bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic architecture of a light-temperature coincidence detector
Authors: Seluzicki Adam , Chory Joanne
Published: November 2024

Light and temperature variations are inescapable in nature. These signals provide daily and seasonal information, guiding life history determinations across many taxa. Here we show that signals from the PHOTOTROPIN2 (PHOT2) blue photoreceptor combine with low temperature information to control flowering. Plants lacking PHOT2 flower later than controls when grown in low ambient temperature. This phenotype is blocked by removal of NON-PHOTOTROPIC HYPOCOTYL 3 (NPH3) and recapitulated by reducing blue light intensity or removing the transcription factor CAMTA2. PHOT2 and CAMTA2 show non-additive genetic interactions in phenotype and gene expression. Network-based co-expression analysis indicates system-level control of key growth modules by PHOT2 and CAMTA2. CAMTA2 is required for low temperature up-regulation ofEHB1, a known NPH3-interacting protein, providing a mechanism of temperature information input to the PHOT-NPH3 blue light signaling system. Together these data describe the genetic architecture of environmental signal integration in this blue light-low temperature coincidence detection module.
Impact of sample size and tissue relevance on T2D gene identification
Authors: Davtian D , Dupuis T , Aly D Mansour , Atabaki-Pasdar N , Walker M , Franks P W , Rutters F , Im HK , Pearson E R , van de Bunt M , Viñuela A , Brown AA
Published: November 2024

Identification of genes and proteins mediating the activity of GWAS variants requires molecular data from disease relevant tissues, but these may be difficult to collect. Using multiple gene expression reference datasets and GWAS summary statistics for T2D we identified 1,818 unique genes associated with T2D. Comparing the performance of different reference datasets, we found that sample size, and not the relevance of the tissue to the disease, was the critical factor in identifying relevant genes. Genes implicated using a well powered expression dataset were also more likely to have multiple lines of genetic evidence. A targeted proteomics reference dataset from plasma samples showed similar power to identify T2D related proteins as gene expression with the same sample size. Accounting for BMI reduces power across all tissues and phenotypes by ∼30%, suggesting that many GWAS links to T2D are mediated by BMI, potentially implicating insulin resistance related effects. Finally, using data from smaller GWAS studies with precisely defined T2D subtypes uncovers genes directly relevant to that subtype, such asLST1, an immune response gene for Severe Autoimmune Diabetes andTRMT2A, involved in beta-cell apoptosis, for Severe Insulin Deficient Diabetes. Our work demonstrates the benefits of well powered reference datasets in accessible tissues and well-defined disease subtypes when studying complex diseases involving multiple tissues.
Community Health Worker Outreach to Assess Confounders of Health
Authors: Takallou Armin , Mitchell Emily , Richardson Gina M. , Frank Brian
Published: November 2024

Background and Objectives

In July 2020, recognizing the potential conflict between COVID-19 quarantine guidelines and other medical and social needs, a university-affiliated family medicine clinic developed a workflow to support patients who test positive for COVID-19. The workflow relies on Community Health Workers (CHWs) to call patients, identify needs, and connect them to community resources, with the goal of reducing barriers to maintaining COVID-19 isolation. The objective of this study was to understand the design, implementation, and maintenance of the workflow to provide guidance for other primary care practices interested in developing similar workflows.

Methods

This qualitative study was conducted in a federally qualified health center. Key informant interviews were conducted with six personnel involved in the workflow. Using a semi-structured interview guide, interviewers asked participants about the design, implementation, maintenance of the workflow, and benefits and harms. Interviews were analyzed using an immersion-crystallization approach.

Results

Across all workflow phases, adaptability and content expertise were reported as essential for workflow success. The main barrier was the lack of coordinated COVID-19-related workflows across the system. Delivery of whole-person care was identified as the primary benefit to both patients and the healthcare system.

Conclusions

Interview participants felt that integrating CHWs into the workflow benefitted patients and the clinic. For other practices interested in implementing a similar workflow, themes for success include a workflow framework built on patient-centeredness, adaptability, and the unique content expertise of CHWs.
Trend Analysis of Hepatitis B and C Virus Infections among Patients at Ambo General Hospital, West Shoa, Ethiopia: Retrospective Study
Authors: Getachew Mulugeta , Teferi Amanuel , Kebede Edosa
Published: November 2024

Background

Hepatitis B and C viruses affect the liver and can cause wider range of disease outcomes. Chronic HBV and/or HCV infection leaves a person susceptible to major liver diseases such liver cirrhosis or hepatic cell cancer later in life. They bear the greater portion of the mortality and morbidity associated with hepatocellular carcinomas and liver cirrhosis.

Methods

A retrospective laboratory record review was conducted at Ambo General Hospital from January 2018 to December 2021. The retrieved data included the date of examination, age, sex and laboratory results of the HBV and HCV. Data were summarized and presented in the form of tables, figures, and frequencies to present the results. The data were analyzed using SPSS and Microsoft Excel.

Results

Over the course of 4 years, a total of 5675 individuals were examined for hepatitis at Ambo general hospital. Of the total individuals examined, 365(6.4%) and 15(2.1%) were positive for HBV and HCV respectively. HBV and HCV mixed infections accounted for 0.6% of the cases. HBV was highest prevalent in males (12.1%) than females (5.72%), while among seropositive of HCV, 7(5.7%) were males and 4(1.0%) were females. HBV and HCV were more prevalent among individuals aged from 45–54 years old 11(11.6%) and 35–44 years old 4(5.6%) respectively. A high percentage of HBV (7.1%) and HCV (5.5%) were seen in the years of 2018 and 2020 respectively.

