bluuebunny/crossref_metadata_2025 huggingface dataset:
DevelopingWolbachia-based disease interventions for an extreme environment
Authors: Ross Perran A. , Elfekih Samia , Collier Sophie , Klein Melissa J. , Lee Su Shyan , Dunn Michael , Jackson Sarah , Zhang Yexin , Axford Jason K. , Gu Xinyue , Nassar Majed S. , Paradkar Prasad N. , Tawfik Essam A. , Jiggins Francis M. , Almalik Abdulaziz M. , Al-Fageeh Mohamed B. , Hoffmann Ary A.
Published: July 2022

Aedes aegyptimosquitoes carrying self-spreading, virus-blockingWolbachiabacteria are being deployed to suppress dengue transmission. However, there are challenges in applying this technology in extreme environments. We introduced twoWolbachiastrains intoAe. aegyptifrom Saudi Arabia for a release program in the hot coastal city of Jeddah.Wolbachiareduced infection and dissemination of dengue virus (DENV2) in Saudi Arabian mosquitoes and showed complete maternal transmission and cytoplasmic incompatibility.Wolbachiareduced mosquito heat tolerance and egg viability, with theWolbachiastrains showing differential thermal stability.Wolbachiaeffects were similar across mosquito genetic backgrounds but we found evidence of local adaptation, with Saudi Arabian mosquitoes having lower egg viability but higher adult desiccation tolerance than Australian mosquitoes. Genetic background effects will influenceWolbachiainvasion dynamics, reinforcing the need to use local genotypes for mosquito release programs, particularly in extreme environments like Jeddah. Our comprehensive characterization ofWolbachiastrains provides a foundation forWolbachia-based disease interventions in harsh climates.
Multibody kinematic optimisation vs body fat: A performance analysis
Authors: Radhakrishnan Vignesh , Patil Samadhan B , Pelah Adar
Published: July 2022

We have analysed the performance of mulitbody kinematic optimisation methods in reducing soft tissue artefacts for subject data of varying body fat percentages. Multibody kinematic optimisation methods are a critical aspect of movement analysis using musculoskeletal modelling software. By minimising soft tissue artefacts, they help in achieving higher fidelity joint kinematics and dynamics analyses. Prior studies have not examined the performance of multibody kinematic optimisation on subjects of varying body fat percentages. Herein, we: 1) have analysed the efficacy of three different multibody kinematic optimisation methods on varying body fat percentages, 2) implemented a novel weighting scheme to reduce error irrespective of body fat percentages. Residual error using gait data of 50 participants of varying body fat percentages was calculated through inverse kinematic analysis using OpenSim(c) musculoskeletal modelling software. The analysis was repeated using a time-based weighting scheme. The residual error of participants with higher body fat percentages was greater by 30% when compared to residual error of participants of lower body fat percentages. Additionally, time-based weighting scheme reduced residual error by 20% on average compared to constant-value weighting scheme. Our results indicate that multibody kinematic optimisation methods are adversely affected by higher body fat percentages and that time-based weighting can provide higher fidelity movement analysis irrespective of body fat percentages. Through our results we aim to develop tools which provide greater precision in obesity-related movement analysis. Such tools could also help address the disparities in rates of obesity associated with different ethnic or socioeconomic background.
Unravelling Key Interactions and the Mechanism of Demethylation during hAGT mediated DNA Repair via Simulations
Authors: G Shruti T , Siddiqui Shakir Ali , Dubey Kshatresh Dutta
Published: July 2022

Alkylating agents possess the biggest threat to the genomic integrity of cell by damaging DNA bases through regular alkylation. Such damages are repaired by several automated machinery inside cell. O6-alkylguanine-DNA alkyltransferase (AGT) is such an enzyme which performs the direct repair of an alkylated guanine base by transferring the alkyl group to a Cysteine residue. In the present study using extensive MD simulations and hybrid QM/MM calculations, we have investigated the key interactions between the DNA lesion and the hAGT enzyme and elucidated the mechanisms of the demethylation of the guanine base. Our simulation shows that the DNA lesion is electrostatically stabilized by the enzyme and the Arg135 of hAGT enzyme provides the main driving force to flip the damaged base into the enzyme. The QM/MM calculations show demethylation of damaged base as a three step in thermodynamically feasible and irreversible manner. Our calculations show that the final products forms via Tyr114 in a facile way in contrast to the previously proposed Lys-mediated route.
Tenotomy-induced muscle atrophy is sex-specific and independent of NFκB
Authors: Meyer Gretchen A. , Thomopoulos Stavros , Abu-Amer Yousef , Shen Karen C.
Published: July 2022

