bluuebunny/crossref_metadata_2025 huggingface dataset:
Holographic sol–gel monoliths: optical properties and application for humidity sensing
Authors: Ilatovskii Daniil A. , Milichko Valentin , Vinogradov Alexander V. , Vinogradov Vladimir V.
Published: May 2018

Sol–gel monoliths based on SiO2, TiO2and ZrO2with holographic colourful diffraction on their surfaces were obtained via a sol–gel synthesis and soft lithography combined method. The production was carried out without any additional equipment at near room temperature and atmospheric pressure. The accurately replicated wavy structure with nanoscale size of material particles yields holographic effect and its visibility strongly depends on refractive index (RI) of materials. Addition of multi-walled carbon nanotubes (MWCNTs) in systems increases their RI and lends absorbing properties due to extremely high light absorption constant. Further prospective and intriguing applications based on the most successful samples, MWCNTs-doped titania, were investigated as reversible optical humidity sensor. Owing to such property as reversible resuspension of TiO2nanoparticles while interacting with water, it was proved that holographic xerogels can repeatedly act as humidity sensors. Materials which can be applied as humidity sensors in dependence on holographic response were discovered for the first time.
Screening for 15 pathogenic viruses in human cell lines registered at the JCRB Cell Bank: characterization of
in vitro
human cells by viral infection
Authors: Shioda Setsuko , Kasai Fumio , Watanabe Ken , Kawakami Kohei , Ohtani Azusa , Iemura Masashi , Ozawa Midori , Arakawa Akemi , Hirayama Noriko , Kawaguchi Eiko , Tano Tomoko , Miyata Sayaka , Satoh Motonobu , Shimizu Norio , Kohara Arihiro
Published: May 2018

Human cell lines have been used in a variety of research fields as an
in vitro
model. These cells are all derived from human tissue samples, thus there is a possibility of virus infection. Virus tests are routinely performed in clinical practice, but are limited in cell lines. In this study, we investigated 15 kinds of viruses in 844 human cell lines registered at the Japanese Collection of Research Bioresources (JCRB) Cell Bank. Our real-time PCR analysis revealed that six viruses, EBV, HTLV-1, HBV, B19V, HHV-6 and HHV-7, were detected in 43 cell lines. Of them, 20 cell lines were transformed by intentional infection
in vitro
with EBV or HTLV-1. Viruses in the other 23 cell lines and one EBV transformed cell line are derived from an
in vivo
infection, including five de novo identifications of EBV, B19V or HHV-7 carriers. Among them, 17 cell lines were established from patients diagnosed with virus-associated diseases. However, the other seven cell lines originated from
in vivo
cells unrelated to disease or cellular tropism. Our approach to screen for a set of 15 viruses in each cell line has worked efficiently to identify these rare cases. Virus tests in cell lines contribute not only to safety assessments but also to investigation of
in vivo
viral infection which can be a characteristic feature of cell lines.
Fabrication and characterization of Ni-decorated h-BN powders with ChCl-EG ionic liquid as addition by electroless deposition
Authors: Yang Qionglian , Ru Juanjian , Song Peng , Hu Mingyu , Feng Jing
Published: May 2018

Ni-decorated h-BN powders are fabricated with ChCl-EG as additive via electroless plating in the paper. As comparison, the different additive concentration of choline chloride-ethylene glycol (ChCl-EG) ionic liquid (0 g l
−1
, 30 g l
−1
, 60 g l
−1
, 90 g l
−1
) is presented. The effects of ChCl-EG concentration are studied, including the surface morphologies, phase analysis of Ni-decorated h-BN powders and the residual Ni
2+
concentration is measured in electroless plating bath. It is demonstrated that the deposition phenomena of nickel particles on h-BN surface is changed with the addition of ChCl-EG. When the concentration of ChCl-EG is 30 g l
−1
, the Ni particles on h-BN surface are in dispersed and spheroid state with the average size of 10–1000 nm. It can be found that 30 g l
−1
ChCl-EG is conducive to the arise of deposition phenomena, which is the formation of the single nickel particle on h-BN surface. Besides, more Ni particles are deposited on h-BN surface with the increase of nickel plating times, which is characterized with scanning electron microscope and transmission electron microscope. Furthermore, the deposition phenomenon and growth mechanism are proposed without and with ChCl-EG as additive to further elaborate the formation of Ni particles on h-BN surface.
BGEN: a binary file format for imputed genotype and haplotype data
Authors: Band Gavin , Marchini Jonathan
Published: April 2018

The impact of modern technology on genetic epidemiology has been significant, with studies comprising millions of individuals assessed at tens of millions of genetic variants now becoming common. Studies on this scale provide logistical and analytic challenges starting with the issue of efficiently storing, transmitting, and accessing underlying data. Here we present a binary file format (the BGEN format) that can store both directly-typed and statistically imputed genotype data, and achieves substantial space savings by data compression and the use of an efficient representation for probabilities. We investigate the properties of this format using imputed data from the UK BiLEVE study, demonstrating both storage efficiency, and fast data loading performance on the order of hundreds of millions of imputed genotypes per second. To make using BGEN as easy as possible, we provide a detailed specification and a freely available reference implementation, and we leverage this by developing additional tools including an indexing tool (bgenix) and an R package (rbgen) that permits loading of BGEN-encoded data into the R statistical programming environment. The UK Biobank is one of a number of projects that have used BGEN for release of imputed data, and we expect the format to continue to be widely implemented and used.
A novel multi-perspective imaging platform (M-PIP) for phenotyping soybean root crowns in the field increases throughput and separation ability of genotype root properties
Authors: Seethepalli Anand , York Larry M. , Almtarfi Hussien , Fritschi Felix B. , Zare Alina
Published: May 2018

