bluuebunny/crossref_metadata_2025_split huggingface dataset:
AvrE1 and HopR1 fromPseudomonas syringaepv.actinidiaeare additively required for full virulence on kiwifruit
Authors: Jayaraman Jay , Yoon Minsoo , Applegate Emma R. , Stroud Erin A. , Templeton Matthew D. 
Published: June 2020

SummaryPseudomonas syringaepv.actinidiaeICMP 18884 biovar 3 (Psa3) produces necrotic lesions during infection of its kiwifruit host. Bacterial growthin plantaand lesion formation are dependent upon a functional type III secretion system (T3S), which translocates multiple effector proteins into host cells. Associated with the T3S locus is the conserved effector locus (CEL), which has been characterised and shown to be essential for the full virulence in otherP. syringaepathovars. Two effectors at the CEL,hopM1andavrE1, as well as anavrE1-related non-CEL effector,hopR1, have been shown to be redundant in the model pathogenP. syringaepv.tomatoDC3000 (Pto), a close relative ofPsa. However, it is not known whether CEL-related effectors are required forPsapathogenicity. ThePsa3allele ofhopM1, and its associated chaperone,shcM, have diverged significantly from their orthologs inPto. Furthermore, the CEL effectorhopAA1-1, as well as a related non-CEL effector,hopAA1-2, have both been pseudogenised. We have shown that HopM1 does not contribute toPsa3virulence due to a truncation inshcM, a truncation conserved in thePsalineage, likely due to the need to evade HopM1-triggered immunity in kiwifruit. We characterised the virulence contribution of CEL and related effectors inPsa3and found that onlyavrE1andhopR1, additively, are required forin plantagrowth and lesion production. This is unlike the redundancy described for these effectors inPtoand indicates that these twoPsa3genes are key determinants essential for kiwifruit bacterial canker disease.
The tumor suppressor microRNA let-7 inhibits human LINE-1 retrotransposition
Authors: Tristán-Ramos Pablo , Rubio-Roldan Alejandro , Peris Guillermo , Sánchez Laura , Amador-Cubero Suyapa , Viollet Sebastien , Cristofari Gael , Heras Sara R. 
Published: June 2020

ABSTRACTNearly half of the human genome is made of transposable elements (TEs) whose activity continues to impact its structure and function. Among them, Long INterspersed Element class 1 (LINE-1 or L1) elements are the only autonomously active TEs in humans. L1s are expressed and mobilized in different cancers, generating mutagenic insertions that could affect malignancy. Tumor suppressor microRNAs are ∼22nt RNAs that post-transcriptionally regulate oncogene expression and are frequently downregulated in cancer. Here we explore whether they also influence L1 mobilization. We found that downregulation of let-7 correlates with accumulation of L1 insertions in human lung cancer. Furthermore, we demonstrate that let-7 binds to the L1 mRNA and impairs the translation of the second L1-encoded protein, ORF2p, reducing its mobilization. Overall, our data uncover a new role for let-7, one of the most relevant microRNAs, which is to maintain somatic genome integrity by restricting L1 retrotransposition.
Tunable phenotypic variability through an autoregulatory alternative sigma factor circuit
Authors: Schwall Christian P. , Loman Torkel , Martins Bruno M.C. , Cortijo Sandra , Villava Casandra , Kusmartsev Vassili , Livesey Toby , Saez Teresa , Locke James C. W. 
Published: June 2020

AbstractGenetically identical individuals in bacterial populations can display significant phenotypic variability. This variability can be functional, for example by allowing a fraction of stress prepared cells to survive an otherwise lethal stress. The optimal fraction of stress prepared cells depends on environmental conditions. However, how bacterial populations modulate their level of phenotypic variability remains unclear. Here we show that the alternative sigma factor σVcircuit inB. subtilisgenerates functional phenotypic variability that can be tuned by stress level, environmental history, and genetic perturbations. Using single-cell time-lapse microscopy and microfluidics, we find the fraction of cells that immediately activate σVunder lysozyme stress depends on stress level and on a memory of previous stress. Iteration between model and experiment reveals that this tunability can be explained by the autoregulatory feedback structure of thesigVoperon. As predicted by the model, genetic perturbations to the operon also modulate the response variability. The conserved sigma-anti-sigma autoregulation motif is thus a simple mechanism for bacterial populations to modulate their heterogeneity based on their environment.
Biophysical characterization of the human K0513 protein
Authors: Nemukondeni Ndivhuwo , Arowolo Afolake , Shonhai Addmore , Zininga Tawanda , Burger Adélle 
Published: June 2020

