bluuebunny/crossref_metadata_2025 huggingface dataset:
Association between ocular biometrical parameters and diabetic retinopathy in Chinese adults with type 2 diabetes mellitus
Authors: Wang Lanhua , Liu Sen , Wang Wei , He Miao , Mo Zhiyin , Gong Xia , Xiong Kun , Li Yuting , Huang Wenyong
Published: February 2020

Purpose

To investigate the association between ocular biometrical parameters and diabetic retinopathy (DR) in ocular treatment naive patients with diabetes.

Methods

This cross-sectional study recruited type 2 diabetes mellitus patients with no history of ocular treatment in Guangzhou, China. The ocular biometrical parameters were obtained by Lenstar, including corneal diameter, central corneal thickness (CCT), corneal curvature (CC), anterior chamber depth (ACD), lens thickness (LT), and axial length (AL). The lens power and axial length-to-cornea radius ratio (AL/CR ratio) were calculated. Spherical equivalent (SE) was determined by auto-refraction after pupil dilation. Multivariate logistic regression analyses were performed to explore the associations of ocular biometry with any DR and vision threatening DR (VTDR).

Results

A total of 1838 patients were included in the final analysis, involving 145 5(79.2%) patients without DR and 383(20.8%) patients with DR. After adjusting confounding factors, any DR was independently associated with AL (OR = 0.84 per 1 mm increase, 95%CI: 0.74, 0.94), lens power (OR = 0.9951 per 1 D increase, 95%CI: 0.9904, 0.9998), and AL/CR ratio (OR = 0.26 per 1 increase, 95%CI: 0.10-0.70). Similarly, the presence of VTDR was independently related to AL (OR = 0.67 per 1 mm increase, 95%CI: 0.54-0.85), lens power (OR = 0.99 per 1 D increase, 95%CI: 0.98, 0.997), and AL/CR ratio (OR = 0.04 per 1 increase, 95%CI: 0.01, 0.25). The CC, corneal diameter, and refractive status were not significantly correlated with presence of DR or VTDR.

Conclusion

Longer AL, deeper ACD, higher lens power, and higher AL/CR ratio may be protective factors against DR. Considering the high prevalence of myopia in the Chinese juvenile population, it is worth paying attention to how the incidence of DR in this generation may change over time.
Low-cost and versatile electrodes for extracellular chronic recordings in rodents
Authors: Franca Arthur S C , van Hulten Josephus A , Cohen Michael X
Published: February 2020

Electrophysiological data are used to investigate fundamental properties of brain function, its relation to cognition, and its dysfunction in diseases. The development of reliable and open-source systems for electrophysiological data acquisition is decreasing the total cost of constructing and operating an electrophysiology laboratory, and facilitates low-cost methods to extract and analyze the data (Siegle et al., 2017). Here we detail our method of building custom-designed low-cost electrodes. These electrodes can be customized and manufactured by any researcher to address a broad set of research questions, further decreasing the final cost of an implanted animal. Finally, we present data showing such an electrode has a good signal quality to record LFP.
Discriminating between sleep and exercise-induced fatigue using computer vision and behavioral genetics
Authors: Schuch Kelsey N. , Govindarajan Lakshmi Narasimhan , Guo Yuliang , Baskoylu Saba N. , Kim Sarah , Kimia Benjamin , Serre Thomas , Hart Anne C.
Published: February 2020

Following prolonged swimming,Caenorhabditis eleganscycle between active swimming bouts and inactive quiescent bouts. Swimming is exercise forC. elegansand here we suggest that inactive bouts are a recovery state akin to fatigue. Previously, analysis of exercise-induced quiescent (EIQ) bouts relied on laborious manual observation, as existing automated analysis methods forC. elegansswimming either cannot analyze EIQ bouts or fail to accurately track animal posture during these bouts. It is known that cGMP-dependent kinase (PKG) activity plays a conserved role in sleep, rest, and arousal. UsingC. elegansEGL-4 PKG, we first validate a novel learning-based computer vision approach to automatically analyzeC. eleganslocomotory behavior and distinguish between activity and inactivity during swimming for long periods of time. We find thatC. elegansEGL-4 PKG function predicts EIQ first bout timing, fractional quiescence, bout number, and bout duration, suggesting that previously described pathways are engaged during EIQ bouts. However, EIQ bouts are likely not sleep as animals are feeding during the majority of EIQ bouts. We find that genetic perturbation of neurons required for otherC. eleganssleep states also does not alter EIQ dynamics. Additionally, we find that EIQ onset is sensitive to age and DAF-16 FOXO function. In summary, we have validated a new behavioral analysis software that enabled a quantitative and detailed assessment of swimming behavior, including EIQ. We found novel EIQ defects in aged animals and animals with mutations in a gene involved in stress tolerance. We anticipate that further use of this software will facilitate the analysis of genes and pathways critical for fatigue and otherC. elegansbehaviors.
Insecticide-free trapping bed-net can mitigate insecticide resistance threat in malaria vector control strategies
Authors: Mouhamadou Chouaibou S. , Luan Kun , Fodjo Behi Kouadio , West Andre , McCord Marian , Apperson Charles S. , Roe R. Michael
Published: February 2020

