bluuebunny/crossref_metadata_2025 huggingface dataset:
The Italian Autism Network (ITAN): A Resource for Molecular Genetics and Biomarker Investigations
Authors: Muglia Pierandrea , Filosi Michele , Ros Lucio Da , Kam-Thong Tony , Nardocci Franco , Trabetti Elisabetta , Ratti Emiliangelo , Rizzini Paolo , Zuddas Alessandro , Bernardina Bernardo Dalla , Domenici Enrico ,   the Italian Autism Network
Published: April 2018

Background

A substantial genetic component accounts for Autism Spectrum Disorders (ASD) aetiology, with some rare and common genetic risk factors recently identified. Large collections of DNAs from thoroughly characterized ASD families are an essential step to confirm genetic risk factors, identify new variants and investigate genotype-phenotype correlations. The Italian Autism Network aimed at constituting a clinical database and a biorepository of samples derived from ASD subjects and first-degree relatives extensively and consistently characterized by child psychiatry centers in Italy.

Methods

The study was approved by the ethical committee of the University of Verona, the coordinating site, and by the local ethical committees of each recruiting site. Certified staff was specifically trained at each site for the overall study conduct, for clinical protocol administration and handling of biological material. A centralized database was developed to collect clinical assessment and medical records from each recruiting site. Children were eligible for recruitment based on the following inclusion criteria: age 4–18 years, at least one parent or legal guardian giving voluntary written consent, meeting DSM-IV criteria for Autistic Disorder or Asperger’s Disorder or Pervasive Developmental Disorder NOS. Affected individuals were assessed by full psychiatric, neurological and physical examination, evaluation with ADI-R and ADOS scales, cognitive assessment with Wechsler Intelligence Scale for Children or Preschool and Primary, Leiter International Performance Scale or Griffiths Mental Developmental Scale. Additional evaluations included language assessment, the Krug Asperger’s Disorder Index, and instrumental examination such as EEG and structural MRI. DNA, RNA and plasma were collected from eligible individuals and relatives. A central laboratory was established to host the biorepository, perform DNA and RNA extraction and lymphocytes immortalisation.

Discussion

The study has led to an extensive collection of biological samples associated with standardised clinical assessments from a network of expert clinicians and psychologists. Eighteen sites have received ADI/ADOS training, thirteen of which have been actively recruiting. The clinical database currently includes information on 812 individuals from 249 families, and the biorepository has samples for 98% of the subjects. This effort has generated a highly valuable resource for conducting clinical and genetic research of ASD, amenable to further expansion.
Differential alteration of IL-8 in liver cancer stem cell enrichment in response to PI3K/Akt/mTOR inhibitors and sorafenib
Authors: Kahraman Deniz Cansen , Kahraman Tamer , Atalay Rengul Cetin
Published: April 2018

Liver cancer stem cells (LCSCs) are derived from damaged and transformed Hepatic progenitor cells (HPCs) during precancerous cirrhosis stage. Ras/Raf/MAPK and PI3K/AKT/mTOR signaling pathways are significantly deregulated in liver cancer. The activation of PI3K/AKT/mTOR pathway in LCSC population is one of the reasons for acquired resistance to Sorafenib in advanced Hepatocellular carcinoma (HCC) patients. Therefore, identifying novel inhibitors targeting this pathway acting on LCSCs is highly essential. We therefore elucidated the bioactivities of small molecule kinase inhibitors on LCSCs acting through PI3K/Akt/mTOR pathway in comparison with DAPT (CSC inhibitor), DNA intercalators and Sorafenib. For this purpose, CD133+/EpCAM+ cells originated from HCC cells were analyzed by flow cytometry and effective inhibitors on LCSCs were further tested for their potential combinatorial effects. Treatment of cells with Sorafenib, and DNA intercalators resulted in enrichment of CD133+/EpCAM+ cells. Yet, mTOR inhibitor Rapamycin, and Notch pathway inhibitor DAPT significantly reduced CD133/EpCAM positivity. Combination studies revealed that sequential treatment strategy, which involves treatment of cells with Rapamycin prior to Sorafenib treatment, decreased the ratio of LCSCs as opposed to Sorafenib treatment alone or Sorafenib treatment prior to Rapamycin. The effect of the inhibitors were also demonstrated with LCSC sphere formation. Additionaly, a large panel of genes involved in cancer pathways were analyzed using Nanostring®nCounter®Technology to identify the differentially expressed genes in Rapamycin, Sorafenib or DAPT treated cells. Pathways involved in stemness (Wnt and Notch pathways) were differentially regulated between Rapamycin or DAPT treated cells and Sorafenib treated cells. Interleukin 8 (IL-8), FLNC, FLNA expressions were down-regulated upon treatment with DAPT or Rapamycin, yet up-regulated upon Sorafenib treatment. Following IL-8 inhibition CD133/EpCAM positivity of cells decreased significantly, indicating that IL-8 signaling is crucial for the conservation of stemness features of cancer cells.