ABSTRACTGlioblastoma multiforme (GBM) is an aggressive grade IV primary malignant tumour which accounts for 78 % of all brain tumours.K0513is a GBM biomarker that is upregulated in the invasive phenotype.K0513is expressed ubiquitously and is reportedly enriched in the cerebral cortex of the brain.K0513is further implicated in signalling pathways involving neuroplasticity, cytoskeletal regulation and apoptosis. The protein encoded byK0513is a prospective biomarker for pancreatic cancer prognosis. However, the gene product ofK0153is not well characterised. This study focused on structure-function characterisation of human K0513 protein. To this end, we employed bioinformatics analysis and biophysical approaches to characterize the protein.In silicostructural characterisation of the human K0513 protein suggests the presence of a SET binding factor 2 (SBF2) domain and a transmembrane region. The SBF2 domain is found in the Myotubularin-related protein 13 (MTMR13), which may function as a nucleotide exchange factor for the RAS-associated GTPase, Rab28. K0513 was predicted to interact with RAS-associated GTPase, Rab3a. Secondary structure prediction revealed K0513 to be predominantly α-helical in nature. The predicted three-dimensional model of K0513 showed a globular fold, suggesting that the protein is water-soluble. K0513 was heterologously expressed inE. coliXL1-Blue cells and subsequent purification yielded 80 % soluble protein. Biophysical characterisation using tryptophan-based fluorescence spectroscopy and limited proteolysis showed the conformation of K0513 is mostly unperturbed in the presence of nucleotides. Interestingly, K0513 was detected in lung carcinoma, fibrosarcoma and cervical adenocarcinoma cells, supporting its possible role in cancer signalling pathways.
Selective vulnerability of aneuploid human cancer cells to inhibition of the spindle assembly checkpoint
Authors: Cohen-Sharir Yael , McFarland James M. , Abdusamad Mai , Marquis Carolyn , Tang Helen , Ippolito Marica R. , Bernhard Sara V. , Laue Kathrin , Malaby Heidi L.H. , Jones Andrew , Kazachkova Mariya , Lyons Nicholas , Nagaraja Ankur , Bass Adam J. , Beroukhim Rameen , Santaguida Stefano , Stumpff Jason , Golub Todd R. , Storchova Zuzana , Ben-David Uri 
Published: June 2020

AbstractSelective targeting of aneuploid cells is an attractive strategy for cancer treatment. Here, we mapped the aneuploidy landscapes of ~1,000 human cancer cell lines and classified them by their degree of aneuploidy. Next, we performed a comprehensive analysis of large-scale genetic and chemical perturbation screens, in order to compare the cellular vulnerabilities between near-diploid and highly-aneuploid cancer cells. We identified and validated an increased sensitivity of aneuploid cancer cells to genetic perturbation of core components of the spindle assembly checkpoint (SAC), which ensures the proper segregation of chromosomes during mitosis. Surprisingly, we also found highly-aneuploid cancer cells to belesssensitive to short-term exposures to multiple inhibitors of the SAC regulatorTTK. To resolve this paradox and to uncover its mechanistic basis, we established isogenic systems of near-diploid cells and their aneuploid derivatives. Using both genetic and chemical inhibition ofBUB1B,MAD2andTTK, we found that the cellular response to SAC inhibition depended on the duration of the assay, as aneuploid cancer cells became increasingly more sensitive to SAC inhibition over time. The increased ability of aneuploid cells to slip from mitotic arrest and to keep dividing in the presence of SAC inhibition was coupled to aberrant spindle geometry and dynamics. This resulted in a higher prevalence of mitotic defects, such as multipolar spindles, micronuclei formation and failed cytokinesis. Therefore, although aneuploid cancer cells can overcome SAC inhibition more readily than diploid cells, the proliferation of the resultant aberrant cells is jeopardized. At the molecular level, analysis of spindle proteins identified a specific mitotic kinesin,KIF18A, whose levels were drastically reduced in aneuploid cancer cells. Aneuploid cancer cells were particularly vulnerable toKIF18Adepletion, andKIF18Aoverexpression restored the sensitivity of aneuploid cancer cells to SAC inhibition. In summary, we identified an increased vulnerability of aneuploid cancer cells to SAC inhibition and explored its cellular and molecular underpinnings. Our results reveal a novel synthetic lethal interaction between aneuploidy and the SAC, which may have direct therapeutic relevance for the clinical application of SAC inhibitors.
Chromosomally unstable tumor cells specifically require KIF18A for proliferation
Authors: Marquis Carolyn , Fonseca Cindy L. , Queen Katelyn A. , Wood Lisa , Vandal Sarah E. , Malaby Heidi L.H. , Clayton Joseph E. , Stumpff Jason 
Published: June 2020

