bluuebunny/crossref_metadata_2025 huggingface dataset:
Perturbing proteomes at single residue resolution using base editing
Authors: Després Philippe C , Dubé Alexandre K , Seki Motoaki , Yachie Nozomu , Landry Christian R
Published: June 2019

Base editors derived from CRISPR-Cas9 systems and DNA editing enzymes offer an unprecedented opportunity for the precise modification of genes, but have yet to be used at a genome-scale throughput. Here, we test the ability of an editor based on a cytidine deaminase, the Target-AID base editor, to systematically modify genes genome-wide using the set of yeast essential genes. We tested the effect of mutating around 17,000 individual sites in parallel across more than 1,500 genes in a single experiment. We identified over 1,100 sites at which mutations have a significant impact on fitness. Using previously determined and preferred Target-AID mutational outcomes, we predicted the protein variants caused by each of these gRNAs. We found that gRNAs with significant effects on fitness are enriched in variants predicted to be deleterious by independent methods based on site conservation and predicted protein destabilization. Finally, we identify key features to design effective gRNAs in the context of base editing. Our results show that base editing is a powerful tool to identify key amino acid residues at the scale of proteomes.
Functional Analysis of FRIGIDA Using Naturally Occurring Variation inArabidopsis thaliana
Authors: Zhang Lei , Jiménez-Gómez José M
Published: June 2019

TheFRIGIDAlocus (FRI, AT4G00650) has been extensively studied inArabidopsis thalianabecause of its role creating flowering time diversity. The FRI protein regulates flowering induction by binding partner proteins on its N- and C-terminus domains and creating a supercomplex that promotes transcription of the floral repressor FLC. Despite the knowledge accumulated on FRI, the function of the highly conserved central domain of the protein is still unknown. Functional characterization of naturally occurring DNA polymorphisms can provide useful information about the role of a protein and the localization of its operative domains. In the case of FRI, deleterious mutations are positively selected and widespread in nature, making them a powerful tool to study the function of the different domains of the protein. Here we explore natural sequence variation in the FRI locus in more than 1000 Arabidopsis accessions. We identify new mutations predicted to compromise the function of the protein and confirm our predictions by cloning 22 different alleles of FRI and expressing them in a common null genetic background. Our analysis allows us to pinpoint two single amino acid changes in the central domain that render the protein non-functional. We show that these two mutations determine the stability and cellular localization of the FRI protein. In summary, our work makes use of natural variants at the FRI locus to help understanding the function of the central domain of the FRI protein.
MicrographCleaner: a python package for cryo-EM micrograph cleaning using deep learning
Authors: Sanchez-Garcia Ruben , Segura Joan , Maluenda David , Sorzano C.O.S. , Carazo J.M.
Published: June 2019

Cryo-EM Single Particle Analysis workflows require from tens of thousands of high-quality particle projections to unveil the three-dimensional structure of macromolecules. Conventional methods for automatic particle picking tend to suffer from high false-positive rates, hurdling the reconstruction process. One common cause of this problem is the presence of carbon and different types of high-contrast contaminations. In order to overcome this limitation, we have developed MicrographCleaner, a deep learning package designed to discriminate which regions of micrographs are suitable for particle picking and which are not in an automatic fashion. MicrographCleaner implements a U-net-like deep learning model trained on a manually curated dataset compiled from over five hundred micrographs. The benchmarking, carried out on about one hundred independent micrographs, shows that MicrographCleaner is a very efficient approach for micrograph preprocessing. MicrographCleaner (micrograph_cleaner_em) package is available at PyPI and Anaconda Cloud and also as a Scipion/Xmipp protocol. Source code is available at https://github.com/rsanchezgarc/micrograph_cleaner_em.
Anin silicoanalysis of robust but fragile gene regulation links enhancer length to robustness
Authors: Barr Kenneth A , Reinitz John , Radulescu Ovidiu
Published: June 2019

1

Organisms must ensure that expression of genes is directed to the appropriate tissues at the correct times, while simultaneously ensuring that these gene regulatory systems are robust to perturbation. This idea is captured by a mathematical concept calledr-robustness, which says that a system is robust to a perturbation in up tor -1 randomly chosen parameters. In this work we use this idea to investigate the robustness of gene regulation using a sequence level model of theDrosophila melanogastergeneeven-skipped. We find that gene regulation can be remarkably sensitive to changes in transcription factor concentrations at the boundaries of expression features, while it is robust to perturbation elsewhere. We also find that the length of sequence used to control an expression feature correlates negatively with the number of nucleotides that are sensitive to mutation in both natural andin silicopredicted enhancers. In all cases, the exact degree of robustness obtained is dependent not only on DNA sequence, but also on the local concentration of regulatory factors. By analyzing both natural and synthetic sequences, we provide strong quantitative evidence that increased sequence length makes gene regulatory systems more robust to genetic perturbation.

