title: Effects Of Video Games On Executive Control, Aggression and Gaming Motivation

abstract:
With the advancements of computer technology and accessible internet, playing video games has become immensely popular across all age groups. Increasing research talks about the cognitive benefits of Video Games. At the same time, video games are stereotyped as an activity for the lazy and unproductive. Within this backdrop, our study aims to understand the effect of video games on Executive control (Visual Scanning and Visual Perception), Aggression, and Gaming Motivation.

Twenty non-gamers were selected and divided into two groups: Action Video Game Players (AVGP) and Non-Action Video Game Players NAVGP). We used two computerized tests: Gabor Orientation Identification Test and Visual Scanning Test (to assess visual perception and visual scanning, respectively) and two questionnaires (to assess aggression and gaming motivation). We found an improvement in visual perception as well as visual scanning following video game training in AVGPs. Interestingly, aggression did not increase with an increase in video game exposure. We also found insignificant changes in gaming motivation after the training, except for self-gratification motives.

Cognitive improvements do not relate to action video games alone, but non-action video games also show promising results to enhance cognition. With better timed and controlled training with video games, aggression as a prospective consequence of video game exposure can also be controlled. We propose targeted video game training as an approach to enhance cognition in non-gamers.


title: Group-level inference of information-based measures for the analyses of cognitive brain networks from neurophysiological data

abstract:
The reproducibility crisis in neuroimaging and in particular in the case of underpowered studies has introduced doubts on our ability to reproduce, replicate and generalize findings. As a response, we have seen the emergence of suggested guidelines and principles for neuroscientists known as Good Scientific Practice for conducting more reliable research. Still, every study remains almost unique in its combination of analytical and statistical approaches. While it is understandable considering the diversity of designs and brain data recording, it also represents a striking point against reproducibility. Here, we propose a non-parametric permutation-based statistical framework, primarily designed for neurophysiological data, in order to perform group-level inferences on non-negative measures of information encompassing metrics from information-theory, machine-learning or measures of distances. The framework supports both fixed- and random-effect models to adapt to inter-individuals and inter-sessions variability. Using numerical simulations, we compared the accuracy in ground-truth retrieving of both group models, such as test- and cluster-wise corrections for multiple comparisons. We then reproduced and extended existing results using both spatially uniform MEG and non-uniform intracranial neurophysiological data. We showed how the framework can be used to extract stereotypical task- and behavior-related effects across the population covering scales from the local level of brain regions, inter-areal functional connectivity to measures summarizing network properties. We also present an open-source Python toolbox called Frites1 that includes the proposed statistical pipeline using information-theoretic metrics such as single-trial functional connectivity estimations for the extraction of cognitive brain networks. Taken together, we believe that this framework deserves careful attention as its robustness and flexibility could be the starting point toward the uniformization of statistical approaches.

Graphical abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

HighlightsO_LIGroup-level statistics for extracting neurophysiological cognitive brain networks
C_LIO_LICombining non-parametric permutations with measures of information
C_LIO_LIFixed- and random-effect models, test- and cluster-wise corrections
C_LIO_LIMulti-level inferences, from local regions to inter-areal functional connectivity
C_LIO_LIA Python open-source toolbox called Frites includes the proposed statistical methods
C_LI

category: neuroscience


title: Rapid fluctuations in functional connectivity of cortical networks encode spontaneous behavior

abstract: Experimental work across a variety of species has demonstrated that spontaneously generated behaviors are robustly coupled to variation in neural activity within the cerebral cortex 1-9. Indeed, functional magnetic resonance imaging (fMRI) data suggest that functional connectivity in cortical networks varies across distinct behavioral states, providing for the dynamic reorganization of patterned activity 5,7,10. However, these studies generally lack the temporal resolution to establish links between cortical signals and the continuously varying fluctuations in spontaneous behavior typically observed in awake animals. Here, we took advantage of recent developments in wide-field, mesoscopic calcium imaging 11 to monitor neural activity across the neocortex of awake mice. Applying a novel approach to quantifying time-varying functional connectivity, we developed a "graph of graphs" method to show that spontaneous behaviors are more accurately represented by fast changes in the correlational structure versus the magnitude of large-scale network activity. Dynamic functional connectivity reveals subnetworks that are not predicted by traditional anatomical atlas-based parcellation of the cortex. These results provide insight into how behavioral information is represented across the mammalian neocortex and demonstrate a new analytical framework for investigating time-varying functional connectivity in neural networks.


title: Pairwise Relative Distance (PRED) is an intuitive and robust metric for assessing vector similarity and class separability

abstract: Scientific studies often require assessment of similarity between ordered sets of values. Each set, containing one value for every dimension or class of data, can be conveniently represented as a vector. The commonly used metrics for vector similarity include angle-based metrics, such as cosine similarity or Pearson correlation, which compare the relative patterns of values, and distance-based metrics, such as the Euclidean distance, which compare the magnitudes of values. Here we evaluate a newly proposed metric, pairwise relative distance (PRED), which considers both relative patterns and magnitudes to provide a single measure of vector similarity. PRED essentially reveals whether the vectors are so similar that their values across the classes are separable. By comparing PRED to other common metrics in a variety of applications, we show that PRED provides a stable chance level irrespective of the number of classes, is invariant to global translation and scaling operations on data, has high dynamic range and low variability in handling noisy data, and can handle multi-dimensional data, as in the case of vectors containing temporal or population responses for each class. We also found that PRED can be adapted to function as a reliable metric of class separability even for datasets that lack the vector structure and simply contain multiple values for each class.


title: Gait as a Quantitative Translational Outcome Measure inAngelman Syndrome

abstract:
Angelman Syndrome (AS) is a genetic neurodevelopmental disorder characterized by developmental delay, lack of speech, seizures, intellectual disability, and walking and balance disorders. Recently, motor ability became an interesting outcome measure in AS, as it is broad including ataxia, hypotonia, delayed and abnormal walking and postural movements and affects nearly every individual with AS. We predict that gait presents a strong opportunity for rigorous, reliable, and quantitative metrics with direct translation to evaluate pharmacological, dietary, and genetic therapies. Numerous motoric deficits have been identified clinically. In this study, we used an innovative, automated gait analysis as well as gold standard motor behavioral assays to further delineate components of motor, coordination, balance, and gait impairments in an AS mouse model across development. Our study demonstrated marked global motoric deficits in AS mice, corroborating many previous reports. Uniquely, this is the first report of nuanced and pertinent aberrations in quantitative spatial and temporal components of gait between AS and wildtype littermate controls, that are analogous in AS individuals. These metrics were followed longitudinally to observe the progression of maladaptive gait in AS, a clinical phenotype. This has not been reported previously and contributes a substantial novel metric for therapeutic development. Taken together, these findings demonstrate the robust translational value in the study of nuanced motor outcomes, i.e., gait, for AS, as well as similar genetic syndromes, in the endeavor of therapeutic screening.

Lay AbstractMotor behaviors, like ambulation, gross and fine motor skills, coordination and balance, are easily quantifiable and readily translational between humans and preclinical rodent models for neurodevelopmental and neurodegenerative disorders, than other domains of behavior. To that end, we investigated gait across development in a mouse model for Angelman Syndrome and elucidated onset, progression, and decline of motor deficits in innovative, nuanced, and clinically relevant manner.


title: Object-scene conceptual regularities reveal fundamental differences between biological and artificial object vision

abstract: Human vision is still largely unexplained. Computer vision made impressive progress on this front, but it is unclear to what extent artificial neural networks approximate human brain strategies. Here, we confirm this gap by testing how biological and artificial systems encode object-scene contextual regularities in natural images. Both systems represent these regularities, but the underlying information processing is markedly different. In human vision, objects and backgrounds are represented separately, with rich domain-specific representations characterizing human visual cortex. Interaction between these components occurs downstream in frontoparietal areas. Conversely, neural networks represent image components in a single entangled representation revealing reduced object-segregation abilities and impoverished domain-specific object spaces. These results show the uniqueness of human vision that allows understanding that images are not just a collection of features and points to the need for developing neural network models with a similar richness of representational content.


title: Anterior thalamic nuclei: A critical substrate for non-spatial paired-associate memory

abstract: The anterior thalamic nuclei (ATN), a central node in a complex memory system, process spatial and temporal memory. Here, we show that ATN lesions do not affect acquisition of a simple odour discrimination or a simple object discrimination in a runway apparatus. The same procedures were used to test learning of an arbitrary association between non-spatial object-odour pairings (A+X or B+Y were rewarded; but not A+Y or B+X). If ATN lesions recapitulate hippocampal function, specifically CA1 function, then they should disrupt acquisition only when an explicit delay (i.e., a 10-second trace) is inserted between the odour and object. Acquisition was completely abolished by ATN lesions, irrespective of the presence of the temporal trace, and despite extensive training (50x12-trial sessions). Faster acquisition with the 10-second trace was found in the sham-lesion rats. During recall, 5 days after criterion, sham rats but not ATN-lesion rats showed elevated Zif268 expression in hippocampal CA1 for the trace compared to no-trace condition; both sham and lesion rats tested in the trace condition showed increased IEG expression in the superficial layers of the prefrontal cortex and retrosplenial cortex. ATN lesions markedly reduced Zif268 expression in the prefrontal cortex and retrosplenial cortex. This is the first evidence that ATN lesions impair non-spatial paired-associate tasks. The findings suggest that the ATN influence memory beyond time and space, and constitute a critical neural structure for learning arbitrary associations even in the task version that is not disrupted by hippocampal lesions.


