bluuebunny/crossref_metadata_2025 huggingface dataset:
High-throughput functional mapping of variants in an arrhythmia gene,KCNE1, reveals novel biology
Authors: Muhammad Ayesha , Calandranis Maria E. , Li Bian , Yang Tao , Blackwell Daniel J. , Harvey M. Lorena , Smith Jeremy E. , Chew Ashli E. , Capra John A. , Matreyek Kenneth A. , Fowler Douglas M. , Roden Dan M. , Glazer Andrew M.
Published: April 2023

Background

KCNE1encodes a 129-residue cardiac potassium channel (IKs) subunit. KCNE1 variants are associated with long QT syndrome and atrial fibrillation. However, most variants have insufficient evidence of clinical consequences and thus limited clinical utility.

Results

Here, we demonstrate the power of variant effect mapping, which couples saturation mutagenesis with high-throughput sequencing, to ascertain the function of thousands of protein coding KCNE1 variants. We comprehensively assayed KCNE1 variant cell surface expression (2,554/2,709 possible single amino acid variants) and function (2,539 variants). We identified 470 loss-of-surface expression and 588 loss-of-function variants. Out of the 588 loss-of-function variants, only 155 had low cell surface expression. The latter half of the protein is dispensable for protein trafficking but essential for channel function. 22 of the 30 KCNE1 residues (73%) highly intolerant of variation were in predicted close contact with binding partners KCNQ1 or calmodulin. Our data were highly concordant with gold standard electrophysiological data (ρ = −0.65), population and patient cohorts (32/38 concordant variants), and computational metrics (ρ = −0.55). Our data provide moderate-strength evidence for the ACMG/AMP functional criteria for benign and pathogenic variants.

Conclusions

Comprehensive variant effect maps ofKCNE1can both provide insight into IKschannel biology and help reclassify variants of uncertain significance.
Genome-scale metabolic models consistently predictin vitrocharacteristics ofCorynebacterium striatum
Authors: Bäuerle Famke , Gusak Gwendolyn O. , Camus Laura , Heilbronner Simon , Dräger Andreas
Published: April 2023

Genome-scale metabolic models (GEMs) are organism specific knowledge bases which can be used to unravel pathogenicity or improve production of specific metabolites in biotechnology applications. The present work combinesin silicoandin vitroapproaches to create and curate strain-specific genome-scale metabolic models ofCorynebacterium striatum. Approaches towards modeling rarely studied organisms are scarce. We introduce a cost-effective and easy experimental protocol which can be adapted to other organisms as well. Furthermore, the comparability of growth kinetics andin silicogrowth rates is discussed. This work introduces five newly created strain-specific genome-scale metabolic models (GEMs) of high quality, satisfying all contemporary standards and requirements. All these models have been benchmarked using the community standard test suite Metabolic Model Testing (MEMOTE) and experimentally validated by laboratory experiments conducted specifically for this purpose. For the curation of those models, the software infrastructurerefineGEMswas developed to work on these models in parallel and to comply with the quality standards for GEMs. The model predictions were confirmed by experimental data and a new comparison metric based on the doubling time was developed to quantify bacterial growth. Future modeling projects can rely on the proposed software, which is independent of specific environmental conditions. The validation approach based on the growth rate calculation is now accessible and closely aligned with biological questions. The curated models are freely available via BioModels and a GitHub repository and can be used. The open-source software refineGEMs is available fromhttps://github.com/draeger-lab/refinegems.
A Novel Risk Assessment Model Predicts Major Bleeding Risk at Admission in Medical Inpatients
Authors: Mittman Benjamin G , Sheehan Megan , Kojima Lisa , Cassachia Nicholas , Lisheba Oleg , Hu Bo , Pappas Matthew , Rothberg Michael B.
Published: May 2023

Background

Venous thromboembolism (VTE) is the leading cause of preventable hospital death in the US. Guidelines from the American College of Chest Physicians and American Society for Hematology recommend providing pharmacological VTE prophylaxis to acutely or critically ill medical patients at acceptable bleeding risk, but there is currently only one validated risk assessment model (RAM) for estimating bleeding risk. We developed a RAM using risk factors at admission and compared it with the International Medical Prevention Registry on Venous Thromboembolism (IMPROVE) model.

Methods

A total of 46,314 medical patients admitted to a Cleveland Clinic Health System hospital from 2017-2020 were included. Data were split into training (70%) and validation (30%) sets with equivalent bleeding event rates in each set. Potential risk factors for major bleeding were identified from the IMPROVE model and literature review. Penalized logistic regression using LASSO was performed on the training set to select and regularize important risk factors for the final model. The validation set was used to assess model calibration and discrimination and compare performance with IMPROVE. Bleeding events and risk factors were confirmed through chart review.

Results

The incidence of major in-hospital bleeding was 0.58%. Active peptic ulcer (OR = 5.90), prior bleeding (OR = 4.24), and history of sepsis (OR = 3.29) were the strongest independent risk factors. Other risk factors included age, male sex, decreased platelet count, increased INR, increased PTT, decreased GFR, ICU admission, CVC or PICC placement, active cancer, coagulopathy, and in-hospital antiplatelet drug, steroid, or SSRI use. In the validation set, the Cleveland Clinic Bleeding Model (CCBM) had better discrimination than IMPROVE (0.86 vs. 0.72, p < .001) and, at equivalent sensitivity (54%), categorized fewer patients as high-risk (6.8% vs. 12.1%, p < .001).

