bluuebunny/crossref_metadata_2025 huggingface dataset:
Peptimetric: Quantifying and visualizing differences in peptidomic data
Authors: Hartman Erik , Mahdavi Simon , Kjellström Sven , Schmidtchen Artur
Published: May 2021

Finding new sustainable means of diagnosing and treating diseases is one of the most pressing issues of our time. In recent years, several endogenous peptides have been found to be both excellent biomarkers for many diseases and to possess important physiological roles which may be utilized in treatments. The detection of peptides has been facilitated by the rapid development of biological mass spectrometry and now the combination of fast and sensitive high resolution MS instruments and stable nano HP-LC equipment sequences thousands of peptides in one single experiment. In most research conducted with these advanced systems, proteolytically cleaved proteins are analyzed and the specific peptides are identified by software dedicated for protein quantification using different proteomics workflows. Analysis of endogenous peptides with peptidomics workflows also benefit from the novel sensitive and advanced instrumentation, however, the generated peptidomic data is vast and subsequently laborious to visualize and examine, creating a bottleneck in the analysis. Therefore, we have created Peptimetric, an application designed to allow researchers to investigate and discover differences between peptidomic samples. Peptimetric allows the user to dynamically and interactively investigate the proteins, peptides, and some general characteristics of multiple samples, and is available as a web application at https://peptimetric.herokuapp.com. To illustrate the utility of Peptimetric, we’ve applied it to a peptidomic dataset of 15 urine samples from diabetic patients and corresponding data from healthy subjects.
Fork Slowing and Reversal as an Adaptive Response to Chronic ATR Inhibition
Authors: Dibitetto Diego , Sanchi Andrea , Sanford Ethan J. , Lopes Massimo , Smolka Marcus B.
Published: May 2021

Inhibitors of the replication stress response kinase ATR are currently being explored in anti-cancer therapy. Acute ATR inhibition is known to impair the proper control of origin firing, DNA repair, and cell cycle, resulting in DNA breaks and mitotic catastrophe. Less is understood about the effects of clinically relevant regimes of ATR inhibition, which involve chronic and low doses of ATR inhibitors (cATRi) to cells. Here we report unexpected molecular effects ofcATRion replication dynamics.cATRistrongly reduces fork speed but has minimal effects on the accumulation of DNA breaks or cell survival.cATRipromotes extensive fork reversal and RAD51- and PARP-mediated fork slowing that correlate with the accumulation of DNA-RNA hybrids. Our work shows that fork reversal is a critical adaptive response ensuring cell survival duringcATRiand that the manipulation of fork reversal causes hypersensitivity tocATRi, increasing the effectiveness of ATR inhibitors in anti-cancer therapies.
Adapting fundamental concepts from insect societies to the demands of bio-ontologies
Authors: Silva Thiago S.R.
Published: May 2021

The present work provides a logical account for translating fundamental concepts in the study of social insects to bio-ontologies, namely ‘colony’ and ‘caste’, which can be used by researchers for describing and organizing entities belonging to nonhuman societies, as well as for the provision of evidential criteria for evaluating cumulative-constitutive explanations of ‘social’ entities. I explore how different properties can provide connectedness of ‘colonies’ and ‘castes’ and discuss the implications of this approach to biological representation and ontology design. Finally, I briefly discuss some limitations in current approaches to demarcate subcategories of ‘castes’.
Out-of-sight or out-of-site? Forays and detection probabilities in single-season occupancy models
Authors: Desrochers André , Blanchette Pierre , Mazerolle Marc J.
Published: May 2021

Occupancy models have become popular in wildlife survey analyses because they account for the frequent failure to detect individuals of targeted species. Those individuals sometimes move outside sampling sites, i.e. exhibit temporary emigration. In such cases, occupancy models may become difficult to interpret or even misleading either at the species or the individual level, because they confound presence at the site, availability for detection given presence, and actual detection by the observer. We quantified the probabilities of these three components with spruce grouse (Falcipennis canadensis) in southern Quebec, Canada. We conducted call-response surveys of 24 grouse monitored by radio-telemetry. We defined sites empirically as circular areas of 83 m radius centered on the observer, corresponding to the maximum detection distance obtained. Based on telemetry locations, grouse were present at the site during 42 % of the surveys. Six stationary grouse were present during surveys, but were never detected. Thus, only individuals that moved in the presence of the observer (89 %) were considered available for detection. Individuals available for detection were detected in 51 % of the cases. We simulated detection histories and built single-season occupancy models, based on the empirical relationship between detection probability and the distance measured between observers and grouse. When temporary emigration was ignored, site occupancy wasψ= 0.89, and the associated probability of detection wasp= 0.23. When instances of temporary emigration were dropped, estimates wereψ= 0.88 andp= 0.41. Using only grouse available for detection, estimates wereψ= 0.87 andp= 0.42. Disentangling the components of detection probabilities had little impact on occupancy estimates, but showed a major effect of temporary emigration on estimated detection probabilities.
Gene flow influences the genomic architecture of local adaptation in six riverine fish species
Authors: Shi Yue , Bouska Kristen L. , McKinney Garrett J. , Dokai William , Bartels Andrew , McPhee Megan V. , Larson Wesley A.
Published: May 2021

