bluuebunny/crossref_metadata_2025 huggingface dataset:
Exploring factors affected timely receiving intravitreal anti-VEGF treatment in patients with Diabetic Macular Edema: a qualitative interview study analyzed with COM-B model
Authors: Li Shu , Pan Jiani , Xu Yan , Tian Shiyu , Dai Zhengyue , Fang Qiong
Published: April 2024

Objectives

To explore factors affected untimely receiving intravitreal anti-Vascular endothelial growth factor (VEGF) injection based on the Capability, Opportunity and Motivation-Behavior (COM-B) model in patients with Diabetic Macular Edema (DME) and regard these factors as main targets for interventions.

Design

An exploratory qualitative study was conducted using semi-structured interviews with patients with DME. The COM-B model was used to guide data collection and analysis.

Setting

The study was carried out in outpatient department of ophthalmology in China.

Participants

24 patients with DME who experienced anti-VEGF treatment at least one injection within one year were recruited using convenience and purposed sampling.

Results

The themes and subthemes were identified. Physical capability included (1) lack of knowledge, (2) high treatment expenditure, and psychological capability included prioritized glycemic control rather than anti-VEGF. Social opportunity included (1) no anti-VEGF available, (2) Recommended eyedrops, laser and oral drug but not mentioned intravitreal anti-VEGF injection, (3) As an optional therapy, selected more convenient treatment rather than anti-VEGF agents, and physical opportunity included (1) no confidence in treatment from doctor, (2) communication between doctors and patients. Reflective motivation included (1) outcome expectancies, and automatic motivation included (1) fear of injection, (2) fear of blindness.

Conclusion

We should attach importance to these eleven factors, especially to effective interaction between doctors and patients, and doctor’s authoritative treatment advice, which interventions were based on in the future.

Strengths and limitations of this study

⇒ The qualitative design was used to understand factors affecting timely intravitreal anti-VEGF injections in patients with DME and to explore the potential measures to change them.

⇒The study highlighted the importance of efficient communication between clinicians and patients.

⇒The study didn’t consider other clinical variables, such as the severity and duration of diabetes, which should be included in the future studies.
Antibody Responses to SARS-Cov-2 among Health Care Workers of a Tertiary Hospital in North-Eastern, Tanzania
Authors: Ibrahim Pendo M , Anthony Felix , Mshana Happiness , Rwegoshola Kevin , Semvua Hadija , Chilongola Jaffu
Published: April 2024

Background

Health Care Workers (HCWs) have been playing crucial role in treating patient with COVID-19. They have a higher occupational risk of contracting the disease than the general population, and a greater chance of them transmitting the disease to vulnerable patients under their care. Given their scarcity and low COVID-19 vaccine acceptance in Africa, it is essential that HCWs are seroprotected and their exposure to COVID-19 minimized. This study was therefore designed to determine IgG antibody response to SARS-CoV-2 among HCWs in North Eastern, Tanzania.

Methodology

This was a cross-sectional study carried out among 273 HCWs at Kilimanjaro Christian Medical Centre (KCMC), a tertiary, zonal referral hospital in Tanzania’s North Eastern region. Stratified sampling was used to select study participants. Data were obtained from each consenting participant using a validated questionnaire. Blood samples were collected for SARS-CoV-2 IgG antibodies quantification by using an indirect ELISA test. RedCap software was used to enter and manage data. Statistical analysis was done by using STATA statistical software version 15 and GraphPad Prism v 9.0. A p-value of < 0.05 was considered the cut-off for statistical significance.

Results

Among 273 HCWS only 37.9 % reported to have received COVID-19 vaccine. Except for one person, all of the participants had SARS-CoV-2 IgG antibody concentrations that were positive, with 64.5% of them having strong seropositivity. Female gender, allied health professionals, active smoking, COVID-19 patient interactions, COVID-19 vaccination receptivity, and adherence to recommended hand hygiene were found to be significant predictors of variation of median SARS-CoV-2 antibody concentration. The usage of personal protective equipment, history of previously testing PCR positive for COVID-19, the number of COVID-19 patient exposure and age were found to cause no significant variation in median antibody concentration among participants.

Conclusions

This study reports a high seroprevalence of SARS-CoV-2 antibodies among healthcare workers in Kilimanjaro Christian Medical Centre. This suggests that HCWs have significant exposure to SARS-CoV-2 despite the low rate of vaccination acceptance even among HCWs. We recommend a strengthened Infectious Prevention and Control (IPC) in hospitals through provision of technical leadership and coordination according to WHO guidelines. We also recommend continued conduction of seroprevalence studies to estimate the magnitude and trends of SARS-CoV-2 infections in different populations in Tanzania. A better understanding of the past, current, and future transmission patterns of infectious pathogens is critical for preparedness and response planning, and to inform the optimal implementation of existing and novel interventions under the current and changing climate.
Reduced Continuity Index with Proactive Esophageal Cooling Compared to Luminal Temperature Monitoring During Radiofrequency Ablation
Authors: Lazarus Catherine , Sherman Jacob , Putzel Natalie , Zagrodzky William , Sharkoski Tiffany , Ro Alex , Nazari Jose , Fisher Westby , Kulstad Erik , Metzl Mark
Published: April 2024

Background

Proactive esophageal cooling is FDA cleared to reduce the likelihood of esophageal injury during radiofrequency ablation for treatment of atrial fibrillation (AF). Long-term follow-up data have also shown improved freedom from arrhythmia with proactive esophageal cooling compared to luminal esophageal temperature (LET) monitoring during pulmonary vein isolation (PVI). One hypothesized mechanism is improved lesion contiguity (as measured by the Continuity Index) with the use of cooling. We aimed to compare the Continuity Index of PVI cases using proactive esophageal cooling to those using LET monitoring.

