bluuebunny/crossref_metadata_2025 huggingface dataset:
Linking cells across single-cell modalities by synergistic matching of neighborhood structure
Authors: Hristov Borislav H. , Bilmes Jeffrey A. , Noble William S.
Published: May 2022

A wide variety of experimental methods are available to characterize different properties of single cells in a complex biosample. However, because these measurement techniques are typically destructive, researchers are often presented with complementary measurements from disjoint subsets of cells, providing a fragmented view of the cell’s biological processes. This creates a need for computational tools capable of integrating disjoint multi-omics data. Because different measurements typically do not share any features, the problem requires the integration to be done in unsupervised fashion. Recently, several methods have been proposed that project the cell measurements into a common latent space and attempt to align the corresponding low-dimensional manifolds. In this study we present an approach, Synmatch, which produces a direct matching of the cells between modalities by exploiting information about neighborhood structure in each modality. Synmatch relies on the intuition that cells which are close in one measurement space should be close in the other as well. This allows us to formulate the matching problem as a constrained supermodular optimization problem over neighborhood structures that can be solved efficiently. We show that our approach successfully matches cells in small real multi-omics datasets and performs favorably when compared to recently published state-of-the-art methods. Further, we demonstrate that Synmatch is capable of scaling to large datasets of thousands of cells. The Synmatch code and data used in this manuscript are available at https://github.com/orgs/Noble-Lab/synmatch
An Open-Source Computational Tool for Measuring Bacterial Biofilm Morphology and Growth Kinetics upon One-Sided Exposure to an Anti-Microbial Source
Authors: Gingichashvili Sarah , Steinberg Doron , Sionov Ronit V. , Feuerstein Osnat , Cohen Noa E.
Published: May 2022

Bacillus subtilis biofilms are well known for their complex and highly adaptive morphology. Indeed, their phenotypical diversity and intra-biofilm heterogeneity make this gram-positive bacterium the subject of many scientific papers on the structure of biofilms. The ‘robustness’ of biofilms is a term often used to describe their level of susceptibility to anti-microbial agents and various mechanical and molecular inhibition/eradication methods. In this paper, we use computational analytics to quantify Bacillus subtilis morphological response to proximity to an anti-microbial source, in the form of the antiseptic chlorhexidine. Chlorhexidine droplets, placed in proximity to Bacillus subtilis macrocolonies at different distances result in morphological changes, quantified using Python-based code, which we have made publicly available. Our results quantify peripheral and inner core deformation as well as differences in cellular viability of the two regions. The results reveal that the inner core, which is often characterized by the presence of wrinkled formations in the macrocolony, is more preserved than the periphery. Furthermore, the paper describes a crescent shaped colony morphology which occurs when the distance from the chlorhexidine source is 0.5 cm, as well as changes observed in the growth substrate of macrocolonies exposed to chlorhexidine.
Profound geroprotection from brief rapamycin treatment in early adulthood by persistently increased intestinal autophagy
Authors: Juricic Paula , Lu Yu-Xuan , Leech Thomas , Drews Lisa F. , Paulitz Jonathan , Lu Jiongming , Nespital Tobias , Azami Sina , Regan Jennifer C. , Funk Emilie , Fröhlich Jenny , Grönke Sebastian , Partridge Linda
Published: May 2022

The licensed drug rapamycin has potential to be repurposed for geroprotection. A key challenge is to avoid adverse side-effects from continuous dosing regimes. Here we show a profound memory effect of brief, early rapamycin treatment of adults, which extended lifespan in Drosophila to the same degree as lifelong dosing. Lasting memory of earlier rapamycin treatment was mediated by elevated autophagy in enterocytes of the gut, accompanied by increased levels of intestinal lysosomal alpha-mannosidase V (LManV), proteins involved in branched-chain amino acid metabolism and lysozyme levels, and by maintained structure and function of the ageing intestine. Brief elevation of autophagy in early adulthood itself induced a long-term increase in autophagy. In mice, a short-term, 3-month treatment in early adulthood also induced a memory effect, with maintenance similar to that seen with chronic treatment, of lysozyme distribution, Man2B1 level in intestinal crypts, Paneth cell architecture and gut barrier function, even 6 months after rapamycin was withdrawn. The geroprotective effects of chronic rapamycin treatment can thus be obtained with a brief pulse of the drug in early adulthood.
Evaluation of sex differences in laser-induced choroidal neovascularization severity, phenotype and disease progression
Authors: Pearsall Elizabeth A.
Published: May 2022

Age-related macular degeneration (AMD) progresses through two phases: a non-exudative “dry” stage that compromises vision but does not involve angiogenesis, and an angiogenic “wet” phase characterized by choroidal neovascularization (CNV), in which neovessels from the choroid break through the Bruch’s membrane to form neovascular lesions in the macula. If left untreated, CNV leads to permanent central blindness, which the current standard of care (anti-VEGF therapy) arrests but does not reverse. In laser-induced CNV, a laser is used to rupture the Bruch’s membrane, prompting the outgrowth of choroidal blood vessels in a wound healing response. This model was used to develop currently available CNV therapeutics, such as intravitreal injection of anti-VEGF and corticosteroid therapies and is considered a gold standard model for CNV. Laser-induced CNV thus remains a highly clinically relevant model of CNV secondary to AMD and other pathologies, such as myopia. A rapidly growing body of research suggests that the pathogenesis of myriad diseases is highly dependent on biological sex, yet most studies use only male animals. This highlights the importance of determining whether the severity and pathogenesis of commonly used models of disease, for example laser-induced CNV, differ between sexes. In the present study, we tracked longitudinal progression and pathogenesis of laser-induced CNV in male and female animals, and found that CNV severity did not differ between sexes. This lack of difference recapitulates findings in human patients with CNV, which have also identified that both sexes are at equal risk of CNV development in the contexts of both age-related macular degeneration induced CNV and myopic CNV.
Mesostats — A multiplexed, low-cost, do-it-yourself continuous culturing system for experimental evolution of mesocosms
Authors: Hansson Erika M , Childs Dylan Z , Beckerman Andrew P
Published: May 2022

