bluuebunny/crossref_metadata_2025 huggingface dataset:
Implementation of 300-mL Rule for Management of Traumatic Hemothorax
Authors: Al Tannir Abdul Hafiz , Biesboer Elise A , Tentis Morgan , Seadler Monica , Patin Bryce B , Golestani Simin , Morris Rachel S , Peschman Jacob , Carver Thomas W , de Moya Marc A
Published: June 2024

BACKGROUND:

Traumatic hemothorax (HTX) is often managed with tube thoracostomy (TT); however, TT carries a high complication rate. In 2017, a guideline was implemented at our Level I trauma center to observe traumatic HTX 300 mL or less in patients who are hemodynamically stable. We hypothesized that this guideline would decrease TT placement without increasing observation failure rates.

STUDY DESIGN:

This was a single-center retrospective review of all adult patients admitted with an HTX on CT before (2015 to 2016) and after (2018 to 2019) the guideline implementation. Exclusion criteria were TT placement before CT scan, absence of CT scan, death within 5 days of admission, and a concurrent pneumothorax more than 20 mm. HTX volume was calculated using CT scan images and Mergo’s formula: V = d
2 × L (where V is the volume, d is the depth, and L is the length). The primary outcome was observation failure, defined as the need for TT, video-assisted thoracoscopic surgery, thoracotomy after repeat imaging or worsening of symptoms, and pulmonary morbidity.

RESULTS:

A total of 357 patients met inclusion criteria, of whom 210 were admitted after guideline implementation. No significant differences in baseline demographics, comorbidities, or injury characteristics across both cohorts were observed. The postimplementation cohort had a significant increase in observation rate (75% vs 59%) and a decrease in TT placement (42% vs 57%). The postimplementation group had a statistically significant shorter hospital (6 vs 8 days) and ICU (2 vs 3 days) length of stay. No significant differences in observation failure, pulmonary complications, 30-day readmission, or 30-day mortality were observed across both cohorts.

CONCLUSIONS:

The implementation of the 300-mL guideline led to a decrease in TT placement without increasing observation failure or complication rates.
A predominately pulmonary activation of complement in a mouse model of severe COVID-19
Authors: Szachowicz Peter J. , Wohlford-Lenane Christine , Heinen Cobey J. , Ghimire Shreya , Xue Biyun , Boly Timothy J. , Verma Abhishek , MašinoviĆ Leila , Bermick Jennifer R. , Perlman Stanley , Meyerholz David K. , Pezzulo Alejandro A. , Zhang Yuzhou , Smith Richard J.H. , McCray Paul B.
Published: June 2024

Evidence from in vitro studies and observational human disease data suggest the complement system plays a significant role in SARS-CoV-2 pathogenesis, although how complement dysregulation develops in patients with severe COVID-19 is unknown. Here, using a mouse-adapted SARS-CoV-2 virus (SARS2-N501YMA30) and a mouse model of severe COVID-19, we identify significant serologic and pulmonary complement activation following infection. We observed C3 activation in airway and alveolar epithelia, and in pulmonary vascular endothelia. Our evidence suggests that while the alternative pathway is the primary route of complement activation, components of both the alternative and classical pathways are produced locally by respiratory epithelial cells following infection, and increased in primary cultures of human airway epithelia in response to cytokine exposure. This locally generated complement response appears to precede and subsequently drive lung injury and inflammation. Results from this mouse model recapitulate findings in humans, which suggest sex-specific variance in complement activation, with predilection for increased C3 activity in males, a finding that may correlate with more severe disease. Our findings indicate that complement activation is a defining feature of severe COVID-19 in mice and lay the foundation for further investigation into the role of complement in COVID-19.
Persistent Neurological Deficits in Mouse PASC Reveal Antiviral Drug Limitations
Authors: Verma Abhishek Kumar , Lowery Shea , Lin Li-Chin , Duraisami Eazhisaivallabi , Abrahante Lloréns Juan E. , Qiu Qiang , Hefti Marco , Yu C. Ron , Albers Mark W. , Perlman Stanley
Published: June 2024

Post-Acute Sequelae of COVID-19 (PASC) encompasses persistent neurological symptoms, including olfactory and autonomic dysfunction. Here, we report chronic neurological dysfunction in mice infected with a virulent mouse-adapted SARS-CoV-2 that does not infect the brain. Long after recovery from nasal infection, we observed loss of tyrosine hydroxylase (TH) expression in olfactory bulb glomeruli and neurotransmitter levels in the substantia nigra (SN) persisted. Vulnerability of dopaminergic neurons in these brain areas was accompanied by increased levels of proinflammatory cytokines and neurobehavioral changes. RNAseq analysis unveiled persistent microglia activation, as found in human neurodegenerative diseases. Early treatment with antivirals (nirmatrelvir and molnupiravir) reduced virus titers and lung inflammation but failed to prevent neurological abnormalities, as observed in patients. Together these results show that chronic deficiencies in neuronal function in SARS-CoV-2-infected mice are not directly linked to ongoing olfactory epithelium dysfunction. Rather, they bear similarity with neurodegenerative disease, the vulnerability of which is exacerbated by chronic inflammation.
The glycoprotein quality control factor Malectin promotes coronavirus replication and viral protein biogenesis
Authors: Davies Jonathan P. , Plate Lars
Published: June 2024