Methods

Continuity Index was calculated for PVI cases at two different hospitals within the same health system using a slightly modified Continuity Index to facilitate both real-time calculation during observation of PVI cases and retrospective determination from recorded cases. The results were then compared between proactively cooled cases and those using LET monitoring.

Results

Continuity Indices for a total of 101 cases were obtained; 77 cases using proactive esophageal cooling and 24 cases using traditional LET monitoring. With proactive esophageal cooling, the average Continuity Index was 2.7 (1.3 on the left pulmonary vein, and 1.5 on the right pulmonary vein). With LET monitoring, the average Continuity Index was 27.3 (14.3 on the left, and 12.9 on the right), for a difference of 24.6 (p < 0.001).

Conclusion

Proactive esophageal cooling during PVI is associated with significantly improved lesion contiguity when compared to LET monitoring. This finding may offer a mechanism for the greater freedom from arrhythmia seen with proactive cooling in long-term follow-up.
ASCVD risk refinement with NT-proBNP for statin allocation among low- and intermediate risk individuals
Authors: Pavlović Jelena , Kavousi Maryam , Ikram M. Kamran , Bos Daniel , Ikram M. Arfan , Leening Maarten J.G.
Published: April 2024

Background

Statin trials targeting low- to intermediate risk individuals, namely MEGA, JUPITER, and HOPE-3, have demonstrated benefit of statin use for primary prevention of atherosclerotic cardiovascular disease (ASCVD), but are poorly reflected in guideline recommendations for primary prevention of ASCVD. N-terminal pro-B-type natriuretic peptide (NT-proBNP) may refine ASCVD risk in low-to intermediate risk individuals eligible for HOPE-3, JUPITER and MEGA, and aid statin initiation in low- to intermediate risk populations.

Methods

5434 participants, aged 45 years and above from the prospective population-based Rotterdam Study, free of ASCVD, heart failure, and diabetes, were included between 1997 and 2008. Eligibility criteria for MEGA, JUPITER, and HOPE-3 trials were checked for each participant. ASCVD event rates, hazard ratios (HR), 5-year numbers needed to treat (NNT5y), and screen (NNS5y) per trial eligible population and NT-proBNP category (≤50, 50-100, and >100 pg/mL) were calculated.

Results

Median age was 61.6 years, 58.9% were women, median NT-proBNP was 60 pg/mL. The proportions of participants eligible for MEGA, JUPITER and HOPE-3 were 34.9%, 10.4% and 23.7%. Incidence rates per 1000 person-years for ASCVD were 10.4 (95%CI: 60.1-67.9) for MEGA, 16.8 (95%CI: 13.6-20.6) for JUPITER, and 12.1 (95%CI: 10.3-14) for HOPE-3. Adjusted HR in trial eligible individuals for NT-proBNP >100 pg/mL compared to ≤50 pg/mL level were 1.73 (95%CI: 1.21-2.47), 1.46 (95%CI: 0.80-2.66) and 1.50 (95%CI: 0.99-2.26), respectively. Estimated NNT5yamong trial eligible individuals with NT-proBNP levels >100 pg/mL based on high-intensity statin treatment, varied from 23 to 34 to prevent one ASCVD event, while NNS5yranged between 56 and 134.

Conclusions

NT-proBNP level >100 pg/mL identifies individuals at the highest ASCVD risk among low- to intermediate risk populations who are likely to benefit from statin treatment at acceptable NNT5yand NNS5y.

Clinical Perspective

What is New?

NT-proBNP level >100 pg/mL can identify individuals at the highest ASCVD risk among low- to intermediate risk populations who are likely to benefit from statin treatment at acceptable numbers needed to treat and screen.

Among apparently healthy individuals without prior ASCVD and diabetes mellitus, 60% was deemed to be at low- to intermediate risk by qualifying for at least one of three RCT based on the trial eligibility criteria, and one out four individuals had NT-proBNP level >100 pg/mL.

What are the Clinical Implications?

NT-proBNP level can be used for risk refining in low- to intermediate risk individuals who are most likely to benefit from statin initiation for ASCVD primary prevention.
Development of a Real-Time Risk Tracking Model for Neurological Deterioration in Ischemic Stroke Patients Based on Blood Pressure Dynamics
Authors: Kang Jihoon , Noh Maeng Seok , Lee Juneyoung , Lee Youngjo , Bae Hee-Joon
Published: April 2024

Objectives

Using the significant link between blood pressure fluctuations and neurological deterioration (ND) in patients with ischemic stroke, this study aims to develop a predictive model capable of real-time tracking of ND risk, enabling timely detection of high-risk periods.