Background

Root crown phenotyping has linked root properties to shoot mass, nutrient uptake, and yield in the field, which increases the understanding of soil resource acquisition and presents opportunities for breeding. The original methods using manual measurements have been largely supplanted by image-based approaches. However, most image-based systems have been limited to one or two perspectives and rely on segmentation from grayscale images. An efficient high-throughput root crown phenotyping system is introduced that takes images from five perspectives simultaneously, constituting the Multi-Perspective Imaging Platform (M-PIP). A segmentation procedure using the Expectation-Maximization Gaussian Mixture Model (EM-GMM) algorithm was developed to distinguish plant root pixels from background pixels in color images and using hardware acceleration (CPU and GPU). Phenes were extracted using MatLab scripts. Placement of excavated root crowns for image acquisition was standardized and is ergonomic. The M-PIP was tested on 24 soybean [Glycine max (L.) Merr.] cultivars released between 1930 and 2005.

Results

Relative to previous reports of imaging throughput, this system provides greater throughput with sustained rates of 1.66 root crowns min-1. The EM-GMM segmentation algorithm with hardware acceleration was able to segment images in 10 s, faster than previous methods, and the output images were consistently better connected with less loss of fine detail. Image-based phenes had similar heritabilities as manual measures with the greatest effect sizes observed for Maximum Radius and Fine Radius Frequency. Correlations were also noted, especially among the manual Complexity score and phenes such as number of roots and Total Root Length. Averaging phenes across perspectives generally increased heritability, and no single perspective consistently performed better than others. Angle-based phenes, Fineness Index, Maximum Width, Holes, Solidity and Width-to-Depth Ratio were the most sensitive to perspective with decreased correlations among perspectives.

Conclusion

The substantial heritabilities measured for many phenes suggest that they are potentially useful for breeding. Multiple perspectives together often produced the greatest heritabilities, and no single perspective consistently performed better than others. Thus, as illustrated here for soybean, multiple perspectives may be beneficial for root crown phenotyping systems. This system can contribute to breeding efforts that incorporate under-utilized root phenotypes to increase food security and sustainability.
Identifying high-priority proteins across the human diseasome using semantic similarity
Authors: Lau Edward , Venkatraman Vidya , Thomas Cody T , Van Eyk Jennifer E , Lam Maggie PY
Published: April 2018

Knowledge of “popular proteins” has been a focus of multiple Human Proteome Organization (HUPO) initiatives and can guide the development of proteomics assays targeting important disease pathways. We report here an updated method to identify prioritized protein lists from the research literature, and apply it to catalog lists of important proteins across multiple cell types, sub-anatomical regions, and disease phenotypes of interest. We provide a systematic collection of popular proteins across 10,129 human diseases as defined by the Disease Ontology, 10,642 disease phenotypes defined by Human Phenotype Ontology, and 2,370 cellular pathways defined by Pathway Ontology. This strategy allows instant retrieval of popular proteins across the human “diseasome”, and further allows reverse queries from protein to disease, enabling functional analysis of experimental protein lists using bibliometric annotations.
Interdependence of EGFR with PTPs on juxtaposed membranes generates a growth factor sensing and responding network
Authors: Stanoev Angel , Mhamane Amit , Schuermann Klaus C. , Grecco Hernán E. , Stallaert Wayne , Baumdick Martin , Brüggemann Yannick , Joshi Maitreyi S. , Roda-Navarro Pedro , Fengler Sven , Stockert Rabea , Roßmannek Lisaweta , Luig Jutta , Koseska Aneta , Bastiaens Philippe I. H.
Published: April 2018

The proto-oncogenic epidermal growth factor receptor (EGFR) is a tyrosine kinase whose sensitivity to growth factors (GFs) and signal duration determines cellular behavior. We resolve how EGFR’s response to epidermal growth factor (EGF) originates from dynamically established recursive interactions with spatially organized protein tyrosine phosphatases (PTPs). Opposed genetic PTP perturbations enabled identification of receptor-like PTPRG/J at the plasma membrane (PM) and endoplasmic reticulum (ER) associated PTPN2 as the major EGFR dephosphorylating activities. Imaging spatial-temporal PTP reactivity then revealed that vesicular trafficking establishes a spatially-distributed negative feedback with PTPN2 that determines signal duration, whereas single cell dose-response analysis uncovered a ROS-mediated toggle switch between autocatalytically activated monomeric EGFR and the tumor suppressor PTPRG that governs EGFR’s sensitivity to EGF. Vesicular recycling of monomeric EGFR unifies the interactions with these PTPs on juxtaposed membranes, dynamically generating a network architecture that can sense and respond to time varying growth factor signals.
Detection of succinate by intestinal tuft cells triggers a type 2 innate immune circuit
Authors: Nadjsombati Marija S. , McGinty John W. , Lyons-Cohen Miranda R. , Pollack Joshua L. , Gowda G.A. Nagana , Erle David J. , Locksley Richard M. , Raftery Daniel , von Moltke Jakob
Published: April 2018