Mosquito-borne malaria kills 429,000 people each year with the problem acute in sub-Saharan Africa. The successes gained with long-lasting pyrethroid treated bed-nets is now in jeopardy because of wide-spread, pyrethroid-resistance in mosquitoes. Using crowd modeling theory normalized for standard bed-net architecture, we were able to design an attract-trap-kill mechanism for mosquitoes that does not require insecticides. Using three-dimensional polyester knitting and heat fixation, trap funnels were developed with high capture efficacy, no egression under worst-case laboratory conditions, and greater durability than current bed-nets sold. Field testing in Africa in WHO huts with Gen1-3 T (trap)-Nets validated our model, and as predicted, Gen3 had the highest efficacy with a 4.3-fold greater trap-kill rate with no deterrence or repellency compared to Permanet 2.0, the most common bed-net in Africa. A T-Net population model was developed based on field data to predict community level mosquito control compared to a pyrethroid bed-net. This model showed the Gen3 T-Net under field conditions in Africa against pyrethroid resistant mosquitoes was 12.7-fold more efficacious than single chemical, pyrethroid treated nets, demonstrating significantly greater mosquito control using bed-nets without insecticides.
Long-term Behavioural Rewriting of Maladaptive Drinking Memories via Reconsolidation-Update Mechanisms
Authors: Gale Grace. , Hennessy Vanessa E. , Walsh Katie. , Kamboj Sunjeev K. , Das Ravi. K.
Published: February 2020

Background

Alcohol use disorders can be conceptualised as a learned pattern of maladaptive alcohol-consumption behaviours. The memories encoding these behaviours centrally contribute to long-term excessive alcohol consumption and are a key therapeutic target. The transient period of memory instability sparked during memory reconsolidation offers a therapeutic window to directlyrewritethese memories using targeted behavioural interventions. However, clinically-relevant demonstrations of the efficacy of this approach are few. We examined key retrieval parameters for destabilising naturalistic drinking memories and the ability of subsequent counterconditioning to effect long-term reductions in drinking.

Methods

Hazardous/harmful beer-drinking volunteers (N=120) were factorially randomised to retrieve (RET) or not retrieve (No RET) alcohol reward memories with (PE) or without (No PE) alcohol reward prediction error. All participants subsequently underwent disgust-basedcounterconditioningof drinking cues. Acute responses to alcohol were assessed pre- and post-manipulation and drinking levels assessed up to 9 months.

Results

Greater long-term reductions in drinking were found when counterconditioning was conducted following retrieval (with and without PE), despite a lack of short-term group differences in motivational responding to acute alcohol. Large variability in acute levels of learning during counterconditioning were noted. ‘Responsiveness’ to counterconditioning predicted subsequent responses to acute alcohol inRET+PEonly, consistent with reconsolidation-update mechanisms.

Conclusions

The longevity of behavioural interventions designed to reduce problematic drinking levels may be enhanced by leveraging reconsolidation-update mechanisms to rewrite maladaptive memory. However, inter-individual variability in levels of corrective learning is likely to determine the efficacy of reconsolidation-updating interventions and should be considered when designing and assessing interventions.
The Druggable Genome as Seen from the Protein Data Bank
Authors: Wang Jiayan , Yazdani Setayesh , Han Ana , Schapira Matthieu
Published: February 2020

Almost twenty years after the human genome was sequenced, the wealth of data produced by the international human genome project has not translated into a significantly improved drug discovery enterprise. This is in part because small molecule modulators that could be used to explore the cellular function of their target proteins and to discover new therapeutic opportunities are only available for a limited portion of the human proteome. International efforts are underway to develop such chemical tools for a few, specific protein families, and a “Target 2035” call to enable, expand and federate these efforts towards a comprehensive chemical coverage of the druggable genome was recently announced. But what is the druggable genome? Here, we systematically review structures of human proteins bound to drug-like ligands available from the protein databank (PDB) and use ligand desolvation upon binding as a druggability metric to draw a landscape of the human druggable genome. We show that the vast majority of druggable protein families, including some highly populated and deeply associated with cancer according to genomic screens, are almost orphan of small molecule ligands, and propose a list of 46 druggable domains representing 3440 human proteins that could be the focus of large chemical probe discovery efforts.
Variation in recombination rate affects detection of outliers in genome scans under neutrality
Authors: Booker Tom R. , Yeaman Sam , Whitlock Michael C.
Published: February 2020

Genome scans can potentially identify genetic loci involved in evolutionary processes such as local adaptation and gene flow. Here, we show that recombination rate variation across a neutrally evolving genome gives rise to mixed sampling distributions of meanFST, a common population genetic summary statistic. In particular, we show that in regions of low recombination the distribution ofestimates have more variance and a longer tail than in more highly recombining regions. Determining outliers from the genome-wide distribution without taking local recombination rate into consideration may therefore increase the frequency of false positives in low recombination regions and be overly conservative in more highly recombining ones. We perform genome-scans on simulated and empiricalDrosophila melanogasterdatasets and, in both cases, find patterns consistent with this neutral model. Similar patterns are observed for other summary statistics used to capture variation in the coalescent process. Linked selection, particularly background selection, is often invoked to explain heterogeneity inacross the genome, but here we point out that even under neutrality, statistical artefacts can arise due to variation in recombination rate. Our results highlight a flaw in the design of genome scan studies and suggest that without estimates of local recombination rate, interpreting the genomic landscape of any summary statistic that captures variation in the coalescent process will be very difficult.
A framework for implementing metaheuristic algorithms using intercellular communication
Authors: Gutiérrez Martín , Ortiz Yerko , Carrión Javier
Published: February 2020