Coronaviruses (CoV) rewire host protein homeostasis (proteostasis) networks through interactions between viral nonstructural proteins (nsps) and host factors to promote infection. With the emergence of SARS-CoV-2, it is imperative to characterize host interactors shared across nsp homologs. Using quantitative proteomics and functional genetic screening, we identify conserved proteostasis interactors of nsp2 and nsp4 that serve pro-viral roles during infection of murine hepatitis virus – a model betacoronavirus. We uncover a glycoprotein quality control factor, Malectin (MLEC), which significantly reduces infectious titers when knocked down. During infection, nsp2 interacts with MLEC-associated proteins and the MLEC-interactome is drastically altered, stabilizing association with the Oligosaccheryltransferase (OST) complex, a crucial component of viral glycoprotein production. MLEC promotes viral protein levels and genome replication through its quality control activity. Lastly, we show MLEC promotes SARS-CoV-2 replication. Our results reveal a role for MLEC in mediating CoV infection and identify a potential target for pan-CoV antivirals.
Delayed cerebrovascular reactivity in individuals with spinal cord injury in the right inferior parietal lobe: a breath-hold functional near-infrared spectroscopy study
Authors: Chen Donna Y. , Di Xin , Karunakaran Keerthana Deepti , Sun Hai , Pal Saikat , Biswal Bharat B.
Published: June 2024

Cerebrovascular reactivity (CVR) reflects the ability of blood vessels to dilate or constrict in response to a vasoactive stimulus, and allows researchers to assess the brain’s vascular health. Individuals with spinal cord injury (SCI) are at an increased risk for autonomic dysfunction in addition to cognitive impairments, which have been linked to a decline in CVR; however, there is currently a lack of brain-imaging studies that investigate how CVR is altered after SCI. In this study, we used a breath-holding hypercapnic stimulus and functional near-infrared spectroscopy (fNIRS) to investigate CVR alterations in individuals with SCI (n = 20, 14M, 6F, mean age = 46.3 ± 10.2 years) as compared to age– and sex-matched able-bodied (AB) controls (n = 25, 19M, 6F, mean age = 43.2 ± 12.28 years). CVR was evaluated by its amplitude and delay components separately by using principal component analysis and cross-correlation analysis, respectively. We observed significantly delayed CVR in the right inferior parietal lobe in individuals with SCI compared to AB controls (linear mixed-effects model, fixed-effects estimate = 6.565, Satterthwaite’s t-test, t = 2.663, p = 0.008), while the amplitude of CVR was not significantly different. The average CVR delay in the SCI group in the right inferior parietal lobe was 14.21 s (sd: 6.60 s), and for the AB group, the average delay in the right inferior parietal lobe was 7.08 s (sd: 7.39 s). CVR delays were also associated with the duration since injury in individuals with SCI, in which a longer duration since injury was associated with a shortened delay in CVR in the right inferior parietal region (Pearson’s r-correlation, r = –0.59, p = 0.04). This study shows that fNIRS can be used to quantify changes in CVR in individuals with SCI, and may be further used in rehabilitative settings to monitor the cerebrovascular health of individuals with SCI.
Understanding the impact of the COVID-19 pandemic and its control measures on women and children: A Zimbabwe case study
Authors: Taruvinga Tinotenda , Chingono Rudo S. , Olaru Ioana D. , Masiye Kenneth , Madanhire Claudius , Munhenzva Sharon , Sibanda Sibusisiwe , Mafuva Lyton , O’Sullivan Natasha , Osman Abdinasir Y. , Deane Kevin , Brandson Tsitsi , Munyanyi Manes , Makoni Annamercy C. , Ngwenya Solwayo , Webb Karen , Chinyanga Theonevus T. , Ferrand Rashida A. , Dixon Justin , Kranzer Katharina , McCoy David
Published: June 2024

COVID-19 presented countries with unprecedented health policy challenges. For low-income countries in particular, policymakers had to contend with both the direct threats posed by COVID-19 as well as the social, educational, and economic harms associated with lockdown and other infection prevention and control measures. We present a holistic and contextualised case study of the direct and indirect impacts of COVID-19 on women and children, with some assessment of their uneven distribution across socio-economic, age and gender groups. We used different types of primary and secondary data from multiple sources to produce a holistic descriptive analysis. Primary data included: qualitative data obtained from 28 in-depth interviews of key informants, six focus group discussions; and 40 household interviews. We also extracted data from government reports and announcements, the District Health Information Software version 2 (DHIS2), newspaper articles and social media, as well as from published research articles. Our findings show that the direct and indirect adverse impacts of COVID-19 were compounded by many years of severe political economic challenges, and consequent deterioration of the healthcare system. The indirect effects of the pandemic had the most severe impacts on the poorest segment of society and widened age and gender inequalities. The pandemic and its accompanying infection prevention and control measures negatively affected health service delivery and uptake. The management of COVID-19 presented enormous challenges to policymakers and public health specialists. These included managing the greatest tension between direct and indirect harms; short-term and long-term effects; and the unequal distribution of harms across different segments of society.
Prevalence of metabolic syndrome among patients with type 2 diabetes mellitus: A cross-sectional study in a tertiary care center of western Nepal
Authors: Karki Manoj , Shrestha Rejma , Dhungana Milan , Rayamajhi Bidhata
Published: June 2024

INTRODUCTION

The coexistence of Metabolic Syndrome in Type 2 diabetic patients significantly increases the risk of stroke and cardiovascular disease. Due to its remarkably high prevalence, metabolic syndrome has gained significant interest over the last decade. Limited information exists regarding the occurrence of Metabolic Syndrome in Type 2 diabetic patients in developing nations like Nepal. Our study aims to determine the prevalence of Metabolic Syndrome among patients with Type 2 Diabetes Mellitus in Western Nepal.

