bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomics for rational autogenous vaccine design to control Campylobacter infection in poultry
Authors: Calland Jessica , Mourkas Evangelos , Pascoe Ben , Sheppard Sam
Published: April 2019

Campylobacter is the leading cause of food-borne gastroenteritis worldwide and the most common cause of infection in humans have been linked to the consumption of contaminated poultry meat. Previous poultry vaccines have provided short term reduction in Campylobacter intestinal load in chickens but have limited commercial efficacy because of high diversity and rapid evolution of strains. Genome-wide association study (GWAS) of isolates from humans and chicken have identified genes associated with survival of Campylobacter through the poultry processing chain. These genes represent targets for vaccine design that would be selectively neutral within the chicken gut and therefore could be sustained in the population. We designed an autogenous vaccine based on isolates with survival-associated genes and monitored the efficacy in the chicken and through processing. First, we sampled for Campylobacter across five broiler farms feeding into one abattoir in Norfolk and characterized genomic diversity using next generation sequencing (NGS), including the identification of survival genes. These data were then used in a predictive model to identify the minimum number of strains to be used in vaccine design based on known immunogenicity of the strains. Second, the vaccine was developed and given at two time-points to a whole farm of breeder chickens. Third, vaccine efficacy was monitored at three time points post-vaccination in vaccinated breeders and their progeny. The cfu/g reduction in the ceacum and neck skin were determined. This study demonstrates the potential for NGS in autogenous vaccine design to reduce harmful strains of bacteria that are carried commensally in livestock.
Clinical evaluation of herPHEgen®: a herpesvirus genotype-to-phenotype antiviral resistance database and testing service
Authors: Mohamed Hodan , Bibby David , Gallagher Eileen , Piorkowska Renata , Gavriel Andros , Manso Carmen , Wallis Nigel , Parry Chris , Zuckerman Mark , Cane Patricia , Bradshaw Daniel , Mbisa Jean
Published: April 2019

Herpes simplex virus type 1 (HSV-1) and 2 (HSV-2) infections may be life-threatening in immunocompromised patients. Antiviral treatment is available but resistance can develop. The gold standard for resistance testing is cell culture-based phenotyping which is slow (3–4 weeks) and has a high (50 %) failure rate. Faster (<10 working days) genotypic testing of viral thymidine kinase (TK) and DNA polymerase (DNApol) can be used with >95 % success rate. However, a reference database for interpreting drug susceptibility from genetic data is lacking. We developed an HSV genotypic test and genotype-to-phenotype drug resistance database. We evaluated the service using 325 clinical samples, previously characterised by phenotypic susceptibility testing, from 248 treatment-experienced patients. The median age was 42.5 years [IQR30.0–51.0] and 50.8 % (n=126) were female. Clinical details were as follows: 42.3 % (n=105) haemato-oncology patients; 12.1 % (n=30) HIV-infected; 4.4 % (n=11) unspecified immunosuppression; 2.4 % (n=6) congenital infection; 1.2 % (n=3) solid organ transplant; 37.5 % (n=93) unknown. HSV-1 was identified in 58.2 % (n=189) samples. Phenotypic testing identified resistance in 63.7 % (n=207) samples. Genotypic testing identified a resistance-associated mutation (RAM) in TK and/or DNApol in 200/207 samples, a positive percent agreement of 96.6 %, whereas a RAM was detected in 1/118 susceptible samples, a negative percent agreement of 99.2 %. Most RAM occurred in TK (n=195; 97.0 %) with few in DNApol (n=32; 15.9 %). In summary, through herPHEgen we have developed a robust HSV resistance testing service, providing clinicians with timely and accurate results. This will improve clinical decision-making, optimising treatment efficacy and minimising toxicity in immunocompromised patients with HSV.
Shiga toxin prophage analysis of clinically relevant enterohaemorrhagic E. coli isolates using Nanopore sequencing
Authors: Yara Daniel , Greig David , Dallman Tim , Jenkins Claire
Published: April 2019

Enterohaemorrhagic E. coli O157 produces different Shiga toxin (Stx) subtypes which can contribute to the development of disease. The advancement of severe disease such as haemolytic uraemic syndrome is significantly associated to Stx2a subtype carriage. Three distinct EHEC lineages exist, where in the UK, stx2a has found in three STEC O157 sub-lineages: Ic, I/II and IIb. Stx encoding phages from the three sub-lineages where examined to determine whether the bacteriophage which conferred the stx2a synthesis are the same or different. Relevant representative EHEC O157 strains were sequenced using the MinION Platform. The sequences were assembled and annotated, allowing Stx encoding prophage identification. Such prophages and constituent genes were then aligned for comparison along with various reference strains. Results reveal that outbreak EHEC strains carry Stx2c encoding prophages and that such prophages were conserved, supporting past studies which suggest a single integration event and clonal expansion of Stx2c bacteriophages. Analysis of Stx genes revealed that some Stx2c phages carry Stx2a encoding genes, suggesting recombination between different Stx encoding phages. Variability was observed for Stx2a encoding phages, suggesting that there are various Stx2a encoding phages circulating in the UK.
Development of bio-inspired protein-based materials as novel transparent adhesives for glass laminates
Authors: Allen Gethin , Griffin Sholeem , Clifford Ben , Phillips Chris , Van Keulen Geertje
Published: April 2019