Microbial experimental evolution allows studying evolutionary dynamics in action and testing theory predictions in the lab. Experimental evolution in chemostats (i.e. continuous flow through cultures) has recently gained increased interest as it allows tighter control of selective pressures compared to static batch cultures, with a growing number of efforts to develop systems that are easier and cheaper to construct. This protocol describes the design and construction of a multiplexed chemostat array (dubbed “mesostats”) designed for cultivation of algae in 16 concurrent populations, specifically intended for studying adaptation to herbicides. We also present control data from several experiments run on the system to show replicability, data illustrating the effects of common issues like leaks, contamination and clumps, and outline possible modifications and adaptations of the system for future research.
Statistical learning of distractor co-occurrences facilitates visual search
Authors: Thorat Sushrut , Quek Genevieve , Peelen Marius V.
Published: May 2022

Visual search is facilitated by knowledge of the relationship between the target and the distractors, including both where the target is likely to be amongst the distractors and how it differs from the distractors. Whether the statistical structure amongst distractors themselves, unrelated to target properties, facilitates search is less well understood. Here, we assessed the benefit of distractor structure using novel shapes whose relationship to each other was learned implicitly during visual search. Participants searched for target items in arrays of shapes that comprised either four pairs of co-occurring distractor shapes (structured scenes) or eight distractor shapes randomly partitioned into four pairs on each trial (unstructured scenes). Across five online experiments (N=1140), we found that after a period of search training, participants were more efficient when searching for targets in structured than unstructured scenes. This structure-benefit emerged independently of whether the position of the shapes within each pair was fixed or variable, and despite participants having no explicit knowledge of the structured pairs they had seen. These results show that implicitly learned co-occurrence statistics between distractor shapes increases search efficiency. Increased efficiency in the rejection of regularly co-occurring distractors may contribute to the efficiency of visual search in natural scenes, where such regularities are abundant.
Spatiotemporal Profiling of Seed-Associated Microbes of an Aquatic, Intermediate Recalcitrant Species,Zizania palustrisL. and the Impact of Anti-Microbial Seed Treatments
Authors: Gietzel Clare , McGilp Lillian , Kimball Jennifer A.
Published: May 2022

Northern wild rice (NWR;Zizania palustrisvar.interior) (NWR) is an ecologically important, annual, aquatic species native to North America, that is also cultivated in irrigated paddies in Minnesota and California. NWR seeds are desiccation-sensitive and must be kept in hydrated conditions, in which viability can decline rapidly within the first two years of storage. During this period, microbial growth is rampant and the relationship between these communities and the viability of NWR seed is unclear. In this study, we cultured and identified bacteria and fungi found in 27 NWR seed stocks, collected over a five-year period from three locations and four NWR genotypes. Results revealed that microbial communities were heavily dependent on seed viability and communities began shifting after one year of seed storage. Fungi became more prominent as years in storage increased suggesting that fungi begin to outcompete bacteria. Spatial analysis of locations and genotypes revealed a core set of microbes found across locations and genotypes.PenicilliumandPseudomonaswere ubiquitous in NWR hydrated seed storage. We also evaluated the efficacy of four antimicrobial treatments at reducing microbial growth in hydrated NWR seed storage. These treatments did not reduce or drastically change microbial growth or seed viability. However, previously undetected microbes were identified after treatments, which suggested a disruption to the major constituents of the microbiome. Overall, this study identified common microbial constituents found in an aquatic, recalcitrant species, adapted for a cold climate, during seed storage and provides a foundation for future studies to evaluate the effect of microbial communities on NWR seed viability during hydrated storage.
Importance of Mobile Genetic Element Immunity in Numerically AbundantTrichodesmiumClades
Authors: Webb Eric A. , Held Noelle A. , Zhao Yiming , Graham Elaina , Conover Asa E. , Semones Jake , Lee Michael D. , Feng Yuanyuan , Fu Feixue , Saito Mak A. , Hutchins David A.
Published: May 2022

