacteria. Here we report the design and discovery of lolamicin, a Gram-negative-specific antibiotic targeting the lipoprotein transport system.

Pairing metagenomics and metaproteomics to characterize ecological niches and metabolic essentiality of gut microbiomes.

The genome of a microorganism encodes its potential functions that can be implemented through expressed proteins. It remains elusive how a protein's selective expression depends on its metabolic essentiality to microbial growth or its ability to claim resources as ecological niches. To reveal a protein's metabolic or ecological role, we developed a computational pipeline, which pairs metagenomics and metaproteomics data to quantify each protein's gene-level and protein-level functional redundancy simultaneously.

Biosynthesis of Macrocyclic Peptides with C-Terminal β-Amino-α-keto Acid Groups by Three Different Metalloenzymes.

Advances in genome sequencing and bioinformatics methods have identified a myriad of biosynthetic gene clusters (BGCs) encoding uncharacterized molecules. By mining genomes for BGCs containing a prevalent peptide-binding domain used for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), we uncovered a new compound class involving modifications installed by a cytochrome P450, a multinuclear iron-dependent non-heme oxidative enzyme (MNIO, formerly DUF692), a cobalamin- and radical -adenosyl-l-methionine-dependent enzyme (B12-rSAM), and a methyltransferase. All enzymes were functionally expressed in sp.