Methods

A total of 3,906 consecutive ischemic stroke patients were recruited. As an initial predictive model, a polytomous logistic regression model, incorporating clinical parameters to estimate a probability of ND occurring within and beyond 12 hours post-stroke onset, was developed. To refine ND risk assessments over time, we subsequently introduced an iterative risk-tracking model that utilizes continuously updated blood pressure measurements. We endeavored to integrate these models, assessing their combined discriminative capacity and clinical utility, with a particular emphasis on pinpointing time periods of increased ND risk.

Results

ND rates were observed at 6.1% within the first 12 hours and 7.3% during the following 60 hours. We noted variations in incidence rates and their distribution over time across predefined patient groups. Significant predictors of ND varied among these subgroups and across different time periods. The iterative risk-tracking model maintained a consistent relationship between blood pressure variables and ND risk across different patient groups, successfully forecasting ND within a 12-hour window. The integrated models achieved an area under the receiver operating characteristic curve (AUC) ranging from 0.68 to 0.76. This performance effectively narrowed down the critical window for ND risk identification without sacrificing predictive accuracy across diverse patient groups. At 90% and 70% sensitivity settings, the combined model precisely identified the periods of highest ND risk, showing slightly higher or comparable specificity and positive predictive values relative to other models.

Conclusion

This study presents a novel approach for real-time monitoring of ND risk in ischemic stroke patients, utilizing BP trends to identify critical periods for potential intervention.
Gpr37 modulates the severity of inflammation-induced GI dysmotility by regulating enteric reactive gliosis
Authors: Robertson Keiramarie , Hahn Oliver , Robinson Beatriz G. , Faruk Arwa T. , Janakiraman Mathangi , Namkoong Hong , Kim Kwangkon , Ye Jiayu , Bishop Estelle Spear , Hall Randy A. , Wyss-Coray Tony , Becker Laren S. , Kaltschmidt Julia A.
Published: April 2024

The enteric nervous system (ENS) is contained within two layers of the gut wall and is made up of neurons, immune cells, and enteric glia cells (EGCs) that regulate gastrointestinal (GI) function. EGCs in both inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) change in response to inflammation, referred to as reactive gliosis. Whether EGCs restricted to a specific layer or region within the GI tract alone can influence intestinal immune response is unknown. Using bulk RNA-sequencing andin situhybridization, we identify G-protein coupled receptorGpr37, as a gene expressed only in EGCs of the myenteric plexus, one of the two layers of the ENS. We show that Gpr37 contributes to key components of LPS-induced reactive gliosis including activation of NF-kB and IFN-y signaling and response genes, lymphocyte recruitment, and inflammation-induced GI dysmotility. Targeting Gpr37 in EGCs presents a potential avenue for modifying inflammatory processes in the ENS.
Glutamylation imbalance leads to photoreceptor cell degeneration
Authors: Mercey Olivier , Gadadhar Sudarshan , Magiera Maria M. , Lebrun Laura , Kostic Corinne , Moulin Alexandre , Arsenijevic Yvan , Janke Carsten , Guichard Paul , Hamel Virginie
Published: April 2024

The stereotypic structure of microtubules, assembled from conserved α/β-tubulin dimers is subject to a complex diversity of Post-translational Modifications (PTMs). PTMs are predicted to fine-tune microtubule properties and interactions with other proteins, thus allowing microtubules to perform specific functions. Cilia accumulate several types of tubulin PTMs, such as polyglutamylation, polyglycylation, detyrosination and acetylation, whose functions are not yet fully understood. Recently, mutations ofAGBL5, coding for the deglutamylating enzyme CCP5, have been associated to retinitis pigmentosa, suggesting that perturbation of polyglutamylation leads to the degeneration of photoreceptor cells. However, the molecular mechanisms underlying this degeneration remain unknown. Here, using super-resolution Ultrastructure Expansion Microscopy in mouse and human photoreceptor cells, we found that most tubulin PTMs are accumulated at the level of the connecting cilium, a structure linking the outer and inner segments of photoreceptor cells. Using mouse models with increased glutamylation (Ccp5-/-andCcp1-/-), or loss of tubulin acetylation (Atat1-/-), we demonstrated that aberrant glutamylation, but not loss of acetylation, resulted in perturbed molecular architecture of the outer segment, with the loss of the bulge region and destabilization of the distal axoneme. Concurrently, we observed a substantial impairment in tubulin glycylation and intraflagellar transport. Altogether our results indicate that glutamylation plays a crucial role in the maintenance of the molecular architecture of the outer segment and point to tubulin PTM imbalance as possible culprit in retinal degeneration.
Integrative multi-omic analysis identifies genes associated with cuticular wax biogenesis in adult maize leaves
Authors: Lin Meng , Bacher Harel , Bourgault Richard , Qiao Pengfei , Matschi Susanne , Vasquez Miguel F. , Mohammadi Marc , van Boerdonk Sarah , Scanlon Michael J. , Smith Laurie G. , Molina Isabel , Gore Michael A.
Published: April 2024