2

Author Summary

Robustness assures that organisms can survive when faced with unpredictable environments or genetic mutations. In this work, we characterize the robustness of gene regulation using an experimentally validated model of the regulation of theDrosophilageneeven-skipped. We use a mathematically precise definition of robustness that allows us to make quantitative comparisons of robustness between different genetic sequences or between different nuclei. From this analysis, we found that genetic sequences that were not previously known to be important for gene regulation reduce sensitivity to genetic perturbation. In contrast, we found that gene regulation can be very sensitive to the levels of regulators. This extreme sensitivity was only observed at the boundaries of expression features, where switch-like behavior is desirable. This highlights the importance of considering context when assessing robustness.
Integrated Approach On Degaradtion Of Azo Dyes Using Laccase Enzyme And Nanoparticle With Its Interaction By In Silco Analysis
Authors: Sridharan Rajalakshmi , Krishnaswamy Veena Gayathri , Murali.K Archana , Rajagopal Revathy , Kumar. D Thirumal , Doss.C George Priya
Published: June 2019

Azo dyes, released by the textile industries causes severe damage to the environment and living organisms. The degradation of azo dyes is widely studied using enzymatic methods. Laccase, is a copper containing enzyme that degrades the azo dyes into less toxic compounds. In this work, Laccase enzyme produced by the alkaliphile Pseudomonas mendocina in the degradation of mixed azo dye showed 0.386 U/Ml activity at pH 8.5. Combination of enzymatic and green synthesised nanoparticle were used in the degradation mixed azo dye. Laccase used in the degradation of mixed azo dyes showed 58.46% in 72 hours while the photocatalytic degradation of mixed azo dyes showed 15.98%. The degradation of azo dyes using copper iodide nanoparticle resulted in 15.835% of mixed azo dye degradation. But it was noticed that combined method removed 62.35% of mixed azo dyes in 60 minutes. Interaction of laccase enzyme with azo dyes using in silico analysis predicted the binding energy of RR (−7.19 kcal/mol), RB (−8.57 kcal/mol) and RBL (−9.17 kcal/mol).
Tankyrase inhibition sensitizes cells to CDK4 blockade
Authors: Foronda Miguel , Tarumoto Yusuke , Schatoff Emma M. , Leach Benjamin I. , Diaz Bianca J , Goswami Sukanya , Shusterman Michael , Vakoc Christopher R. , Dow Lukas E
Published: June 2019

Tankyrase (TNKS) 1/2 are positive regulators of WNT signaling by controlling the activity of the β-catenin destruction complex. TNKS inhibitors provide an opportunity to suppress hyperactive WNT signaling in tumors, however, they have shown limited anti-proliferative activity as a monotherapy in human cancer cell lines. Here we perform a kinome-focused CRISPR screen to identify potential effective drug combinations with TNKS inhibition. We show that the loss of CDK4, but not CDK6, synergizes with TNKS1/2 blockade to drive G1 cell cycle arrest and senescence. Through precise modelling of cancer-associated mutations using cytidine base editors, we show that this therapeutic approach is absolutely dependent on suppression of canonical WNT signaling by TNKS inhibitors and is effective in cells from multiple epithelial cancer types. Together, our results suggest that combined WNT and CDK4 inhibition might provide a potential therapeutic strategy for difficult-to-treat epithelial tumors.
The causal role of circulating vitamin D concentrations in human complex traits and diseases: a large-scale Mendelian randomization study
Authors: Jiang Xia , Ge Tian , Chen Chia-Yen
Published: June 2019

Vitamin D has been associated with a variety of human complex traits and diseases in observational studies, but a causal relationship remains unclear. To examine a putative causal effect of vitamin D across phenotypic domains and disease categories, we conducted Mendelian randomization (MR) analyses using genetic instruments associated with circulating 25-hydroxyvitamin D [25(OH)D] concentrations. We leveraged genome-wide significant 25(OH)D-associated SNPs (N=138) from a meta-analysis combining a vitamin D GWAS conducted in 401,460 white British UK Biobank (UKBB) participants and an independent vitamin D GWAS including 42,274 samples of European ancestry, and examined 190 large-scale health-related GWAS spanning a broad spectrum of complex traits, diseases and biomarkers. We applied multiple MR methods to estimate the causal effect of vitamin D while testing and controlling for potential biases from horizontal pleiotropy. Consistent with previous findings, genetically predicted increased 25(OH)D levels significantly decreased the risk of multiple sclerosis (OR=0.824; 95%CI=0.689-0.986). The protective effect estimate was consistent across different MR methods and four different multiple sclerosis GWAS with varying sample sizes and genotyping platforms. On the contrary, we found limited evidence in support of a causal effect of 25(OH)D on anthropometric traits, obesity, cognitive function, sleep behavior, breast and prostate cancer, and autoimmune, cardiovascular, metabolic, neurological and psychiatric traits and diseases, and blood biomarkers. Our results may inform ongoing and future randomized clinical trials of vitamin D supplementation.
Mixture Network Regularization of Generalized Linear Model With Application in Genomics Data
Authors: Li Kaiqiao , Li Jialiang , Wang Xuefeng , Kuan Pei Fen
Published: June 2019