Conclusions

From a large population of medical inpatients, we developed and validated a RAM to accurately predict bleeding risk at admission. The CCBM may be used in conjunction with VTE risk calculators to decide between mechanical and pharmacological prophylaxis for at-risk patients.
1,25-dihydroxyvitamin D3 potentiates the innate immune response of peripheral blood mononuclear cells from Japanese Black cattle
Authors: Oyamada Youki , Iizasa Ei’ichi , Usa Amane , Otomaru Konosuke
Published: April 2023

1,25-dihydroxyvitamin D3(1,25(OH)2D3), a bioactive Vitamin D, is known to regulate immune responses in mammals. However, its impact on the innate immune responses of Japanese Black cattle, which are beef cattle endemic to Japan, remains unknown. Thus, in this study, we investigated the effect of 1,25(OH)2D3on the immune responses of PBMC from Japanese Black cattle. PBMC were cultured with or without 1,25(OH)2D3for measurement of cell viability, and stimulated with or without 1,25(OH)2D3and lipopolysaccharide (LPS) for measurement of the gene expressions. As the results, the treatment of 1,25(OH)2D3increased the cell viability. It also upregulated antibacterial peptides,DEFB10andLAPwith or without LPS stimulation. Moreover, 1,25(OH)2D3enhanced the inflammatory responses,CXCL8with LPS stimulation andNOS2with or without LPS stimulation, while reducing the expression of anti-inflammatory cytokineIL10 with or without LPS stimulation, leading to an inflammatory phenotype. However, in contrast to humans and mice, 1,25(OH)2D3did not alter the expression ofTNFand downregulatedTREM1with LPS treatment. These results suggest that 1,25(OH)2D3potentiates the innate immune responses of Japanese Black cattle, albeit with different effects and mechanisms as compared to humans and mice.
Building alternative splicing and evolution-aware sequence-structure maps for protein repeats
Authors: Szatkownik Antoine , Zea Diego Javier , Richard Hugues , Laine Elodie
Published: April 2023

Alternative splicing of repeats in proteins provides a mechanism for rewiring and fine-tuning protein interaction networks. In this work, we developed a robust and versatile method, ASPRING, to identify alternatively spliced protein repeats from gene annotations. ASPRING leverages evolutionary meaningful alternative splicing-aware hierarchical graphs to provide maps between protein repeats sequences and 3D structures. We re-think the definition of repeats by explicitly accounting for transcript diversity across several genes/species. Using a stringent sequence-based similarity criterion, we detected over 5,000 evolutionary conserved repeats by screening virtually all human protein-coding genes and their orthologs across a dozen species. Through a joint analysis of their sequences and structures, we extracted specificity-determining sequence signatures and assessed their implication in experimentally resolved and modelled protein interactions. Our findings demonstrate the widespread alternative usage of protein repeats in modulating protein interactions and open avenues for targeting repeat-mediated interactions.

Highlights

Robust detection of alternatively used repeated protein regions in evolution

The approach relies on sequence similarity and identifies conserved signatures

Mapping of the repeats onto protein isoform 3D models predicted by AlphaFold

5 000 repeats detected over the human coding fraction, about one third disordered

Assessment of the structural coverage of their interactions with protein partners
Only Zn2+and Fe2+out of 12 cations can fold ALS-linked nascent hSOD1
Authors: Lim Liangzhong , Kang Jian , Song Jianxing
Published: April 2023

153-residue copper-zinc superoxide dismutase 1 (hSOD1) is the first gene whose mutation was linked to FALS, while wild-type hSOD1 aggregation is associated with SALS. So far >180 ALS-causing mutations have been identified within hSOD1, but the underlying mechanism still remains enigmatic. Mature hSOD1 is extremely stable constrained by a disulfide bridge to adopt a Greek-key β-barrel fold that houses copper and zinc cofactors. Conversely, nascent hSOD1 is unfolded and prone to aggregation, requiring Zn2+to initiate folding to a coexistence of folded and unfolded states. Recent studies demonstrate mutations disrupting Zn2+-binding correlate with their capacity to form toxic aggregates. Therefore, to decode the role of cations in hSOD1 folding provide not only mechanistic insights, but also therapeutic prospects for hSOD1-linked ALS. Here by NMR, we visualized the effect of 12 cations, encompassing 8 essential for humans (Na+, K+, Ca2+, Zn2+, Mg2+, Mn2+,Cu2+,Fe2+), 3 mimicking zinc (Ni2+, Cd2+, Co2+), and environmentally abundant Al3+. Surprisingly, most cations, including Zn2+-mimics, exhibited negligible binding or induction for folding of nascent hSOD1. Cu2+displayed extensive binding to the unfolded state but induced severe aggregation. Unexpectedly, here for the first time Fe2+was deciphered to have Zn2+-like folding-inducing ability. Surprisingly, Zn2+failed to induce folding of H80S/D83S-hSOD1, while Fe2+could. By contrast, Zn2+could trigger folding of G93A-hSOD1, but Fe2+failed. Notably, pre-existing Fe2+disrupted the Zn2+-induced folding of G93A-hSOD1. Comparing with ATP-induced folded state, our results delineate that hSOD1 maturation requires: 1) intrinsic folding capacity encoded by the sequence; 2) specific Zn2+-coordination; 3) disulfide formation and Cu-load catalyzed by hCCS. This study decodes a previously-unknown interplay of cations in controlling the initial folding of hSOD1, thus not only underscoring the critical role of Zn2+in hSOD1-associated ALS, but also suggesting novel hSOD1-dependent mechanisms for Cu2+/Fe2+-induced cytotoxicity likely relevant to other diseases and aging.
Detection of Ghost Introgression from Phylogenomic Data Requires a Full-Likelihood Approach
Authors: Pang Xiao-Xu , Zhang Da-Yong
Published: April 2023