The nuclear factor-κB (NFκB) pathway is a major thoroughfare for skeletal muscle atrophy and is driven by diverse stimuli. Targeted inhibition of NFκB through its canonical mediator IKKβ effectively mitigates loss of muscle mass across many conditions, from denervation to unloading to cancer. In this study, we used gain- and loss-of-function mouse models to examine the role of NFκB in muscle atrophy following rotator cuff tenotomy – a model of chronic rotator cuff tear. IKKβ was knocked down or constitutively activated in muscle-specific inducible transgenic mice to elicit a 2-fold gain or loss of NFκB signaling. Surprisingly, neither knockdown of IKKβ nor overexpression of caIKKβ significantly altered the loss of muscle mass following tenotomy. This finding was consistent across measures of architectural adaptation (fiber cross-sectional area, fiber length, fiber number), tissue pathology (fibrosis and fatty infiltration) and intracellular signaling (ubiquitin-proteasome, autophagy). Intriguingly, late-stage tenotomy-induced atrophy was exacerbated in male mice compared to female mice. This sex specificity was driven by ongoing decreases in fiber cross-sectional area, which paralleled the accumulation of large autophagic vesicles in male, but not female muscle. These findings suggest that tenotomy-induced atrophy is not dependent on NFκB and instead may be regulated by autophagy in a sex-specific manner.
RET enhancer haplotype-dependent remodeling of the human fetal gut development program
Authors: Chatterjee Sumantra , Fries Lauren E. , Yaacov Or , Hu Nan , Berk-Rauch Hanna E. , Chakravarti Aravinda
Published: July 2022

Hirschsprung disease (HSCR) is associated with deficiency of the receptor tyrosine kinase RET, resulting in loss of cells of the enteric nervous system (ENS) during fetal gut development. The major contribution to HSCR risk is from common sequence variants in RET enhancers with additional risk from rare coding variants in many genes. Here, we demonstrate that these RET enhancer variants specifically alter the human fetal gut development program through significant decreases in gene expression of RET, members of the RET-EDNRB gene regulatory network (GRN), other HSCR genes, and an altered transcriptome with 2,382 differentially expressed genes with diverse neuronal and mesenchymal functions. A parsimonious hypothesis for these results is that beyond RET’s direct effect on its GRN, it also has a major role in enteric neural crest derived cell (ENCDC) precursor proliferation, its deficiency reducing ENCDCs with relative expansion of non-ENCDC cells. Thus, genes reducing RET proliferative activity can potentially cause HSCR. One such class is the 23 RET-dependent transcription factors enriched in early gut development. We show that their knockdown in human neuroblastoma SK-N-SH cells reduces RET and/or EDNRB gene expression, expanding the RET-EDNRB GRN. The human embryos we studied had major remodeling of the gut transcriptional but were unlikely to have had HSCR: thus, genetic changes in addition to those in RET are required for a significant enough reduction in ENCDCs to cause aganglionosis.
Genomics of viruses infecting green and purple sulfur bacteria in two euxinic lakes
Authors: Hesketh-Best P. J. , Bosco-Santos A. , Garcia S. L. , Werne J. P. , Gilhooly W. P. , Silveira C. B.
Published: July 2022

Viral infections of marine bacteria modulate the rates of primary production and the cycling of organic and inorganic matter in the world’s oceans. Here, we investigated the hypothesis that viral infections influence the ecology of purple and green sulfur bacteria (PSB and GSB) in anoxic and sulfidic (euxinic) lakes, modern analogs of early Earth oceans. Over 200 high and medium quality viral contigs were identified in long-read metagenomes from the sediments and water column of Lime Blue and Poison Lake, respectively. We compared these sequences with 94 predicted prophages identified in the complete genomes of PSB (n = 213) and GSB (n = 33). Viral genomes carrying psbA, encoding the small subunit of photosystem II protein, were present in all three datasets (sediment, water column, and complete genomes). The ubiquity of these genes suggests that PSB and GSB viruses interfere with the light reactions of sulfur-oxidizing autotrophs in a process similar to viral modulation of photosynthesis in Cyanobacteria. Viruses predicted to infect PSB and GSB also encoded auxiliary metabolic genes involved in reductive sulfur assimilation as cysteine, a pathway not yet described in these sulfur bacteria, as well as genes involved in pigment production (crtF) and carbon fixation (CP12, zwf, PGD). These observations highlight the potential for viral modulation of metabolic markers used as proxies to interpret biogeochemical processes in early Earth oceans.
ArtiaX: An Electron Tomography Toolbox for the Interactive Handling of Sub-Tomograms in UCSF ChimeraX
Authors: Ermel Utz H. , Arghittu Serena M. , Frangakis Achilleas S.
Published: July 2022

Cryo-electron tomography analysis involves the selection of macromolecular complexes to be used for subsequent sub-tomogram averaging and structure determination. Here, we describe a plugin developed for UCSF ChimeraX that allows for the display, selection, and editing of particles within tomograms. Positions and orientations of selected particles can be manually set, modified and inspected in real-time, both on screen and in virtual reality, and exported to various file formats. The plugin allows for the parallel visualization of particles stored in several meta data lists, in the context of any 3D image that can be opened with UCSF ChimeraX. The particles are rendered in user-defined colors or using colormaps, such that individual classes or groups of particles, cross-correlation coefficients or other types of information can be highlighted to the user. The implemented functions are fast, reliable and intuitive, exploring the broad range of features in UCSF ChimeraX. They allow for a fluent human-machine interaction, which enables an effective understanding of the sub-tomogram processing pipeline, even for non-specialist users.
Novel leaf-root coordination driven by leaf water storage tissues in mangroves
Authors: Cao Jingjing , Yang Qingpei , Chen Jing , Lu Mingzhen , Ren Weizheng , Xiong Yanmei , Pei Yuxin , Kong Deliang
Published: July 2022

