bluuebunny/crossref_metadata_2025 huggingface dataset:
Prohibitin depletion extends lifespan of a TORC2/SGK-1 mutant through autophagy
Authors: Hernando-Rodríguez Blanca , Pérez-Jiménez Mercedes M. , Rodríguez-Palero María Jesús , Pla Antoni , Martínez-Bueno Manuel David , de la Cruz Ruiz Patricia , Gatsi Roxani , Artal-Sanz Marta
Published: October 2019

Mitochondrial prohibitins (PHB) are highly conserved proteins with a peculiar effect on lifespan. While PHB depletion shortens lifespan of wild type animals, it enhances longevity of a plethora of metabolically compromised mutants, including target of rapamycin complex 2 (TORC2) mutantssgk-1andrict-1. Here, we show thatsgk-1mutants have impaired mitochondrial homeostasis, lipogenesis, yolk formation and autophagy flux due to alterations in membrane lipid and sterol homeostasis. Remarkably, all these features are suppressed by PHB depletion. Lifespan analysis shows that autophagy and the mitochondrial unfolded protein response (UPRmt), but not mitophagy, are required for the enhanced longevity caused by PHB depletion insgk-1mutants. We hypothesize that UPRmtinduction upon PHB depletion extends lifespan ofsgk-1mutants through autophagy. Our results strongly suggest that PHB depletion suppresses the autophagy defects ofsgk-1mutants by altering membrane lipid composition at ER-mitochondria contact sites, where TORC2 localizes.
Aberrant connectivity in auditory precision encoding in schizophrenia spectrum disorder and across the continuum of psychotic-like experiences
Authors: Larsen Kit Melissa , Dzafic Ilvana , Darke Hayley , Pertile Holly , Carter Olivia , Sundram Suresh , Garrido Marta I.
Published: October 2019

Background

The ability to generate a precise internal model of statistical regularities is impaired in schizophrenia. Predictive coding accounts of schizophrenia suggest that psychotic symptoms may be explained by a failure to build precise beliefs or a model of the world. The precision of this model may vary with context. For example, in a noisy environment the model will be more imprecise compared to a model built in an environment with lower noise. However compelling, this idea has not yet been empirically studied in schizophrenia. Methods: In this study, 62 participants engaged in a stochastic mismatch negativity paradigm with high and low precision. We included inpatients with a schizophrenia spectrum disorder (N=20), inpatients with a psychiatric disorder but without psychosis (N=20), and healthy controls (N=22), with comparable sex ratio and age distribution. Bayesian mapping and dynamic causal modelling were employed to investigate the underlying microcircuitry of precision encoding of auditory stimuli. Results: We found strong evidence (exceedance p > 0.99) for differences in the underlying connectivity associated with precision encoding between the three groups as well as on the continuum of psychotic-like experiences assessed across all participants. Critically, we show changes in interhemispheric connectivity between the two inpatient groups, with some connections further aligning on the continuum of psychotic-like experiences. Conclusions: While our results suggest continuity in backward connectivity alterations with psychotic-like experiences regardless of diagnosis, they also point to specificity for the schizophrenia spectrum disorder group in interhemispheric connectivity alterations.
B cells extract antigens using Arp2/3-generated actin foci interspersed with linear filaments
Authors: Roper Sophie I. , Wasim Laabiah , Malinova Dessislava , Way Michael , Cox Susan , Tolar Pavel
Published: October 2019

Antibody production depends on B cell internalization and presentation of antigens to helper T cells. To acquire antigens displayed by antigen-presenting cells, B cells form immune synapses and extract antigens by the mechanical activity of the acto-myosin cytoskeleton. While cytoskeleton organization driving the initial formation of the B cell synapse has been studied, how the cytoskeleton supports antigen extraction remains poorly understood. Here we show that after initial cell spreading, F-actin in B cell synapses forms a highly dynamic pattern composed of actin foci interspersed with linear filaments and myosin IIa. The foci are generated by Arp2/3-mediated branched-actin polymerization and stochastically associate with antigen clusters to mediate internalization. However, antigen extraction also requires the activity of formins, which reside near the foci and produce the interspersed filaments. Thus, a cooperation of branched-actin foci supported by linear filaments underlies B cell mechanics during antigen extraction.
Gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure
Authors: Zrimec Jan , Buric Filip , Muhammad Azam Sheikh , Chen Rhongzen , Verendel Vilhelm , Töpel Mats , Zelezniak Aleksej
Published: October 2019