High dimensional genomics data in biomedical sciences is an invaluable resource for constructing statistical prediction models. With the increasing knowledge of gene networks and pathways, such information can be utilized in the statistical models to improve prediction accuracy and enhance model interpretability. However, in certain scenarios the network structure may only be partially known or subject to inaccuracy. Thus, the performance of statistical models incorporating such network structure may be compromised. In this paper, we propose a weighted sparse network learning method by optimally combining a data driven network with sparsity property to prior known or partially known network to address this issue. We show that our proposed model attains the oracle property and achieves a parsimonious structure in high dimensional setting for different types of outcomes including continuous, binary and survival data. Simulations studies show that our proposed model is robust and outperforms existing methods. Case study on melanoma gene expression further demonstrates that our proposed model achieves good operating characteristics in identifying informative genes and predicting survival risk. An R package glmaag implementing our method is available on the Comprehensive R Archive Network (CRAN).
Mapping gene regulatory networks of primary CD4+T cells using single-cell genomics and genome engineering
Authors: Gate Rachel E. , Kim Min Cheol , Lu Andrew , Lee David , Shifrut Eric , Subramaniam Meena , Marson Alexander , Ye Chun J.
Published: June 2019

Gene regulatory programs controlling the activation and polarization of CD4+T cells are incompletely mapped and the interindividual variability in these programs remain unknown. We sequenced the transcriptomes of ~160k CD4+T cells from 9 donors following pooled CRISPR perturbation targeting 140 regulators. We identified 134 regulators that affect T cell functionalization, includingIRF2as a positive regulator of Th2polarization. Leveraging correlation patterns between cells, we mapped 194 pairs of interacting regulators, including known (e.g.BATFandJUN) and novel interactions (e.g.ETS1andSTAT6). Finally, we identified 80 natural genetic variants with effects on gene expression, 48 of which are modified by a perturbation. In CD4+T cells, CRISPR perturbations can influencein vitropolarization and modify the effects oftransandcisregulatory elements on gene expression.
Generalizing movement patterns following shoulder fixation
Authors: Maeda Rodrigo S. , Zdybal Julia M. , Gribble Paul L. , Pruszynski J. Andrew
Published: June 2019

A common goal of motor learning is generalizing newly learned movement patterns beyond the training context. Here we tested whether learning a new physical property of the arm during self-initiated reaching generalizes to new arm configurations. One hundred human participants performed a single-joint elbow reaching task and/or countered mechanical perturbations that created pure elbow motion. Participants did so with the shoulder joint either free to rotate or locked by the robotic manipulandum. With the shoulder free, we found activation of shoulder extensor muscles for pure elbow extension trials, as required to counter the interaction torques that arise at the shoulder due to forearm rotation. After locking the shoulder joint, we found a substantial reduction in shoulder muscle activity that developed slowly over many trials. This reduction is appropriate because locking the shoulder joint cancels the interaction torques that arise at the shoulder to do forearm rotation and thus removes the need to activate shoulder muscles. In our first three experiments, we tested whether this reduction generalizes when reaching is self-initiated in (1) a different initial shoulder orientation, (2) a different initial elbow orientation and (3) for a different reach distance/speed. We found reliable generalization across initial shoulder orientation and reach distance/speed but not for initial elbow orientation. In our fourth experiment, we tested whether generalization is also transferred to feedback control by applying mechanical perturbations and observing reflex responses in a distinct shoulder orientation. We found robust transfer to feedback control.

New & Noteworthy

Here we show that learning to reduce shoulder muscles activity following shoulder fixation generalizes to other movement conditions but does not generalize globally, indicating that the nervous system does not implement such learning by modifying a general internal model of arm dynamics.

Disclosures

The authors declare no conflict of interest.
Epitope - based peptide vaccine against glycoprotein G of Nipah henipavirus using immunoinformatics approaches
Authors: Mohammed Arwa A. , Shantier Shaza W. , Mustafa Mujahed I. , Osman Hind K. , Elmansi Hashim E. , Osman Isam-Aldin A. , Mohammed Rawan A. , Abdelrhman Fatima A. , Elnnewery Mihad E. , Yousif Einas M. , M.Mustafa Marwa , Elfadol Nafisa M. , Abdalla Alaa I. , Mahmoud Eiman , Eltay Ahmed A. , Ahmed yassir A. , Hassan Mohamed A.
Published: June 2019

Background

Nipah virus (NiV) is a member of the genus Henipavirus of the family Paramyxoviridae, characterized by high pathogenicity and endemic in South Asia, first emerged in Malaysia in 1998. The case-fatality varies from 40% to 70% depending on the severity of the disease and on the availability of adequate healthcare facilities. At present no antiviral drugs are available for NiV disease and the treatment is just supportive. Clinical presentation ranges from asymptomatic infection to fatal encephalitis. Bats are the main reservoir for this virus, which can cause disease in humans and animals. The last investigated NiV outbreak has occurred in May 2018 in Kerala.

Objective

This study aims to predict effective epitope-based vaccine against glycoprotein G of Nipah henipavirus using immunoinformatics approaches.

Methods and Materials

Glycoprotein G of Nipah henipavirus sequence was retrieved from NCBI. Different prediction tools were used to analyze the nominee’s epitopes in BepiPred-2.0: Sequential B-Cell Epitope Predictor for B-cell, T-cell MHC class II & I. Then the proposed peptides were docked using Autodock 4.0 software program.