This project aims to develop Chaplins, functional amyloid proteins from Streptomyces sp., into a novel nano-thin adhesive material for the defence industry through combining existing protein-based technology with a composite partner. Chaplin proteins were extracted from a range of wild-type strains, while a synthetic promoter system was developed to express and secrete chaplins, which are typically difficult to express and purify. Chaplin proteins were found to have potentially useful adhesive properties and we have been investigating their application in optically transparent adhesives, since adhesives currently used to bond laminated transparent materials are prone to water ingress resulting in degradation of optical clarity and delamination. These adhesives could also be lighter, thinner, and have a lower environmental impact. To determine the potential of this material as a novel synbio-adhesive for bonding glass and polycarbonate we have investigated the bonding ability and transparency of natural and engineered amyloid proteins, both alone and with partner biopolymers and bulking materials. We are now exploring ways to improve the properties of the proteins by modifying the amino acid sequences, incorporating binding domains to the composite partner and via chemical modifications. Our projects has provided proof-of-concept for the use of bio-inspired amyloid protein-based materialscompounds as both adhesives and corrosion resistant metal coatings. Supported by Defence and Security Accelerator (DASA), Defence Science and Technology Laboratory (Dstl) project grants CDE100367 and ACC101824.
Potential glycoengineered anti-Burkholderia vaccines by exploiting the bacterial O-glycosylation machinery
Authors: Wang Guan-bo , Glaser Lena , Ingram Rebecca , Valvano Miguel
Published: April 2019

Previously, we discovered a protein O-glycosylation (ogc) cluster conserved in all Burkholderia species, which glycosylates proteins with a trisaccharide glycan. Sera from Burkholderia-infected patients produce anti-glycan antibodies, suggesting that the Burkholderia protein glycosylation pathway can be exploited for potential vaccine development. Here, we successfully produced two prototypes of anti-Burkholderia vaccines: a recombinant glycoprotein-based vaccine and an E. coli LPS-display vaccine. To generate the former, we constructed a plasmid carrying a chimeric gene encoding three glycosylation sequons fused to the cholera toxin B subunit. The presence of the glycan was observed in recombinant proteins expressed in B. cenocepacia parental strain, but not in proteins expressed by the glycosyltransferase-deficient ΔpglLstrain, as determined by SDS-PAGE and fluorescent lectin blots. For the development of an E. coli LPS-display vaccine, we constructed a plasmid expressing the ogc cluster, which was introduced into an E. coli strain unable to synthesize O-antigen but carrying the O-antigen ligase WaaL. Our results show that the LPS of this strain contained an additional moiety consistent with the B. cenocepacia trisaccharide glycan, as demonstrated by silver-stained LPS gels and lectin blot. This extra moiety was not detected in aΔwaaL mutant. These results suggest that the plasmid was able to provide the necessary functions for the synthesis and membrane translocation of the lipid-linked trisaccharide, which became a substrate for the WaaL ligase and incorporation into the E. coli LPS. Therefore, we demonstrate that the O-glycosylation pathway can be manipulated for the construction of potential anti-Burkholderia vaccines.
Increased predominance of HIV-1 CRF01_AE and its recombinants in the Philippines
Authors: Chen Yue , Hora Bhavna , DeMarco Todd , Berba Regina , Register Heidi , Hood Sylvia , Carter Meredith , Stone Mars , Pappas Andrea , Sanchez Ana M. , Busch Michael , Denny Thomas N. , Gao Feng
Published: April 2019

The growth rate of new HIV infections in the Philippines was the fastest of any countries in the Asia-Pacific region between 2010 and 2016. To date, HIV-1 subtyping results in the Philippines have been determined by characterizing only partial viral genome sequences. It is not known whether recombination occurs in the majority of unsequenced genome regions. Near-full-length genome (NFLG) sequences were obtained by amplifying two overlapping half genomes from plasma samples collected between 2015 and 2017 from 23 newly diagnosed infected individuals in the Philippines. Phylogenetic analysis showed that the newly characterized sequences were CRF01_AE (14), subtype B (3), CRF01/B recombinants (5) and a CRF01/CRF07/B recombinant (1). All 14 CRF01_AE formed a tight cluster, suggesting that they were derived from a single introduction. The time to the most recent common ancestor (tMRCA) for CRF01_AE in the Philippines was 1995 (1992–1998), about 10–15 years later than that of CRF01_AE in China and Thailand. All five CRF01/B recombinants showed distinct recombination patterns, suggesting ongoing recombination between the two predominant circulating viruses. The identification of partial CRF07_BC sequences in one CRF01/CRF07/B recombinant, not reported previously in the Philippines, indicated that CRF07_BC may have been recently introduced into that country from China, where CRF07_BC is prevalent. Our results show that the major epidemic strains may have shifted to an increased predominance of CRF01_AE and its recombinants, and that other genotypes such as CRF07_BC may have been introduced into the Philippines.
Simple study designs in ecology produce inaccurate estimates of biodiversity responses
Authors: Christie Alec P. , Amano Tatsuya , Martin Philip A. , Shackelford Gorm E. , Simmons Benno I. , Sutherland William J.
Published: April 2019

Ecologists use a wide range of study designs to estimate the impact of interventions or threats but there are no quantitative comparisons of their accuracy. For example, while it is accepted that simpler designs, such as After (sampling sites post-impact without a control), Before-After (BA) and Control-Impact (CI), are less robust than Randomised Controlled Trials (RCT) and Before-After Control-Impact (BACI) designs, it is not known how much less accurate they are.