title: Modulation of the renin-angiotensin system inhibits memory advantage for negative emotional material via decreasing hippocampus activation and its coupling with the amygdala

abstract: Exaggerated arousal and dysregulated emotion-memory interactions are key pathological dysregulations that accompany the development of post-traumatic stress disorder (PTSD). Current treatments for PTSD are of moderate efficacy and preventing the dysregulations already during exposure to threatening events may attenuate the development of PTSD-symptomatology. In a preregistered double-blind, between-subject, placebo-controlled pharmaco-fMRI design, the present proof-of-concept study examined the potential of a single dose of angiotensin II type 1 receptor (AT1R) antagonist losartan (LT) to attenuate the mnemonic advantage of threatening stimuli and the underlying neural mechanism via combining an emotional subsequent memory paradigm with LT (n=29) or placebo treatment (n=30) and a surprise memory test after 24h washout. LT generally improved memory performance and abolished emotional memory enhancement for negative yet not positive material while emotional experience during encoding remained intact. LT further suppressed hippocampus activity during encoding of subsequently remembered negative stimuli. On the network level LT reduced coupling between hippocampus and basolateral amygdala during successful memory formation of negative stimuli. Our findings suggest that LT may have the potential to attenuate memory formation for negative yet not positive information by decreasing hippocampus activity and its functional coupling strength with amygdala. These findings suggest a promising potential of LT to prevent preferential encoding and remembering of negative events, a mechanism that could prevent the emotion-memory dysregulations underlying the development of PTSD-symptomatology.


title: Soldier neural architecture is temporarily modality-specialized but poorly predicted by repertoire size in the stingless bee Tetragonisca angustula

abstract: Individual heterogeneity within societies provides opportunities to test hypotheses about adaptive neural investment in the context of group cooperation. Here we explore neural investment in defense specialist soldiers of the eusocial stingless bee (Tetragonisca angustula) which are age sub-specialized on distinct defense tasks, and have an overall higher lifetime task repertoire than other sterile workers within the colony. Consistent with predicted behavioral demands, soldiers had higher relative visual (optic lobe) investment than non-soldiers but only during the period when they were performing the most visually demanding defense task (hovering guarding). As soldiers aged into the less visually demanding task of standing guarding this difference disappeared. Neural investment was otherwise similar across all colony members. Despite having larger task repertoires, soldiers had similar absolute brain size and smaller relative brain size compared to other workers, meaning that lifetime task repertoire size was a poor predictor of brain size. Together, our results are consistent with the specialized but flexible defense strategies of this species, broadening our understanding of how neurobiology mediates age and morphological task specialization in highly cooperative societies.


title: Lupus Gut Microbiota Transplants Cause Autoimmunity and Inflammation

abstract:
BackgroundThe etiology of systemic lupus erythematosus (SLE) is multifactorial. Recently, growing evidence suggests that the microbiota plays a role in SLE, yet whether gut microbiota participates in the development of SLE remains largely unknown. To investigate this issue, we carried out 16s rDNA sequencing analyses in a cohort of 18 female un-treated active SLE patients and 7 female healthy controls, and performed fecal microbiota transplantation from patients and healthy controls to germ-free mice.

ResultsCompared to the healthy controls, we found no significant different microbial diversity but some significantly different species in SLE patients including Turicibacter genus and other 5 species. Fecal transfer from SLE patients to germ free (GF) C57BL/6 mice caused GF mice to develop a series of lupus-like phenotyptic features, which including an increased serum autoimmune antibodies, and imbalanced cytokines, altered distribution of immune cells in mucosal and peripheral immune response, and upregulated expression of genes related to SLE in recipient mice that received SLE fecal microbiota transplantation (FMT). Moreover, the metabolism of histidine was significantly altered in GF mice treated with SLE patient feces, as compared to those which received healthy fecal transplants.

ConclusionsOverall, our results describe a causal role of aberrant gut microbiota in contributing to the pathogenesis of SLE. The interplay of gut microbial and histidine metabolism may be one of the mechanisms intertwined with autoimmune activation in SLE.

category: immunology


title: Insights into the nutritional properties and microbiome diversity in sweet and sour yogurt manufactured in Bangladesh

abstract: Yogurt quality mainly depends on nutritional properties, microbial diversity and purity of starter culture. This study aimed to assess the nutritional composition and microbiome diversity in yogurt. Microbial diversity was analyzed by 16S and 18S rRNA based high-throughput sequencing. Significantly (P<0.05) higher pH, fat, moisture, total solid and solid-non-fat contents (%) were observed in sweet yogurt whereas sour varieties had significantly higher ash and minerals. Metagenomic investigation showed that 44.86% and 55.14% reads were assigned to bacterial and fungal taxa, respectively, with significantly higher taxonomic richness in sour yogurt. A significant difference in bacterial (Ppermanova=0.001) and fungal (Ppermanova=0.013) diversity between sweet and sour yogurt was recorded. We detected 76 bacterial and 70 fungal genera across these samples which were mostly represented by Firmicutes (>92%) and Ascomycota (98%) phyla, respectively. Among the detected genera, 36.84% bacterial and 22.86% fungal genera were found in both yogurt types. Our results suggest that Streptococcus (50.82%), Lactobacillus (39.92%), Enterobacter (4.85%), Lactococcus (2.84%) and Aeromonas (0.65%) are the most abundant bacterial genera, while Kluyveromyces (65.75%), Trichosporon (8.21%), Clavispora (7.19%), Candida (6.71%), Iodophanus (2.22%), Apiotrichum (1.94%), and Issatchenkia (1.35%) are the most abundant fungal genera in yogurt metagenomes. This is the first study on nutritional properties and microbiome diversity of Bangladeshi yogurt that would be a benchmark for safe production of quality yogurt by commercial manufacturers.

category: microbiology


title: Dynamics of transcription elongation are finely tuned by dozens of regulatory factors

abstract: Understanding the complex network and dynamics that regulate transcription elongation requires the quantitative analysis of RNA polymerase II (Pol II) activity in a wide variety of regulatory environments. We performed native elongating transcript sequencing (NET-seq) in 41 strains of S. cerevisiae lacking known elongation regulators, including RNA processing factors, transcription elongation factors, chromatin modifiers, and remodelers. We found that the opposing effects of these factors balance transcription elongation dynamics. Different sets of factors tightly regulate Pol II progression across gene bodies so that Pol II density peaks at key points of RNA processing. These regulators control where Pol II pauses with each obscuring large numbers of potential pause sites that are primarily determined by DNA sequence and shape. Genes that are sensitive to disruptions in transcription elongation tend to couple changes in Pol II pausing and antisense transcription to transcription output. Our findings collectively show that the regulation of transcription elongation by a diverse array of factors affects gene expression levels and co-transcriptional processing by precisely balancing Pol II activity.

category: molecular biology


title: Estimation of Cross-Species Introgression Rates using Genomic Data Despite Model Unidentifiability

abstract: Full likelihood implementations of the multispecies coalescent with introgression (MSci) model takes the genealogical fluctuation across the genome as a major source of information to infer the history of species divergence and gene flow using multilocus sequence data. However, MSci models are known to have unidentifiability issues, whereby different models or parameters make the same predictions about the data and cannot be distinguished by the data. Previous studies have focused on heuristic methods based on gene trees, and does not make an efficient use of the information in the data. Here we study the unidentifiability of MSci models under the full likelihood methods. We characterize the unidentifiability of the bidirectional introgression (BDI) model, which assumes that gene flow occurs in both directions. We derive simple rules for arbitrary BDI models, which create unidentifiability of the label-switching type. In general, an MSci model with k BDI events has 2k unidentifiable modes or towers in the posterior, with each BDI event between sister species creating within-model parameter unidentifiability and each BDI event between non-sister species creating between-model unidentifiability. We develop novel algorithms for processing Markov chain Monte Carlo (MCMC) samples to remove label-switching problems and implement them in the BPP program. We analyze real and synthetic data to illustrate the utility of the BDI models and the new algorithms. We discuss the unidentifiability of heuristic methods and provide guidelines for the use of MSci models to infer gene flow using genomic data.

category: evolutionary biology


title: The rs1421085 variant within FTO promotes but not inhibits thermogenesis and is potentially associated with human migration

abstract: Disease-associated GWAS loci are predominantly scattered among noncoding regions of the human genome, which impedes causality estimation. One lead risk signal of obesity-rs1421085 T>C within the FTO gene-is reported to functional in vitro but lack of organismal evidence. Here, we established global and the brown-adipocyte specific locus-knock-in mice to recapitulate this homologous variant in humans, and discovered the minor allele (C-allele) as one candidate thermogenic locus. Mice carrying the C-alleles showed increased thermogenic capacity and a resistance to high-fat diet-induced adiposity. In terms of mechanism, the knock-in models showed enhanced FTO expression, while FTO knockdown or inhibition effectively eliminated the increased thermogenic ability of brown adipocytes. In humans, the C-allele was associated with lower birthweight, and its allele frequency increases following the environmental temperature decreases. Cumulatively, these findings demonstrated rs1421085 T>C as a functional variant regulating whole-body thermogenesis, and this variation was possibly related to early human migration from hot to cold environments.

category: genetics


title: Analysis of genetic dominance in the UK Biobank

abstract: Classical statistical genetic theory defines dominance as a deviation from a purely additive effect. Dominance is well documented in model organisms and plant/animal breeding; outside of rare monogenic traits, however, evidence in humans is limited. We evaluated dominance effects in >1,000 phenotypes in the UK Biobank through GWAS, identifying 175 genome-wide significant loci (P < 4.7 x 10-11). Power to detect non-additive loci is low: we estimate a 20-30 fold increase in sample size is required to detect dominance loci to significance levels observed at additive loci. By deriving a new dominance form of LD-score regression, we found no evidence of a dominance contribution to phenotypic variance tagged by common variation genome-wide (median fraction 5.73 x 10-4). We introduce dominance fine-mapping to explore whether the more rapid decay of dominance linkage disequilibrium can be leveraged to find causal variants. These results provide the most comprehensive assessment of dominance trait variation in humans to date.


title: ALGAEFUN with MARACAS, microALGAE FUNctional enrichment tool for MicroAlgae RnA-seq and Chip-seq AnalysiS

abstract:
BackgroundMicroalgae are emerging as promising sustainable sources for biofuels, biostimulants in agriculture, soil bioremediation, feed and human nutrients. Nonetheless, the molecular mechanisms underpinning microalgae physiology and the biosynthesis of compounds of biotechnological interest are largely uncharacterized. This hinders the development of microalgae full potential as cell-factories. The recent application of omics technologies into microalgae research aims at unraveling these systems. Nevertheless, the lack of specific tools for analysing omics raw data generated from microalgae to provide biological meaningful information are hampering the impact of these technologies. The purpose of ALGAEFUN with MARACAS consists in providing researchers in microalgae with an enabling tool that will allow them to exploit transcriptomic and cistromic high-throughput sequencing data.