Abstract

In recent years, the study of hybridization and introgression has made significant progress, with ghost introgression - the transfer of genetic material from extinct or unsampled lineages to extant species - emerging as a key area for research. Accurately identifying ghost introgression, however, presents a challenge. To address this issue, we focused on simple cases involving three species with a known phylogenetic tree. Using mathematical analyses and simulations, we evaluated the performance of popular phylogenetic methods, including HyDe and PhyloNet/MPL, and the full-likelihood method, Bayesian Phylogenetics and Phylogeography (BPP), in detecting ghost introgression. Our findings suggest that heuristic approaches relying on site patterns or gene tree topologies struggle to differentiate ghost introgression from introgression between sampled non-sister species, frequently leading to incorrect identification of donor and recipient species. The full-likelihood method BPP using multilocus sequence alignments, by contrast, is capable of detecting ghost introgression in phylogenomic datasets. We analyzed a real-world phylogenomic dataset of 14 species ofJaltomata(Solanaceae) to showcase the potential of full-likelihood methods for accurate inference of introgression.
The phospholipid biosynthesis enzyme PlsB contains three distinct domains for membrane association, lysophosphatidic acid synthesis and dimerization
Authors: Li Yumei , Li Anjie , Liu Zhenfeng
Published: April 2023

Biosynthesis of phospholipids is fundamental for membrane biogenesis in all living organisms. As a member of the Glycerol-3-phosphate (G3P) Acyltransferase (GPAT) family, PlsB is a crucial enzyme catalyzing the first step of phospholipid synthesis by converting G3P and fatty acyl-coenzyme A (CoA)/acyl-carrier protein (ACP) into lysophosphatidic acid and free CoA (CoASH)/ACP. In bacterial cells, PlsB participates in the formation of persister cells related to multidrug tolerance, and is hence considered as a potential target for anti-persister therapy. By using the single-particle cryo-electron microscopy (cryo-EM) method, we have solved the structure of full-length PlsB fromThemomonas haemolytica(ThPlsB) at 2.79 Å resolution. TheThPlsB protein forms a homodimer withC2 symmetry and each monomer contains three distinct domains, namely the amino-terminal domain (NTD), the middle catalytic domain (MCD) and the carboxy-terminal domain (CTD). For the first time, we have unraveled the binding sites of a fatty acyl-CoA and a 1,2-dioleoyl-sn-glycero-3-phosphate (DOPA) molecule in the MCD of PlsB. The interactions betweenThPlsB and the membrane involve two surface-exposed amphipathic regions located in the NTD and MCD respectively. The results of structural and biochemical analyses suggest a membrane surface association-catalysis coupling model for the PlsB-mediated biosynthesis of lysophosphatidic acid occurring at the membrane-cytosol interface.
The relationship between hyperglycaemia on admission and patient outcome is modified by hyperlactatemia and diabetic status: a retrospective analysis of the eICU collaborative research database
Authors: Fitzgerald Oisin , Perez-Concha Oscar , Gallego-Luxan Blanca , Rudd Lachlan , Jorm Louisa
Published: May 2023

Both blood glucose and lactate are well-known predictors of organ dysfunction and mortality in critically ill patients. Previous research has shown that concurrent adjustment for glucose and lactate modifies the relationship between these variables and patient outcomes, including blunting of the association between blood glucose and patient outcome. We aim to investigate the relationship between ICU admission blood glucose and hospital mortality while accounting for lactate and diabetic status. Across 43,250 ICU admissions, weighted to account for missing data, we assessed the predictive ability of several logistic regression and generalised additive models that included blood glucose, blood lactate and diabetic status. We found that inclusion of blood glucose marginally improved predictive performance in all patients: AUC-ROC 0.665 vs 0.659, with a greater degree of improvement seen in non- diabetics: AUC-ROC 0.675 vs 0.663. Inspection of the estimated risk profiles revealed the standard U-shaped risk profile for blood glucose was only present in non-diabetic patients after controlling for blood lactate levels. Future research should aim to utilise observational data to estimate whether interventions such as insulin further modify this effect, with the goal of informing future RCTs of interventions targeting glycaemic control in the ICU.
No Laughing White Matter: Cortical Cholinergic Pathways and Cognitive Decline in Parkinson’s Disease
Authors: Crockett Rachel A. , Wilkins Kevin B. , Aditham Sudeep , Brontë-Stewart Helen M.
Published: May 2023

Background

Approximately one third of recently diagnosed Parkinson’s disease (PD) patients experience cognitive decline. The nucleus basalis of Meynert (NBM) degenerates early in PD and is crucial for cognitive function. The two main NBM white matter pathways include a lateral and medial trajectory. However, research is needed to determine which pathway, if any, are associated with PD-related cognitive decline.

Methods

Thirty-seven PD patients with no mild cognitive impairment (MCI) were included in this study. Participants either developed MCI at 1-year follow up (PD MCI-Converters; n=16) or did not (PD no-MCI; n=21). Mean diffusivity (MD) of the medial and lateral NBM tracts were extracted using probabilistic tractography. Between-group differences in MD for each tract was compared using ANCOVA, controlling for age, sex, and disease duration. Control comparisons of the internal capsule MD were also performed. Associations between baseline MD and cognitive outcomes (working memory, psychomotor speed, delayed recall, and visuospatial function) were assessed using linear mixed models.