The colony-forming cyanobacteriaTrichodesmiumspp. are considered one of the most important nitrogen-fixing genera in the warm, low nutrient, open ocean. Despite this central biogeochemical role, many questions about their evolution, physiology, and trophic interactions remain unanswered. To address these questions, we describe the genetic potential of the genus via significantly improved genomic assemblies of strainsTrichodesmium thiebautiiH94,Trichodesmium erythraeum2175, and 17 newTrichodesmiummetagenome-assembled genomes (MAGs, >50% complete) from hand-picked,Trichodesmiumcolonies spanning the Atlantic Ocean. Phylogenomics identified ∼four N2fixing clades ofTrichodesmiumacross the transect, withT. thiebautiidominating the colony-specific reads. Pangenomic analyses showed that allT. thiebautiiMAGs are enriched in defense mechanisms and encode a vertically inherited Type III-B Clustered Regularly Interspaced Short Palindromic Repeats and associated protein-based immunity system (CRISPR-Cas hereafter). Surprisingly, this CRISPR-Cas system was absent in allT. erythraeumgenomes and MAGs, vertically inherited byT. thiebautii, and correlated with increased signatures of horizontal gene transfer. Multiple lines of evidence indicate that the CRISPR-Cas system is functional in situ: 1.TrichodesmiumCRISPR spacer sequences with 100% identical hits to field-assembled, putative phage genome fragments were identified, 2. HighTrichodesmiumspacer sequence variability indicating rapid adaptation, and 3. metaproteomic and transcriptomic expression analyses detecting the CRISPR-Cas system components inTrichodesmiumcolonies from the Atlantic and Pacific Oceans. These data suggest that phage or mobile genetic element immunity inT. thiebautiicould contribute to their success, gene diversity, and numerical dominance overT. erythraeumin the oceans, thus warranting furtherTrichodesmiumvirome investigations.

Significance statement

Our work identifies CRISPR-Cas immunity as a phylogenetically distinct, environmentally expressed factor in the speciation of closely related N2-fixingTrichodesmiumclades. These findings suggest that differential phage predation and resistance could be a previously overlooked selective pressure in the genus, potentially leading to the current numerical dominance ofT. thiebautiioverT. erythraeumin the oceans. Furthermore, while the currently CO2-limitedT. erythraeumis expected to be a ‘winner’ of anthropogenic climate change, their predicted higher phage sensitivity thanT. thiebautiicould challenge this outcome.
Histone H2A serine-1 phosphorylation is a chaperone dependent signal for dimerization with H2B and for enhanced deposition
Authors: Onikubo Takashi , Wang Wei-Lin , Shechter David
Published: May 2022

Multiple histone chaperones and histone modifications are involved in the folding, transport, and re-lease of histones onto newly replicated DNA. Little is known about histone H2A-H2B pre-deposition his-tone modifications and their regulation of histone deposition. We previously showed that H2A serine 1 phosphorylation (H2AS1ph) is enriched on the soluble egg histones and on zygotic chromatin in Xenopus embryos. Here, we demonstrate that H2AS1 phosphorylation is required for a timely incorporation of H2A-H2B into the pronuclear chromatin. Our analysis revealed that exogenous H2AS1A-H2B dimers were poorly incorporated into pronuclei in egg extract compared with wildtype and H2AS1E-H2B dimers. Chaperone-mediated deposition using histones purified from pronuclei showed that neither Nap1 nor Nucleoplasmin (Npm2) histone deposition was directly affected by endogenous histone posttranslational modification. We further demonstrate that H2AS1 phosphorylation was dependent on Npm2 and required H2B. Surprisingly, Nap1 was incapable of promoting H2AS1 phosphorylation. These results suggest that serine 1 phosphorylation signals a specific state of H2A-H2B dimer bound by Nucleoplasmin. Neither Npm2 nor Nap1 exhibited preference for binding H2AS1A or H2AS1E mutant histones or dimers with H2B in vitro. We propose that H2AS1 phosphorylation is a pre-deposition modification that signals for the proper dimerization of H2A-H2B, which in turn activates downstream effectors leading to H2A-H2B deposition.
Vegetation formation in Staphylococcus aureus endocarditis inversely correlates with RNAIII and sarA expression in invasive clonal complex 5 (CC5) isolates
Authors: Kinney Kyle J. , Stach Jessica M. , Kulhankova Katarina , Brown Matthew , Salgado-Pabón Wilmara
Published: May 2022

Infective endocarditis (IE) is one of the most feared and lethal diseases caused by Staphylococcus aureus. Once established, the infection is fast-progressing and tissue destructive. S. aureus of the clonal complex 5 (CC5) commonly cause IE yet are severely understudied. IE results from bacterial colonization and formation of tissue biofilms (known as vegetations) on injured or inflamed cardiac endothelium. S. aureus IE is promoted by adhesins, coagulases, and superantigens, with the exotoxins and exoenzymes likely contributing to tissue destruction and dissemination. Expression of the large repertoire of virulence factors required for IE and sequelae is controlled by complex regulatory networks. We investigated the temporal expression of the global regulators agr (RNAIII), rot, sarS, sarA, sigB, and mgrA in 8 invasive CC5 isolates and established intrinsic expression patterns associated with IE outcomes. We show that vegetation formation, as tested in the rabbit model of IE, inversely correlates with RNAIII and sarA expression during growth in Todd-Hewitt broth (TH). Large vegetations with severe sequelae arise from strains with high-level expression of colonization factors but slower transition towards expression of the exotoxins. Overall, strains proficient in vegetation formation, a hallmark of IE, exhibit lower expression of RNAIII and sarA. Simultaneous high expression of RNAIII, sarA, sigB, and mgrA is the one phenotype assessed in this study that fails to promote IE. Thus, RNAIII and sarA expression that provides for rheostat control of colonization and virulence genes, rather than an on and off switch, promote both vegetation formation and lethal sepsis.
A Coxiella burnetii effector interacts with the host PAF1 complex and suppresses the innate immune response
Authors: Fischer Natasha Lopes , Boyer Mark A. , Bradley William P. , Spruce Lynn A. , Fazelinia Hossein , Shin Sunny
Published: May 2022