ResultsALGAEFUN with MARACAS consists of two different tools. First, MARACAS (MicroAlgae RnA-seq and Chip-seq AnalysiS) implements a fully automatic computational pipeline receiving as input RNA-seq (RNA sequencing) or ChIP-seq (chromatin immunoprecipitation sequencing) raw data from microalgae studies. MARACAS generates sets of differentially expressed genes or lists of genomic loci for RNA-seq and ChIP-seq analysis respectively. Second, ALGAEFUN (microALGAE FUNctional enrichment tool) is a web-based application where gene sets generated from RNA-seq analysis as well as lists of genomic loci from ChIP-seq analysis can be used as input. On the one hand, it can be used to perform Gene Ontology and biological pathways enrichment analysis over gene sets. On the other hand, using the results of ChIP-seq data analysis, it identifies a set of potential target genes and analyses the distribution of the loci over gene features. Graphical representation of the results as well as tables with gene annotations are generated and can be downloaded for further analysis.

ConclusionsALGAEFUN with MARACAS provides an integrated environment for the microalgae research community that facilitates the process of obtaining relevant biological information from raw RNA-seq and ChIP-seq data. These applications are designed to assist researchers in the interpretation of gene lists and genomic loci based on functional enrichment analysis. ALGAEFUN with MARACAS is publicly available on https://greennetwork.us.es/AlgaeFUN/.

category: bioinformatics


title: Deep graph learning of inter-protein contacts

abstract:
MotivationInter-protein (interfacial) contact prediction is very useful for in silico structural characterization of protein-protein interactions. Although deep learning has been applied to this problem, its accuracy is not as good as intra-protein contact prediction.

ResultsWe propose a new deep learning method GLINTER (Graph Learning of INTER-protein contacts) for interfacial contact prediction of dimers, leveraging a rotational invariant representation of protein tertiary structures and a pretrained language model of multiple sequence alignments (MSAs). Tested on the 13th and 14th CASP-CAPRI datasets, the average top L/10 precision achieved by GLINTER is 54.35% on the homodimers and 51.56% on all the dimers, much higher than 30.43% obtained by the latest deep learning method DeepHomo on the homodimers and 14.69% obtained by BIPSPI on all the dimers. Our experiments show that GLINTER-predicted contacts help improve selection of docking decoys.

Contactjinboxu@gmail.com


title: Designing peptide drug with archaeal antimicrobial peptides against multidrug resistant bacterial biofilms and human diseases: an in silico approach

abstract: Novel peptide therapeutics have been the cardinal part of modern-day research. Such therapies are being incorporated to prevent the adverse effects of globally emerging multi-drug resistant bacteria and various chronic human diseases which pose a great risk to the present world. In this study, we have designed a novel peptide therapy involving archaeal antimicrobial peptides. In silico predictions assign the peptide construct to be antigenic, non-allergenic, non-toxic and having stable physicochemical properties. The secondary and tertiary structures of the construct were predicted. The tertiary structure was refined for improving the quality of the predicted model. Computational tools predicted intracellular receptors in Escherichia coli, Klebsiella pneumoniae and the human body to be possible binding targets of the construct. In silico docking of modelled peptide with predicted targets, showed prominent results against targets for complex human diseases and that of bacterial infections. The stability of those docked complexes was confirmed with computational studies of conformational dynamics. Certainly, the designed peptide could be a potent therapeutic against multi-drug resistant bacteria as well as several human diseases.


title: In silico design of bioactive chimeric peptide from archaeal antimicrobial peptides


title: Estimation of effective concentrations enforced by complex linker architectures using conformational ensembles.

abstract: Proteins and protein assemblies often tether interaction partners to strengthen interactions, to regulate activity through auto-inhibition or -activation, or to boost enzyme catalysis. Tethered reactions are regulated by the architecture of the tether, which defines an effective concentration of the interactor. Effective concentrations can be estimated theoretically for simple linkers via polymer models, but there is currently no general method for estimating effective concentrations for complex linker architectures consisting of both flexible and folded domains. We describe how effective concentrations can be estimated computationally for any protein linker architecture by defining a realistic conformational ensemble. We benchmark against prediction from a worm-like chain and values measured by competition experiments and find minor differences likely due to excluded volume effects. Systematic variation of the properties of flexible and folded segments show that the effective concentration is mainly determined by the combination of the total length of flexible segments and the distance between the termini of the folded domains. We show that a folded domain in a disordered linker can increase the effective concentration beyond what can be achieved by a fully disordered linker by focusing the end-to-end distance at the appropriate spacing. This suggests that complex linker architecture may have advantages over simple flexible linkers and emphasizes that annotation as a linker should depend on the molecular context.

category: biophysics


title: Targeted Reactivation of X-linked Endogenous FOXP3 Gene from X-chromosome Inactivation in Human Female Breast Cancer Cells

abstract: Unlike autosomal tumor suppressors, which must be inactivated by a two-hit Knudson mechanism, X-linked tumor suppressors can be inactivated by a single hit due to X-chromosome inactivation (XCI). Here, we argue that targeted reactivation of the non-mutated allele from XCI offers a potential therapy for female breast cancers. Towards this goal, we developed a dual CRISPR interference and activation (CRISPRi/a) approach for simultaneously silencing and reactivating multiple X-linked genes using two orthogonal, nuclease-deficient CRISPR/Cas9 (dCas9) proteins. We verified the efficacy for use of Streptococcus pyogenes (Sp) dCas9-KRAB for silencing XIST and Staphylococcus aureus (Sa) dCas9-VPR for activating FOXP3 in various cell lines of human female breast cancers. We confirmed CRISPR reactivation of the non-mutated copy of FOXP3 from XCI in human breast cancer CRL2316 cells, which express a synonymous heterozygous mutation (p.L266L; c.798G>C) in the coding region of FOXP3. Further, simultaneous silencing of XIST from XCI led to enhanced and prolonged FOXP3 reactivation. We optimized CRISPRa by fusing SadCas9 to the demethylase TET1 and observed enhanced FOXP3 activation. Analysis of the conserved CpG-rich region of FOXP3 intron 1 confirmed that CRISPRi/a-mediated simultaneous FOXP3 activation and XIST silencing were accompanied by elevated H4 acetylation, including H4K5ac, H4K8ac, and H4K16ac, and H3K4me3 and lower DNA methylation. This indicates that CRISPRi/a targeting to XIST and FOXP3 loci alters their transcription and their nearby epigenetic modifications. The simultaneous activation and repression of the X-linked, endogenous FOXP3 and XIST from XCI offers a useful research tool and a potential therapeutic for female breast cancers. This approach also provides new routes of targeted therapy for other X-chromosome-linked genetic disorders.

category: cancer biology


title: Reconfigurable asymmetric protein assemblies through implicit negative design

abstract: Asymmetric multi-protein complexes that undergo subunit exchange play central roles in biology, but present a challenge for protein design. The individual components must contain interfaces enabling reversible addition to and dissociation from the complex, but be stable and well behaved in isolation. Here we employ a set of implicit negative design principles to generate beta sheet mediated heterodimers which enable the generation of a wide variety of structurally well defined asymmetric assemblies. Crystal structures of the heterodimers are very close to the design models, and unlike previously designed orthogonal heterodimer sets, the subunits are stable, folded and monomeric in isolation and rapidly assemble upon mixing. Rigid fusion of individual heterodimer halves to repeat proteins yields central assembly hubs that can bind two or three different proteins across different interfaces. We use these connectors to assemble linearly arranged hetero-oligomers with up to 6 unique components, branched hetero-oligomers, closed C4-symmetric two-component rings, and hetero-oligomers assembled on a cyclic homo-oligomeric central hub, and demonstrate such complexes can readily reconfigure through subunit exchange. Our approach provides a general route to designing asymmetric reconfigurable protein systems.

category: synthetic biology


title: Spatio-temporally efficient coding assigns functions to hierarchical structures of the visual system

abstract: Hierarchical structures constitute a wide array of brain areas, including the visual system. One of the important questions regarding visual hierarchical structures is to identify computational principles for assigning functions that represent the external world to hierarchical structures of the visual system. Given that visual hierarchical structures contain both bottom-up and top-down pathways, the derived principles should encompass these bidirectional pathways. However, existing principles such as predictive coding do not provide an effective principle for bidirectional pathways. Therefore, we propose a novel computational principle for visual hierarchical structures as spatio-temporally efficient coding underscored by the efficient use of given resources in both neural activity space and processing time. This coding principle optimises bidirectional information transmissions over hierarchical structures by simultaneously minimising temporal differences in neural responses and maximising entropy in neural representations. Simulations demonstrated that the proposed spatio-temporally efficient coding was able to assign the function of appropriate neural representations of natural visual scenes to visual hierarchical structures. Furthermore, spatio-temporally efficient coding was able to predict well-known phenomena, including deviations in neural responses to unlearned inputs and bias in preferred orientations. Our proposed spatio-temporally efficient coding may facilitate deeper mechanistic understanding of the computational processes of hierarchical brain structures.


title: Diet-induced modifications to human microbiome reshape colonic homeostasis in irritable bowel syndrome

abstract: Changes in microbiome composition have been associated with a wide array of human diseases, turning the human microbiota into an attractive target for therapeutic intervention. Yet clinical translation of these findings requires the establishment of causative connections between specific microbial taxa and their functional impact on host tissues. Here, we colonized gut organ cultures with longitudinal microbiota samples collected from newly-diagnosed and therapy-naive irritable bowel syndrome (IBS) patients under low-FODMAP (fermentable Oligo-, Di-, Mono- saccharides and Polyols) diet. We show that post-diet microbiota regulates intestinal expression of inflammatory and neuro-muscular gene-sets. Specifically, we identify Bifidobacterium adolescentis as a diet-sensitive pathobiont that alters tight junction integrity and disrupts gut barrier functions. Collectively, we present a unique pathway discovery approach for mechanistic dissection and identification of functional diet-host-microbiota modules. Our data support the hypothesis that the gut microbiota mediates the beneficial effects of low-FODMAP diet, and reinforce the potential feasibility of microbiome based-therapies in IBS.