Results

PD MCI-Converters had significantly greater MD of both NBM tracts compared to PD no-MCI (p<.001). No difference was found in the control region (p=.06). Trends were identified between: 1) lateral tract MD, poorer visuospatial performance (p=.05) and working memory decline (p=.04); and 2) medial tract MD and reduced psychomotor speed (p=.03).

Conclusions

Reduced integrity of the NBM tracts is evident in PD patients up to one year prior to the development of MCI. Thus, deterioration of the NBM tracts in PD may be an early marker of those at risk of cognitive decline.
Disturbed laterality of non-rapid eye movement sleep oscillations in post-stroke human sleep: a pilot study
Authors: Simpson Benjamin K. , Rangwani Rohit , Abbasi Aamir , Chung Jeffrey M. , Reed Chrystal M. , Gulati Tanuj
Published: May 2023

Sleep is known to promote recovery post-stroke. However, there is a paucity of data profiling sleep oscillations post-stroke in the human brain. Recent rodent work showed that resurgence of physiologic spindles coupled to sleep slow oscillations(SOs) and concomitant decrease in pathological delta(δ) waves is associated with sustained motor performance gains during stroke recovery. The goal of this study was to evaluate bilaterality of non-rapid eye movement (NREM) sleep-oscillations (namely SOs,δ-waves, spindles and their nesting) in post-stroke patients versus healthy control subjects. We analyzed NREM-marked electroencephalography (EEG) data in hospitalized stroke-patients (n=5) and healthy subjects (n=3) from an open-sourced dataset. We used a laterality index to evaluate symmetry of NREM oscillations across hemispheres. We found that stroke subjects had pronounced asymmetry in the oscillations, with a predominance of SOs,δ-waves, spindles and nested spindles in one hemisphere, when compared to the healthy subjects. Recent preclinical work classified SO-nested spindles as restorative post-stroke andδ-wave-nested spindles as pathological. We found that the ratio of SO-nested spindles laterality index toδ-wave-nested spindles laterality index was lower in stroke subjects. Using linear mixed models (which included random effects of concurrent pharmacologic drugs), we found large and medium effect size forδ-wave nested spindle and SO-nested spindle, respectively. Our results indicate considering laterality index of NREM oscillations might be a useful metric for assessing recovery post-stroke and that factoring in pharmacologic drugs may be important when targeting sleep modulation for neurorehabilitation post-stroke.
Predicting Virus Fitness: Towards a structure-based computational model
Authors: Thakur Shivani , Kepp Kasper Planeta , Mehra Rukmankesh
Published: May 2023

Predicting the impact of new emerging virus mutations is of major interest in surveillance and for understanding the evolutionary forces of the pathogen. The SARS-CoV-2 surface spike-protein (S-protein) binds to human ACE2 receptors as a critical step in host cell infection. At the same time, S-protein binding to human antibodies neutralizes the virus and prevents interaction with ACE2. Here we combine these two binding properties in a simple virus fitness model, using structure-based computation of all possible mutation effects averaged over 10 ACE2 complexes and 10 antibody complexes of the S-protein (∼3,80,000 computed mutations), and validated the approach against diverse experimental binding/escape data of ACE2 and antibodies. The ACE2-antibody selectivity change caused by mutation (i.e., the differential change in binding to ACE2 vs. immunity-inducing antibodies) is proposed to be a key metric of fitness model, enabling systematic error cancelation when evaluated. In this model, new mutations become fixated if they increase the selective binding to ACE2 relative to circulating antibodies, assuming that both are present in the host in a competitive binding situation. We use this model to categorize viral mutations that may best reach ACE2 before being captured by antibodies. Our model may aid the understanding of variant-specific vaccines and molecular mechanisms of viral evolution in the context of a human host.
Identifying core MRI sequences for reliable automatic brain metastasis segmentation
Authors: Buchner Josef A , Peeken Jan C , Etzel Lucas , Ezhov Ivan , Mayinger Michael , Christ Sebastian M , Brunner Thomas B , Wittig Andrea , Menze Björn , Zimmer Claus , Meyer Bernhard , Guckenberger Matthias , Andratschke Nicolaus , El Shafie Rami A , Debus Jürgen , Rogers Susanne , Riesterer Oliver , Schulze Katrin , Feldmann Horst J , Blanck Oliver , Zamboglou Constantinos , Ferentinos Konstantinos , Bilger Angelika , Grosu Anca L , Wolff Robert , Kirschke Jan S , Eitz Kerstin A , Combs Stephanie E , Bernhardt Denise , Rückert Daniel , Piraud Marie , Wiestler Benedikt , Kofler Florian
Published: May 2023

Background

Many automatic approaches to brain tumor segmentation employ multiple magnetic resonance imaging (MRI) sequences. The goal of this project was to compare different combinations of input sequences to determine which MRI sequences are needed for effective automated brain metastasis (BM) segmentation.

Methods

We analyzed preoperative imaging (T1-weighted sequence ± contrast-enhancement (T1/T1-CE), T2-weighted sequence (T2), and T2 fluid-attenuated inversion recovery (T2-FLAIR) sequence) from 339 patients with BMs from six centers. A baseline 3D U-Net with all four sequences and six U-Nets with plausible sequence combinations (T1-CE, T1, T2-FLAIR, T1-CE+T2-FLAIR, T1-CE+T1+T2-FLAIR, T1-CE+T1) were trained on 239 patients from two centers and subsequently tested on an external cohort of 100 patients from five centers.