Conclusion

According to WHO criteria, the total prevalence of hepatitis B and C in our study is moderate, and the prevalence of HBV is significantly higher than that of HCV. Although, there are annual fluctuations in the prevalence. As a result, it is critical to improve coverage of services in healthcare facilities and raise community awareness regarding the means of transmission, prevention and control of hepatitis B and C virus infection.
Pulmonary barotrauma in COVID-19 patients: Experience from a tertiary university hospital
Authors: Chai Jian Hai , Masdar Azlina , Mohamad Yusof Aliza , Wan Mat Wan Rahiza
Published: November 2024

Introduction: Mechanical ventilation (MV) in COVID-19 patients is often complicated with pulmonary barotrauma. The aim of this study was to determine the incidence and risk factors associated with the development of pulmonary barotrauma in mechanically ventilated COVID-19 patients.Materials and methods:We included all mechanically ventilated COVID-19 patients who were aged 18 and above whom admitted to COVID ICU between January 2021 and June 2022. Patients who developed pulmonary barotrauma prior to or within 24 hours of ICU admission, iatrogenic pneumothorax, readmitted to ICU and ventilated for other causes than respiratory failure due to COVID-19 were excluded. The data for demographic, vaccination status, ventilator settings, laboratory data, steroid and immunomodulator therapies received were analysed. Univariate and multivariate analysis were carried out to determine the risk factors and outcome.Results:Medical records of 204 patients were included. The incidence of pulmonary barotrauma was 22.5%. Lower C-reactive protein (CRP) value on admission to ICU and FiO2prescription in the first week of MV, utilisation of higher PEEP in the second week of MV and longer ventilator days predisposed patients to pulmonary barotrauma (p = 0.039, p = 0.049, p = 0.021, p = 0.036 respectively). Pulmonary barotrauma increased the duration of ICU stay (p = 0.006) and all-cause ICU mortality (p = 0.009).Conclusion:Lower level of CRP and FiO2prescription, higher use of PEEP and longer ventilator days were the independent risk factors in our study population to develop pulmonary barotrauma which increased their duration of ICU stay and all-cause ICU mortality.
Diagnostic value of neutrophil gelatinase-associated lipocalin and neutrophil-to-lymphocyte ratio in type 2 diabetes mellitus individuals with reduced estimated glomerular filtration rate(eGFR): A case-control study in a municipal hospital in Ghana
Authors: Adofo Ayirebi Allwell , Boadu Wina Ivy Ofori , Sackey Benedict , Antwi-Boateng Lilian , Adoba Prince , Adu Patrick , Boachie Joseph , Twumasi Stephen , Frimpong Joseph , Ekow Korsah Emmanuel , Ansah Ezekial , Senu Ebenezer , Arele Ansah Eugene , Nii Martey Antonio Daniel , Marfowaa Afua , Opoku Antwi Isaac , Agyemang Sah John , Baba Domosie Joachim , Khalifah Abiba , Asamoah Evans Adu , Obirikorang Christian , Addai-Mensah Otchere , Anto Enoch Odame
Published: November 2024

Introduction

Serum neutrophil gelatinase-associated lipocalin (sNGAL), a renal tubular marker, and Neutrophil-to-Lymphocyte Ratio (NLR), a haematological inflammatory marker are two biomarkers that have recently received attention, because of their association with kidney disease. This study examined the diagnostic value sNGAL and NLR in type 2 diabetes mellitus (T2DM) patients with reduced eGFR.

Materials and methods

In this hospital-based case-control research, 97 T2DM participants and 70 healthy subjects were included. Participants’ information was documented using a structured questionnaire and patient case records. Venous blood was drawn from each participant to evaluate absolute neutrophil and lymphocyte count ratio, glycosylated haemoglobin (HBA1c), creatinine, sNGAL, and fasting blood glucose.

Results

sNGAL and NLR were higher in diabetes patients with reduced eGFR than those with normal eGFR and control (p < 0.05). sNGAL level was negative correlated with eGFR among both good (r= -0.317,p= 0.036) and poor (r= -0.544,p< 0.001) glycaemic-controlled T2DM subjects with reduced eGFR. A negative correlation was observed between NLR and eGFR among poor glycaemic-controlled T2DM subjects with reduced eGFR (r= -0.329,p= 0.016). At a cut off of 8.87 µg/L and 2.34 respectively, sNGAL and NLR were found to be good predictors of nephropathy among T2DM patients (AUC=100.0, p< 0.0001 and AUC=76.0, p< 0.0001 respectively) with sNGAL being the superior marker.

Conclusions

sNGAL and NLR have important diagnostic value for diabetic with reduced eGFR. Whiles sNGAL showed superiority and is recommended, NLR can serve as a less expensive and readily measurable alternative biomarker for diabetic patients with reduced eGFR, particularly in poorly controlled diabetes. These two markers can be added to the available array of tests used to indicate nephropathy in type 2 diabetics to help clinicians in better management of the disease.
Beyond Image Recognition: Applying Deep Learning to List-Type Medical Data for Risk Prediction
Authors: Kondo Gaku
Published: November 2024

Objective

The purpose of our research was to develop efficient utilization of Deep Learning to the list-type data in which medical characteristics are arranged.