Metaheuristic procedures (MH) have been a trend driving Artificial Intelligence (AI) researchers for the past 50 years. A variety of tools and applications (not only in Computer Science) stem from these techniques. Also, MH frequently rely on evolution, a trademark process involved in cell colony growth. Generally, MH are used to approximate the solution to difficult problems but require a large amount of computational resources. Cell colonies harboring synthetic distributed circuits using intercell communication offer a direction for tackling this problem, as they process information in a massively parallel fashion. In this work, we propose a framework that maps MH elements to synthetic circuits in growing cell colonies. The framework relies on cell-cell communication mechanisms such as quorum sensing (QS) and bacterial conjugation. As a proof-of-concept, we also implemented the workflow associated to the framework, and tested the execution of two specific MH (Genetic Algorithms and Simulated Annealing) encoded as synthetic circuits on thegrosimulator. Furthermore, we show an example of how our framework can be extended by implementing another kind of computational model: The Cellular Automaton. This work seeks to lay the foundations of mappings for implementing AI algorithms in a general manner using Synthetic Biology constructs in cell colonies.
ContamLD: Estimation of Ancient Nuclear DNA Contamination Using Breakdown of Linkage Disequilibrium
Authors: Nakatsuka Nathan , Harney Éadaoin , Mallick Swapan , Mah Matthew , Patterson Nick , Reich David
Published: February 2020

We report a method,ContamLD, for estimating autosomal ancient DNA (aDNA) contamination by measuring the breakdown of linkage disequilibrium in a sequenced individual due to the introduction of contaminant DNA, leveraging the idea that contaminants should have haplotypes uncorrelated to those of the studied individual. Using simulated data, we confirm thatContamLDaccurately infers contamination rates with low standard errors (e.g. less than 1.5% standard error in cases with <10% contamination and data from at least 500,000 sequences covering SNPs). This method is optimized for application to aDNA, leveraging characteristic aDNA damage patterns to provide calibrated contamination estimates. Availability:https://github.com/nathan-nakatsuka/ContamLD.
Cohorting KPC+ Klebsiella pneumoniae (KPC-Kp) positive patients – a genomic exposé of cross-colonization hazards in a long-term acute care hospital (LTACH)
Authors: Hawken Shawn E. , Hayden Mary K. , Lolans Karen , Yelin Rachel D. , Weinstein Robert A. , Lin Michael Y. , Snitkin Evan S.
Published: February 2020

Objective

Cohorting patients who are colonized or infected with multidrug-resistant organisms (MDROs) has been demonstrated to protect uncolonized patients from acquiring MDROs in healthcare settings. A neglected aspect of cohorting is the potential for cross-transmission within the cohort and the possibility of colonized patients acquiring secondary isolates with additional antibiotic resistance traits. We searched for evidence of cross-transmission of KPC+ Klebsiella pneumoniae (KPC-Kp) colonization among cohorted patients in a long-term acute care hospital (LTACH), and evaluated the impact of secondary acquisitions on resistance potential.

Design

Genomic epidemiological investigation

Setting

A high-prevalence LTACH during a bundled intervention that included cohorting KPC-Kp-positive patients.

Methods

Whole-genome sequencing (WGS) and location data were analyzed to identify potential cases of cross-transmission between cohorted patients.

Results

Secondary KPC-Kp isolates from 19 of 28 admission-positive patients were more closely related to another patient’s isolate than to their own admission isolate. In 14 of these 19 cases there was strong genomic evidence for cross-transmission (<10 SNVs) and the majority of these patients occupied shared cohort floors (12 cases) or rooms (5 cases) at the same time. Of the 14 patients with strong genomic evidence of acquisition, 12 acquired antibiotic resistance genes not found in their primary isolates.

Conclusions

Acquisition of secondary KPC-Kp isolates carrying distinct antibiotic resistance genes was detected in nearly half of cohorted patients. These results highlight the importance of healthcare provider adherence to infection prevention protocols within cohort locations, and motivate future studies to assess whether multiple-strain acquisition increases risk of adverse patient outcomes.
Clonal Evolution of Acute Myeloid Leukemia Revealed by High-Throughput Single-Cell Genomics
Authors: Morita Kiyomi , Wang Feng , Jahn Katharina , Kuipers Jack , Yan Yuanqing , Matthews Jairo , Little Latasha , Gumbs Curtis , Chen Shujuan , Zhang Jianhua , Song Xingzhi , Thompson Erika , Patel Keyur , Bueso-Ramos Carlos , DiNardo Courtney D , Ravandi Farhad , Jabbour Elias , Andreeff Michael , Cortes Jorge , Konopleva Marina , Bhalla Kapil , Garcia-Manero Guillermo , Kantarjian Hagop , Beerenwinkel Niko , Navin Nicholas , Futreal P Andrew , Takahashi Koichi
Published: February 2020