Intracellular bacteria such as the pathogen Coxiella burnetii inject effector proteins into the host cell that promote productive infection. One common strategy of pathogen effectors is to suppress host immune responses to enable pathogen replication. The C. burnetii type IV secretion system translocates a large number of effectors into host cells that collectively promote intracellular bacterial replication, but the individual functions of most of these effectors are poorly understood. In this study, we describe a C. burnetii effector, CBU1314, that localizes to the nucleus and inhibits NF-κB-, MAPK-, and type I IFN-dependent gene expression. Mechanistically, we find that CBU1314 interacts with the PAF1 complex (PAF1C), a central host transcriptional complex that regulates expression of inflammatory genes in innate immune cells. Notably, we find that PAF1 promotes immune gene expression in response to various immune agonists and C. burnetii infection. Moreover, we find that PAF1 is critical for restricting intracellular C. burnetii replication. Overall, our findings uncover PAF1C as a host target of a C. burnetii effector and reveal new insight into how intracellular bacterial pathogens subvert cell- intrinsic innate defenses.

Significance

Intracellular bacteria often employ secreted effector proteins to modulate cellular processes and survive intracellularly. The study of these effectors can provide valuable insight into microbial pathogenesis and host biology. Here, we describe a Coxiella burnetii effector that inhibits multiple host signaling pathways and modulates the innate immune response. This effector interacts with the host PAF1 complex (PAF1C), a central regulator of transcription. Furthermore, we show that PAF1 is necessary for maximal gene expression downstream of various innate immune receptors and restricts bacterial replication during infection. Overall, our study elucidates the function of a C. burnetii effector in evading the immune response and provides insight into the role of PAF1C in cell-intrinsic defense against bacterial pathogens.
Is single nucleus ATAC-seq accessibility a qualitative or quantitative measurement?
Authors: Miao Zhen , Kim Junhyong
Published: May 2022

Single nucleus ATAC-seq is a key assay for gene regulation analysis. Existing approaches to scoring feature matrices from sequencing reads are inconsistent with each other, creating differences in downstream analysis, and displaying artifacts. We show that even with sparse single cell data, quantitative counts are informative for estimating a cell’s regulatory state, which calls for consistent treatment. We propose Paired-Insertion-Counting (PIC) as a uniform method for snATAC-seq feature characterization.
Intrinsic furin-mediated cleavability of the spike S1/S2 site from SARS-CoV-2 variant B.1.1.529 (Omicron)
Authors: Lubinski Bailey , Jaimes Javier A. , Whittaker Gary R.
Published: May 2022

The ability of SARS-CoV-2 to be primed for viral entry by the host cell protease furin has become one of the most investigated of the numerous transmission and pathogenicity features of the virus. SARS-CoV-2 The variant B.1.1.529 (Omicron) emerged in late 2020 and has continued to evolve and is now present in several distinct sub-variants. Here, we analyzed the “furin cleavage site” of the spike protein of SARS-CoV-2 B.1.1.529 (Omicron variant) in vitro, to assess the role of two key mutations (spike, N679K and P681H) that are common across all subvariants compared to the ancestral B.1 virus and other notable lineages. We observed significantly increased intrinsic cleavability with furin compared to an original B lineage virus (Wuhan-Hu1), as well as to two variants, B.1.1.7 (Alpha) and B.1.617 (Delta) that subsequently had wide circulation. Increased furin-mediated cleavage was attributed to the N679K mutation, which lies outside the conventional furin binding pocket. Our findings suggest that B.1.1.529 (Omicron variant) has gained genetic features linked to intrinsic furin cleavability, in line with its evolution within the population as the COVID-19 pandemic has proceeded.
A remarkable expansion of oligopeptide transporter genes in rust fungi (Pucciniales) suggests a specialization in nutrients acquisition for obligate biotrophy
Authors: Guerillot Pamela , Salamov Asaf , Louet Clémentine , Morin Emmanuelle , Frey Pascal , Grigoriev Igor V. , Duplessis Sébastien
Published: May 2022

Nutrients acquisition by rust fungi during their biotrophic growth has been assigned to a few transporters expressed in haustorial infection structures. We performed a comparative genomic analysis of all transporter genes (hereafter termed transportome) classified according to the Transporter Classification Database (TCDB) focusing specifically on rust fungi (order Pucciniales) versus other species in the Dikarya. We also surveyed expression of transporter genes in the poplar rust fungus for which transcriptomics data are available across the whole life cycle. Despite a significant increase in gene number, rust fungi presented a reduced transportome compared to a vast majority of fungi in the Dikarya. However, a few transporter families in the subclass Porters showed significant expansions. Noteworthy, three metal transport-related families involved in the import, export and sequestration of metals were expanded in Pucciniales and expressed at various stages of the rust life cycle suggesting a tight regulation of metal homeostasis. The most remarkable gene expansion in the Pucciniales was observed for the oligopeptide transporter (OPT) family with 25 genes in average compared to seven to 14 genes in the other surveyed taxonomical ranks. A phylogenetic analysis showed several specific expansion events at the root of the order Pucciniales with subsequent expansions in rust taxonomical families. The OPT genes showed dynamic expression patterns along the rust life cycle and more particularly during infection of the poplar host tree, suggesting a specialization for the acquisition of nitrogen and sulfur through the transport of oligopeptides from the host during biotrophic growth.
CandidatusNealsonbacteria (OD1) are biomass recycling ectosymbionts of methanogenic archaea in a stable benzene-degrading enrichment culture
Authors: Chen Xu , Molenda Olivia , Brown Christopher T. , Toth Courtney R. A. , Guo Shen , Luo Fei , Howe Jane , Nesbø Camilla L. , He Christine , Montabana Elizabeth A. , Cate Jamie H. D. , Banfield Jillian F. , Edwards Elizabeth A.
Published: May 2022