Conclusion

PI3K/Akt/mTOR pathway inhibitors alter hepatic CSC composition and gene expression in favor or to the detriment of cancer stem cell survival. Blockade of IL-8 signaling provides a promising therapeutic approach for prevention of LCSC enrichment.
Co-evolution networks of HIV/HCV are modular with direct association to structure and function
Authors: Quadeer Ahmed Abdul , Morales-Jimenez David , McKay Matthew R.
Published: April 2018

Mutational correlation patterns found in population-level sequence data for the Human Immunodeficiency Virus (HIV) and the Hepatitis C Virus (HCV) have been demonstrated to be informative of viral fitness. Such patterns can be seen as footprints of the intrinsic functional constraints placed on viral evolution under diverse selective pressures. Here, considering multiple HIV and HCV proteins, we demonstrate that these mutational correlations encode a modular co-evolutionary structure that is tightly linked to the structural and functional properties of the respective proteins. Specifically, by introducing a robust statistical method based on sparse principal component analysis, we identify near-disjoint sets of collectively-correlated residues (sectors) having mostly a one-to-one association to largely distinct structural or functional domains. This suggests that the distinct phenotypic properties of HIV/HCV proteins often give rise to quasi-independent modes of evolution, with each mode involving a sparse and localized network of mutational interactions. Moreover, individual inferred sectors of HIV are shown to carry immunological significance, providing insight for guiding targeted vaccine strategies.

Author summary

HIV and HCV cause devastating infectious diseases for which no functional vaccine exists. A key problem is that while immune cells may induce individual mutations that compromise viral fitness, this is typically restored through other “compensatory” mutations, leading to immune escape. These compensatory pathways are complicated and remain poorly understood. They do, however, leave co-evolutionary markers which may be inferred from measured sequence data. Here, by introducing a new robust statistical method, we demonstrated that the compensatory networks employed by both viruses exhibit a remarkably simple decomposition involving small and near-distinct groups of protein residues, with most groups having a clear association to biological function or structure. This provides insights that can be harnessed for the purpose of vaccine design.
Ethane-dependent synthesis of polyhydroxyalkanoates by the obligate methanotrophMethylocystis parvusOBBP
Authors: Jaewook Myung , Flanagan James C. A. , Galega Wakuna M. , Waymouth Robert M. , Criddle Craig S.
Published: April 2018

Under conditions of nutrient-limited growth, Type II obligate methanotrophs oxidize C1compounds, such as methane or methanol and accumulate intracellular granules of poly(3-hydroxybutyrate) (P3HB). Here, we report that, under same nutrient-limited conditions, the Type II obligate methanotrophMethylocystis parvusOBBP can use ethane as its sole carbon and energy source for synthesis P3HB granules, accumulating up to 35 ± 4 wt% P3HB.13C-NMR spectra of the P3HB confirmed incorporation of13C from [13C2]ethane. Moreover, when valerate was added as a co-substrate with ethane, oxidation of the ethane supported synthesis of the copolymer poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV).

IMPORTANCE

The presence of ethane in natural gas is often considered undesirable for methanotroph-based biotechnology due to the C1specialization of obligate methanotrophs and concerns about inhibitory byproducts arising from methane monooxygenase-mediated cometabolism of ethane. This work establishes that co-oxidation of ethane and further metabolism in the absence of methane can support synthesis of the valuable polyhydroxyalkanoate bioplastics P3HB and PHBV.
NLMR and landscapetools: An integrated environment for simulating and modifying neutral landscape models in R
Authors: Sciaini Marco , Fritsch Matthias , Scherer Cédric , Simpkins Craig Eric
Published: April 2018

Neutral landscape models (NLMs) simulate landscape patterns based on theoretical distributions and can be used to systematically study the effect of landscape structure on ecological processes. NLMs are commonly used in landscape ecology to enhance the findings of field studies as well as in simulation studies to provide an underlying landscape. However, their creation so far has been limited to software that is platform dependent, does not allow a reproducible workflow or is not embedded in R, the prevailing programming language used by ecologists.

Here, we present two complementary R packages NLMR and land-scapetools, that allow users to generate, manipulate and analyse NLMs in a single environment. They grant the simulation of the widest collection of NLMs found in any single piece of software thus far while allowing for easy manipulation in a self-contained and reproducible workflow. The combination of both packages should stimulate a wider usage of NLMs in landscape ecology. NLMR is a comprehensive collection of algorithms with which to simulate NLMs. landscapetools provides a utility toolbox which facilitates an easy workflow with simulated neutral landscapes and other raster data.

We show two example applications that illustrate potential use cases for NLMR and landscapetools: First, an agent-based simulation study in which the effect of spatial structure on disease persistence was studied. Here, spatial heterogeneity resulted in more variable disease outcomes compared to the common well-mixed host assumption. The second example shows how increases in spatial scaling can introduce biases in calculated landscape metrics.