Initiation of immune responses requires innate immune sensing, but immune detection of the helminths, protists, and allergens that stimulate type 2 immunity remains poorly understood. In the small intestine, type 2 immune responses are regulated by a tuft cell-ILC2 signaling circuit. Tuft cells express components of a canonical taste transduction pathway, including the membrane channel TRPM5, but the ligands and receptors that activate tuft cells in the small intestine are unknown. Here we identify succinate as the first ligand that activates intestinal tuft cells to initiate type 2 immune responses. Using mRNA-Seq on tuft cells from different tissues, we show that all tuft cells express the intracellular taste transduction pathway, but expression of upstream receptors is tissue-specific. In the small intestine, tuft cells express the succinate receptor SUCNR1. Remarkably, providing succinate in drinking water is sufficient to induce a multifaceted type 2 immune response in the murine small intestine, involving all known components of the tuft-ILC2 circuit. The helminthNippostrongylus brasiliensissecretes succinate as a metabolite, and sensing of both succinate andN. brasiliensisrequires tuft cells and TRPM5, suggesting a novel paradigm in which type 2 immunity monitors microbial metabolism. Manipulation of succinate sensing may have therapeutic benefit in numerous intestinal diseases.
Cargo-Loading of Misfolded Proteins into Extracellular Vesicles: The CSPα-EV Export Pathway
Authors: Pink Desmond , Donnelier Julien , Lewis John , Braun Janice E.A.
Published: April 2018

Extracellular vesicles (EVs) are secreted vesicles of diverse size and cargo that are implicated in the cell-to-cell transmission of disease-causing-proteins in several neurodegenerative diseases. Mutant huntingtin, the disease-causing entity in Huntington’s disease, has an expanded polyglutamine track at the N terminus that causes the protein to misfold and form toxic intracellular aggregates. In Huntington’s disease, mutant huntingtin aggregates are transferred between cells by an unknown route. We have previously identified a cellular pathway that is responsible for the export of mutant huntingtin via extracellular vesicles, given the heterogeneity of EVs, here we examine the specific EVs involved. In this work we expressed a form of polyglutamine expanded huntingtin (GFP-tagged 72Qhuntingtinexon1) in cells to assess the EVs involved in cellular export. We demonstrate that the molecular chaperone, cysteine string protein (CSPα; DnaJC5), mediates export of disease-causing-polyglutamine-expanded huntingtin cargo via two distinct vesicle populations of 180-240nm and 15-30μm. In doing so, our data links the molecular chaperone, CSPα, and the packaging of pathogenic misfolded huntingtin into two separate extracellular vesicles pathways.
Human 5′ UTR design and variant effect prediction from a massively parallel translation assay
Authors: Sample Paul J. , Wang Ban , Reid David W. , Presnyak Vlad , McFadyen Iain , Morris David R. , Seelig Georg
Published: April 2018

Predicting the impact of cis-regulatory sequence on gene expression is a foundational challenge for biology. We combine polysome profiling of hundreds of thousands of randomized 5′ UTRs with deep learning to build a predictive model that relates human 5′ UTR sequence to translation. Together with a genetic algorithm, we use the model to engineer new 5′ UTRs that accurately target specified levels of ribosome loading, providing the ability to tune sequences for optimal protein expression. We show that the same approach can be extended to chemically modified RNA, an important feature for applications in mRNA therapeutics and synthetic biology. We test 35,000 truncated human 5′ UTRs and 3,577 naturally-occurring variants and show that the model accurately predicts ribosome loading of these sequences. Finally, we provide evidence of 47 SNVs associated with human diseases that cause a significant change in ribosome loading and thus a plausible molecular basis for disease.
Optimizing the identification of causal variants across varying genetic architectures in crops
Authors: Miao Chenyong , Yang Jinliang , Schnable James C.
Published: April 2018

Background

Association studies use statistical links between genetic markers and variation in a phenotype’s value across many individuals to identify genes controlling variation in the target phenotype. However, this approach, particularly conducted on a genome-wide scale (GWAS), has limited power to identify the genes responsible for variation in traits controlled by complex genetic architectures.

Results

Here we employ simulation studies utilizing real-world genotype datasets from association populations in four species with distinct minor allele frequency distributions, population structures, and patterns linkage disequilibrium to evaluate the impact of variation in both heritability and trait complexity on both conventional mixed linear model based GWAS and two new approaches specifically developed for complex traits. Mixed linear model based GWAS rapidly losses power for more complex traits. FarmCPU, a method based on multi-locus mixed linear models, provides the greatest statistical power for moderately complex traits. A Bayesian approach adopted from genomic prediction provides the greatest statistical power to identify causal genetic loci for extremely complex traits.