title: The utility of a closed breeding colony of Peromyscus leucopus for dissecting complex traits

abstract: Although Peromyscus leucopus (deermouse) is not considered a genetic model system, its genus is well suited for addressing several questions of biologist interest, including the genetic bases of longevity, behavior, physiology, adaptation, and its ability to serve as a disease vector. Here we explore a diversity outbred approach for dissecting complex traits in Peromyscus leucopus, a non-traditional genetic model system. We take advantage of a closed colony of deer-mice founded from 38 individuals between 1982 and 1985 and subsequently maintained for 35+ years ([~]40-60 generations). From 405 low-pass ([~]1X) short-read sequenced deermice we accurately imputed genotypes at 17,751,882 SNPs. Conditional on observed genotypes for a subset of 297 individuals, simulations were conducted in which a QTL contributes 5% to a complex trait under three different genetic models. The power of either a haplotype- or marker-based statistical test was estimated to be 15-25% to detect the hidden QTL. Although modest, this power estimate is consistent with that of DO/HS mice and rat experiments for an experiment with [~]300 individuals. This limitation in QTL detection is mostly associated with the stringent significance threshold required to hold the genome-wide false positive rate low, as in all cases we observe considerable linkage signal at the location of simulated QTL, suggesting a larger panel would exhibit greater power. For the subset of cases where a QTL was detected, localization ability appeared very desirable at [~]1-2Mb. We finally carried out a GWAS on a demonstration trait, bleeding time. No tests exceeded the threshold for genome-wide significance, but one of four suggestive regions co-localizes with Von Willebrand factor. Our work suggests that complex traits can be dissected in founders-unknown P. leucopus colony mice in much the same manner as founders-known DO/HS mice and rats, with genotypes obtained from low pass sequencing data. Our results further suggest that the DO/HS approach can be powerfully extended to any system in which a founders-unknown closed colony has been maintained for several dozen generations.


title: Genetic parameters of colostrum and calf serum antibodies in Swedish dairy cattle

abstract:
BackgroundColostrum with sufficient IgG content is essential for the newborn calf, as it provides passive immunity which substantially affects the probability of survival during rearing. Failure of passive transfer occurs when a calf does not absorb enough antibodies from the colostrum as indicated by less than 10 g/L of IgG in calf serum. Besides delayed access to colostrum, this can be due to low IgG production of the mother or poor IgG absorption by the calf. The aim of this study was to estimate the genetic background of antibody levels and indicator traits for antibodies in colostrum and calf serum, and their correlation with milk production and health.

ResultsColostrum data were available from 1340 cows with at least one calving and calf serum data were available from 886 calves from these cows. Antibody concentrations were estimated using refractometry (digital Brix refractometer for colostrum and optical refractometer for serum) as indicator traits and established using ELISAs to determine total IgG and natural antibodies [NAb] of various antibody isotypes in colostrum and serum. Colostrum traits had heritabilities ranging from 0.16 to 0.31 with repeatabilities from 0.21 to 0.55. Brix had positive genetic correlations with all colostrum antibody traits including total IgG (0.68). Calf serum antibody concentrations had heritabilities ranging from 0.25 to 0.59, with a significant maternal effect accounting for 17 to 27% of the variance. When calves later in life produced their first lactation, lactation-average somatic cell score was found to be negatively correlated with NAb in calf serum.

ConclusionsOur results suggest that antibody levels in colostrum and calf serum can be increased by means of selection.


title: Polymer microparticles prolong delivery of the 15-PGDH inhibitor SW033291

abstract:
As the prevalence of age-related fibrotic diseases continues to increase, novel antifibrotic therapies are emerging to address clinical needs. However, many novel therapeutics for managing chronic fibrosis are small-molecule drugs that require frequent dosing to attain effective concentrations. While bolus parenteral administrations have become standard clinical practice, an extended delivery platform would achieve steady state concentrations over a longer time period with fewer administrations. This study lays the foundation for the development of a sustained release platform for the delivery of (+)SW033291, a potent, small-molecule inhibitor of the 15-hydroxyprostaglandin dehydrogenase (15-PGDH) enzyme, which has previously demonstrated efficacy in a murine model of pulmonary fibrosis. Herein, we leverage fine-tuned cyclodextrin microparticles - specifically {beta}-CD microparticles ({beta}-CD MPs) - to extend the delivery of 15-PGDH inhibitor, (+)SW033291, to over one week.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/456403v1_ufig1.gif" ALT="Figure 1">
View larger version (14K):
org.highwire.dtl.DTLVardef@13aed1dorg.highwire.dtl.DTLVardef@1a541eaorg.highwire.dtl.DTLVardef@8a9fd5org.highwire.dtl.DTLVardef@1038a77_HPS_FORMAT_FIGEXP  M_FIG C_FIG

category: bioengineering


title: Structural basis for channel conduction in the pump-like channelrhodopsin ChRmine

abstract: ChRmine1, a recently-discovered bacteriorhodopsin-like cation-conducting channelrhodopsin1, 2, exhibits puzzling properties (unusually-large photocurrents, exceptional red-shift in action spectrum, and extreme light-sensitivity) that have opened up new opportunities in optogenetics1, 3-5. ChRmine and its homologs function as light-gated ion channels, but by primary sequence more closely resemble ion pump rhodopsins; the molecular mechanisms for passive channel conduction in this family of proteins, as well as the unusual properties of ChRmine itself, have remained mysterious. Here we present the cryo-electron microscopy structure of ChRmine at 2.0 [A] resolution. The structure reveals striking architectural features never seen before in channelrhodopsins including trimeric assembly, a short transmembrane-helix 3 unwound in the middle of the membrane, a prominently-twisting extracellular-loop 1, remarkably-large intracellular cavities and extracellular vestibule, and an unprecedented hydrophilic pore that extends through the center of the trimer, separate from the three individual monomer pores. Electrophysiological, spectroscopic, and computational analyses provide insight into conduction and gating of light-gated channels with these distinct design features, and point the way toward structure-guided creation of novel channelrhodopsins for optogenetic applications in biology.


title: Citrus Huanglongbing is an immune-mediated disease that can be treated by mitigating reactive oxygen species triggered cell death of the phloem tissues caused by Candidatus Liberibacter asiaticus

abstract: The immune system is critical for keeping animals and plants healthy from pathogens. However, immune-mediated diseases are also common for human. Immune-mediated diseases have not been reported for plants. Here, we present evidence that citrus Huanglongbing (HLB), caused by phloem-colonizing Candidatus Liberibacter asiaticus (CLas), is an immune-mediated disease. CLas infection of Citrus sinensis stimulated systemic and chronic immune response in the phloem tissues including reactive oxygen species (ROS) production as indicated by H2O2, callose deposition, and induction of immune related genes. Systemic cell death of companion and sieve element cells, but not surrounding parenchyma cells, was observed following ROS production triggered by CLas. ROS production triggered by CLas localized in phloem tissues. The H2O2 concentration in exudates extracted from phloem enriched bark tissue of CLas infected plants reached a threshold of killing citrus protoplast cells, which was suppressed by uric acid (a ROS scavenger) and gibberellin. Foliar spray of HLB positive citrus with antioxidants (uric acid and rutin) and gibberellin significantly reduced both H2O2 concentrations and cell death in phloem tissues induced by CLas and reduced HLB symptoms. RNA-seq analyses of CLas infected and health C. sinensis support that CLas causes oxidative stress. In sum, HLB is an immune-mediated disease and both mitigating ROS via antioxidants and promoting plant growth can reduce cell death of the phloem tissues caused by CLas, thus controlling HLB.

category: plant biology


title: Musicians and non-musicians consonant/dissonant perception investigated by EEG and fMRI

abstract:
The perception of two (or more) simultaneous musical notes, depending on their pitch interval(s), could be broadly categorized as consonant or dissonant. Previous studies have suggested that musicians and non-musicians adopt different strategies when discerning music intervals: the frequency ratio (perfect fifth or tritone) for the former, and frequency differences (e.g., roughness vs. non-roughness) for the latter. To extend and replicate this previous finding, in this follow-up study we reran the ElectroEncephaloGraphy (EEG) experiment, and separately collected functional magnetic resonance imaging (fMRI) data of the same protocol. The behavioral results replicated our previous findings that musicians used pitch intervals and nonmusicians roughness for consonant judgments. And the ERP amplitude differences between groups in both frequency ratio and frequency differences were primarily around N1 and P2 periods along the midline channels. The fMRI results, with the joint analyses by univariate, multivariate, and connectivity approaches, further reinforce the involvement of midline and related-brain regions in consonant/dissonance judgments. Additional representational similarity analysis (or RSA), and the final spatio-temporal searchlight RSA (or ss-RSA), jointly combined the fMRI-EEG into the same representational space, providing final support on the neural substrates of neurophysiological signatures. Together, these analyses not just exemplify the importance of replication, that musicians rely more on top-down knowledge for consonance/dissonance perception; but also demonstrate the advantages of multiple analyses in constraining the findings from both EEG and fMRI.

