bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spo0A suppressessinlocus expression inClostridioides difficile
Authors: Dhungel Babita Adhikari , Govind Revathi 
Published: February 2020

AbstractClostridioides difficileis the leading cause of nosocomial infection and is the causative agent of antibiotic-associated diarrhea. The severity of the disease is directly associated with the production of toxins, and spores are responsible for the transmission and persistence of the organism. Previously we characterizedsinlocus regulators SinR and SinR’, where SinR is the regulator of toxin production and sporulation, while the SinR’ acting as its antagonist. InBacillus subtilis, Spo0A, the master regulator of sporulation, regulates SinR, by regulating the expression of its antagonistsinI. However, the role of Spo0A in the expression ofsinRandsinR’inC. difficileis not yet reported. In this study, we testedspo0Amutants in three differentC. difficilestrains R20291, UK1, and JIR8094, to understand the role of Spo0A insinlocus expression. Western blot analysis revealed thatspo0Amutants had increased SinR levels. The qRT-PCR analysis for its expression further supported this data. By carrying out genetic and biochemical assays, we have shown that Spo0A can bind to the upstream region of this locus to regulates its expression. This study provides vital information that Spo0A regulatessinlocus, which controls critical pathogenic traits such as sporulation, toxin production, and motility inC. difficile.IMPORTANCEClostridioides difficileis the leading cause of antibiotic-associated diarrheal disease in the United States. During infection,C. difficile sporesgerminate, and the vegetative bacterial cells produce toxins that damage host tissue. InC. difficile,sinlocus is known to regulate both sporulation and toxin production. In this study, we have shown that Spo0A, the master regulator of sporulation to control thesinlocus expression. We performed various genetic and biochemical experiments to show that Spo0A directly regulates the expression of this locus by binding to its upstream DNA region. This observation adds new detail to the gene regulatory network that connects sporulation and toxin production in this pathogen.
PLZF is a new substrate of CRBN with thalidomide and 5-hydroxythalidomide
Authors: Yamanaka Satoshi , Murai Hidetaka , Saito Daisuke , Abe Gembu , Tokunaga Etsuko , Iwasaki Takahiro , Takahashi Hirotaka , Takeda Hiroyuki , Suzuki Takayuki , Shibata Norio , Tamura Koji , Sawasaki Tatsuya 
Published: February 2020

AbstractThalidomide induces cereblon (CRBN)-dependent degradation of proteins. Human cytochrome P450s are thought to provide two monohydroxylated metabolites from thalidomide, and the metabolites are also considered to be involved in thalidomide effects. However, it remains unclear. We report that human PLZF/ZBTB16 is a target protein of CRBN with thalidomide and its derivatives, and that 5-hydroxythalidomide has high potential for degrading PLZF. Using a human transcription factor protein array produced by a wheat cell-free protein synthesis system, PLZF was found to bind to CRBN with thalidomide. PLZF is degraded by the CRL4CRBNcomplex with thalidomide and its derivatives. Mutagenesis analysis revealed that both 1st and 3rd zinc finger domains conserved in vertebrates are recognized for thalidomide-dependent binding and degradation by CRBN. In chicken limbs, knockdown of Plzf induced skeletal abnormalities, and Plzf was degraded after thalidomide or 5-hydroxythalidomide treatment. Our findings suggest that PLZF is a pivotal substrate involving thalidomide-induced teratogenesis.
Post-traumatic osteoarthritis development is not modified by postnatal chondrocyte deletion of CCN2
Authors: Keenan Craig M , Ramos-Mucci Lorenzo , Kanakis Ioannis , Milner Peter I , Leask Andrew , Abraham David , Bou-Gharios George , Poulet Blandine 
Published: February 2020