Conclusions

Using estimates of the complexity of the genetic architecture of target traits can guide the selection of appropriate statistical methods and improve the overall accuracy and power of GWAS.
U1 snRNP regulates chromatin retention of noncoding RNAs
Authors: Yin Yafei , Yuyang Lu J. , Zhang Xuechun , Shao Wen , Xu Yanhui , Li Pan , Hong Yantao , Zhang Qiangfeng Cliff , Shen Xiaohua
Published: April 2018

Thousands of noncoding transcripts exist in mammalian genomes, and they preferentially localize to chromatin. Here, to identify cis-regulatory elements that control RNA-chromatin association, we developed a high-throughput method named RNA element for subcellular localization by sequencing (REL-seq). Coupling REL-seq with random mutagenesis (mutREL-seq), we discovered a key 7-nt U1 recognition motif in chromatin-enriched RNA elements. Reporter assays indicated a direct role for U1 snRNP recognition in regulating RNA-chromatin localization. Globally, U1 motifs and U1 binding are strongly enriched in long noncoding RNA (lncRNA) transcripts. Inhibition of U1 snRNA, and of U2 to a lesser degree, led to global reduction in chromatin association of hundreds of lncRNAs. For promoter- and enhancer-associated noncoding RNAs, U1 binds to their genomic neighborhoods, and their chromatin association depends on both U1 and U2 snRNAs. These findings reveal that U1 snRNP, perhaps together with the splicing machinery, acts widely to promote the chromatin association of noncoding transcripts.
The MarR Family Regulator BmrR is involved in Bile Tolerance ofBifidobacterium longumBBMN68 via Controlling the Expression of an ABC-Transporter
Authors: Xu Qi , Zhai Zhengyuan , An Haoran , Yang Yang , Yin Jia , Wang Guohong , Ren Fazheng , Hao Yanling
Published: April 2018

In order to colonize the human gastrointestinal tract and exert their beneficial effects, bifidobacteria must effectively cope with the toxic bile salts in the intestine, but the molecular mechanism underlying bile tolerance is poorly understood. In this study, heterologous expression of a MarR family transcriptional regulator BmrR significantly reduced ox-bile resistance ofLactococcus lactisNZ9000, suggesting that it might play a role in bile stress response.In silicoanalysis combined with RT-PCR assay demonstrated thatbmrRwas co-transcribed withbmrAandbmrB,which encoded multidrug resistance (MDR) ABC transporters. Promoter prediction and EMSA assay revealed that BmrR could autoregulate thebmrRABoperon by binding tobmrbox (ATTGTTG-6nt-CAACAAT) in the promoter region. Moreover, heterologous expression ofbmrAandbmrBinL. lactisshowed 20.77-fold higher tolerance to 0.10% ox-bile compared to wild type strain. In addition, ox-bile could disrupt the DNA binding activity of BmrR as a ligand. Taken together, our findings indicate thatbmrRABoperon is autoregulated by transcriptional regulator BmrR and ox-bile serves as an inducer to activate the bile efflux transporter BmrAB in response to bile stress inB. longumBBMN68.

Importance

Bifidobacteria are natural inhabitants of the human intestinal tract. Some bifidobacterial strains are used as probiotics in fermented dairy production because of their health-promoting effects. Following consumption, bifidobacteria finally colonize the lower intestinal tract where the concentration of bile salts remains nearly 0.05% to 2.0%. Bile salts as detergent-like antimicrobial compounds can cause disruption of the cellular membrane, protein misfolding and DNA damage. Therefore, tolerance to physiological bile stress is indeed essential for bifidobacteria to survive and exert the probiotic effects in gastrointestinal tract. InB. longumBBMN68, the MarR-type regulator BmrR was involved in bile stress response by auto-regulatingbmrRABoperon and ox-bile as an inducer could increase the expression of BmrAB transporter to enhance the bile tolerance of BBMN68.This is the first report about functional analysis ofbmrRABoperon in bile stress response, which will provide new insight into bile tolerance mechanisms inBifidobacteriumand other bacteria.
Forces on nascent polypeptides during membrane insertion and translocation via the Sec translocon
Authors: Niesen Michiel J.M. , Müller-Lucks Annika , Hedman Rickard , von Heijne Gunnar , Miller Thomas F.
Published: April 2018

During ribosomal translation, nascent polypeptide chains (NCs) undergo a variety of physical processes that determine their fate in the cell. Translation arrest peptide (AP) experiments are used to measure the external pulling forces that are exerted on the NC at different lengths during translation. To elucidate the molecular origins of these forces, a recently developed coarsegrained molecular dynamics (CGMD) is used to directly simulate the observed pulling-force profiles, thereby disentangling contributions from NC-translocon and NC-ribosome interactions, membrane partitioning, and electrostatic coupling to the membrane potential. This combination of experiment and theory reveals mechanistic features of Sec-facilitated membrane integration and protein translocation, including the interplay between transient interactions and conformational changes that occur during ribosomal translation to govern protein biogenesis.
Anthropogenic habitat alteration leads to rapid loss of adaptive variation and restoration potential in wild salmon populations
Authors: Thompson Tasha Q. , Bellinger Renee M. , O’Rourke Sean M. , Prince Daniel J. , Stevenson Alexander E. , Rodrigues Antonia T. , Sloat Matthew R. , Speller Camilla F. , Yang Dongya Y. , Butler Virginia L. , Banks Michael A. , Miller Michael R.
Published: April 2018