Studying the genetic basis of leaf wax composition and its correlation with leaf cuticular conductance (gc) is crucial for improving crop water-use efficiency. The leaf cuticle, which comprises a cutin matrix and various waxes, functions as an extracellular hydrophobic layer, protecting against water loss upon stomatal closure. To address the limited understanding of genes associated with the natural variation of leaf cuticular waxes and their connection togc, we conducted statistical genetic analyses using leaf transcriptomic, metabolomic, and physiological data sets collected from a maize (Zea maysL.) panel of ∼300 inbred lines. Through a random forest analysis with 60 cuticular wax traits, it was shown that high molecular weight wax esters play an important role in predictinggc. Integrating results from genome-wide and transcriptome-wide studies (GWAS and TWAS) via a Fisher’s combined test revealed 231 candidate genes detected by all three association tests. Among these, 11 genes exhibit known or predicted roles in cuticle-related processes. Throughout the genome, multiple hotspots consisting of GWAS signals for several traits from one or more wax classes were discovered, identifying four additional plausible candidate genes and providing insights into the genetic basis of correlated wax traits. Establishing a partially shared genetic architecture, we identified 35 genes for bothgcand at least one wax trait, with four considered plausible candidates. Our study uncovered the genetic control of maize leaf waxes, establishing a link between wax composition andgc, with implications for potentially breeding more water-use efficient maize.

SIGNIFICANCE STATEMENT

We exploited natural variation in the abundance of maize leaf cuticular waxes to identify genetic determinants of wax composition and its relationship to cuticle function as a barrier against water loss. We identified a set of strongly supported candidate genes with plausible functions in cuticular wax biosynthesis or deposition and added to the evidence for wax esters as the most important wax for water barrier function, offering new tools for modification of cuticle-dependent traits.
Computational functions of precisely balanced neuronal assemblies in an olfactory memory network
Authors: Meissner-Bernard Claire , Jenkins Bethan , Rupprecht Peter , Bouldoires Estelle Arn , Zenke Friedemann , Friedrich Rainer W. , Frank Thomas
Published: April 2024

Structured connectivity in the brain organizes information by constraining neuronal dynamics. Theoretical models predict that memories are represented by balanced assemblies of excitatory and inhibitory neurons, but the existence and functions of such EI assemblies are difficult to explore. We addressed these issues in telencephalic area Dp of adult zebrafish, the homolog of piriform cortex, using computational modeling, population activity measurements, and optogenetic perturbations. Modeling revealed that precise balance of EI assemblies is important to prevent not only excessive firing rates (“runaway activity”) but also the stochastic occurrence of high pattern correlations (“runaway correlations”). Consistent with model-derived predictions, runaway correlations emerged in Dp when synaptic balance was perturbed by optogenetic manipulations of fast-spiking feedback interneurons. Moreover, runaway correlations were driven by sparse subsets of strongly active neurons, rather than by a general broadening of tuning curves. These results reveal novel computational functions of EI assemblies in an autoassociative olfactory memory network and support the hypothesis that EI assemblies organize information on continuous representational manifolds rather than discrete attractor landscapes.
RummaGEO: Automatic Mining of Human and Mouse Gene Sets from GEO
Authors: Marino Giacomo B. , Clarke Daniel J. B. , Deng Eden Z. , Ma’ayan Avi
Published: April 2024

The Gene Expression Omnibus (GEO) is a major open biomedical research repository for transcriptomics and other omics datasets. It currently contains millions of gene expression samples from tens of thousands of studies collected by many biomedical research laboratories from around the world. While users of the GEO repository can search the metadata describing studies for locating relevant datasets, there are currently no methods or resources that facilitate global search of GEO at the data level. To address this shortcoming, we developed RummaGEO, a webserver application that enables gene expression signature search of a large collection of human and mouse RNA-seq studies deposited into GEO. To develop the search engine, we performed offline automatic identification of sample conditions from the uniformly aligned GEO studies available from ARCHS4. We then computed differential expression signatures to extract gene sets from these studies. In total, RummaGEO currently contains 135,264 human and 158,062 mouse gene sets extracted from 23,395 GEO studies. Next, we analyzed the contents of the RummaGEO database to identify statistical patterns and perform various global analyses. The contents of the RummaGEO database are provided as a web-server search engine with signature search, PubMed search, and metadata search functionalities. Overall, RummaGEO provides an unprecedented resource for the biomedical research community enabling hypothesis generation for many future studies. The RummaGEO search engine is available from:https://rummageo.com/.
The chromatin conformation landscape of Alzheimer’s disease
Authors: Nativio R , Lan Y , Donahue G , Shcherbakova O , Barnett N , Titus KR , Chandrashekar H , Phillips-Cremins JE , Bonini NM , Berger SL
Published: April 2024

We have been investigating epigenetic alterations in the brain during human aging and Alzheimer’s disease (AD), and have evidence for histone acetylation both protecting the aging epigenome and driving AD. Here we extend our studies to chromatin architecture via looping studies, and with binding studies of key proteins required for looping: CTCF and RAD21. We detected changes in CTCF and RAD21 levels and localization, finding major changes in CTCF in AD compared to fewer changes in healthy aging. In our study of 3D genome conformation changes, we identified stable topological associating domains (TADs) in Old and AD; in contrast, in AD, there is loss of interaction at genomic sites/loops within TADs, likely reflecting the loss of CTCF. We identified genes and potential transcription factor binding at the loops that are lost in AD. in addition, we found enrichment of CTCF peak losses for AD eQTLs, suggesting that architectural dysfunction has a role in Alzheimer’s. Functional experiments lowering the homologues of several key genes in aDrosophilamodel of Aβ42 toxicity exacerbate neurodegeneration. Taken together, these data indicate both functional protections and losses occur in the Alzheimer’s brain genome compared to normal aging.
Scribbleknockdown induced metastasis tracking, identification of its associated novel molecular candidates through Proteome andin silicostudies
Authors: Singh Jyotsna , Srikrishna Saripella
Published: April 2024