METHODS

This prospective cross-sectional study was conducted at the Universal College of Medical Sciences (UCMS) among patients with Type 2 Diabetes Mellitus. Patients with gestational diabetes mellitus, Type I Diabetes Mellitus, and those aged less than 20 were excluded. Metabolic syndrome has been diagnosed based on the definition given by the International Diabetes Federation.

RESULTS

The study involved 123 patients with a mean age of 61.44 ± 12.88 years, predominantly female (55.3%). Of these patients, 42.3% were classified as Obese. The overall prevalence of Metabolic Syndrome in Type 2 Diabetes Mellitus patients was 61%, comprising 75 cases. The most common component in our study was hypertension, with 82 cases (66.7%), followed by central obesity with 81 cases (65.9%). Among patients with Metabolic Syndrome, 66.7% had an estimated glomerular filtration rate (eGFR) in the 60-89 ml/min range. In females, central obesity was the most common component, while in males, hypertension was the most common component of Metabolic Syndrome.

CONCLUSION

The prevalence of Metabolic Syndrome in patients with Type 2 Diabetes Mellitus was high. Therefore, timely detection and management of Metabolic Syndrome is crucial in preventing consequences and premature mortality in individuals with Type 2 Diabetes Mellitus.
SalmonellaTyphi Haplotype 58 (H58) Biofilm Formation and Genetic Variation in Typhoid Fever Patients with Gallstones in an Endemic Setting in Kenya
Authors: Muturi Peter , Wachira Peter , Wagacha Maina , Mbae Cecilia , Kavai Susan , Mugo Michael , Muhammed Musa , González Juan F. , Kariuki Samuel , Gunn John S.
Published: June 2024

The causative agent of typhoid fever,Salmonella entericaserovar Typhi, is a human restricted pathogen. Human carriers, 90% of whom have gallstones in their gallbladder, continue to shed the pathogen after treatment. The genetic mechanisms involved in establishing the carrier state are poorly understood, butS. Typhi is thought to undergo specific genetic changes within the gallbladder as an adaptive mechanism. In the current study, we aimed to identify biofilm forming ability and the genetic differences in longitudinal clinicalS. Typhi isolates from asymptomatic carriers with gallstones in Nairobi, Kenya. Whole genome sequences were analyzed from 22S. Typhi isolates, 20 from stool and 2 from blood samples, all genotype 4.3.1 (H58). Nineteen strains were from four patients also diagnosed with gallstones, of whom, three had typhoid symptoms and continued to shedS. Typhi after treatment. All isolates had point mutations in the quinolone resistance determining region (QRDR) and only sub-lineage 4.3.1.2EA3 encoded multidrug resistance genes. There was no variation in antimicrobial resistance patterns among strains from the same patient/household. Non-multidrug resistant (MDR), isolates formed significantly stronger biofilmsin vitrothan the MDR isolates, p<0.001. A point mutation within thetreBgene (treBA383T) was observed in strains isolated after clinical resolution from patients living in 75% of the households. Missense mutations in Vi capsular polysaccharide genes,tviEP263S was also observed in 18% of the isolates. This study provides insights into the role of typhoid carriage, biofilm formation, AMR genes and genetic variations inS.Typhi from asymptomatic carriers.

Importance

Although typhoid fever has largely been eliminated in high income countries, it remains a major global public health concern especially among low- and middle-income countries. The bacteria responsible for this infectious disease,SalmonellaTyphi, has limited ability to replicate outside the human host and human carriers serve as a reservoir of infection. Typhoid is a common infection in parts of sub-Saharan Africa and Asia, and is endemic in our study setting. Our research findings on differences inS.Typhi strains causing typhoid fever and carriage will influence public health approaches aimed at reducing carriage and transmission ofS. Typhi.
Inequalities in Compliance with the Two-Dose Measles Vaccination in Peruvian Children Aged 12 to 59 Months in 2023
Authors: Intimayta-Escalante Claudio , Tapia-Sequeiros Gustavo , Cueva-Cañola Luis E.
Published: June 2024

Introduction

Inadequate measles vaccination coverage leads to outbreaks that affect the pediatric population in Peru. The aim of this study was to evaluate sociodemographic inequalities related to the coverage and compliance in the two-dose measles vaccination schedule among Peruvian children in 2023.

Methods

An analytical cross-sectional study was conducted using data from a national Peruvian survey. Mothers aged 15 to 49 with children aged 12 to 59 months were included. Sociodemographic and health characteristics of the mother and child were considered sources of inequality. Prevalence ratios (PR) were calculated to measure the characteristics associated with adherence to the measles vaccination schedule. Inequality analysis was assessed using the Erreygers Concentration Index (ECI).

Results

A total of 8,148 households were evaluated. Vaccination coverage was identified as 85.9% (95%CI: 94.7 – 87.1) for the first dose and 53.9% (95%CI: 52.1 – 55.7) for the second dose. In the inequality analysis, mothers with no education (CI: -0.57), aged 15 to 17 years (CI: -0.38), residing in the jungle (CI: -0.41) or highlands (CI: -0.26), and without health insurance (CI: -0.01) showed greater inequality in adherence to the vaccination schedule. Additionally, adherence to growth and development check-ups in infants was a source of inequality (CI: -0.09).