Understanding how gene flow influences adaptive divergence is important for predicting adaptive responses. Theoretical studies suggest that when gene flow is high, clustering of adaptive genes in fewer genomic regions would protect adaptive alleles from among-population recombination and thus be selected for, but few studies have tested this hypothesis with empirical data. Here, we used RADseq to generate genomic data for six fish species with contrasting life histories from six reaches of the Upper Mississippi River System, USA. We then conducted genome scans for genomic islands of divergence to examine the distribution of adaptive loci and investigated whether these loci were found in inversions. We found that gene flow varied among species, and adaptive loci were clustered more tightly in species with higher gene flow. For example, the two species with the highest overall FST (0.03 - 0.07) and therefore lowest gene flow showed little evidence of clusters of adaptive loci, with adaptive loci spread uniformly across the genome. In contrast, nearly all adaptive loci in the species with the lowest FST (0.0004) were found in a single large putative inversion. Two other species with intermediate gene flow (FST ~ 0.004) also showed clustered genomic architectures, with most islands of divergence clustered on a few chromosomes. These results provide important empirical evidence to support the hypothesis that increasingly clustered architectures of local adaptation are associated with high gene flow. Our study utilized a unique system with species spanning a large gradient of life histories to highlight the importance of gene flow in shaping adaptive divergence.
The FusX TALE Base Editor (FusXTBE) for rapid mitochondrial DNA programming of human cells in vitro and zebrafish disease models in vivo
Authors: Sabharwal Ankit , Kar Bibekananda , Restrepo-Castillo Santiago , Holmberg Shannon R. , Kendall Benjamin Luke , Cotter Ryan P. , WareJoncas Zachary , Clark Karl J. , Ekker Stephen C.
Published: May 2021

Functional analyses of mitochondria have been hampered by few effective approaches to manipulate mtDNA and a lack of existing animal models. Recently a TALE-derived base editor was shown to induce C-to-T (or G-to-A) sequence changes in mtDNA. We report here the FusX TALE Base Editor (FusXTBE) to facilitate broad-based access to TALE mitochondrial base editing technology. TALE Writer is a de novo in silico design tool to map potential mtDNA base editing sites. FusXTBE was demonstrated to function with comparable activity to the initial base editor in human cells in vitro. Zebrafish embryos were used as a pioneering in vivo test system, with FusXTBE inducing 90+% editing efficiency in mtDNA loci, the first example of majority mtDNA heteroplasmy induction in any system. Gene editing specificity as precise as a single nucleotide was observed in vivo for a protein-coding gene. Non-destructive genotyping enables single animal mtDNA analyses for downstream biological functional genomics applications. FusXTBE is a new gene editing toolkit for exploring important questions in mitochondrial biology and genetics.
Predictive uncertainty in mechanistic models of cellular processes calibrated to experimental data
Authors: Irvin Michael W. , Ramanathan Arvind , Lopez Carlos F.
Published: May 2021

Mathematical models are often used to explore network-driven cellular processes from a systems perspective. However, a dearth of quantitative data suitable for model calibration leads to models with parameter unidentifiability and questionable predictive power. Here we introduce a Bayesian and Machine-Learning based Measurement Model approach to explore how quantitative and non-quantitative data constrain models of apoptosis execution within a missing data context. We find two orders of magnitude more ordinal (e.g. immunoblot) data are necessary to achieve accuracy comparable to quantitative (e.g. fluorescence) data. Notably, ordinal and nominal (e.g. immunostain) non-quantitative data synergize to reduce model uncertainty and improve accuracy. Further, model prediction accuracy and certainty strongly depend on rigorous data-driven formulations of the measurement, and the size and make-up of the datasets. Finally, we demonstrate the potential of a data-driven Measurement Model approach to identify model features that could lead to informative experimental measurements and improve model predictive power.
Galbut virus infection minimally influences Drosophila melanogaster fitness traits in a strain and sex-dependent manner
Authors: Cross Shaun T. , Brehm Ali L. , Dunham Tillie J. , Rodgers Case P. , Borlee Grace I. , Stenglein Mark D.
Published: May 2021

Galbut virus (family Partitiviridae) infects Drosophila melanogaster and can be transmitted vertically from infected mothers or infected fathers with near perfect efficiency. This form of super-Mendelian inheritance should drive infection to 100% prevalence, and indeed galbut virus is ubiquitous in wild D. melanogaster populations. But on average only about 60% of individual flies are infected. One possible explanation for this apparent paradox is that a subset of flies are resistant to infection. Although galbut virus infected flies seem healthy, infection may be sufficiently costly to drive selection for resistant hosts, thereby decreasing overall prevalence. To test this hypothesis, we quantified a variety of fitness-related traits in galbut virus infected flies from two lines from the Drosophila Genetic Reference Panel (DGRP). Galbut virus infected flies had slightly decreased average lifespan and total offspring production, but these decreases were mostly not statistically significant. Galbut virus DGRP-517 flies pupated and eclosed slightly faster than their uninfected counterparts. Some galbut virus infected flies exhibited altered sensitivity to viral, bacterial, and fungal pathogens. Galbut virus infection produced minimal changes to host mRNA levels as measured by RNA sequencing, consistent with minimal phenotypic changes. The microbiome composition of flies was not measurably perturbed by galbut virus infection. Differences in phenotype attributable to galbut virus infection varied as a function of fly sex and DGRP strain and were generally dwarfed by larger differences attributable to strain and sex. Thus, galbut virus infection does produce measurable phenotypic changes, with changes being minor, offsetting, and possibly net negative.