Simplifying the workflow around handling NLMs should encourage an uptake in the usage of NLMs. NLMR and landscapetools are both generic frameworks that can be used in a variety of applications and are a further step to having a unified simulation environment in R for answering spatial research questions.
BPscore: an effective metric for meaningful comparisons of structural chromosome segmentations
Authors: Zaborowski Rafal , Wilczyński Bartek
Published: April 2018

Studying the 3D structure of chromosomes is an emerging field flourishing in recent years because of rapid development of experimental approaches for studying chromosomal contacts. This has led to numerous studies providing results of segmentation of chromosome sequences of different species into so called Topologically Associating Domains (TADs). As the number of such studies grows steadily and many of them make claims about the perceived differences between TAD structures observed in different conditions, there is a growing need for good measures of similarity (or dissimilarity) between such segmentations. We provide here a BP score, which is a relatively simple distance metric based on the bipartite matching between two segmentations. In this paper, we provide the rationale behind choosing specifically this function and show its results on several different datasets, both simulated and experimental. We show that not only the BP score is a proper metric satisfying the triangle inequality, but that it is providing good granularity of scores for typical situations occuring between different TAD segmentations. We also introduce local variant of the BP metric and show that in actual comparisons between experimental datasets, the local BP score is correlating with the observed changes in gene expression and genome methylation. In summary, we consider the BP score a good foundation for analysing the dynamics of chromosome structures. The methodology we present in this work could be used by many researchers in their ongoing analyses making it a popular and useful tool.

Author summary

Many researchers are interested in the chromosomal structure, its function and dynamics. Over the recent years, chromosome conformation capture (3C) methods have become the main source of experimental data on the subject and the Topologically Associating Domains (TADs) have become the de-facto standard unit of chromosomal structure. Many methods have been developed for TAD calling and the 3C experiments have been done in multiple conditions giving us a multitude of chromosomal segmentations describing the most atomic differences in chromosomal structure between conditions. Until now, such segmentations were compared mostly by very rough measures, such as the Jaccard coefficient or TAD overlaps or very general metrics like the variation of information coefficient. This has limited the researchers in the analysis of differential TAD segmentations, and practically prevented any proper analysis of TAD dynamics between conditions. Our approach has the potential to facilitate such analyses by providing researchers with mathematically sound metric that is designed specifically for the purpose and tested on both simulated and experimental data. Additionally, we provide a local variant of our measure that is a natural derivative of the BP score that can indicate which parts of the chromosomes are undergoing the most significant structural reorganizations.
Limb- and tendon-specificAdamtsl2deletion identifies a soft tissue mechanism modulating bone length
Authors: Hubmacher Dirk , Thacker Stetson , Adams Sheila M. , Birk David E. , Schweitzer Ronen , Apte Suneel S.
Published: April 2018

Disproportionate distal limb shortening is the hallmark of acromelic dysplasias. Among them, geleophysic dysplasia is a rare, frequently lethal condition characterized by severe short stature, musculoskeletal, cardiac, pulmonary, and skin anomalies. Geleophysic dysplasia results from dominant fibrillin-1 (FBN1) or recessiveADAMTSL2mutations, suggesting a functional link between ADAMTSL2 and FBN1. Mice lacking ADAMTSL2 die at birth, precluding analysis of postnatal skeletal growth and mechanisms underlying the skeletal anomalies of geleophysic dysplasia. We show thatAdamtsl2is expressed in limb soft tissues, predominantly in tendon. Expression in developing bones is limited to their terminal cell layers that are destined to become articular cartilage and is absent in growth plate cartilage.Adamtsl2conditional deletion in limb mesenchyme usingPrxl-Cre led to an acromelic dysplasia, providing a suitable model for investigation of geleophysic dysplasia. Unexpectedly, conditionalAdamtsl2deletion usingScx-Cre, a tendon-specific deleter, also impaired skeletal growth. Specific morphogenetic anomalies were seen in Achilles tendon, along with FBN1 accumulation. Thus, ADAMTSL2, shown here to bind fibrillin microfibrils in vitro, limits fibrillin microfibril formation in tendons and promotes tendon growth. The findings suggest that reduced bone growth in geleophysic dysplasia results from external tethering by short tendons rather than intrinsic growth plate anomalies.
A generic normalization method for proper quantification in untargeted proteomics screening
Authors: Anjo Sandra Isabel , Simões Isaura , Castanheira Pedro , Grãos Mário , Manadas Bruno
Published: April 2018

The label-free quantitative mass spectrometry methods, in particular, the SWATH-MS approach, have gained popularity and became a powerful technique for comparison of large datasets. In the present work, it is introduced the use of recombinant proteins as internal standards for untargeted label-free methods. The proposed internal standard strategy reveals a similar intragroup normalization capacity when compared with the most common normalization methods, with the additional advantage of maintaining the overall proteome changes between groups (which are lost using other methods). Therefore, the proposed strategy is able to maintain a good performance even when large qualitative and quantitative differences in sample composition are observed, such as the ones induced by biological regulation (as observed in secretome and other biofluids’ analyses) or by enrichment approaches (such as immunopurifications). Moreover, this approach corresponds to a cost-effective alternative, easier to implement than the current stable-isotope labeling internal standards, therefore being an appealing strategy for large quantitative screening, as clinical cohorts for biomarker discovery.
Bisulfite-free, Base-resolution, and Quantitative Sequencing of Cytosine Modifications
Authors: Liu Yibin , Siejka Paulina , Velikova Gergana , Yuan Fang , Tomkova Marketa , Bai Chunsen , Chen Lei , Bi Ying , Schuster-Boeckler Benjamin , Song Chun-Xiao
Published: April 2018

The deamination of unmodified cytosine to uracil by treatment with bisulfite has for decades been the gold standard for sequencing epigenetic DNA modifications including 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). However, this harsh chemical reaction degrades the majority of the DNA and generates sequencing libraries with low complexity. Here, we present a novel bisulfite-free and base-resolution sequencing method, TET Assisted Pic-borane Sequencing (TAPS), for detection of 5mC and 5hmC. TAPS relies on mild reactions, detects modifications directly without affecting unmodified cytosines and can be adopted to detect other cytosine modifications. Compared with bisulfite sequencing, TAPS results in higher mapping rates, more even coverage and lower sequencing costs, enabling higher quality, more comprehensive and cheaper methylome analyses.