Interactions among root and leaf traits (in particular, leaf hydraulic and leaf economics traits) are fundamental in generating diverse strategies in land plants, yet it remains a knowledge gap in mangrove plants that experiences saline stress distinct from most other vascular plants. Here, we tested the trait relationships in mangrove plants and compared them with typical land plants (non-mangrove). Consistent with non-mangrove plants, leaf hydraulic and economics traits were decoupled in mangrove plants. However, mangrove leaf economics traits correlated strongly with root hydraulic traits, which are normally decoupled in non-mangrove plants. Moreover, we observed a unique scaling relationship between leaf dry mass per area and root hydraulic traits in mangroves. The novel coordination between leaves and roots arises from the wide-presence of leaf water storage tissues in mangroves, and this potentially represents a new paradigm with which we look into the ecology, physiology and evolution of this important vegetation.
PROTEIN CODING VARIATION IN OUTBRED LABORATORY MOUSE STOCKS PROVIDES A MOLECULAR BASIS FOR DISTINCT RESEARCH APPLICATIONS
Authors: Cornes Belinda , Paisie Carolyn , Swanzey Emily , Schile Andrew , Brackett Kelly , Reinholdt Laura , Srivastava Anuj
Published: July 2022

Outbred laboratory mice (Mus musculus) are readily available and have high fecundity, making them a popular choice for biomedical research, especially toxicological and pharmacological applications. Direct high throughput genome sequencing (HTS) of these widely used research animals is an important genetic quality control measure that ensures research reproducibility. HTS data have been used to confirm the common origin of outbred stocks and to molecularly define distinct outbred populations. But these data have also revealed unexpected population structure and homozygosity in some populations; genetic features that emerge when outbred stocks are not properly maintained. We used exome sequencing to discover and interrogate protein coding variation in a newly established population of Swiss-derived outbred stock (J:ARC) that is closely related to other, commonly used CD-1 outbred populations. We used these data to describe the genetic architecture of the J:ARC population including heterozygosity, minor allele frequency, LD decay, and we defined the novel, protein-coding sequence variation. These data reveal the expected genetic architecture for a properly maintained outbred stock and provide a basis for on-going genetic quality control. We also compared these data to protein coding variation found in a multiparent outbred stock, the Diversity Outbred (J:DO). We found that the more recently derived, multiparent outbred stock has significantly higher interindividual variability, greater overall genetic variation, higher heterozygosity, and fewer novel variants than the Swiss derived J:ARC stock. However, among the novel variants found in the J:DO stock, significantly more are predicted to be protein-damaging. That individuals from this population can tolerate a higher load of potentially damaging variants highlights the buffering effects of allelic diversity and the differing selective pressures in these stocks. While both outbred stocks offer significant individual heterozygosity, our data provide a molecular basis for their intended applications, where the J:DO are best suited for studies requiring maximum, population-level genetic diversity and power for mapping, while the J:ARC are best suited as a general-purpose outbred stock with robust fecundity, relatively low allelic diversity, and less potential for extreme phenotypic variability.
The genetics of immune and infection phenotypes in wild mice, Mus musculus domesticus
Authors: Cheynel Louise , Lazarou Luke , Riley Eleanor M. , Viney Mark
Published: July 2022

Wild animals are under constant threat from a wide range of micro- and macroparasites in their environment. Animals make immune responses against parasites, and these are important in affecting the dynamics of parasite populations. Individual animals vary in their anti-parasite immune responses. Genetic polymorphism of immune-related loci contributes to inter-individual differences in immune responses, but most of what we know in this regard comes from studies of humans or laboratory animals; there are very few such studies of wild animals naturally infected with parasites. Here we have investigated the effect of polymorphism in immune-related loci (the MHC, and genes coding for cytokines and Toll-like receptors) on a wide range of immune and infection phenotypes in UK wild house mice, Mus musculus domesticus. We found strong effects of polymorphisms in various MHC and cytokine coding loci on both immune measures (antibody concentration and cytokine production) and on infection phenotypes (infection with mites, worms and viruses). Our study provides a comprehensive view of how polymorphism of immune-related loci affects immune and infection phenotypes in naturally infected wild rodent populations.
Biofilm competency of Desulfovibrio vulgaris Hildenborough facilitates colonization in the gut and represses adenoma development in a rat model of colon cancer
Authors: Busi Susheel Bhanu , De León Kara B. , Montonye Dan R. , Wall Judy D. , Landgraf James Amos-
Published: July 2022