Significance StatementIn this study, the neural correlates of consonant and dissonant perception has been revisited with both EEG and fMRI. Behavioral results of the current study well replicated the pattern of our earlier work (Kung et al., 2014), and the ERP results, though showing that both musicians and nonmusicians processed rough vs. non-rough notes similarly, still supported the top-down modulation in musicians likely through long-term practice. The fMRI results, combining univariate (GLM contrast and functional connectivity) and multivariate (MVPA searchlight and RSA on voxel-, connectivity-, and spatio-temporal RSA searchlight-level) analyses, commonly speak to lateralized and midline regions, at different time windows, as the core brain networks that underpin both musicians and nonmusicians consonant/dissonant perceptions.


title: Long-term effects of moderate concussive brain injury during adolescence on synaptic and tonic GABA currents in dentate projection neurons.

abstract: Progressive physiological changes in the hippocampal dentate gyrus circuits following traumatic brain injury contribute to temporal evolution of neurological sequelae. Although early posttraumatic changes in dentate synaptic and extrasynaptic GABA currents have been reported, whether they evolve over time and remain distinct between the two projection neuron classes, granule cells and semilunar granule cells, has not been evaluated. We examined changes in tonic GABA currents and spontaneous inhibitory postsynaptic currents (sIPSCs) and in dentate projection neurons one and three month after moderate concussive fluid percussion injury (FPI) in adolescent rats. Granule cell tonic GABA current amplitude remained elevated up to one month after FPI, but decreased to levels comparable to age-matched controls by three months postinjury. Granule cell sIPSC frequency, which we previously reported to be increased one week after FPI, remained higher than in age-matched controls at one month and was significantly reduced three months after FPI. In contrast to the early decrease, tonic GABA current amplitude and sIPSC frequency in semilunar granule cell was not different from controls three months after FPI. The switch in granule cell inhibitory inputs from early increase to subsequent decrease could contribute to the delayed emergence of cognitive deficits and seizure susceptibility after brain injury.


title: Immune competence and spleen size scale with colony status in the naked mole-rat

abstract: Naked mole-rats (NM-R; Heterocephalus glaber) live in multi-generational colonies with a social hierarchy, show low cancer incidence and long life-spans. Here we asked if such extreme physiology might have an immune component. The spleen is the largest lymphoid organ and plays an essential role in response to immunological insults and may participate in combating cancer and slowing ageing. We investigated the anatomy, molecular composition and function of the NM-R spleen using RNA-sequencing and histological analysis in healthy animals. We found that spleen size in healthy NM-Rs varies considerably. We therefore classified NM-Rs according to spleen size as NM-Rs with small spleens or enlarged spleens. Animals with enlarged spleens showed potentially better anti-microbial profiles and were much more likely to have a high rank within the colony. Splenomegaly was associated with infection in sick NM-Rs, but not in NM-Rs with enlarged spleens. In all healthy NM-Rs splenic erythropoiesis, megakaryopoiesis and myelopoiesis were increased, but B lymphopoiesis was reduced and splenic marginal zone showed markedly altered morphology when compared to other rodents. However, in NM-Rs lymphocytes were found in secondary sites such as lymph nodes, gut lymphoid nodules and thymus. Thus, the NM-R spleen is a major site of adult hematopoiesis under normal physiological conditions. Overall, the NM-R immune system seems to rely mainly on innate immune responses with a more restricted adaptive immune response. We propose that the anatomical plasticity of the spleen might be regulated by social interaction and gives immunological advantage to increase the life-span of higher ranked animals.


title: Hyperactive chemotaxis contributes to anti-TNFα treatment resistance in inflammatory bowel disease

abstract:
Background & AimsAnti-tumour necrosis factor-alpha (anti-TNF) agents have been used for inflammatory bowel disease (IBD), however, it has up to 30% non-response rate. Identifying molecular pathways and finding reliable diagnostic biomarkers for patient response to anti-TNF treatment are clearly needed.

MethodsPublicly available transcriptomic data from IBD patients receiving anti-TNF therapy was systemically collected and integrated. In silico flow cytometry approaches and MetaScape were applied to evaluate immune cell populations and to perform gene enrichment analysis, respectively. Genes identified within enrichment pathways validated in neutrophils were tracked in an anti-TNF-treated animal model (with lipopolysaccharide (LPS)-induced inflammation). The receiver operating characteristic (ROC) curve was applied to all genes to identify the best prediction biomarkers.

ResultsA total of 449 samples were retrieved from control, baseline and after primary anti-TNF therapy or placebo. No statistically significant differences were observed between anti-TNF treatment responders and non-responders at baseline in immune microenvironment scores. Neutrophils, endothelial and B cell populations were higher in baseline non-responders and chemotaxis pathways may contribute to the treatment resistance. Genes related to chemotaxis pathways were significantly up-regulated in LPS-induced neutrophils but no statistically significant changes were observed in neutrophils treated with anti-TNF. Interleukin 13 receptor subunit alpha 2 (IL13RA2) is the best predictor (ROC: 80.7%, 95% CI: 73.8% - 87.5%) with a sensitivity of 68.13% and specificity of 84.93%, and significantly higher in non-responders compared to responders (p < 0.0001).

ConclusionsHyperactive chemotaxis influences responses to anti-TNF treatment and IL13RA2 is a potential biomarker to predict anti-TNF treatment response.


title: Optimal dynamic incentive scheduling for Hawk-Dove evolutionary games

abstract: The Hawk-Dove mathematical game offers a paradigm of the trade-offs associated with aggressive and passive behaviors. When two (or more) populations of players (animals, insect populations, countries in military conflict, economic competitors, microbial communities, populations of co-evolving tumor cells, or reinforcement learners adopting different strategies) compete, their success or failure can be measured by their frequency in the population (successful behavior is reinforced, unsuccessful behavior is not), and the system is governed by the replicator dynamical system. We develop a time-dependent optimal-adaptive control theory for this nonlinear dynamical system in which the payoffs of the Hawk-Dove payoff matrix are dynamically altered (dynamic incentives) to produce (bang-bang) control schedules that (i) maximize the aggressive population at the end of time T, and (ii) minimize the aggressive population at the end of time T. These two distinct time-dependent strategies produce upper and lower bounds on the outcomes from all strategies since they represent two extremizers of the cost function using the Pontryagin maximum (minimum) principle. We extend the results forward to times nT (n = 1, ..., 5) in an adaptive way that uses the optimal value at the end of time nT to produce the new schedule for time (n + 1)T. Two special schedules and initial conditions are identified that produce absolute maximizers and minimizers over an arbitrary number of cycles for 0 [≤] T [≤] 3. For T > 3, our optimum schedules can drive either population to extinction or fixation. The method described can be used to produce optimal dynamic incentive schedules for many different applications in which the 2 x 2 replicator dynamics is used as a governing model.


title: Reconsidering the validity of transcriptome-wide association studies

abstract: Transcriptome-wide association studies (TWAS)1-5, which aim to detect relationships between gene expression and a phenotype, are commonly used for secondary analysis of genome-wide association study (GWAS) results. Results of TWAS analyses are often interpreted as indicating a genetically mediated relationship between gene expression and the phenotype, but because the traditional TWAS framework does not model the uncertainty in the expression quantitative trait loci (eQTL) effect estimates6,7, this interpretation is not justified. In this study we outline the implications of this issue. Using simulations, we show severely inflated type 1 error rates for TWAS when evaluating a null hypothesis of no genetic relationship between gene expression and the phenotype. Moreover, in our application to real data only 51% of the TWAS associations were confirmed with local genetic correlation8 analysis, an approach which correctly evaluates the same null. Our results thus demonstrate that TWAS is unsuitable for investigating genetic relationships between gene expression and a phenotype.


title: A nanopore ion source delivers single amino acid and peptide ions directly into the gas phase

abstract: A technology for sequencing single proteins would expand our understanding of biology and improve the detection and treatment of disease [1]. Approaches based on fluorosequencing [2], nanopores [3, 4], and tunneling spectroscopy [5] are under development and show promise. However, only mass spectrometry (MS) has demonstrated an ability to identify amino acids with minimal degeneracy [6]. We envision sequencing a protein by fragmenting it and delivering its constituent amino acids into a mass spectrometer in sequential order, but existing ion sources employ a background gas that scrambles the spatial ordering of ions and degrades their transmission. Here we report an ion source comprising a glass capillary with a sub-100 nm diameter pore that emits amino acid ions from aqueous solution directly into vacuum. Emitted ions travel collision-less trajectories before striking a single-ion detector. We measured unsolvated ions of 16 different amino acids as well as glutathione and two of its post-translationally modified variants.


title: Quaternary structure independent folding of voltage-gated ion channel pore domain subunits

abstract: Every voltage-gated ion channel (VGIC) superfamily member has an ion conducting pore consisting of four pore domain (PD) subunits that are each built from a common plan comprising an antiparallel transmembrane helix pair, a short, obliquely positioned helix (the pore helix), and selectivity filter. The extent to which this structure, the VGIC-PD fold, relies on the extensive quaternary interactions observed in PD assemblies is unclear. Here, we present crystal structures of three bacterial voltage-gated sodium channel (BacNaO_SCPLOWVC_SCPLOW) pores that adopt a surprising set of non-canonical quaternary structures and yet maintain the native tertiary structure of the PD monomer. This context-independent structural robustness demonstrates that the VGIC-PD fold, the fundamental VGIC structural building block, can adopt its native-like tertiary fold independent of native quaternary interactions. In line with this observation, we find that the VGIC-PD fold is not only present throughout the VGIC superfamily and other channel classes but has homologs in diverse transmembrane and soluble proteins. Characterization of the structures of two synthetic Fabs (sFabs) that recognize the VGIC-PD fold shows that such sFabs can bind purified full-length channels and indicates that non-canonical quaternary PD assemblies can occur in the context of complete VGICs. Together, our data demonstrate that the VGIC-PD structure can fold independently of higher-order assembly interactions and suggest that full-length VGIC PDs can access previously unknown non-canonical quaternary states. These PD properties have deep implications for understanding how the complex quaternary architectures of VGIC superfamily members are achieved and point to possible evolutionary origins of this fundamental VGIC structural element.


title: Respiratory Alkalosis Provokes Spike-Wave Discharges in Seizure- Prone Rats

abstract: Hyperventilation reliably provokes seizures in patients diagnosed with absence epilepsy. Despite this predictable patient response, the mechanisms that enable hyperventilation to powerfully activate absence seizure-generating circuits remain entirely unknown. Using the WAG/Rij rat, an established rodent model of absence epilepsy, we demonstrate that absence seizures are highly sensitive to arterial carbon dioxide, suggesting that seizure-generating circuits are sensitive to pH. Moreover, hyperventilation consistently activated neurons within the intralaminar nuclei of the thalamus, a structure implicated in seizure generation. We show that intralaminar thalamus also contains pH-sensitive neurons. Collectively, these observations suggest that hyperventilation activates pH-sensitive neurons of the intralaminar nuclei to provoke absence seizures.


