bluuebunny/crossref_metadata_2025 huggingface dataset:
High throughput screen in a co-culture model to uncover therapeutic strategies to potentiate the cancer-inhibiting properties of the tumor-stroma in pancreatic cancer
Authors: Mason James , Cumming Joshua , Eriksson Anna U. , Binder Carina , Dongre Mitesh , Patthey Cedric , Espona-Fiedler Margarita , Chorell Erik , Öhlund Daniel
Published: March 2022

Pancreatic stellate cells (PSCs) differentiate into multiple subtypes of cancer associated fibroblasts (CAFs) that modulate disease progression in pancreatic ductal adenocarcinoma (PDAC). CAF subtypes demonstrate functional heterogeneity in tumor development, with conflicting consequences for disease progression. Here, we show that myofibroblastic CAFs (myCAFs), but not inflammatory CAFs (iCAFs), can act to restrain tumor cell growth in an in vitro PDAC model of tumor organoids co-cultured with PSCs. Inhibiting myCAF formation by TGF-β pathway inhibition improved tumor organoid growth, indicating that manipulating the balance of CAF subtypes may be exploited as a therapeutic approach. We therefore conducted a high throughput screen of approximately 36,000 compounds on the co-culture model to find novel compounds to inhibit PDAC tumor cell growth via CAF manipulation. We identify a new role for GNF-5, a known Abelson tyrosine kinase (Abl) inhibitor, in the context of PDAC as a compound that inhibits tumor cell growth in co-culture; an effect that was accompanied by an induction of the myCAF phenotype around tumor organoids. This highlights the therapeutic potential of novel therapies targeting specific CAF subtypes in PDAC.
Interspecies isobaric labeling-based quantitative proteomics reveals protein changes in the ovary of Aedes aegypti co-infected with ZIKV and Wolbachia
Authors: Ramos Luis Felipe Costa , Martins Michele , Murillo Jimmy Rodriguez , Domont Gilberto Barbosa , de Oliveira Danielle Maria Perpétua , Nogueira Fábio César Sousa , Maciel-de-Freitas Rafael , Junqueira Magno
Published: March 2022

Zika is a vector-borne disease caused by an arbovirus (ZIKV) and overwhelmingly transmitted by Ae. aegypti. This disease is linked to adverse fetal outcomes, mostly microcephaly in newborns, and other clinical aspects such as acute febrile illness and neurologic complications, for example, Guillain-Barré syndrome. One of the actual most promising strategies to mitigate arbovirus transmission involves releasing Ae. aegypti mosquitoes carrying the maternally inherited endosymbiont bacteria Wolbachia pipientis. The presence of Wolbachia is associated with a reduced susceptibility to arboviruses and a fitness cost in mosquito life-history traits as fecundity and fertility. However, the mechanisms by which Wolbachia influences metabolic pathways leading to differences in egg production remains poorly known. To investigate the impact of co-infections on the reproductive tract of the mosquito, we applied an isobaric labeling-based quantitative proteomic strategy to investigate the influence of Wolbachia wMel and ZIKV infection in Ae. aegypti ovaries. To the best of our knowledge, this is the most complete proteome of Ae. aegypti ovaries reported so far, with a total of 3,913 proteins identified, also,were able to quantify a total of 1,044 Wolbachia proteins in complex sample tissue of Ae. aegypti ovary.. Furthermore, we discuss proteins and pathways altered in Ae. aegypti during ZIKV infections, Wolbachia infections, co-infection Wolbachia/ZIKV, and compared with no infection, focusing on immune and reproductive aspects of Ae. aegypti. The modified aspects were mostly related to the immune priming enhancement by Wolbachia presence and the modulation of the Juvenile Hormone pathway caused by both microorganisms infection.

Highlights

Proteome changes in Ae. aegypti, Wolbachia, and ZIKV interactions

A great diversity of Wolbachia proteins were quantified in Ae. aegypti ovary

Juvenile Hormone pathway is modulated by both infections

Wolbachia enhances Ae. aegypti immune priming mechanism

ZIKV unsettles host immune response by reducing antimicrobial peptides production

Coinfection triggers oxidative stress and a lack of vitellogenin precursors
Dual inhibition of vacuolar ATPase and TMPRSS2 is required for complete blockade of SARS-CoV-2 entry into cells
Authors: Icho Simoun , Rujas Edurne , Muthuraman Krithika , Tam John , Liang Huazhu , Harms Shelby , Liao Mingmin , Falzarano Darryl , Julien Jean-Philippe , Melnyk Roman A.
Published: March 2022