AbstractCCN2 is a matricellular protein involved in several critical biological processes. In particular, CCN2 is involved in cartilage development and in osteoarthritis. CCN2 null mice exhibit a range of skeletal dysmorphisms, highlighting its importance in regulating matrix formation during development, however its role in adult cartilage remains unclear. The aim of this study was to determine the role of CCN2 in postnatal chondrocytes in models of post-traumatic osteoarthritis (PTOA). CCN2 deletion was induced in articular chondrocytes of male transgenic mice at 8 weeks of age. PTOA was induced in knees either surgically or non-invasively by repetitive mechanical loading at 10 weeks of age. Knee joints were harvested, scanned with micro-CT, and processed for histology. Sections were stained with toluidine blue and scored using the OARSI grading system. In the non-invasive model cartilage lesions were present in the lateral femur but no significant differences were observed between wildtype (WT) and CCN2 knockout (KO) mice 6 weeks post-loading. In the surgical model, severe cartilage degeneration was observed in the medial compartments but no significant differences were observed between WT and CCN2 KO mice at 2, 4, and 8 weeks post-surgery. We conclude that CCN2 deletion in chondrocytes did not modify the development of PTOA in mice, suggesting that chondrocyte expression of CCN2 in adults is not a critical player in protecting cartilage from the degeneration associated with PTOA.Summary StatementPost-natal deletion of CCN2 in chondrocytes does not affect the development of post-traumatic osteoarthritis in mice.
Downward Gazing for Steadiness
Authors: Koren Yogev , Mairon Rotem , Sofer Ilay , Parmet Yisrael , Ben-Shahar Ohad , Bar-Haim Simona 
Published: February 2020

AbstractWhen walking on an uneven surface or complex terrain, humans tend to gaze downward. Previous investigations indicate that visual information can be used for online control of stepping. Behavioral investigations suggest that, during walking, the availability of visual information increases stepping accuracy, but probably through a feedforward control mechanism. Consequently, downward gazing (DWG) is usually interpreted as a strategy used to acquire useful information for online and/or feedforward control of stepping.Visual information is not exclusively used for guiding locomotion; a wealth of literature has been published on the usefulness of visual information for feedback postural control. Critically, postural control has been shown to be sensitive to the visual flow arising from the respective motion of the individual and the 3D environment.To investigate whether DWG can be used to enhance feedback control of posture, rather than feedforward/online control of gait, we conducted a series of experiments that explore this possible interplay. Through these experiments we were able to show that DWG, just a few steps ahead, results in a steadier standing and walking posture, without the need for accuracy. Moreover, we were able to demonstrate that humans resort to DWG when walking stability is compromised, even when destabilizing features were visually unpredictable.This series of experiments provides sufficient evidence of the possible interplay between visual information used for guiding locomotion and that used for postural control. Moreover, this evidence raises concerns regarding the way we interpret gaze behavior without the knowledge of the type and use of the information gathered.
Two particle picking procedures for filamentous proteins: SPHIRE-crYOLO filament mode and SPHIRE-STRIPER
Authors: Wagner Thorsten , Lusnig Luca , Pospich Sabrina , Stabrin Markus , Schönfeld Fabian , Raunser Stefan 
Published: February 2020

AbstractStructure determination of filamentous molecular complexes involves the selection of filaments from cryo-EM micrographs. The automatic selection of helical specimens is particularly difficult and thus many challenging samples with issues such as contamination or aggregation are still manually picked. Here we present two approaches for selecting filamentous complexes: one uses a trained deep neural network to identify the filaments and is integrated in SPHIRE-crYOLO, the other one, called SPHIRE-STRIPER, is based on a classical line detection approach. The advantage of the crYOLO based procedure is that it accurately performs on very challenging data sets and selects filaments with high accuracy. Although STRIPER is less precise, the user benefits from less intervention, since in contrast to crYOLO, STRIPER does not require training. We evaluate the performance of both procedures on tobacco mosaic virus and filamentous F-actin data sets to demonstrate the robustness of each method.
Crystallography of lamin A facilitated by chimeric fusions
Authors: Stalmans Giel , Lilina Anastasia V. , Strelkov Sergei V. 
Published: February 2020