Results

The model based on T1-CE alone achieved the best segmentation performance for BM segmentation with a median Dice similarity coefficient (DSC) of 0.96. Models trained without T1-CE performed worse (T1-only: DSC = 0.70 and T2-FLAIR-only: DSC = 0.73). For edema segmentation, models that included both T1-CE and T2-FLAIR performed best (DSC = 0.93), while the remaining four models without simultaneous inclusion of these both sequences reached a median DSC of 0.81-0.89.

Conclusions

A T1-CE-only protocol suffices for the segmentation of BMs. The combination of T1-CE and T2-FLAIR is important for edema segmentation. Missing either T1-CE or T2-FLAIR decreases performance. These findings may improve imaging routines by omitting unnecessary sequences, thus allowing for faster procedures in daily clinical practice while enabling optimal neural network-based target definitions.
Single-cell dissection of the immune response after acute myocardial infarction
Authors: van Blokland Irene V. , Oelen Roy , Groot Hilde E. , Benjamins Jan Walter , Pekayvaz Kami , Losert Corinna , Knottenberg Viktoria , Heinig Matthias , Nicolai Leo , Stark Konstantin , van der Harst Pim , Franke Lude H. , van der Wijst Monique G. P.
Published: May 2023

The role of the immune system during and in response to acute myocardial infarction (MI) is poorly characterized but is an important driver of recurrent cardiovascular events. Anti-inflammatory drugs have shown promising effects on lowering this recurrency risk, but broadly impair the immune system and may induce severe side effects. To overcome these challenges a more detailed understanding of the immune response to myocardial infarction is needed.

For this, we compared peripheral blood mononuclear cell (PBMC) single-cell RNA-sequencing expression and plasma protein profiles over time (hospital admission, 24h and 6-8 weeks after STEMI) in 38 patients and in comparison to 38 controls (95,995 diseased and 33,878 control PBMCs). Compared to controls, we observed a relative increase in classical monocytes and a decrease in CD56dimnatural killer cells in STEMI patients at admission, and these differences persisted until 24h after STEMI. The monocytes also showed the largest gene expression changes in each of the conditions, which was associated with changes in toll-like receptor, IFN and IL-1 signaling activity. Finally, a targeted protein cardiovascular biomarker panel revealed 33/92 plasma proteins to be changed after STEMI. Interestingly, three of these proteins were found to be affected by coronary artery disease-associated genetic risk variation, disease status and time after STEMI. Indicating the importance of taking all these aspects into consideration when defining potential future therapies.

Altogether, our analyses have revealed the immunological pathways that are disturbed upon MI, and in which cell type and during which stage of the disease this occurs. Additionally, we also provide insights in which patients are expected to benefit most from anti-inflammatory treatments, by identifying the genetic variants and disease stage at which these variants affect the outcome of these (drug-targeted) pathways. These findings advance our knowledge of the immune response after MI and provide further guidance for future therapeutic studies.
Disruptions of Hierarchical Cortical Organisation in Early Psychosis and Schizophrenia
Authors: Holmes Alexander , Levi Priscila T. , Chen Yu-Chi , Chopra Sidhant , Aquino Kevin M. , Pang James C. , Fornito Alex
Published: May 2023

Background

The cerebral cortex is organised hierarchically along an axis that spans unimodal sensorimotor to transmodal association areas. This hierarchy is often characterised using low-dimensional embeddings, termed gradients, of inter-regional functional coupling estimates measured with resting-state functional magnetic resonance imaging (fMRI). Such analyses may offer insights into the pathophysiology of schizophrenia, which is frequently linked to dysfunctional interactions between association and sensorimotor areas.

Methods

To examine disruptions of hierarchical cortical function across distinct stages of psychosis, we applied diffusion map embedding to two independent fMRI datasets: one comprised 114 patients with early psychosis and 48 controls, and the other comprising 50 patients with established schizophrenia and 121 controls. We then analysed the primary sensory-fugal and secondary visual-to-sensorimotor gradients of each participant in both datasets.

Results

There were no significant differences in regional gradient scores between patients with early psychosis and controls. Patients with established schizophrenia showed significant differences in the secondary, but not primary, gradient relative to controls. Gradient differences in schizophrenia were characterised by lower within-network dispersion in the Dorsal Attention (pFDR<.001), Visual (pFDR=.003), Frontoparietal (pFDR=.018), and Limbic (pFDR=.020) networks and lower between-network dispersion between the Visual network and other networks (pFDR<.001).

Conclusions

These findings indicate that differences in cortical hierarchical function occur along the secondary visual-to-sensorimotor axis rather than the primary sensory-fugal axis, as previously thought. The absence of differences in early psychosis suggests that visual-sensorimotor abnormalities may emerge as the illness progresses.
Becoming a resilient scientist series: An intervention program
Authors: Han H. Anna , Klenke Ulrike , McNulty Laurie Chaikind , Scheiner Annie , Milgram Sharon L.
Published: May 2023