An essential step in the infection life cycle of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the proteolytic activation of the viral spike (S) protein, which enables membrane fusion and entry into the host cell. Two distinct classes of host proteases have been implicated in the S protein activation step: cell-surface serine proteases, such as the cell-surface transmembrane protease, serine 2 (TMPRSS2), and endosomal cathepsins, leading to entry through either the cell-surface route or the endosomal route, respectively. In cells expressing TMPRSS2, inhibiting endosomal proteases using non-specific cathepsin inhibitors such as E64d or lysosomotropic compounds such as hydroxychloroquine fails to prevent viral entry, suggesting that the endosomal route of entry is unimportant; however, mechanism-based toxicities and poor efficacy of these compounds confound our understanding of the importance of the endosomal route of entry. Here, to identify better pharmacological agents to elucidate the role of the endosomal route of entry, we profiled a panel of molecules identified through a high throughput screen that inhibit endosomal pH and/or maturation through different mechanisms. Among the three distinct classes of inhibitors, we found that inhibiting vacuolar-ATPase using the macrolide bafilomycin A1 was the only agent able to potently block viral entry without associated cellular toxicity. Using both pseudotyped and authentic virus, we showed that bafilomycin A1 inhibits SARS-CoV-2 infection both in the absence and presence of TMPRSS2. Moreover, synergy was observed upon combining bafilomycin A1 with Camostat, a TMPRSS2 inhibitor, in neutralizing SARS-CoV-2 entry into TMPRSS2-expressing cells. Overall, this study highlights the importance of the endosomal route of entry for SARS-CoV-2 and provides a rationale for the generation of successful intervention strategies against this virus that combine inhibitors of both entry pathways.
Is Melanopsin Activation Affecting Large Field Color Matching Functions?
Authors: Barrionuevo Pablo , Filgueira Clemente Paz , Cao Dingcai
Published: March 2022

Color theory is based on the exclusive activation of cones. However, since the discovery of melanopsin expressing cells in the human retina, evidence of its intrusion in brightness and color vision is increasing. We aimed to assess if differences between peripheral or large field and foveal color matches can be accounted for melanopsin activation or rod intrusion. Photopic color matches by young observers showed that differences between extrafoveal and foveal results cannot be explained by rod intrusion. Furthermore, statistical analyses on existing color matching functions suggest a role of melanopsin activation, particularly, in Large Field S Fundamentals.
The Balbiani body is formed by microtubule-controlled molecular condensation of Buc in early oogenesis
Authors: Kar Swastik , Deis Rachael , Ahmad Adam , Bogoch Yoel , Dominitz Avichai , Shvaizer Gal , Sasson Esther , Mytlis Avishag , Ben-Zvi Ayal , Elkouby Yaniv M.
Published: March 2022

Vertebrate oocyte polarity has been observed for two centuries and is essential for embryonic axis formation and germline specification, yet its underlying mechanisms remain unknown. In oocyte polarization, critical RNA-protein (RNP) granules delivered to the oocyte’s vegetal pole, are stored by the Balbiani body (Bb), a membraneless organelle conserved across species from insects to humans. However, the mechanisms of Bb formation are still unclear. Here, we elucidate mechanisms of Bb formation in zebrafish through developmental biomolecular condensation. Using super-resolution microscopy, live imaging, biochemical, and genetic analysesin-vivo, we demonstrate that Bb formation is driven by molecular condensation through phase-separation of the essential intrinsically disordered protein Bucky ball (Buc). Live imaging, molecular analyses, and FRAP experimentsin-vivoreveal Buc-dependent changes in the Bb condensate’s dynamics and apparent material properties, transitioning from liquid-like condensates to a solid-like stable compartment. Furthermore, we identify a multi-step regulation by microtubules that controls Bb condensation: first through dynein-mediated trafficking of early condensing Buc granules, then by scaffolding condensed granules, likely through molecular crowding, and finally by caging the mature Bb to prevent overgrowth and maintain shape. These regulatory steps ensure the formation of a single intact Bb, which is considered essential for oocyte polarization and embryonic development. Our work offers insight into the long-standing question of the origins of embryonic polarity in non-mammalian vertebrates, support a paradigm of cellular control over molecular condensation by microtubules, and highlight biomolecular condensation as a key process in female reproduction.
Structure of the human RAD17-RFC clamp loader and 9-1-1 checkpoint clamp bound to a dsDNA-ssDNA junction
Authors: Day Matthew , Oliver Antony W. , Pearl Laurence H.
Published: March 2022

The RAD9-RAD1-HUS1 (9-1-1) clamp forms one half of the DNA damage checkpoint system that signals the presence of substantial regions of single-stranded DNA arising from replication fork collapse or resection of DNA double strand breaks. Loaded at the 5’-recessed end of a dsDNA-ssDNA junction by the RAD17-RFC clamp loader complex, the phosphorylated C-terminal tail of the RAD9 subunit of 9-1-1 engages with the mediator scaffold TOPBP1 which in turn activates the ATR kinase, localised through the interaction of its constitutive partner ATRIP with RPA-coated ssDNA.

Using cryogenic electron microscopy (cryoEM) we have determined the structure of a complex of the human RAD17-RFC clamp loader bound to human 9-1-1, engaged with a dsDNA-ssDNA junction. The structure answers the key questions of how RAD17 confers specificity for 9-1-1 over PCNA, and how the clamp loader specifically recognises the recessed 5’ DNA end and fixes the orientation of 9-1-1 on the ssDNA.
Structural and biochemical insights into lipid transport by VPS13 proteins
Authors: Adlakha Jyoti , Hong Zhouping , Li PeiQi , Reinisch Karin M.
Published: March 2022