AbstractAll proteins of the intermediate filament (IF) family contain the signature central α-helical domain which forms a coiled-coil dimer. Because of its length, past structural studies relied on a ‘divide-and-conquer’ strategy whereby fragments of this domain were recombinantly produced, crystallized and analysed using X-rays. Here we describe a further development of this approach towards structural studies of nuclear IF protein lamin. To this end, we have fused lamin A fragments to short N- and C-terminal capping motifs which provide for the correct formation of parallel, in-register coiled-coil dimers. As the result, a chimeric construct containing lamin A residues 17-70 C-terminally capped by the Eb1 domain was solved to 1.83 Å resolution. Another chimera containing lamin A residues 327-403 N-terminally capped by the Gp7 domain was solved to 2.9 Å. In the latter case the capping motif was additionally modified to include a disulphide bridge at the dimer interface. We discuss multiple benefits of fusing coiled-coil dimers with such capping motifs, including a convenient crystallographic phasing by either molecular replacement or sulphur single-wavelength anomalous dispersion (S-SAD) measurements.
SULF1 suppresses Wnt3A-driven growth of bone metastatic prostate cancer in perlecan-modified 3D cancer-stroma-macrophage triculture models
Authors: da Costa Fabio Henrique Brasil , Lewis Michael , Truong Anna , Carson Daniel , Farach-Carson Mary 
Published: February 2020

AbstractBone marrow stroma influences metastatic prostate cancer (PCa) progression, latency, and recurrence. At sites of PCa bone metastasis, cancer-associated fibroblasts and tumor-associated macrophages interact to establish a perlecan-rich desmoplastic stroma. As a heparan sulfate proteoglycan, perlecan (HSPG2) stores and stabilizes growth factors, including heparin-binding Wnt3A, a positive regulator of PCa cell growth. Because PCa cells alone do not induce CAF production of perlecan in the desmoplastic stroma, we sought to discover the sources of perlecan and its growth factor-releasing modifiers SULF1, SULF2, and heparanase in PCa cells and xenografts, bone marrow fibroblasts, and macrophages. SULF1, produced primarily by bone marrow fibroblasts, was the main glycosaminoglycanase present, a finding validated with primary tissue specimens of PCa metastases with desmoplastic bone stroma. Expression of bothHSPG2andSULF1was concentrated inαSMA-rich stroma near PCa tumor nests, where infiltrating pro-tumor TAMs also were present. To decipher SULF1’s role in the reactive bone stroma, we created a bone marrow biomimetic hydrogel incorporating perlecan, PCa cells, macrophages, and fibroblastic bone marrow stromal cells. Finding that M2-like macrophages increased levels ofSULF1andHSPG2produced by fibroblasts, we examined SULF1 function in Wnt3A-mediated PCa tumoroid growth in tricultures. Comparing control orSULF1knockout fibroblastic cells, we showed that SULF1 reduces Wnt3A-driven growth, cellularity, and cluster number of PCa cells in our 3D model. We conclude that SULF1 can suppress Wnt3A-driven growth signals in the desmoplastic stroma of PCa bone metastases, andSULF1loss favors PCa progression, even in the presence of pro-tumorigenic TAMs.
New Radiological Classification of Glioma and validation with the survival analysis
Authors: Kamble Akshaykumar Nana , Agrawal Nidhi K , Koundal Surabhi , Bhargava Salil , Kamble Abhaykumar Nana 
Published: February 2020

AbstractRadiology based classification of glioma independent of histological or genetic markers predicting survival of patients is an unmet need. Until now radiology is chasing these markers rather than focussing directly on the clinical outcome. Our study is first of its kind to come up with the independent new radiological classification of gliomas encompassing both low-and high-grade gliomas under single classification system.TCGA-LGG and REMBRANDT public domain dataset of glioma were analyzed as training and testing dataset respectively. Based on MRI images, gliomas were classified into six types in detailed classification & three types in simplified classification system. Survival analysis using Kaplan Meier and Cox regression was done. Secondary objective was to evaluate the sensitivity and specificity of novel signs with existing histological and genetic markers.The study predicted survival in both training and testing dataset independent of genetic or histological information. Novel signs, “Ball on Christmas tree” sign(highly specific), Type-4 lineage sign(highly sensitive) identifies IDH-wild and high-grade gliomas (grade-III and IV) while Type-2 lineage sign showed good specificity in identifying 1p19q non co-deleted IDH-mutated, ATRX del/mutated, Grade-II gliomas. There is a substantial interobserver agreement for the classification and novel signs. New radiological classification of glioma predicts the survival of patients independent of genetic or histological information. This can act as a scaffolding to formulate and streamline the treatment guidelines for glioma patients. This classification has potential of improving the quality of care of glioma patients by predicting the survival without the need of invasive biopsy.
The low complexity regions in the C-terminus are essential for the subcellular localisation of Leishmania casein kinase 1 but not for its activity
Authors: Martel Daniel , Pine Stewart , Bartsch Katharina , Clos Joachim , Späth Gerald F. , Rachidi Najma 
Published: February 2020