The Candidate Phyla Radiation (CPR) is a very large group of bacteria with no pure culture representatives, first discovered by metagenomic analyses. Within the CPR, candidate phylum Parcubacteria (previously referred to as OD1) within the candidate superphylum Patescibacteria is prevalent in anoxic sediments and groundwater. Previously, we had identified a specific member of the Parcubacteria (referred to as DGGOD1a) as an important member of a methanogenic benzene-degrading consortium. Phylogenetic analyses herein place DGGOD1a within theCandidateclade Nealsonbacteria. Because of its persistence over many years, we hypothesized thatCa. Nealsonbacteria DGGOD1a must serve an important role in sustaining anaerobic benzene metabolism in the consortium. To try to identify its growth substrate, we amended the culture with a variety of defined compounds (pyruvate, acetate, hydrogen, DNA, phospholipid), as well as crude culture lysate and three subfractions thereof. We observed the greatest (10 fold) increase in the absolute abundance ofCa. Nealsonbacteria DGGOD1a only when the consortium was amended with crude cell lysate. These results implicateCa. Nealsonbacteria in biomass recycling. Fluorescent in situ hybridization and cryogenic transmission electron microscope images revealed thatCa. Nealsonbacteria DGGOD1a cells were attached to larger archaealMethanothrixcells. This apparent epibiont lifestyle was supported by metabolic predictions from a manually curated complete genome. This is one of the first examples of bacterial-archaeal episymbiosis and may be a feature of otherCa. Nealsonbacteria found in anoxic environments.
In silico identification of novel peptides as potential modulators of Aβ42 Amyloidogenesis
Authors: Kundal Kavita , Paramasivam Santhosh , Mitra Amit , Sarkar Nandini
Published: May 2022

Alzheimer’s Disease is a neurodegenerative disease for which no cure is available at present. The presence of amyloid plaques in the extracellular space of neural cells is the key feature of this fatal disease. Amyloid-Beta (Aβ) is a 40-42 amino acid peptide and the main component of amyloid plaques. This peptide is produced by the proteolysis of Amyloid Precursor Protein by presenilin. Deposition of 42 residual Aβ peptides forms fibrils structure, leading to disruption of neuron synaptic transmission, inducing neural cell toxicity, ultimately leading to neuron death. To modulate the amyloidosis of Aβ peptides, various novel peptides have been investigated via molecular docking and molecular dynamic simulation studies. The sequence-based peptides were designed and investigated for their interaction with Aβ42 monomer and fibril using the molecular docking method, and their influence on the structural stability of target proteins was studied using molecular simulations. According to the docking results, amongst all the synthetic peptides, the peptide YRIGY (P6) has the highest binding affinity with Aβ42 fibril, and the peptide DKAPFF (P12) shows better binding with Aβ42 monomer. Moreover, simulation results also suggest that the higher the binding affinity, the better the inhibitory action. From these findings, it is suggested that both the peptides can modulate the amyloidogenesis, but peptide (P6) has better potential for the disaggregation of the fibrils, whereas peptide P12 stabilizes the native structure of the Aβ42 monomer more effectively and hence can serve as a potential amyloid inhibitor. Thus, these peptides can be explored as therapeutic agents against Alzheimer’s Disease.
Subcortical brain volumes in young infants exposed to antenatal maternal depression: Findings from a South African birth cohort
Authors: Groenewold Nynke A. , Wedderburn Catherine J. , Pellowski Jennifer A. , Fouché Jean-Paul , Michalak Liza , Roos Annerine , Woods Roger P. , Narr Katherine L. , Zar Heather J. , Donald Kirsten A. , Stein Dan J.
Published: May 2022

Background

Several studies have reported enlarged amygdala and smaller hippocampus volumes in children and adolescents exposed to maternal depression. It is unclear whether similar volumetric differences are detectable in the infants’ first weeks of life, following exposurein utero. We investigated subcortical volumes in 2-to-6 week old infants exposed to antenatal maternal depression (AMD) from a South African birth cohort.

Methods

AMD was measured with the Beck Depression Inventory 2ndedition (BDI-II) at 28-32 weeks gestation. T2-weighted structural images were acquired during natural sleep on a 3T Siemens Allegra scanner. Subcortical regions were segmented based on the University of North Carolina neonatal brain atlas. Volumetric estimates were compared between AMD-exposed (BDI-II⍰20) and unexposed (BDI-II<14) infants, adjusted for age, sex and total intracranial volume using analysis of covariance.

Results

Larger volumes were observed in AMD-exposed (N=49) compared to unexposed infants (N=75) for the right amygdala (1.98% difference,p=0.039) and bilateral caudate nucleus (left: 5.78% difference, p=0.001; right: 6.06% difference,p<0.001). A significant AMD-by-sex interaction was found for the hippocampus (left:F(1,118)=4.80,p=0.030; right:F(1,118)=5.16,p=0.025), reflecting greater volume in AMD-exposed females (left: 5.09% difference,p=0.001, right: 3.53% difference,p=0.010), but not males.