Importance

Virology has largely focused on viruses that cause unmistakable phenotypic changes. But metagenomic surveys are revealing that persistent virus infections are extremely common, even in apparently healthy organisms. The extent to which these persistent viruses impact host fitness and evolution remains largely unclear. Here we study fitness impacts of a partitivirus named galbut virus that is ubiquitous in wild D. melanogaster populations. Despite efficient biparental vertical transmission, galbut virus is present in only just over half of wild flies. We quantified various fitness-related traits in galbut virus infected and uninfected fly lines and found that infection produced small but measurable changes in host phenotype that in aggregate may reduce fly fitness. Further studies that take advantage of this virus that naturally infects a premier model organism that is easy to study in the wild will shed further light on the persistent virus-host dynamics that may actually represent most viral infections.
School start times and academic achievement - a systematic review on grades and test scores
Authors: Biller Anna M. , Meissner Karin , Winnebeck Eva C. , Zerbini Giulia
Published: May 2021

School start times have been at the centre of many scientific and political debates given the accumulating evidence that bell times are generally too early, and thus lead to an epidemic of sleep restriction in the student population. Recent media attention has conveyed the message that later school starts not only improve sleep but also result in better academic achievement. Several studies have been recently published on this topic requiring a comprehensive review of the results to clarify the relationship between later school start times and academic achievement to inform the general public and policy makers.

To this end, we conducted a systematic review of the current literature on school starting times and academic achievement in middle and high school students, considering grades and standardised test scores as achievement measures. We followed the PRISMA guidelines for searching, including, and reporting relevant literature and identified 21 studies for detailed analysis. Evidence quality of included studies was assessed with a pre-defined risk of bias assessment using modified items from the GRADE scheme and ROBINS-I tool.

About half of the reviewed studies reported no (positive or negative) effect of delaying school times on grades and test scores, while the other half reported either mixed or positive results. Given the strong heterogeneity of included studies, we grouped them according to various characteristics, such as academic outcomes, dose of delay, evidence quality, or study design to identify potential hidden effects. Despite this, we could not identify any generalisable effect beyond single studies as to whether delaying school times has clear beneficial effects on academic performance.

Given that grades and scores determine future career trajectories and predict future success, the question whether school start times contribute to academic achievement is of great interest for the general public and needs to be further clarified. Mechanistically, it is very likely that improved sleep leads to or mediates improved cognitive performance and learning, but definitive conclusions on whether this also translates into better grades and scores across all students requires better evidence at this stage. Importantly, this does not preclude other positive outcomes of later start times such as improved sleep (quality), motivation or learning but draws attention on current gaps and shortcomings. To this end, we also highlight critical methodological aspects and provide suggestions to increase the evidence-level and to guide the direction of research in future studies.
A baseline transcriptional signature associates with clinical malaria risk in RTS,S/AS01-vaccinated African children
Authors: Moncunill Gemma , Carnes Jason , Young William Chad , Carpp Lindsay N. , Rosa Stephen De , Campo Joseph J. , Nhabomba Augusto J. , Mpina Maximillian , Jairoce Chenjerai , Finak Greg , Haas Paige , Murie Carl , Van Phu , Sanz Héctor , Dutta Sheetij , Mordmüller Benjamin , Agnandji Selidji T. , Díez-Padrisa Núria , Williams Nana A. , Aponte John J. , Valim Clarissa , Neafsey Daniel E. , Daubenberger Claudia , McElrath Juliana , Dobaño Carlota , Stuart Ken , Gottardo Raphael
Published: May 2021

In a phase 3 trial in African infants/children, the RTS,S/AS01 (GSK) vaccine showed moderate efficacy against clinical malaria. We aimed to identify RTS,S/AS01-induced signatures associated with clinical malaria by analyzing antigen-stimulated peripheral blood mononuclear cells sampled from a subset of trial participants at baseline and month 3 (one month post-third dose). RTS,S/AS01 vaccination was associated with downregulation of B-cell and monocyte-related blood transcriptional modules (BTMs) and upregulation of T-cell related BTMs, as well as higher month 3 (vs baseline) circumsporozoite protein (CSP)-specific CD4+T-cell responses. There were few RTS,S/AS01-associated BTMs whose month 3 levels correlated with malaria risk. In contrast, baseline levels of BTMs associated with dendritic cells and with monocytes (among others) correlated with malaria risk. A cross-study analysis supported generalizability of the baseline dendritic cell- and monocyte-related BTM correlations with malaria risk to healthy, malaria-naïve adults, suggesting inflammatory monocytes may inhibit protective RTS,S/AS01-induced responses.
One year of SARS-CoV-2: Genomic characterization of COVID-19 outbreak in Qatar
Authors: Benslimane Fatiha M. , Al Khatib Hebah A. , Al-Jamal Ola , Albatesh Dana , Boughattas Sonia , Ahmed Ayeda A , Bensaad Meryem , Younuskunju Shameem , Mohamoud Yasmin A , Badr Mashael Al , Mohamed Abdalla A. , El-Kahlout Reham A. , Al-Hamad Tasneem , Elgakhlab Dina , Al-Kuwari Fatima H. , Saad Chadi , Jeremijenko Andrew , Al-Khal Abdullatif , Al-Maslamani Muna A. , Bertollini Roberto , Al-Kuwari Einas A. , Al-Romaihi Hamad E. , Al-Marri Salih , Al-Thani Mohammed , Badji Radja M. , Mbarek Hamdi , Al-Sarraj Yasser , Malek Joel A , Ismail Said I. , Abu-Raddad Laith J. , Coyle Peter V. , Al Thani Asmaa A. , Yassine Hadi M.
Published: May 2021

