Pangenomic analysis of the bacterial cellulose-producing genera Komagataeibacter and Novacetimonas.

Bacterial cellulose (BC) holds significant commercial potential due to its unique structural and chemical properties, making it suitable for applications in electronics, medicine, and pharmaceuticals. However, large-scale BC production remains limited by challenges in bacterial performance. In this study, we compared 79 microbial genomes from three genera-Komagataeibacter, Novacetimonas, and Gluconacetobacter-to investigate their pangenomes, genetic diversity, and evolutionary relationships.

A time-calibrated salamander phylogeny including 765 species and 503 genes.

Recent time-calibrated amphibian phylogenies agree on the family-level relationships among extant salamanders but had disparate sampling regimes and inferred very different divergence times. For example, a recent phylogenomic study based on 220 nuclear loci had limited taxon sampling (41 species) and estimated relatively young divergence dates, whereas a more extensive supermatrix study based on 15 genes and 481 species estimated dates that were 22-45 million years older for major clades. Here, we combined phylogenomic and supermatrix approaches to estimate the largest salamander phylogeny to date based on molecular markers.

The role of uncertainty and negative feedback loops in the evolution of induced immune defenses.

Organisms use constitutive or induced defenses against pathogens and other external threats. Constitutive defenses are constantly on, whereas induced defenses are activated when needed. Each of these strategies has costs and benefits, which can affect the type of defense that evolves in response to pathogens.

Unifying considerations and evidence of macrophage activation mosaicism through human CSF1R and M1/M2 genes.

Addressing the mononuclear phagocyte system (MPS) and macrophage M1/M2 activation is important in diagnosing hematological disorders and inflammatory pathologies and designing therapeutic tools. CSF1R is a reliable marker to identify all circulating MPS cells and tissue macrophages in humans using a single surface protein. CSF1R permits the quantification and isolation of monocyte and dendritic cell (DC) subsets in conjunction with CD14, CD16, and CD1c and is stable across the lifespan and sexes in the absence of overt pathology.

Lunar-linked biological rhythms in the immune system of freshwater three-spined stickleback.

Immune responses are widely accepted to be under circadian regulation via a molecular clock, with many practical consequences, but much less is known of how other biological rhythms could affect the immune system. In this study, we search for lunar rhythms (circalunar, circasemilunar, and circatidal cycles) in the immune expression of the recently marine-derived freshwater fish, the low-plate morph of the three-spined stickleback. We employed time series of immune expression (mRNA) measurements for 14 immune-associated genes, representing a variety of immunological pathways.

Resolving selfish and spiteful interdependent conflict.

Interdependence occurs when individuals have a stake in the success or failure of others, such that the outcomes experienced by one individual also generate costs or benefits for others. Discussion on this topic has typically focused on positive interdependence (where gains for one individual result in gains for another) and on the consequences for cooperation. However, interdependence can also be negative (where gains for one individual result in losses for another), which can spark conflict.

Thioredoxin is a metabolic rheostat controlling regulatory B cells.

Metabolic programming is important for B cell fate, but the bioenergetic requirement for regulatory B (B) cell differentiation and function is unknown. Here we show that B cell differentiation, unlike non-B cells, relies on mitochondrial electron transport and homeostatic levels of reactive oxygen species (ROS). Single-cell RNA sequencing analysis revealed that TXN, encoding the metabolic redox protein thioredoxin (Trx), is highly expressed by B cells, unlike Trx inhibitor TXNIP which was downregulated.

The distorting effects of producer strategies: Why engagement does not reveal consumer preferences for misinformation.

A great deal of empirical research has examined who falls for misinformation and why. Here, we introduce a formal game-theoretic model of engagement with news stories that captures the strategic interplay between (mis)information consumers and producers. A key insight from the model is that observed patterns of engagement do not necessarily reflect the preferences of consumers.

Management of Newly Diagnosed Multiple Myeloma Today, and in the Future.