Materials and Methods

We conducted a survey of blood donors, focusing on the rare adverse reaction of falling. In addition to all cases of fainting, we randomly selected a control group of donors who did not fall. This data was then converted into a two-dimensional format suitable for analysis with a convolutional neural network (CNN). We used an under sampling method to randomly divide the dataset into training and testing sets. Finally, we used the CNN and a logistic regression model to predict the probability of fainting, calculate anomaly scores, and rank the risk of falling.

Results

The convolutional neural network (CNN) identified 3 out of 10 falls among the group with the top 1% of anomaly scores. In contrast, the logistic regression model failed to identify any falls within the same top 1% anomaly score group.

Conclusion

Applying information converted into two-dimensional data to Deep Learning by using anomaly detection together was useful to narrow down with high-risk group. Although these findings require validation in a larger and more diverse population, the success of this approach in predicting falls after blood donation suggests its potential for predicting other rare adverse events in healthcare, such as adverse drug reactions, complications from medical procedures, or even disease outbreaks.
Engagement in antenatal and HIV care among pregnant women before and after Option B+ policy implementation in South Africa
Authors: Hwang Candice , Jinga Nelly , Dheda Mukesh , Mhlongo Otty , Phungula Pinky , Clouse Kate , Huffman Mark D. , Fox Matthew P. , Maskew Mhairi
Published: November 2024

Background

Substantial gains have been made in South Africa in the prevention of vertical transmission of HIV over the past decade.

Objectives

to determine whether engagement in antenatal and HIV care among pregnant Women Living with HIV (WLWH) differed after Option B+ implementation.

Methods

We analysed cohort data from a pregnancy and birth defects surveillance system in KwaZulu-Natal (KZN). We report on two co-primary outcomes related to engagement in HIV care: 1) timing and number of ANC visits during the pregnancy period; and 2) timing of ART initiation (both self-reported ART use in interviews and observed initiation of treatment in maternal records). The association of policy era on the timing of ANC presentation was assessed using log-binomial regression modelling. We also report proportions initiating ART before or during pregnancy stratified by policy era.

Results

Data from 40,357 women, including 16,016 (40%) WLWH were analysed. During the Option B+ era, 24% of pregnant WLWH attended their first antenatal care visit during the first trimester, compared to 16% during the Option B era (RR=1.52;95%CI=1.41-1.64). The proportion of women living with HIV who initiated ART prior to pregnancy was also higher during the Option B+ era compared to the Option B era, though this result was limited by missingness in the data.

Conclusions

Engagement in antenatal and HIV care improved after Option B+ implementation. In the Option B+ era, South Africa has made significant progress towards the goal of eliminating mother-to-child transmission of HIV.

What this study adds

There has been an increase in the proportion of pregnant WLWH initiating ART prior to pregnancy and presenting for antenatal care (ANC) during the first trimester.

The findings suggest improved timing and frequency of ANC visits during pregnancy, moving towards the UNAIDS 2025 targets.
Immune cell distributions in the blood of healthy individuals at high genetic risk of Parkinson’s disease
Authors: Deecke Laura , Goldeck David , Ohlei Olena , Homann Jan , Demuth Ilja , Bertram Lars , Pawelec Graham , Lill Christina M.
Published: November 2024

The immune system likely plays a key role in Parkinson’s disease (PD) pathophysiology. Thus, we investigated whether immune cell compositions are already altered in healthy individuals at high genetic risk for PD. We quantified 92 immune cell subtypes in the blood of 442 individuals using multicolor flow cytometry. Polygenic risk scores (PGS) for PD were calculated based on genome-wide significant SNPs (n = 87) from a large genome-wide association study (n = 1,530,403). Linear regression analyses did not reveal significant associations between PGS and any immune cell subtype (FDR = 0.05). Nominally significant associations were observed for NKG2C+ B cells (p = 0.026) in the overall sample. Older participants at increased genetic PD risk also showed a higher proportion of myeloid dendritic cells (p = 0.019) and CD27+CD4+ memory T cells (p = 0.043). Several immune cells were nominally statistically associated in women only. These findings suggest that major alterations of immune cells only occur later in the progression of PD.
A Canado-European external validation of the Kidney Transplant Failure Score
Authors: Chatton Arthur , Feugo Kevin Assob , Pilote Émilie , Cardinal Héloïse , Platt Robert W. , Schnitzer Mireille E.
Published: November 2024

In kidney transplantation, obtaining early information about the risk of graft failure helps physicians and patients anticipate a potential return to dialysis or retransplantation. Clinical prediction models are commonly used to obtain such risk estimation, but their performance needs to be continuously evaluated in various contexts. We propose an external validation study of theKidney Transplant Failure Scorein a pooled sample of 3,144 patients transplanted between 2010 and 2015 in France, Belgium, Norway and Canada. This score is used at the first transplantation anniversary to predict the probability of graft failure over the following seven years. The target population was defined as adult recipients of a kidney from a neurologically deceased donor without graft failure in the first year post-transplantation. Graft failure was defined as a return to dialysis. Around 10% of patients returned to dialysis, and 12.6% died during the seven-year follow-up. The KTFS authors fitted a Cox model and then adjusted its coefficients to maximize the discrimination, yielding the KTFS final version. We evaluated the performance of the initial and final versions of the KTFS, as well as the performance of another model we developed to consider death as a competing event. All KTFS versions yielded similarly good discrimination (area under the time-dependant receiver operating curve around from 0.79 [0.76-0.82] to 0.80 [0.77-0.84]), while the discrimination-optimized one presented important miscalibration. Clinical utility, assessed through net benefit, was also the lowest for the discrimination-optimized version. Our results warn against using the current KTFS version and recommend using either the initial coefficients or the competing risk-based ones instead.