Compared to the general population, science trainees experience challenges and heightened stressors that often lead to adverse mental health outcomes. With COVID-19, the stressors of social distancing, isolation, truncated lab time, and uncertainty about the future have all likely exacerbated these issues. Now, more than ever, practical and effective interventions are vitally needed to address the core causes of stress among science trainees and increase their resilience. This paper introduces a new resilience program targeted to biomedical trainees and scientists – Becoming a Resilient Scientist Series (BRS), a multi-part workshop complemented by facilitated group discussions all aimed at bolstering resilience, particularly in the context of academic and research environments. To assess the program’s efficacy, participants completed resilience measures and related assessments before and after completing the series. The results demonstrate that BRS significantly enhances trainee resilience (primary outcome) and reduces perceived stress, anxiety, and work-related presenteeism, as well as increased adaptability, self-awareness, and self-efficacy (secondary outcomes). Furthermore, program participants reported a high level of satisfaction, a strong willingness to recommend the program to others, and perceived positive changes in their resilience skills. To the best of our knowledge, this is the first resilience program designed explicitly for biomedical trainees and scientists, tailored to their unique professional culture and work environment.
Did knowledge, attitudes, and practices matter during the second wave of COVID-19 pandemic in Bangladesh? Results from a web-based cross-sectional study
Authors: Khan Md. Robin , Hossain Md. Jamal , Islam Md. Ariful , Zaman Shadid Uz , Islam Mohammad Touhidul , Haque Md. Anamul , Islam Md. Rabiul , Ripa Farhana Alam , Islam Md. Monirul , Ahmmed Foyez
Published: May 2023

Globally, health promotion measures have been undertaken in preventing the emergence and spread of coronavirus disease 2019 (COVID-19). However, whether these measures influence public awareness and behaviors is unclear and evidence is limited in particular in low-and-middle income country. We conducted an online survey among internet users in Bangladesh to understand the status and attributes of their knowledge, attitudes and practices towards COVID-19 during second wave of the pandemic when COVID educational information was more accessible to the public. Survey data were analyzed using descriptive statistics, Chi-square tests, and multivariate logistic regression analysis. Of 964 respondents, 40.2%, 51.5%, and 64.3% had good knowledge, confident attitudes, and proper practices towards COVID-19, respectively. The multivariate regression analysis found that the knowledge and practice scores were associated (p<0.05) with gender, age, and occupation. Females had better knowledge and practices compared to males (p<0.05). There were major gaps in awareness, attitudes, and practices among internet users in particular males and elders that needs to be addressed to control the further spread of COVID-19 infections before at least COVID-19 vaccine become accessible at population level in Bangladesh.
GATA3 ZnF2-defective mutant condensation underlies type I IFN-activating in breast cancer
Authors: Chen Yatao , Wan Yajie , Pei Xiaoying , Wang Tan , Ma Zhifang , Chen Liming
Published: May 2023

Zinc finger (ZnF) transcription factors (TFs) consist of ZnF-containing DNA-binding domains (DBDs) and intrinsically disordered region (IDR)-containing activation domains (ADs). Recent studies have suggested that liquid-liquid phase separation (LLPS) is the fundamental mechanism underlying human health and disease, with ZnF TFs activating gene expression through the LLPS capacity of their IDR-containing ADs. However, little is known about how the well-folded DBD of ZnF TFs is involved in their LLPS mechanism. GATA3 is one of the most frequently mutated genes in breast cancer, and its encoded protein GATA3, which contains two ZnFs (ZnF1 and ZnF2) in its DBD, is a master regulator of immunity. Here, we show that GATA3 undergoes LLPS in cells and in vitro, and its DBD plays an important regulatory role. Mechanistically, ZnF2 in the DBD contains two arginine amino acids (R329 and R330) that provide critical charges to regulate GATA3 LLPS and DNA binding by generating multivalent electrostatic interactions. Functionally, we demonstrated that ZnF2-regulated GATA3 LLPS is the mechanism underlying the multifaceted function of GATA3 in breast cancer development and immune regulation, where aberrant GATA3 LLPS caused by artificial or breast cancer-associated ZnF2-defective mutations by reducing Suv39H1 protein stability showed significantly reduced potential in promoting breast cancer development and exhibited remarkably enhanced capacities for activating type I interferon signaling. Since ZnF is a common feature in the DBDs of ZnF TFs, by describing GATA3 as a proof-of-principle, our data suggest that ZnF-regulated LLPS may be a general mechanism underlying the multifaceted function of ZnF TFs in human health and disease.
Single cell transcriptomics of the human parasiteSchistosoma mansonifirst intra-molluscan stage reveals tentative tegumental and stem cell regulators
Authors: Soria Carmen L. Diaz , Attenborough Teresa , Lu Zhigang , Graham Jennie , Hall Christopher , Thompson Sam , Andrews Toby G. R. , Rawlinson Kate A. , Berriman Matthew , Rinaldi Gabriel
Published: May 2023

Background

Schistosomiasis is a major Neglected Tropical Disease, caused by the infection with blood flukes in the genusSchistosoma. To complete the life cycle, the parasite undergoes asexual and sexual reproduction within an intermediate snail host and a definitive mammalian host, respectively. The intra-molluscan phase provides a critical amplification step that ensures a successful transmission. However, the cellular and molecular mechanisms underlying the development of the intra-molluscan stages remain poorly understood.

Methods

S. mansonimother sporocysts were dissociated into single cell suspensions, and live cells enriched and sequenced using the single cell 10X Genomics Chromium platform. We defined somatic and stem/germinal cell clusters, identified cell type-enriched Gene Ontology (GO) terms, and predicted transcription factor binding sites for key marker genes.