Conclussion

Measles vaccination coverage did not reach the minimum values required to prevent outbreaks in Peru. The factors contributing to inequality in vaccination coverage included education level, age, region of residence, area of residence, health insurance status, and adherence to growth and development check-ups.
Sitetack: A Deep Learning Model that Improves PTM Prediction by Using Known PTMs
Authors: Gutierrez Clair S. , Kassim Alia A. , Gutierrez Benjamin D. , Raines Ronald T.
Published: June 2024

Post-translational modifications (PTMs) increase the diversity of the proteome and are vital to organismal life and therapeutic strategies. Deep learning has been used to predict PTM locations. Still, limitations in datasets and their analyses compromise success. Here we evaluate the use of known PTM sites in prediction via sequence-based deep learning algorithms. Specifically, PTM locations were encoded as a separate amino acid before sequences were encoded via word embedding and passed into a convolutional neural network that predicts the probability of a modification at a given site. Without labeling known PTMs, our model is on par with others. With labeling, however, we improved significantly upon extant models. Moreover, knowing PTM locations can increase the predictability of a different PTM. Our findings highlight the importance of PTMs for the installation of additional PTMs. We anticipate that including known PTM locations will enhance the performance of other proteomic machine learning algorithms.
Plant interaction traits determine the biomass of arbuscular mycorrhizal fungi and bacteria in soil
Authors: Lewe Natascha , Keyzers Robert A. , Tylianakis Jason M. , Deslippe Julie R.
Published: June 2024

Plant-arbuscular mycorrhizal fungal (AMF) mutualisms play key roles in the biodiversity and productivity of ecosystems. Yet we have limited understanding of the functional roles of plants as AMF generalists or specialists, and the consequences of these plant interaction traits for soil ecosystems are virtually unknown. We grew eight pasture plant species under two experimental conditions and determined their root AMF communities by sequencing. We determined plant species interaction traits with AMF using a set of numeric and phylogenetic α-, β– and γ-diversities and characterized plant species’ relative interaction generalism for AMF. We used lipid analysis of rhizosphere soils and Bayesian modelling to explore how host interaction traits affected carbon allocation to AMF and bacteria. Plant interaction traits for AMF appear to be stable despite large variation in edaphic conditions and AMF pools. We show that host interaction generalism was associated with opposite patterns of bacterial and AMF biomass; the phylogenetic diversity of host interactions was positively associated with AMF biomass whereas the richness of host interactions was negatively associated with bacterial biomass in rhizosphere soils. Explicit consideration of plant interaction niches may enhance understanding of how changes in biodiversity affect ecosystem carbon cycling.

Open research statement

This publication does not use novel code, and the bioinformatic and statistic pipelines for this manuscript will be made available athttps://github.com/NLewe/Bayes-interaction-niche.

Raw data will be made available at NCBI as BioProject: PRJNA997080
APOE4 increases energy metabolism in APOE-isogenic iPSC-derived neurons
Authors: Budny Vanessa , Knöpfli Yannic , Meier Debora , Zürcher Kathrin , Bodenmann Chantal , Peter Siri L. , Müller Terry , Tardy Marie , Cortijo Cedric , Tackenberg Christian
Published: June 2024

The apolipoprotein E4 (APOE4) allele represents the major genetic risk factor for Alzheimer’s disease (AD). In contrast, APOE2 is known to lower the AD risk while APOE3 is defined as risk neutral. APOE plays a prominent role in the bioenergetic homeostasis of the brain, and early-stage metabolic changes have been detected in brains of AD patients. Although APOE is primarily expressed by astrocytes in the brain, neurons also have been shown as source for APOE. However, little is known about the differential role of the three APOE isoforms for neuronal energy homeostasis. In this study, we generated pure human neurons (iN cells) from APOE-isogenic induced pluripotent stem cells (iPSCs), expressing either APOE2, APOE3, APOE4 or carrying an APOE-knockout (KO) to investigate APOE isoform-specific effects on neuronal energy metabolism. We showed that endogenously produced APOE4 enhanced mitochondrial ATP production in APOE-isogenic iN cells but not in the corresponding iPS cell line. This effect neither correlated with the expression levels of mitochondrial fission or fusion proteins, nor with the intracellular or secreted levels of APOE, which were similar for APOE2, APOE3 and APOE4 iN cells. ATP production and basal respiration in APOE-KO iN cells strongly differed from APOE4 and more closely resembled APOE2 and APOE3 iN cells indicating a gain-of-function mechanism of APOE4 rather than a loss-of-function. Taken together, our findings in APOE isogenic iN cells reveal an APOE genotype-dependent and neuron-specific regulation of oxidative energy metabolism.
PT-seq: A method for metagenomic analysis of phosphorothioate epigenetics in complex microbial communities
Authors: Yuan Yifeng , DeMott Michael S. , Byrne Shane R. ,   the Global Microbiome Conservancy, Dedon Peter C.
Published: June 2024

Among dozens of known epigenetic marks, naturally occurring phosphorothioate (PT) DNA modifications are unique in replacing a non-bridging phosphate oxygen with redox-active sulfur and function in prokaryotic restriction-modification and transcriptional regulation. Interest in PTs has grown due to the widespread distribution of thednd, ssp, andbrxgenes among bacteria and archaea, as well as the discovery of PTs in 5-10% of gut microbes. Efforts to map PTs in complex microbiomes using existing next-generation and direct sequencing technologies have failed due to poor sensitivity. Here we developed PT-seq as a high-sensitivity method to quantitatively map PTs across genomes and metagenomically identify PT-containing microbes in complex genomic mixtures. Like other methods for mapping PTs in individual genomes, PT-seq exploits targeted DNA strand cleavage at PTs by iodine, followed by sequencing library construction using ligation or template switching approaches. However, PT-specific sequencing reads are dramatically increased by adding steps to heat denature the DNA, block pre-existing 3’-ends, fragment DNA after T-tailing, and enrich iodine-induced breaks using biotin-labeling and streptavidin beads capture. Iterative optimization of the sensitivity and specificity of PT-seq is demonstrated with individual bacteria and human fecal DNA.
Comparative neuroimaging of the carnivoran brain: Neocortical sulcal anatomy
Authors: Boch Magdalena , Karadachka Katrin , Loh Kep Kee , Benn R. Austin , Roumazeilles Lea , Bertelsen Mads F. , Manger Paul R , Wriggelsworth Ethan , Spiro Simon , Spocter Muhammad A. , Johnson Philippa J. , Avelino-de-Souza Kamilla , Patzke Nina , Lamm Claus , Miller Karla L. , Sallet Jerome , Khrapitchev Alexandre A. , Tendler Benjamin C , Mars Rogier B.
Published: June 2024