Lay summary

French nephrologists have used the Kidney Transplant Failure Score (KTFS) for nearly fifteen years to predict kidney graft failure eight years after the transplantation. Because predictive performance decreases over time, we first verified that the score could still predict correctly in France and also in other countries. Then, we compared the different KTFS formulas to find that the one currently used is suboptimal and should be avoided. Our findings show that the KTFS is still a reliable source of information for both kidney recipients and nephrologists when using its first version.
Investigating the Role of Zinc in Mitigating Blood Lead Levels Toxicity on Gut Microbiome Diversity: NHANES 2007-2010
Authors: Ayres Kathyrn R , Liuzzi Juan P. , Lewis Freeman C. , Mobarki Huda M.
Published: November 2024

Introduction

Zinc is an essential micronutrient used in many biological functions including maintaining the gut microbial diversity. Many environmental factors, such as lead exposure, have been shown to disrupt diversity. The purpose of this study was to determine whether zinc serves as a protective factor against elevated blood lead levels (BLL) on gut microbiome diversity.

Methods

The 2007-2008 and 2009-2010 NHANES datasets were utilized to conduct a cross-sectional complex survey analysis aimed at determining whether zinc intake acts as a protective factor against changes in microbiome diversity associated with BLL, using enterolactone (ENL) as a biomarker. A multiple linear regression was conducted to evaluate whether an interaction between BLL and zinc intake could predict ENL. The model included BLL, zinc intake and their interaction, along with additional covariates such as gender, fiber intake and BMI.

Results

BMI, fiber intake, and gender were identified as covariates through diagnostic analysis and stepwise regression and were included in the final model. Sequential variable selection revealed that fiber intake was a confounding variable in the relationship between zinc and ENL levels (p = 0.543), while gender was identified as a confounding factor between BLL and ENL levels (p = 0.173). After controlling for fiber intake, zinc intake was not significantly associated with predicting microbiome diversity (p = 0.101). Additionally, no significant interaction between zinc and BLL was observed in predicting ENL levels (p = 0.079).

Conclusion

Zinc intake did not play a crucial role in mitigating the toxicity of BLL exposure on gut microbiome diversity. However, the model did reveal important confounding variables, such as gender and fiber intake, which should be considered when using ENL as a biomarker. The public health implications suggest that dietary interventions focusing on fiber intake and managing BMI could be key in maintaining a diverse microbiome.
COVID-19 disease and economic burden in adults in six Latin American Countries before nationwide vaccination program: Ministry of Health databases assessment and systematic literature review
Authors: Espinola Natalia , Loudet Cecilia I. , Luxardo Rosario , Moreno Carolina , Kyaw Moe H. , Spinardi Julia , Mendoza Carlos Fernando , Carballo Carolina M. , Dantas Ana Carolina , Abalos Maria Gabriela , Ballivian Jamile , Navarro Emiliano , Bardach Ariel
Published: November 2024

Introduction and objective

The COVID-19 pandemic had a significant disease burden on the healthcare system worldwide. There is limited reliable national data on COVID-19 associated morbidity, mortality, and healthcare costs in Latin America. This study explored the COVID-19 disease and economic burden in Argentina, Brazil, Chile, Colombia, Mexico, and Peru in the pre-vaccination period.

Methods

We analyzed national databases and conducted a systematic review of the published literature on COVID-19 in adults aged 18 years and above. We reported cases, death rates, years of life lost, and excess mortality associated with COVID-19 in pre-vaccination period. In addition, we used a cost of illness analysis to estimate the direct medical costs associated with COVID-19. All costs are reported in US dollars as of 2023.

Results

Before the national COVID vaccination program rollout, the average incidence rate of COVID-19 in adults aged 18 and above was 6,741 per 100,000 persons. Approximately 91% of the cases were mild, 7% were moderate/severe, and 2% were critical. Among 2,201,816 hospitalized cases, 27.8% were in intensive care, and 17.5% required mechanical ventilation. The country-specific data varied greatly across Latin American countries, with hospitalization admission: 469-18,096 per 100,000, excess mortality: 76-557 per 100,000, and years of life lost: 241,089-3,312,346. Direct medical costs ranged from US$258 million to US$10,437 million, representing approximately 2%-5% of national health expenditure.

Conclusion

COVID-19 imposed a substantial public health and economic burden on Latin American countries during the pre-vaccination period. The findings should help policymakers to make informed decisions and allocate resources effectively to improve national strategies around surveillance, preventive and treatment strategies to control the spread of COVID-19 disease in the future.
Influence of Factor V Leiden mutation and Protein C/S deficiencies on preeclampsia among Sudanese women
Authors: Abdon Faris , Elamin Maha , Bakheit Khalid Hussein
Published: November 2024

Background

Preeclampsia (PE) is a serious pregnancy complication that poses significant health risks to both mothers and babies. Genetic factors like thrombophilia mutations and deficiencies in natural anticoagulants might contribute to its development, but their exact roles are not well understood, especially among Sudanese women.