Understanding the genetic regulatory code that governs gene expression is a primary, yet challenging aspiration in molecular biology that opens up possibilities to cure human diseases and solve biotechnology problems. However, the fundamental question of how each of the individual coding and non-coding regions of the gene regulatory structure interact and contribute to the mRNA expression levels remains unanswered. Considering that all the information for gene expression regulation is already present in living cells, here we applied deep learning on over 20,000 mRNA datasets in 7 model organisms ranging from bacteria to Human. We show that in all organisms, mRNA abundance can be predicted directly from the DNA sequence with high accuracy, demonstrating that up to 82% of the variation of gene expression levels is encoded in the gene regulatory structure. Coding and non-coding regions carry both overlapping and orthogonal information and additively contribute to gene expression levels. By searching for DNA regulatory motifs present across the whole gene regulatory structure, we discover that motif interactions can regulate gene expression levels in a range of over three orders of magnitude. The uncovered co-evolution of coding and non-coding regions challenges the current paradigm that single motifs or regions are solely responsible for gene expression levels. Instead, we show that the correct combination of all regulatory regions must be established in order to accurately control gene expression levels. Therefore, the holistic system that spans the entire gene regulatory structure is required to analyse, understand, and design any future gene expression systems.
Reward-based improvements in motor control are driven by multiple error-reducing mechanisms
Authors: Codol Olivier , Holland Peter J. , Manohar Sanjay G. , Galea Joseph M.
Published: October 2019

Reward has a remarkable ability to invigorate motor behaviour, enabling individuals to select and execute actions with greater precision and speed. However, if reward is to be exploited in applied settings such as rehabilitation, a thorough understanding of its underlying mechanisms is required. Although reward-driven enhancement of movement execution has been proposed to occur through enhanced feedback control, an untested alternative is that it is driven by increased arm stiffness, an energy-consuming process that increases limb stability. First, we demonstrate that during reaching reward improves selection and execution performance concomitantly without interference. Computational analysis revealed that reward led to both an increase in feedback correction during movement and a reduction in motor noise near the target. We provide novel evidence that this noise reduction is driven by a reward-dependent increase in arm stiffness. Therefore, reward drives multiple error-reduction mechanisms which enable individuals to invigorate motor performance without compromising accuracy.
No evidence for motion dazzle in an evolutionary citizen science game
Authors: Hughes Anna E. , Griffiths David , Troscianko Jolyon , Kelley Laura A.
Published: October 2019

The motion dazzle hypothesis posits that high contrast geometric patterns can cause difficulties in tracking a moving target, and has been argued to explain the patterning of animals such as zebras. Research to date has only tested a small number of patterns, offering equivocal support for the hypothesis. Here, we take a genetic programming approach to allow patterns to evolve based on their fitness (time taken to capture) and thus find the optimal strategy for providing protection when moving. Our ‘Dazzle Bug’ citizen science game tested over 1.5 million targets in a touch screen game at a popular visitor attraction. Surprisingly, we found that targets lost pattern elements during evolution and became closely background matching. Modelling results suggested that targets with lower motion energy were harder to catch. Our results indicate that low contrast, featureless targets offer the greatest protection against capture when in motion, challenging the motion dazzle hypothesis.
Development of Candida auris microsatellite typing and its application on a global collection of isolates
Authors: de Groot Theun , Puts Ynze , Berrio Indira , Chowdhary Anuradha , Meis Jacques F.
Published: October 2019

Candida auris is a pathogenic yeast that causes invasive infections with high mortality. Infections most often occur in intensive care units of healthcare facilities. It is crucial to trace the source and prevent further spread of C. auris during an outbreak setting, therefore, genotyping of C. auris is required. To enable fast and cost-effective genotyping, we developed a microsatellite typing assay for C. auris.