Results and Conclusions

Peptide TVYHCSAVY shows a very strong binding affinity to MHC I alleles while FLIDRINWI shows a very strong binding affinity to MHC II and MHC I alleles. This indicates a strong potential to formulate a new vaccine, especially with the peptide FLIDRINWI that is likely to be the first proposed epitope-based vaccine against glycoprotein G of Nipah henipavirus. This study recommends an in-vivo assessment for the most promising peptides especially FLIDRINWI.
Inorganic salts and compatible solutes help mesophilic bacteria inhabit the high temperature waters of a Trans-Himalayan sulfur-borax spring
Authors: Mondal Nibendu , Roy Chayan , Peketi Aditya , Alam Masrure , Mapder Tarunendu , Mandal Subhrangshu , Fernandes Svetlana , Bhattacharya Sabyasachi , Rameez Moidu Jameela , Haldar Prabir Kumar , Volvoikar Samida Prabhakar , Nandi Nilanjana , Bhattacharya Tannisha , Mazumdar Aninda , Chakraborty Ranadhir , Ghosh Wriddhiman
Published: June 2019

While geographically-/geologically-distinct hot springs harbor different levels of microbial diversity, some of them encompass several such taxa which have no strain reported for laboratory growth at >45°C. We, therefore, hypothesized that native geomicrobial factors could be potent determinants of the microbial habitability of hot spring environments. To test this hypothesis, aquatic microbial communities were revealed metataxonomically, and considered in the context of spring-water chemistry, along the 85-14°C hydrothermal gradient of a sulfur-boron spring namedLotus Pondlocated at 4,436 m, within the Puga geothermal area of the Indian Trans-Himalayan region of Ladakh. Water samples were studied from four distinct sites alongLotus Pond’s spring-water transit from the vent to an adjacent river calledRulang. Insinuations obtained from geomicrobiological data were tested via pure-culture growth experiments in habitat-inspired media. Microbial diversities were found to be high at all the sample-sites; majority of the genera identified at the 70-85°C sites were found to have no report of laboratory growth at >45°C; concurrently, these sample-sites had high concentrations of the kosmotropic solutes boron, lithium, sodium, sulfide, thiosulfate and sulfate, which are known to biophysically stabilize macromolecules. Based on the universal thermodynamic status of these solutes, we conjectured that they may be instrumental in helping mesophiles withstand highin situtemperatures. Corroboratively, growth experiments with a mesophilic, 80°C-isolate,ParacoccusSMMA_5 showed that at 50°C and 70°C, depending on the incubation-time, lithium/boron/sulfate/sodium/glycine-betaine either increases the number of colony-forming units present in the culture or arrests decline of the same. Incubations at 70°C, followed by fluorescein diacetate staining and flow cytometry, showed that these solutes keep more cells under viable condition than in ready-to-divide state. We concluded that kosmotropes and compatible solutes help mesophiles overcome the chaotropic effects of heat by augmenting such indigenous, entropy-minimizing biophysical mechanisms that apparently trade-off cell division for cell viability.
Dolosigranulum pigrum cooperation and competition in human nasal microbiota
Authors: Brugger Silvio D. , Eslami Sara M. , Pettigrew Melinda M. , Escapa Isabel F. , Henke Matthew T. , Kong Yong , Lemon Katherine P.
Published: June 2019

Background

Multiple epidemiological studies identify Dolosigranulum pigrum as a candidate beneficial bacterium based on its positive association with health, including negative associations with nasal/nasopharyngeal colonization by the pathogenic species Staphylococcus aureus and Streptococcus pneumoniae.

Results

Using a multipronged approach to gain new insights into D. pigrum function, we observed phenotypic interactions and predictions of genomic capacity that support a role for microbe-microbe interactions involving D. pigrum in shaping the composition of human nasal microbiota. We identified in vivo community-level and in vitro phenotypic cooperation by specific nasal Corynebacterium species. Also, D. pigrum inhibited S. aureus growth in vitro. Whereas, robust inhibition of S. pneumoniae required both D. pigrum and a nasal Corynebacterium together, and not either alone. D. pigrum L-lactic-acid production was insufficient to account for these inhibitions. Genomic analysis of 11 strains revealed that D. pigrum has a small genome (average 1.86 Mb) and multiple predicted auxotrophies consistent with D. pigrum relying on its human host and cocolonizing bacteria for key nutrients. Further, the accessory genome of D. pigrum encoded a diverse repertoire of biosynthetic gene clusters, some of which may have a role in microbe-microbe interactions.

Conclusions

These new insights into D. pigrum’s functions advance the field from compositional analysis to genomic and phenotypic experimentation on a potentially beneficial bacterial resident of the human upper respiratory tract and lay the foundation for future animal and clinical experiments.
Functional connectome linking child-parent relationships with psychological problems in adolescence
Authors: Itahashi Takashi , Okada Naohiro , Ando Shuntaro , Yamasaki Syudo , Koshiyama Daisuke , Morita Kentaro , Yahata Noriaki , Koike Shinsuke , Nishida Atsushi , Kasai Kiyoto , Hashimoto Ryu-ichiro
Published: June 2019