Objective

To assess the relationship between the Factor V Leiden (FVL) thrombophilic mutation and reduced levels of natural anticoagulants Protein C (PC) and Protein S (PS) with the occurrence of PE among Sudanese women.

Methods and materials

We conducted a case-control study that included a total of 300 women, divided equally into three groups: 100 with PE, 100 healthy pregnant women, and 100 healthy non-pregnant women. To detect FVL mutations, we used PCR-RFLP analysis. Levels of PC and PS were measured using colorimetric assays. We applied logistic regression analyses to assess the relationships between these variables and the risk of developing PE.

Results

Our findings showed no significant link between FVL mutations and PE (p=.390). PC levels on their own did not emerge as significant independent predictors of PE (OR 1.01, 95% CI 0.99–1.02, p=.419). However, women with low PC and S levels were strongly associated with PE in both univariate and multivariate analyses (OR 77.67, 95% CI 8.97– 672.5, p<.001). This combination was significantly more common in the PE group than in the control group (p<.001). Additionally, reduced PS levels were significantly associated with an increased risk of PE.

Conclusion

Combined PC/PS deficiencies are strongly associated with PE among Sudanese women, indicating a significant role of these natural anticoagulants in the disease’s pathogenesis. FVL mutation was not significantly linked with PE in this population.
Nanoscale Optical Imaging, Reconstruction, and Spatial Analysis of Whole Mouse Glomeruli
Authors: Ali Adilijiang , Liu Zixuan , Ye Kenan , Guan Yun , Chen Siying , Liu Tingxuan , Guo Ziyu , Wong Madeline K. , Vasquez Pedro , Poudel Chetan , Mustonen Benjamin C. , Eng Diana G. , Pippin Jeffrey W. , Shankland Stuart J. , Wang Sheng , Vaughan Joshua C.
Published: November 2024

Renal glomeruli have traditionally been studied by micrometer-scale optical microscopy to interrogate overall physiology or molecular distributions and by nanoscale electron microscopy to interrogate the ultrastructure of thin sections. While these approaches are powerful, they have been limited in their ability to obtain detailed views of the glomeruli as holistic 3D functional units. To fill this knowledge gap, we have developed a novel pipeline for imaging, reconstructing, and analyzing whole mouse glomeruli at 100 nm resolution using super-resolution fluorescence microscopy. This pipeline integrates both manual and machine learning approaches to annotate and analyze glomerular structures. Using this method, we created 18 detailed glomerulus models, from a range of healthy, aged, and model diseased mice, that outline all major structures and cell types. These models have been made publicly accessible in an online repository, providing a valuable resource for further studies. Our results also uncovered a diverse set of novel phenotypes including nuclear enlargement in all glomerular cell types in aging and disease, as well as an aging-related pattern of regional thickening of the Bowman’s capsule basement membrane near the tubular-glomerular junction.
Drivers of antibiotic resistance in two monsoon-impacted Indian urban rivers receiving untreated wastewater
Authors: Bagra Kenyum , Singh Harshita , Klümper Uli , Singh Gargi
Published: November 2024

Rivers in India receive 78.7% of untreated sewage from cities and towns making it a potential global “hotspot” for AMR. During monsoon, flooding is common in most Indian cities bringing in fecal contamination in storm runoff. Identifying the major driving factors contributing to the elevated levels of AMR in these rivers is essential to combat AMR proliferation. Determining whether the introduction of ARBs and ARGs through fecal pollution or subsequent (co-) selection for ARGs through chemical pollutants is responsible for the rise and spread of AMR is important in mitigation efforts. To achieve this, we targeted two rivers in northern India which received untreated wastewater and assessed the level of two fecal indicators (E. coliandintI1) and wastewater-associated ARGs (ermF,sul1,sul2, andtetW) along with heavy metals (Ag, Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, and Zn). Water and sediment samples were collected in triplicates at 5-6 locations for each river. Consequently, to evaluate how seasonality affects the ARG levels as well as their drivers in these heavily polluted rivers, sampling campaigns were carried out during three seasons: in summer (pre-monsoon), during monsoon, and post-monsoon in winter. We here demonstrate that the main source for the river resistome in the Bindal and Rispana is the constant inflow of untreated wastewater throughout the year and not the co-selection of ARGs due to the presence of heavy metals. This may be true for many Indian rivers that receive untreated or partially treated wastewater. The rainfall adds to the ARG abundance of the river instead of diluting it. MGEintI1 is more reliable thanE. colias an indicator for fecal pollution and horizontal gene transfer. Heavy metals, despite being present in the river in higher concentrations than the MCSC, no evidence for co-selection was observed.
Streamlining Asymmetry Quantification in Fetal Mouse Imaging: A Semi-Automated Pipeline Supported by Expert Guidance
Authors: Rolfe S.M. , Mao D. , Maga A. M.
Published: November 2024