VPS13 proteins are proposed to function at contact sites between organelles as bridges for lipids to move directionally and in bulk between organellar membranes. VPS13s are anchored between membranes via interactions with receptors, including both peripheral or integral membrane proteins. Here we present the crystal structure of VPS13s adaptor binding domain (VAB) complexed with a Pro-X-Pro peptide recognition motif present in one such receptor, the integral membrane protein Mcp1p, and show biochemically that other Pro-X-Pro motifs bind the VAB in the same site. We further demonstrate that Mcp1p and another integral membrane protein that interacts directly with human VPS13A, XK, are scramblases. This finding supports an emerging paradigm of a partnership between bulk lipid transport proteins and scramblases. Scramblases can re-equilibrate lipids between membrane leaflets as lipids are removed from or inserted into, respectively, the cytosolic leaflet of donor and acceptor organelles in the course of protein-mediated transport.
IRE1α/XBP1 pathway expression is impaired in pediatric cholestatic liver disease explants
Authors: Kriegermeier Alyssa , Hyon Angela , LeCuyer Brian , Hubchak Susan , Liu Xiaoying , Green Richard M.
Published: March 2022

Background/Aims

Cholestatic liver diseases (CLD) are the leading indication for pediatric liver transplantation. Increased intrahepatic bile acid concentrations cause endoplasmic reticulum (ER) stress and the unfolded protein response (UPR) is activated to maintain homeostasis. UPR dysregulation, including the inositol-requiring enzyme 1α/X-box protein 1 (IRE1α/XBP1) pathway, is associated with several adult liver diseases. We evaluated hepatic UPR expression in pediatric patients with end-stage CLD and hypothesize that an inability to appropriately activate the hepatic IRE1α/XBP1 pathway is associated with the pathogenesis of CLD.

Methods

We evaluated 34 human liver explants. Cohorts included: pediatric CLD (Alagille, ALGS, and progressive familial intrahepatic cholestasis, PFIC), pediatric non-cholestatic liver disease controls (autoimmune hepatitis, AIH), adult CLD, and normal controls. We performed RNA-seq, quantitative PCR, and western blotting to measure expression differences of the hepatic UPR and other signaling pathways.

Results

Metascape pathway analysis demonstrated that the KEGG ‘protein processing in ER’ pathway was downregulated in pediatric CLD compared to normal controls. Pediatric CLD had decreased hepatic IRE1α/XBP1 pathway gene expression and decreased protein expression of p-IRE1α compared to normal controls. These CLD changes were not disease-specific to ALGS or PFIC. IRE1α/XBP1 pathway gene expression was decreased in pediatric CLD compared to AIH disease controls.

Conclusion

Pediatric CLD explants have decreased gene and protein expression of the protective IRE1α/XBP1 pathway and down-regulated KEGG protein processing in the ER pathways. IRE1α/XBP1 pathway expression differences occur when compared to both normal and non-cholestatic disease controls. Attenuated expression of the IRE1α/XBP1 pathway is associated with cholestatic diseases and could be targeted to treat pediatric CLD.
State-of-the-art estimation of protein model accuracy using AlphaFold
Authors: Roney James P. , Ovchinnikov Sergey
Published: March 2022

The problem of predicting a protein’s 3D structure from its primary amino acid sequence is a longstanding challenge in structural biology. Recently, approaches like AlphaFold have achieved remarkable performance on this task by combining deep learning techniques with coevolutionary data from multiple sequence alignments of related protein sequences. The use of coevolutionary information is critical to these models’ accuracy, and without it their predictive performance drops considerably. In living cells, however, the 3D structure of a protein is fully determined by its primary sequence and the biophysical laws that cause it to fold into a low-energy configuration. Thus, it should be possible to predict a protein’s structure from only its primary sequence by learning a highly-accurate biophysical energy function. We provide evidence that AlphaFold has learned such an energy function, and uses coevolution data to solve the global search problem of finding a low-energy conformation. We demonstrate that AlphaFold’s learned potential function can be used to rank the quality of candidate protein structures with state-of-the-art accuracy, without using any coevolution data. Finally, we explore several applications of this potential function, including the prediction of protein structures without MSAs.
Implicit sensorimotor adaptation is preserved in Parkinson’s Disease
Authors: Tsay Jonathan S. , Najafi Tara , Schuck Lauren , Wang Tianhe , Ivry Richard B.
Published: March 2022

Our ability to enact successful goal-directed actions involves multiple learning processes. Among these processes, implicit motor adaptation ensures that the sensorimotor system remains finely tuned in response to changes in the body and environment. Whether Parkinson’s Disease (PD) impacts implicit motor adaptation remains a contentious area of research: whereas multiple reports show impaired performance in this population, many others show intact performance. While there are a range of methodological differences across studies, one critical issue is that performance in many of the studies may reflect a combination of implicit adaptation and strategic re-aiming. Here, we revisited this controversy using a visuomotor task designed to isolate implicit adaptation. In two experiments, we found that adaptation in response to a wide range of visual perturbations (3° - 45°) was similar in PD and matched control participants. Moreover, in a meta-analysis of previously published work, we found that the mean effect size contrasting PD and controls across 16 experiments was not significant. Together, these analyses indicate that implicit adaptation is preserved in PD, offering a fresh perspective on the role of the basal ganglia in sensorimotor learning.