Carnivorans are an important study object for comparative neuroscience, as they exhibit a wide range of behaviours, ecological adaptations, and social structures. Previous studies have mainly examined relative brain size, but a comprehensive understanding of brain diversity requires the investigation of other aspects of their neuroanatomy. Here, we obtained primarily post-mortem brain scans from eighteen species of the order Carnivora, reconstructed their cortical surfaces, and examined neocortical sulcal anatomy to establish a framework for systematic inter-species comparisons. We observed distinct regional variations in sulcal anatomy, potentially related to the species' behaviour and ecology. Arctoidea species with pronounced forepaw dexterity exhibited complex sulcal configurations in the presumed somatosensory cortex but low sulcal complexity in the presumed visual and auditory occipitotemporal cortex. Canidae had the largest number of unique major sulci with a unique sulcus in the occipital cortex and highly social canids featuring an additional frontal cortex sulcus. We also observed differentially complex occipito-temporal sulcal patterns in Felidae and Canidae, indicative of changes in auditory and visual areas that may be related to foraging strategies and social behaviour. In conclusion, this study presents an inventory of the sulcal anatomy of a number of rarely studied carnivoran brains and establishes a framework and novel avenues for further investigations employing a variety of neuroimaging modalities to reveal more about carnivoran brain diversity.
Disruption of recombination machinery alters the mutational landscape in plant organellar genomes
Authors: Waneka Gus , Broz Amanda K. , Wold-McGimsey Forrest , Zou Yi , Wu Zhiqiang , Sloan Daniel B.
Published: June 2024

Land plant organellar genomes have extremely low rates of point mutation yet also experience high rates of recombination and genome instability. Characterizing the molecular machinery responsible for these patterns is critical for understanding the evolution of these genomes. While much progress has been made towards understanding recombination activity in land plant organellar genomes, the relationship between recombination pathways and point mutation rates remains uncertain. The organellar targetedmutShomolog MSH1 has previously been shown to suppress point mutations as well as non-allelic recombination between short repeats inArabidopsis thaliana. We therefore implemented high-fidelity Duplex Sequencing to test if other genes that function in recombination and maintenance of genome stability also affect point mutation rates. We found small to moderate increases in the frequency of single nucleotide variants (SNVs) and indels in mitochondrial and/or plastid genomes ofA. thalianamutant lines lackingradA,recA1, orrecA3. In contrast,osb2andwhy2mutants did not exhibit an increase in point mutations compared to wild type (WT) controls. In addition, we analyzed the distribution of SNVs in previously generated Duplex Sequencing data fromA. thalianaorganellar genomes and found unexpected strand asymmetries and large effects of flanking nucleotides on mutation rates in WT plants andmsh1mutants. Finally, using long- read Oxford Nanopore sequencing, we characterized structural variants in organellar genomes of the mutant lines and show that different short repeat sequences become recombinationally active in different mutant backgrounds. Together, these complementary sequencing approaches shed light on how recombination may impact the extraordinarily low point mutation rates in plant organellar genomes.
A map of canine sequence variation relative to a Greenland wolf outgroup
Authors: Nguyen Anthony , Schall Peter Z , Kidd Jeffrey M
Published: June 2024

For over 15 years, canine genetics research relied on a reference assembly from a Boxer breed dog named Tasha (i.e., canFam3.1). Recent advances in long-read sequencing and genome assembly have led to the development of numerous high-quality assemblies from diverse canines. These assemblies represent notable improvements in completeness, contiguity, and the representation of gene promoters and gene models. Although genome graph and pan-genome approaches have promise, most genetic analyses in canines rely upon the mapping of Illumina sequencing reads to a single reference. The Dog10K consortium, and others, have generated deep catalogs of genetic variation through an alignment of Illumina sequencing reads to a reference genome obtained from a German Shepherd Dog named Mischka (i.e., canFam4, UU_Cfam_GSD_1.0). However, alignment to a breed-derived genome may introduce bias in genotype calling across samples. Since the use of an outgroup reference genome may remove this effect, we have reprocessed 1,929 samples analyzed by the Dog10K consortium using a Greenland wolf (mCanLor1.2) as the reference. We efficiently performed remapping and variant calling using a GPU-implementation of common analysis tools. The resulting call set removes the variability in genetic differences seen across samples and breed relationships revealed by principal component analysis are not affected by the choice of reference genome. Using this sequence data, we inferred the history of population sizes and found that village dog populations experienced a 9-13 fold reduction in historic effective population size relative to wolves.
Hallmarks of tumor-experienced T cells are absent in multiple myeloma patients from diagnosis through maintenance therapy
Authors: Shasha Carolyn , Glass David R. , Moelhman Ernest , Islas Laura , Tian Yuan , Szeto Gregory L. , Peng Tao , Song Xiaoling , Wurscher Michelle , Bumol Thomas F. , Torgerson Troy R. , Greenberg Philip D. , Green Damian J. , Newell Evan W.
Published: June 2024