Asymmetry is a key feature of numerous developmental disorders and in phenotypic screens is often used as a readout for environmental or genetic perturbations to normal development. A better understanding of the genetic basis of asymmetry and its relationship to disease susceptibility will help unravel the complex genetic and environmental factors and their interactions that increase risk in a range of developmental disorders. Large-scale imaging datasets offer opportunities to work with sample sizes needed to detect and quantify differences in morphology beyond severe deformities while also posing challenges to manual phenotyping protocols. In this work, we introduce a semi-automated open-source workflow to quantify abnormal asymmetry of craniofacial structures that integrates expert anatomical knowledge. We apply this workflow to explore the role of genes contributing to abnormal asymmetry by deep phenotyping 3D fetal microCT images from knockout strains acquired as part of the Knockout Mouse Phenotyping Program (KOMP2). Four knockout strains:Ccdc186,Acvr2a,Nhlh1, andFam20cwere identified with highly significant asymmetry in craniofacial regions, making them good candidates for further analysis into their potential roles in asymmetry and developmental disorders.

Summary Statement

We introduce an open-source, semi-automated pipeline to detect abnormally asymmetric phenotypes in 3D scans of fetal mice to explore the relationship between facial asymmetry, perturbed development, and developmental instability.
StreptococcusPhage Genomes Reveal Extensive Diversity, New Taxonomic Insights, and Novel Endolysin-Derived Antimicrobial Peptides
Authors: Karim Daniyal , Mondal Shakhinur Islam , Rolin Mohimenul Haque , Jewel Nurnabi Azad , Hoque Hammadul , Buttimer Colin , Rahman Md Mahfuzur , Azad Abul Kalam , Akter Arzuba
Published: November 2024

The global rise of antibiotic-resistant bacteria, particularly amongStreptococcusspecies, poses an escalating public health threat. Traditional antibiotic development has proven inadequate, making innovative approaches such as bacteriophage-based therapies promising alternatives. A deep understanding of phage biology at the genomic level is essential for advancing therapeutic applications. Here, we analyzed 709Streptococcusphage genomes to bridge gaps in genomic diversity and propose revisions toStreptococcusphage taxonomy. The phage genomes were clustered based on shared proteins, resulting in 66 clusters and 35 singletons with significant variation in genome characteristics. Through proteome phylogeny, average nucleotide identity, and inter-cluster core genes, we propose 21 new family-level classifications and 296 genus-level subclusters, providing an updated framework forStreptococcusphage taxonomy. Further analysis revealed diverse domain architectures inStreptococcusphage endolysins, including previously unreported structures. Specific domains were associated with distinct streptococcal hosts, suggesting adaptive evolution. We also observed variation in endolysin gene organization, with purifying selection acting on most sites, though some were subject to diversifying selection. Additionally, 182 novel endolysin-derived antimicrobial peptides (AMPs) were identified, some exhibiting antifungal, antiviral, cell-penetrating and non-toxic properties. Molecular dynamics and docking simulations demonstrated high stability and strong binding affinity of peptides EP-39 and EP-121 to theStreptococcus pneumoniaevirulence factor autolysin. This is the first comprehensive comparative study ofStreptococcusphage genomes, providing critical insights into phage diversity and taxonomy. It also highlights the therapeutic potential of endolysin-derived AMPs against multidrug-resistantStreptococcusstrains. Further experimental validation is required to assess their clinical potential.
TFAP2C is a key regulator of intrauterine trophoblast cell invasion and deep hemochorial placentation
Authors: Dominguez Esteban M. , Moreno-Irusta Ayelen , Scott Regan L. , Iqbal Khursheed , Soares Michael J.
Published: November 2024

Transcription factor AP-2 gamma (TFAP2C) has been identified as a key regulator of the trophoblast cell lineage and hemochorial placentation. The rat possesses deep placentation characterized by extensive intrauterine trophoblast cell invasion, which resembles human placentation.Tfap2c isexpressed in multiple trophoblast cell lineages, including invasive trophoblast cells situated within the uterine-placental interface of the rat placentation site. Global genome-editing was used to explore the biology ofTfap2cin rat placenta development. Homozygous global disruption ofTfap2cresulted in prenatal lethality. Heterozygous global disruption ofTfap2cwas associated with diminished invasive trophoblast cell infiltration into the uterus. The role of TFAP2C in the invasive trophoblast cell lineage was explored using Cre-lox conditional mutagenesis. Invasive trophoblast cell-specific disruption ofTfap2cresulted in inhibition of intrauterine trophoblast cell invasion and intrauterine and postnatal growth restriction. The invasive trophoblast cell lineage was not impaired following conditional monoallelic disruption ofTfap2c. In summary, TFAP2C contributes to the progression of distinct stages of placental development. TFAP2C is a driver of early events in trophoblast cell development and reappears later in gestation as an essential regulator of the invasive trophoblast cell lineage. A subset of TFAP2C actions on trophoblast cells are dependent on gene dosage.
Functional diversity in the output of the primate retina
Authors: Kling A. , Cooler S. , Manookin M.B. , Rhoades C. , Brackbill N. , Field G. , Rieke F. , Sher A. , Litke A. , Chichilnisky E.J.
Published: November 2024