SummaryChromosomal instability (CIN), characterized by frequent missegregation of chromosomes during mitosis, is a hallmark of tumor cells caused by changes in the dynamics and control of microtubules that comprise the mitotic spindle1–3. Thus, CIN tumor cells may respond differently than normal diploid cells to treatments that target mitotic spindle regulation. We tested this idea by inhibiting a subset of kinesin motor proteins that control spindle microtubule dynamics and mechanics but are not required for the proliferation of near-diploid cells. Our results indicated that KIF18A was required for proliferation of CIN cells derived from triple negative breast cancer or colorectal cancer tumors but was not required in near-diploid cells. CIN tumor cells exhibited mitotic delays, multipolar spindles due to centrosome fragmentation, and increased cell death following inhibition of KIF18A. Sensitivity to KIF18A knockdown was strongly correlated with centrosome fragmentation, which required dynamic microtubules but did not depend on bipolar spindle formation or mitotic arrest. Our results indicate the altered spindle microtubule dynamics characteristic of CIN tumor cells can be exploited to reduce the proliferative capacity of CIN cells.
Allele-specific endogenous tagging and quantitative analysis of beta-catenin in colorectal cancer cells
Authors: Ambrosi Giulia , Voloshanenko Oksana , Eckert Antonia F. , Kranz Dominique , Nienhaus G. Ulrich , Boutros Michael 
Published: June 2020

ABSTRACTWnt signaling plays important roles in development, homeostasis, and tumorigenesis. Mutations in β-catenin that activate Wnt signaling have been found in colorectal and hepatocellular carcinomas. However, the dynamics of wild-type and mutant forms of β-catenin are not fully understood. Here, we genome-engineered fluorescently tagged alleles of the endogenous β-catenin in a colorectal cancer cell line. Wild-type and oncogenic mutant alleles were tagged with different fluorescent proteins, enabling the analysis of both variants in the same cell. We analyzed the properties of both β-catenin alleles using immunoprecipitation, immunofluorescence and fluorescence correlation spectroscopy approaches, revealing distinctly different biophysical properties. In addition, activation of Wnt signaling by treatment with a GSK3β inhibitor or a truncatingAPCmutation modulated the wild-type allele to mimic the properties of the mutant β-catenin allele. The one-step tagging strategy demonstrates how genome engineering can be employed for the parallel functional analysis of different genetic variants.
Hi-C deconvolution of a textile-dye degrader microbiome reveals novel taxonomic landscapes and link phenotypic potential to individual genomes
Authors: Sánchez-Reyes Ayixon , Bretón-Deval Luz , Mangelson Hayley , Salinas-Peralta Ilse , Sanchez-Flores Alejandro 
Published: June 2020