Paternal- and maternal-child relationships are associated with partly distinct psychobehavioral problems, which often manifest differently between boys and girls. In order to understand neural mechanisms underlying complicated mappings between child-parent relationship and adolescents’ problems, we used a dataset of early adolescents (N=93) and separately estimated the effects of paternal- and maternal-child relationships on resting-state functional connectivity and problems in boys and girls. General linear models identified the effects of paternal- and maternal-child relationships in different sets of functional connectivity, which we termed functional brain connectomes associated with paternal- and maternal-child relationship (FBCp and FBCm), respectively. Subsequent connectome-based models using these FBCs significantly predicted aggressive behaviors only for boys and internalizing problems selectively only girls. Lastly, a causal discovery method identified causal paths from daughter-mother relationship to FBCm, and then to daughter’s internalizing problems. These observations highlight sex-dependent mechanisms linking child-parent relationship, brain, and psychobehavioral problems in early adolescence.
Norvaline reduces blood pressure and induces diuresis in rats with inherited stress-induced arterial hypertension
Authors: Gilinsky Michael A. , Polityko Yulia K. , Markel Arkady L. , Latysheva Tatyana V. , Samson Abraham O. , Polis Baruh , Naumenko Sergey E.
Published: June 2019

Growing evidence suggests that increased arginase activity affects vital bioprocesses in various systems and universally mediates the pathogenesis of numerous metabolic diseases. The adverse effects of arginase are associated with a severe decline in L-arginine bioavailability, which leads to nitric oxide synthase substrate insufficiency, uncoupling, and, eventually, to superoxide anion generation and substantial reduction of nitric oxide (NO) synthesis. In cooperation, it contributes to chronic oxidative stress and endothelial dysfunction, which might lead to hypertension and atherosclerosis.

Recent preclinical investigations point to arginase as a promising therapeutic target in ameliorating metabolic and vascular dysfunctions. In the present study, adult rats with inherited stress-induced arterial hypertension (ISIAH) were used as a model of hypertension. Wistar rats served as normotensive controls. Experimental animals were intraperitoneally administered for seven days with non-proteinogenic amino acid L-norvaline (30 mg/kg/day), which is a potent arginase inhibitor, or with the vehicle. Blood pressure (BP), body weight, and diuresis were monitored. The changes in blood and urine levels of creatinine, urea, and NO metabolites were analyzed.

We observed a significant decline in BP and induced diuresis in ISIAH rats following the treatment. The same procedure did not affect the BP of control animals. Remarkably, the treatment had no influence upon glomerular filtration rate in two experimental groups, just like the daily excretion of creatinine and urea. Conversely, NO metabolites levels were amplified in normotonic but not in hypertensive rats following the treatment.

The data indicate that L-norvaline is a potential antihypertensive agent, and deserves to be clinically investigated. Moreover, we suggest that changes in blood and urine are causally related to the effect of L-norvaline upon the BP regulation.
Reproducible microbial community dynamics of two drinking water systems treating similar source waters
Authors: Potgieter Sarah C , Dai Zihan , Havenga Minette , Vosloo Solize , Sigudu Makhosazana , Pinto Ameet J , Venter Stefanus N
Published: June 2019

Understanding whether the spatial-temporal dynamics of the drinking water microbiome are reproducible in full-scale drinking water systems is an important step towards devising engineering strategies to manipulate it. Yet, direct comparisons across full-scale drinking water systems are challenging because multiple factors, from source water to treatment process choice and configuration, can be unique to each system. This study compared the spatial-temporal dynamics of the drinking water microbiome in two drinking water treatment plants (DWTPs) with identical sequence of treatment strategies treating source waters from the same river system and with treated drinking water distributed in same large-scale (but independent) distribution system (DWDS) with similar disinfectant residual regiment. Dissimilarities in source water communities were tempered by the pre-disinfection treatments, resulting in highly similar post-filtration microbial communities between the two systems. However, high community turnover due to disinfection resulted in highly dissimilar microbial communities in the finished water between the two systems. Interestingly however, the microbial communities in the two systems increased in similarity during transit through the DWDS despite presence of a disinfectant residual. Overall our study finds that the drinking water microbiome demonstrated reproducible spatial and temporal dynamics within both independent but nearly identical DWTPs and their corresponding DWDSs.

Graphical abstract
Intensity warping for multisite MRI harmonization
Authors: Wrobel J , Martin ML , Bakshi R , Calabresi PA , Elliot M , Raolf D , Gur RC , Gur RE , Henry RG , Nair G , Oh J , Papinutto N , Pelletier D , Reich DS , Rooney W , Satterthwaite TD , Stern W , Prabhakaran K , Sicotte N , Shinohara RT , Goldsmith J ,   on behalf of the NAIMS Cooperative
Published: June 2019

In multisite neuroimaging studies there is often unwanted technical variation across scanners and sites. These “scanner effects” can hinder detection of biological features of interest, produce inconsistent results, and lead to spurious associations. We assess scanner effects in two brain magnetic resonance imaging (MRI) studies where subjects were measured on multiple scanners within a short time frame, so that one could assume any differences between images were due to technical rather than biological effects. We propose mica (multisite image harmonization by CDF alignment), a tool to harmonize images taken on different scanners by identifying and removing within-subject scanner effects. Our goals in the present study were to (1) establish a method that removes scanner effects by leveraging multiple scans collected on the same subject, and, building on this, (2) develop a technique to quantify scanner effects in large multisite trials so these can be reduced as a preprocessing step. We found that unharmonized images were highly variable across site and scanner type, and our method effectively removed this variability by warping intensity distributions. We further studied the ability to predict intensity harmonization results for a scan taken on an existing subject at a new site using cross-validation.
Targeting pathogenic Lafora bodies in Lafora disease using an antibody-enzyme fusion
Authors: Brewer M. Kathryn , Uittenbogaard Annette , Austin Grant , McCarthy John J. , Segvich Dyann M. , DePaoli-Roach Anna , Roach Peter J. , Hodges Bradley L. , Zeller Jill , Pauly James R. , McKnight Tracy , Armstrong Dustin , Gentry Matthew S.
Published: June 2019