Phenotypic variation is critical for the long-term persistence of species and populations. Anthropogenic activities have caused substantial shifts and reductions in phenotypic variation across diverse taxa, but the underlying mechanism (i.e., phenotypic plasticity and/or genetic evolution) and potential to recover previous phenotypic characteristics are unclear. Here we investigate changes in adult migration characteristics of wild salmon populations caused by dam construction and other anthropogenic habitat modifications. Strikingly, we find that dramatic allele frequency change (i.e., genetic evolution) from strong selection at a single locus explains the rapid phenotypic shift observed after recent dam construction. Furthermore, ancient DNA analysis confirms the abundance of a specific allele associated with adult migration type in historical habitat that will soon become accessible through a large restoration (i.e., dam removal) project. However, analysis of contemporary samples suggests the restoration will be challenged by loss of the allele from potential source populations. These results highlight the need to conserve and restore critical adaptive variation before the potential for recovery is lost.
Genome-wide DNA methylation patterns in Autism Spectrum Disorder and mitochondrial function
Authors: Stathopoulos Sofia , Gaujoux Renaud , O’Ryan Colleen
Published: April 2018

Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterised by phenotypic heterogeneity and overlapping co-morbidities. The genetic architecture of ASD is complex, with 100’s of risk genes cumulatively contributing to the aetiology of ASD. Epigenetic mechanisms, particularly DNA methylation, have been associated with ASD. The vast majority of ASD molecular research has focused on Northern European populations, with a paucity of data from Africa. This study examines genome-wide DNA methylation patterns in a novel cohort of South African children with ASD and matched, unrelated controls. We performed a whole-genome DNA methylation screen using the Illumina 450K Human Methylation Array. We identify differentially methylated loci associated with ASD across 898 genes (p-value ≤ 0.05). Using a pathway analysis framework, we find nine enriched canonical pathways implicating 32 of the significant genes in our ASD cohort. These pathways converge on two crucial biological processes: mitochondrial metabolism and protein ubiquitination, both hallmarks of mitochondrial function. The involvement of mitochondrial function in ASD aetiology is in line with the recently reported transcriptomic dysregulation associated with the disorder. The differentially methylated genes in our cohort overlap with the gene co-expression modules identified in brain tissue from five major neurological disorders, including ASD. We find significant enrichment of three gene modules, two of which are classified as Mitochondrial and were significantly downregulated in ASD brains. Furthermore, we find significant overlap between differentially methylated and differentially expressed genes from our dataset with a RNA seq dataset from ASD brain tissue. This overlap is particularly significant across the Occipital brain region (padj= 0.0002) which has known association to ASD. Our differential methylation data recapitulate the expression differences of genes and co-expression module functions observed in ASD brain tissue which is consistent with a central role for DNA-methylation leading to mitochondrial dysfunction in the aetiology of ASD.
A Monte Carlo method forin silicomodeling and visualization of Waddington’s epigenetic landscape with intermediate details
Authors: Zhang Xiaomeng , Chong Ket Hing , Zheng Jie
Published: April 2018

Waddington’s epigenetic landscape is a classic metaphor for describing the cellular dynamics during the development modulated by gene regulation. Quantifying Waddington’s epigenetic landscape by mathematical modeling would be useful for understanding the mechanisms of cell fate determination. A few computational methods have been proposed for quantitative modeling of landscape; however, to model and visualize the landscape of a high dimensional gene regulatory system with realistic details is still challenging. Here, we propose a Monte Carlo method for modeling the Waddington’s epigenetic landscape of a gene regulatory network (GRN). The method estimates the probability distribution of cellular states by collecting a large number of time-course simulations with random initial conditions. By projecting all the trajectories into a 2-dimensional plane of dimensionsiandj, we can approximately calculate the quasi-potentialU(xi,xj) = −lnP(xi,xj), whereP(xi,xj) is the estimated probability of an equilibrium steady state or a non-equilibrium state. A state with locally maximal probability corresponds to a locally minimal potential and such a state is called an attractor. Compared to the state-of-the-art methods, our Monte Carlo method can quantify the global potential landscape (or emergence behavior) of GRN for a high dimensional system. The same topography of landscape can be produced from deterministic or stochastic time-course simulations. The potential landscapes show that not only attractors represent stability, but the paths between attractors are also part of the stability or robustness of biological systems. We demonstrate the novelty and reliability of our method by plotting the potential landscapes of a few published models of GRN. Besides GRN-driven landscapes of cellular dynamics, the algorithm proposed can also be applied to studies of global dynamics (or emergence behavior) of other dynamical systems.
Bracketing phenotypic limits of mammalian hybridization
Authors: Savriama Yoland , Valtonen Mia , Kammonen Juhana , Rastas Pasi , Smolander Olli-Pekka , Lyyski Annina , Häkkinen Teemu J. , Corfe Ian J. , Gerber Sylvain , Salazar-Ciudad Isaac , Paulin Lars , Holm Liisa , Löytynoja Ari , Auvinen Petri , Jernvall Jukka
Published: April 2018

