bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic action of the Sec machinery during initiation, protein translocation and termination revealed by single molecule fluorescence
Authors: Fessl Tomas , Watkins Daniel , Oatley Peter , Allen William J. , Corey Robin A. , Horne Jim E. , Baldwin Steve A. , Radford Sheena E. , Collinson Ian , Tuma Roman 
Published: January 2018

AbstractProtein translocation across cell membranes is a ubiquitous process required for protein secretion and membrane protein insertion. This is mediated, for the majority of proteins, by the highly conserved Sec machinery. The bacterial translocon – SecYMKEG – resides in the plasma membrane, where translocation is driven through rounds of ATP hydrolysis by the cytoplasmic SecA ATPase, and the proton motive force (PMF). We have used single molecule Förster resonance energy transfer (FRET) alongside a combination of confocal and total internal reflection microscopy to gain access to SecY pore dynamics and translocation kinetics on timescales spanning milliseconds to minutes. This allows us to dissect and characterise the translocation process in unprecedented detail. We show that SecA, signal sequence, pre-protein and ATP hydrolysis each have important and specific roles in unlocking and opening the Sec channel, priming it for transport. After channel opening, translocation proceeds in two phases: an initiation phase independent of substrate length, and a length-dependent transport phase with an intrinsic translocation rate of ~ 40 amino acids per second for the model pre-protein substrate proOmpA. The initiation and translocation phases are both coupled to ATP hydrolysis while termination is ATP-independent. Distributions of translocation rates reflect the stochastic nature of the translocation process and are consistent with the recently proposed Brownian ratchet model [Allenet al.doi: 10.7554/eLife.15598]. The results allow us unparalleled access to the kinetics of the complex reaction and provide a framework for understanding the molecular mechanism of protein secretion.
Loss of Trem2 in microglia leads to widespread disruption of cell co-expression networks in mouse brain
Authors: Carbajosa Guillermo , Malki Karim , Lawless Nathan , Wang Hong , Ryder John W. , Wozniak Eva , Wood Kristie , Mein Charles A. , Dobson Richard J.B. , Collier David A. , O’Neill Michael J. , Hodges Angela K. , Newhouse Stephen J. 
Published: January 2018

AbstractRare heterozygous coding variants in the Triggering Receptor Expressed in Myeloid cells 2 (TREM2) gene, conferring increased risk of developing late-onset Alzheimer's disease, have been identified. We examined the transcriptional consequences of the loss of Trem2 in mouse brain to better understand its role in disease using differential expression and coexpression network analysis of Trem2 knockout and wild-type mice. We generated RNA-Seq data from cortex and hippocampus sampled at 4 and 8 months. Using brain cell type markers and ontology enrichment, we found subnetworks with cell type and/or functional identity. We primarily discovered changes in an endothelial-gene enriched subnetwork at 4 months, including a shift towards a more central role for the Amyloid Precursor Protein (App) gene, coupled with widespread disruption of other cell-type subnetworks, including a subnetwork with neuronal identity. We reveal an unexpected potential role of Trem2 in the homeostasis of endothelial cells that goes beyond its known functions as a microglial receptor and signalling hub, suggesting an underlying link between immune response and vascular disease in dementia.
A novel system for online fertility monitoring based on milk progesterone
Authors: Adriaens Ines , Saeys Wouter , Huybrechts Tjebbe , Lamberigts Chris , François Liesbeth , Geerinckx Katleen , Leroy Jo , De Ketelaere Bart , Aernouts Ben 
Published: January 2018

ABSTRACTTimely identification of a cow’s reproduction status is essential to minimize fertilityrelated losses on dairy farms. This includes optimal estrus detection, pregnancy diagnosis and the timely recognition of early embryonic death and ovarian problems. On farm milk progesterone (P4) analysis could indicate all of these fertility events simultaneously. However, milk P4 measurements are subject to a large variability both in terms of measurement errors and absolute values between cycles. In this study, an innovative monitoring system based on milk P4 using the principles of synergistic control is presented. Instead of using filtering techniques and fixed thresholds, the present system employs an individually updated online model to describe the P4 profile, combined with a statistical process control chart to identify the cow’s fertility status. The inputs for the latter are the residuals of the online model, corrected for the concentration-dependent variability which is typical for milk P4 measurements. The objective of this paper is to present the developed methodology and give an indication of its use on farm. To this end, the system was validated on the P4 profiles of 38 dairy cows. The positive predictive value for luteolysis followed by estrus was 100%, meaning that the monitoring system picked up all estrous periods identified by the experts. Pregnancy or embryonic mortality was characterized by the absence or detection of luteolysis following an insemination, respectively. For thirteen cows, no luteolysis was detected by the system within the 25-32 days after insemination, indicating pregnancy, which was confirmed later by rectal palpation. It was also shown that the system is able to cope with deviating P4 profiles having prolonged follicular or luteal phases, which may suggest the occurrence of cysts. Future research is recommended for optimizing sampling frequency, prediction of the optimal insemination window and the establishment of rules to detect problems based on deviating P4 patterns.INTERPRETIVE SUMMARY. Progestrone-based online fertility monitoring. Adriaens.Milk progesterone based monitoring systems can be valuable for indicating fertility events in dairy cows, as the evolution of the milk progesterone levels can be related to acyclicity, estrus, pregnancy, and ovarian problems. We developed a system to translate raw progesterone measurements into clear information for the farmer, based on a mathematical model and a statistical control chart. In this way, a detailed image of a cow’s reproduction status on-farm can be obtained and fertility-related losses minimized.
Diverse spatial organization of photosynthetic membranes among purple nonsulfur bacteria
Authors: LaSarre Breah , Kysela David T. , Stein Barry D. , Ducret Adrien , Brun Yves V. , McKinlay James B. 
Published: January 2018