One Sentence Summary

A bisulfite-free and base-resolution method to directly sequence epigenetically modified cytosine.
Complete functional mapping of infection- and vaccine-elicited antibodies against the fusion peptide of HIV
Authors: Dingens Adam S. , Acharya Priyamvada , Haddox Hugh K. , Rawi Reda , Xu Kai , Chuang Gwo-Yu , Wei Hui , Mascola John R. , Carragher Bridget , Potter Clinton S. , Overbaugh Julie , Kwong Peter D. , Bloom Jesse D.
Published: April 2018

Eliciting broadly neutralizing antibodies (bnAbs) targeting envelope (Env) is a major goal of HIV vaccine development, but cross-clade breadth from immunization has only sporadically been observed. Recently, Xu et al (2018) elicited cross-reactive neutralizing antibody responses in a variety of animal models using immunogens based on the epitope of bnAb VRC34.01. The VRC34.01 antibody, which was elicited by natural human infection, targets the N terminus of the Env fusion peptide, a critical component of the virus entry machinery. Here we precisely characterize the functional epitopes of VRC34.01 and two vaccine-elicited murine antibodies by mapping all single amino-acid mutations to the BG505 Env that affect viral neutralization. While escape from VRC34.01 occurred via mutations in both fusion peptide and distal interacting sites of the Env trimer, escape from the vaccine-elicited antibodies was mediated predominantly by mutations in the fusion peptide. Cryo-electron microscopy of four vaccine-elicited antibodies in complex with Env trimer revealed focused recognition of the fusion peptide and provided a structural basis for development of neutralization breadth. Together, these functional and structural data suggest that the breadth of vaccine-elicited antibodies targeting the fusion peptide can be enhanced by specific interactions with additional portions of Env. Thus, our complete maps of viral escape provide a template to improve the breadth or potency of future vaccine-induced antibodies against Env’s fusion peptide.

Author summary

A major goal of HIV-1 vaccine design is to elicit antibodies that neutralize diverse strains of HIV-1. Recently, some of us elicited such antibodies in animal models using immunogens based on the epitope of a broad antibody (VRC34.01) isolated from an infected individual. Further improving these vaccine-elicited antibody responses will require a detailed understanding of how the resulting antibodies target HIV’s envelope protein (Env). Here, we used mutational antigenic profiling to precisely map the epitope of two vaccine-elicited antibodies and the template VRC34.01 antibody. We did this by quantifying the effect of all possible amino acid mutations to Env on antibody neutralization. Although all antibodies target a similar region of Env, we found clear differences in the functional interaction of Env with the vaccine- and infection-elicited antibodies. We combined these functional data with structural analyses to identify antibody–Env interactions that could improve the breadth of vaccine-elicited antibodies, and thereby help to refine vaccination schemes to achieve broader responses.
Novel anionic cecropins from the spruce budworm feature a poly-L-aspartic acid C-terminus
Authors: Maaroufi Halim , Cusson Michel , Levesque Roger C.
Published: April 2018

Cecropins form a family of amphipathic α-helical cationic peptides with broad-spectrum antibacterial properties and potent anticancer activity. The emergence of bacteria and cancer cells showing resistance to cationic antimicrobial peptides (CAMPs) has fostered a search for new, more selective and more effective alternatives to CAMPs. With this goal in mind, we looked for cecropin homologs in the genome and transcriptome of the spruce budworm,Choristoneura fumiferana. Not only did we find paralogs of the conventional cationic cecropins (Cfcec+), our screening also led to the identification of previously uncharacterized anionic cecropins (Cfcec−), featuring a poly-L-aspartic acid C-terminus. Comparative peptide analysis indicated that the C-terminal helix of Cfcec−is amphipathic, unlike that of Cfcec+, which is hydrophobic. Interestingly, molecular dynamics simulations pointed to the lower conformational flexibility of Cfcec−peptides, relative to that of Cfcec+. Phylogenetic analysis suggests that the evolution of distinct Cfcec+and Cfcec−peptides may have resulted from an ancient duplication event within the Lepidoptera. Our analyses also indicated that Cfcec−shares characteristics with entericidins, which are involved in bacterial programmed cell death, lunasin, a peptide of plant origins with antimitotic effects, and APC15, a subunit of the anaphase-promoting complex. Finally, we found that both anionic and cationic cecropins contain a BH3-like motif (G-[KQR]-[HKQNR]-[IV]-[KQR]) that could interact with Bcl-2, a protein involved in apoptosis; this observation is congruent with previous reports indicating that cecropins induce apoptosis. Altogether, our observations suggest that cecropins may provide templates for the development of new anticancer drugs.

Graphical abstract

Highlights

Genes encoding novel anionic cecropins (Cfcec−), featuring a C-terminal poly-L-aspartic acid, were found in the genome of the spruce budworm,Choristoneura fumiferana.