Human epidemiological and animal model studies have shown that the presence of colon cancer is associated with certain microbiota. Previous human colon cancer case-control reports and our preclinical model studies identify several bacterial taxa correlating with the suppression of tumor growth. This includes a sulfate-reducing bacteria from the genus Desulfovibrio, which correlates with fewer tumors and decreased phenotype penetrance as early as 1 month of age in rats. However, other studies have shown that Desulfovibrio spp. are decreased in relative abundance in healthy patient controls. To address this disparity we treated PIRC rats, a model of human familial colon cancer that harbored a complex gut microbiota, with biofilm-forming and biofilm-deficient strains of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH). We found that the biofilm-forming DvH strain could stably colonize the rat colon, with the bacteria detected even at 3.5 months post treatment. The biofilm-deficient DvH mutant only transiently colonized the rat colon and was no longer detected in fecal samples one-week post treatment. The colonic adenoma burden at four months of age was significantly reduced in rats colonized with the biofilm- forming DvH compared to those treated with the biofilm-deficient DvH. We found a differential shift in the endogenous gut microbiota (GM) structure over time, with a notable increase in known mucin degraders in the buffer-treated control and biofilm-deficient DvH treated groups. These latter groups of rats also showed a higher level of expression of MUC2 in the colon, which encodes for the sulfonated mucin 2 expressed primarily in the gut and trachea. We also detected more dissolved sulfide in the feces from rats treated with either buffer or biofilm-deficient DvH compared to rats colonized with the biofilm-competent DvH. We found that the in vitro biofilm- forming capacity of DvH enabled in vivo engraftment of this bacterium within a complex GM population, altering the bacterial composition, and significantly reducing tumor burden in PIRC rats.
Conformation and structural dynamics of the Xist lncRNA A-repeats
Authors: Jones Alisha N. , Gabel Frank , Bohn Stefan , Wolfe Gregory , Sattler Michael
Published: July 2022

LncRNAs are emerging to play crucial roles in the regulation of many essential cellular processes and have been linked to human disease, but a detailed understanding of their structure and how this relates to underlying molecular mechanisms is still limited. The structure that a lncRNA adopts can interconvert between multiple conformations. However, characterizing the structure and dynamics is challenging given their large size. Here, we present an integrated approach, combining biochemical and biophysical techniques to investigate the core structural elements and conformational dynamics of the A-repeats of the lncRNA Xist. We combine chemical RNA structure probing, SAXS, NMR-spectroscopy and cryo-EM to comprehensively describe the conformational landscape of the Xist A-repeats. We show that under native-like conditions, the A-repeats are modular, comprising building blocks made from stable AUCG tetraloop hairpins and inter-repeat dimers separated by flexible uracil-rich regions. The structural core of the A-repeats involves dimerization of sequential repeats to form two subdomains, comprising repeats 1-4 and 5-8. The overall topology of the A-repeats is dynamic, with structural variability linked to the uracil-rich linker regions. Our results rationalize context and buffer-dependent structural variations of the Xist lncRNA. The integrative approach presented here establishes a general pipeline for investigating lncRNA structure and dynamics.

GRAPHICAL ABSTRACT
Microtubule severing enzymes oligomerization and allostery: a tale of two domains
Authors: Macke Amanda C. , Kelly Maria S. , Varikoti Rohith Anand , Mullen Sarah , Groves Daniel , Forbes Clare , Dima Ruxandra I.
Published: July 2022

Severing proteins are nanomachines from the AAA+ (ATPases associated with various cellular activities) superfamily whose function is to remodel the largest cellular filaments, microtubules. The standard AAA+ machines adopt hexameric ring structures for functional reasons, while being primarily monomeric in the absence of the nucleotide. Both major severing proteins, katanin and spastin, are believed to follow this trend. However, studies proposed that they populate lower-order oligomers in the presence of co-factors, which are functionally relevant. Our simulations show that the preferred oligomeric assembly is dependent on the binding partners, and on the type of severing protein. Essential dynamics analysis predicts that the stability of an oligomer is dependent on the strength of the interface between the helical bundle domain (HBD) of a monomer and the convex face of the nucleotide binding domain (NBD) of a neighboring monomer. Hot spots analysis found that the region consisting of the HBD tip and the C-terminal (CT) helix is the only common element between the allosteric networks responding to nucleotide, substrate, and inter-monomer binding. Clustering analysis indicates the existence of multiple pathways for the transition between the secondary structure of the HBD tip in monomers and the structure(s) it adopts in oligomers.
Transcriptome analysis of the binucleate ciliate Tetrahymena thermophila with asynchronous nuclear cell cycles
Authors: Zhang L , Cervantes MD , Pan S , Lindsley J , Dabney A , Kapler GM
Published: July 2022

As a prototypic ciliated protozoan, Tetrahymena thermophila harbors two functionally and physically distinct nuclei within a shared cytoplasm. During vegetative growth, the ‘cell cycles’ of the diploid germline micronucleus and polyploid somatic macronucleus are offset. Micronuclear S phase initiates just before cell division and is completed in daughter cells prior to the onset of macronuclear S phase. Whereas mitotic micronuclear division occurs mid-cell cycle, amitotic macronuclear division immediately precedes cytokinesis. Here we report the first RNA-seq analysis across the cell cycle of a binucleated organism. RNA was isolated at 30 min intervals across 1.5 vegetative cell cycles, starting with a macronuclear G1 population synchronized by centrifugal elutriation. Using MetaCycle, 3244 of the predicted 26,000+T. thermophila genes were shown to be cell cycle regulated. Proteins that are required in micro- and macronuclei exhibit a single mRNA peak that correlates with their macronuclear function, while the expression of nucleus-limited protein-coding genes, including nucleoporins and importins, peak prior to their respective nucleus-specific role. Cyclin D and cyclin A/B genes showed distinct expression patterns that predict nucleus-specific functions. Clustering of periodically expressed genes revealed seven gene expression patterns. Four clusters have known PANTHER GO biological processes that are overrepresented for G1/S and G2/M phase functions. We propose that these clusters encode known and novel factors that coordinate micro- and macronuclear-specific events such as mitosis, amitosis, DNA replication and cell division.
Multi-omics analysis of sarcospan overexpression in mdx skeletal muscle reveals compensatory remodeling of cytoskeleton-matrix interactions that promote mechanotransduction pathways
Authors: McCourt Jackie L. , Stearns-Reider Kristen M. , Mamsa Hafsa , Shu Cynthia , Afsharinia Mohammad Hossein , Gibbs Elizabeth M. , Shin Kara M. , Kurmangaliyev Yerbol Z. , Schmitt Lauren R. , Hansen Kirk C. , Crosbie Rachelle H.
Published: July 2022