ABSTRACTIn diverse bacteria, proper cellular physiology requires the utilization of protein- or membrane-bound compartments that afford specific metabolic capabilities. One such compartment is the light-harvesting intracytoplasmic membrane (ICM) of purple nonsulfur bacteria (PNSB). Here we reveal that ICMs are subject to differential spatial organization among PNSB. We visualized ICMs in live cells of fourteen PNSB species by exploiting the natural autofluorescence of the photosynthetic machinery. We then quantitatively characterized ICM localization using automated computational analysis of autofluorescence patterns within single cells across the population. Our studies revealed that ICMs are localized in distinct subcellular patterns that differ between species; some PNSB elaborate ICMs throughout the cell, while others spatially restrict ICM to varying degrees. The most highly-restricted ICMs were localized in a specific pattern corresponding to progression of cell growth and division. An identical pattern of ICM restriction was conserved across at least two genera. Phylogenetic and phenotypic comparisons established that ICM localization and ICM architecture are not strictly interdependent and that neither trait fully correlates with the evolutionary relatedness of the species. This discovery of new diversity in bacterial cell organization has implications for understanding both the mechanisms underpinning spatial arrangement of bacterial compartments and the potential benefits of adopting different spatiotemporal patterns.
Higher performers upregulate brain signal variability in response to more feature-rich visual input
Authors: Garrett Douglas D. , Epp Samira , Kleemeyer Maike , Lindenberger Ulman , Polk Thad A. 
Published: January 2018

AbstractThe extent to which brain responses differ across varying cognitive demands is referred to as “neural differentiation,” and greater neural differentiation has been associated with better cognitive performance in older adults. An emerging approach has examined within-person neural differentiation using moment-to-moment brain signal variability. A number of studies have found that brain signal variability differs by cognitive state; however, the factors that cause signal variability to rise or fall on a given task remain understudied. We hypothesized that top performers would modulate signal variability according to the complexity of sensory input, upregulating variability when processing more feature-rich stimuli. In the current study, 46 older adults passively viewed face stimuli and house stimuli during fMRI. Low-level analyses of our stimuli showed that house images were more feature-rich than faces, and subsequent computational modelling of ventral visual stream responses (HMAX) revealed that houses were more feature-rich especially in V1/V2-like model layers. Notably, we then found that participants exhibiting greater face-to-house upregulation of brain signal variability in V1/V2 (higher for house relative to face stimuli) also exhibited more accurate, faster, and more consistent behavioral performance on a battery of offline visuo-cognitive tasks. Further, control models revealed that face-house modulation of mean brain signal was relatively insensitive to offline cognition, providing further evidence for the importance of brain signal variability for understanding human behavior. We conclude that the ability to align brain signal variability to the complexity of perceptual input may mark heightened trait-level behavioral performance in older adults.
Substrate deformations induce directed keratinocyte migration
Authors: Zarkoob Hoda , Chinnathambi Sathivel , Selby John C. , Sander Edward A. 
Published: January 2018