Conclusions

Volumetric differences in subcortical regions can be detected in AMD-exposed infants soon after birth, suggesting structural changes may occurin utero. Female infants might exhibit volumetric changes that are not observed in male infants. The potential mechanisms underlying these early volumetric differences, and their significance for long-term child mental health, require further investigation.
Usage and awareness of antiviral medications for COVID-19
Authors: Kojima N , Klausner JD
Published: May 2022

We surveyed people that recently tested positive for SARS-CoV-2 to assess the frequency and correlates of early treatment seeking behavior. Among high risk respondents, 66.0% were aware of treatment for COVID-19 and 36.3% had sought treatment, however only 1.7% reported use of an antiviral for SARS-CoV-2 infection. More public outreach is needed to raise awareness of the benefits of treatment for COVID-19.
SORLA mediates endocytic uptake of proIAPP and protects against islet amyloid deposition
Authors: Shih Alexis Z.L. , Chen Yi-Chun , Verchere C. Bruce , Willnow Thomas E.
Published: May 2022

Aims/ hypothesis

Sorting-related receptor with type A repeats (SORLA) is a neuronal sorting receptor that prevents accumulation of amyloid-beta peptides, the main constituent of senile plaques in Alzheimer disease. Recent transcriptomic studies show that SORLA transcripts are also found in pancreatic islet beta cells, yet the role of SORLA in islets is unclear so far. Based on its protective role in reducing amyloid burden in the brain, we hypothesized that SORLA may have a similar function in the pancreas, regulating islet amyloid plaque formation from islet amyloid polypeptide (IAPP).

Methods

We generated human IAPP transgenic mice lacking SORLA (hIAPP:SORLA KO) to assess the consequences of receptor deficiency for islet histopathology and functionin vivo. Using both primary islet cells and established cell lines, we further investigated the molecular mechanisms whereby SORLA controls the cellular metabolism and accumulation of IAPP.

Results

Loss of SORLA activity in hIAPP:SORLA KO resulted in a significant increase in islet amyloid deposits and associated islet cell death as compared to hIAPP:SORLA WT animals expressing the receptor. Aggravated islet amyloid deposition was observed in mice fed a normal chow diet, not requiring high-fat diet feeding typically needed to induce islet amyloidosis in mouse models. Furtherin vitrostudies showed that SORLA binds to and mediates the endocytic uptake of proIAPP, but not mature IAPP, delivering the propeptide to an endolysosomal fate.

Conclusions/interpretation

SORLA functions as a clearance receptor specific for proIAPP, protecting against islet amyloid deposition and associated cell death caused by IAPP.
Conservation and divergence of canonical and non-canonical imprinting in murids
Authors: Albert Julien Richard , Kobayashi Toshihiro , Inoue Azusa , Monteagudo-Sánchez Ana , Kumamoto Soichiro , Takashima Tomoya , Miura Asuka , Oikawa Mami , Miura Fumihito , Takada Shuji , Hirabayashi Masumi , Korthauer Keegan , Kurimoto Kazuki , Greenberg Maxim , Lorincz Matthew , Kobayashi Hisato
Published: May 2022

Background

Genomic imprinting affects gene expression in a parent-of-origin manner and has a profound impact on complex traits including growth and behaviour. While the rat is widely used to model human pathophysiology, few imprinted genes have been identified in this murid. To systematically identify imprinted genes and genomic imprints in the rat, we used low input methods for genome-wide analyses of gene expression and DNA methylation to profile embryonic and extra-embryonic tissues at allele-specific resolution.

Results

We identify 14 and 26 imprinted genes in these tissues, respectively, with 10 of these genes imprinted in both tissues. Comparative analyses with mouse revealed that orthologous imprinted gene expression and associated canonical DNA methylation imprints are conserved in the embryo proper of the Muridae family. However, only 3 paternally expressed imprinted genes are conserved in the extra-embryonic tissue of murids, all of which are associated with non-canonical H3K27me3 imprints. The discovery of 8 novel non-canonical imprinted genes unique to the rat is consistent with more rapid evolution of extra-embryonic imprinting. Meta-analysis of novel imprinted genes revealed multiple mechanisms by which species-specific imprinted expression may be established, including H3K27me3 deposition in the oocyte, the birth of ZFP57 binding motifs and the insertion of endogenous retroviral promoters.

Conclusions

In summary, we provide a comprehensive list of imprinted loci in the rat, reveal the extent of conservation of imprinted gene expression, and identify potential mechanisms responsible for the evolution of species-specific imprinting.
Rising Temperature Drives Tipping Points in Mutualistic Networks†
Authors: Bhandary Subhendu , Deb Smita , Dutta Partha Sharathi
Published: May 2022

The effect of climate warming on species physiological parameters, including growth rate, mortality rate, and handling time, is well established from empirical data. However, with an alarming rise in global temperature more than ever, predicting the interactive influence of these changes on mutualistic communities remains uncertain. Using 139 real plant-pollinator networks sampled across the globe and a modelling approach, we study the impact of species’ individual thermal responses on mutualistic communities. We show that at low mutualistic strength plant-pollinator networks are at potential risk of rapid transitions at higher temperatures. Evidently, generalist species plays a critical role in guiding tipping points in mutualistic networks. Further, we derive stability criteria for the networks in a range of temperatures using a two-dimensional reduced model. We identify network structures that can ascertain the delay of a community collapse. Until the end of this century, many real mutualistic networks can be under the threat of sudden collapse, and we frame strategies to mitigate them. Together, our results indicate that knowing individual species thermal responses and network structure can improve predictions for communities facing rapid transitions.
Birth and Death in Terminal Complement Pathway
Authors: Sharma Ashutosh , Gupta Saumya , Patil Ajinkya Bharatraj , Vijay Nagarjun
Published: May 2022