Dysregulation of the bone marrow (BM) niche in multiple myeloma (MM) alters the composition and state of resident immune cells, potentially impeding anti-tumor immunity. One common mechanism of immune inhibition in solid tumors is the induction of exhaustion in tumor-specific T cells. However, the extent of T cell tumor recognition and exhaustion is not well-characterized in MM. As the specific mechanisms of immune evasion are critical for devising effective therapeutic strategies, we deeply profiled the CD8+T cell compartment of newly-diagnosed MM (NDMM) patients for evidence of tumor reactivity and T cell exhaustion. We applied single-cell multi-omic sequencing and antigen-specific mass cytometry to longitudinal BM and peripheral blood (PB) samples taken from timepoints spanning from diagnosis through induction therapy, autologous stem cell transplant (ASCT), and maintenance therapy. We identified an exhausted-like population that lacked several canonical exhaustion markers, was not significantly enriched in NDMM patients, and consisted of small, nonpersistent clones. We also observed an activated population with increased frequency in the PB of NDMM patients exhibiting phenotypic and clonal features consistent with homeostatic, antigen-nonspecific activation. However, there was no evidence of “tumor-experienced” T cells displaying hallmarks of terminal exhaustion and/or tumor-specific activation/expansion in NDMM patients at any timepoint.
No Miracle, Just a Mineral: The Not-So-Magical Antimicrobial World of Chlorine Dioxide
Authors: Dudek-Wicher R. , Brożyna M. , Paleczny J. , Mączyńska B. , Dudek B. , Migdał P. , Dołowacka-Jóźwiak A. , Fischer J. , Junka A.
Published: June 2024

This study evaluates thein vitroantimicrobial efficacy and cytotoxicity of acidified sodium chlorite (ASC), a source of chlorine dioxide. Despite its controversial promotion in alternative medicine as a cure-all solution, known as “Miracle Mineral Solution” (MMS), the data on its factual medicinal activity is very limited. Therefore, we aimed to elucidate the activity of ASC against biofilms ofStaphylococcus aureus, Pseudomonas aeruginosa, Enterococcus faecalis, Streptococcus mutans, Pseudomonas aeruginosa, Escherichia coli, andLactobacillus sp. The study also investigated the in vitrocytotoxic effects of ASC towards eukaryotic fibroblasts and inin vivomodel ofGalleria mellonellalarvae. Our findings demonstrate that these concentrations of ASC which can effectively eradicate biofilms, also pose potential health risks due to theirin vitroandin vivocytotoxicity. It implies that ASC applied in human can lead to damage to the mucous membrane of the gastrointestinal tract. This research contributes to the ongoing debate on the safety and efficacy of chlorine dioxide in clinical applications, highlighting the need for precise dosing to avoid mucosal damage in therapeutic contexts.
Genomic analysis revealed hotspots of genetic adaptation and risk of disappearance in the Brazilian goat populations
Authors: Sobrinho Francisco de A. Diniz , Coelho Ronaldo Cunha , de Oliveira Moura Jeane , do Nascimento Igor Ferreira , Bajay Miklos Maximiliano , Branco Carvalho Leonardo Castelo , Britto Fábio Barros , Rocha Sarmento José Lindenberg , M. Ribeiro Azevedo Danielle Maria , Mastrangelo Salvatore , de Araújo Adriana Mello
Published: June 2024

We accessed a 50K Illumina SNP genotype dataset from two important goat breeds of the Brazilian semi- arid region to analyze the abundance and length of runs of homozygosity (ROH). This analysis aims to elucidate the importance of adaptation history in the genome of the Brazilian goat populations and to measure genomic inbreeding. Heterozygosity-rich regions (HRR) or genome regions of high genetic variability provide clues about how diversity might be associated with increased fitness, avoiding deleterious homozygous alleles. Overall, 22,872 ROH were identified. The average number of ROH per individual ranged from 74.73 (Anglo-Nubian commercial breed) to 173.85 (Marota landrace). Analysis of the distribution of runs of homozygosity according to their size showed that, for both breeds, the majority of ROH were in the short (<2.0 Mb) category (65.6%). ROH-based inbreeding (FROH) revealed low levels in Anglo-Nubian (0.0627) and high levels in Marota (0.1419), likely due to a reduction in effective population size over generations in the Marota landrace. We defined islands of ROH and HRR and identified common regions in the Marota goat, where genes related to various traits such as embryonic development, body growth, lipid homeostasis, and brain functions are located. These results indicate that such regions are associated with many traits and have therefore been under selective pressure in these goat breeds reared for different purposes.
The FGFR inhibitor Rogaratinib reduces microglia reactivity and synaptic loss in TBI
Authors: Rehman Rida , Froehlich Albrecht , olde Heuvel Florian , Elsayed Lobna , Boeckers Tobias , Huber-Lang Markus , Morganti-Kossmann Cristina , Roselli Francesco
Published: June 2024

Background

Traumatic brain injury (TBI) induces an acute reactive state of microglia, which contribute to secondary injury processes through phagocytic activity and release of cytokines. Several receptor tyrosine kinases (RTK) are activated in microglia upon TBI, and their blockade may reduce the acute inflammation and decrease the secondary loss of neurons; thus RTKs are potential therapeutic targets. We have previously demonstrated that several members of the FGFR family are transiently phosporylated upon TBI; the availability for drug repurposing of FGFR inhibitors makes worthwhile the elucidation of the role of FGFR in the acute phases of the response to TBI and the effect of FGFR inhibition.