Divergence between Cfcec+and Cfcec−could be the result of an ancient duplication event within the Lepidoptera.

There is an apparent relationship between motifs observed in cecropin peptides and apoptosis.

Anionic cecropins from the spruce budworm display characteristics suggesting they could have anticancer activity
Benchmarking tree and ancestral sequence inference for B cell receptor sequences
Authors: Davidsen Kristian , Matsen Frederick A.
Published: April 2018

B cell receptor sequences evolve during affinity maturation according to a Darwinian process of mutation and selection. Phylogenetic tools are used extensively to reconstruct ancestral sequences and phylogenetic trees from affinity-matured sequences. In addition to using general-purpose phylogenetic methods, researchers have developed new tools to accommodate the special features of B cell sequence evolution. However, the performance of classical phylogenetic techniques in the presence of B cell-specific features is not well understood, nor how much the newer generation of B cell specific tools represent an improvement over classical methods. In this paper we benchmark the performance of classical phylogenetic and new B cell-specific tools when applied to B cell receptor sequences simulated from a forward-time model of B cell receptor affinity maturation towards a mature receptor. We show that the currently used tools vary substantially in terms of tree structure and ancestral sequence inference accuracy. Furthermore, we show that there are still large performance gains to be achieved by modeling the special mutation process of B cell receptors. These conclusions are further strengthened with real data using the rules of isotype switching to count possible violations within each inferred phylogeny.
Computational Disease Subtyping based on Joint Analysis of Clinical and Genomic Data
Authors: Diaz Diana , Bollig-Fischer Aliccia , Kotov Alexander
Published: April 2018

Objective

To investigate application of non-negative tensor decomposition for disease subtype discovery based on joint analysis of clinical and genomic data.

Data and Methods

Somatic mutation profiles including 11,996 genes of 503 breast cancer patients from the Cancer Genome Atlas (TCGA) along with 11 clinical variables and markers of these patients were used to construct a binary third-order tensor. CANDECOMP/PARAFAC method was applied to decompose the constructed tensor into rank-one component tensors. Definitions of breast cancer verotypes were constructed from the patient, gene and clinical vectors corresponding to each component tensor. Patient membership proportions in the identified verotypes were utilized in a Cox proportional hazards model to predict their survival.

Results

Qualitative evaluation of the verotypes obtained by tensor factorization indicates that they correspond to clinically meaningful breast cancer subtypes. While some components correspond to the known HER2- or ER-positive breast cancer subtypes, other components correspond to a variant of triple negative subtype and a cohort of patients with high mutation load of tumor suppressor genes. Quantitative evaluation indicates that the Cox model utilizing computationally discovered breast cancer verotypes is more accurate (AUC=0.5796) at predicting patient survival than the Cox models utilizing random patient membership proportions in cancer subtypes (AUC=0.4056) as well as patient membership proportions in genotypes (AUC=0.4731) and phenotypes (AUC=0.5047) obtained by non-negative factorization of the somatic mutation and clinical matrices.

Conclusion

Non-negative factorization of a binary tensor constructed from clinical and genomic data enables high-throughput discovery of breast cancer verotypes that are effective at predicting patient survival.
Shared Data Science Infrastructure for Genomics Data
Authors: Bagher Hamid , Muppiral Usha , Severin Andrew J , Rajan Hridesh
Published: April 2018

Background

Creating a computational infrastructure to analyze the wealth of information contained in data repositories that scales well is difficult due to significant barriers in organizing, extracting and analyzing relevant data. Shared Data Science Infrastructures like Boa can be used to more efficiently process and parse data contained in large data repositories. The main features of Boa are inspired from existing languages for data intensive computing and can easily integrate data from biological data repositories.

Results

Here, we present an implementation of Boa for Genomic research (BoaG) on a relatively small data repository: RefSeq’s 97,716 annotation (GFF) and assembly (FASTA) files and metadata. We used BoaG to query the entire RefSeq dataset and gain insight into the RefSeq genome assemblies and gene model annotations and show that assembly quality using the same assembler varies depending on species.

Conclusions

In order to keep pace with our ability to produce biological data, innovative methods are required. The Shared Data Science Infrastructure, BoaG, can provide greater access to researchers to efficiently explore data in ways previously not possible for anyone but the most well funded research groups. We demonstrate the efficiency of BoaG to explore the RefSeq database of genome assemblies and annotations to identify interesting features of gene annotation as a proof of concept for much larger datasets.
Enrichment of rare protein truncating variants in amyotrophic lateral sclerosis patients
Authors: Farhan Sali M.K. , Howrigan Daniel P. , Abbott Liam E. , Byrnes Andrea E. , Churchhouse Claire , Phatnani Hemali , Smith Bradley N. , Topp Simon D. , Rampersaud Evadnie , Wu Gang , Wuu Joanne , Gubitz Amelie , Klim Joseph R. , Mordes Daniel A. , Ghosh Sulagna ,   CReATe Consortium, FALS Consortium, ALSGENS Consortium, Eggan Kevin , Rademakers Rosa , McCauley Jacob L. , Schüle Rebecca , Züchner Stephan , Benatar Michael , Taylor J. Paul , Nalls Mike A. , Traynor Bryan , Shaw Christopher E. , Goldstein David B. , Harms Matthew B. , Daly Mark J. , Neale Benjamin M.
Published: April 2018