Results

Six cell clusters comprising stem/germinal, two tegument, muscle, neuron, and parenchyma were identified and validated by Fluorescencein situHybridisation (FISH). GO term analysis predicted key biological processes for each of the clusters. Using the Self-Assembling Manifold (SAM) algorithm, three sub-clusters were identified within the stem/germinal cell population. Furthermore, transcription factor binding sites and putative transcription factors were predicted for stem/germinal and tegument clusters.

Conclusions

We report a spatially validated single cell transcriptomic analysis of the first intra-molluscan stage ofS. mansoni.Key cell regulators were identified, paving the way for future analyses to unveil their role during the parasite development and interaction with its intermediate host.
Molecular Mechanisms Underlying Medium-Chain Free Fatty Acid-regulated Activity of the Phospholipase PlaF fromPseudomonas aeruginosa
Authors: Gentile Rocco , Modric Matea , Thiele Björn , Jaeger Karl-Erich , Kovacic Filip , Schott-Verdugo Stephan , Gohlke Holger
Published: May 2023

PlaF is a membrane-bound phospholipase A1fromP. aeruginosathat is involved in remodeling membrane glycerophospholipids (GPLs) and modulation of virulence-associated signaling and metabolic pathways. Previously, we identified the role of medium-chain free fatty acids (FFA) in inhibiting PlaF activity and promoting homodimerization, yet the underlying molecular mechanism remained elusive. Here, we used unbiased and biased molecular dynamics simulations and free energy computations to assess how PlaF interacts with FFAs localized in the water milieu surrounding the bilayer or within the bilayer, and how these interactions regulate PlaF activity. Medium-chain FFAs localized in the upper bilayer leaflet can stabilize inactive dimeric PlaF, likely through interactions with charged surface residues as experimentally validated. Potential of mean force (PMF) computations indicate that membrane-bound FFAs may facilitate the activation of monomeric PlaF by lowering the activation barrier of changing into a tilted, active configuration. We estimated that the coupled equilibria of PlaF monomerization-dimerization and tilting at the physiological concentration of PlaF lead to the majority of PlaF forming inactive dimers when in a cell membrane loaded with decanoic acid (C10). This is in agreement with a suggestedin vivoproduct feedback loop and GC-MS profiling results indicating that PlaF catalyzes the release of C10 fromP. aeruginosamembranes. Additionally, we found that C10 in the water milieu can access the catalytic site of active monomeric PlaF, contributing to the competitive component of C10-mediated PlaF inhibition. Our study provides mechanistic insights into how medium-chain FFA may regulate the activity of PlaF, a potential bacterial drug target.
Specification of distinct cell types in a sensory-adhesive organ for metamorphosis in theCionalarva
Authors: Johnson Christopher J. , Razy-Krajka Florian , Zeng Fan , Piekarz Katarzyna M. , Biliya Shweta , Rothbächer Ute , Stolfi Alberto
Published: May 2023

The papillae of tunicate larvae contribute sensory, adhesive, and metamorphosis-regulating functions that are crucial for the biphasic lifestyle of these marine, non-vertebrate chordates. We have identified additional molecular markers for at least five distinct cell types in the papillae of the model tunicateCiona,allowing us to further study the development of these organs. Using tissue-specific CRISPR/Cas9-mediated mutagenesis and other molecular perturbations, we reveal the roles of key transcription factors and signaling pathways that are important for patterning the papilla territory into a highly organized array of different cell types and shapes. We further test the contributions of different transcription factors and cell types to the production of the adhesive glue that allows for larval attachment during settlement, and to the processes of tail retraction and body rotation during metamorphosis. With this study, we continue working towards connecting gene regulation to cellular functions that control the developmental transition between the motile larva and sessile adult ofCiona.
Enzyme stability-activity trade-off : new insights from protein stability weaknesses and evolutionary conservation
Authors: Hou Qingzhen , Rooman Marianne , Pucci Fabrizio
Published: May 2023

A general limitation of the use of enzymes in biotechnological processes under sometimes non-physiological conditions is the complex interplay between two key quantities, enzyme activity and stability, where the increase of one is often associated with the decrease of the other. A precise stability-activity trade-off is necessary for the enzymes to be fully functional, but its weight in different protein regions and its dependence on environmental conditions is not yet elucidated. To advance this issue, we used the formalism that we have recently developed to effectively identify stability strength and weakness regions in protein structures, and applied it to a large set of globular enzymes with known experimental structure and catalytic sites. Our analysis showed a striking oscillatory pattern of free energy compensation centered on the catalytic region. Indeed, catalytic residues are usually non-optimal with respect to stability, but residues in the first shell around the catalytic site are, on the average, stability strengths and thus compensate for this lack of stability; residues in the second shell are weaker again, and so on. This trend is consistent across all enzyme families. It is accompanied by a similar, but less pronounced, pattern of residue conservation across evolution. In addition, we analyzed cold- and heat-adapted enzymes separately and highlighted different patterns of stability strengths and weaknesses, which provide insight into the longstanding problem of catalytic rate enhancement in cold environments. The successful comparison of our stability and conservation results with experimental fitness data, obtained by deep mutagenesis scanning, led us to propose criteria for improving catalytic activity while maintaining enzyme stability, a key goal in enzyme design.
Structural Insights into the Iron Nitrogenase Complex
Authors: Schmidt Frederik V. , Schulz Luca , Zarzycki Jan , Oehlmann Niels N. , Prinz Simone , Erb Tobias J. , Rebelein Johannes G.
Published: May 2023