Significance statement

Among multiple motor learning processes, implicit adaptation ensures that our motor system remains exquisitely calibrated. Whether Parkinson’s disease affects implicit motor adaptation has been a point of controversy. We revisited this issue using a visuomotor task designed to isolate implicit adaptation and found that individuals with PD and matched controls showed indistinguishable performance. A meta-analysis based on data from 16 previous experiments yielded a similar null result, strongly supporting the notion that implicit adaptation is preserved in PD.
The impact of COVID-19 non-pharmaceutical interventions on future respiratory syncytial virus transmission in South Africa
Authors: Bents Samantha , Viboud Cécile , Grenfell Bryan , Hogan Alexandra , Tempia Stefano , Gottberg Anne von , Moyes Jocelyn , Walaza Sibongile , Cohen Cheryl , Baker Rachel
Published: March 2022

In response to the COVID-19 pandemic, the South African government employed various nonpharmaceutical interventions (NPIs) in order to reduce the spread of SARS-CoV-2. In addition to mitigating transmission of SARS-CoV-2, these public health measures have also functioned in slowing the spread of other endemic respiratory pathogens. Surveillance data from South Africa indicates low circulation of respiratory syncytial virus (RSV) throughout the 2020-2021 Southern Hemisphere winter seasons. Here we fit age-structured epidemiological models to national surveillance data to predict the 2022 RSV outbreak following two suppressed seasons. We project a 32% increase in the peak number of monthly hospitalizations among infants ≤ 2 years, with older infants (6-23 month olds) experiencing a larger portion of severe disease burden than typical. Our results suggest that hospital system readiness should be prepared for an intense RSV season in early 2022.
Response to COVID-19 booster vaccinations in seronegative people with MS
Authors: Tallantyre Emma C , Scurr Martin J , Vickaryous Nicola , Richards Aidan , Anderson Valerie , Baker David , Chance Randy , Evangelou Nikos , George Katila , Giovannoni Gavin , Harding Katharine E , Hibbert Aimee , Ingram Gillian , Jolles Stephen , Jones Meleri , Kang Angray S , Loveless Samantha , Moat Stuart J , Robertson Neil P , Rios Francesca , Schmierer Klaus , Willis Mark , Godkin Andrew , Dobson Ruth
Published: March 2022

Background

Uncertainties remain about the benefit of a 3rd COVID-19 vaccine for people with attenuated response to earlier vaccines. This is of particular relevance for people with multiple sclerosis (pwMS) treated with anti-CD20 therapies and fingolimod, who have substantially reduced antibody responses to initial vaccine course.

Methods

PwMS taking part in a seroprevalence study without a detectable IgG response following COVID-19 vaccines 1&2 were invited to participate. Participants provided a dried blood spot +/-venous blood sample 2-12 weeks following COVID-19 vaccine 3. Humoral and T cell responses to SARS-CoV-2 spike protein and nucleocapsid antigen were measured. The relationship between evidence of prior COVID-19 infection and immune response to COVID-19 vaccine 3 was evaluated using Fishers exact test.

Results

Of 81 participants, 79 provided a dried blood spot sample, of whom 38 also provided a whole blood sample; 2 provided only whole blood. Anti-SARS-CoV-2-spike IgG seroconversion post-COVID-19 vaccine 3 occurred in 26/79 (33%) participants; 26/40 (65%) had positive T-cell responses. Overall, 31/40 (78%) demonstrated either humoral or cellular immune response post-COVID-19 vaccine 3. There no association between laboratory evidence of prior COVID-19 infection and anti-spike seroconversion following COVID-19 vaccine 3.

Conclusions

Approximately one third of pwMS who were seronegative after initial COVID-19 vaccination seroconverted after booster (third) vaccination, supporting the use of boosters in this group. Almost 8 out of 10 had a measurable immune response following 3rd COVID-19 vaccine.

Key messages

What is already known

The benefits of COVID vaccination are well described. It is unknown whether there is additional benefit afforded from a third COVID-19 vaccination in those people who have failed to mount a serological response to their initial vaccine course.

What this study adds

Approximately one third of people with MS in our study, all of whom had failed to response to initial vaccine course, developed anti-spike antibodies following a third COVID-19 vaccine. Two-thirds of participants had T cell response to vaccination. No people taking fingolimod appeared to mount a T cell response to vaccination.

How this study might influence practice

These findings highlight potential benefits of booster vaccinations to a substantial proportion of immunosuppressed people who have failed to respond to initial vaccination course. The clinical correlates of antibody and T-cell responses to COVID-19 remain uncertain but they are almost certainly associated with milder subsequent disease in the general population.
Maternal diet and gut microbiota influence predisposition to cardiovascular disease in the offspring
Authors: Jama Hamdi , Dona Malathi S.I. , Dinakis Evany , Nakai Michael , Paterson Madeleine R. , Shihata Waled , Krstevski Crisdion , Cohen Charles. D. , Weeks Kate L. , Farrugia Gabriella E. , Johnson Chad , Salimova Ekaterina , Donner Daniel , Kiriazis Helen , Kaipananickal Harikrishnan , Okabe Jun , Anderson Dovile , Creek Darren J. , Mackay Charles R. , El-Osta Assam , Pinto Alexander R. , Kaye David M. , Marques Francine Z
Published: March 2022

Cardiovascular disease is one of the most significant causes of death globally, especially in regions where unhealthy diets are prevalent and dietary fibre intake is low.1,2 Fibre, particularly prebiotic types that feed gut microbes, is essential for maintaining healthy gut microbial ecosystems.3 One assumption has been that cardiovascular health relates directly to lifestyle choices in adult life. Here, we show in mice that some of these benefits operate from the prenatal stage and relate to the diet and gut microbiome of the mother. Intake of fibre during pregnancy shaped the mothers’ gut microbiome, which had a lasting founding effect on the offspring’s microbial composition and function. Maternal fibre intake during pregnancy significantly changed the cardiac cellular and molecular landscape in the offspring, protecting them against the development of cardiac hypertrophy, remodelling, and inflammation. These suggest a role for foetal exposure to maternal-derived gut microbial metabolites, which are known to cross the placenta and drive epigenetic changes. Maternal fibre intake led to foetal epigenetic reprogramming of the atrial natriuretic peptide gene (Nppa), protective against heart failure. These results underscore the importance of dietary intake and the gut microbiome of the mother during pregnancy for cardiovascular disease in the offspring.
Environmental DNA sequencing data from algal blooms in Lake Erie using Oxford Nanopore MinION
Authors: Koeppel Alexander F. , Goodrum Will , Steffen Morgan , Wurch Louie , Turner Stephen D.
Published: March 2022