Qatar, a state that has a diverse population consisting mainly of foreign residents, has experienced a large COVID19 outbreak. In this study, we report on 2634 SARS-CoV-2 whole-genome sequences from infected patients in Qatar between March-2020 and March-2021, representing 1.5% of all positive cases in this period. Despite the restrictions on international travel, the viruses sampled from the populace of Qatar mirrored nearly the entire global population’s genomic diversity with nine predominant viral lineages that were sustained by local transmission chains and the emergence of mutations that are likely to have originated in Qatar. We reported an increased number of mutations and deletions in B.1.1.7 and B.1.351 lineages in a short period. These findings raise the imperative need to continue the ongoing genomic surveillance that has been an integral part of the national response to monitor the SARS-CoV-2 profile and re-emergence in Qatar.
An approximate Bayesian approach for estimation of the reproduction number under misreported epidemic data
Authors: Gressani Oswaldo , Faes Christel , Hens Niel
Published: May 2021

In epidemic models, the effective reproduction number is of central importance to assess the transmission dynamics of an infectious disease and to orient health intervention strategies. Publicly shared data during an outbreak often suffers from two sources of misreporting (underreporting and delay in reporting) that should not be overlooked when estimating epidemiological parameters. The main statistical challenge in models that intrinsically account for a misreporting process lies in the joint estimation of the time-varying reproduction number and the delay/underreporting parameters. Existing Bayesian approaches typically rely on Markov chain Monte Carlo (MCMC) algorithms that are extremely costly from a computational perspective. We propose a much faster alternative based on Laplacian-P-splines (LPS) that combines Bayesian penalized B-splines for flexible and smooth estimation of the time-varying reproduction number and Laplace approximations to selected posterior distributions for fast computation. Assuming a known generation interval distribution, the incidence at a given calendar time is governed by the epidemic renewal equation and the delay structure is specified through a composite link framework. Laplace approximations to the conditional posterior of the spline vector are obtained from analytical versions of the gradient and Hessian of the log-likelihood, implying a drastic speed-up in the computation of posterior estimates. Furthermore, the proposed LPS approach can be used to obtain point estimates and approximate credible intervals for the delay and reporting probabilities. Simulation of epidemics with different combinations for the underreporting rate and delay structure (one-day, two-day and weekend delays) show that the proposed LPS methodology delivers fast and accurate estimates outperforming existing methods that do not take into account underreporting and delay patterns. Finally, LPS is illustrated on two real case studies of epidemic outbreaks.
Clinical characteristics and COVID-19 outcomes in a regional cohort of pediatric patients with rheumatic diseases
Authors: Clemente Daniel , Udaondo Clara , de Inocencio Jaime , Nieto Juan Carlos , del Río Pilar Galán , Fernández Antía García , Palomo Jaime Arroyo , Bachiller-Corral Javier , Robledillo Juan Carlos Lopez , Leon Leticia , Abasolo Lydia , Boteanu Alina
Published: May 2021

Background

This study aimed to assess the baseline characteristics and clinical outcomes of coronavirus disease 2019 (COVID-19) in pediatric patients with rheumatic and musculoskeletal diseases (RMD) and identify the risk factors associated with symptomatic or severe disease defined as hospital admission, intensive care admission or death.

Methods

An observational longitudinal study was conducted during the first year of pandemic SARS-CoV-2 (1stMarch 2020 to 1stMarch 2021). All pediatric patients attended at the rheumatology outpatient clinic of six tertiary hospital in Madrid, Spain, with a medical diagnosis of RMD and COVID-19 were included. Main outcomes were symptomatic disease and hospital admission. The covariates were sociodemographic, clinical, and treatments. We ran a multivariable logistic regression model to assess risk factors for outcomes.

Results

The study population included 77 pediatric patients. Mean age was 11.88 (4.04) years Of these, 30 patients were asymptomatic, 41 had a mild or moderate disease and other 6 patients (7.79%) required hospital admission related to COVID-19. The median length of stay was 5 (2–20) days and there was no death. Previous comorbidities increased the risk for symptomatic disease and hospital admission. Compared with outpatients, the factor independently associated with hospital admission was the use of glucocorticoids (OR 1.08; p=0.00). No statistically significant findings for symptomatic COVID-19 were found in the final model.