title: Characteristic core voxels in normal individuals revealed by hyperbolic disc embedding and k-core percolation on resting state fMRI

abstract: Hyperbolic disc embedding and k-core percolation reveal the core structure of the functional connectivity on resting-state fMRI (rsfMRI). Inter-voxel relations were visualized on embedded hyperbolic discs, and their core composition was traced using k-core percolation. Using 180 normal adults rsfMRI data from the Human Connectome Project database, scale- free intervoxel connectivity represented by IC-voxels composition, while visualized on hyperbolic discs using [Formula] model, showed the expected change of the largest component decreasing its size on k-core percolation eventually yielding the core structures of individuals. This kmax-core voxels-ICs composition revealed such stereotypes of individuals as visual network dominant, default mode network dominant, and distributed patterns. Characteristic core structures of resting-state brain connectivity of normal subjects disclosed the distributed or asymmetric contribution of voxels to the kmax-core, which suggests the hierarchical dominance of certain IC subnetworks characteristic to subgroups of individuals at rest.


title: Crosstalk between myosin II and formin functions in the regulation of force generation and actomyosin dynamics in stress fibers

abstract:
REF52 fibroblasts have a well-developed contractile machinery, the most prominent elements of which are actomyosin stress fibers with highly ordered organization of actin and myosin IIA filaments. The relationship between contractile activity and turnover dynamics of stress fibers is not sufficiently understood. Here, we simultaneously measured the forces exerted by stress fibers (using traction force microscopy or micropillar array sensors) and the dynamics of actin and myosin (using photoconversion-based monitoring of actin incorporation and high-resolution fluorescence microscopy of myosin II light chain). Our data revealed new features of the crosstalk between myosin II-driven contractility and stress fiber dynamics. During normal stress fiber turnover, actin incorporated all along the stress fibers and not only at focal adhesions. Incorporation of actin into stress fibers/focal adhesions, as well as actin and myosin II filaments flow along stress fibers, strongly depends on myosin II activity. Myosin II-dependent generation of traction forces does not depend on incorporation of actin into stress fibers per se, but still requires formin activity. This previously overlooked function of formins in maintenance of the actin cytoskeleton connectivity could be the main mechanism of formin involvement in traction force generation.

Highlights* Cell traction forces are measured together with visualization of actomyosin flow
* Actin turnover depends on formin and myosin II activities
* Traction forces depend not only on myosin II, but also on formins
* Traction force generation may require formin-dependent cytoskeleton connectivity

category: cell biology


title: Niche theory for within-host parasite dynamics: Analogies to food web modules via feedback loops

abstract: Why do parasites exhibit a wide dynamical range within their hosts? For instance, why can a parasite only sometimes successfully infect its host? Why do some parasites exhibit large fluctuations? Why do two parasites coinfect, exclude each other, or win only sometimes over another (via priority effects)? For insights, we turn to food webs. An omnivory model (IGP) blueprints one parasite competing with immune cells for host energy (PIE), and a competition model (keystone predation, KP) mirrors a new coinfection model (2PIE). We then draw analogies between models using feedback loops. We translate those loops into the intraspecific direct (DE) and indirect effects (IE) that create various dynamics. Three points arise. First, a prey or parasite can flip between stable and oscillatory coexistence with their enemy with weakening IE and strengthening DE. Second, even with comparable loop structure, a parasite cannot exhibit priority effects seen in IGP due to constraints imposed by production of immune cells. Third, despite simpler loop structure, KP predicts parallel outcomes in the two-parasite model due to comparable structure of interactions between competing victims and their resources and enemies. Hence, food web models offer powerful if imperfect analogies to feedbacks underlying the dynamical repertoire of parasites within hosts.

category: ecology


title: ColabFold - Making protein folding accessible to all

abstract:
ColabFold offers accelerated protein structure and complex predictions by combining the fast homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. ColabFolds 40 - 60x faster search and optimized model use allows predicting close to a thousand structures per day on a server with one GPU. Coupled with Google Colaboratory, ColabFold becomes a free and accessible platform for protein folding. ColabFold is open-source software available at github.com/sokrypton/ColabFold. Its novel environmental databases are available at colabfold.mmseqs.com

Contactmilot.mirdita@mpibpc.mpg.de, so@fas.harvard.edu, martin.steinegger@snu.ac.kr


title: Fanconi Anemia Pathway Deficiency Drives Copy Number Variation in Squamous Cell Carcinomas

abstract: Fanconi anemia (FA), a model syndrome of genome instability, is caused by a deficiency in DNA interstrand crosslink (ICL) repair resulting in chromosome breakage1-3. The FA repair pathway comprises at least 22 FANC proteins including BRCA1 and BRCA24-6, and protects against carcinogenic endogenous and exogenous aldehydes7-10. Individuals with FA are hundreds to thousands-fold more likely to develop head and neck (HNSCC), esophageal and anogenital squamous cell carcinomas (SCCs) with a median onset age of 31 years11. The aggressive nature of these tumors and poor patient tolerance of platinum and radiation-based therapy have been associated with short survival in FA11-16. Molecular studies of SCCs from individuals with FA (FA SCCs) have been limited, and it is unclear how they relate to sporadic HNSCCs primarily driven by tobacco and alcohol exposure or human papillomavirus (HPV) infection17. Here, by sequencing FA SCCs, we demonstrate that the primary genomic signature of FA-deficiency is the presence of a high number of structural variants (SVs). SVs are enriched for small deletions, unbalanced translocations, and fold-back inversions that arise in the context of TP53 loss. The SV breakpoints preferentially localize to early replicating regions, common fragile sites, tandem repeats, and SINE elements. SVs are often connected forming complex rearrangements. Resultant genomic instability underlies elevated copy number alteration (CNA) rates of key HNSCC-associated genes, including PIK3CA, MYC, CSMD1, PTPRD, YAP1, MXD4, and EGFR. In contrast to sporadic HNSCC, we find no evidence of HPV infection in FA HNSCC, although positive cases were identified in gynecologic tumors. A murine allograft model of FA pathway-deficient SCC was enriched in SVs, exhibited dramatic tumor growth advantage, more rapid epithelial-to-mesenchymal transition (EMT), and enhanced autonomous inflammatory signaling when compared to an FA pathway-proficient model. In light of the protective role of the FA pathway against SV formation uncovered here, and recent findings of FA pathway insufficiency in the setting of increased formaldehyde load resulting in hematopoietic stem cell failure and carcinogenesis18-20, we propose that high copy-number instability in sporadic HNSCC may result from functional overload of the FA pathway by endogenous and exogenous DNA crosslinking agents. Our work lays the foundation for improved FA patient treatment and demonstrates that FA SCC is a powerful model to study tumorigenesis resulting from DNA crosslinking damage.


title: Defective Slc7a7 transport reduces systemic arginine availability compromising erythropoiesis and iron homeostasis

abstract: SLC7A7 encodes for y+LAT1, a cationic amino acid transporter expressed on the basolateral membrane of epithelial cells and macrophages. Mutations in human SLC7A7 cause lysinuric protein intolerance (LPI), a rare autosomal disorder with a variety of clinical symptoms. Citrulline and a low protein diet are widely used to treat the main symptoms of LPI; however, the hematological and immunological abnormalities in LPI remain poorly understood and difficult to manage by established treatments. Here, we show that erythropoietin levels are significantly diminished in mice lacking Slc7a7, which reduces the number of erythroblast precursors, resulting in mature red blood cells with a smaller mean corpuscular volume. Ex vivo analysis demonstrated that erythrocytes from Slc7a7-deficient mice were phagocytosed more by bone marrow-derived macrophages. Gene expression analysis of sorted red pulp macrophages (RPMs) from Slc7a7-deficient mice indicated that this cell population had higher erythrophagocytic activity, but preserved heme catabolic activity. The increase in erythrophagocytosis resulted in iron accumulation in macrophages and tissues, and ultimately led to RPM apoptosis. Surprisingly, ablation of Slc7a7 in myeloid cells failed to trigger tissue iron accumulation or changes in the RPM population, indicating that the expression of this gene in macrophages is not key for the development of iron accumulation in tissue. Finally, restoration of serum erythropoietin levels in Slc7a7-deficient mice re-established normal erythropoiesis and erythrophagocytosis and prevented the accumulation of iron in tissues. Thus, erythropoietin has a fundamental role in the immune-hematological alterations of LPI in mice, revealing a new crucial role for this hormone in this disease.


title: Erythropoietin supplementation ameliorates the immunological and hematological deficiencies of lysinuric protein intolerance in mice


title: SUMO E2/E3 Enzyme Co-Recognize Substrates and Confers High Substrates Specificity

abstract:
Although various technologies can determine protein-protein interaction affinity, Kd, current approaches require at least one interacting protein to be purified. Here, we present a development of high-throughput approach to determine protein interaction affinity for un-purified interacting proteins using quantitative FRET assay. We developed this approach first using SUMO E2 conjugating enzyme, Ubc9, and SUMO substrate, RanGap1c. The interaction affinities from two purified proteins and two unpurified proteins in the presence of BSA, bacterial extracts or two mixtures are all in excellent agreement with that obtained from the SPR measurement. We then applied this approach to determine the interaction affinities of SUMO E3 PIAS1 and Ubc9 with a SUMO substrate, influenza virus protein, NS1, and, for the first time, the SUMO E3 ligase-substrate interaction affinity is determined, which enables us to provide a kinetics explanation for the two-enzyme substrate recognition mode. In general, our studies allow high-throughput determination of protein interacting affinity without any purification, and both the approach and scientific discoveries can be applied to proteins that are difficult to be expressed in general.