ABSTRACTCell migration is an essential part of many (patho)physiological processes in the body, including keratinocyte re-epithelialization of healing wounds. Recent interest in the mechanobiology of tissues suggests that physical forces and mechanical cues from the wound bed (in addition to biochemical signals) may also play an important role in the healing process. Previously, we explored this possibility and found that polyacrylamide (PA) gel stiffness affected primary human keratinocyte behavior and that mechanical deformations in soft (~1.2 kPA) PA gels produced by neighboring cells appeared to influence the process ofde novoepithelial sheet formation. In order to clearly demonstrate that keratinocytes do respond to such deformations, we conducted a series of experiments where we observed the response of single keratinocytes to a prescribed local substrate deformation that mimicked a neighboring cell or evolving multicellular aggregate via a servo-controlled microneedle. We also examined the effect of adding either Y27632, a rho kinase inhibitor, or blebbistatin, a non-muscle myosin II inhibitor, on the response of the cells to PA gel deformations. The results of this study indicate that keratinocytes do sense and respond to mechanical signals comparable to those that originate from substrate displacements imposed by neighboring cells, a finding that could have important implications for the process of keratinocyte re-epithelialization that takes place during normal and pathologic wound healing. Furthermore, the Rho/ROCK pathway and the engagement of NM II are both essential to the observed process of substrate deformation-directed keratinocyte migration.
Structure of the Core of the Type Three Secretion System Export Apparatus
Authors: Kuhlen Lucas , Abrusci Patrizia , Johnson Steven , Gault Joseph , Deme Justin , Caesar Joseph , Dietsche Tobias , Mebrhatu Mehari Tesfazgi , Ganief Tariq , Macek Boris , Wagner Samuel , Robinson Carol V. , Lea Susan M. 
Published: January 2018

SummaryExport of proteins through type three secretion systems is critical for bacterial motility and virulence of many major bacterial pathogens. Three putative integral membrane proteins (FliP/FliQ/FliR) are suggested to form the core of an export gate in the inner membrane, but their structure, assembly and location within the final nanomachine remain unclear. We here present the structure of this complex at 4.2 Å by cryo-electron microscopy. None of the subunits adopt canonical integral membrane protein topologies and common helix-turn-helix structural elements allow them to form a helical assembly with 5:4:1 stoichiometry. Fitting of the structure into reconstructions of intact secretion systems localize the export gate as a core component of the periplasmic portion of the machinery, and cross-linking experiments confirm this observation. This study thereby identifies the export gate as a key element of the secretion channel and implies that it primes the helical architecture of the components assembling downstream.One Sentence SummaryThe core of the T3SS export gate forms a supra-membrane helical assembly
Enabling the hypothesis-driven prioritization of ligand candidates in big databases: Screenlamp and its application to GPCR inhibitor discovery for invasive species control
Authors: Raschka Sebastian , Scott Anne M. , Liu Nan , Gunturu Santosh , Huertas Mar , Li Weiming , Kuhn Leslie A. 
Published: January 2018

AbstractWhile the advantage of screening vast databases of molecules to cover greater molecular diversity is often mentioned, in reality, only a few studies have been published demonstrating inhibitor discovery by screening more than a million compounds for features that mimic a known three-dimensional ligand. Two factors contribute: the general difficulty of discovering potent inhibitors, and the lack of free, user-friendly software to incorporate project-specific knowledge and user hypotheses into 3D ligand-based screening. The Screenlamp modular toolkit presented here was developed with these needs in mind. We show Screenlamp’s ability to screen more than 12 million commercially available molecules and identify potentin vivoinhibitors of a G protein-coupled bile acid receptor within the first year of a discovery project. This pheromone receptor governs sea lamprey reproductive behavior, and to our knowledge, this project is the first to establish the efficacy of computational screening in discovering lead compounds for aquatic invasive species control. Significant enhancement in activity came from selecting compounds based on one of the hypotheses: that matching two distal oxygen groups in the three-dimensional structure of the pheromone is crucial for activity. Six of the 15 most active compounds met these criteria. A second hypothesis – that presence of an alkyl sulfate side chain results in high activity – identified another 6 compounds in the top 10, demonstrating the significant benefits of hypothesis-driven screening.
Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data
Authors: Coudray Alexandre , Battenhouse Anna M. , Bucher Philipp , Iyer Vishwanath R. 
Published: January 2018

ABSTRACTTo detect functional somatic mutations in tumor samples, whole-exome sequencing (WES) is often used for its reliability and relative low cost. RNA-seq, while generally used to measure gene expression, can potentially also be used for identification of somatic mutations. However there has been little systematic evaluation of the utility of RNA-seq for identifying somatic mutations. Here, we develop and evaluate a pipeline for processing RNA-seq data from glioblastoma multiforme (GBM) tumors in order to identify somatic mutations. The pipeline entails the use of the STAR aligner 2-pass procedure jointly with MuTect2 from GATK to detect somatic variants. Variants identified from RNA-seq data were evaluated by comparison against the COSMIC and dbSNP databases, and also compared to somatic variants identified by exome sequencing. We also estimated the putative functional impact of coding variants in the most frequently mutated genes in GBM. Interestingly, variants identified by RNA-seq alone showed better representation of GBM-related mutations cataloged by COSMIC. RNA-seq-only data substantially outperformed the ability of WES to reveal potentially new somatic mutations in known GBM-related pathways, and allowed us to build a high-quality set of somatic mutations common to exome and RNA-seq calls. Using RNA-seq data in parallel with WES data to detect somatic mutations in cancer genomes can thus broaden the scope of discoveries and lend additional support to somatic variants identified by exome sequencing alone.
Increased PHGDH expression uncouples hair follicle cycle progression and promotes inappropriate melanin accumulation
Authors: Mattaini Katherine R. , Sullivan Mark R. , Lau Allison N. , Fiske Brian P. , Bronson Roderick T. , Vander Heiden Matthew G. 
Published: January 2018