Short tandem repeats (STRs) in C. auris were identified, and a novel STR typing assay for C. auris was developed using 4 panels of three multiplex PCRs. Having shown that the microsatellite typing assay was highly reproducible and specific, a robust set of 444 C. auris isolates was investigated to identify genotypic diversity. In concordance with whole-genome sequencing (WGS) analysis we identified five major different C. auris clusters, namely, South-America, South-Asia, Africa, East-Asia and Iran. Overall, a total of 40 distinct genotypes were identified, with the largest variety in the East Asian clade. Comparison with WGS demonstrated that isolates with <20 SNPs are mostly not differentiated by STR analysis, while isolates with 30 or more SNPs usually have differences in one or more STR markers.

Altogether, a highly reproducible and specific microsatellite typing assay for C. auris was developed, which distinguishes the five different C. auris clades in identical fashion to WGS, while most isolates differing >20 SNPs, as determined via WGS, are also separated. This new C. auris specific genotyping technique is a rapid, reliable, cost-effective alternative to WGS analysis to speedily investigate outbreaks.

Importance

Candida auris is an emerging fungal pathogen now recognized as a threat to public health. The pathogen has spread worldwide and mainly causes hospital associated outbreaks. To track and trace outbreaks and to relate them to new introductions from elsewhere, whole genome sequencing and amplified fragment length polymorphism (AFLP) have been used for molecular typing. While the former is costly and only available in few centers, AFLP is a complicated technique and standardization is not possible. We describe a novel simple microsatellite genotyping technique based on small tandem repeats in the C. auris genome. Further we show that this microsatellite based genotyping technique has been proven comparable to WGS. Overall, this work provides a novel, rapid, reliable and cost-effective method of molecular outbreaks investigations of C. auris.
Targeting the Pregnane X Receptor Using Microbial Metabolite Mimicry
Authors: Dvořák Zdeněk , Kopp Felix , Costello Cait M. , Kemp Jazmin S. , Li Hao , Vrzalová Aneta , Štěpánková Martina , Bartoňková Iveta , Jiskrová Eva , Poulíková Karolína , Vyhlídalová Barbora , Nordstroem Lars U. , Karunaratne Chamini , Ranhotra Harmit , Mun Kyu Shik , Naren Anjaparavanda P. , Murray Iain , Perdew Gary H. , Brtko Julius , Toporova Lucia , Schon Arne , Wallace William G. , Walton William G. , Redinbo Matthew R. , Sun Katherine , Beck Amanda , Kortagere Sandhya , Neary Michelle C. , Chandran Aneesh , Vishveshwara Saraswathi , Cavalluzzi Maria M. , Lentini Giovanni , Cui Julia Yue , Gu Haiwei , March John C. , Chaterjee Shirshendu , Matson Adam , Wright Dennis , Flannigan Kyle L. , Hirota Simon A. , Sartor R. Balfour , Mani Sridhar
Published: October 2019

The human pregnane X receptor (PXR), a master regulator of drug metabolism, has important roles in intestinal homeostasis and abrogating inflammation. Existing PXR ligands have substantial off-target toxicity. Based on prior work that established microbial (indole) metabolites as PXR ligands, we proposed microbial metabolite mimicry as a novel strategy for drug discovery that allows to exploit previously unexplored parts of chemical space. Here we report functionalized indole-derivatives as first-in-class non-cytotoxic PXR agonists, as a proof-of-concept for microbial metabolite mimicry. The lead compound, FKK6, binds directly to PXR protein in solution, induces PXR specific target gene expression in, cells, human organoids, and mice. FKK6 significantly represses pro-inflammatory cytokine production cells and abrogates inflammation in mice expressing the human PXR gene. The development of FKK6 demonstrates for the first time that microbial metabolite mimicry is a viable strategy for drug discovery and opens the door to mine underexploited regions of chemical space.
TLR5 participates in the TLR4 receptor complex and biases towards MyD88-dependent signaling in environmental lung injury
Authors: Hussain Salik , Johnson Collin G , Sciurba Joseph , Meng Xianglin , Stober Vandy P , Liu Caini , Cyphert-Daly Jaime M , Bulek Katarzyna , Qian Wen , Solis Alma , Sakamachi Yosuke , Trempus Carol S , Aloor Jim J , Gowdy Kym M , Foster W. Michael , Hollingsworth John W , Tighe Robert M , Li Xiaoxia , Fessler Michael B , Garantziotis Stavros
Published: October 2019