Harmful Algal Blooms (HABs) pose a significant and increasing risk, both to human health and to the Blue Economy. Genomics approaches to early detection promise to help mitigate these risks. We have developed and prototyped HABSSED (HAB Surveillance by Sequencing of Environmental DNA), a portable, reliable, rapid, low-cost pipeline for detecting HABs in the field using 3rd generation sequencing with the Oxford Nanopore MinION device. We demonstrated the efficacy of our approach by sequencing existing samples collected from a National Oceanic and Atmospheric Administration (NOAA) Great Lakes Environmental Research Laboratory (GLERL) on Lake Erie. We sequenced environmental DNA (eDNA) from samples drawn before, during, and after a Microcystis bloom, and estimate the abundanced of HAB-associated taxa. While sequencing results showed some evidence of human and E. coli contamination, we find that the abundance of Mycrocystis and other HAB-associated orgnisms significantly differs between pre- and post-bloom environments. Here we describe the publicly available sequencing data that was generated as part of this research, which is available in the Sequence Read Archive (SRA) under accession number PRJNA812770.
Graph-based algorithms for phase-type distributions
Authors: Røikjer Tobias , Hobolth Asger , Munch Kasper
Published: March 2022

Phase-type distributions model the time until absorption in continuous or discrete-time Markov chains on a finite state space. The multivariate phase-type distributions have diverse and important applications by modeling rewards accumulated at visited states. However, even moderately sized state spaces make the traditional matrix-based equations computationally infeasible. State spaces of phase-type distributions are often large but sparse, with only a few transitions from a state. This sparseness makes a graph-based representation of the phase-type distribution more natural and efficient than the traditional matrix-based representation. In this paper, we develop graph-based algorithms for analyzing phase-type distributions. In addition to algorithms for state space construction, reward transformation, and moments calculation, we give algorithms for the marginal distribution functions of multivariate phase-type distributions and for the state probability vector of the underlying Markov chains of both time-homogeneous and time-inhomogeneous phase-type distributions. The algorithms are available as a numerically stable and memory-efficient open source software package written in C named ptdalgorithms. This library exposes all methods in the programming languages C and R. We compare the running time of ptdalgorithms to the fastest tools using a traditional matrix-based formulation. This comparison includes the computation of the probability distribution, which is usually computed by exponentiation of the sub-intensity or sub-transition matrix. We also compare time spent calculating the moments of (multivariate) phase-type distributions usually defined by inversion of the same matrices. The numerical results of our graph-based and traditional matrix-based methods are identical, and our graph-based algorithms are often orders of magnitudes faster. Finally, we demonstrate with a classic problem from population genetics how ptdalgorithms serves as a much faster, simpler, and completely general modeling alternative.
Associations between locus coeruleus MRI contrast and physiological responses to acute stress in younger and older adults
Authors: Bachman Shelby L. , Nashiro Kaoru , Yoo Hyunjoo , Wang Diana , Thayer Julian F. , Mather Mara
Published: March 2022

Acute stress activates the brain’s locus coeruleus (LC)-noradrenaline system. Recent studies indicate that a magnetic resonance imaging (MRI)-based measure of LC structure is associated with better cognitive outcomes in later life. Yet despite the LC’s documented role in promoting physiological arousal during acute stress, no studies have examined whether MRI-assessed LC structure is related to arousal responses to acute stress. In this study, 102 younger and 51 older adults completed an acute stress induction task while we assessed multiple measures of physiological arousal (heart rate, breathing rate, systolic and diastolic blood pressure, sympathetic tone, and heart rate variability, HRV). We used turbo spin echo MRI scans to quantify LC MRI contrast as a measure of LC structure. We applied univariate and multivariate approaches to assess how LC MRI contrast was associated with arousal at rest and during acute stress reactivity and recovery. In older participants, having higher caudal LC MRI contrast was associated with greater stress-related increases in systolic blood pressure and decreases in HRV, as well as lower HRV during recovery from acute stress. These results suggest that having higher caudal LC MRI contrast in older adulthood is associated with more pronounced physiological responses to acute stress. Further work is needed to confirm these patterns in larger samples of older adults.
Gram-negative Antimicrobial spectrum of Ulmus pumila
Authors: Schafer Josh , Puga Troy B. , Miller Sha’Rai T. , Agbedanu Prince N.
Published: March 2022

Purpose

This study explores the antimicrobial spectrum of Ulmus pumila by screening commonly infectious gram-negative bacteria for susceptibility. Currently, many gram-negative bacteria are developing resistance to recommended antibiotic therapies used in clinical practice. It is imperative that we continue to explore new antimicrobial compounds in order to help combat the global health issue of antibiotic resistance.