Treatment options have expanded rapidly and widely in the past two decades for patients with multiple myeloma. Triplet novel agent-based induction regimens have been accepted as the standard practice wordwide over the last decade both for transplant-eligible and non-eligible patients. The addition of anti-CD38 monoclonal antibodies as part of quadruplet regimens has led to even deeper and longer-lasting responses.

sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data.

Class-switch recombination (CSR) is an integral part of B cell maturation. Here we present sciCSR (pronounced 'scissor', single-cell inference of class-switch recombination), a computational pipeline that analyzes CSR events and dynamics of B cells from single-cell RNA sequencing (scRNA-seq) experiments. Validated on both simulated and real data, sciCSR re-analyzes scRNA-seq alignments to differentiate productive heavy-chain immunoglobulin transcripts from germline 'sterile' transcripts.

Eco-evolutionary trade-offs in the dynamics of prion strain competition.

Prion and prion-like molecules are a type of self-replicating aggregate protein that have been implicated in a variety of neurodegenerative diseases. Over recent decades, the molecular dynamics of prions have been characterized both empirically and through mathematical models, providing insights into the epidemiology of prion diseases and the impact of prions on the evolution of cellular processes. At the same time, a variety of evidence indicates that prions are themselves capable of a form of evolution, in which changes to their structure that impact their rate of growth or fragmentation are replicated, making such changes subject to natural selection.

Diversification of immunoglobulin genes by gene conversion in the domestic chicken ( domesticus).

Sustainable modern poultry production depends on effective protection against infectious diseases and a diverse range of antibodies is key for an effective immune response. In the domestic chicken, somatic gene conversion is the dominant process in which the antibody immunoglobulin genes are diversified. Affinity maturation by somatic hypermutation (SHM) also occurs, but the relative contribution of gene conversion versus somatic hypermutation to immunoglobulin (Ig) gene diversity is poorly understood.

Group reciprocity and the evolution of stereotyping.

Stereotypes are generalized beliefs about groups of people, which are used to make decisions and judgements about them. Although such heuristics can be useful when decisions must be made quickly, or when information is lacking, they can also serve as the basis for prejudice and discrimination. In this paper, we study the evolution of stereotypes through group reciprocity.

Multi-Omics Reveals Mechanisms of Partial Modulation of COVID-19 Dysregulation by Glucocorticoid Treatment.

Treatments for COVID-19 infections have improved dramatically since the beginning of the pandemic, and glucocorticoids have been a key tool in improving mortality rates. The UK's National Institute for Health and Care Excellence guidance is for treatment to be targeted only at those requiring oxygen supplementation, however, and the interactions between glucocorticoids and COVID-19 are not completely understood. In this work, a multi-omic analysis of 98 inpatient-recruited participants was performed by quantitative metabolomics (using targeted liquid chromatography-mass spectrometry) and data-independent acquisition proteomics.

Metabolomics Markers of COVID-19 Are Dependent on Collection Wave.

The effect of COVID-19 infection on the human metabolome has been widely reported, but to date all such studies have focused on a single wave of infection. COVID-19 has generated numerous waves of disease with different clinical presentations, and therefore it is pertinent to explore whether metabolic disturbance changes accordingly, to gain a better understanding of its impact on host metabolism and enable better treatments. This work used a targeted metabolomics platform (Biocrates Life Sciences) to analyze the serum of 164 hospitalized patients, 123 with confirmed positive COVID-19 RT-PCR tests and 41 providing negative tests, across two waves of infection.

Pandemic, Epidemic, Endemic: B Cell Repertoire Analysis Reveals Unique Anti-Viral Responses to SARS-CoV-2, Ebola and Respiratory Syncytial Virus.