Background

The dystrophin-glycoprotein complex (DGC) is a critical adhesion complex of the muscle cell membrane, providing a mechanical link between the extracellular matrix (ECM) and the cortical cytoskeleton that stabilizes the sarcolemma during repeated muscle contractions. One integral component of the DGC is the transmembrane protein, sarcospan (SSPN). Overexpression of SSPN in the skeletal muscle of mdx mice (murine model of DMD) restores muscle fiber attachment to the ECM in part through an associated increase in utrophin and integrin adhesion complexes at the cell membrane, protecting the muscle from contraction-induced injury. In this study, we utilized transcriptomic and ECM protein-optimized proteomics data sets from wild-type, mdx, and mdx transgenic (mdxTG) skeletal muscle tissues to identify pathways and proteins driving the compensatory action of SSPN overexpression.

Methods

The tibialis anterior and quadriceps muscles were isolated from wild-type, mdx, and mdxTG mice and subjected to bulk RNA-Seq and global proteomics analysis using methods to enhance capture of ECM proteins. Data sets were further analyzed through the Ingenuity Pathway Analysis (QIAGEN) and integrative gene set enrichment to identify candidate networks, signaling pathways, and upstream regulators.

Results

Through our multi-omics approach, we identified 3 classes of differentially expressed genes and proteins in mdxTG muscle, included those that were: 1) unrestored (significantly different from wild-type, but not from mdx), 2) restored (significantly different from mdx, but not from wild-type), and 3) compensatory (significantly different from both wild-type and mdx). We identified signaling pathways that may contribute to the rescue phenotype, most notably cytoskeleton and ECM organization pathways. ECM optimized-proteomics revealed an increased abundance of collagens II, V, and XI, along with β-spectrin in mdxTG samples. Using Ingenuity Pathway Analysis, we identified upstream regulators that are computationally predicted to drive compensatory changes, revealing a possible mechanism of SSPN rescue through a rewiring of cell-ECM bidirectional communication. We found that SSPN overexpression results in upregulation of key signaling molecules associated with regulation of cytoskeleton organization and mechanotransduction, including Rho, RAC, and Wnt.

Conclusions

Our findings indicate that SSPN overexpression rescues dystrophin deficiency partially through mechanotransduction signaling cascades mediated through components of the ECM and the cortical cytoskeleton.
Precise control of neural activity using dynamically optimized electrical stimulation
Authors: Shah Nishal P. , Phillips A.J. , Madugula Sasi , Lotlikar Amrith , Gogliettino Alex R. , Hays Madeline , Grosberg Lauren , Brown Jeff , Dusi Aditya , Tandon Pulkit , Hottowy Pawel , Dabrowski Wladyslaw , Sher Alexander , Litke Alan M. , Mitra Subhasish , Chichilnisky E.J.
Published: July 2022

Neural implants have the potential to restore lost sensory function by electrically evoking the complex naturalistic activity patterns of neural populations. However, it can be difficult to predict and control evoked neural responses to simultaneous multi-electrode stimulation due to nonlinearity of the responses. We present a solution to this problem and demonstrate its utility in the context of a bi-directional retinal implant for restoring vision. A dynamically optimized stimulation approach encodes incoming visual stimuli into a rapid, greedily chosen, temporally dithered and spatially multiplexed sequence of simple stimulation patterns. Stimuli are selected to optimize the reconstruction of the visual stimulus from the evoked responses. Temporal dithering exploits the slow time scales of downstream neural processing, and spatial multiplexing exploits the independence of responses generated by distant electrodes. The approach was evaluated using an experimental laboratory prototype of a retinal implant: large-scale, high-resolution multi-electrode stimulation and recording of macaque and rat retinal ganglion cellsex vivo. The dynamically optimized stimulation approach substantially enhanced performance compared to existing approaches based on static mapping between visual stimulus intensity and current amplitude. The modular framework enabled parallel extensions to naturalistic viewing conditions, incorporation of perceptual similarity measures, and efficient implementation for an implantable device. A direct closed-loop test of the approach supported its potential use in vision restoration.