The visual image transmitted by the retina to the brain has long been understood in terms of spatial filtering by the center-surround receptive fields of retinal ganglion cells (RGCs). Recently, this textbook view has been challenged by the stunning functional diversity and specificity observed in ∼40 distinct RGC types in the mouse retina. However, it is unclear whether the ∼20 morphologically and molecularly identified RGC types in primates exhibit similar functional diversity, or instead exhibit center-surround organization at different spatial scales. Here, we reveal striking and surprising functional diversity in macaque and human RGC types using large-scale multi-electrode recordings from isolated macaque and human retinas. In addition to the five well-known primate RGC types, 18-27 types were distinguished by their functional properties, likely revealing several previously unknown types. Surprisingly, many of these cell types exhibited striking non-classical receptive field structure, including irregular spatial and chromatic properties not previously reported in any species. Qualitatively similar results were observed in recordings from the human retina. The receptive fields of less-understood RGC types formed uniform mosaics covering visual space, confirming their classification, and the morphological counterparts of two types were established using single-cell recording. The striking receptive field diversity was paralleled by distinctive responses to natural movies and complexity of visual computation. These findings suggest that diverse RGC types, rather than merely filtering the scene at different spatial scales, instead play specialized roles in human vision.
Elongation of the nascent avian foregut requires coordination of intrinsic and extrinsic cell behaviors
Authors: Powell Olivia , Garcia Emily , Sriram Vanshika , Qu Yi , Nerurkar Nandan L.
Published: November 2024

The foregut tube gives rise to the lungs and upper gastrointestinal tract, enabling vital functions of respiration and digestion. How the foregut tube forms during embryonic development has historically received considerable attention, but over the past few decades this question has primarily been addressed indirectly through studies on morphogenesis of the primitive heart tube, a closely related process. As a result, many aspects of foregut development remain unresolved. Here, we exploit the accessibility of the chick embryo to study the initial formation of the foregut tube, combining embryology with fate mapping, live imaging, and biomechanical analyses. The present study reveals that the foregut forms and elongates over a narrower time window than previously thought, and displays marked dorso-ventral and left-right asymmetries early in its development. Through tissue-specific ablation of endoderm along the anterior intestinal portal, we confirm its central biomechanical role in driving foregut morphogenesis, despite not directly contributing cells to the elongating tube. We further confirm the important role of this cell population in formation of the heart tube, with evidence that this role extends to later stages of cardiac looping as well. Together, these data reveal the need for an intricate balance between intrinsic cell behaviors and extrinsic forces for normal foregut elongation, and set the stage for future studies aimed at understanding the underlying molecular cues that coordinate this balance.

GRAPHICAL ABSTRACT
Mitochondrial NADK2-dependent NADPH controls Tau oligomer uptake in human neurons
Authors: Pardo Evelyn , Kim Taylor , Wallrabe Horst , Zengeler Kristine E. , Sagar Vijay Kumar , Mingledorff Garnett , Sun Xuehan , Periasamy Ammasi , Lukens John R. , Bloom George S. , Norambuena Andrés
Published: November 2024

Alterations in NADH and NADPH metabolism are associated with aging, cancer, and Alzheimer’s Disease. Using 2P-FLIM imaging of the mitochondrial NAD(P)H in live human neurons and PS19 mouse brains, we show that tau oligomers (TauO) upregulate the mitochondrialde novoNADPH synthesis through NADK2. This process controls LRP1-mediated internalization of TauO, setting a vicious cycle for further TauO internalization. Thus, mitochondrial NADK2-dependent NADPH controls a key step in TauO toxicity.
A Structural Mechanism for Noncanonical GPCR Signal Transduction in the Hedgehog Pathway
Authors: Steiner William P. , Iverson Nathan , Venkatakrishnan Varun , Wu Jian , Stepniewski Tomasz Maciej , Michaelson Zachary , Bröckel Jan W. , Zhu Ju-Fen , Bruystens Jessica , Lee Annabel , Nelson Isaac , Bertinetti Daniela , Arveseth Corvin D. , Tan Gerald , Spaltenstein Paul , Xu Jiewei , Hüttenhain Ruth , Kay Michael , Herberg Friedrich W. , Selent Jana , Anand Ganesh S. , Dunbrack Roland L. , Taylor Susan S. , Myers Benjamin R.
Published: November 2024

The Hedgehog (Hh) signaling pathway is fundamental to embryogenesis, tissue homeostasis, and cancer. Hh signals are transduced via an unusual mechanism: upon agonist-induced phosphorylation, the noncanonical G protein-coupled receptor SMOOTHENED (SMO) binds the catalytic subunit of protein kinase A (PKA-C) and physically blocks its enzymatic activity. By combining computational structural approaches with biochemical and functional studies, we show that SMO mimics strategies prevalent in canonical GPCR and PKA signaling complexes, despite little sequence or secondary structural homology. An intrinsically disordered region of SMO binds the PKA-C active site, resembling the PKA regulatory subunit (PKA-R) / PKA-C holoenzyme, while the SMO transmembrane domain binds a conserved PKA-C interaction hub, similar to other GPCR-effector complexes. In contrast with prevailing GPCR signal transduction models, phosphorylation of SMO promotes intramolecular electrostatic interactions that stabilize key structural elements within the SMO cytoplasmic domain, thereby remodeling it into a PKA-inhibiting conformation. Our work provides a structural mechanism for a central step in the Hh cascade and defines a paradigm for disordered GPCR domains to transmit signals intracellularly.
Viral vector-mediatedSLC9A6gene replacement reduces cerebellar dysfunction in theshakerrat model of Christianson syndrome
Authors: Anderson Collin J , Figueroa Karla P , Paul Sharan , Gandelman Mandi , Dansithong Warunee , Katakowski Joseph A , Scoles Daniel R. , Pulst Stefan M
Published: November 2024