SUMMARYCopy number gain of thePHGDHgene that encodes the first enzyme of the serine biosynthesis pathway is found in some human cancers, including a subset of melanomas. In order to study the effect of increasedPHGDHexpression in tissuesin vivo, we generated mice harboring aPHGDHtetOallele that allows tissue-specific, doxycycline-inducible PHGDH expression. Tissues and cells derived fromPHGDHtetOmice exhibit increased serine biosynthesis. Histological examination of skin tissue fromPHGDHtetOmice reveals the presence of melanin granules in anagen II hair follicles, despite the fact that melanin synthesis is normally closely coupled to the hair follicle cycle and does not begin until later in the cycle. This phenotype occurs in the absence of any global change in hair follicle cycle timing. The inappropriate presence of melanin early in the hair follicle cycle following PHGDH expression is also accompanied by increased melanocyte abundance in anagen II skin. Together, these data support a model in which PHGDH expression affects melanocyte proliferation and/or differentiation and may provide insight into how PHGDH expression impacts normal melanocyte biology to promote melanoma.SIGNIFICANCEThe significance behind copy number gain ofPHGDHin human cancers is unclear. In this study, we generate a mouse model that mimicsPHGDHgene copy number gain and characterize its effect on normal tissues. Increased PHGDH expression yields a phenotype of aberrant melanin production, which indicates that PHGDH expression may play a role in normal melanocyte biology. This result may provide insight into whyPHGDHcopy number gain is observed in melanoma more frequently than in most other tumor types.
Massive surface membrane expansion without involvement of classical exocytic mechanisms
Authors: Fine Michael , Bricogne Christopher , Hilgemann Donald W. 
Published: January 2018

AbstractActivation of TMEM16F, a Ca2+ -dependent ion channel and lipid scramblase, causes massive surface membrane expansion in multiple cell types by unresolved mechanisms. We describe here that membrane expansion reflects opening of deeply invaginating surface membrane compartments when anionic phospholipids are lost from the cytoplasmic membrane leaflet. Compartments that open contain vesicle-associated membrane proteins (VAMPs) and can open with as little as one micromolar free Cai2+. Cationic peptides that sequester anionic phospholipids open the compartments from the cytoplasmic side without Ca2+. Monovalent cations facilitate membrane expansion via coupled permeation with anionic phospholipids through TMEM16F. When monovalent cation concentrations are reduced, membrane expansion can be reversed by changing ion gradients and membrane voltage. Depolarization closes the compartments by generating inward cation gradients through TMEM16F that promote influx of anionic phospholipids. In summary, TMEM16F-mediated membrane expansion likely does not reflect exocytosis but rather the relaxation of constrictions that close surface membrane invaginations.SummaryThe surface membrane of diverse cell types can be remodeled by opening and closing surface invaginations that are held shut by proteins that bind negatively charged lipids and constrict the orifices of these compartments.
Genetic Diversity and Distributional Pattern of Ammonia Oxidizing Archaea Lineages in the Global Oceans
Authors: Cheung Shunyan , Mak Wingkwan , Xia Xiaomin , Lu Yanhong , Liu Hongbin 
Published: January 2018

SummaryIn the study, we used miTAG approach to analyse the distributional pattern of the ammonium oxidizing archaea (AOA) lineages in the global oceans using the metagenomics datasets of the Tara Oceans global expedition (2009-2013). Using ammonium monooxygenase alpha subunit gene as biomarker, the AOA communities were obviously segregated with water depth, except the upwelling regions. Besides, the AOA communities in the euphotic zones are more heterogeneous than in the mesopelagic zones (MPZs). Overall, water column A clade (WCA) distributes more evenly and widely in the euphotic zone and MPZs, while water column B clade (WCB) and SCM-like clade mainly distribute in MPZ and high latitude waters, respectively. At fine-scale genetic diversity, SCM1-like and 2 WCA subclades showed distinctive niche separation of distributional pattern. The AOA subclades were further divided into ecological significant taxonomic units (ESTUs), which were delineated from the distribution pattern of their corresponding subclades. For examples, ESTUs of WCA have different correlation with depth, nitrate to silicate ratio and salinity; SCM1-like-A was negatively correlated with irradiation; the other SCM-like ESTUs preferred low temperature and high nutrient conditions, etc. Our study provides new insight to the genetic diversity of AOA in global scale and its connections with environmental factors.