Lafora disease (LD) is a fatal childhood epilepsy and a non-classical glycogen storage disorder with no effective therapy or cure. LD is caused by recessive mutations in theEPM2AorEPM2Bgenes that encode the glycogen phosphatase laforin and an E3 ubiquitin ligase malin, respectively. A hallmark of LD is the intracellular accumulation of abnormal and insoluble α-linked polysaccharide deposits known as Lafora bodies (LBs) in several tissues, including most regions of the brain. In mouse models of LD, genetic reduction of glycogen synthesis eliminates LB formation and rescues the neurological phenotype. Since multiple groups have confirmed that neurodegeneration and epilepsy result from LB accumulation, a major focus in the field has shifted toward the development of therapies that reduce glycogen synthesis or target LBs for degradation with the goal of treating LD. Herein, we identify the optimal enzymes for degrading LBs, and we develop a novel therapeutic agent by fusing human pancreatic α-amylase to a cellpenetrating antibody fragment. This antibody-enzyme fusion (VAL-0417) degrades LBsin vitro, shows robust cellular uptake, and significantly reduces the LB loadin vivoinEpm2a-/- mice. VAL-0417 is a promising therapeutic for the treatment of LD and a putative precision therapy for an intractable epilepsy. Antibody-enzyme fusions represent a new class of antibody-based drugs that could be utilized to treat glycogen storage disorders and other diseases.

One Sentence Summary

An antibody-enzyme fusion delivering an amylase degrades the toxic polyglucosan bodies that cause Lafora disease, a fatal childhood epilepsy.
Artisanal and farmer bread making practices differently shape fungal species community composition in French sourdoughs
Authors: Michel Elisa , Masson Estelle , Bubbendorf Sandrine , Lapicque Léocadie , Nidelet Thibault , Segond Diego , Guézenec Stéphane , Marlin Thérèse , Devillers Hugo , Rué Olivier , Onno Bernard , Legrand Judith , Sicard Delphine ,   the participating bakers
Published: June 2019

Abstract

Preserving microbial diversity in food systems is one of the many challenges to be met to achieve food security and quality. Although industrialization led to the selection and spread of specific fermenting microbial strains, there are still ongoing artisanal processes that may allow the conservation of a wider species diversity and genetic diversity. We examined whether the diversity of artisanal practices could lead to an increased level in fungal species diversity for bread making. We used an interdisciplinary participatory research approach including bakers, psycho-sociologists and microbiologists to analyze French bread making practices and describe fungal communities in naturally fermented sourdough of 27 bakers and 12 farmer bakers. Bread making practices were classified in two groups: the farmer-like practice group and the artisanal-like practice group. The well-known bakery yeast,Saccharomyces cerevisiae, was dominant (i.e. with a relative abundance over 50%) in only 24% of sourdoughs while other yeast species, belonging to theKazachstaniagenus, were dominant in 54% of sourdoughs. Bread making practices were found to drive the distribution of fungal species across sourdoughs. The most striking bread making practice effect was the occurrence ofKazachstania humilisin sourdoughs made with artisanal-like practices and the occurrence ofKazachstania bulderiin sourdoughs made with farmer-like practices. Phenotypic divergences between sourdough and nonsourdough strains were found forK. humilisbut not forK. bulderi. Overall, our results showed that preserving bread making practice diversity allows the preservation of a higher species and phenotypic diversity in microbial communities.
Cell-in-the-loop pattern formation with optogenetically emulated cell-to-cell signaling
Authors: Perkins Melinda Liu , Benzinger Dirk , Arcak Murat , Khammash Mustafa
Published: June 2019

1

Designing and implementing synthetic biological pattern formation remains a challenge due to underlying theoretical complexity as well as the difficulty of engineering multicellular networks bio-chemically. Here, we introduce a “cell-in-the-loop” approach where living cells interact through in silico signaling, establishing a new testbed to interrogate theoretical principles when internal cell dynamics are incorporated rather than modeled. We present a theory that offers an easy-to-use test to predict the emergence of contrasting patterns in gene expression among laterally inhibiting cells. Guided by the theory, we experimentally demonstrated spontaneous checkerboard patterning in an optogenetic setup where cell-to-cell signaling was emulated with light inputs calculated in silico from real-time gene expression measurements. The scheme successfully produced spontaneous, persistent checkerboard patterns for systems of sixteen patches, in quantitative agreement with theoretical predictions. Our research highlights how tools from dynamical systems theory may inform our understanding of patterning, and illustrates the potential of cell-in-the-loop for engineering synthetic multicellular systems.
Spinal V3 interneurons and left-right coordination in mammalian locomotion
Authors: Danner Simon M. , Zhang Han , Shevtsova Natalia A. , Borowska Joanna , Rybak Ilya A. , Zhang Ying
Published: June 2019