We simulate a step-change response of a population to an environmental impact using empirically-derived estimates of the major parameters. We use five ecological study designs to estimate the effect of this impact and evaluate each one by determining the percentage of simulations in which they accurately estimate the direction and magnitude of the environmental impact. We also simulate different numbers of replicates and assess several accuracy thresholds.

We demonstrate that BACI designs could be 1.1-1.5 times more accurate than RCTs, 2.9-4.1 times more accurate than BA, 3.8-5.6 times more accurate than CI, and 6.8-10.8 times more accurate than After designs, when estimating to within ±30% of the true effect (depending on the sample size). We also found that increasing sample size substantially increases the accuracy of BACI designs but only increases the precision of simpler designs around a biased estimate; only by using more robust designs can accuracy increase. Modestly increasing replication of both control and impact sites also increased the accuracy of BACI designs more than substantially increasing replicates in just one of these groups.

We argue that investment into using more robust designs in ecology, where possible, is extremely worthwhile given the inaccuracy of simpler designs, even when using large sample sizes. Based on our results we propose a weighting system that quantitatively ranks the accuracy of studies based on their study design and the number of replicates used. We hope these ‘accuracy weights’ enable researchers to better account for study design in evidence synthesis when assessing the reliability of a range of studies using a variety of designs.
Beat-based and memory-based temporal expectations in rhythm: similar perceptual effects, different underlying mechanisms
Authors: Bouwer Fleur L. , Honing Henkjan , Slagter Heleen A.
Published: April 2019

Predicting the timing of incoming information allows the brain to optimize information processing in dynamic environments. Behaviorally, temporal expectations have been shown to facilitate processing of events at expected time points, such as sounds that coincide with the beat in musical rhythm. Yet, temporal expectations can develop based on different forms of structure in the environment, not just the regularity afforded by a musical beat. Little is still known about how different types of temporal expectations are neurally implemented and affect performance. Here, we orthogonally manipulated the periodicity and predictability of rhythmic sequences to examine the mechanisms underlying beat-based and memory-based temporal expectations, respectively. Behaviorally and using EEG, we looked at the effects of beat-based and memory-based expectations on auditory processing when rhythms were task relevant or task irrelevant. At expected time points, both beat-based and memory-based expectations facilitated target detection and led to attenuation of P1 and N1 responses, even when expectations were task-irrelevant (unattended). For beat-based expectations, we additionally found reduced target detection and enhanced N1 responses for events at unexpected time points (e.g., off-beat), regardless of the presence of memory-based expectations or task relevance. This latter finding supports the notion that periodicity selectively induces rhythmic fluctuations in neural excitability and furthermore indicates that while beat-based and memory-based expectations may similarly affect auditory processing of expected events, their underlying neural mechanisms may be different.
Neurostructural Heterogeneity in Youth with Internalizing Symptoms
Authors: Kaczkurkin Antonia N. , Sotiras Aristeidis , Baller Erica B. , Calkins Monica E. , Chand Ganesh B. , Cui Zaixu , Erus Guray , Fan Yong , Gur Raquel E. , Gur Ruben C. , Moore Tyler M. , Roalf David R. , Rosen Adon F.G. , Ruparel Kosha , Shinohara Russell T. , Varol Erdem , Wolf Daniel H. , Davatzikos Christos , Satterthwaite Theodore D.
Published: April 2019

Internalizing disorders such as anxiety and depression are the most common psychiatric disorders, frequently begin in youth, and exhibit marked heterogeneity in treatment response and clinical course. It is increasingly recognized that symptom-based classification approaches to internalizing disorders do not align with underlying neurobiology. An alternative to classifying psychopathology based on clinical symptoms is to identify neurobiologically-informed subtypes based on brain imaging data. We used a recently developed semi-supervised machine learning method (HYDRA) to delineate patterns of neurobiological heterogeneity within youth with internalizing symptoms using structural imaging data collected at 3T from a large community-based sample of 1,141 youth. Using volume and cortical thickness, cross-validation methods indicated a highly stable solution (ARI=.66; permutation-basedpfdr< .001) and identified two subtypes of internalizing youth. Subtype 1, defined by smaller brain volumes and reduced cortical thickness, was marked by impaired cognitive performance and higher levels of psychopathology than both Subtype 2 and typically developing youth. Using resting-state fMRI and diffusion images not considered during clustering, we found that Subtype 1 also showed reduced amplitudes of low-frequency fluctuations in fronto-limbic regions at rest, as well as reduced fractional anisotropy in white matter tracts such as the parahippocampal cingulum bundle and the uncinate fasciculus. In contrast, Subtype 2 showed intact cognitive performance, greater volume, cortical thickness, and amplitudes during rest compared to Subtype 1 and typically developing youth, despite still showing clinically significant levels of psychopathology. Identification of biologically-grounded subtypes of internalizing disorders may assist in targeting early interventions and assessing longitudinal prognosis.
Revisiting the regulation of the capsular polysaccharide biosynthesis gene cluster inStaphylococcus aureus
Authors: Keinhörster Daniela , Salzer Andrea , Duque-Jaramillo Alejandra , George Shilpa E. , Marincola Gabriella , Lee Jean C. , Weidenmaier Christopher , Wolz Christiane
Published: April 2019