One of the pervasive features of cancer is the diversity of mutations found in malignant cells within the same tumor; a phenomenon called clonal diversity or intratumor heterogeneity. Clonal diversity allows tumors to adapt to the selective pressure of treatment and likely contributes to the development of treatment resistance and cancer recurrence. Thus, the ability to precisely delineate the clonal substructure of a tumor, including the evolutionary history of its development and the co-occurrence of its mutations, is necessary to understand and overcome treatment resistance. However, DNA sequencing of bulk tumor samples cannot accurately resolve complex clonal architectures. Here, we performed high-throughput single-cell DNA sequencing to quantitatively assess the clonal architecture of acute myeloid leukemia (AML). We sequenced a total of 556,951 cells from 77 patients with AML for 19 genes known to be recurrently mutated in AML. The data revealed clonal relationship among AML driver mutations and identified mutations that often co-occurred (e.g.,NPM1/FLT3-ITD, DNMT3A/NPM1, SRSF2/IDH2,andWT1/FLT3-ITD) and those that were mutually exclusive (e.g.,NRAS/KRAS, FLT3-D835/ITD, andIDH1/IDH2) at single-cell resolution. Reconstruction of the tumor phylogeny uncovered history of tumor development that is characterized by linear and branching clonal evolution patterns with latter involving functional convergence of separately evolved clones. Analysis of longitudinal samples revealed remodeling of clonal architecture in response to therapeutic pressure that is driven by clonal selection. Furthermore, in this AML cohort, higher clonal diversity (≥4 subclones) was associated with significantly worse overall survival. These data portray clonal relationship, architecture, and evolution of AML driver genes with unprecedented resolution, and illuminate the role of clonal diversity in therapeutic resistance, relapse and clinical outcome in AML.
DNA Methylation Repels Binding of HIF Transcription Factors to Maintain Tumour Immunotolerance
Authors: D’anna Flora , Dyck Laurien Van , Xiong Jieyi , Zhao Hui , Berrens Rebecca V. , Smedt Julie De , Bieniasz-Krzywiec Pawel , Chandra Vikas , Schoonjans Luc , Matthews Jason , Minnoye Liesbeth , Qian Junbin , Amorim Ricardo , Khorasanizadeh Sepideh , Borre Marie De , Savvides Savvas N. , Simon Celeste , Carmeliet Peter , Reik Wolf , Rastinejad Fraydoon , Mazzone Massimiliano , Thienpont Bernard , Lambrechts Diether
Published: February 2020

Abstract

Background

Hypoxia is pervasive in cancer and other diseases. Cells sense and adapt to hypoxia by activating hypoxia-inducible transcription factors (HIFs), but it is still an outstanding question why cell types differ in their transcriptional response to hypoxia.

Results

Here, we report that HIFs fail to bind CpG dinucleotides that are methylated in their consensus binding sequence, both inin vitrobiochemical binding assays andin vivostudies of differentially methylated isogenic cell lines. Based on in silico structural modelling, we show that 5-methylcytosine indeed causes steric hindrance in the HIF binding pocket. A model wherein cell-type-specific methylation landscapes, as laid-down by the differential expression and binding of other transcription factors under normoxia control cell-type-specific hypoxia responses is observed. We also discover ectopic HIF binding sites in repeat regions which are normally methylated. Genetic and pharmacological DNA demethylation, but also cancer-associated DNA hypomethylation, expose these binding sites, inducing HIF-dependent expression of cryptic transcripts. In line with such cryptic transcripts being more prone to cause double-stranded RNA and viral mimicry, we observe low DNA methylation and high cryptic transcript expression in tumours with high immune checkpoint expression, but not in tumours with low immune checkpoint expression, where they would compromise tumour immunotolerance. In a low-immunogenic tumour model, DNA demethylation upregulates cryptic transcript expression in a HIF-dependent manner, causing immune activation and reducing tumour growth.

Conclusions

Our data elucidate the mechanism underlying cell-type specific responses to hypoxia, and suggest DNA methylation and hypoxia to underlie tumour immunotolerance.
The sudden emergence of aNeisseria gonorrhoeaestrain with reduced susceptibility to extended-spectrum cephalosporins, Norway
Authors: Osnes Magnus N. , Didelot Xavier , de Korne-Elenbaas Jolinda , Alfsnes Kristian , Brynildsrud Ola B , Syversen Gaute , Nilsen Øivind , de Blasio Birgitte F. , Caugant Dominique A , Eldholm Vegard
Published: February 2020

TheNeisseria gonorrhoeaemultilocus sequence type (ST) 7827 emerged in dramatic fashion in Norway in the period 2016-2018. Here, we aim to determine what enabled it to establish and spread so quickly. In Norway, ST-7827 isolates were almost exclusively isolated from men. Phylogeographic analyses demonstrated an Asian origin of the ST with multiple importation events to Europe. The ST was uniformly resistant to fluoroquinolones and associated with reduced susceptibility to both azithromycin and the extended-spectrum cephalosporins (ESC) cefixime and ceftriaxone. We identified additional independent events of acquisition ofpenAandporBalleles in Europe, associated with further reduction in cefixime and ceftriaxone susceptibility, respectively. Transmission of the ST was largely curbed in Norway in 2019, but our results indicate the existence of a reservoir in Europe. The worrisome drug resistance profile and rapid emergence of ST-7827 calls for close monitoring of the situation.
Visual input into theDrosophila melanogastermushroom body
Authors: Li Jinzhi , Mahoney Brennan Dale , Jacob Miles Solomon , Caron Sophie Jeanne Cécile
Published: February 2020