Method

3g of freshly harvested leaves and flower samples of Ulmus pumila were extracted in 15 ml of 95% ethanol. The mixture was filtered to remove the debris and sterile blank discs were soaked in the clear filtrate (samples) or the extraction solvent (as background controls) for 20 minutes. Glycerol stocks of bacteria were scaled in LB broth and Muller Hinton agar was prepared with 38g of agar in a liter of water. A 100-microliter suspension of the scaled bacteria was diluted with 9 ml of 1% saline solution and 100 microliters of this saline dilution was plated. Sterile paper discs that were infused with extracts (samples) or vehicle control (95% ethanol) were placed on the freshly plated bacterial plates and incubated at 37 degree Celsius overnight. Zones of inhibition were recorded as a measure of antibacterial activity.

Result

Ulmus pumila demonstrated antimicrobial activity against the following gram-negative bacteria: E. coli (16 mm mean zone of clearing), P. vulgaris (15 mm mean zone of clearing), E. cloacae (20.5 mm mean zone of clearing), and K. pneumoniae (16 mm mean zone of clearing).

Conclusion

Ulmus pumila displayed antimicrobial activity against various species of gram-negative bacteria including E. coli, P. vulgaris, K. pneumonaie, and E. cloacae. Ulmus pumila has also previously demonstrated activity against some species of gram-positive bacteria. By this discovery, Ulmus pumila has the potential to serve as a broad-spectrum antimicrobial agent with activity against both gram-positive and gram-negative bacteria.
Effectiveness of Community-Based Rehabilitation (CBR) centres for improving physical fitness for community-dwelling older adults: a systematic review protocol
Authors: Xin Wei , Xu Dan , Dou Zulin , Jacques Angela , Umbella Josephine , Hill Anne-Marie
Published: March 2022

Introduction

The increasing ageing population has become a substantial challenge for both health care and social services in many Asian countries. There is a high incidence of chronic diseases and comorbidities in older populations, leading to impairments and functional disability. Functional disability may result in loss of independence, reduced quality of life and increased care needs. Community-based rehabilitation (CBR) aims to promote equality of opportunity and improve the social inclusion of individuals living with disability. CBR also provides rehabilitation to improve physical, mental, and social outcomes. However, there is limited evidence regarding the effectiveness of CBR for improving older adults’ physical fitness. The aim of this systematic review is to synthesise the evidence for the effectiveness of interventions delivered by CBR centres on physical fitness of community-dwelling older adults in Asian countries.

Methods and analysis

A search on four English databases (CINAHL, Medline, Scopus and Proquest) and two Chinese databases (China National Knowledge Internet and Wanfang Database) will be conducted, from inception to 15 November 2021. Both English and Chinese publications will be included. Experimental and quasi-experimental studies using any type of control group will be included. The primary outcomes are physical fitness (capacity to perform activities and tasks). Secondary outcomes are performance of activities of daily living and health-related quality of life. The quality of all included studies will be assessed using the Joanna Briggs Institute (JBI) standardised critical appraisal tools. Two reviewers will independently complete study screening, selection, quality appraisal, and data extraction. Quantitative data where possible will be pooled in statistical meta-analysis. All statistical analyses will be performed using Review Manager (Rev Man) V.5.3 software.

Ethics and dissemination

Ethical approval is not required for this review. The findings of this review will be disseminated electronically through a peer-reviewed publication and conference presentations.

PROSPERO registration number

CRD42021292088

Strengths and limitations

Findings and evidence in this review will be summarised and graded using the Grading of Recommendations, Assessment, Development and Evaluation Pro (GRADEPro) approach.

A comprehensive literature search using both English and Chinese language databases will be conducted.

Studies included in the review may measure different outcomes which may limit pooling in meta-analysis.

Differences in populations and interventions delivered in the included studies may result in high levels of heterogeneity, leading to less certainty about the recommendations from the review.
A shared genetic signature for common chronic pain conditions and its impact on biopsychosocial traits
Authors: Farrell Scott F. , Kho Pik-Fang , Lundberg Mischa , Campos Adrián I. , Rentería Miguel E. , de Zoete Rutger M. J. , Sterling Michele , Ngo Trung Thanh , Cuéllar-Partida Gabriel
Published: March 2022

The multifactorial nature of chronic pain with its numerous comorbidities presents a formidable challenge in disentangling their aetiology. Here, we performed genome-wide association studies of eight regional chronic pain types using UK Biobank data (N=4,037–79,089 cases; N=239,125 controls), followed by bivariate linkage disequilibrium-score regression and latent causal variable analyses to determine (respectively) their genetic correlations and genetic causal proportion (GCP) parameters with 1,492 other complex traits. We report evidence of a shared genetic signature across common chronic pain types as their genetic correlations and GCP parameter directions were broadly consistent across a wide array of biopsychosocial traits. Across 5,942 significant genetic correlations, 570 trait pairs could be explained by a causal association (|GCP| > 0.6; 5% false discovery rate), including 82 traits affected by pain while 488 contributed to an increased risk of chronic pain such as certain somatic pathologies (e.g., musculoskeletal), psychiatric traits (e.g., depression), socioeconomic factors (e.g., occupation) and medical comorbidities (e.g., cardiovascular disease). This data-driven study has demonstrated a novel & efficient strategy for identifying genetically supported risk & protective traits to enhance the design of interventional trials targeting underlying causal factors and help accelerate the development of more effective treatments with broader clinical utility.
Comparison of CRISPR/Cas9-mediated megabase-scale genome deletion methods in mouse embryonic stem cells
Authors: Miyata Masayuki , Yoshida Junko , Takagishi Itsuki , Horie Kyoji
Published: March 2022