Commissural interneurons (CINs) mediate interactions between rhythm-generating locomotor circuits located on each side of the spinal cord and are necessary for left-right limb coordination during locomotion. While glutamatergic V3 CINs have been implicated in left-right coordination, their functional connectivity remains elusive. Here, we addressed this issue by combining experimental and modeling approaches. We employed Sim1Cre/+; Ai32 mice, in which light-activated Channelrhodopsin-2 was selectively expressed in V3 interneurons. Fictive locomotor activity was evoked by NMDA and 5-HT in the isolated neonatal lumbar spinal cord. Flexor and extensor activities were recorded from left and right L2 and L5 ventral roots, respectively. Bilateral photoactivation of V3 interneurons increased the duration of extensor bursts resulting in a slowed down on-going rhythm. At high light intensities, extensor activity could become sustained. When light stimulation was shifted toward one side of the cord, the duration of extensor bursts still increased on both sides, but these changes were more pronounced on the contralateral side than on the ipsilateral side. Additional bursts appeared on the ipsilateral side not seen on the contralateral side. Further increase of the stimulation could suppress the contralateral oscillations by switching to a sustained extensor activity, while the ipsilateral rhythmic activity remained. To delineate the function of V3 interneurons and their connectivity, we developed a computational model of the spinal circuits consisting of two (left and right) rhythm generators (RGs) interacting via V0V, V0D and V3 CINs. Both types of V0 CINs provided mutual inhibition between the left and right flexor RG centers and promoted left-right alternation. V3 CINs mediated mutual excitation between the left and right extensor RG centers. These interactions allowed the model to reproduce our current experimental data, while being consistent with previous data concerning the role of V0V and V0D CINs in securing left-right alternation and the changes in left-right coordination following their selective removal. We suggest that V3 CINs provide mutual excitation between the spinal neurons involved in the control of left and right extensor activity, which may promote left-right synchronization during locomotion.
NMRdock: Lightweight and Modular NMR Processing
Authors: East Kyle W. , Leith Andrew , Ragavendran Ashok , Delaglio Frank , Lisi George P.
Published: June 2019

NMR is a widely employed tool in chemistry, biology, and physics for the study of molecular structure and dynamics. Advances in computation have produced scores of software programs necessary for the processing and analysis of NMR data. However, the production of NMR software has been largely overseen by academic labs, each with their own preferred OS, environment, and dependencies. This lack of broader standardization and the complexity of installing and maintaining NMR-related software creates a barrier of entry into the field. To further complicate matters, as computation evolves, many aging software packages become deprecated. To reduce the barrier for newcomers and to prevent deprecation of aging software, we have created the NMRdock container. NMRdock utilizes containerization to package NMR processing and analysis programs into a single, easy-to-install Docker image that can be run on any modern OS. The current image contains two bedrock NMR data processing programs (NMRPipe and NMRFAM Sparky). However, future development of NMRdock aims to add modules for additional analysis programs to build a library of tools in a standardized and easy-to-implement manner. NMRdock is open source and free to download at https://compbiocore.github.io/nmrdock/.
The temporal transcription factor E93 controls dynamic enhancer activity and chromatin accessibility during development
Authors: Nystrom Spencer L. , Niederhuber Matthew J. , McKay Daniel J.
Published: June 2019

How temporal cues combine with spatial inputs to control gene expression during development is poorly understood. Here, we test the hypothesis that theDrosophilatranscription factor E93 controls temporal gene expression by regulating chromatin accessibility. Precocious expression of E93 early in wing development reveals that it can simultaneously activate and deactivate different target enhancers. Notably, the precocious patterns of enhancer activity resemble the wild-type patterns that occur later in development, suggesting that provision of E93 alters the competence of enhancers to respond to spatial cues. Genomic profiling reveals that precocious E93 expression is sufficient to regulate chromatin accessibility at a subset of its targets. These accessibility changes mimic those that normally occur later in development, indicating that precocious E93 accelerates the wild-type developmental program. Further, we find that target enhancers that do not respond to precocious E93 in early wings become responsive after a developmental transition, suggesting that parallel temporal pathways work alongside E93. These findings support a model wherein E93 expression functions as an instructive cue that defines a broad window of developmental time through control of chromatin accessibility.
Reaction mechanisms of Pol IV, RDR2 and DCL3 drive RNA channeling in the siRNA-directed DNA methylation pathway
Authors: Singh Jasleen , Mishra Vibhor , Wang Feng , Huang Hsiao-Yun , Pikaard Craig S.
Published: June 2019

In eukaryotes with multiple small RNA pathways the mechanisms that channel RNAs within specific pathways are unclear. Here, we reveal the reactions that account for channeling in the siRNA biogenesis phase of the Arabidopsis RNA-directed DNA methylation pathway. The process begins with template DNA transcription by NUCLEAR RNA POLYMERASE IV (Pol IV) whose atypical termination mechanism, induced by nontemplate DNA basepairing, channels transcripts to the associated RNA-dependent RNA polymerase, RDR2. RDR2 converts Pol IV transcripts into double-stranded RNAs then typically adds an extra untemplated 3’ terminal nucleotide to the second strands. The dicer endonuclease, DCL3 cuts resulting duplexes to generate 24 and 23nt siRNAs. The 23nt RNAs bear the untemplated terminal nucleotide of the RDR2 strand and are underrepresented among ARGONAUTE4-associated siRNAs. Collectively, our results provide mechanistic insights into Pol IV termination, Pol IV-RDR2 coupling and RNA channeling from template DNA transcription to siRNA guide strand/passenger strand discrimination.
PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline
Authors: Shteynberg David D , Deutsch Eric W , Campbell David S , Hoopmann Michael R , Kusebauch Ulrike , Lee Dave , Mendoza Luis , Midha Mukul , Sun Zhi , Whetton Anthony D , Moritz Robert L
Published: June 2019