The ability to integrate input from different sensory systems is a fundamental property of many brains. Yet, the patterns of neuronal connectivity that underlie such multisensory integration remain poorly characterized. TheDrosophila melanogastermushroom body — an associative center required for the formation of olfactory and visual memories — is an ideal system to investigate how different sensory channels converge in higher-order brain centers. The neurons connecting the mushroom body to the olfactory system have been described in great detail, but input from other sensory systems remains poorly defined. Here, we use a range of anatomical and genetic techniques to identify two novel types of mushroom body input neuron that connect visual processing centers — namely the lobula and the posterior lateral protocerebrum — to the dorsal accessory calyx of the mushroom body. Together with previous work that described a pathway conveying visual information from the medulla to the ventral accessory calyx of the mushroom body (Vogt et al., 2016), our study defines a second, parallel pathway that is anatomically poised to convey information from the visual system to the dorsal accessory calyx. This connectivity pattern — the segregation of the visual information into two separate pathways — could be a fundamental feature of the neuronal architecture underlying multisensory integration in associative brain centers.
Deep predictive coding accounts for emergence of complex neural response properties along the visual cortical hierarchy
Authors: Dora S. , Bohte S. M. , Pennartz C.M.A.
Published: February 2020

Predictive coding provides a computational paradigm for modelling perceptual processing as the construction of representations accounting for causes of sensory inputs. Here, we develop a scalable, deep predictive coding network that is trained using a Hebbian learning rule. Withouta prioriconstraints that would force model neurons to respond like biological neurons, the model exhibits properties similar to those reported in experimental studies. We analyze low- and high-level properties such as orientation selectivity, object selectivity and sparseness of neuronal populations in the model. As reported experimentally, image selectivity increases systematically across ascending areas in the model hierarchy. A further emergent network property is that representations for different object classes become more distinguishable from lower to higher areas. Thus, deep predictive coding networks can be effectively trained using biologically plausible principles and exhibit emergent properties that have been experimentally identified along the visual cortical hierarchy.

Significance Statement

Understanding brain mechanisms of perception requires a computational approach based on neurobiological principles. Many deep learning architectures are trained by supervised learning from large sets of labeled data, whereas biological brains must learn from unlabeled sensory inputs. We developed a Predictive Coding methodology for building scalable networks that mimic deep sensory cortical hierarchies, perform inference on the causes of sensory inputs and are trained by unsupervised, Hebbian learning. The network models are well-behaved in that they faithfully reproduce visual images based on high-level, latent representations. When ascending the sensory hierarchy, we find increasing image selectivity, sparseness and generalizability for object classification. These models show how a complex neuronal phenomenology emerges from biologically plausible, deep networks for unsupervised perceptual representation.
Assessment of different seedling production techniques ofEuterpe edulis
Authors: Regnier Leonardo Lima Pereira , Salatino Maria Luiza Faria
Published: February 2020

Euterpe edulisis an endangered species with high importance ecologically and economically. Seedling production seems to be one of the most important alternatives to population recovery. Besides that, the knowledge of seedling production methods’ influence over germination is very restricted. Thus, this study aimed to evaluate the effects of parent populations, germination conditions, and the substrate to commercial seedling production ofE. edulis. Nine thousand seven hundred and thirteen seeds were distributed between the heated water and control, greenhouse and open-field treatments. The parent population presented high differences between most of the germination indexes. Influencing the germination rate, mean germination time and germination speed, but not affecting synchrony and uncertainty indexes. Heated water treatment did not affect any of the studied indexes, presenting a close pattern of germination over time, indicating it is an appropriate method for seedling production. Greenhouse and open-field treatment presented variations at the same indexes affected in the parent population analysis. The most profitable method forE. edulisseed germination was the greenhouse production method, which provided the best indexes results.
Physiological and Metabolic Features of Mice with CRISPR/Cas9-Mediated Loss-of-Function in Growth Hormone-Releasing Hormone
Authors: Icyuz Mert , Fitch Michael P. , Zhang Fang , Challa Anil K. , Sun Liou Y.
Published: February 2020

Our previous study demonstrated that the loss of growth hormone releasing hormone (GHRH) results in increased lifespan and improved metabolic homeostasis in the mouse model generated by classical embryonic stem cell based gene-targeting method. In this study, we targeted the GHRH gene using the CRISPR/Cas9 technology to avoid passenger alleles/mutations and performed in-depth physiological and metabolic characterization. In agreement with our previous observation, male and female GHRH-/-mice have significantly reduced body weight and enhanced insulin sensitivity when compared to wild type littermates. Dual-energy X-ray absorptiometry showed that there were significant decreases in lean mass, bone mineral content and density, and a dramatic increase in fat mass of GHRH-/-mice when compared to wild type littermates. Indirect calorimetry measurements including oxygen consumption, carbon dioxide production and energy expenditure were dramatically reduced in GHRH-/-mice compared to wild type mice. Respiratory exchange ratio was significantly lower in GHRH-/-mice during the light cycle, but not during the dark cycle, indicating a circadian related metabolic shift towards fat utilization in the growth hormone deficient mice. The novel CRISPR/Cas9 GHRH-/-mice are exhibiting the consistent and unique physiological and metabolic characteristics, which might mediate the longevity effects of growth hormone deficiency in mice.
Consensus mutagenesis and ancestral reconstruction provide insight into the substrate specificity and evolution of the front-end Δ6-desaturase family
Authors: Li Dongdi , Damry Adam M. , Petrie James R. , Vanhercke Thomas , Singh Surinder P. , Jackson Colin J.
Published: February 2020