The genome contains large functional units ranging in size from hundreds of kilobases to megabases, such as gene clusters, promoter-enhancer loops, and topologically associating domains. To analyze these large functional units, the technique of deleting the entire functional unit is effective. However, deletion of such large regions is less efficient than conventional genome editing, especially in cultured cells, and a method that can ensure success is anticipated. Here, we compared methods to delete the 2.5-Mb Krüppel-associated box zinc finger protein (KRAB-ZFP) gene cluster on chromosome 4 in mouse embryonic stem cells using CRISPR/Cas9. Three methods were used: first, deletion by non-homologous end joining (NHEJ); second, homology-directed repair (HDR) using a single-stranded oligodeoxynucleotide (ssODN) with 70-bp homology arms; and third, HDR employing targeting vectors with a selectable marker and 1-kb homology arms. NHEJ-mediated deletion was achieved in 9% of the transfected cells. The deletion frequency of NHEJ and HDR was found to be comparable when the ssODN was transfected. Deletion frequency was highest when targeting vectors were introduced, with deletions occurring in 31–63% of the drug-resistant clones. Biallelic deletion was observed when targeting vectors were used. This study will serve as a benchmark for the introduction of large deletions into the genome.
Tracking SARS-CoV-2 Omicron diverse spike gene mutations identifies multiple inter-variant recombination events
Authors: Ou Junxian , Lan Wendong , Wu Xiaowei , Zhao Tie , Duan Biyan , Yang Peipei , Ren Yi , Quan Lulu , Zhao Wei , Seto Donald , Chodosh James , Wu Jianguo , Zhang Qiwei
Published: March 2022

The current pandemic of COVID-19 is fueled by more infectious emergent Omicron variants. Ongoing concerns of emergent variants include possible recombinants, as genome recombination is an important evolutionary mechanism for the emergence and re-emergence of human viral pathogens. Although recombination events among SARS-CoV-1 and MERS-CoV were well-documented, it has been difficult to detect the recombination signatures in SARS-CoV-2 variants due to their high degree of sequence similarity. In this study, we identified diverse recombination events between two Omicron major subvariants (BA.1 and BA.2) and other variants of concern (VOCs) and variants of interest (VOIs), suggesting that co-infection and subsequent genome recombination play important roles in the ongoing evolution of SARS-CoV-2. Through scanning high-quality completed Omicron spike gene sequences, eighteen core mutations of BA.1 variants (frequency >99%) were identified (eight in NTD, five near the S1/S2 cleavage site, and five in S2). BA.2 variants share three additional amino acid deletions with the Alpha variants. BA.1 subvariants share nine common amino acid mutations (three more than BA.2) in the spike protein with most VOCs, suggesting a possible recombination origin of Omicron from these VOCs. There are three more Alpha-related mutations (del69-70, del144) in BA.1 than BA.2, and therefore BA.1 may be phylogenetically closer to the Alpha variant. Revertant mutations are found in some dominant mutations (frequency >95%) in the BA.1 subvariant. Most notably, multiple additional amino acid mutations in the Delta spike protein were also identified in the recently emerged Omicron isolates, which implied possible recombination events occurred between the Omicron and Delta variants during the on-going pandemic. Monitoring the evolving SARS-CoV-2 genomes especially for recombination is critically important for recognition of abrupt changes to viral attributes including its epitopes which may call for vaccine modifications.
Direct and indirect neurogenesis generate a mosaic of distinct glutamatergic projection neuron types in cerebral cortex
Authors: Huilgol Dhananjay , Levine Jesse M , Galbavy William , Wang Bor-Shuen , He Miao , Suryanarayana Shreyas M , Huang Z. Josh
Published: March 2022

Variations in size and complexity of the cerebral cortex result from differences in neuron number and composition, which are rooted in evolutionary changes in direct and indirect neurogenesis (dNG and iNG) mediated by radial glial progenitors and intermediate progenitors, respectively. How dNG and iNG differentially contribute to cortical neuronal number, diversity, and connectivity are unknown. Establishing a genetic fate-mapping method to differentially visualize dNG and iNG in mice, we found that while both dNG and iNG contribute to all cortical structures, iNG contributes the largest relative proportions to the hippocampus and neocortex compared to insular and piriform cortex, claustrum, and the pallial amygdala. Within the neocortex, whereas dNG generates all major glutamatergic projection neuron (PN) classes, iNG differentially amplifies and diversifies PNs within each class; the two neurogenic pathways generate distinct PN types and assemble fine mosaics of lineage-based cortical subnetworks. Our results establish a ground-level lineage framework for understanding cortical development and evolution by linking foundational progenitor types and neurogenic pathways to PN types.

Highlights

- A genetic strategy for differential visualization of direct and indirect neurogenesis in the same animal.