Immunoglobulin gene heterogeneity reflects the diversity and focus of the humoral immune response towards different infections, enabling inference of B cell development processes. Detailed compositional and lineage analysis of long read IGH repertoire sequencing, combining examples of pandemic, epidemic and endemic viral infections with control and vaccination samples, demonstrates general responses including increased use of in both Zaire Ebolavirus (EBOV) and COVID-19 patient cohorts. We also show unique characteristics absent in Respiratory Syncytial Virus or yellow fever vaccine samples: EBOV survivors show unprecedented high levels of class switching events while COVID-19 repertoires from acute disease appear underdeveloped.

Inequality, identity, and partisanship: How redistribution can stem the tide of mass polarization.

The form of political polarization where citizens develop strongly negative attitudes toward out-party members and policies has become increasingly prominent across many democracies. Economic hardship and social inequality, as well as intergroup and racial conflict, have been identified as important contributing factors to this phenomenon known as "affective polarization." Research shows that partisan animosities are exacerbated when these interests and identities become aligned with existing party cleavages.

Radical and Ionic Mechanisms in Rearrangements of -Tolyl Aryl Ethers and Amines Initiated by the Grubbs-Stoltz Reagent, EtSiH/KOBu.

Rearrangements of tolyl aryl ethers, amines, and sulfides with the Grubbs-Stoltz reagent (EtSiH + KOBu) were recently announced, in which the ethers were converted to -hydroxydiarylmethanes, while the (tol)(Ar)NH amines were transformed into dihydroacridines. Radical mechanisms were proposed, based on prior evidence for triethylsilyl radicals in this reagent system. A detailed computational investigation of the rearrangements of the aryl tolyl ethers now instead supports an anionic Truce-Smiles rearrangement, where the initial benzyl anion can be formed by either of two pathways: (i) direct deprotonation of the tolyl methyl group under basic conditions or (ii) electron transfer to an initially formed benzyl radical.

Empowering patients with the PREPARE advance care planning program results in reciprocal clinician communication.

Background: The patient-directed PREPAREforYourCare.org program empowers patients to participate in advance care planning (ACP) discussions with clinicians. Our goal was to determine whether PREPARE could reciprocally increase clinician ACP communication.

The Influence of Emotions on Treatment Decisions About Low-Risk Thyroid Cancer: A Qualitative Study.

Little is known about the role of emotions in treatment decisions for thyroid cancer. We aimed to characterize the emotional content of patient-surgeon communication during decision-making about low-risk thyroid cancer treatment. We audio-recorded conversations about treatment for clinically low-risk thyroid cancer or biopsy suspicious for thyroid cancer between patients ( = 30) and surgeons ( = 9) in two diverse, academic hospitals in the United States.

"Do You Smoke?" Physician-Patient Conversations About Smoking and Lung Cancer.

This study examined how physicians initiated and navigated conversations about smoking with patients with lung cancer. While there are numerous health benefits associated with smoking cessation in patients with advanced lung cancer, conversations about smoking cessation are infrequent and often lack tangible cessation support. We conducted a qualitative inductive content analysis on transcripts of conversations (n = 58) recorded during an initial appointment between a physician and a standardized patient (SP).

Tissue and regional expression patterns of dicistronic tRNA-mRNA transcripts in grapevine (Vitis vinifera) and their evolutionary co-appearance with vasculature in land plants.

Transfer RNAs (tRNA) are crucial adaptor molecules between messenger RNA (mRNA) and amino acids. Recent evidence in plants suggests that dicistronic tRNA-like structures also act as mobile signals for mRNA transcripts to move between distant tissues. Co-transcription is not a common feature in the plant nuclear genome and, in the few cases where polycistronic transcripts have been found, they include non-coding RNA species, such as small nucleolar RNAs and microRNAs.

The natural selection of good science.

Scientists in some fields are concerned that many published results are false. Recent models predict selection for false positives as the inevitable result of pressure to publish, even when scientists are penalized for publications that fail to replicate. We model the cultural evolution of research practices when laboratories are allowed to expend effort on theory, enabling them, at a cost, to identify hypotheses that are more likely to be true, before empirical testing.