Marine algae are a major source of omega (ω)-3 long-chain polyunsaturated fatty acids (ω3-LCPUFAs), which are conditionally essential nutrients in humans and a target for industrial production. The biosynthesis of these molecules in marine algae begins with the desaturation of fatty acids by Δ6-desaturases and enzymes from different species display a range of specificities towards ω3 and ω6 LCPUFAs. In the absence of a molecular structure, the structural basis for the variable substrate specificity of Δ6-desaturases is poorly understood. Here we have conducted a consensus mutagenesis and ancestral protein reconstruction-based analysis of the Δ6-desaturase family, focusing on the ω3-specific Δ6-desaturase fromMicromonas pusilla(MpΔ6des) and the bispecific (ω3/ω6) Δ6-desaturase fromOstreococcus tauri(OtΔ6des). Our characterization of consensus amino acid substitutions in MpΔ6des revealed that residues in diverse regions of the protein, such as the N-terminal cytochrome b5 domain, can make important contributions to determining substrate specificity. Ancestral protein reconstruction also suggests that some extant Δ6-desaturases, such as OtΔ6des, could have adapted to different environmental conditions by losing specificity for ω3-LCPUFAs. This dataset provides a map of regions within Δ6-desaturases that contribute to substrate specificity and could facilitate future attempts to engineer these proteins for use in biotechnology.
Large home range scavengers support higher rates of carcass removal
Authors: Gutiérrez-Cánovas Cayetano , Moleón Marcos , Mateo-Tomás Patricia , Olea Pedro P. , Sebastián-González Esther , Sánchez-Zapata José Antonio
Published: February 2020

Vertebrate scavenger communities vary in species composition across the globe, and include a wide array of species with diverse ecological strategies and life-histories that support essential ecosystem functions, such as carrion removal. While previous studies have mostly focussed on how community aspects such as species richness and composition affect carrion consumption rates, it remains unclear whether this important function of scavengers is better explained by the dominance of key functional traits or niche complementarity as a result of a diverse functional representation.

Here, we test three competitive hypotheses to assess if carrion consumption in vertebrate scavenger communities depends on: i) the presence of key dominant traits (functional identity hypothesis), ii) functional diversity that promotes niche complementarity (functional diversity hypothesis), or iii) the accumulation of individuals and species, irrespective of their trait representation (functional equivalence). To explore these hypotheses, we used five study areas in Spain and South Africa, which represent a gradient of scavenger biodiversity, i.e., ranging from communities dominated by facultative scavengers, such as generalists and meso-predators, to those including vultures and large carnivores.

Within study areas, traits that characterise obligate scavengers or large carnivores (e.g. mean home range, proportion of social foragers) were positively linked to rapid carrion consumption, while the biomass of functional groups including facultative scavengers were either weakly or negatively associated with carrion consumption.

When combining all study areas, higher rates of carrion consumption were related to scavenger communities dominated by species with large home ranges (e.g.Gypsvultures), which was found to be a key trait. In contrast, metrics describing functional diversity (functional dispersion) and functional equivalence (species richness and abundance) had lower predictive power in explaining carrion consumption patterns.

Our data support the functional identity hypothesis as a better framework for explaining carrion consumption rates than functional diversity or equivalence. Our findings contribute to understanding the mechanisms sustaining ecosystem functioning in vertebrate communities and reinforce the role of obligate scavengers and large carnivores as keystone species in terrestrial ecosystems.
The Nef protein of the macrophage tropic HIV-1 strain AD8 counteracts human Bst-2/tetherin
Authors: Giese Sebastian , Lawrence Scott P. , Mazzon Michela , Nijmeijer Bernadien M. , Marsh Mark
Published: February 2020

Bst-2/tetherin inhibits the release of numerous enveloped viruses by physically attaching nascent particles to infected cells during the process of viral budding from the cell surface. Tetherin also restricts human immunodeficiency viruses (HIV), and pandemic main (M) group HIV-1s are thought to exclusively rely on their Vpu proteins to overcome tetherin-mediated restriction of virus release. However, at least one M group HIV-1 strain, the macrophage-tropic primary AD8 isolate, is unable to expressvpudue to a mutation in its translation initiation codon. Here, using primary monocyte-derived macrophages (MDMs), we show that AD8 was able to use its Nef protein to compensate for the absence of Vpu and restore virus release to wild type levels. We demonstrate that HIV-1 AD8 Nef reduces endogenous tetherin levels from the cell surface, physically separating it from the site of viral budding and thus preventing HIV retention. Mechanistically, AD8 Nef enhances l-tetherin internalisation, leading to perinuclear accumulation of the restriction factor. Finally, we show that Nef proteins from other HIV strains also display varying degrees of tetherin antagonism. Overall, this is the first report showing that M group HIV-1s can use an accessory protein other than Vpu to antagonise human tetherin.
Nanobody mediated neutralization reveals an Achilles heel for norovirus
Authors: Koromyslova Anna D. , Devant Jessica Michelle , Kilic Turgay , Sabin Charles D. , Malak Virginie , Hansman Grant S.
Published: February 2020