Impact Statement

A novel method of electrical stimulation to precisely control neural activity for sensory restoration exhibits improvements in visual stimulus reconstruction, enables efficient hardware design, and extends to naturalistic conditions.
Identification of hub genes and key pathways in pediatric Crohn’s disease using next generation sequencing and bioinformatics analysis
Authors: Vastrad Basavaraj , Vastrad Chanabasayya
Published: July 2022

Pediatric Crohn Disease (CD) also known as inflammatory bowel diseases, affects millions of people all over the world. The aim of this investigation is to identify the key genes in CD and uncover their potential functions. We downloaded the next generation sequencing (NGS) dataset GSE101794 from the Gene Expression Omnibus (GEO) database. The NGS dataset GSE101794 was used to screen differentially expressed genes (DEGs) between samples from patients with CD and healthy controls. Gene ontology (GO) and REACTOME pathway enrichment analyses were applied for the DEGs. Subsequently, a protein - protein interaction (PPI) network, modules, miRNA- hub gene regulatory network and TF - hub gene regulatory network were constructed to identify hub genes, miRNAs and TFs. Receiver operating characteristic curve (ROC) analysis was applied to validate the hub genes. A total of 957 DEGs were identified, including 478 up regulated genes and 479 down regulated genes. GO and REACTOME results suggested that several Go terms and pathways are involved in response to stimulus, extracellular region, signaling receptor binding, small molecule metabolic process, membrane, transporter activity, immune system and biological oxidations. The top centrality hub genes MDFI, MNDA, FBXO6, TFRC, STAT1, DPP4, MME, SLC39A4, APOA1 and TMEM25 were screened out as the critical genes among the DEGs from the PPI network, modules, miRNA-hub gene regulatory network and TF-hub gene regulatory network. This investigation identified key genes and signal pathways, which might help us improve our understanding of the molecular mechanisms of CD and identify some novel therapeutic targets for CD.
High conservation of the dental plaque microbiome community across populations with differing subsistence strategies and levels of market integration
Authors: Velsko Irina M. , Gallois Sandrine , Stahl Raphaela , Henry Amanda G. , Warinner Christina
Published: July 2022

Industrialization - including urbanization, participation in the global food chain, and consumption of heavily processed foods - is thought to drive substantial shifts in the human microbiome. While diet strongly influences stool microbiome composition, the influence of diet on the oral microbiome, and particularly dental plaque, is largely speculative. Here we investigated whether dental plaque microbial communities are distinctly different across populations with dissimilar subsistence strategies and degree of industrialized market integration. Using a metagenomic approach, we compared the dental plaque microbiomes of Baka foragers and Nzime subsistence agriculturalists in Cameroon (n = 46) with the dental plaque and calculus microbiomes of highly industrialized populations in North America and Europe. We found that differences in microbial taxonomic composition between populations were minimal, with high conservation of abundant microbial taxa and no significant differences in microbial diversity related to dietary practices. Instead, we find that the major source of variation in dental plaque microbial species composition is related to tooth location and oxygen availability, and may be influenced by toothbrushing or other dental hygiene measures. Our results support that dental plaque, in contrast to the stool microbiome, maintains an inherent stability against ecological perturbations in the oral environment.
Replication origin mapping in the malaria parasite Plasmodium falciparum
Authors: Totañes Francis Isidore Garcia , Gockel Jonas , Chapman Sarah E. , Bártfai Richárd , Boemo Michael A. , Merrick Catherine J.
Published: July 2022

The malaria parasite Plasmodium falciparum replicates via schizogony: a fundamentally unusual type of cell cycle involving asynchronous replication of multiple nuclei within the same cytoplasm. It also has one of the most A/T-biased genomes ever sequenced. Here, we present the first comprehensive study of the specification and activation of DNA replication origins during Plasmodium schizogony. Potential replication origins were found to be abundant, with ORC1-binding sites detected every ∼800 bp throughout the genome. They had no motif enrichment, but were biased towards areas of higher G/C content. Origin activation was then measured at single-molecule resolution via new DNAscent technology that measures fork movement by detecting base analogues BrdU and EdU in DNA sequenced on the Oxford nanopore platform (https://github.com/MBoemo/DNAscent). DNAscent-called origins were found to be much less dense than ORC1-binding sites, with origins activated preferentially in areas of low transcriptional activity. Consistently, replication forks moved fastest through the most lowly transcribed genes, suggesting that conflicts between transcription and origin firing inhibit efficient replication, and that P. falciparum has evolved its S-phase to minimise such conflicts.
A system-level view on the function of natural eukaryotic biomes through taxonomically resolved metabolic pathway profiling
Authors: Gutierrez Jayson , Hablützel Pascal I.
Published: July 2022