Conclusion

Our data found no differences in COVID-19 outcomes between children-onset rheumatic diseases. Our results suggest that associated comorbidities and being in treatment with glucocorticoids increase the risk of hospital admission.
The microbiome of Lotus nodules varies with plant health in a species-specific manner
Authors: Crosbie Duncan B. , Mahmoudi Maryam , Radl Viviane , Brachmann Andreas , Schloter Michael , Kemen Eric , Marín Macarena
Published: May 2021

Nitrogen fixation is carried out inside nodules of legumes by symbiotic rhizobia. Rhizobia dominate the nodule microbiome, however other non-rhizobial bacteria also colonise root nodules. It is not clear whether these less abundant nodule colonisers impact nodule function. In order to investigate the relationship between the nodule microbiome and nodule function as influenced by the soil microbiome, we used a metabarcoding approach to characterise the communities inside Lotus burttii, Lotus japonicus and Lotus corniculatus nodules from plants that were either starved or healthy resulting from inoculations with different soil suspensions in a closed pot experiment. We found that the nodule microbiome of all tested Lotus species differed according to inoculum, but only that of L. burttii varied with plant health. Using a machine learning algorithm, we also found that among the many non-rhizobial bacteria inside the nodule, amplicon sequence variants that were related to Pseudomonas were the most indicative signatures of a healthy plant nodule microbiome. These results support the hypothesis that legume nodule endophytes may play a role in the overall success of root-nodule symbiosis, albeit in a plant host specific manner.
Concurrent invasions by European starlings (Sturnus vulgaris) suggest selection on shared genomic regions even after genetic bottlenecks
Authors: Hofmeister Natalie R. , Stuart Katarina , Warren Wesley C. , Werner Scott J. , Bateson Melissa , Ball Gregory F. , Buchanan Katherine L. , Burt David W. , Cardilini Adam P.A. , Cassey Phillip , De Meyer Tim , George Julia , Meddle Simone L. , Rowland Hannah M. , Sherman Craig D.H. , Sherwin William , Berghe Wim Vanden , Rollins Lee Ann , Clayton David F.
Published: May 2021

A species’ success during the invasion of new areas hinges on an interplay between demographic processes and the outcome of localized selection. Invasive European Starlings (Sturnus vulgaris) established populations in Australia and North America in the 19th century. Here, we compare whole-genome sequences among native and independently introduced European Starling populations from three continents to determine how demographic processes interact with rapid adaptive evolution to generate similar genetic patterns in these recent and replicated invasions. Our results confirm that a post-bottleneck expansion may in fact support local adaptation. We find that specific genomic regions have differentiated even on this short evolutionary timescale, and suggest that selection best explains differentiation in at least two of these regions. This infamous and highly mobile invader adapted to novel selection (e.g., extrinsic factors), perhaps in part due to the demographic boom intrinsic to many invasions.
Corticotropin-Releasing Factor Induces Functional And Structural Synaptic Remodelling In Acute Stress
Authors: Vandael Dorien , Wierda Keimpe , Vints Katlijn , Baatsen Pieter , De Groef Lies , Moons Lieve , Rybakin Vasily , Gounko Natalia V.
Published: May 2021

Biological responses to internal and external stress factors involve highly conserved mechanisms, using a tightly coordinated interplay of many factors. Corticotropin-releasing factor (CRF) plays a central role in organizing these lifesaving physiological responses to stress. We show that CRF rapidly and reversibly changes Schaffer Collateral input into hippocampal CA1 pyramidal cells (PC), by modulating both functional and structural aspects of these synapses. Host exposure to acute stress, in vivo CRF injection, and ex vivo CRF application all result in fast de novo formation and remodeling of existing dendritic spines. Functionally, CRF leads to a rapid increase in synaptic strength of Schaffer collateral input into CA1 neurons, e.g. increase in spontaneous neurotransmitter release, paired-pulse facilitation and repetitive excitability and improves long-term synaptic plasticity: LTP and LTD. In line with the changes in synaptic function, CRF increases the number of presynaptic vesicles, induces redistribution of vesicles towards the active zone increases active zone size, and improves the alignment of the pre- and post-synaptic compartments. Together, CRF rapidly enhances synaptic communication in the hippocampus, potentially playing a crucial role in the enhanced memory consolidation in acute stress.
Tetraspanin Cd9b and Cxcl12a/Cxcr4b have a synergistic effect on the control of collective cell migration
Authors: Marsay KS , Greaves S , Mahabaleshwar H , Ho CM , Roehl H , Monk PN , Carney T. J. , Partridge LJ
Published: May 2021

Collective cell migration is essential for embryonic development and homeostatic processes. During zebrafish development, the posterior lateral line primordium (pLLP) navigates along the embryo flank by collective cell migration. The chemokine receptors, Cxcr4b and Cxcr7b, as well as their cognate ligand, Cxcl12a, are essential for this process. We corroborate that knockdown of the zebrafish cd9 tetraspanin orthologue, cd9b, results in mild pLL abnormalities. Through generation of CRISPR and TALEN mutants, we show that cd9a and cd9b function partially redundantly in pLLP migration, which is delayed in the cd9b single and cd9a; cd9b double mutants. This delay led to a transient reduction in neuromast numbers. Loss of both Cd9a and Cd9b sensitized embryos to reduced Cxcr4b and Cxcl12a levels. Together these results provide evidence that Cd9 modulates collective cell migration of the pLLP during zebrafish development. One interpretation of these observations is that Cd9 contributes to more effective chemokine signalling.
Mitochondria serve as axonal shuttle for Cox7c mRNA through mechanism that involves its mitochondrial targeting signal
Authors: Cohen Bar , Golani-Armon Adi , Altman Topaz , Savulescu Anca F. , Mhlanga Musa M. , Perlson Eran , Arava Yoav S.
Published: May 2021