An increasing number of mammalian species have been shown to have a history of hybridization and introgression based on genetic analyses. Only relatively few fossils, however, preserve genetic material and morphology must be used to identify the species and determine whether morphologically intermediate fossils could represent hybrids. Because dental and cranial fossils are typically the key body parts studied in mammalian paleontology, here we bracket the potential for phenotypically extreme hybridizations by examining uniquely preserved cranio-dental material of a captive hybrid between gray and ringed seals. We analyzed how distinct these species are genetically and morphologically, how easy it is to identify the hybrids using morphology, and whether comparable hybridizations happen in the wild. We show that the genetic distance between these species is more than twice the modern human-Neanderthal distance, but still within that of morphologically similar species-pairs known to hybridize. In contrast, morphological and developmental analyses show gray and ringed seals to be highly disparate, and that the hybrid is a predictable intermediate. Genetic analyses of the parent populations reveal introgression in the wild, suggesting that gray-ringed seal hybridization is not limited to captivity. Taken together, gray and ringed seals appear to be in an adaptive radiation phase of evolution, showing large morphological differences relative to their comparatively modest genetic distance. Because morphological similarity does not always correlate with genetic distance in nature, we postulate that there is considerable potential for mammalian hybridization between phenotypically disparate taxa.
Exome sequencing in families with severe mental illness identifies novel and rare variants in genes implicated in Mendelian neuropsychiatric syndromes
Authors: Ganesh Suhas , Husayn Ahmed P , Nadella Ravi Kumar , More Ravi Prabhakar , Sheshadri Manasa , Viswanath Biju , Rao Mahendra , Jain Sanjeev ,   The ADBS consortium, Mukherjee Odity
Published: April 2018

Introduction

Severe Mental Illnesses (SMI), such as bipolar disorder and schizophrenia, are highly heritable, and have a complex pattern of inheritance. Genome wide association studies detect a part of the heritability, which can be attributed to common genetic variation. Examination of rare variants with Next Generation Sequencing (NGS) may add to the understanding of genetic architecture of SMIs.

Methods

We analyzed 32 ill subjects (with diagnosis of Bipolar Disorder, n=26; schizophrenia, n=4; schizoaffective disorder, n=1 schizophrenia like psychosis, n=1) from 8 multiplex families; and 33 healthy individuals by whole exome sequencing. Prioritized variants were selected by a 4-step filtering process, which included deleteriousness by 5 in silico algorithms; sharing within families, absence in the controls and rarity in South Asian sample of Exome Aggregation Consortium.

Results

We identified a total of 42 unique rare, non-synonymous deleterious variants in this study with an average of 5 variants per family. None of the variants were shared across families, indicating a ‘private’ mutational profile. Twenty (47.6%) of the variant harboring genes identified in this sample have been previously reported to contribute to the risk of neuropsychiatric syndromes. These include genes which are related to neurodevelopmental processes, or have been implicated in different monogenic syndromes with a severe neurodevelopmental phenotype.

Conclusion

NGS approaches in family based studies are useful to identify novel and rare variants in genes for complex disorders like SMI. The study further validates the phenotypic burden of rare variants in Mendelian disease genes, indicating pleiotropic effects in the etiology of severe mental illnesses.
ovoDco-selection: a method for enriching CRISPR/Cas9-edited alleles inDrosophila
Authors: Ewen-Campen Ben , Perrimon Norbert
Published: April 2018

Screening for successful CRISPR/Cas9 editing events remains a time consuming technical bottleneck in the field ofDrosophilagenome editing. This step can be particularly laborious for events that do not cause a visible phenotype, or those which occur at relatively low frequency. A promising strategy to enrich for desired CRISPR events is to co-select for an independent CRISPR event that produces an easily detectable phenotype. Here, we describe a simple negative co-selection strategy involving CRISPR-editing of a dominant female sterile allele,ovoD1. In this system (“ovoDco-selection”), the only functional germ cells in injected females are those that have been edited at theovoD1locus, and thus 100% of the offspring of these flies have undergone editing of at least one locus. We demonstrate thatovoDco-selection can be used to enrich for knock-out mutagenesis via nonhomologous end-joining (NHEJ), and for knock-in alleles via homology-directed repair (HDR). Altogether, our results demonstrate thatovoDco-selection reduces the amount of screening necessary to isolate desired CRISPR events inDrosophila.
Distinct ‘pattern of autofluorescence’ of acute ischemic stroke patients’ skin and fingernails: A novel diagnostic biomarker for acute ischemic stroke
Authors: Wu Danhong , Zhang Mingchao , Tao Yue , Yu Haibo , Li Yujia , Zhang Shufan , Chu Tianqing , Zou Xiaofeng , Chen Xin , Ying Weihai
Published: April 2018

Abstract

Early and economical diagnosis of acute ischemic stroke (AIS) is pivotal for therapeutic efficacy, particularly for the settings where medical imaging resource is deficient. We have obtained evidence supporting our hypothesis that collective properties of the green autofluorescence (AF) of the fingernails and certain skin’s positions may be a novel diagnostic biomarker for AIS: Both the green AF intensity and AF asymmetry of the AIS patients in their Index Fingernails and most examined skin’s positions were significantly higher than that of the healthy subjects and the Non-AIS subjects. ROC analyses and machine learning-based analyses on the AF properties showed that AUC was 0.93 and 0.87, respectively, for differentiating the AIS patients from the healthy subjects and for differentiating the AIS patients from the Non-AIS subjects. The AIS patients had significantly higher AF intensity and AF asymmetry at several examined positions, compared to those of the patients of Parkinson’s disease, pulmonary infection and transient ischemic attack. The AUC was 0.79 – 0.88 for differentiating AIS patients from each of these diseases. There was evidence suggesting that the AF originates from keratins. Collectively, our study has indicated that the characteristic AIS’s ‘Pattern of AF’ is a novel diagnostic biomarker for the disease. The ‘Pattern of AF Technology’ holds excellent potential to become a new non-invasive, label-free and economical diagnostic approach for AIS, which is particularly valuable when MRI or CT imaging resource is deficient.
Optical alignment device for two-photon microscopy
Authors: Galiñanes Gregorio L. , Marchand Paul J. , Turcotte Raphaёl , Pellat Sebastien , Ji Na , Huber Daniel
Published: May 2018