High-throughput sequencing of environmental samples has dramatically improved our understanding of the molecular activities of complex microbial communities in their natural environments. For instance, by enabling taxonomic profiling and differential gene expression analysis, microbiome studies have revealed intriguing associations between community structure and ecosystem functions. However, the effectiveness of sequence data analysis to characterize the functioning of microbial ecosystems at the systems level (e.g. metabolic pathways) and at high taxonomic resolution has thus far been limited by the quality and scope of reference sequence databases. In this work, we applied state of the art bioinformatics tools to leverage publicly available genome/gene sequences for a wide array of (mostly eukaryotic) planktonic organisms to build a customized protein sequence database. Based on this, our goal is to conduct a systems-level interrogation of environmental samples, which can effectively augment the insights obtained through traditional gene-centric analysis (i.e. analysis of single gene expression profiles at the genome-wide level). To achieve this, we utilized the popular HUMAnN pipeline, which has proven effective at delineating taxon-specific metabolic pathways that may be actively contributing to the overall functioning of a microbiome. To test the efficacy of our database customization for mapping metabolic pathway activities in complex planktonic ecosystems, we reanalyzed previously published metatranscriptome datasets derived from different marine environments. Our results demonstrate that database customization can substantially improve our ability to quantitatively assess core metabolic processes across taxonomically diverse marine microbiomes, which have so far remained largely uncharacterized at the systems level. By further expanding on the taxonomic and functional complexity of our database with newly released high-quality genome assemblies and gene catalogs for marine microbes, we aim to improve our ability to map the molecular traits that drive changes in the composition and functioning of marine planktonic networks through space and time.
Interdependent progression of bidirectional sister replisomes in E. coli
Authors: Chen P.J. , McMullin A.B. , Visser B.J. , Mei Q. , Rosenberg S.M. , Bates D.
Published: July 2022

Bidirectional DNA replication complexes initiated from the same origin remain colocalized in a factory configuration for part or all of their lifetimes. However, there is little evidence that sister replisomes are functionally interdependent, and the consequence of factory replication is unknown. Here, we investigated the functional relationship between sister replisomes in E. coli, which naturally exhibits both factory and solitary configurations in the same replication cycle. Using an inducible transcription factor roadblocking system, we found that blocking one replisome caused a significant decrease in overall progression and velocity of the sister replisome. Remarkably, progression was impaired only if the block occurred while sister replisomes were still in a factory configuration – blocking one fork had no significant effect on the other replisome when sister replisomes were physically separate. Disruption of factory replication also led to increased fork stalling and requirement of fork restart mechanisms. These results suggest that physical association between sister replisomes is important for establishing an efficient and uninterrupted replication program. We discuss the implications of our findings on mechanisms of replication factory structure and function, and cellular strategies of replicating problematic DNA such as highly transcribed segments.
Presynaptic contact and activity opposingly regulate postsynaptic dendrite outgrowth
Authors: Heckman Emily L. , Doe Chris Q.
Published: July 2022

The organization of neural circuits determines nervous system function. Variability can arise during neural circuit development (e.g. neurite morphology, axon/dendrite position). To ensure robust nervous system function, mechanisms must exist to accommodate variation in neurite positioning during circuit formation. Previously we developed a model system in the Drosophila ventral nerve cord to conditionally induce positional variability of a proprioceptive sensory axon terminal, and used this model to show that when we altered the presynaptic position of the sensory neuron, its major postsynaptic interneuron partner modified its dendritic arbor to match the presynaptic contact, resulting in functional synaptic input (Sales et al., 2019). Here we investigate the cellular mechanisms by which the interneuron dendrites detect and match variation in presynaptic partner location and input strength. We manipulate the presynaptic sensory neuron by (a) ablation; (b) silencing or activation; or (c) altering its location in the neuropil. From these experiments we conclude that there are two opposing mechanisms used to establish functional connectivity in the face of presynaptic variability: presynaptic contact stimulates dendrite outgrowth locally, whereas presynaptic activity inhibits postsynaptic dendrite outgrowth globally. These mechanisms are only active during an early larval critical period for structural plasticity. Collectively, our data provide new insights into dendrite development, identifying mechanisms that allow dendrites to flexibly and robustly respond to developmental variability in presynaptic location and input strength.
ArcRegulates a Second-Guessing Cognitive Bias During Naturalistic Foraging Through Effects on Discrete Behavior Modules
Authors: Ravens Alicia , Stacher-Hörndli Cornelia N. , Emery Jared , Steinwand Susan , Shepherd Jason D. , Gregg Christopher
Published: July 2022

Foraging involves innate decision heuristics that are adapted for the wild but can cause economically suboptimal cognitive biases in some contexts. The mechanisms underlying cognitive biases are poorly understood but are likely genetic. Here, we investigate foraging in fasted mice using a naturalistic paradigm and uncover an innate “second-guessing” cognitive bias that involves repeatedly investigating an empty former food patch instead of consuming available food. Second-guessing prevents mice from maximizing feeding benefits in the task. Since learning and memory are involved, we tested roles for the synaptic plasticity gene,Arc,and found thatArc−/−mice show a specific lack of second-guessing.Arc−/−males reap benefits by increasing food consumption. Unsupervised machine learning decompositions of foraging show thatArcaffects discrete, stereotyped foraging sequences that we call modules within a rich naturalistic behavioral landscape. Thus, our study reports a second- guessing cognitive bias, ethological roles forArcin naturalistic foraging, and links between genetically determined foraging modules and cognitive bias in decision making.
PBAF loss leads to DNA damage-induced inflammatory signaling through defective G2/M checkpoint maintenance
Authors: Feng Hugang , Lane Karen A. , Roumeliotis Theodoros I. , Jeggo Penny A. , Somaiah Navita , Choudhary Jyoti S. , Downs Jessica A.
Published: July 2022