Human norovirus frequently causes outbreaks of acute gastroenteritis. Although discovered more than five decades ago, antiviral development has, until recently, been hampered by the lack of a reliable human norovirus cell culture system. Nevertheless, a lot of pathogenesis studies were accomplished using murine norovirus (MNV), which can be grown routinely in cell culture. In this study, we analysed a sizeable library of Nanobodies that were raised against the murine norovirus virion with the main purpose of developing Nanobody-based inhibitors. We discovered two types of neutralizing Nanobodies and analysed the inhibition mechanisms using X-ray crystallography, cryo-EM, and cell culture techniques. The first type bound on the top region of the protruding (P) domain. Interestingly, the Nanobody binding region closely overlapped the MNV receptor-binding site and collectively shared numerous P domain-binding residues. In addition, we showed that these Nanobodies competed with the soluble receptor and this action blocked virion attachment to cultured cells. The second type bound at a dimeric interface on the lower side of the P dimer. We discovered that these Nanobodies disrupted a structural change in the capsid associated with binding co-factors (i.e., metal cations/bile acid). Indeed, we found that capsids underwent major conformational changes following addition of Mg2+or Ca2+. Ultimately, these Nanobodies directly obstructed a structural modification reserved for a post-receptor attachment stage. Altogether, our new data show that Nanobody-based inhibition could occur by blocking functional and structural capsid properties.

AUTHOR SUMMARY

This research discovered and analysed two different types of MNV neutralizing Nanobodies. The top-binding Nanobodies sterically inhibited the receptor-binding site, whereas the dimeric-binding Nanobodies interfered with a structural modification associated with co-factor binding. Moreover, we found that the capsid contained a number of vulnerable regions that were essential for viral replication. In fact, the capsid appeared to be organized in a state of flux, which could be important for co-factor/receptor binding functions. Blocking these capsid-binding events with Nanobodies directly inhibited essential capsid functions. Moreover, a number of MNV-specific Nanobody binding epitopes were comparable to human norovirus-specific Nanobody inhibitors. Therefore, this additional structural and inhibition information could be further exploited in the development of human norovirus antivirals.
The acetyltransferase Eco1 elicits cohesin dimerization during S phase
Authors: Shi Di , Zhao Shuaijun , Zuo Mei-Qing , Zhang Jingjing , Hou Wenya , Dong Meng-Qiu , Cao Qinhong , Lou Huiqiang
Published: February 2020

Sister chromatid cohesion is established by Eco1 in S phase. Nevertheless, the exact consequence of Eco1-catalyzed acetylation is unknown, and the cohesive state remains highly controversial. Here we show that self-interactions of cohesin subunits Scc1/Rad21 and Scc3 occur in a DNA replication-coupled manner in both yeast and human. Through cross-linking mass spectrometry and VivosX analysis of purified cohesin, we show that a subpopulation of cohesin may exist as dimers. Importantly, cohesin-cohesin interaction becomes significantly compromised when Eco1 is depleted. On the other hand, deleting either deacetylase Hos1 or Eco1 antagonist Wpl1/Rad61 results in an increase (e.g., from ∼20% to 40%) of cohesin dimers. These findings suggest that cohesin dimerization is controlled by common mechanisms as the cohesion cycle, thus providing an additional layer of regulation for cohesin to execute various functions such as sister chromatid cohesion, DNA repair, gene expression, chromatin looping and high-order organization.

Author Summary

Cohesin is a ring that tethers sister chromatids since their synthesis during S phase till their separation in anaphase. According to the single-ring model, one ring holds twin sisters. Here we show a conserved cohesin-cohesin interaction from yeast to human. A subpopulation of cohesin is dimerized concomitantly with DNA replication. Cohesin dimerization is dependent on the acetyltransferase Eco1 and counteracted by the anti-establishment factor Wpl1 and deacetylase Hos1. Approximately 20% of cellular cohesin complexes are measured to be dimers, close to the level of Smc3 acetylation by Eco1 in vivo. These findings provide evidence to support the double-ring model in sister chromatid cohesion.
A Novel Performance Metric for Multiclass Subject Invariant Brain Computer Interfaces with Imbalanced Classes
Authors: Sherwood Jesse , Lowe Jesse , Derakhshani Reza
Published: February 2020

[Finding suitable common feature sets for use in multiclass subject independent brain-computer interface (BCI) classifiers is problematic due to characteristically large inter-subject variation of electroencephalographic signatures. We propose a wrapper search method using a one versus the rest discrete output classifier. Obtaining and evaluating the quality of feature sets requires the development of appropriate classifier metrics. A one versus the rest classifier must be evaluated by a scalar performance metric that provides feedback for the feature search algorithm. However, the one versus the rest discrete classifier is prone to settling into degenerate states for difficult discrimination problems. The chance of occurrence of degeneracy increases with the number of classes, number of subjects and imbalance between the number of samples in the majority and minority classes. This paper proposes a scalar Quality (Q)-factor to compensate for classifier degeneracy and to improve the convergence of the wrapper search. The Q-factor, calculated from the ratio of sensitivity to specificity of the confusion matrix, is applied as a penalty to the accuracy (1-error rate). This method is successfully applied to a multiclass subject independent BCI using 10 untrained subjects performing 4 motor tasks in conjunction with the Sequential Floating Forward Selection feature search algorithm and Support Vector Machine classifiers.]
The haemodynamics of the human placenta in utero
Authors: Dellschaft Neele S. , Hutchinson George , Shah Simon , Jones Nia W. , Bradley Chris , Leach Lopa , Platt Craig , Bowtell Richard , Gowland Penny A.
Published: February 2020