Two-photon excitation fluorescence microscopy has revolutionized our understanding of brain structure and function through the high resolution and large penetration depth it offers. Investigating neural structures in vivo requires gaining optical access to the brain, which is typically achieved by replacing a part of the skull with one or several layers of cover glass windows. To compensate for the spherical aberrations caused by the presence of these layers of glass, collar-correction objectives are typically used. However, the efficiency of this correction has been shown to depend significantly on the tilt angle between the glass window surface and the optical axis of the imaging system. Here we expand these observations and characterize the effect of the tilt angle on the collected fluorescence signal with thicker windows (double cover glass) and compare these results with an objective devoid of collar-correction. Finally, we present a simple optical alignment device designed to rapidly minimize the tilt angle in vivo and align the optical axis of the microscope perpendicularly to the glass window, thereby significantly improving the imaging quality. The performance of the device is demonstrated in an in vivo setting and a tilt-correction procedure is described, enabling the accurate alignment (<0.2°) of the cover glass with the imaging plane in only few iterations.
Minor sequence modifications in temporin B cause drastic changes in antibacterial potency and selectivity by fundamentally altering membrane activity
Authors: Manzo Giorgia , Ferguson Philip M. , Gustilo V. Benjamin , Bui Tam T. , Drake Alex F. , Atkinson R. Andrew , Batoni Giovanna , Lorenz Christian D. , Phoenix David A. , Mason A. James
Published: May 2018

Antimicrobial peptides (AMPs) are a potential source of new molecules to counter the increase in antimicrobial resistant infections but a better understanding of their properties is required to understand their native function and for effective translation as therapeutics. Details of the mechanism of their interaction with the bacterial plasma membrane are desired since damage or penetration of this structure is considered essential for AMP activity. Relatively modest modifications to AMP primary sequence can induce substantial changes in potency and/or spectrum of activity but, hitherto, have not been predicted to substantially alter the mechanism of interaction with the bacterial plasma membrane. Here we use a combination of molecular dynamics simulations, circular dichroism, solid-state NMR and patch clamp to investigate the extent to which temporin B and its analogues can be distinguished both in vitro and in silico on the basis of their interactions with model membranes. Enhancing the hydrophobicity of the N-terminus and cationicity of the C-terminus in temporin B improves its membrane activity and potency against both Gram-negative and Gram-positive bacteria. In contrast, enhancing the cationicity of the N-terminus abrogates its ability to trigger channel conductance and renders it ineffective against Staphylococcus aureus while nevertheless enhancing its potency against Escherichia coli. Our findings suggest even closely related AMPs may target the same bacterium with fundamentally differing mechanisms of action.
PLK4 is a microtubule-associated protein that self assembles promoting de novo MTOC formation
Authors: Gouveia Susana Montenegro , Zitouni Sihem , Kong Dong , Duarte Paulo , Gomes Beatriz Ferreira , Sousa Ana Laura , Tranfield Erin M. , Hyman Antony , Loncarek Jadranka , Bettencourt-Dias Monica
Published: May 2018

Summary statement

PLK4 binds to microtubules and self assembles into supramolecular assemblies that recruit tubulin and trigger de novo MTOC formation in Xenopus laevis extracts.

The centrosome is an important microtubule-organizing center (MTOCs) in animal cells and it consists of two barrel-shaped structures (centrioles), surrounded by the pericentriolar material (PCM), which nucleates microtubules. PCM components form condensates, supramolecular assemblies that concentrate microtubule nucleators. Centrosomes can form close to an existing structure (canonical duplication) or de novo. How centrosomes form de novo is not known. PLK4 is a master driver of centrosome biogenesis, which is critical to recruit several centriole components. Here, we investigate the beginning of centrosome biogenesis, taking advantage of Xenopus egg extracts, where we and others have shown that PLK4 can induce de novo MTOC formation (Eckerdt et al., 2011; Zitouni et al., 2016). Surprisingly, we observe that in vitro, PLK4 can self-assemble into supramolecular assemblies that recruit α/β-tubulin. In Xenopus extracts, PLK4 supramolecular assemblies additionally recruit the PLK4 substrate STIL and the microtubule nucleator, γ-tubulin, and form acentriolar MTOCs de novo. The assembly of these robust microtubule asters is independent of dynein, similarly to centrosomes. We suggest a new mechanism of action for PLK4, where it forms a self-organizing catalytic scaffold that recruits centriole components, PCM factors and α/β-tubulin, leading to MTOC formation.
Hotspot mutations and ColE1 plasmids contribute to the fitness ofSalmonellaHeidelberg in poultry litter
Authors: Oladeinde Adelumola , Cook Kimberly , Orlek Alex , Zock Greg , Herrington Kyler , Cox Nelson , Lawrence Jodie Plumblee , Hall Carolina
Published: May 2018