The PBRM1 subunit of the PBAF (SWI/SNF) chromatin remodeling complex is mutated in ∼40% of clear cell renal cancers. PBRM1 loss has been implicated in responses to immunotherapy in renal cancer, but the mechanism is unclear. DNA damage-induced inflammatory signaling is an important factor determining immunotherapy response. This response is kept in check by the G2/M checkpoint, which prevents progression through mitosis with unrepaired damage. We found that in the absence of PBRM1, p53-dependent p21 up-regulation is delayed after DNA damage, leading to defective transcriptional repression by the DREAM complex and premature entry into mitosis. Consequently, DNA damage-induced inflammatory signaling pathways are activated by cytosolic DNA. Notably, p53 is infrequently mutated in renal cancer, so PBRM1 mutational status is critical to G2/M checkpoint maintenance. Moreover, we found that the ability of PBRM1 deficiency to predict response to immunotherapy correlates with expression of the cytosolic DNA-sensing pathway in clinical samples. These findings have implications for therapeutic responses in renal cancer.
Persistent up-regulation of polyribosomes at synapses during long-term memory, reconsolidation, and extinction of associative memory
Authors: Ostroff Linnaea E. , Cain Christopher K.
Published: July 2022

Local protein synthesis at synapses can provide a rapid supply of proteins to support synaptic changes during consolidation of new memories, but its role in the maintenance or updating of established memories is unknown. Consolidation requires new protein synthesis in the period immediately following learning, whereas established memories are resistant to protein synthesis inhibitors. We have previously reported that polyribosomes are up-regulated in the lateral amygdala (LA) during consolidation of aversive-cued Pavlovian conditioning. In this study, we used serial section electron microscopy reconstructions to determine whether the distribution of dendritic polyribosomes returns to baseline during the long-term memory phase. Relative to control groups, long-term memory was associated with up-regulation of polyribosomes throughout dendrites, including in dendritic spines of all sizes. Retrieval of a consolidated memory by presentation of a small number of cues induces a new, transient requirement for protein synthesis to maintain the memory, while presentation of a large number of cues results in extinction learning, forming a new memory. One hour after retrieval or extinction training, the distribution of dendritic polyribosomes was similar except in the smallest spines, which had more polyribosomes in the extinction group. Our results demonstrate that the effects of learning on dendritic polyribosomes are not restricted to the transient translation-dependent phase of memory formation. Cued Pavlovian conditioning induces persistent synapse strengthening in the LA that is not reversed by retrieval or extinction, and dendritic polyribosomes may therefore correlate generally with synapse strength as opposed to recent activity or transient translational processes.
Assessing the importance of sex in a hippocampus-dependent behavioral test battery in C57BL/6NTac mice
Authors: Stevanovic Korey D. , Fry Sydney A. , DeFilipp Jemma M.S. , Wu Nicholas , Bernstein Briana J. , Cushman Jesse D.
Published: July 2022

Inclusion of male and female subjects in behavioral neuroscience research requires a concerted effort to characterize sex differences in standardized behavioral assays. Sex differences in hippocampus-dependent assays have been widely reported but are still poorly characterized. In the present study, we conducted a parametric analysis of spontaneous alternation, object recognition, and fear conditioning in a commonly used control strain, C57BL/6NTac. Our findings show largely similar performance between males and females across the majority of behavioral end points. However, we identified an important difference in nonassociative fear sensitization, whereby females showed an enhanced fear response to the 75-dB tone that is used as the conditional stimulus. In addition, we observed an impairment in object location performance in females that was ameliorated by more extensive habituation to handling. Together, these findings argue that sex differences in nonassociative fear responses to both novel auditory cues and novel objects need to be considered when designing and interpreting cognitive assays in C57BL/6 mice. Furthermore, this elevated fear sensitization could serve as a novel approach to model the increased incidence of anxiety disorders in women.
Toward a public sector asset optimization strategy: the case of Indonesia
Authors: Nanang Rustanto , Susilawati Connie , Skitmore Martin
Published: July 2022

Purpose

Governments in developing countries manage their considerable state assets for public service delivery directly. In Indonesia, the Directorate of State Asset Management responsible for developing the national strategy for state asset optimization requires the determination of key elements and prioritization tools. The purpose of this paper is to show that a simple calculation using the combination of the balanced scorecard (BCS) and analytical hierarchy process (AHP) will help in the prioritization of strategy development.

Design/methodology/approach

A questionnaire survey of 131 multistakeholder respondents to identify the most important key elements and the best alternative for asset optimization was done in this study.

Findings

The respondents agree on the most important key elements, and that the best alternative for asset optimization is the efficient maintenance of assets. Competitive human resources comprise the recommended second key element, and that improvements in asset performance and value will improve public service as the second-highest alternative. This study also shows the importance of the integration of asset optimization in existing government strategic instruments supported by a comprehensive data set related to public assets and their performance.

Originality/value

This paper provides a new contribution to integrating asset optimization strategies as the core of the organization’s performance and prioritization strategies. Additional BSC perspectives are suggested, with the inclusion of AHP for prioritization. In addition, this study includes the opinions of all the stakeholders, from external users to the central management. The flexibility of the tools to adapt to the existing strategic framework will allow their application by different agencies and in different countries.