AbstractMicrobial biodiversity is represented by genomic landscapes populating dissimilar environments on earth. These genomic landscapes usually contain microbial functional signatures connected with the community phenotypes. Here we assess the genomic microbiodiversity landscape of a river associated microbiome enriched with 200 mg.mL−1of anthraquinone Deep-Blue 35 (™); we subjected to nutritional selection a composite sample from four different sites from a local river basin (Morelos, Mexico). This paper explores the resultant textile-dye microbiome, and infer links between predicted biodegradative functions and the individual genome fractions. By using a proximity-ligation deconvolution method, we deconvoluted 97 genome composites, with 80% of this been potentially novel species associated with the textile-dye environment. The main determinants of taxonomic composition were the generaMethanobacterium,Clostridium, andCupriavidusconstituting 50, 22, and 11 % of the total population profile respectively; also we observe an extended distribution of novel taxa without clear taxonomic standing. Removal of 50% chemical oxygen demand (COD) with 23% decolorization was observed after 30 days after dye enrichment. By metagenome wide analysis we postulate that sequence elements related to catalase-peroxidase, polyphenol oxidase, and laccase enzymes may be causally associated with the textile-dye degradation phenotype under our study conditions. This study prompts rapid genomic screening in order to select statistically represented functional features, reducing costs, and experimental efforts. As well as predicting phenotypes within complex communities under environmental pressures.
Rhes, a Striatal Enriched Protein, Regulates Post-Translational Small-Ubiquitin-like-Modifier (SUMO) Modification of Nuclear Proteins and Alters Gene Expression
Authors: Rivera Oscar , Sharma Manish , Shahani Neelam , Ramírez-Jarquín Uri Nimrod , Crynen Gogce , Karunadharma Pabalu , McManus Francis , Pierre Thibault , Subramaniam Srinivasa 
Published: June 2020

ABSTRACTRhes (Ras homolog enriched in the striatum) is a multifunctional protein that orchestrates striatal toxicity, motor behaviors and abnormal movements associated with dopaminergic signaling, Huntington disease and Parkinson disease signaling in the striatum. Rhes engineers membranous tunneling nanotube-like structures and promotes intercellular protein and cargoes transport. Recent study revealed Rhes also regulates mitophagy via the Nix receptor. Despite these studies, the mechanisms through which Rhes mediates these diverse functions remains unclear. Rhes belongs to a small GTPase family member and consists of a unique C-terminal Small Ubiquitin-like Modifier (SUMO) E3-like domain that promotes the post-translational modification (PTM) of proteins with SUMO (SUMOylation) by promoting “cross-SUMOylation” of SUMO enzymes SUMO E1 (Aos1/Uba2) and SUMO E2 ligase (Ubc-9). However, the identity of the SUMO substrates of Rhes remains largely unknown. By combining high throughput interactome and SUMO proteomics we report that Rhes regulates the SUMOylation of nuclear proteins that are involved in the regulation of gene transcription. While Rhes has increased the SUMOylation of histone deacetylase 1 (HDAC1) and histone 2B, it had decreased the SUMOylation of heterogeneous nuclear ribonucleoprotein M (HNRNPM), protein polybromo-1 (PBRM1) and E3 SUMO-protein ligase (PIASy). We also found that Rhes itself is SUMOylated at 5 different lysine residues (K32, K110, K114, K120, K124 and K245). Furthermore, we found that Rhes regulates the expression of genes involved in cellular morphogenesis and differentiation in the striatum, in a SUMO-dependent manner. Our findings thus provide a previously undescribed role for Rhes in regulating SUMOylation of nuclear targets and in orchestrating striatal gene expression via the SUMOylation.
Single molecule microscopy reveals key physical features of repair foci in living cells
Authors: Miné-Hattab Judith , Heltberg Mathias , Villemeur Marie , Guedj Chloé , Mora Thierry , Walczak Aleksandra M. , Dahan Maxime , Taddei Angela 
Published: June 2020

ABSTRACTIn response to double strand breaks (DSB), repair proteins accumulate at damaged sites, forming membrane-less sub-compartments or foci. Here we explored the physical nature of these foci, using single molecule microscopy in living cells. Rad52, the functional homolog of BRCA2 in yeast, accumulates at DSB sites and diffuses ~6 times faster within repair foci than the focus itself, exhibiting confined motion. The Rad52 confinement radius coincides with the focus size: foci resulting from 2 DSBs are twice larger in volume that the ones induced by a unique DSB and the Rad52 confinement radius scales accordingly. In contrast, molecules of the single strand binding protein Rfa1 follow anomalous diffusion similar to the focus itself or damaged chromatin. We conclude that while most Rfa1 molecules are bound to the ssDNA, Rad52 molecules are free to explore the entire focus possibly reflecting the existence of a liquid droplet around damaged DNA.
Being diagnosed with autism in adulthood: a personal case study
Authors: Henley Ross 
Published: June 2020

Purpose
This paper aims to report the personal experiences of an adult male diagnosed with autism at the age of 48 years.