Methods

A closed, blunt, weight-drop mild TBI protocol was employed. The pan-FGFR inhibitor Rogaratinib was administered to mice 30min after the TBI and daily up to 7 days post injury. Phosphor-RTK Arrays and proteomic antibody arrays were used to determine target engagement and large-scale impact of the FGFR inhibitor. pFGFR1 and pFGFR3 immunostaining were employed for validation. As outcome parameters of the TBI injury immunostainings for NeuN, VGLUT1, VGAT at 7dpi were considered.

Results

Inhibition of FGFR during TBI restricted phosphorylation of FGFR1, FGFR3, FGFR4 and ErbB4. Phosphorylation of FGFR1 and FGFR3 during TBI was traced back to Iba1+ microglia. Rogaratinib substantially dowregulated the proteomic signature of the neuroimmunological response to trauma, including the expression of CD40L, CXCR3, CCL4, CCR4, ILR6, MMP3 and OPG. Protracted Rogaratinib treatment exhibited a neuroprotective effect on neuronal density at 7dpi and limited the loss of excitatory (vGLUT+) synapses.

Conclusion

The FGFR family is involved in the early induction of reactive microglia in TBI. FGFR inhibition selectively prevented FGFR phosphorylation in the microglia, dampened the overall neuroimmunological response and enhanced the preservation of neuronal and synaptic integrity. Thus, FGFR inhibitors display potential as microglial modulators in TBI.
Short heat shock factor A2 confers heat sensitivity inArabidopsis: Insights into heat resistance and growth balance
Authors: Chen Wanxia , Zhao Jiaqi , Tao Zhanxia , Zhang Shan , Bei Xiujuan , Lu Wen , Qi Xiaoting
Published: June 2024

Cells prevent heat damage through a highly conserved canonical heat stress response (HSR) in which heat shock factors (HSFs) bind heat shock elements (HSEs) to activate heat shock proteins (HSPs). Plants generate short HSFs that originate from HSF splicing variants, but little is known about S-HSFs. Although an enhanced canonical HSR confers thermotolerance, its hyperactivation inhibits plant growth. How this process is prevented to ensure proper plant growth has not been determined. Here, we report thatArabidopsisS-HsfA2, S-HsfA4c, and S-HsfB1 confer extreme heat (45°C) sensitivity and represent new kinds of HSF with a unique truncated DNA-binding domain (tDBD) that binds a new heat-regulated element (HRE). The HRE conferred a minimal promoter response to heat and exhibited heat stress sensing and transmission patterns. We used S-HsfA2 to investigate whether and how S-HSFs prevent hyperactivation of the canonical HSR.HSP17.6B,a direct target gene of HsfA2, conferred thermotolerance, but its overexpression caused HSR hyperactivation. We revealed that S-HsfA2 alleviated this hyperactivation in two different ways. 1) S-HsfA2 negatively regulatesHSP17.6B viathe HRE-HRE-like element, thus constructing a noncanonical HSR (S-HsfA2-HRE-HSP17.6B) to antagonistically repress HsfA2-activatedHSP17.6Bexpression. 2) S-HsfA2 binds to the DBD of HsfA2 to prevent HsfA2 from binding to HSEs, eventually attenuating HsfA2-activatedHSP17.6Bpromoter activity. Overall, our findings underscore the biological importance of S-HSFs, namely, preventing plant heat tolerance hyperactivation to maintain proper growth.

Graphical Abstract
Functional carbohydrate-active enzymes acquired by horizontal gene transfer from plants in the whiteflyBemisia tabaci
Authors: Colinet D , Haon M , Drula E , Boyer M , Grisel S , Belliardo C , Koutsovoulos GD , Berrin JG , Danchin EGJ
Published: June 2024

Carbohydrate-active enzymes (CAZymes) involved in the degradation of plant cell walls and/or the assimilation of plant carbohydrates for energy uptake are widely distributed in microorganisms. In contrast, they are less frequent in animals, although there are exceptions, including examples of CAZymes acquired by horizontal gene transfer (HGT) from bacteria or fungi in several of phytophagous arthropods and plant-parasitic nematodes. Although the whiteflyBemisia tabaciis a major agricultural pest, knowledge of HGT-acquired CAZymes in this phloem-feeding insect of the Hemiptera order (subfamily Aleyrodinae) is still lacking. We performed a comprehensive and accurate detection of HGT candidates inB. tabaciand identified 136 HGT events, 14 of which corresponding to CAZymes. TheB. tabaciHGT-acquired CAZymes were not only of bacterial or fungal origin, but some were also acquired from plants. Biochemical analysis revealed that members of the glycoside hydrolase families 17 (GH17) and 152 (GH152) acquired from plants are functional beta-glucanases with different substrate specificities, suggesting distinct roles. These two CAZymes are the first characterized GH17 and GH152 glucanases in an animal. We identified a lower number of HGT events in the related AleyrodinaeTrialeurodes vaporariorum, with only three HGT-acquired CAZymes, including a GH152 glucanase, with phylogenetic analysis suggesting a unique HGT event in the ancestor of the Aleyrodinae. Another GH152 CAZyme, most likely independently acquired from plants, was also identified in two plant cell-feeding insects of the Thysanoptera order, highlighting the importance of plant-acquired CAZymes in the biology of piercing-sucking insects.