AbstractCasein Kinase 1 (CK1) family members are serine/threonine protein kinases ubiquitously expressed in eukaryotic organisms. They are involved in a wide range of important cellular processes, such as membrane trafficking, or vesicular transport in organisms from yeast to humans. Due to its broad spectrum of action, CK1 activity and expression is tightly regulated by a number of mechanisms, including subcellular sequestration. Defects in CK1 regulation, localisation or the introduction of mutations in the CK1 coding sequence are often associated with important diseases such as cancer. Increasing evidence suggest that the manipulation of host cell CK1 signalling pathways by intracellular pathogens, either by exploiting the host CK1 or by exporting the CK1 of the pathogen into the host cell may play an important role in infectious diseases. Leishmania CK1.2 is essential for parasite survival and released into the host cell, playing an important role in host pathogen interactions. Although Leishmania CK1.2 has dual role in the parasite and in the host cell, nothing is known about its parasitic localisation and organelle-specific functions. In this study, we show that CK1.2 is a ubiquitous kinase, which is present in the cytoplasm, associated to the cytoskeleton and localised to various organelles, indicating potential roles in kinetoplast and nuclear segregation, as well as ribosomal processing and motility. Furthermore, using truncated mutants, we show for the first time that the two low complexity regions (LCR) present in the C-terminus of CK1.2 are essential for the subcellular localisation of CK1.2 but not for its kinase activity, whereas the deletion of the N-terminus leads to a dramatic decrease in CK1.2 abundance. In conclusion, our data on the localisation and regulation of Leishmania CK1.2 contribute to increase the knowledge on this essential kinase and get insights into its role in the parasite.
Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
Authors: Maynard Kristen R. , Collado-Torres Leonardo , Weber Lukas M. , Uytingco Cedric , Barry Brianna K. , Williams Stephen R. , Catallini Joseph L. , Tran Matthew N. , Besich Zachary , Tippani Madhavi , Chew Jennifer , Yin Yifeng , Kleinman Joel E. , Hyde Thomas M. , Rao Nikhil , Hicks Stephanie C. , Martinowich Keri , Jaffe Andrew E. 
Published: February 2020

AbstractWe used the 10x Genomics Visium platform to define the spatial topography of gene expression in the six-layered human dorsolateral prefrontal cortex (DLPFC). We identified extensive layer-enriched expression signatures, and refined associations to previous laminar markers. We overlaid our laminar expression signatures onto large-scale single nuclei RNA sequencing data, enhancing spatial annotation of expression-driven clusters. By integrating neuropsychiatric disorder gene sets, we showed differential layer-enriched expression of genes associated with schizophrenia and autism spectrum disorder, highlighting the clinical relevance of spatially-defined expression. We then developed a data-driven framework to define unsupervised clusters in spatial transcriptomics data, which can be applied to other tissues or brain regions where morphological architecture is not as well-defined as cortical laminae. We lastly created a web application for the scientific community to explore these raw and summarized data to augment ongoing neuroscience and spatial transcriptomics research (http://research.libd.org/spatialLIBD).
A Quantitative Sequencing Framework for Absolute Abundance Measurements of Mucosal and Lumenal Microbial Communities
Authors: Barlow Jacob T. , Bogatyrev Said R. , Ismagilov Rustem F. 
Published: February 2020