InStaphylococcus aureus, the capsular polysaccharide (CP) protects against phagocytosis, but also hinders adherence to endothelial cells and matrix proteins. Its biosynthesis is tightly controlled resulting in a heterogeneous phenotype within a population and CP being mainly detectable in non-growing cells. Capsular biosynthesis genes are encoded by a conservedcapA-Poperon whose expression is driven by an upstream promoter element (Pcap) in front ofcapA. The organization of Pcapis poorly understood, as is the interplay of different regulators that influence the early-Off/late-Heterogeneouscaptranscription pattern. Here, we demonstrate that Pcapcontains a main SigB-dependent promoter. The SigB consensus motif overlaps with a previously described inverted repeat that is crucial forcapexpression. The essentiality of the inverted repeat is derived from this region acting as a SigB binding site rather than as an operator site for the proposedcapactivators RbsR and MsaB. Furthermore, Pcapcontains an extensive upstream region harboring a weak SigA-dependent promoter and binding sites for thecaprepressors SaeR, CodY and Rot. We show that heterogeneous CP synthesis is determined by the combination of SigB activity and repressor binding to the upstream region. The direct SigB dependency and the upstream repressors are also sufficient to explain the temporal gene expression pattern at the transcriptional level. However, CP synthesis remains growth phase-dependent even whencapAtranscription is rendered constitutive, suggesting additional post-transcriptional regulatory circuits. Thus, the interference of multiple repressors with SigB-dependent promoter activity as well as post-transcriptional mechanisms ensure the appropriate regulation of CP synthesis.

Importance

The majority of bacterial pathogens produce an array of polysaccharides on their surface which are important virulence factors and thus serve as attractive vaccine candidates. However, the synthesis and assembly of these structures is highly variable and tightly regulated at various levels. In the human pathogenStaphylococcus aureus, the synthesis of the capsular polysaccharide (CP) is dependent on a complex regulatory network which ensures that CP is produced only in a fraction of stationary phase cells. Here, we determined main regulators that drive the peculiar CP expression pattern. We found that the interplay of the transcriptional repressors Sae, CodY and Rot with the alternative Sigma factor B is responsible for early-Off/late-Heterogeneous expression at the transcriptional level. The data also implicates post-transcriptional mechanisms that may act to avoid conflict in precursor usage by machineries involved in either synthesis of CP or other glycopolymers in growing bacterial cells.
HAMAP rules as SPARQL A portable annotation pipeline for genomes and proteomes
Authors: Bolleman Jerven , de Castro Eduoard , Baratin Delphine , Gehant Sebastien , Cuche Beatrice A. , Auchincloss Andrea H. , Coudert Elisabeth , Hulo Chantal , Masson Patrick , Pedruzzi Ivo , Rivoire Catherine , Xenarios Ioannis , Redaschi Nicole , Bridge Alan
Published: April 2019

Motivation

Genome and proteome annotation pipelines are generally custom built and therefore not easily reusable by other groups, which leads to duplication of effort, increased costs, and suboptimal results. One cost-effective way to increase the data quality in public databases is to encourage the adoption of annotation standards and technological solutions that enable the sharing of biological knowledge and tools for genome and proteome annotation.

Results

We have translated the rules of our HAMAP proteome annotation pipeline to queries in the W3C standard SPARQL 1.1 syntax and applied them with two off-the-shelf SPARQL engines to UniProtKB/Swiss-Prot protein sequences described in RDF format. This approach is applicable to any genome or proteome annotation pipeline and greatly simplifies their reuse.

Availability

HAMAP SPARQL rules and documentation are freely available for download from the HAMAP FTP site ftp://ftp.expasy.org/databases/hamap/hamapsparql.tar.gz under a CC-BY-ND 4.0 license. The annotations generated by the rules are under the CC-BY 4.0 license.

Contact

hamap@sib.swiss

Supplementary information

Supplementary data are included at the end of this document.
cT-DNA in Linaria vulgaris L. is multicopy, inverted and homogenized
Authors: Vladimirov Ivan A. , Pavlova Olga A. , Polev Dmitrii E. , Bogomaz Denis I.
Published: April 2019

The phenomenon of evolutionary fixation of agrobacterial sequences (cT-DNA or cellular transferred DNA) in plant genomes is well known in nature. It was previously considered, that all of cT-DNA-containing species, except Linaria vulgaris, have multiple inverted cT-DNA repeats. Deep studying of general features of cT-DNA brings us closer to understanding the causes and mechanisms of its fixation in plants genomes. We combined multiple long-range PCR with genome walking for studying extended structure of cT-DNA. Using digital PCR method, we estimated copy number of cT-DNA elements. NGS with low covering allows us to develop a set of microsatellite markers, also used for copy number estimation. According to new data, cT-DNA elements in L. vulgaris form an inverted complex repeat of two simple direct repeats. After cT-DNA integration, cT-DNA sequence duplication events took place at least two times. The phenomenon of concerted evolution of cT-DNA sequences as well as some details of this process have been shown for the first time.