Background

Christianson syndrome (CS) is an x-linked recessive neurodevelopmental and neurodegenerative condition characterized by severe intellectual disability, cerebellar degeneration, ataxia, and epilepsy. Mutations to theSLC9A6gene encoding NHE6 are responsible for CS, and we recently demonstrated that a mutation to the ratSlc9a6gene causes a similar phenotype in the spontaneousshakerrat model, which exhibits cerebellar degeneration with motor dysfunction. In previous work, we used the PhP.eB-L7-Slc9a6-GFP adeno-associated viral (AAV) vector to demonstrate that gene replacement in Purkinje cells reduced theshakermotor and molecular phenotype.

Methods

We carried out a 20-week longitudinal study evaluating the impact of Purkinje cell-specific gene replacement on ataxia and tremor. Taking advantage of the high homology between humanSLC9A6and ratSlc9a6, we tested a more clinically relevant construct, AAV9-CAG-hSLC9A6 AAV vector in theshakerrat. In both experimental cohorts, we performed molecular studies to evaluate expression of NHE6 and key cerebellar markers. We then characterized the relationship between molecular markers and motor function, as well between tremor and ataxia.

Results

Administration of either of PhP.eB-L7-Slc9a6-GFP or AAV9-CAG-hSLC9A6 AAV vectors led to significant improvement in the molecular and motor phenotypes. The abundance of each disease-relevant cerebellar proteins was significantly correlated to motor ataxia. Further, we found that the relationship between cerebellar ataxia and tremor devolved over time, with disease modifying therapy disrupting their temporal relationship.

Conclusions

These findings impact futureSLC9A6-targeted gene therapy efforts for CS and strongly support gene replacement as a viable therapeutic strategy. Furthermore, tremor and ataxia phenotypes may arise from dissociable cerebellar mechanisms.

Graphical Abstract
Analysis of sparse animal social networks
Authors: Mylne Helen K , Abell Jackie , Beale Colin M , Brent Lauren JN , Bro-Jørgensen Jakob , Evans Kate E , DA Hart Jordan , Sakala Dabwiso , Simpamba Twakundine , Youldon David , Franks Daniel W
Published: November 2024

Low-density social networks can be common in animal societies, even among species generally considered to be highly social. Social network analysis is commonly used to analyse animal societal structure, but edge weight (strength of association between two individuals) estimation methods designed for dense networks can produce biased measures when applied to low-density networks. Frequentist methods suffer when data availability is low, because they contain an inherent flat prior that will accept any possible edge weight value, and contain no uncertainty in their output. Bayesian methods can accept alternative priors, so can provide more reliable edge weights that include a measure of uncertainty, but they can only reduce bias when sensible prior values are selected. Currently, neither accounts for zero-inflation, so they produce edge weight estimates biased towards stronger associations than the true social network, which can be seen through diagnostic plots of data quality against output estimate. We address this by adding zero-inflation to the model, and demonstrate the process using group-based data from a population of male African savannah elephants. We show that the Bayesian approach performs better than the frequentist to reduce the bias caused by these problems, though the Bayesian requires careful consideration of the priors. We recommend the use of a Bayesian framework, but with a conditional prior that allows the modelling of zero-inflation. This reflects the fact that edge weight derivation is a two-step process: i) probability of ever interacting, and ii) frequency of interaction for those who do. Additional conditional priors could be added where the biology requires it, for example in a society with strong community structure, such as female elephants in which kin structure would create additional levels of social clustering. Although this approach was inspired by reducing bias observed in sparse networks, it could have value for networks of all densities.
A chaotrope-based approach for rapidin vitroassembly and loading of bacterial microcompartment shells
Authors: Range Kyleigh L. , Chiang Timothy K. , Pramanik Arinita , Landa Joel F. , Snyder Samuel N. , Zuo Xiaobing , Tiede David M. , Utschig Lisa M. , Hegg Eric L. , Sutter Markus , Kerfeld Cheryl A. , Ralston Corie Y.
Published: November 2024

Bacterial microcompartments (BMCs) are proteinaceous organelles that self-assemble into selectively permeable shells that encapsulate enzymatic cargo. BMCs enhance catalytic pathways by reducing crosstalk among metabolites, preventing harmful intermediates from leaking into the cytosol, and increasing reaction efficiency via enzyme colocalization. The intrinsic properties of BMCs make them attractive for biotechnological engineering. However,in vivoexpression methods for shell synthesis have significant drawbacks that limit the potential design space for these nanocompartments. Here we describe the development of a new, efficient, and rapid method forin vitroassembly of BMC shells from their protein building blocks. Our method enables large-scale construction of BMC shells by utilizing urea as a chaotropic agent to control self-assembly, and provides an approach for encapsulation of both biotic and abiotic cargo under a broad range of reaction conditions. We demonstrate an enhanced level of control over the assembly of BMC shellsin vitroand expand the design parameter space for engineering BMC systems with specialized and enhanced catalytic properties.