The cytolytic activity of the membrane attack complex (MAC) has a crucial role in the complement-mediated elimination of pathogens. Terminal complement pathway (TCP) genes encode the proteins that form the MAC. Although the TCP genes are well conserved within most vertebrate species, the early evolution of the TCP genes is poorly understood. Based on the comparative genomic analysis of the early evolutionary history of the TCP homologs, we evaluated four possible scenarios that could have given rise to the vertebrate TCP. Currently available genomic data support a scheme of complex sequential protein domain gains that may be responsible for the birth of the vertebrateC6gene. The subsequent duplication and divergence of this vertebrateC6gene formed theC7, C8α,C8β, andC9genes. Compared to the widespread conservation of TCP components within vertebrates, we discovered thatC9has disintegrated in the genomes of galliform birds. Publicly available genome and transcriptome sequencing datasets of chicken from Illumina short read, PacBio long read, and Optical mapping technologies support the validity of the genome assembly at theC9locus. In this study, we have generated a >120X coverage whole-genome Chromium 10x linked-read sequencing dataset for the chicken and used it to verify the loss of theC9gene in the chicken. We find multiple CR1 (chicken repeat 1) element insertions within and near the remnant exons ofC9in several galliform bird genomes. The reconstructed chronology of events shows that the CR1 insertions occurred afterC9gene loss in an early galliform ancestor. Our study ofC6gene birth in an early vertebrate ancestor andC9gene death in galliform birds provides insights into the evolution of the TCP.
Towards Synthetic PETtrophy: EngineeringPseudomonas putidafor concurrent polyethylene terephthalate (PET) monomer metabolism and PET hydrolase expression
Authors: Brandenberg Oliver F. , Schubert Olga T. , Kruglyak Leonid
Published: May 2022

Background

Biocatalysis offers a promising path for plastic waste management and valorization, especially for hydrolysable plastics such as polyethylene terephthalate (PET). Microbial whole-cell biocatalysts for simultaneous PET degradation and growth on PET monomers would offer a one-step solution toward PET recycling or upcycling. We set out to engineer the industry-proven bacteriumPseudomonas putidafor (i) metabolism of PET monomers as sole carbon sources, and (ii) efficient concurrent extracellular expression of PET hydrolases. We pursued this approach for both PET and the related polyester polybutylene adipate co-terephthalate (PBAT), aiming to learn about the determinants and potential applications of bacterial polyester-degrading biocatalysts.

Results

P. putidawas engineered to metabolize the PET and PBAT monomer terephthalic acid (TA) through genomic integration of four tphII operon genes fromComamonas sp. E6. Efficient cellular TA uptake was enabled by a point mutation in the nativeP. putidamembrane transporter mhpT. Metabolism of the PET and PBAT monomers ethylene glycol and 1,4-butanediol was achieved through adaptive laboratory evolution. We then used fast design-build-test-learn cycles to engineer extracellular PET hydrolase expression, including tests of (i) the three PET hydrolases LCC, HiC, and IsPETase; (ii) genomic versus plasmid-based expression, using expression plasmids with high, medium, and low cellular copy number; (iii) three different promoter systems; (iv) three membrane anchor proteins for PET hydrolase cell surface display; and (v) a 30-mer signal peptide library for PET hydrolase secretion. PET hydrolase surface display and secretion was successfully engineered but often resulted in host cell fitness costs, which could be mitigated by promoter choice and altering construct copy number. Plastic biodegradation assays with the best PET hydrolase expression constructs genomically integrated into our monomer-metabolizingP. putidastrains resulted in various degrees of plastic depolymerization, although self-sustaining bacterial growth remained elusive.

Conclusion

Our results show that balancing extracellular PET hydrolase expression with cellular fitness under nutrient-limiting conditions is a challenge. The precise knowledge of such bottlenecks, together with the vast array of PET hydrolase expression tools generated and tested here, may serve as a baseline for future efforts to engineerP. putidaor other bacterial hosts towards becoming efficient whole-cell polyester-degrading biocatalysts.
FGF signaling promotes precursor spreading for adult adipogenesis in Drosophila
Authors: Lei Yuting , Huang Yuwei , Yang Ke , Cao Xueya , Song Yuzhao , Martín-Blanco Enrique , Pastor-Pareja José C.
Published: May 2022

Knowledge of adipogenetic mechanisms is essential to understand and treat conditions affecting organismal metabolism and adipose tissue health. In Drosophila, mature adipose tissue (fat body) exists in larvae and adults. In contrast to the well-known development of the larval fat body from the embryonic mesoderm, adult adipogenesis has remained mysterious. Furthermore, conclusive proof of its physiological significance is lacking. Here, we show that the adult fat body originates from a pool of undifferentiated mesodermal precursors that migrate from the thorax into the abdomen during metamorphosis. Through in vivo imaging, we found that these precursors spread from the ventral midline and cover the inner surface of the abdomen in a process strikingly reminiscent of embryonic mesoderm migration, requiring FGF signaling as well. FGF signaling guides migration dorsally and regulates adhesion to the substrate. After spreading is complete, precursor differentiation involves fat accumulation and cell fusion that produces mature binucleate and tetranucleate adipocytes. Finally, we show that flies where adult adipogenesis is impaired by knock down of FGF receptor Heartless or transcription factor Serpent display ectopic fat accumulation in oenocytes and decreased resistance to starvation. Our results reveal that adult adipogenesis occurs de novo during metamorphosis and demonstrate its crucial physiological role.
Neuromuscular denervation and deafferentation but not motor neuron death are disease features in the Smn2B/- mouse model of SMA
Authors: Carlini Maria J. , Triplett Marina K. , Pellizzoni Livio
Published: May 2022