We have shown, that L. vulgaris, as well as other cT-DNA containing species, has inverted structure of repeats. This fact indicates possible existence of some general causes and mechanisms of cT-DNA fixation in plant genomes during evolution.
coMethDMR: Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies
Authors: Gomez Lissette , Odom Gabriel J. , Young Juan I. , Martin Eden R. , Liu Lizhong , Chen Xi , Griswold Anthony J. , Gao Zhen , Zhang Lanyu , Wang Lily
Published: April 2019

Recent technology has made it possible to measure DNA methylation profiles in a cost-effective and comprehensive genome-wide manner using array-based technology for epigenome-wide association studies. However, identifying differentially methylated regions (DMRs) remains a challenging task because of the complexities in DNA methylation data. Supervised methods typically focus on the regions that contain consecutive highly significantly differentially methylated CpGs in the genome, but may lack power for detecting small but consistent changes when few CpGs pass stringent significance threshold after multiple comparison. Unsupervised methods group CpGs based on genomic annotations first and then test them against phenotype, but may lack specificity because the regional boundaries of methylation are often not well defined. We present coMethDMR, a flexible, powerful, and accurate tool for identifying DMRs. Instead of testing all CpGs within a genomic region, coMethDMR carries out an additional step that selects co-methylated sub-regions first. Next, coMethDMR tests association between methylation levels within the sub-region and phenotype via a random coefficient mixed effects model that models both variations between CpG sites within the region and differential methylation simultaneously. coMethDMR offers well-controlled Type I error rate, improved specificity, focused testing of targeted genomic regions, and is available as an open-source R package.
Probing dynamical cortical gating of attention with concurrent TMS-EEG
Authors: Okazaki Yuka O. , Mizuno Yuji , Kitajo Keiich
Published: April 2019

Background

Attention facilitates gating of information from the sending brain area to receiving areas, with this being achieved by dynamical change in effective connectivity between cortices. However, it is difficult to assess effective connectivity, which refers to the causal influence of one cortical area on another.

Objective

The aim of this study is to directly probe the effective connectivity between cortical areas, which is modulated by covertly shifted attention, excluding the thalamic influence.

Methods

Transcranial magnetic stimulation (TMS) was used to directly perturb the right retinotopic visual cortex in task-relevant (TR) and task-irrelevant (TIR) networks, and the impact of this was tracked to other areas by concurrent use of electroencephalography (EEG).

Results

Key finding was that TMS to the TR hemisphere led to a stronger evoked potential than did
stimulation to the TIR hemisphere. Moreover, stronger beta- and gamma-band effective connectivities assessed as lagged phase synchronizations between stimulated areas and other areas were observed when TMS was delivered to the TR area. These effects were more enhanced when they preceded more prominent alpha lateralization, which is known to be associated with gating information.

Conclusion

Our results indicate that attention-regulated cortical excitability and feedforward dynamical effective connectivity can be probed by direct cortical stimulation to the TR or TIR area, thereby bypassing thalamic gating. These results bear out the idea that TMS-EEG could help to characterize changes in the functional architecture of brain networks that are required for rapid adaptation to the environment or due to brain diseases.

Highlights

Attention-regulated cortical excitability and effective connectivity were probed by TMS-EEG.

Stronger TMS evoked potentials were observed in the task-relevant visual hemisphere.

Strong effective connectivity between task-relevant visual cortex and other areas were found.
Effects of compassion training on brain responses to suffering others
Authors: Ashar Yoni K. , Andrews-Hanna Jessica R. , Halifax Joan , Dimidjian Sona , Wager Tor D.
Published: April 2019

What are the active ingredients and brain mechanisms of compassion training? To address these questions, we conducted a three-armed randomized trial (N = 57) of compassion meditation (CM). We compared a four-week CM program delivered by smartphone application to i) a placebo condition, in which participants inhaled sham oxytocin, which they were told would enhance compassion, and ii) a familiarity control condition, designed to control for increased familiarity with suffering others. Functional MRI was collected while participants listened to narratives describing suffering others at pre- and post-intervention. CM increased brain responses to suffering others in the medial orbitofrontal cortex (mOFC) relative to both the placebo and familiarity control conditions, and in the nucleus accumbens relative to the familiarity control condition. Results support the specific efficacy of CM beyond effects of expectancy, demand characteristics, and increased familiarity with suffering others, and implicate affective and motivational pathways as brain mechanisms of CM.

Author Note

Funded by the John Templeton Foundation’s Positive Neuroscience project (PIs Wager and Dimidjian), with additional support from NIH R01 R01DA035484 (PI Wager). Gratitude to research assistants Jenifer Mutari, Robin Kay, Scott Meyers, Nicholas Peterson, and Brandin Williams for help with data collection.
DRPnet - Automated Particle Picking in Cryo-Electron Micrographs using Deep Regression
Authors: Nguyen Nguyen P. , Gotberg Jacob , Ersoy Ilker , Bunyak Filiz , White Tommi
Published: April 2019