To discover novel genetic risk factors underlying amyotrophic lateral sclerosis (ALS), we aggregated exomes from 3,864 cases and 7,839 ancestry matched controls. We observed a significant excess of ultra-rare and rare protein-truncating variants (PTV) among ALS cases, which was primarily concentrated in constrained genes; however, a significant enrichment in PTVs does persist in the remaining exome. Through gene level analyses, known ALS genes, SOD1, NEK1, and FUS, were the most strongly associated with disease status. We also observed suggestive statistical evidence for multiple novel genes including DNAJC7, which is a highly constrained gene and a member of the heat shock protein family (HSP40). HSP40 proteins, along with HSP70 proteins, facilitate protein homeostasis, such as folding of newly synthesized polypeptides, and clearance of degraded proteins. When these processes are not regulated, misfolding and accumulation of degraded proteins can occur leading to aberrant protein aggregation, one of the pathological hallmarks of neurodegeneration.
Permanent neuroglial remodeling of the retina following infiltration of CSF1R-inhibition resistant peripheral monocytes
Authors: Paschalis Eleftherios I , Lei Fengyang , Zhou Chengxin , Kapoulea Vassiliki , Dana Reza , Chodosh James , Vavvas Demetrios G. , Dohlman Claes H.
Published: April 2018

Previous studies have demonstrated that ocular injury can lead to prompt infiltration of bone marrow-derived peripheral monocytes into the retina. However, the ability of these cells to integrate into the tissue and become microglia has not been studied. Here we show that such peripheral monocytes not only infiltrate into the retina after ocular injury, but that they engraft permanently, migrate to the three distinct microglia strata, and adopt a microglia-like morphology. However, contrary to the original microglia, after injury the engrafted peripheral monocytes are resistant to depletion by colony stimulating factor 1 receptor (CSF1R) inhibitor and remain pro-inflammatory, expressing high levels of major histocompatibility complex II (MHC-II) for the long-term. In the absence of ocular injury, on the other hand, the peripheral monocytes that repopulate the retina after CSF1R inhibition remain sensitive to CSF1R inhibition and can be re-depleted. The observed permanent neuroglia remodeling after injury constitutes a major potential immunological change that may contribute to progressive retinal degeneration. These findings may be relevant also to other degenerative conditions of the retina and central nervous system.

Significance statement: Ocular injury causes permanent neuroglia remodeling that promotes neuroinflammation.
Comparison between three concentration techniques for diagnosing intestinal parasites
Authors: Trabelsi Sonia , Hanachi Majdi , Cheikhrouhou Sarra , Aloui Dorsaf , Bouchekoua Meriam , Khaled Samira
Published: April 2018

Background

Intestinal parasitoses still are a noticeable threat to public health. The direct diagnosis of such parasites requires the use of concentration techniques, whose sensitivities for protozoan cysts and helminth eggs are far from equal.

Aim

To compare the Willis, Ritchie and Bailenger concentration techniques in terms of parasite recovery, cost, time, and biosafety.

Methods

This prospective study analysed 236 stool specimens for intestinal parasites using the direct wet smear and the above-mentioned concentration techniques applied separately.

Results

Biphasic techniques identified significantly more positive specimens for intestinal parasites than the Willis technique, the latter leading to less concentrated and more altered parasitic elements on microscopy. No statistically significant difference emerged from comparing Ritchie’s and Bailenger’s methods. The Willis technique was the safest, yet the costliest and the most time-consuming of the studied methods.

Conclusions

Even though the hazardous reagents employed may raise legitimate concerns over their health implications, biphasic techniques prove to be uncostly, quick to perform, and highly sensitive for detecting faecal parasites, therefore ensuring a safe diagnosis for routine stool examinations.
Novel features in the structure of P-glycoprotein (ABCB1) in the post-hydrolytic state as determined at 7.9Å resolution
Authors: Thonghin Nopnithi , Collins Richard F. , Barbieri Alessandro , Shafi Talha , Siebert Alistair , Ford. Robert C.
Published: April 2018

P-glycoprotein (ABCB1) is a ATP-binding cassette transporter that plays an important role in the removal of drugs and xenobiotic compounds from the cell. It is also associated with multi-drug resistance in cancer. Here we report novel features of the cryo-EM-derived structure of P-glycoprotein in the post-hydrolytic state: The cytosolic nucleotide-binding domains (NBDs) are separated despite ADP remaining bound to the NBDs. Gaps in the TMDs that connect to the inner hydrophilic cavity are back-filled by detergent head-groups from the annular detergent micelle and are close to two regions predicted to delineate two pseudo-symmetry-related drug-binding sites. In this conformation, the (newly-resolved) N-terminal extension, NBD-TMD linker region and gap-filling detergents all appear to impede NBD dimerisation. We propose a model for the mechanism of action of the exporter where ATP will be bound to the protein for most of the time, consistent with the high physiological ATP concentrationsin vivo.
Dissecting the control mechanisms for DNA replication and cell division inE. coli
Authors: Micali Gabriele , Grilli Jacopo , Marchi Jacopo , Osella Matteo , Lagomarsino Marco Cosentino
Published: April 2018