We have used MRI to provide important new insights into the function of the human placentain utero. We have measured slow net flow and high net oxygenation in the placentain vivo, which are consistent with efficient delivery of oxygen from mother to fetus. Our experimental evidence substantiates previous hypotheses on the effects of spiral artery remodellingin utero, and also indicates rapid venous drainage from the placenta, which is important since the outflow has been largely neglected in the past. Furthermore, beyond Braxton Hicks contractions, which involve the entire uterus, we have identified a new physiological phenomenon, the ‘utero-placental pump’, by which the placenta and underlying uterine wall contract independently of the rest of the uterus, expelling maternal blood from the intervillous space.
Markers of Acute Toxicity in Pancreatic Beta-Cells Exposed to Lethal Doses of the Organochlorine Pollutant DDT Determined by a Proteomic Approach
Authors: Pavlíková Nela , Šrámek Jan , Jelínek Michael , Halada Petr , Kovář Jan
Published: February 2020

Many compounds have the potential to harm pancreatic beta-cells; organochlorine pollutants belong to those compounds. In this work, we aimed to find markers of acute toxicity of p,p‘-DDT among proteins expressed in human pancreatic beta-cells NES2Y and visible at 2-D electrophoresis. We exposed NES2Y cells to a lethal dose of p,p‘-DDT (150 μM) for 24 hours and 30 hours and determined changes in protein expression using 2-D electrophoresis. We also stained the cells exposed to p,p‘-DDT to visualize the altered phenotype of the exposed cells. Among proteins with changed expression, we identified proteins involved in ER stress (GRP78, and endoplasmin), mitochondrial proteins (GRP75, ECHM, IDH3A, NDUS1, and NDUS3), proteins with potential to change the cell morphology (EFHD2, TCPA, NDRG1, and ezrin), and some other proteins (HNRPF, HNRH1, K2C8, vimentin, PBDC1, EF2, PCNA, biliverdin reductase, G3BP1, FRIL, and HSP27). These proteins can be used as markers of acute DDT toxicity.
A novel factor essential for unconventional secretion of chitinase Cts1
Authors: Reindl Michèle , Stock Janpeter , Hussnaetter Kai P. , Genc Aycin , Brachmann Andreas , Schipper Kerstin
Published: February 2020

Subcellular targeting of proteins is essential to orchestrate cytokinesis in eukaryotic cells. During cell division ofUstilago maydis, for example, chitinases must be specifically targeted to the fragmentation zone at the site of cell division to degrade remnant chitin and thus separate mother and daughter cells. Chitinase Cts1 is exported to this location via an unconventional secretion pathway putatively operating in a lock-type manner. The underlying mechanism is largely unexplored. Here, we applied a forward genetic screen based on UV mutagenesis to identify components essential for Cts1 export. The screen revealed a novel factor termed Jps1 lacking known protein domains. Deletion of the corresponding gene confirmed its essential role for Cts1 secretion. Localization studies demonstrated that Jps1 colocalizes with Cts1 in the fragmentation zone of dividing yeast cells. While loss of Jps1 leads to exclusion of Cts1 from the fragmentation zone and strongly reduced unconventional secretion, deletion of the chitinase does not disturb Jps1 localization. Yeast-two hybrid experiments suggest that the two proteins interact. In essence, we identified a novel component of unconventional secretion that functions in the fragmentation zone to enable export of Cts1. We hypothesize that Jps1 acts as an anchoring factor, supporting the proposed novel lock-type mechanism of unconventional secretion.
Mechanisms underlying the cooperation between loss of epithelial polarity and Notch signaling during neoplastic growth in Drosophila
Authors: Logeay Rémi , Géminard Charles , Lassus Patrice , Rodríguez-Vázquez Miriam , Kantar Diala , Héron-Milhavet Lisa , Fischer Bettina , Bray Sarah J. , Colinge Jacques , Djiane Alexandre
Published: February 2020

Aggressive neoplastic growth can be initiated by a limited number of genetic alterations, such as the well-established cooperation between loss of cell architecture and hyperactive signaling pathways. However, our understanding of how these different alterations interact and influence each other remains very incomplete. Using Drosophila paradigms of imaginal wing disc epithelial growth, we have monitored the changes in Notch pathway activity according to the polarity status of cells (scrib mutant). We show that the scrib mutation impacts the direct transcriptional output of the Notch pathway, without altering the global distribution of Su(H), the Notch dedicated transcription factor. The Notch-dependent neoplasms require however, the action of a group of transcription factors, similar to those previously identified for Ras/scrib neoplasm (namely AP-1, Stat92E, Ftz-F1, and bZIP factors), further suggesting the importance of this transcription factor network during neoplastic growth. Finally our work highlights some Notch/scrib specificities, in particular the role of the PAR domain containing bZIP transcription factor and Notch direct target Pdp1 for neoplastic growth.