Localized protein synthesis plays a key role in spatiotemporal regulation of the cellular proteome. Neurons, which extend axons over long distances, heavily depend on this process. However, the mechanisms by which axonal mRNAs are transported to protein target sites are not fully understood. Here, we describe a novel role for mitochondria in shuttling a nuclear encoded mRNA along axons. Fractionation analysis and smFISH revealed that the mRNA encoding Cox7c protein is preferentially associated with mitochondria from a neuronal cell line and from primary motor neuron axons. Live cell imaging of MS2-tagged Cox7c or Cryab control mRNA in primary motor neurons further confirmed the preferential colocalization of Cox7c mRNA with mitochondria. More importantly, Cox7c demonstrated substantial cotransport with mitochondria along axons. Intriguingly, the coding region, rather than the 3’UTR, was found to be the key domain for the cotransport. Furthermore, we show that puromycin treatment as well as hindering the synthesis of the mitochondrial targeting signal (MTS) reduced the colocalization. Overall, our results reveal a novel mRNA transport mode which exploits mitochondria as a shuttle and translation of the MTS as a recognition feature. Thus, mitochondria may play a role in spatial regulation of the axonal transcriptome and self-sustain their own proteome at distant neuronal sites.
Epigenetic repression of Wnt receptors in AD: a role for Sirtuin2-induced H4K16ac deacetylation of Frizzled1 and Frizzled7 promoters
Authors: Palomer Ernest , Martin-Flores Núria , Jolly Sarah , Pascual-Vargas Patricia , Benvegnù Stefano , Podpolny Marina , Teo Samuel , Vaher Kadi , Saito Takashi , Saido Takaomi C , Whiting Paul , Salinas Patricia C
Published: May 2021

Growing evidence supports a role for deficient Wnt signalling in Alzheimer′s disease (AD). First, the Wnt antagonist DKK1 is elevated in AD brains and is required for amyloid-β-induced synapse loss. Second, LRP6 Wnt co-receptor is required for synapse integrity and three variants of this receptor are linked to late-onset AD. However, the expression/role of other Wnt signalling components remain poorly explored in AD. Wnt receptors Frizzled1 (Fzd1), Fzd5, Fzd7 and Fzd9 are of interest due to their role in synapse formation/plasticity. Our analyses showed reducedFZD1andFZD7mRNA levels in the hippocampus of human early AD stages and in the hAPPNLGF/NLGFmouse model. This transcriptional downregulation was accompanied by reduced levels of the pro-transcriptional histone mark H4K16ac and a concomitant increase of its deacetylase Sirt2 atFzd1andFzd7promoters in AD.In vitroandin vivoinhibition of Sirt2 rescuedFzd1andFzd7mRNA expression and H4K16ac levels at their promoters. In addition, we showed that Sirt2 recruitment toFzd1andFzd7promoters is dependent on FoxO1 activity in AD, thus acting as a co-repressor. Finally, we found reduced levels of Sirt2 inhibitory phosphorylation in nuclear samples from human early AD stages with a concomitant increased in the Sirt2 phosphatase PP2C. This results in hyperactive nuclear Sirt2 and favoursFzd1andFzd7repression in AD. Collectively, our findings define a novel role for nuclear hyperactivated Sirt2 in repressingFzd1andFzd7expressionviaH4K16ac deacetylation in AD. We propose Sirt2 as an attractive target to ameliorate AD pathology.
Cellulonodin-2 and Lihuanodin: Lasso Peptides with an Aspartimide Post-translational Modification
Authors: Cao Li , Beiser Moshe , Koos Joseph D. , Orlova Margarita , Elashal Hader E. , Schröder Hendrik V. , Link A. James
Published: May 2021

Lasso peptides are a family of ribosomally synthesized and post-translationally modified peptides (RiPPs) defined by their threaded structure. Besides the class-defining isopeptide bond, other post-translational modifications (PTMs) that further tailor lasso peptides have been previously reported. Using genome mining tools, we identified a subset of lasso peptide biosynthetic gene clusters (BGCs) that are colocalized with protein L-isoaspartyl methyltransferase (PIMT) homologs. PIMTs have an important role in protein repair, restoring isoaspartate residues formed from asparagine deamidation to aspartate. Here we report a new function for PIMT enzymes in the post-translational modification of lasso peptides. The PIMTs associated with lasso peptide BGCs first methylate an L-aspartate sidechain found within the ring of the lasso peptide. The methyl ester is then converted into a stable aspartimide moiety, endowing the lasso peptide ring with rigidity relative to its unmodified counterpart. We describe the heterologous expression and structural characterization of two examples of aspartimide-modified lasso peptides from thermophilic Gram-positive bacteria. The lasso peptide cellulonodin-2 is encoded in the genome of actinobacterium Thermobifida cellulosilytica, while lihuanodin is encoded in the genome of firmicute Lihuaxuella thermophila. Additional genome mining revealed PIMT-containing lasso peptide BGCs in 48 organisms. In addition to heterologous expression, we have reconstituted PIMT-mediated aspartimide formation in vitro, showing that lasso peptide-associated PIMTs transfer methyl groups very rapidly as compared to canonical PIMTs. Furthermore, in stark contrast to other characterized lasso peptide PTMs, the methyltransferase functions only on lassoed substrates.