Spinal muscular atrophy (SMA) is a neurodegenerative disease characterized by loss of motor neurons and skeletal muscle atrophy which is caused by ubiquitous deficiency in the survival motor neuron (SMN) protein. Several cellular defects contribute to sensory-motor circuit pathology in SMA mice, but the underlying mechanisms have often been studied in one mouse model without validation in other available models. Here, we used Smn2B/- mice to investigate specific behavioral, morphological, and functional aspects of SMA pathology that we previously characterized in the SMNΔ7 model. Smn2B/- SMA mice on a pure FVB/N background display deficits in body weight gain and muscle strength with onset in the second postnatal week and median survival of 19 days. Morphological analysis revealed severe loss of proprioceptive synapses on the soma of motor neurons and prominent denervation of neuromuscular junctions (NMJs) in axial but not distal muscles. In contrast, no evidence of cell death emerged from analysis of several distinct pools of lumbar motor neurons known to be lost in the disease. Moreover, SMA motor neurons from Smn2B/- mice showed robust nuclear accumulation of p53 but lack of phosphorylation of serine 18 at its amino-terminal, which selectively marks degenerating motor neurons in the SMNΔ7 mouse model. These results indicate that NMJ denervation and deafferentation, but not motor neuron death, are conserved features of SMA pathology in Smn2B/- mice.
Breakpoint models shown no evidence of thresholds in recreational response to increasing wildfire smoke in the American West
Authors: Clark Matt , Killion Alexander , Williamson Matthew A. , Hillis Vicken
Published: May 2022

Ambient wildfire smoke in the American West has worsened considerably in recent decades, while the number of individuals recreating outdoors has simultaneously surged. Wildfire smoke poses a serious risk to human health, especially during long periods of exposure and during exercise. Here we aggregate data on black carbon, a major component of wildfire smoke, and recreational visitation in 32 U.S. national parks from 1980 - 2019 to examine how visitors respond to wildfire smoke. We hypothesize that visitor response may exhibit a threshold effect where ambient smoke reduces visitation after a critical level, but not before. We develop a series of breakpoint models to test this hypothesis. Overall, these models show little to no effect of ambient smoke on visitation to the 32 parks tested, even when allowing for critical thresholds at the extreme upper ranges of the smoke data. This suggests that wildfire smoke does not significantly alter behavior of park attendance. This finding has implications for the management of recreation areas, public health, and climate change adaptation broadly.
Deep sequencing of a large family of isogenic mice enables complex variants discovery and accurate phenotype mapping
Authors: Villani Flavia , Sasani Thomas A , Maksimov Mikhail , Gunturkun Mustafa Hakan , Ma Nichole , Ren Yu-yu , Rothschild Daphna , Chen Hao , Lu Lu , Dumont Beth L , Harris Kelley , Gymrek Melissa , Colonna Vincenza , Pritchard Jonathan K , Palmer Abraham A , Williams Robert W , Ashbrook David G
Published: May 2022

The BXD family of recombinant inbred mice were developed by crossing and inbreeding progeny of C57BL/6J and DBA/2J strains. This family is the largest and most extensively phenotyped mammalian experimental genetic resource. Although used in genetics for 52 years, we do not yet have comprehensive data on DNA variants segregating in the BXDs. Using linked-read whole-genome sequencing, we sequenced 152 members of the family at about 40X coverage and quantified most variants. We identified 6.25 million polymorphism segregating at a near-optimal minor allele frequency of 0.42. We also defined two other major variants: strain-specific de novo singleton mutations and epoch-specific de novo polymorphism shared among subfamilies of BXDs. We quantified per-generation mutation rates of de novo variants and demonstrate how founder-derived, strain-specific, and epoch-specific variants can be analyzed jointly to model genome-phenome causality. This integration enables forward and reverse genetics at scale, rapid production of any of more than 10,000 diallel F1 hybrid progeny to test predictions across diverse environments or treatments. Combined with five decades of phenome data, the BXD family and F1 hybrids are a major resource for systems genetics and experimental precision medicine.
RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription
Authors: Abuhashem Abderhman , Chivu Alexandra G. , Zhao Yixin , Rice Edward J. , Siepel Adam , Danko Charles G. , Hadjantonakis Anna-Katerina
Published: May 2022

Promoter-proximal RNA Pol II pausing is a critical step in transcriptional control. Pol II pausing has been studied predominantly in tissue culture systems. While Pol II pausing has been shown to be required for mammalian development, the phenotypic and mechanistic details of this requirement are unknown. Here, we find that loss of RNA Pol II pausing stalls pluripotent state transitions in the epiblast of the early mouse embryo. Using Nelfb-/- mice and a novel NELFB- degron mouse embryonic stem cells, we show that mouse ES cells (mESCs) representing the naive state of pluripotency successfully initiate a transition program, but fail to balance levels of induced and repressed genes and enhancers in the absence of NELF. Consistently, we find an increase in chromatin-associated NELF during pluripotency transitions. Overall, our work reveals the molecular and phenotypic roles of Pol II pausing in pluripotency and introduces Pol II pausing as a modulator of cell state transitions.