Metastasis is the primary cause of cancer associated death globally. Loss of function ofScribble, a cell polarity regulator/tumor suppressor gene, is associated with many forms of human cancer but its role in cell proliferation and metastasis remains unknown. We generated metastatic cancer inDrosophilausing UAS-GAL4 system, through knockdown ofScribblein the wing imaginal discs and tracked metastasis events from 0hr early pupae to 84hrs late pupae using fluorescence microscope. Here, we report, for the first time, that knockdown ofScribblealone could lead to the development of primary tumor in the wing imaginal discs, which is capable of establishing metastasis, leading to secondary tumor formation, eventually resulting in absolute pupal lethality. Further, we checked a metastasis biomarker, MMP1 levels during pre-and post-metastatic phases inDrosophilapupae using qRT-PCR and Western blot analysis. In addition, we analyzed the proteome ofScribbleknockdown induced tumor-bearing pupae by 2-D gel electrophoresis followed by MALDI-TOF MS to identify novel proteins involved in the process of tumorigenesis and metastasis. We identified six differentially expressed proteins, Obp 99b, Fer2LCH,CG13492, Hsp23, Ubiquitin and Colt inScribknockdown pupae compared to wild-type and validated their expression at the transcriptional level using qRT-PCR.In-silicostudies show these novel protein interaction withScrib. Thus, our results suggested that loss ofScribalone causes metastasis, without the need for cooperative interaction with oncogenicRas.The newly identified Fer2LCH (ferritin) and colt proteins could be important candidates for therapeutic target againstScribassociated cell proliferation and metastasis.
Bioinformatics analysis and validation of differentially expressed miRNA in the sperm of partners of patients with unexplained recurrent miscarriages
Authors: Tian Hui , Zhao Xiao-Xi
Published: April 2024

Background

Recurrent miscarriage is a common multifactorial disease, and even after systematic examination, the cause of the miscarriages cannot be determined in approximately 50% of patients. However, currently, few examinations are conducted for partners of patients with recurrent miscarriages. The contribution of spermatozoa to new individuals is not limited to half of the diploid genome. Recent studies have shown that spermatozoa add several components to oocytes, including a complex RNA population that plays an important role in paternal chromatin packaging, sperm maturation and empowerment, fertilisation, early embryogenesis, and developmental maintenance. In view of this, we constructed a sperm miRNA expression profile of partners of patients with unexplained recurrent miscarriages and explored the relationship between unexplained recurrent miscarriages and differential miRNA expression in sperm.

Methods

Semen samples were obtained from the partners of patients with unexplained recurrent miscarriages treated at the affiliated hospital of Inner Mongolia Medical University, as well as healthy men who underwent physical examinations between July 2021 and February 2023. The miRNA expression profiles of the sperm in the two groups were detected using high-throughput sequencing. Bioinformatics analysis of differentially expressed miRNAs was performed to predict target genes and their action pathways and verify the expression levels of paternal miRNAs in known embryos in the study and control groups through RT-PCR technology.

Result

A total of 83 differentially expressed miRNAs were detected between the two groups, of which 39 were significantly upregulated and 44 were significantly downregulated. The results showed that spermatic hsa-miR-34c-5p, hsa-miR-1285-3p, hsa-miR-486-3p, and hsa-miR-146b-3p may regulate the occurrence of unexplained recurrence through the Ras, PI3K-Akt, and MAPK signalling pathways in the bioinformatics analysis. The expression of hsa-miR-34c-5 in spouses of patients with unexplained miscarriage recurrence was downregulated (p < 0.001). Binary logistic regression analysis showed that low expression of hsa-miR-34c-5p was a high-risk factor for recurrent miscarriage (odds ratio [OR] = 4.344; 95% confidence interval [CI], 1.119–16.857; p < 0.05).

Conclusion

The occurrence of unexplained recurrent miscarriages is associated with the differential expression of key miRNAs in the sperms of patients’ spouses.
Development of a recombineering system for the acetogenEubacterium limosumwith Cas9 counterselection for markerless genome engineering
Authors: Sanford Patrick A. , Woolston Benjamin M.
Published: April 2024

Eubacterium limosumis a Clostridial acetogen that efficiently utilizes a wide range of single-carbon substrates and contributes to metabolism of health-associated compounds in the human gut microbiota. These traits have led to interest in developing it as a platform for sustainable CO2-based biofuel production to combat carbon emissions, and for exploring the importance of the microbiota in human health. However, synthetic biology and metabolic engineering inE. limosumhave been hindered by the inability to rapidly make precise genomic modifications. Here, we screened a diverse library of recombinase proteins to develop a highly efficient oligonucleotide-based recombineering system based on the viral recombinase RecT. Following optimization, the system is capable of catalyzing ssDNA recombination at an efficiency of up to 2%. Addition of a Cas9 counterselection system allows recombination to reach an efficiency of up to 100%, enabling creation of genomic point mutations in a scarless and markerless manner. We deployed this system to create a clean knockout of the extracellular polymeric substance (EPS) gene cluster, generating a strain incapable of biofilm formation. This approach is rapid and simple, not requiring laborious homology arm cloning, and can readily be retargeted to almost any genomic locus. This work overcomes a major bottleneckEubacterium limosumgenetic engineering by enabling precise genomic modifications, and provides both a roadmap and associated recombinase plasmid library for developing similar systems in other Clostridia of interest.