Abstract

Selection of individual protein particles in cryo-electron micrographs is an important step in single particle analysis. In this study, we developed a deep learning-based method to automatically detect particle centers from cryoEM micrographs. This is a challenging task because of the low signal-to-noise ratio of cryoEM micrographs and the size, shape, and grayscale-level variations in particles. We propose a double convolutional neural network (CNN) cascade for automated detection of particles in cryo-electron micrographs. Particles are detected by the first network, a fully convolutional regression network (FCRN), which maps the particle image to a continuous distance map that acts like a probability density function of particle centers. Particles identified by FCRN are further refined (or classified) to reduce false particle detections by the second CNN. This approach, entitled Deep Regression Picker Network or “DRPnet”, is simple but very effective in recognizing different grayscale patterns corresponding to 2D views of 3D particles. Our experiments showed that DRPnet’s first CNN pretrained with one dataset can be used to detect particles from a different datasets without retraining. The performance of this network can be further improved by re-training the network using specific particle datasets. The second network, a classification convolutional neural network, is used to refine detection results by identifying false detections. The proposed fully automated “deep regression” system, DRPnet, pretrained with TRPV1 (EMPIAR-10005) [1], and tested onβ-galactosidase (EMPIAR-10017) [2] andβ-galactosidase (EMPIAR-10061) [3], was then compared to RELION’s interactive particle picking. Preliminary experiments resulted in comparable or better particle picking performance with drastically reduced user interactions and improved processing time.
Disentangling unity from diversity in developmental psychopathology
Authors: Mendes Lorenna Sena Teixeira , Polanczyk Guilherme Vanoni , Rohde Luis Augusto , Salum Giovanni Abrahão
Published: April 2019

Developmental psychopathology has been a fruitful space for the investigation of the validity of multidimensionality. Nonetheless, previous studies in the field have not tested a model with a fine-grained division within the internalizing and externalizing spectra that also accounts for the contribution of a general psychopathology factor. The aim of this study is to test the validity and reliability of a theoretically-driven bifactor model with one general dimension and ten specific dimensions of psychopathology: fear, somatic complaints, distressful thoughts, low mood, low motivation/energy, inattention-hyperactivity, temper loss, aggression, noncompliance, and low concern for others. Our study evaluated 2,511 children aged 6-14 years-old from the Brazilian High-Risk Cohort for Psychiatric Disorders. There was support for the model in terms of its fit to the data, reliability, and external validity. Our findings highlight the potential of combined fine-grained approaches with models disentangling unity from diversity in developmental psychopathology.
Reconstructing the transcriptional ontogeny of maize and sorghum supports an inverse hourglass model of inflorescence development
Authors: Leiboff Samuel , Hake Sarah
Published: April 2019

Assembling meaningful comparisons between species is a major limitation in studying the evolution of organismal form. To understand development in maize and sorghum, closely-related species with architecturally distinct inflorescences, we collected RNAseq profiles encompassing inflorescence body plan specification in both species. We reconstructed molecular ontogenies from 40 B73 maize tassels and 47 BT×623 sorghum panicles and separated them into transcriptional stages. To discover new markers of inflorescence development, we used random forest machine learning to determine stage by RNAseq. We used two descriptions of transcriptional conservation to identify hourglass-like developmental stages. Despite short evolutionary ancestry of 12 million years, we found maize and sorghum inflorescences are most different during their hourglass-like stages of development, following an ‘inverse-hourglass’ model of development. We discuss if agricultural selection may account for the rapid divergence signatures in these species and the observed separation of evolutionary pressure and developmental reprogramming.

Highlights

Transcript dynamics identify maize tassel and sorghum panicle developmental stages

Random forest predicts developmental age by gene expression, providing molecular markers and anin silicostaging application

Maize and sorghum inflorescences are most similar when committing stem cells to a determinant fate

Expression conservation identifies hourglass-like stage, but transcriptomes diverge, similar to ‘inverse hourglass’ observations in cross-phyla animal embryo comparisons
ABioTrans: A Biostatistical tool for Transcriptomics Analysis
Authors: Yutong Zou , Thuy Tien Bui , Selvarajoo Kumar
Published: April 2019

Here we report a bio-statistical/informatics tool, ABioTrans, developed in R for gene expression analysis. The tool allows the user to directly read RNA-Seq data files deposited in the Gene Expression Omnibus or GEO database. Operated using any web browser application, ABioTrans provides easy options for multiple statistical distribution fitting, Pearson and Spearman rank correlations, PCA, k-means and hierarchical clustering, differential expression analysis, Shannon entropy and noise (square of coefficient of variation) analyses, as well as Gene ontology classifications.

Availability and implementation

ABioTrans is available at https://github.com/buithuytien/ABioTrans

Operating system(s): Platform independent (web browser)

Programming language: R (R studio)

Other requirements: Bioconductor genome wide annotation databases, R-packages (shiny, LSD, fitdistrplus, actuar, entropy, moments, RUVSeq, edgeR, DESeq2, NOISeq, AnnotationDbi, ComplexHeatmap, circlize, clusterProfiler, reshape2, DT, plotly, shinycssloaders, dplyr, ggplot2). These packages will automatically be installed when the ABioTrans.R is executed in R studio.