Abstract Figure
Microbial phylogenetic relatedness links to distinct successional patterns of bacterial and fungal communities
Authors: Lin Qiang , Dini-Andreote Francisco , Meador Travis B. , Angel Roey , Meszárošová Lenka , Heděnec Petr , Li Lingjuan , Baldrian Petr , Frouz Jan
Published: May 2021

Development of soil microbial communities along ecological succession is crucial for ecosystem recovery and maintenance. However, mechanisms mediating microbial community dynamics and co-occurrence patterns along ecological succession remain unclear. Here, we explored community dynamics and taxa co-occurrence patterns in bacterial and fungal communities across a well-established chronosequence of post-mining lands spanning 54 years of recovery. Meanwhile, by synthesizing previous studies and ecological theories, we devised two conceptual models that integrate microbial phylogeny with patterns in community dynamics and in taxa co-occurrence. We further tested these models by using empirical data. At early successional stages, bacterial community structures became increasingly phylogenetically clustered with soil age, which was co-determined by the environmental selection from soil vegetation cover and by heterogeneous responses of less phylogenetically similar bacteria to the increasing resource availability along succession. At later successional stages, bacterial community phylogenetic structures displayed progressively lower variability. The fungal community phylogenetic structures varied relatively less and were independent of soil age, soil properties and vegetation cover, which was attributed to the dominance of stochastic processes in community turnover along succession. Network analysis revealed a decrease in bacterial co-occurrence complexity along succession, which aligned with a decrease in average pairwise phylogenetic distances between co-occurring bacteria. These patterns together implied a decrease in potential bacterial cooperation that was probably mediated by increasing resource availability along succession. The increased complexity of fungal co-occurrence along succession was independent of phylogenetic distances between co-occurring fungi. This study provides new sights into ecological mechanisms underlying bacterial and fungal community succession.
Genetic structure correlates with ethnolinguistic diversity in eastern and southern Africa
Authors: Atkinson Elizabeth G. , Dalvie Shareefa , Pichkar Yakov , Kalungi Allan , Majara Lerato , Stevenson Anne , Abebe Tamrat , Akena Dickens , Alemayehu Melkam , Ashaba Fred K. , Atwoli Lukoye , Baker Mark , Chibnik Lori B. , Creanza Nicole , Daly Mark J. , Fekadu Abebaw , Gelaye Bizu , Gichuru Stella , Injera Wilfred E. , James Roxanne , Kariuki Symon M. , Kigen Gabriel , Koen Nastassja , Koenen Karestan C. , Koenig Zan , Kwobah Edith , Kyebuzibwa Joseph , Musinguzi Henry , Mwema Rehema M. , Neale Benjamin M. , Newman Carter P. , Newton Charles R.J.C. , Ongeri Linnet , Ramachandran Sohini , Ramesar Raj , Shiferaw Welelta , Stein Dan J. , Stroud Rocky E. , Teferra Solomon , Yohannes Mary T. , Zingela Zukiswa , Martin Alicia R. ,   NeuroGAP-Psychosis Study Team
Published: May 2021

African populations are the most diverse in the world yet are sorely underrepresented in medical genetics research. Here, we examine the structure of African populations using genetic and comprehensive multigenerational ethnolinguistic data from the Neuropsychiatric Genetics of African Populations-Psychosis study (NeuroGAP-Psychosis) consisting of 900 individuals from Ethiopia, Kenya, South Africa, and Uganda. We find that self-reported language classifications meaningfully tag underlying genetic variation that would be missed with consideration of geography alone, highlighting the importance of culture in shaping genetic diversity. Leveraging our uniquely rich multi-generational ethnolinguistic metadata, we track language transmission through the pedigree, observing the disappearance of several languages in our cohort as well as notable shifts in frequency over three generations. We find suggestive evidence for the rate of language transmission in matrilineal groups having been higher than that for patrilineal ones. We highlight both the diversity of variation within the African continent, as well as how within-Africa variation can be informative for broader variant interpretation; many variants appearing rare elsewhere are common in parts of Africa. The work presented here improves the understanding of the spectrum of genetic variation in African populations and highlights the enormous and complex genetic and ethnolinguistic diversity within Africa.
A Modular Platform for Streamlining Automated Cryo-FIB Workflows
Authors: Klumpe Sven , Fung Herman K. H. , Goetz Sara K. , Zagoriy Ievgeniia , Hampoelz Bernhard , Zhang Xiaojie , Erdmann Philipp S. , Baumbach Janina , Müller Christoph W. , Beck Martin , Plitzko Jürgen M. , Mahamid Julia
Published: May 2021

Lamella micromachining by focused ion beam milling at cryogenic temperature (cryo-FIB) has matured into a preparation method widely used for cellular cryo-electron tomography. Due to the limited ablation rates of low Ga+ ion beam currents required to maintain the structural integrity of vitreous specimens, current preparation protocols are time-consuming and labor intensive. The improved stability of new generation cryo-FIB instruments now enables automated operations. Here, we present an open-source software tool, SerialFIB, for creating automated and customizable cryo-FIB preparation protocols. The software encompasses a graphical user interface for easy execution of routine lamellae preparations, a scripting module compatible with available python packages, and interfaces with 3-dimensional correlative light and electron microscopy (CLEM) tools. The software enables the streamlining of advanced cryo-FIB protocols such as multi-modal imaging, CLEM guided preparation and in situ lamella lift-out procedures. Our software therefore provides a foundation for further development of advanced cryogenic imaging and sample preparation protocols.
A hybridoma-derived monoclonal antibody with high homology to the aberrant myeloma light chain
Authors: Pornnoppadol Ghasidit , Zhang Boya , Desai Alec A. , Berardi Anthony , Remmer Henriette A. , Tessier Peter M. , Greineder Colin F.
Published: May 2021