Nitrogenases are best known for catalysing the reduction of dinitrogen to ammonia at a complex metallic cofactor. Recently, nitrogenases were shown to reduce carbon dioxide (CO2) and carbon monoxide to hydrocarbons, offering a pathway to recycle carbon waste into hydrocarbon products. Among the nitrogenase family the iron nitrogenase is the isozyme with the highest wildtype activity for the reduction of CO2, but the molecular architecture facilitating these activities remained unknown. Here, we report a 2.35-Å cryogenic electron microscopy structure of the Fe nitrogenase complex fromRhodobacter capsulatus,revealing an [Fe8S9C-(R)-homocitrate]-cluster in the active site. The enzyme complex suggests that the AnfG-subunit is involved in cluster stabilisation, substrate channelling and confers specificity between nitrogenase reductase and catalytic components. Moreover, the structure highlights a different interface between the two catalytic halves of the iron and the molybdenum nitrogenase, potentially influencing the intra-subunit ‘communication’ and thus the nitrogenase mechanism.
Development of tools to detect and identify strains belonging to thePseudomonas syringaespecies complex responsible for vein clearing of zucchini
Authors: Lacault Caroline , Briand Martial , Jacques Marie-Agnès , Darrasse Armelle
Published: May 2023

Vein clearing of zucchini (VCZ) is a seed-borne bacterial disease that affects young plants ofCucurbita peposubsp.pepo. VCZ agents are distributed into four phylogenetic clusters within the clades 2a and 2ba of the phylogroup 2 ofPseudomonas syringaespecies complex. Strains belonging to clades 2b and 2d are sometimes isolated from zucchini seeds but have not been associated with VCZ epidemics. Development of tools able to identify VCZ agents is important to better control the disease. Primers were designed to implement a seven-gene MLSA scheme on a collection of strains isolated from zucchini seeds. A clear predominance of strains with a host range on cucurbits limited to the genusCucurbita(cluster 2ba-A) and the presence of VCZ strains in a fifth cluster (2ba-C) were evidenced. PCR tests were designed to characterize VCZ clusters and a multiplex qPCR test was proposed to distinguish strains having narrow cucurbit host range, associated to the presence ofavrRpt2andsylC,from broad host range strains associated to the presence ofhopZ5andsylC. Additional qPCR tests targeting clade 2b and 2d were also designed to gain insights onP. syringaestrains that could be isolated from cucurbits. Specificity of these tools was evaluatedin silicoon the whole NCBI database andin vitroon a strain collection, showing a 100% inclusivity, except for the test dedicated to clade-2b strains, and an exclusivity ranging from to 96.7% to 100%. These different tools are intended to serve phylogenetic studies, epidemiological monitoring and seed testing.
Collection of Biospecimens from the Inspiration4 Mission Establishes the Standards for the Space Omics and Medical Atlas (SOMA)
Authors: Overbey Eliah G. , Ryon Krista , Kim JangKeun , Tierney Braden , Klotz Remi , Ortiz Veronica , Mullane Sean , Schmidt Julian C. , MacKay Matthew , Damle Namita , Najjar Deena , Matei Irina , Patras Laura , Medina J. Sebastian Garcia , Kleinman Ashley , Hirschberg Jeremy Wain , Proszynski Jacqueline , Narayanan S. Anand , Schmidt Caleb M. , Afshin Evan E. , Innes Lucinda , Saldarriaga Mateo Mejia , Schmidt Michael A. , Granstein Richard D. , Shirah Bader , Yu Min , Lyden David , Mateus Jaime , Mason Christopher E.
Published: May 2023

The SpaceX Inspiration4 mission provided a unique opportunity to study the impact of spaceflight on the human body. Biospecimen samples were collected from the crew at different stages of the mission, including before (L-92, L-44, L-3 days), during (FD1, FD2, FD3), and after (R+1, R+45, R+82, R+194 days) spaceflight, creating a longitudinal sample set. The collection process included samples such as venous blood, capillary dried blood spot cards, saliva, urine, stool, body swabs, capsule swabs, SpaceX Dragon capsule HEPA filter, and skin biopsies, which were processed to obtain aliquots of serum, plasma, extracellular vesicles, and peripheral blood mononuclear cells. All samples were then processed in clinical and research laboratories for optimal isolation and testing of DNA, RNA, proteins, metabolites, and other biomolecules. This paper describes the complete set of collected biospecimens, their processing steps, and long-term biobanking methods, which enable future molecular assays and testing. As such, this study details a robust framework for obtaining and preserving high-quality human, microbial, and environmental samples for aerospace medicine in the Space Omics and Medical Atlas (SOMA) initiative, which can also aid future experiments in human spaceflight and space biology.
The Role of Lrig1 in the Development of the Colonic Epithelium
Authors: Hopton Rachel E. , Jahahn Nicholas J. , Zemper Anne E.
Published: May 2023

Growth and specification of the mouse intestine occurs in utero and concludes after birth. While numerous studies have examined this developmental process in the small intestine, far less is known about the cellular and molecular cues required for colon development. In this study, we examine the morphological events leading to crypt formation, epithelial cell differentiation, areas of proliferation, and the emergence and expression of a stem and progenitor cell marker Lrig1. Through multicolor lineage tracing, we show Lrig1 expressing cells are present at birth and behave as stem cells to establish clonal crypts within three weeks after birth. In addition, we use an inducible knockout mouse to eliminate Lrig1 during colon development and show loss of Lrig1 restrains proliferation within a critical developmental time window, without impacting colonic epithelial cell differentiation. Our study illustrates the morphological changes that occur during crypt development and the importance of Lrig1 in the developing colon.