Salmonella entericasubsp.entericaserovar Heidelberg (S.Heidelberg) is a clinically-important serovar linked to food-borne illness, and commonly isolated from poultry. Investigations of a large, multistate outbreak in the USA in 2013 identified poultry litter (PL) as an important extra-intestinal environment that may have selected for specificS.Heidelberg strains. Poultry litter is a mixture of bedding materials and chicken excreta that contains chicken gastrointestinal (GI) bacteria, undigested feed, feathers, and other materials of chicken origin. In this study, we performed a series of controlled laboratory experiments which assessed the microevolution of two S. Heidelberg strains (SH-2813 and SH-116) in PL previously used to raise 3 flocks of broiler chickens. The strains are closely related at the chromosome level, differing from the reference genome by 109 and 89 single nucleotide polymorphisms/InDels, respectively. Whole genome sequencing was performed on 86 isolates recovered after 0, 1, 7 and 14 days of microevolution in PL. Only strains carrying an IncX1 (37kb), 2 ColE1 (4 and 6kb) and 1 ColpVC (2kb) plasmids survived more than 7 days in PL. Competition experiments showed that carriage of these plasmids was associated with increased fitness. This increased fitness was associated with an increased copy number of IncX1 and ColE1 plasmids. Further, all Col plasmid-bearing strains had hotspot mutations in 37 loci on the chromosome and in 3 loci on the IncX1 plasmid. Additionally, we observed a decrease in susceptibility to tobramycin, kanamycin, gentamicin, neomycin and fosfomycin for Col plasmid-bearing strains. Our study demonstrates how positive selection from poultry litter can change the evolutionary path of S. Heidelberg.
Adaptation after vastus lateralis denervation in rats suggests neural regulation of joint stresses and strains
Authors: Alessando Cristiano , Rellinger Benjamin A. , Barroso Filipe O. , Tresch Matthew C.
Published: May 2018

In order to produce movements, muscles must act through joints. The translation from muscle force to limb movement is mediated by internal joint structures that permit movement in some directions but constrain it in others. Although muscle forces acting against constrained directions will not affect limb movements, such forces can cause excess stresses and strains in joint structures, leading to pain or injury. In this study, we hypothesized that the central nervous system (CNS) chooses muscle activations to avoid excess joint stresses and strains. We evaluated this hypothesis by examining adaptation strategies after selective paralysis of a muscle acting at the rat knee. We show that the CNS compromises between restoration of task performance and regulation of joint stresses and strains. These results have significant implications to our understanding of the neural control of movements, suggesting that common theories emphasizing task performance are insufficient to explain muscle activations during behaviors.
Enterococcus faecalisCRISPR-Cas is a robust barrier to conjugative antibiotic resistance dissemination in the murine intestine
Authors: Price Valerie J. , McBride Sara W. , Hullahalli Karthik , Chatterjee Anushila , Duerkop Breck A. , Palmer Kelli L.
Published: May 2018

CRISPR-Cas systems are barriers to horizontal gene transfer (HGT) in bacteria. Little is known about CRISPR-Cas interactions with conjugative plasmids, and studies investigating CRISPR-Cas/plasmid interactions inin vivomodels relevant to infectious disease are lacking. These are significant gaps in knowledge because conjugative plasmids disseminate antibiotic resistance genes among pathogensin vivo, and it is essential to identify strategies to reduce the spread of these elements. We use enterococci as models to understand the interactions of CRISPR-Cas with conjugative plasmids.Enterococcus faecalisis a native colonizer of the mammalian intestine and harbors pheromone-responsive plasmids (PRPs). PRPs mediate inter- and intraspecies transfer of antibiotic resistance genes. We assessedE. faecalisCRISPR-Cas anti-PRP activity in the mouse intestine and under varyingin vitroconditions. We observed striking differences in CRISPR-Cas efficiencyin vitroversusin vivo. With few exceptions, CRISPR-Cas blocked intestinal PRP dissemination, whilein vitro, the PRP frequently escaped CRISPR-Cas defense. Our results further the understanding of CRISPR-Cas biology by demonstrating that standardin vitroexperiments do not adequately model thein vivoanti-plasmid activity of CRISPR-Cas. Additionally, our work identifies several variables that impact the apparentin vitroanti-plasmid activity of CRISPR-Cas, including planktonic versus biofilm settings, different donor/recipient ratios, production of a plasmid-encoded bacteriocin, and the time point at which matings are sampled. Our results are clinically significant because they demonstrate that barriers to HGT encoded by normal human microbiota can have significant impacts onin vivoantibiotic resistance dissemination.

Importance

CRISPR-Cas is a type of immune system encoded by bacteria that is hypothesized to be a natural impediment to the spread of antibiotic resistance genes. In this study, we directly assessed the impact of CRISPR-Cas on antibiotic resistance dissemination in the mammalian intestine and under varyingin vitroconditions. We observed a robust effect of CRISPR-Cas onin vivobut notin vitrodissemination of antibiotic resistance plasmids in the native mammalian intestinal colonizerEnterococcus faecalis. We conclude that standard laboratory experiments currently do not appropriately model thein vivoconditions where antibiotic resistance dissemination occurs betweenE. faecalisstrains. Moreover, our results demonstrate that CRISPR-Cas encoded by native members of the mammalian intestinal microbiota can block the spread of antibiotic resistance plasmids.