Understanding how singleE. colicells coordinate the timing of cell division with genome replication would unlock a classic problem of biology, and open the way to address cell-cycle progression at the single-cell level. Several recent studies produced new data and proposed different models, based on the hypothesis that replication-segregation is the bottleneck process for cell division. However, due to the apparent contrast in both experimental results and proposed mechanisms, the emerging picture is fragmented and unclear. In this work, we re-evaluate jointly available data and models, and we show that, while each model contains useful insights, none of the proposed models, as well as generalizations based on the same assumptions, correctly describes all the correlation patterns observed in data. This analysis leads us to conclude that the assumption that replication is the bottleneck process for cell division is too restrictive. Instead, we propose that two concurrent cycles responsible for division and initiation of DNA replication together set the time of cell division. This framework correctly captures available data and allows us to select a nearly constant added size per origin between subsequent initiations as the most likely mechanism setting initiation of replication.
Endothelin receptor Aa regulates proliferation and differentiation of Erb-dependant pigment progenitors in zebrafish
Authors: Camargo-Sosa Karen , Colanesi Sarah , Müller Jeanette , Schulte-Merker Stefan , Stemple Derek , Elizabeth Patton E. , Kelsh Robert N.
Published: April 2018

Skin pigment patterns are important, being under strong selection for multiple roles including camouflage and UV protection. Pigment cells underlying these patterns form from adult pigment stem cells (APSCs). In zebrafish, APSCs derive from embryonic neural crest cells, but sit dormant until activated to produce pigment cells during metamorphosis. The APSCs are set-aside in an ErbB signaling dependent manner, but the mechanism maintaining quiescence until metamorphosis remains unknown. Mutants for a pigment pattern gene,parade, exhibit ectopic pigment cells localised to the ventral trunk. We show thatparadeencodes Endothelin receptor Aa, expressed in the blood vessels. Using chemical genetics, coupled with analysis of cell fate studies, we show that the ectopic pigment cells derive from APSCs. We propose that a novel population of APSCs exists in association with medial blood vessels, and that their quiescence is dependent upon Endothelin-dependent factors expressed by the blood vessels.

Lay Abstract

Pigment patterns are crucial for the many aspects of animal biology, for example, providing camouflage, enabling mate selection and protecting against UV irradiation. These patterns are generated by one or more pigment cell-types, localised in the skin, but derived from specialised stem cells (adult pigment stem cells, APSCs). In mammals, such as humans, but also in birds and fish, these APSCs derive from a transient population of multipotent progenitor cells, the neural crest. Formation of the adult pigment pattern is perhaps best studied in the zebrafish, where the adult pigment pattern is formed during a metamorphosis beginning around 21 days of development. The APSCs are set-aside in the embryo around 1 day of development, but then remain inactive until that metamorphosis, when they become activated to produce the adult pigment cells. We know something of how the cells are set-aside, but what signals maintain them in an inactive state is a mystery. Here we study a zebrafish mutant, calledparade, which shows ectopic pigment cells in the embryo. We clone theparadegene, identifying it asednraaencoding a component of a cell-cell communication process, which is expressed in blood vessels. By characterising the changes in the neural crest and in the pigment cells formed, and by combining this with an innovative assay identifying drugs that prevent the ectopic cells from forming, we deduce that the ectopic cells in the larva derive from precocious activation of APSCs to form pigment cells. We propose that a novel population of APSCs are associated with the blood vessels, that these are held in a quiescent state by signals coming from these vessels, and that these signals depend uponednraa. Together this opens up an exciting opportunity to identify the signals maintaining APSC quiescence in zebrafish.
Imaging beyond the super-resolution limits using ultrastructure expansion microscopy (UltraExM)
Authors: Gambarotto D. , Zwettler F. U. , Cernohorska M. , Fortun D. , Borgers S. , Heine J. , Schloetel J. G. , Reuss M. , Unser M. , Boyden E. S. , Sauer M. , Hamel V. , Guichard P.
Published: April 2018

For decades, electron microscopy (EM) was the only method able to reveal the ultrastructure of cellular organelles and molecular complexes because of the diffraction limit of optical microscopy. In recent past, the emergence of superresolution fluorescence microscopy enabled the visualization of cellular structures with so far unmatched spatial resolution approaching virtually molecular dimensions. Despite these technological advances, currently super-resolution microscopy does not permit the same resolution level as provided by electron microscopy, impeding the attribution of a protein to an ultrastructural element. Here, we report a novel method of near-native expansion microscopy (UltraExM), enabling the visualization of preserved ultrastructures of macromolecular assemblies with subdiffraction-resolution by standard optical microscopy. UltraExM revealed for the first time the ultrastructural localization of tubulin glutamylation in centrioles. Combined with super-resolution microscopy, UltraExM unveiled the centriolar chirality, an ultrastructural signature, which was only visualizable by electron microscopy.
Cell-cell contact dictates life or death decisions following CD95 activation in cancer
Authors: Gülcüler Balta Gülce S. , Monzel Cornelia , Kleber Susanne , Beaudouin Joel , Kaindl Thomas , Thiemann Meinolf , Wirtz Christian R. , Tanaka Motomu , Martin-Villalba Ana
Published: April 2018