Graphical Abstract
HIV-1 controllers possess a unique CD8+ T-cell activation phenotype and loss of control is associated with increased expression of exhaustion markers
Authors: Jones Amber D , Capriotti Zachary , Santos Erin , Lin Angel , Duyne Rachel Van , Smith Stephen , Klase Zachary
Published: April 2024

HIV-1 controllers are a rare population of individuals that exhibit spontaneous control of HIV-1 infection without antiretroviral therapy. These controllers can be categorized based on the level and mechanism of control. Understanding the mechanisms by which controllers maintain and eventually lose this ability would be highly valuable in HIV-1 cure or vaccine research. We explored whether CD8+ T cell exhaustion plays a role in the maintenance and loss of control by examining immune characteristics of HIV-1 controllers and controllers who lost control within the duration of the study. Previous work revealed the ability of CD8+ T-cells isolated from HIV-1 controllers to suppress HIV-1 replication in matched CD4+ T-cellsex vivo. Using flow cytometry, we analyzed exhaustion marker expression on CD8+ T-cells from these controllers and determined that they maintain a unique exhaustion profile as compared to HIV-negative individuals and standard progressors. The low level of T-cell exhaustion seen in controllers was reversed when these individuals lost control and showed increased viral loads. Immune checkpoint blockade targeting exhaustion markers was able to restoreex vivocontrol by CD8+ T-cells from former controllers. These results suggest that CD8+ T cell exhaustion compromises the ability to control viral replication in HIV-1 controllers.

AUTHOR SUMMARY

Despite the use of antiretroviral therapy, HIV continues to be a major public health issue that affects the lives of millions of people. Some infected people can control viral infection without therapy. The mechanism by which some people can control HIV infection at low, but detectable levels is unknown. In this study we examined the state of cytotoxic CD8+ T-cells in a group of HIV controllers and found that controllers maintain low levels of markers for a chronic state of activation called exhaustion. Loss of control correlated with increase in exhausted T-cells and for individuals who had recently lost control of infection we could restore protection in the cell culture dish by using immune checkpoint blockade drugs that affect exhaustion.
Impact of Prescribed Fire on Soil Microbial Communities in a Southern Appalachian Forest Clearcut
Authors: Rafie S.A.A , Blentlinger L. , Putt A. D. , Williams D. E. , Joyner D. C. , Campa M. F. , Schubert M. J. , Hoyt K. P. , Horn S. P. , Franklin J. A. , Hazen T. C.
Published: April 2024

Escalating wildfire frequency and severity, exacerbated by shifting climate patterns, pose significant ecological and economic challenges. Prescribed burns, a common forest management tool, aim to mitigate wildfire risks and protect biodiversity. Nevertheless, understanding the impact of prescribed burns on soil and microbial communities in temperate mixed forests, considering temporal dynamics and slash fuel types, remains crucial. Our study, conducted at the University of Tennessee Forest Resources AgResearch and Education Center in Oak Ridge, TN, employed controlled burns across various treatments, and the findings indicate that low-intensity prescribed burns have none or minimal short-term effects on soil parameters but may alter soil nutrient concentrations, as evidenced by significant changes in porewater acetate, formate, and nitrate concentrations. These burns also induce shifts in microbial community structure and diversity, with Proteobacteria and Acidobacteria increasing significantly post-fire, possibly aiding soil recovery. In contrast, Verrucomicrobia showed a notable decrease over time, and other specific microbial taxa correlated with soil pH, porewater nitrate, ammonium, and phosphate concentrations. Our research contributes to understanding the intricate relationships between prescribed fire, soil dynamics, and microbial responses in temperate mixed forests in the Southern Appalachian Region, which is valuable for informed land management practices in the face of evolving environmental challenges.
A Novel Magnetic Field Device: Effects of Magnetic Fields on Planktonic Yeasts and Fungal Mats
Authors: Bandara Akila , Li Enoki , Charlebois Daniel A.
Published: April 2024

Microorganisms evolved within the geomagnetic field and can be affected by magnetic field exposure. However, the mechanisms underlying many magnetic phenomena in microbes remain to be elucidated. We develop a 3D-printed magnetic field exposure device to perform experiments on microbes. This device is designed in AutoCAD, modeled in COMSOL, and validated using a Gaussmeter. Using the magnetic field exposure device, we perform static magnetic field experiments on different strains of the budding yeastSaccharomyces cerevisiae. We find that static magnetic field exposure slows the spatially-structured expansion of yeast mats that expands in two dimensions, but not yeast mats that expand in three dimensions, across the surface of semi-solid media. We also find that magnetic fields do not affect the growth of yeast cells in well-mixed liquid media. This study provides a novel device for magnetic field exposure experiments on microorganisms and advances our understanding of the effects of magnetic fields on fungi.