Spectral matching sequence database search engines commonly used on mass spectrometry-based proteomics experiments excel at identifying peptide sequence ions, and in addition, possible sequence ions carrying post-translational modifications (PTMs), but most do not provide confidence metrics for the exact localization of those PTMs when several possible sites are available. Localization is absolutely required for downstream molecular cell biology analysis of PTM function in vitro and in vivo. Therefore, we developed PTMProphet, a free and open-source software tool integrated into the Trans-Proteomic Pipeline, which reanalyzes identified spectra from any search engine for which pepXML output is available to provide localization confidence to enable appropriate further characterization of biologic events. Localization of any type of mass modification (e.g., phosphorylation) is supported. PTMProphet applies Bayesian mixture models to compute probabilities for each site/peptide spectrum match where a PTM has been identified. These probabilities can be combined to compute a global false localization rate at any threshold to guide downstream analysis. We describe the PTMProphet tool, its underlying algorithms and demonstrate its performance on ground-truth synthetic peptide reference datasets, one previously published small dataset, one new larger dataset, and also on a previously published phospho-enriched dataset where the correct sites of modification are unknown. Data have been deposited to ProteomeXchange with identifier PXD013210.
Insights from a general, full-likelihood Bayesian approach to inferring shared evolutionary events from genomic data: Inferring shared demographic events is challenging
Authors: Oaks Jamie R. , L’Bahy Nadia , Cobb Kerry A.
Published: June 2019

Factors that influence the distribution, abundance, and diversification of species can simultaneously affect multiple evolutionary lineages within or across communities. These include changes to the environment or inter-specific ecological interactions that cause ranges of multiple species to contract, expand, or fragment. Such processes predict temporally clustered evolutionary events across species, such as synchronous population divergences and/or changes in population size. There have been a number of methods developed to infer shared divergences or changes in population size, but not both, and the latter has been limited to approximate methods. We introduce a full-likelihood Bayesian method that uses genomic data to estimate temporal clustering of an arbitrary mix of population divergences and population-size changes across taxa. Using simulated data, we find that estimating the timing and sharing of demographic changes tends to be inaccurate and sensitive to prior assumptions, which is in contrast to accurate, precise, and robust estimates of shared divergence times. We also show previous estimates of co-expansion among five Alaskan populations of threespine sticklebacks (Gasterosteus aculeatus) were likely driven by prior assumptions and ignoring invariant characters. We conclude by discussing potential avenues to improve the estimation of synchronous demographic changes across populations.
Regular Architecture (RegArch): A standard expression language for describing protein architectures
Authors: Ortega Davi R. , Jensen Grant J.
Published: June 2019

Domain architecture – the arrangement of features in a protein – exhibits syntactic patterns similar to the grammar of a language. This feature enables pattern mining for protein function prediction, comparative genomics, and studies of molecular evolution and complexity. To facilitate such work, here we propose Regular Architecture (RegArch), an expression language to describe syntactic patterns in protein architectures. Like the well-known Regular Expressions for text, RegArchs codify positional and non-positional patterns of elements into nested JSON objects. We describe the standard and provide a reference implementation in JavaScript to parse RegArchs and match annotated proteins.
Bactericidal efficiency and mechanism of specifically targeted antimicrobial peptides optimized based on structural and functional relationships
Authors: Tan Peng , Lai Zhenheng , Zhu Yongjie , Shao Changxuan , Akhtar Muhammad Usman , Li Weifen , Zheng Xin , Shan Anshan
Published: June 2019

In contrast to traditional broad-spectrum antibiotics, it is difficult for bacteria to develop resistance to most specifically targeted antimicrobial peptides (STAMPs), moreover, they can maintain a normal ecological balance and provide long-term protection for the body. However, therapeutic applications of STAMPS are hindered by their weak activity, and imperfect specificity as well as lack of knowledge to understand their structure-activity relationships. To further investigate the effects of different parameters on the biological activities of STAMPs, a peptide sequence, WKKIWKDPGIKKWIK, was truncated, extended, and provided with an increased charge and altered amphipathicity. In addition, a novel template modification method was introduced, in which a phage-displayed peptide that recognized and bound to E. coli cells was attached at the end of the sequence. Compared with the traditional template modification method, peptide 11, which contained a phage-displayed peptide at the C-terminus, exhibited superior narrow-spectrum antibacterial activity against E. coli compared to that of parental peptide 2, and the activity and specificity of 11 were increased by 5.0 and 2.4 times, respectively. Additionally, 11 showed low cell toxicity and relatively desirable salt, serum, acid and alkaline stability. In this study, 11 specifically killed E. coli by causing cytoplasmic membrane rupture and cytosol leakage. In summary, these findings are useful for improving the activity and specificity of STAMPs and show that peptide 11 is better able to combat the growing threat of E. coli infections.