O_LIProtein interaction dissociation constant, Kd, determination without any protein purification;
C_LIO_LICo-recognition of substrates by two enzymes in one reaction;
C_LIO_LIPotential affinity improvement mechanism of substrate recognition revealed with kinetics parameters in vivo.
C_LI

category: biochemistry


title: Constructing Functional Networks of Phosphorylation Sites Using Co-Phosphorylation

abstract: Protein phosphorylation is a ubiquitous regulatory mechanism that plays a central role in cellular signaling. According to recent estimates, up to 70% of human proteins can be phosphorylated. Therefore, characterization of phosphorylation dynamics is critical for understanding a broad range of biological and biochemical processes. Technologies based on mass spectrometry are rapidly advancing to meet the needs for high-throughput screening of phosphorylation. These technologies enable untargeted quantification of thousands of phosphorylation sites in a given sample. Many labs are already utilizing these technologies to comprehensively characterize signaling landscapes by examining perturbations with drugs and knockdown approaches, or by assessing diverse phenotypes in cancers, neuro-degerenational diseases, infectious diseases, and normal development. Here, we comprehensively investigate the concept of "co-phosphorylation", defined as the correlated phosphorylation of a pair of phosphosites across various biological states. We integrate nine publicly available phospho-proteomics datasets for various diseases (including breast cancer, ovarian cancer and Alzhemiers disease) and utilize functional data related to sequence, evolutionary histories, kinase annotations, and pathway annotations to investigate the functional relevance of co-phosphorylation. Our results across a broad range of studies consistently show that functionally associated sites tend to exhibit significant positive or negative co-phosphorylation. Specifically, we show that co-phosphorylation can be used to predict with high precision the sites that are on the same pathway or that are targeted by the same kinase. Overall, these results establish co-phosphorylation as a useful resource for analyzing phospho-proteins in a network context, which can help extend our knowledge on cellular signaling and its dysregulation.

category: systems biology


title: Arg1+ microglia are critical for shaping cognition in female mice

abstract: Diversity within microglia, the resident brain immune cells, is reported. Whether microglial subsets constitute different subtypes with intrinsic properties and unique functions has not been fully elucidated. Here, we describe a microglial subtype characterized by the expression of the enzyme Arginase-1, i.e. Arg1 +microglia, which is found predominantly in the cholinergic neuron-rich forebrain region during early postnatal development. Arg1+ microglia are frequently observed in close apposition to neurons and exhibit a distinctive molecular signature reflecting a reactive profile. Arg1 deficiency in microglia results in impaired dendritic spine maturation in the hippocampus where cholinergic neurons project, and cognitive behavioural deficiencies in female mice. Our results expand on microglia diversity and provide insights into distinctive spatiotemporal functions exerted by microglial subtypes.


title: Nos2-/- mice infected with M. tuberculosis develop neurobehavioral changes and immunopathology mimicking human central nervous system tuberculosis

abstract:
BackgroundUnderstanding the pathophysiology of central nervous system tuberculosis (CNS-TB) is hampered by the lack of a good pre-clinical model that mirrors the human CNS-TB infection. We developed a murine CNS-TB model that demonstrates neurobehavioral changes with similar immunopathology with human CNS-TB.

MethodsWe injected two Mycobacterium tuberculosis (M.tb) strains, H37Rv and CDC1551, respectively, into two mouse strains, C3HeB/FeJ and Nos2-/- mice, either into the third ventricle or intravenous. We compared the neurological symptoms, histopathological changes and levels of adhesion molecules, chemokines, and inflammatory cytokines in the brain induced by the infections through different routes in different strains.

ResultsIntra-cerebroventricular infection of Nos2-/- mice with M.tb led to development of neurological signs and more severe brain granulomas compared to C3HeB/FeJ mice. Compared with CDC1551 M.tb, H37Rv M.tb infection resulted in a higher neurobehavioral score and earlier mortality. Intra-cerebroventricular infection caused necrotic neutrophil-dominated pyogranulomas in the brain relative to intravenous infection which resulted in disseminated granulomas and mycobacteraemia. Histologically, intra-cerebroventricular infection of Nos2-/- mice with M.tb resembled human CNS-TB brain biopsy specimens. H37Rv intra-cerebroventricular infected mice demonstrated higher brain concentrations of inflammatory cytokines, chemokines and adhesion molecule ICAM-1 than H37Rv intravenous-infected mice.

ConclusionsIntra-cerebroventricular infection of Nos2-/- mice with H37Rv creates a murine CNS-TB model that resembled human CNS-TB immunopathology, exhibiting the worst neurobehavioral score with a high and early mortality reflecting disease severity and its associated neurological morbidity. Our murine CNS-TB model serves as a pre-clinical platform to dissect host-pathogen interactions and evaluate therapeutic agents for CNS-TB.


title: Faster rates of molecular sequence evolution in reproduction-related genes and in species with hypodermic sperm morphologies

abstract: Sexual selection drives the evolution of many striking behaviours and morphologies, and should leave signatures of selection at loci underlying these phenotypes. However, while loci thought to be under sexual selection often evolve rapidly, few studies have contrasted rates of molecular sequence evolution at such loci across lineages with different sexual selection contexts. Furthermore, work has focused on separate sexed animals, neglecting alternative sexual systems. We investigate rates of molecular sequence evolution in hermaphroditic flatworms of the genus Macrostomum. Specifically, we compare species that exhibit contrasting sperm morphologies, strongly associated with multiple convergent shifts in the mating strategy, reflecting different sexual selection contexts. Species donating and receiving sperm in every mating have sperm with bristles, likely to prevent sperm removal. Meanwhile, species that hypodermically inject sperm lack bristles, potentially as an adaptation to the environment experienced by hypodermic sperm. Combining functional annotations from the model, M. lignano, with transcriptomes from 97 congeners, we find genus-wide faster sequence evolution in reproduction-related versus ubiquitously-expressed genes, consistent with stronger sexual selection on the former. Additionally, species with hypodermic sperm morphologies had elevated molecular sequence evolution, regardless of a genes functional annotation. These genome-wide patterns suggest reduced selection efficiency following shifts to hypodermic mating, possibly due to higher selfing rates in these species. Moreover, we find little evidence for convergent amino acid changes across species. Our work not only shows that reproduction-related genes evolve rapidly also in hermaphroditic animals, but also that well-replicated contrasts of different sexual selection contexts can reveal underappreciated genome-wide effects.


title: Diversity and evolution of amphibian pupil shapes

abstract: Pupil constriction has important functional consequences for animal vision, yet the evolutionary mechanisms underlying diverse pupil sizes and shapes, often among animals that occupy optically similar environments, are poorly understood. We aimed to quantify the diversity and evolution of pupil shapes among amphibians and test for potential correlations to ecology based on functional hypotheses. Using photographs, we surveyed pupil shape and the orientation of the constricted pupil across adults of 1293 amphibian species, 72 families, and 3 orders, and additionally for larval life stages for all families of frogs and salamanders with a biphasic ontogeny. Pupil shape is exceptionally diverse in amphibians with evolutionary transitions throughout the amphibian tree of life. For amphibians with a biphasic life history, we found that pupils change in many species that occupy distinct habitats before and after metamorphosis. Finally, we found that non-elongated (round or diamond) constricted pupils were correlated with species inhabiting consistently dim light environments (burrowing and aquatic species) and that elongated pupils (vertical and horizontal) were more common in species with larger absolute eye sizes. We propose that amphibians provide a valuable group within which to explore the anatomical, physiological, optical, and ecological mechanisms underlying the evolution of pupil shape.


title: Predicted responses to selection across the climatic range of a rainforest Drosophila without local adaptation: environmental variation limits trait divergence along ecological gradients

abstract: Evolutionary responses to environmental change require heritable variation in traits under selection. Both heritability and selection vary with the environment, and may also covary, meaning that environmental variation can be an important source of evolutionary constraint. However, estimates of heritability and selection along environmental gradients in the field are rare. We estimated environmental variation in selection on three traits (cold tolerance, heat tolerance and wing size) of the rainforest fly Drosophila birchii by transplanting flies in cages along two elevational gradients in north-east Queensland, Australia, and calculating the genetic covariance of trait values with cage productivity at each elevation. We estimated heritability of each trait from laboratory crosses, and environmental variation in heritability of wing size from the correlation of mothers and daughters in cages at each elevation. We then used estimates of selection and heritability to predict selection responses along the elevation gradients. Laboratory assays revealed low-moderate genetic variation in all traits and low covariation among traits, suggesting the potential for a strong response to selection. Estimated selection responses predicted divergence of cold tolerance with elevation at one gradient. However, this was not observed at either gradient, with no difference between high and low elevation populations for this trait. Despite substantial variation in heritability (and predicted selection response) of wing size, this appeared random with respect to elevation, preventing overall divergence and suggesting that local environmental variation constrains evolutionary responses along natural ecological gradients. Such an effect, if widespread, may significantly slow evolutionary responses to environmental change.


title: Genetic analysis of early phenology in lentil identifies distinct loci controlling component traits

abstract: Reproductive phenology is well known to be a key feature of crop adaptation to diverse ecogeographic variation and management practices. Lentil is one of the founder pulse crops of middle-eastern Neolithic agriculture, and the modern-day domesticated lentil germplasm is generally considered to form three broad adaptation groups: Mediterranean, South Asian and northern temperate, which correspond approximately to the major global production environments. Understanding the molecular basis of these adaptations is crucial to maximise efficiency of breeding programs. Here, we use a QTL approach to dissect the earliness that is characteristic of the South Asian pilosae ecotype, and that suits it to the typically short winter cropping season. We identified two loci, DTF6a and DTF6b, at which dominant alleles confer early flowering. We show that, although these loci can interact in an additive manner, DTF6a alone is sufficient to confer early flowering even in extremely short photoperiods. Comparisons with closely related legume species confirmed the presence of a conserved cluster of three FT orthologs among potential candidate genes in the region, and expression analysis in near-isogenic material showed that the early dtf6a allele is associated with a strong derepression of the FTa1 gene in particular. Analysis of sequence variation revealed the presence of a 7.4 kb deletion in the FTa1-FTa2 intergenic region in the pilosae parent, and a wide survey of over 400 accessions with diverse origin showed that the dtf6a allele is dominant in South Asia material. Collectively, these results contribute to understanding the molecular basis of global adaptation in lentil, and further emphasize the importance of this conserved genomic region for adaptation in temperate legumes generally.