Why it matters

Microorganisms have evolved to function, survive, and reproduce in Earth’s magnetic field. However, the mechanisms underlying magnetic phenomena in microorganisms are unknown. This is especially true for fungi, which are important microorganisms for microbiological research, industrial application, and infectious disease. To elucidate mechanisms driving magnetic phenomena, we need devices to perform controlled experiments in a variety of conditions. We develop a 3D-printed magnetic field exposure device using computer-aided design, physics modeling software, and a magnetometer. Using this novel magnetic field device, we discover that magnetic fields can slow the growth of yeast on agar plates, but that magnetic fields do not affect the growth of yeast in liquid media.
Impact of Obesity on the CCR6-CCL20 Axis in Epidermal γδ T Cells and IL-17A Production in Murine Wound Healing and Psoriasis
Authors: Lawler William , Castellanos Tanya , Engel Emma , Alvizo Cristian R. , Kasler Antolette , Bshara-Corson Savannah , Jameson Julie M.
Published: April 2024

Obesity is associated with comorbidities including type 2 diabetes, chronic nonhealing wounds and psoriasis. Normally skin homeostasis and repair is regulated through the production of cytokines and growth factors derived from skin-resident cells including epidermal γδ T cells. However epidermal γδ T cells exhibit reduced proliferation and defective growth factor and cytokine production during obesity and type 2 diabetes. One of the genes modulated in epidermal γδ T cells during obesity and type 2 diabetes is CCR6, which is the receptor for CCL20. CCL20 is elevated in the skin during obesity and type 2 diabetes. Here we identify a subset of murine epidermal γδ T cells that expresses CCR6 in response to activationin vitroand post-wounding or psoriasis induction with imiquimodin vivo. We show that CCL20 stimulates epidermal γδ T cells to produce IL-17 suggesting CCR6 regulates the IL-17 axis as in dermal γδ T cells. Further, epidermal γδ T cells upregulate CCR6 and produce IL-17 during murine models of wound repair and psoriasis. Obesity increases CCR6 and IL-17 expression by epidermal γδ T cells during wound repair but has less of an effect during psoriasis. These findings have novel implications for the regulation of a specific population of IL-17-producing epidermal γδ T cells during skin damage and inflammation.
Coral long-term recovery after bleaching: implications for sexual reproduction and physiology
Authors: Padilla-Gamiño JL , Timmins-Schiffman E , Lenz EA , White SJ , Axworthy J , Potter A , Lopez J , Wang F
Published: April 2024

This study examined the long-term impacts of coral bleaching on the reproduction and physiology ofMontipora capitata, a dominant reef-building coral in Hawaiʻi. We monitored bleached and non-bleached colonies during and after a natural coral bleaching event in 2014 and analyzed reproductive traits and transcriptomic signatures eight months later. Our study shows that non-bleached and bleached colonies successfully produced gametes. Colonies that bleached had smaller oocytes, and development was slower than in colonies that did not bleach. Corals with different vulnerabilities to bleaching exhibited distinct transcriptomic responses eight months after a bleaching event. Those more prone to bleaching showed suppression of transcripts associated with sperm motility, calcification, and immunity. We found distinct transcriptomic signatures between fringing and patch reefs, suggesting local adaptation and/or acclimatization. To conserve coral reefs and better understand how they will be affected by future heat stress, we need to track which colonies survive and examine how their physiological and reproductive processes are impacted in the short- and long-term. This is critical as consecutive bleaching events become more frequent, and corals have less time to recover. Our study provides valuable molecular and reproductive data that can be used for conservation and management purposes. This information can help us identify signs of coral vulnerability and resilience to bleaching, project how future bleaching events will affect coral reproduction, determine which traits are most at risk, and assess which sites are more likely to be compromised.
Breaking Down the Bottlebrush: Atomically-Detailed Structural Dynamics of Mucins
Authors: Kearns Fiona L. , Rosenfeld Mia A. , Amaro Rommie E.
Published: April 2024

Mucins, the biomolecular components of mucus, are glycoproteins that form a thick physical barrier at all tissue-air interfaces, forming a first line of defense against pathogens. Structural features of mucins and their interactions with other biomolecules remain largely unexplored due to challenges associated with their high-resolution characterization. Combining limited mass spectrometry glycomics and protein sequencing data, we present all-atom, explicitly solvated molecular dynamics simulations of a major respiratory mucin, MUC5B. We detail key forces and degrees of freedom imposed by the extensive O-glycosylation, which imbue the canonically observed bottlebrush-like structures to these otherwise intrinsically disordered protein backbones. We compare our simulation results to static structures observed in recent scanning tunneling microscopy experiments, as well as other published experimental efforts. Our work presents a generalizable framework for investigating the dynamics and interactions of mucins, which can inform on structural details currently inaccessible to experimental techniques.
ScRNA-seq and scATAC-seq reveal that sertoli cell mediate spermatogenesis disorders through stage-specific communications in non-obstructive azoospermia
Authors: Wang Shimin , Wang Hongxian , Jin Bicheng , Yan Hongli , Zheng Qingliang , Zhao Dong
Published: April 2024