Cancer cells react to CD95 activation with either apoptotic or tumorigenic responses. Yet, the determinants of these two antithetic reactions are fundamentally not understood. Here, we show that pre-confined CD95L molecules activate apoptosis of cancer cells in-vitro. For particular CD95L pre-confinement, apoptosis activation is most efficient. Surprisingly, in tumor models, the same pre-confinement yields enhanced proliferation of cancer cells. This shift is rooted in cell-cell interactions, as proliferation was also observed in tumorspheres in-vitro. Indeed, proliferation required death-domain tyrosine phosphorylation of CD95 that was facilitated by cell-cell contacts, whereas decreasing the levels of global tyrosine kinase activity favored apoptosis. Altogether, the response to CD95 activation is cell context-dependent and tunable by CD95L pre-confinement, thereby opening therapeutic opportunities in cancer.

One Sentence Summary

Cell-cell contact tunes tyrosine-kinase activity thereby dictating life or death upon CD95 activation by pre-confined CD95L.
Quantifying multi-layered expression regulation in response to stress of the endoplasmic reticulum
Authors: Rendleman Justin , Cheng Zhe , Maity Shuvadeep , Kastelic Nicolai , Munschauer Mathias , Allgoewer Kristina , Teo Guoshou , Zhang Yun Bin , Lei Amy , Parker Brian , Landthaler Markus , Freeberg Lindsay , Kuersten Scott , Choi Hyungwon , Vogel Christine
Published: April 2018

The mammalian response to endoplasmic reticulum (ER) stress dynamically affects all layers of gene expression regulation. We quantified transcript and protein abundance along with footprints of ribosomes and non-ribosomal proteins for thousands of genes in cervical cancer cells responding to treatment with tunicamycin or hydrogen peroxide over an eight hour time course. We identify shared and stress-specific significant regulatory events at the transcriptional and post-transcriptional level and at different phases of the experiment. ER stress regulators increase transcription and translation at different times supporting an adaptive response. ER stress also induces translation of genes from serine biosynthesis and one-carbon metabolism indicating a shift in energy production. Discordant regulation of DNA repair genes suggests transcriptional priming in which delayed translation fine-tunes the early change in the transcriptome. Finally, case studies on stress-dependent alternative splicing and protein-mRNA binding demonstrate the ability of this resource to generate hypotheses for new regulatory mechanisms.
B7-H1(PD-L1) confers chemoresistance through ERK and p38 MAPK pathway in tumor cells
Authors: Wu Xiaosheng , Li Yanli , Liu Xin , Cao Siyu , Harrington Susan M. , Chen Chunhua , Mansfiled Aaron S. , Dronca Roxana S. , Park Sean S. , Yan Yiyi , Kwon Eugene D. , Wang Liewei , Ling Kun , Dong Haidong
Published: April 2018

Development of resistance to chemotherapy and immunotherapy is a major obstacle in extending the survival of patients with cancer. Although several molecular mechanisms have been identified that can contribute to chemoresistance, the role of immune checkpoint molecules in tumor chemoresistance remains underestimated. It has been recently observed that overexpression of B7-H1(PD-L1) confers chemoresistance in human cancers, however the underlying mechanisms are unclear. Here we show that the development of chemoresistance depends on the increased activation of ERK pathway in tumor cells overexpressing B7-H1. Conversely, B7-H1 deficiency renders tumor cells susceptible to chemotherapy in a cell-context dependent manner through activation of the p38 MAPK pathway. B7-H1 in tumor cells associates with the catalytic subunit of a DNA-dependent serine / threonine protein kinase (DNA-PKcs). DNA-PKcs is required for the activation of ERK or p38 MAPK in tumors expressing B7-H1, but not in B7-H1 negative or B7-H1 deficient tumors. Ligation of B7-H1 by anti-B7-H1 monoclonal antibody (H1A) increased the sensitivity of human triple negative breast tumor cells to cisplatin therapy in vivo. Our results suggest that B7-H1(PD-L1) expression in cancer cells modifies their chemosensitivity towards certain drugs and targeting B7-H1 intracellular signaling pathway is a new way to overcome cancer chemoresistance.
The three regimes of spatial recovery
Authors: Zelnik Yuval R. , Arnoldi Jean-Francois , Loreau Michel
Published: April 2018

An enduring challenge for ecology is identifying the drivers of ecosystem and population stability. In a spatially explicit context, key features to consider are landscape spatial structure, local interactions, and dispersal. Substantial work has been done on each of these features as a driver of stability, but little is known on the interplay between them. Missing has been a more integrative approach, able to map and identify different dynamical regimes, and thus to predict a system’s response to perturbations. Here we first consider a simple scenario, i.e. the recovery of a homogeneous metapopulation from a single localized pulse disturbance. The analysis of this scenario reveals three fundamental recovery regimes: Isolated Regime when dispersal is not significant, Rescue Regime when dispersal mediates recovery, and Mixing Regime when perturbations spread throughout the system. Despite its simplicity, our approach leads to remarkably general predictions. These include the qualitatively different outcomes of various scenarios of habitat fragmentation, the surprising benefits of local extinctions on population persistence at the transition between regimes, and the productivity shifts of metacommunities in a changing environment. This study thus provides context to known results and insight into future directions of research.