title: Structures of Tweety Homolog Proteins TTYH2 and TTYH3 reveal a Ca2+-dependent switch from intra- to inter-membrane dimerization

abstract: Tweety homologs (TTYHs) comprise a conserved family of transmembrane proteins found in eukaryotes with three members (TTYH1-3) in vertebrates. They are widely expressed in mammals including at high levels in the nervous system and have been implicated in cancers and other diseases including epilepsy, chronic pain, and viral infections. TTYHs have been reported to form Ca2+- and cell volume-regulated anion channels structurally distinct from any characterized protein family with potential roles in cell adhesion, migration, and developmental signaling. To provide insight into TTYH family structure and function, we determined cryo-EM structures of Mus musculus TTYH2 and TTYH3 in lipid nanodiscs. TTYH2 and TTYH3 adopt a novel fold which includes an extended extracellular domain with a partially solvent exposed pocket that may be an interaction site for hydrophobic molecules. In the presence of Ca2+, TTYH2 and TTYH3 form homomeric cis-dimers bridged by extracellularly coordinated Ca2+. Strikingly, in the absence of Ca2+, TTYH2 forms trans-dimers that span opposing membranes across a ~130 [A] intermembrane space as well as a monomeric state. All TTYH structures lack ion conducting pathways and we do not observe TTYH2-dependent channel activity in cells. We conclude TTYHs are not pore forming subunits of anion channels and their function may involve Ca2+-dependent changes in quaternary structure, interactions with hydrophobic molecules near the extracellular membrane surface, and/or association with additional protein partners.


title: Magnetic Nanoprobes for Spatio-Mechanical Manipulation in Single Cells

abstract: Magnetic nanoparticles (MNPs) are widely known as valuable agents for biomedical applications. Yet, for their successful application within cells they need to fulfill a variety of demands such as monodispersity, biocompatibility or sufficient magnetic response. Given these prerequisites, MNPs may be used for remote, non-invasive manipulation, where their spatial redistribution or force response in a magnetic field provides a fine-tunable stimulus to a cell. Here, we investigate the properties of two different MNPs and their suitability for spatio-mechanical manipulations: semisynthetic magnetoferritin nanoparticles and fully synthetic  nanoflower-shaped iron-oxide nanoparticles. Next to characterizing their structure, surface potential and magnetic response, we monitor the MNP performance in a living cell environment using fluorescence microscopy and confirm their biocompatibility. We then demonstrate their capability to spatially redistribute and to respond to magnetic force gradients inside a cell. Our remote manipulation assays present these tailored magnetic materials as suitable agents for applications in magnetogenetics, biomedicine or nanomaterial research.


title: Multiple Channel Electrocardiogram QRS Detection by Temporal Pattern Search

abstract: A highly constrained temporal pattern search ("TEPS") based multiple channel heartbeat detector is described. TEPS generates sequences of peaks and statistically scores them according to: 1) peak time coherence across channels; 2) peak prominence; 3) temporal regularity; and 4) number of skipped beats. TEPS was tested on 31 records of three channel capacitive electrode data from the UnoViS automobile database. TEPS showed a sensitivity (SE) of 91.3% and a false discovery rate (FDR) of 3.0% compared to an SE and FDR of 75.3% and 65.0% respectively for a conventional single channel detector (OSEA) applied separately to the three channels. The peak matching window was 30ms. The percentage of 5 second segments with average heart rates within 5 beats/minute of reference was also measured. In 6 of the 31 records, TEPS percentage was at least 30% greater than OSEAs. TEPS was also applied to synthetic data comprising a known signal corrupted with calibrated amounts of noise. At a fixed SE of 85%, increasing the number of channels from one to two resulted in an improvement of approximately 5dB in noise resistance, while increasing the number of channels from two to four resulted in an improvement of approximately 3dB in noise resistance. The quantification of noise resistance as a function of the number of channels could help guide the development of wearable electrocardiogram monitors.


title: On-chip light diffraction imaging of nano structures in the guanine platelet

abstract: Light projection over short distances can minimize the size of photonic devices, e.g., head-mounted displays and lens-free microscopes. Small lenses or light condensers without typical lenses are essential for light control in micron-scale spaces. In this work, micro-platelets floating in water are used for light projection near the image sensor. These platelets, which are made from guanine, have nanohole gratings and demonstrate light diffraction toward specific directions. By setting a thin water layer on the image sensors cover glass, each platelet in water forms column-or bar-code-shaped images on the screen. The projected image shapes and colors are inferred to contain information about nano-structures present in the guanine platelet. The proposed down-sized imaging technique can realize extremely compact and portable imagers for nanoscale object detection.


title: Optimized analysis for sensitive detection and analysis of single proteins via interferometric scattering microscopy

abstract: It has been shown that interferometric detection of Rayleigh scattering (iSCAT) can reach an exquisite sensitivity for label-free detection of nano-matter, down to single proteins. The sensitivity of iSCAT detection is intrinsically limited by shot noise, which can be indefinitely improved by employing higher illumination power or longer integration times. In practice, however, a large speckle-like background and technical issues in the experimental setup limit the attainable signal-to-noise ratio. Strategies and algorithms in data analysis are, thus, crucial for extracting quantitative results from weak signals, e.g. regarding the mass (size) of the detected nano-objects or their positions. In this article, we elaborate on some algorithms for processing iSCAT data and identify some key technical as well as conceptual issues that have to be considered when recording and interpreting the data. The discussed methods and analyses are made available in the extensive python-based platform, PiSCAT[§].


title: A Generic Force Field for Simulating Native Protein Structures Using Dissipative Particle Dynamics

abstract: A coarse-grained force field for molecular dynamics simulations of native structures of proteins in a dissipative particle dynamics (DPD) framework is developed. The parameters for bonded interactions are derived by mapping the bonds and angles for 20 amino acids onto target distributions obtained from fully atomistic simulations in explicit solvent. A dual-basin potential is introduced for stabilizing backbone angles, to cover a wide spectrum of protein secondary structures. The backbone dihedral potential enables folding of the protein from an unfolded initial state to the folded native structure. The proposed force field is validated by evaluating structural properties of several model peptides and proteins including the SARS-CoV-2 fusion peptide, consisting of -helices, {beta}-sheets, loops and turns. Detailed comparisons with fully atomistic simulations are carried out to assess the ability of the proposed force field to stabilize the different secondary structures present in proteins. The compact conformations of the native states were evident from the radius of gyration as well as the high intensity peaks of the root mean square deviation histograms, which were found to lie below 0.4 nm. The Ramachandran-like energy landscape on the phase space of backbone angles ({theta}) and dihedrals ({phi}) effectively captured the conformational phase space of -helices at [~]({phi} = 50{degrees},{theta} = 90{degrees}) and {beta}-strands at [~]({phi} = {+/-}180{degrees},{theta} = 90{degrees} - 120{degrees}). Furthermore, the residue-residue native contacts are also well reproduced by the proposed DPD model. The applicability of the model to multidomain complexes is assessed using lysozyme as well as a large  helical bacterial pore-forming toxin, cytolysin A. Our studies illustrate that the proposed force field is generic, and can potentially be extended for efficient in-silico investigations of membrane bound polypeptides and proteins using DPD simulations.


title: Comparative genomic and pan-genomic characteristion of Staphylococcus epidermidis from different sources unveils the molecular basis and potential biomarkers of pathogenic strains

abstract:
Coagulase-negative Staphylococcus (CoNS) is the most common pathogen causing traumatic endophthalmitis, Staphylococcus epidermidis is the most common species which colonizes human skin, eye surfaces and nasal cavity and is the main cause of nosocomial infection, specially foreign body-related bloodstream infections (FBR-BSIs). Although some studies have reported the genome characteristics of S. epidermidis, a comprehensive understanding of its pathogenicity and the genome of ocular trauma-sourced strains is still lacking. In this study, we sequenced, analyzed and reported the whole genomes of 11 ocular trauma-sourced samples of S. epidermidis that caused traumatic endophthalmitis. By integrating publicly available genomes, we obtained a total of 187 S. epidermidis samples from healthy and diseased eyes, skin, respiratory tract and blood. Combined with pangenome, phylogenetic and comparative genomic analyses, our study supported that S. epidermidis, regardless of niche source, exhibits two founder lineages with different pathogenicities. Moreover, we identified potential biomarkers associated with the virulence of S. epidermidis, namely, essD, uhpt, sdrF, sdrG, fbe and icaABCDR. The essD and uhpt genes have high homology with esaD and hpt in Staphylococcus aureus, showing that the genomes of S. epidermidis and S. aureus may have communicated during evolution, while the sdrF, sdrG, fbe, and icaABCDR genes are related to biofilm formation. Compared to S. epidermidis from blood sources, ocular-sourced strains causing intraocular infection had no direct relationship with biofilm formation. In conclusion, this study not only provided additional data resources for studies on S. epidermidisis, but also improved understanding of the evolution and pathogenicity of different source strains.

ImportantsIn this study, we comprehensively analysied and reported the whole genome sequence (WGS) of the strains that caused traumatic endophthalmitis. Through comparative genomic analyses among 187 S. epidermidis samples from healthy and diseased eyes, skin, respiratory tract and blood, we identified 10 potential biomarkers of pathogenic strains. Finally, we revealed S. epidermidis-induced traumatic endophthalmitis may be independent of biofilm formation. Overall, our data may facilitate comparative research of S. epidermidis and provide clinical value for identifying pathogenic or contaminating strains.


title: Orchestrated Restructuring Events During Secretory Granule Maturation Mediate Intragranular Cargo Segregation

abstract: Regulated secretion is an essential process where proteins are packaged into membranous secretory vesicles. However, the details of cargo packaging and secretory granule maturation are largely unknown. Here, we demonstrate that multiple distinct proteins undergo intragranular restructuring during secretory granule maturation in vivo, resulting in spatial segregation of distinct protein components within the same granule. Furthermore, through a combination of genetics and multimodality imaging, we demonstrate the molecular identity of each distinct intragranular structure. We further identify temporally-regulated genes that are essential for the restructuring events, including those controlling pH (Vha16-1), Cl- ions (Clic and ClC-c) and Ca2+ ions (fwe). Finally, we show that altered cargo glycosylation influences dimensions of these structures, thereby affecting secretory granule morphology. This study elucidates key steps and factors involved in intragranular, rather than intergranular segregation of cargo through regulated restructuring events during secretory granule maturation. Understanding how multiple distinct proteins are efficiently packaged into and secreted from the same secretory granule may provide insight into diseases resulting from defects in secretion.