- dNG and iNG differentially contribute to piriform cortex, basolateral amygdala, hippocampus, and neocortex

- Whereas dNG generates all major PN classes, iNG differentially amplifies and diversifies PNs within each class

- dNG and iNG construct distinct cortical projection subnetworks.
HormoneBayes: a novel Bayesian framework for the analysis of pulsatile hormone dynamics
Authors: Voliotis Margaritis , Abbara Ali , Prague Julia K , Veldhuis Johannes D. , Dhillo Waljit S , Tsaneva-Atanasova Krasimira
Published: March 2022

The hypothalamus is the central regulator of reproductive hormone secretion. Pulsatile secretion of gonadotropin releasing hormone (GnRH) is fundamental to physiological stimulation of the pituitary gland to release luteinizing hormone (LH) and follicle stimulating hormone (FSH). Furthermore, GnRH pulsatility is altered in common reproductive disorders such as polycystic ovary syndrome (PCOS) and hypothalamic amenorrhea (HA). LH is measured routinely in clinical practice using an automated chemiluminescent immunoassay method and is the gold standard surrogate marker of GnRH. LH can be measured at frequent intervals (e.g., 10 minutely) to assess GnRH/LH pulsatility. However, this is rarely done in clinical practice because it is resource intensive, and there is no user-friendly and accessible method for computational analysis of the LH data available to clinicians. Here we presenthormoneBayes, a novel open-access Bayesian framework that can be easily applied to reliably analyze serial LH measurements to assess LH pulsatility. The framework utilizes parsimonious models to simulate hypothalamic signals that drive LH dynamics, together with state-of-the-art (sequential) Monte-Carlo methods to infer key parameters and latent hypothalamic dynamics. We show that this method provides estimates for key pulse parameters including inter-pulse interval, secretion and clearance rates and identifies LH pulses in line with the current gold-standard deconvolution method. We show that these parameters can distinguish LH pulsatility in different clinical contexts including in reproductive health and disease in men and women (e.g., healthy men, healthy women before and after menopause, women with HA or PCOS). A further advantage ofhormoneBayesis that our mathematical approach provides a quantified estimation of uncertainty. Our framework will complement methods enabling real-timein-vivohormone monitoring and therefore has the potential to assist translation of personalized, data-driven, clinical care of patients presenting with conditions of reproductive hormone dysfunction.
Shared and distinct genetic etiologies for different types of clonal hematopoiesis
Authors: Brown Derek W. , Cato Liam D. , Zhao Yajie , Nandakumar Satish K. , Bao Erik L. , Gardner Eugene J. , DePaulis Alexander , Rehling Thomas , Song Lei , Yu Kai , Chanock Stephen J. , Perry John R. B. , Sankaran Vijay G. , Machiela Mitchell J.
Published: March 2022

Clonal hematopoiesis (CH) – age-related expansion of mutated hematopoietic clones – can differ in frequency and cellular fitness. Descriptive studies have identified a spectrum of events (coding mutations in driver genes (CHIP), gains/losses and copy-neutral loss of chromosomal segments (mCAs), and loss of sex chromosomes). Co-existence of different CH events raises key questions as to their origin, selection, and impact. Here, we report analyses of sequence and genotype array data in up to 482,378 individuals from UK Biobank, demonstrating shared genetic architecture across different types of CH. These data highlighted evidence for a cellular evolutionary trade-off between different forms of CH, with LOY occurring at lower rates in individuals carrying mutations in established CHIP genes. Furthermore, we observed co-occurrence of CHIP and mCAs with overlap at TET2, DNMT3A, and JAK2, in which CHIP precedes mCA acquisition. Individuals carrying these overlapping somatic mutations had a large increase in risk of future hematological malignancy (HR=17.31, 95% CI=9.80-30.58, P=8.94×10−23), which is significantly elevated compared to individuals with non-overlapping CHIP and autosomal mCAs (Pheterogeneity=8.83×10−3). Finally, we leverage the shared genetic architecture of these CH traits to identify 15 novel loci associated with blood cancer risk.
Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events
Authors: Allen George , Weiss Benjamin , Panasenko Olesya , Huch Susanne , Villanyi Zoltan , Albert Benjamin , Dilg Daniel , Zagatti Marina , Schaughency Paul , Liao Susan E. , Corden Jeff , Polte Christine , Shore David , Ignatova Zoya , Pelechano Vicent , Collart Martine A.
Published: March 2022

Background

The Ccr4-Not complex is most well known as the major eukaryotic deadenylase. However, several studies have uncovered roles of the complex, in particular of the Not subunits, unrelated to deadenylation and relevant for translation. In particular, the existence of Not condensates that regulate translation elongation dynamics have been reported. Typical studies that evaluate translation efficiency rely on soluble extracts obtained after disruption of cells and ribosome profiling. Yet cellular mRNAs in condensates can be actively translated and may not be present in such extracts.

Results

In this work, by analyzing soluble and insoluble mRNA decay intermediates in yeast, we determine that insoluble mRNAs are enriched for ribosomes dwelling at non-optimal codons compared to soluble mRNAs. mRNA decay is higher for soluble RNAs, but the proportion of co-translational degradation relative to the overall mRNA decay is higher for insoluble mRNAs. We show that depletion of Not1 and Not4 inversely impact mRNA solubilities and, for soluble mRNAs, ribosome dwelling according to codon optimality. Depletion of Not4 solubilizes mRNAs with lower non-optimal codon content and higher expression that are rendered insoluble by Not1 depletion. By contrast, depletion of Not1 solubilizes mitochondrial mRNAs, which are rendered insoluble upon Not4 depletion.

Conclusion

Our results reveal that mRNA solubility defines dynamics of co-translation events and is oppositely regulated by Not1 and Not4, a mechanism that we additionally determine may already be set by Not1 promoter association in the nucleus.