E. Smith

Arbitrium phages can manipulate each other's lysis - lysogeny decisions

The paper shows that Arbitrium phages from different species can influence each other's lysis-lysogeny decisions through peptide-based communication, leading to fitness advantages and coevolution.

Structural characterization of two full length γδTCR/CD3 complexes

This study reports cryoEM structures of two full-length γδ TCR/CD3 complexes, revealing similarities to β TCRs but with highly mobile extracellular domains and a dimeric assembly in one complex.

Variable rates of SARS-CoV-2 evolution in chronic infections

This study analyzes within-host SARS-CoV-2 evolution in chronic infections, finding variable rates of evolution and evidence of subpopulation structure.

Human long noncoding RNA, VILMIR, is induced by major respiratory viral infections and modulates the host interferon response

This study identifies VILMIR, a novel lncRNA upregulated by respiratory viral infections and IFN-β, which modulates the host interferon response.

A comparison between full-length 16S rRNA Oxford Nanopore sequencing and Illumina V3-V4 16S rRNA sequencing in head and neck cancer tissues

This study compares full-length 16S rRNA sequencing using Oxford Nanopore Technology (FL-ONT) with Illumina V3-V4 short-read sequencing in head and neck cancer tissues, finding FL-ONT provides better resolution at lower taxonomic levels.

Pre-challenge gut microbial signature predicts RhCMV/SIV vaccine efficacy in rhesus macaques

The paper identifies a gut microbial signature predictive of RhCMV/SIV vaccine efficacy in rhesus macaques using 16S rRNA analysis and compositional data techniques.

A study on tomato brown rugose fruit virus longevity in soil and virion susceptibility to various pH treatments contributes to optimization of a soil disinfection protocol

This study investigates ToBRFV longevity in soil and virion stability across pH levels, finding that virus infectivity declines over time and is reduced by alkaline treatments.

The effects of cell-cell orientation in modeling the hallmarks of lung cancer in vitro

This study compares 3D tumoroid and 2D cultures of lung cancer cells to assess how cell-cell orientation affects cancer-related features and finds that 3D cultures better mimic primary human lung cancer.

Rules, hypergraphs, and probabilities: the three-level analysis of chemical reaction systems and other stochastic stoichiometric population processes

The paper develops a three-level framework for analyzing stochastic chemical reaction systems, showing how constraints at earlier levels influence dynamics at later levels and applying it to biological sugar-phosphate chemistry.

Disruption of myelin structure and oligodendrocyte maturation in a pigtail macaque model of congenital Zika infection

This study investigates the effects of prenatal Zika virus exposure on fetal myelin structure and oligodendrocyte maturation in pigtail macaques, finding disruptions in myelin formation and gene expression related to oligodendrocyte development.

Target-based discovery of a broad spectrum flukicide

The paper identifies a new flukicide, BZQ, effective against both Fasciola and Schistosoma species by targeting a conserved TRPMPZQ ion channel.

Characterizing Subcortical Structural Heterogeneity in Autism

This study examines subcortical structural differences in autism using MRI data, finding localized shape variations rather than volumetric differences, with age-related patterns observed.

Elevated peripheral and nervous system inflammation is associated with decreased short-chain fatty acid levels in Zika-virus infected macaques

This study links reduced short-chain fatty acid levels with elevated inflammation in Zika-virus infected macaques, suggesting microbial dysfunction contributes to CNS and systemic inflammation.

Quantitative analysis of morphogenesis and growth dynamics in an obligate intracellular bacterium

This paper develops quantitative tools to study the growth and morphology of Rickettsia parkeri, showing MreB is required for its shape and growth.

A Vaccinia-based system for directed evolution of GPCRs in mammalian cells

This paper develops a Vaccinia-based system to evolve GPCRs in mammalian cells, improving stability and expression, and demonstrating functional receptor properties.

A deep learning approach for improved detection of homologous recombination deficiency from shallow genomic profiles

This paper introduces a deep learning model to detect homologous recombination deficiency from shallow whole genome sequencing data, achieving high accuracy comparable to deeper sequencing methods.

Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis

This study identifies gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis, finding that vancomycin treatment promotes bacteria that induce regulatory T cells and ameliorate disease.

The retromer complex regulates C. elegans development and mammalian ciliogenesis

This study shows the retromer complex is essential for C. elegans development and mammalian ciliogenesis, with a role in CP110 removal from the mother centriole.

Beyond fitness: selection and information flow through the constructive steps in lifecycles

This paper generalizes the concept of fitness and information flow in evolutionary genetics to include constructive steps beyond replication in autocatalytic processes.

Monogamy in a moment: how do brief social interactions change over time in pair-bonded zebra finches (Taeniopygia guttata)?

This study examines how brief social interactions change during pair bonding in zebra finches, finding that females are more active and calling rates peak initially, but behavioral coordination remains unaffected by pairing stage.

A natural single-guide RNA repurposes Cas9 to autoregulate CRISPR-Cas expression

The paper shows that a long-form tracrRNA acts as a natural single guide to repress Cas9 expression, revealing a regulatory mechanism in CRISPR-Cas systems.

Analytical and Clinical Comparison of Three Nucleic Acid Amplification Tests for SARS-CoV-2 Detection

This study compares three SARS-CoV-2 nucleic acid amplification tests, finding similar limit of detection but differences in absolute quantification and clinical performance.

Differential B-cell receptor signaling requirement for adhesion of mantle cell lymphoma cells to stromal cells

The paper identifies differential B-cell receptor signaling requirements for adhesion of mantle cell lymphoma cell lines to stromal cells, showing that inhibition of BCR signaling reduces adhesion in JeKo-1 but not REC-1 cells.

Accelerated single cell seeding in relapsed multiple myeloma

This study uses whole genome sequencing to show that relapsed multiple myeloma exhibits accelerated systemic seeding driven by chemotherapy-induced mutations and clonal expansion of single myeloma cells.

In silico screening of GMQ-like compounds reveals guanabenz and sephin1 as new allosteric modulators of acid-sensing ion channel 3

The paper identifies guanabenz and sephin1 as new allosteric modulators of ASIC3 through in silico screening of FDA-approved drugs and electrophysiological validation.

Systematic profiling of full-length immunoglobulin and T-cell receptor repertoire diversity in rhesus macaque through long read transcriptome sequencing

This study uses long-read sequencing to profile full-length Ig and TCR repertoires in rhesus macaques, revealing significant diversity missed by traditional methods.

Inflammation induced by influenza virus impairs innate control of human pneumococcal carriage

This study shows that influenza virus infection impairs innate immune responses to pneumococcal carriage in the nose, increasing bacterial density through cytokine-driven mechanisms.

Effect of Live Attenuated Influenza Vaccine on Pneumococcal Carriage

This study tests if LAIV affects pneumococcal carriage in humans, finding transient increases in bacterial density but no overall change in acquisition rates.

Resurrecting ancestral genes in bacteria to interpret ancient biosignatures

This paper resurrects ancestral bacterial carbonic anhydrase proteins to link ancient environmental conditions with biosignatures preserved in the geological record.

The Rise of the Middle Author: Investigating Collaboration and Division of Labor in Biomedical Research using Partial Alphabetical Authorship

This paper analyzes authorship patterns in biomedical research, showing that middle authors' contributions have increased significantly over time despite being undervalued.