Design/methodology/approach
A personal case study methodology was used to illustrate the journey to autism diagnosis, the experience of diagnosis and post-diagnosis support.

Findings
This case study illustrates how stress and mental health difficulties can precede autism diagnosis in adults. The personal experiences detailed highlight how an adult autism diagnosis can bring about positive change, prompting increased self-knowledge and coping skills, improved relationships and. Furthermore, it highlights how a supportive employer can make reasonable adjustments in the workplace to improve productivity of an autistic employee.

Research limitations/implications
This case study has implications for various practice issues, including post-diagnosis counselling and access to support for autistic adults nationally.

Originality/value
This paper provides an original case study highlighting the personal experiences of an adult diagnosed with autism.
On the numerical integration in generalized/extended finite element method analysis for crack propagation problems
Authors: Campos Bruna Caroline , Barros Felício Bruzzi , Penna Samuel Silva 
Published: June 2020

Purpose
The purpose of this paper is to evaluate some numerical integration strategies used in generalized (G)/extended finite element method (XFEM) to solve linear elastic fracture mechanics problems. A range of parameters are here analyzed, evidencing how the numerical integration error and the computational efficiency are improved when particularities from these examples are properly considered.

Design/methodology/approach
Numerical integration strategies were implemented in an existing computational environment that provides a finite element method and G/XFEM tools. The main parameters of the analysis are considered and the performance using such strategies is compared with standard integration results.

Findings
Known numerical integration strategies suitable for fracture mechanics analysis are studied and implemented. Results from different crack configurations are presented and discussed, highlighting the necessity of alternative integration techniques for problems with singularities and/or discontinuities.

Originality/value
This study presents a variety of fracture mechanics examples solved by G/XFEM in which the use of standard numerical integration with Gauss quadratures results in loss of precision. It is discussed the behaviour of subdivision of elements and mapping of integration points strategies for a range of meshes and cracks geometries, also featuring distorted elements and how they affect strain energy and stress intensity factors evaluation for both strategies.
A novel trust model for fog computing using fuzzy neural networks and weighted weakest link
Authors: Zineddine Mhamed 
Published: June 2020

PurposeTrust is one of the main pillars of many communication and interaction domains. Computing is no exception. Fog computing (FC) has emerged as mitigation of several cloud computing limitations. However, selecting a trustworthy node from the fog network still presents serious challenges. This paper aims to propose an algorithm intended to mitigate the trust and the security issues related to selecting a node of a fog network.Design/methodology/approachThe proposed model/algorithm is based on two main concepts, namely, machine learning using fuzzy neural networks (FNNs) and the weighted weakest link (WWL) algorithm. The crux of the proposed model is to be trained, validated and used to classify the fog nodes according to their trust scores. A total of 2,482 certified computing products, in addition to a set of nodes composed of multiple items, are used to train, validate and test the proposed model. A scenario including nodes composed of multiple computing items is designed for applying and evaluating the performance of the proposed model/algorithm.FindingsThe results show a well-performing trust model with an accuracy of 0.9996. Thus, the end-users of FC services adopting the proposed approach could be more confident when selecting elected fog nodes. The trained, validated and tested model was able to classify the nodes according to their trust level. The proposed model is a novel approach to fog nodes selection in a fog network.Research limitations/implicationsCertainly, all data could be collected, however, some features are very difficult to have their scores. Available techniques such as regression analysis and the use of the experts have their own limitations. Experts might be subjective, even though the author used the fuzzy group decision-making model to mitigate the subjectivity effect. A methodical evaluation by specialized bodies such as the security certification process is paramount to mitigate these issues. The author recommends the repetition of the same study when data form such bodies is available.Originality/valueThe novel combination of FNN and WWL in a trust model mitigates uncertainty, subjectivity and enables the trust classification of complex FC nodes. Furthermore, the combination also allowed the classification of fog nodes composed of diverse computing items, which is not possible without the WWL. The proposed algorithm will provide the required intelligence for end-users (devices) to make sound decisions when requesting fog services.