No restriction of usage for non-academic.
CCDC186 controls dense-core vesicle cargo sorting by exit
Authors: Cattin-Ortolá Jérôme , Topalidou Irini , Lau Ho-Tak , Hummer Blake , Asensio Cedric S. , Ong Shao-En , Ailion Michael
Published: April 2019

The regulated release of peptide hormones depends on their packaging into dense-core vesicles (DCVs). Two models have been proposed for DCV cargo sorting. The “sorting by entry” model proposes that DCV cargos selectively enter nascent DCVs at the trans-Golgi network (TGN). The “sorting by exit” model proposes that sorting occurs by the post-TGN removal of non-DCV cargos and retention of mature DCV cargos. Here we show that the coiled-coil protein CCDC186 controls sorting by exit.Ccdc186KO insulinoma cells secrete less insulin, fail to retain insulin and carboxypeptidase E in mature DCVs at the cell periphery, and fail to remove carboxypeptidase D from immature DCVs. A mutation affecting the endosome-associated recycling protein (EARP) complex causes similar defects in DCV cargo retention and removal. CCDC186 and EARP may act together to control the post-Golgi retention of cargos in mature DCVs.
Zebrafish GPR161 Contributes to Basal Hedgehog Repression in a Tissue-specific Manner
Authors: Tschaikner Philipp , Regele Dominik , Salvenmoser Willi , Geley Stephan , Stefan Eduard , Aanstad Pia
Published: April 2019

Hedgehog (Hh) ligands act as morphogens to direct patterning and proliferation during embryonic development. Protein kinase A (PKA) is a central negative regulator of Hh signalling, and in the absence of Hh ligands, PKA activity prevents inappropriate expression of Hh target genes. The Gαs- coupled receptor Gpr161 contributes to the basal Hh repression machinery by activating PKA, although the extent of this contribution is unclear. Here we show that loss of Gpr161 in zebrafish leads to constitutive activation of low-, but not high-level Hh target gene expression in the neural tube. In contrast, in the myotome, both high- and low-level Hh signalling is constitutively activated in the absence of Gpr161 function. Our results suggest that the relative contribution of Gpr161 to basal repression of Hh signalling is tissue-specific. Distinct combinations of G-protein-coupled receptors may allow the fine-tuning of PKA activity to ensure the appropriate sensitivity to Hh across different tissues.
Neuronal aging potentiates beta-amyloid generation via amyloid precursor protein endocytosis
Authors: Burrinha Tatiana , Gomes Ricardo , Terrasso Ana Paula , Almeida Cláudia Guimas
Published: April 2019

Aging increases the risk of Alzheimer’s disease (AD). During normal aging synapses decline and β-Amyloid (Aβ) accumulates. An Aβ defective clearance with aging is postulated as responsible for Aβ accumulation, although a role for increased Aβ production with aging can also lead to Aβ accumulation. To test this hypothesis, we established a long-term culture of primary mouse neurons that mimics neuronal aging (lysosomal lipofuscin accumulation and synapse decline). Intracellular endogenous Aβ42 accumulated in aged neurites due to increased amyloid-precursor protein (APP) processing. We show that APP processing is up-regulated by a specific age-dependent increase in APP endocytosis. Endocytosed APP accumulated in early endosomes that, in turn were found augmented in aged neurites. APP processing and early endosomes up-regulation was recapitulated in vivo. Finally, we found that inhibition of Aβ production reduced the decline in synapses in aged neurons. We propose that potentiation of APP endocytosis by neuronal aging increases Aβ production, which contributes to aging-dependent decline in synapses.

How aging increases the risk of Alzheimer’s disease is not clear. We show that normal neuronal aging increases the intracellular production of β-amyloid, due to an upregulation of the amyloid precursor protein endocytosis. Importantly, increased Aβ production contributes to the aging-dependent synapse loss.
Split-Belt walking induces changes in active, but not passive, perception of step length
Authors: Sombric Carly , Gonzalez-Rubio Marcela , Torres-Oviedo Gelsy
Published: April 2019

The estimation of limbs’ position is critical for motor control. While motor adaptation changes the estimation of limb position in volitional arm movements, this has not been observed in locomotion. We hypothesized that split-belt walking with the legs moving at different speeds changes the estimation of the legs’ position when taking a step. Thus, we assessed young subjects’ perception of step length (i.e., inter-feet distance at foot landing) when they moved their legs (active perception) or these were moved by the experimenter (passive perception). Step length’s active, but not passive perception was altered by split-belt walking; indicating that adapted efferent inputs changed the perceived limbs’ position without changing information from sensory signals. These perceptual shifts were sensitive to how they were tested: they were observed in the trailing, but not the leading leg, and they were more salient when tested with short than long step lengths. Our results suggest that sensory changes following motor adaptation might arise from mismatched limb position estimates from different sensory sources (i.e., proprioception and vision), which is less prominent in walking. We also speculate that split-belt walking could improve the deficient perception of step length post-stroke, which contributes to their gait asymmetry impairing patients’ mobility.
An in vitro model maintaining taxon-specific functional activities of the gut microbiome
Authors: Li Leyuan , Abou-Samra Elias , Ning Zhibin , Zhang Xu , Mayne Janice , Wang Janet , Cheng Kai , Walker Krystal , Stintzi Alain , Figeys Daniel
Published: April 2019