Non-obstructive azoospermia (NOA) belongs to male infertility due to spermatogenesis failure. However, evidence for cell type-specific abnormalities of spermatogenesis disorders in NOA remains lacking. We performed single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) on testicular tissues from patients with obstructive azoospermia(OA) and NOA. HE staining confirmed the structural abnormalities of the seminiferous tubules in NOA patients. We identified 12 germ cell subtypes (spermatogonial stem cell-0 (SSC0), SSC1, SSC2, diffing-spermatogonia (Diffing-SPG), diffed-spermatogonia (Diffed-SPG), pre-leptotene (Pre-Lep), leptotene-zygotene (L-Z), pachytene (Pa), diplotene (Di), spermatids-1 (SPT1), SPT2, and SPT3) and 8 Sertoli cell subtypes (SC1-SC8). Among them, three novel Sertoli cell subtypes phenotypes were identified, namely SC4/immature, SC7/mature, and SC8/further mature Sertoli cells. For each germ or Sertoli cell subtype, we identified unique new markers, among which immunofluorescence confirmed co-localization of ST3GAL4, A2M, ASB9, and TEX19 and DDX4 (classical marker of germ cell). PRAP1, BST2, and CCDC62 were co-expressed with SOX9 (classical marker of Sertoli cell) in testes tissues also confirmed by immunofluorescence. The interaction between germ cell subtypes and Sertoli cell subtypes exhibits stage-specific-matching pattern, as evidenced by SC1/2/5/7 involving in SSC0-2 development, SC3 participating in the whole process of spermiogenesis, SC4/6 participating in Diffing and Diffed-SPG development, and SC8 involving in the final stage of SPT3. This pattern of specific interactions between subtypes of germ cell and Sertoli cell was confirmed by immunofluorescence of novel markers in testes tissues. The interaction was mainly contributed by Notch1/2/3 signaling. Our study profiled the single-cell transcriptome of human spermatogenesis and provided many potentials molecular markers for developing testicular puncture specific marker kits for NOA patients.

Impact statement

The specific interactions between Sertoli cell subtypes and different stages of germ subgroups maintain normal development of germ cells. SC3 subtype absence may be the key factor leading to NOA.
Consensus Guideline for the Management of Peritoneal Metastases in Patients with Neuroendocrine Neoplasms
Authors: Turaga Kiran
Published: April 2024

Background

Neuroendocrine neoplasms (NEN) with peritoneal metastases (PM) represent a complex clinical challenge due to low incidence and heterogeneous phenotypes. This manuscript describes the results of a national consensus aimed at addressing clinical management of patients with NEN-PMs.

Methods

An update of the 2018 Chicago consensus guidelines was conducted using a modified Delphi technique, encompassing two rounds of voting. The levels of agreement for various pathway blocks were rigorously assessed. Key systemic therapy concepts were summarized by content experts. Supporting evidence was evaluated via a rapid literature review.

Results

Overall, the level of evidence for the management of PM in this disease was universally low. In total, 107 participants responded in the first round, with 88/107 (82%) participating in the second round. Strong consensus (> 90%) was achieved in 5/7 (71%) and 7/7 (100%) blocks in rounds I and II respectively. A multidisciplinary approach including psychosocial and wellness assessments received a strong positive recommendation. Management of NENs with PMs was organized according to disease grade and symptom profiles. In grade 1 and 2 well-differentiated NENs, cytoreductive surgery (CRS) received strong support (>95%) following the management of functional syndromes (if present). For grade 3 well-differentiated NENs, systemic therapy is the primary recommendation, with surgical resection considered in select cases. Poorly differentiated NENs (i.e. neuroendocrine carcinomas) are predominantly treated with chemotherapy.

Conclusion

Given limited evidence, the consensus-driven clinical pathway offers vital clinical guidance for the management on NENs with PM. The need for high-quality evidence remains critical to the field.
Consensus Guideline for the Management of Patients with Peritoneal Mesothelioma
Authors:   PSM Writing Group,   PSM Consortium Group, Turaga Kiran K
Published: April 2024

Background

Treatment of peritoneal mesothelioma (PeM) poses significant challenges owing to its rare incidence, heterogeneity and limited clinical evidence. This manuscript describes results from a national consensus aimed at addressing management of PeM.

Methods

An update of the 2018 Chicago Consensus Guidelines was conducted using a Modified Delphi technique, encompassing two rounds of voting. The levels of agreement for various pathway blocks were assessed.

Results

Of 101 participants responding in the first round of Modified Delphi voting, 95 (94%) responded in the second round. Over 90% consensus was achieved in 5/6 and 6/6 pathway blocks in rounds I and II, respectively. Observation was recommended for benign neoplasms, with guidance for interventions in the presence of symptoms or concerning clinicopathologic features. For malignant pathology, management was outlined based on a multidisciplinary assessment of patient characteristics, disease histology, and predictive success of medical and surgical interventions. Additional emphasis was placed on multimodal therapy for Intermediate-Risk and appropriate High-Risk patients. A rapid review demonstrated limited availability of data and inconclusive findings regarding optimal systemic therapy timing. There was unanimous support for considering clinical trial enrollment.

Conclusions

Given limited evidence, the consensus-driven pathway provides essential guidance regarding the management of PeM. To further direct clinical care, additional dedicated research to generate higher-quality evidence is needed.