The identification of antibody variable regions in the heavy (VH) and light (VL) chains from hybridomas is necessary for the production of recombinant, sequence-defined monoclonal antibodies (mAbs) and antibody derivatives. This process has received renewed attention in light of recent reports of hybridomas having unintended specificities due to the production of non-antigen specific heavy and/or light chains for the intended antigen. Here we report a surprising finding and potential pitfall in variable domain sequencing of an anti-human CD63 hybridoma. We amplified multiple VL genes from the hybridoma cDNA, including the well-known aberrant Sp2/0 myeloma VK and a unique, full-length VL. After finding that the unique VL failed to yield a functional antibody, we discovered an additional full-length sequence with surprising similarity (~95% sequence identify) to the non-translated myeloma kappa chain but with a correction of its key frameshift mutation. Expression of the recombinant mAb confirmed that this highly homologous sequence is the antigen-specific light chain. Our results highlight the complexity of PCR-based cloning of antibody genes and strategies useful for identification of correct sequences.
Transcriptional states of retroelement-inserted regions and KRAB zinc finger protein association regulate DNA methylation of retroelements in human male germ cells
Authors: Fukuda Kei , Makino Yoshinori , Kaneko Satoru , Okada Yuki , Ichiyanagi Kenji , Shinkai Yoichi
Published: May 2021

DNA methylation, repressive histone modifications, and PIWI-interacting RNAs are essential for controlling retroelement silencing in mammalian germ lines. Dysregulation of retroelement silencing is associated with male sterility. Although retroelement silencing mechanisms have been extensively studied in mouse germ cells, little progress has been made in humans. Here, we show that the Krüppel-associated box domain zinc finger proteins (KRAB-ZFPs) are associated with DNA methylation of retroelements in human primordial germ cells (hPGCs), and hominoid-specific retroelement SINE-VNTR-Alus (SVA) is subjected to transcription-directed de novo DNA methylation during human spermatogenesis. Furthermore, we show that the degree of de novo DNA methylation in SVAs varies among human individuals, which confers a significant inter-individual epigenetic variation in sperm. Collectively, our results provide potential molecular mechanisms for the regulation of retroelements in human male germ cells.
The unfolded protein response of the endoplasmic reticulum supports mitochondrial biogenesis by buffering non-imported proteins
Authors: Knöringer Katharina , Groh Carina , Krämer Lena , Stein Kevin C. , Hansen Katja G. , Herrmann Johannes M. , Frydman Judith , Boos Felix
Published: May 2021

Almost all mitochondrial proteins are synthesized in the cytosol and subsequently targeted to mitochondria. The accumulation of non-imported precursor proteins occurring upon mitochondrial dysfunction can challenge cellular protein homeostasis. Here we show that blocking protein translocation into mitochondria results in the accumulation of mitochondrial membrane proteins at the endoplasmic reticulum, thereby triggering the unfolded protein response (UPRER). Moreover, we find that mitochondrial membrane proteins are also routed to the ER under physiological conditions. The levels of ER-resident mitochondrial precursors is enhanced by import defects as well as metabolic stimuli that increase the expression of mitochondrial proteins. Under such conditions, the UPRER is crucial to maintain protein homeostasis and cellular fitness. We propose the ER serves as a physiological buffer zone for those mitochondrial precursors that can’t be immediately imported into mitochondria while engaging the UPRER to adjust the ER proteostasis capacity to the extent of precursor accumulation.
Cell-free Expression of Proton-Coupled Folate Transporter in the Presence of Nanodiscs
Authors: Do Hoa Quynh , Bassil Carla M. , Andersen Elizabeth I. , Jansen Michaela
Published: May 2021

The Proton-Coupled Folate Transporter (PCFT) is a transmembrane transport protein that controls the absorption of dietary folates in the small intestine. PCFT also mediates uptake of chemotherapeutically used antifolates into tumor cells. PCFT has been identified within lipid rafts observed in phospholipid bilayers of plasma membranes, a micro environment that is altered in tumor cells. The present study aimed at investigating the impact of different lipids within Lipid-protein nanodiscs (LPNs), discoidal lipid structures stabilized by membrane scaffold proteins, to yield soluble PCFT expression in an E. coli lysate-based cell-free transcription/translation system. In the absence of detergents or lipids, we observed PCFT quantitatively as precipitate in this system. We then explored the ability of LPNs to support solubilized PCFT expression when present during in-vitro translation. LPNs consisted of either dimyristoyl phosphatidylcholine (DMPC), palmitoyl-oleoyl phosphatidylcholine (POPC), or dimyristoyl phosphatidylglycerol (DMPG). While POPC did not lead to soluble PCFT expression, both DMPG and DMPC supported PCFT translation directly into LPNs, the latter in a concentration dependent manner. The results obtained through this study provide insights into the lipid preferences of PCFT. Membrane-embedded or solubilized PCFT will enable further studies with diverse biophysical approaches to enhance the understanding of the structure and molecular mechanism of folate transport through PCFT.

Highlights

Cell free expression of PCFT without any lipids or detergents resulted in quantitative precipitation of in-situ synthesized PCFT.

Additives for expression of PCFT in the soluble fraction were identified.