Significance statement

Carbohydrate-active enzymes (CAZymes) are crucial for sugar metabolism. Those involved in plant cell wall degradation are usually absent from animal genomes. In this study, we explored CAZyme repertoires in the genomes of several insects: the phloem-feeding whiteflyBemisia tabaci, a major agricultural pest, and the related greenhouse whiteflyTrialeurodes vaporariorum, as well as two Thysanoptera species that feed on plant cell contents. We identified several cases of CAZymes acquired from plant via horizontal gene transfer in the genome of these insects. Notably, we showed that twoB. tabaciCAZymes of plant origin function as glucanases with distinct substrate specificities, potentially helping the insect to overcome plant defenses. Overall, these findings enhance our understanding of how the ability to feed on plants evolved in insects.
Piximi - An Images to Discovery web tool for bioimages and beyond
Authors: Moser Levin M , Gogoberidze Nodar , Papaleo Andréa , Lucas Alice , Dao David , Friedrich Christoph A , Paavolainen Lassi , Molnar Csaba , Stirling David R , Hung Jane , Wang Rex , Tromans-Coia Callum , Li Bin , Evans Edward L , Eliceiri Kevin W , Horvath Peter , Carpenter Anne E , Cimini Beth A
Published: June 2024

Deep learning has greatly accelerated research in biological image analysis yet it often requires programming skills and specialized tool installation. Here we present Piximi, a modern, no-programming image analysis tool leveraging deep learning. Implemented as a web application at Piximi.app, Piximi requires no installation and can be accessed by any modern web browser. Its client-only architecture preserves the security of researcher data by running all computation locally. Piximi offers four core modules: a deep learning classifier, an image annotator, measurement modules, and pre-trained deep learning segmentation modules. Piximi is interoperable with existing tools and workflows by supporting import and export of common data and model formats. The intuitive researcher interface and easy access to Piximi allows biological researchers to obtain insights into images within just a few minutes. Piximi aims to bring deep learning-powered image analysis to a broader community by eliminating barriers to entry.
The distribution of beneficial mutational effects between two sister yeast species poorly explains natural outcomes of vineyard adaptation
Authors: Longan Emery R. , Fay Justin C.
Published: June 2024

Domesticated strains ofSaccharomyces cerevisiaehave adapted to resist copper and sulfite, two chemical stressors commonly used in winemaking.S. paradoxus, has not adapted to these chemicals despite being consistently present in sympatry withS. cerevisiaein vineyards. This contrast represents a case of apparent evolutionary constraints favoring greater adaptive capacity inS. cerevisiae. In this study, we used a comparative mutagenesis approach to test whetherS. paradoxusis mutationally constrained with respect to acquiring greater copper and sulfite resistance. For both species, we assayed the rate, effect size, and pleiotropic costs of resistance mutations and sequenced a subset of 150 mutants isolated from our screen. We found that the distributions of mutational effects displayed by the two species were very similar and poorly explained the natural pattern. We also found that chromosome VIII aneuploidy and loss of function mutations inPMA1confer copper resistance in both species, whereas loss of function mutations inREG1were only a viable route to copper resistance inS. cerevisiae. We also observed a singlede novoduplication of theCUP1gene inS. paradoxusbut none inS. cerevisiae. For sulfite, loss of function mutations inRTS1andKSP1confer resistance in both species, but mutations inRTS1have larger average effects inS. paradoxus. Our results show that even when the distributions of mutational effects are largely similar, species can differ in the adaptive paths available to them. They also demonstrate that assays of the distribution of mutational effects may lack predictive insight concerning adaptive outcomes.
Degradation Bottlenecks and Resource Competition in Transiently and Stably Engineered Mammalian Cells
Authors: Gabrielli Jacopo , Di Blasi Roberto , Kontoravdi Cleo , Ceroni Francesca
Published: June 2024

Degradation tags, otherwise known as degrons, are portable sequences that can be used to alter protein stability. Here, we report that degron-tagged proteins compete for cellular degradation resources in engineered mammalian cells leading to coupling of the degradation rates of otherwise independently expressed proteins when constitutively targeted human degrons are adopted. By adopting inducible bacterial and plant degrons we also highlight how orthogonality and uncoupling of synthetic construct degradation from the native machinery can be achieved. We show the effect of this competition to be dependent on the context of the degrons where C-terminal degradation appears to impact competition the most across our tested settings. We then build a genomically integrated capacity monitor tagged with different degrons and confirm resource competition between genomic and transiently expressed DNA constructs. This work expands the characterisation of resource competition in engineered mammalian cells to degradation also including integrated systems, providing a framework for the optimisation of heterologous expression systems to advance applications in fundamental and applied biological research.
A transformer model forde novosequencing of data-independent acquisition mass spectrometry data
Authors: Sanders Justin , Wen Bo , Rudnick Paul , Johnson Rich , Wu Christine C. , Oh Sewoong , MacCoss Michael J. , Noble William Stafford
Published: June 2024

A core computational challenge in the analysis of mass spectrometry data is thede novosequencing problem, in which the generating amino acid sequence is inferred directly from an observed fragmentation spectrum without the use of a sequence database. Recently, deep learning models have made significant advances inde novosequencing by learning from massive datasets of high-confidence labeled mass spectra. However, these methods are primarily designed for data-dependent acquisition (DDA) experiments. Over the past decade, the field of mass spectrometry has been moving toward using data-independent acquisition (DIA) protocols for the analysis of complex proteomic samples due to their superior specificity and reproducibility. Hence, we present a newde novosequencing model called Cascadia, which uses a transformer architecture to handle the more complex data generated by DIA protocols. In comparisons with existing approaches forde novosequencing of DIA data, Cascadia achieves state-of-the-art performance across a range of instruments and experimental protocols. Additionally, we demonstrate Cascadia’s ability to accurately discoverde novocoding variants and peptides from the variable region of antibodies.