AbstractA fundamental goal in microbiome studies is to determine which microbes affect host physiology. Standard methods for determining changes in microbial taxa measure relative microbial abundances, which cannot capture absolute changes. Moreover, studies often focus on a single site (usually stool), although microbial demographics differ substantially among gastrointestinal (GI) locations. Here, we developed a quantitative framework to accurately measure absolute abundances of individual bacterial taxa by combining the precision of digital PCR with the high-throughput nature of 16S rRNA gene amplicon sequencing. In a murine ketogenic-diet study, we compared microbial loads in lumenal and mucosal samples at several sites along the GI tract. Measurements of absolute (but not relative) abundances revealed decreases in total microbial loads on the ketogenic diet and enabled us to accurately determine the effect of the diet on each taxon at each GI location. Quantitative measurements also revealed different patterns in how the ketogenic diet affected each taxon’s abundance in stool and small-intestine mucosa samples. This rigorous quantitative microbial analysis framework applied to samples from relevant GI locations will enable mapping microbial biogeography of the mammalian GI tract and more accurately capture the changes of microbial taxa in experimental microbiome studies.
Unique structural features of mammalian NEIL2 DNA glycosylase prime its activity for diverse DNA substrates and environments
Authors: Eckenroth Brian E. , Cao Vy , Averill April M. , Dragon Julie A. , Doublié Sylvie 
Published: February 2020

SUMMARYOxidative damage on DNA arising from both endogenous and exogenous sources can result in base modifications that promote errors in replication as well as generate sites of base loss (abasic sites) that present unique challenges to maintaining genomic integrity. These lesions are excised by DNA glycosylases in the first step of the base excision repair pathway. Here we present the first crystal structure of a NEIL2 glycosylase, an enzyme active on cytosine oxidation products and abasic sites. The structure reveals an unusual “open” conformation not seen in NEIL1 or NEIL3 orthologs. NEIL2 is predicted to adopt a “closed” conformation when bound to its substrate. Combined crystallographic and solution scattering studies show the enzyme to be conformationally dynamic in a manner distinct among the NEIL glycosylases and provide insight into the unique substrate preference of the enzyme. Additionally, we characterized three cancer variants of human NEIL2, namely S140N, G230W, and G303R.
The Effect of a Virtual No-Step Zone on Balance Control in Walking
Authors: Fettrow Tyler , DiBianca Stephen , dos Santos Fernando Vanderlinde , Reimann Hendrik , Jeka John 
Published: February 2020

AbstractHumans need to actively control their upright posture during walking to avoid loss of balance. We do not have a comprehensive theory for how humans regulate balance during walking, especially in complex environments. Balance must be maintained in a variety of contexts including crowded city side-walks, rocky nature trails, walks on the beach, or fast-paced sporting events. The nervous system must process many aspects of the environment to produce an appropriate motor output in order to maintain balance on two legs. We have previously identified three balance mechanisms that young healthy adults use to maintain balance while walking: 1) The ankle roll mechanism, a modulation of ankle inversion/eversion; 2) The foot placement mechanism, a shift of the swing foot placement; and 3) The push-off mechanism, a modulation of the ankle plantarflexion angle during double stance. We know that these mechanisms are interdependent and can be influenced by internal factors such as the phase of the gait cycle and walking cadence. Here we seek to determine whether there are changes in neural control of balance when walking in the presence of environmental constraints. Subjects walked on a selfpaced treadmill while immersed in a virtual environment that provides three different colored pathways. Subjects were instructed not to step in theNo-Step Zone, which appeared either on the right or left side of the subject. While walking, subjects received balance perturbations in the form of galvanic vestibular stimulation, providing the sensation of falling sideways, either toward theNo-Stepzone or toward theNeutralzone on the other side. The results indicate that the use of the balance mechanisms are subtly altered depending on whether the perceived fall is toward theNo-Stepor theNeutralzone. This experiment provides further evidence that the balance control system during walking is extremely flexible, recruiting multiple mechanisms at different times in the gait cycle to adapt to environmental constraints.