The gut microbiome is a new target for therapeutics. In vitro high-throughput culture models could provide time-and-cost saving solutions to discover microbiome responses to drugs. Unfortunately, there has been no report of in vitro models capable of maintaining functional and compositional profiles resembling the in vivo gut microbiome. Here, we developed and validated a high-throughput culturing model named Mipro to maintain individuals’ microbiomes. The Mipro model quintupled viable bacteria count while maintained the functional and compositional profiles of individuals’ gut microbiomes. Comparison of taxon-specific functions between pre -and-post culture microbiomes showed Pearson’s correlation coefficient r of 0.83 ± 0.03. Moreover, the Mipro model also exhibited a high degree of in vitro – in vivo correlation (Pearson’s r of 0.68 ± 0.09) in microbial responses to metformin in mice fed a high-fat diet. Mipro provides a highly simulated gut microbiome for high-throughput investigation of drug-microbiome interactions.
Quantifying the Payments for Ecosystem Services among hydrologic units in Zhujiang River Basin, China based on the indicator of Optional Capacity Value
Authors: Yang Haile , Zhao Bin , Chen Jiakuan
Published: April 2019

Ecosystem services (ES) are fundamental to human being’s livelihoods, production and survival. However, the spatial mismatch between ES supply and demand is a common phenomenon. Payments for Ecosystem Services (PES) provide a way to promote the complementary advantages and benefits equilibrium between ES supplier and beneficiary. At present, PES is mainly based on the tradeoff between the profit and loss of ecological conservation. The quantifying of PES mainly uses the opportunity cost of ES supplier and follows the principle of additionality, which neglects the benefits that arise from the basic (contrast to additional) ES experienced by ES beneficiary and ignores the rights and interests of ES supplier who supplies the basic ES. To resolve this problem, we proposed that we should set the value of ES experienced by ES beneficiary as the quantitative indicator of PES. Here, we introduced a new indicator (optional capacity value, OCV) to implement this idea. The ES OCV indicates the optional capacity of supporting the total value produced by human being’s economic and social activities provided by the total volume of an ES. In this paper, we calculated the ES OCV of water provision in Zhujiang River Basin (Pearl River Basin), China. Then, we discussed three scenarios of quantifying PES, based on the principles of (1) interests sharing and responsibilities bearing and (2) equal pay for equal work. The results showed that the ES OCV could describe the conditions that water resources in a hydrologic unit not only provide benefits to the hydrologic unit itself, but also provide benefits to downstream hydrologic units, and then could be a quantitative indicator for PES. This research provides a new PES scheme which would promote the coordinated development and ecological conservation among the regions with mismatch between ES supply and demand.
The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons
Authors: Batista Rita A. , Moreno-Romero Jordi , Qiu Yichun , van Boven Joram , Santos-González Juan , Figueiredo Duarte D. , Köhler Claudia
Published: April 2019

MADS-box transcription factors are ubiquitous in eukaryotic organisms and play major roles during plant development. Nevertheless, their function in seed development remains largely unknown. Here we show that the imprinted Arabidopsis thaliana MADS-box TF PHERES1 (PHE1) is a master regulator of paternally expressed imprinted genes, as well as of non-imprinted key regulators of endosperm development. PHE1 binding sites show distinct epigenetic modifications on maternal and paternal alleles, correlating with parental-specific transcriptional activity. Importantly, we show that the CArG-box-like DNA-binding motifs bound by PHE1 have been distributed by RC/Helitron transposable elements. Our data provide an example of molecular domestication of these elements, which by distributing PHE1 binding sites throughout the genome, have facilitated the recruitment of crucial endosperm regulators into a single transcriptional network.
Genetic analysis of the transition from wild to domesticated cotton (G. hirsutumL.)
Authors: Grover Corrinne E. , Yoo Mi-Jeong , Lin Meng , Murphy Matthew D. , Harker David B. , Byers Robert L. , Lipka Alexander E. , Hu Guanjing , Yuan Daojun , Conover Justin L. , Udall Joshua A. , Paterson Andrew H. , Gore Michael A. , Wendel Jonathan F.
Published: April 2019

The evolution and domestication of cotton is of great interest from both economic and evolutionary standpoints. Although many genetic and genomic resources have been generated for cotton, the genetic underpinnings of the transition from wild to domesticated cotton remain poorly known. Here we generated an intraspecific QTL mapping population specifically targeting domesticated cotton phenotypes. We used 466 F2individuals derived from an intraspecific cross between the wildGossypium hirsutumvar.yucatanense(TX2094) and the elite cultivarG. hirsutumcv. Acala Maxxa, in two environments, to identify 120 QTL associated with phenotypic changes under domestication. While the number of QTL recovered in each subpopulation was similar, only 22 QTL were considered coincident (i.e., shared) between the two locations, eight of which shared peak markers. Although approximately half of QTL were located in the A-subgenome, many key fiber QTL were detected in the D-subgenome, which was derived from a species with unspinnable fiber. We found that many QTL are environment-specific, with few shared between the two environments, indicating that QTL associated withG. hirsutumdomestication are genomically clustered but environmentally labile. Possible candidate genes were recovered and are discussed in the context of the phenotype. We conclude that the evolutionary forces that shape intraspecific divergence and domestication in cotton are complex, and that phenotypic transformations likely involved multiple interacting and environmentally responsive factors.

An F2population between wild and domesticated cotton was used to identify QTL associated with selection under domestication. Multiple traits characterizing domesticated cotton were evaluated, and candidate genes underlying QTL are described for all traits. QTL are unevenly distributed between subgenomes of the domesticated polyploid, with many fiber QTL located on the genome derived from the D parent, which does not have spinnable fiber, but a majority of QTL overall located on the A subgenome. QTL are many (120) and environmentally labile. These data, together with candidate gene analyses, suggest recruitment of many environmentally responsive factors during cotton domestication.