Lung disease causes significant morbidity and mortality, and is exacerbated by environmental injury, e.g. through lipopolysaccharide (LPS) or ozone (O3). Toll-like receptors (TLRs) orchestrate immune responses to injury by recognizing pathogen- or danger-associated molecular patterns. TLR4, the prototypic receptor for LPS, also mediates inflammation after O3, triggered by endogenous hyaluronan. Regulation of TLR4 signaling is incompletely understood. TLR5, the flagellin receptor, is expressed in alveolar macrophages, and regulates immune responses to environmental injury. Usingin vivoanimal models of TLR4-mediated inflammations (LPS, O3, hyaluronan), we show that TLR5 impacts thein vivoresponse to LPS, hyaluronan and O3. We demonstrate that immune cells of human carriers of a dominant negative TLR5 allele have decreased inflammatory response to O3exposureex vivoand LPS exposurein vitro. Using primary murine macrophages, we find that TLR5 physically associates with TLR4 and biases TLR4 signaling towards the MyD88 pathway. Our results suggest an updated paradigm for TLR4/TLR5 signaling.
Defining epidermal basal cell states during skin homeostasis and wound healing using single-cell transcriptomics
Authors: Haensel Daniel , Jin Suoqin , Cinco Rachel , Sun Peng , Nguyen Quy , Cang Zixuan , Dragan Morgan , Gong Yanwen , MacLean Adam L , Kessenbrock Kai , Gratton Enrico , Nie Qing , Dai Xing
Published: October 2019

Our knowledge of transcriptional heterogeneities in epithelial stem/progenitor cell compartments is limited. Epidermal basal cells sustain cutaneous tissue maintenance and drive wound healing. Previous studies have probed basal cell heterogeneity in stem/progenitor potential, but a non-biased dissection of basal cell dynamics during differentiation is lacking. Using single-cell RNA-sequencing coupled with RNAScope and fluorescence lifetime imaging, we identify three non-proliferative and one proliferative basal cell transcriptional states in homeostatic skin that differ in metabolic preference and become spatially partitioned during wound re-epithelialization. Pseudotemporal trajectory and RNA velocity analyses produce a quasi-linear differentiation hierarchy where basal cells progress fromCol17a1high/Trp63highstate to early response state, proliferate at the juncture of these two states, or become growth arrested before differentiating into spinous cells. Wound healing induces plasticity manifested by dynamic basal-spinous interconversions at multiple basal states. Our study provides a systematic view of epidermal cellular dynamics supporting a revised “hierarchical-lineage” model of homeostasis.
A Bayesian Non-parametric Mixed-Effects Model of Microbial Phenotypes
Authors: Tonner Peter D. , Darnell Cynthia L. , Bushell Francesca M.L. , Lund Peter A. , Schmid Amy K. , Schmidler Scott C.
Published: October 2019

Substantive changes in gene expression, metabolism, and the proteome are manifested in overall changes in microbial population growth. Quantifying how microbes grow is therefore fundamental to areas such as genetics, bioengineering, and food safety. Traditional parametric growth curve models capture the population growth behavior through a set of summarizing parameters. However, estimation of these parameters from data is confounded by random effects such as experimental variability, batch effects or differences in experimental material. A systematic statistical method to identify and correct for such confounding effects in population growth data is not currently available. Further, our previous work has demonstrated that parametric models are insufficient to explain and predict microbial response under non-standard growth conditions. Here we develop a hierarchical Bayesian non-parametric model of population growth that identifies the latent growth behavior and response to perturbation, while simultaneously correcting for random effects in the data. This model enables more accurate estimates of the biological effect of interest, while better accounting for the uncertainty due to technical variation. Additionally, modeling hierarchical variation provides estimates of the relative impact of various confounding effects on measured population growth.
Saak Transform-Based Machine Learning for Light-Sheet Imaging of Cardiac Trabeculation
Authors: Ding Yichen , Gudapati Varun , Lin Ruiyuan , Fei Yanan , Song Sibo , Chang Chih-Chiang , Baek Kyung In , Wang Zhaoqiang , Roustaei Mehrdad , Kuang Dengfeng , Jay Kuo C.-C. , Hsiai Tzung K.
Published: October 2019

Recent advances in light-sheet fluorescence microscopy (LSFM) enable 3-dimensional (3-D) imaging of cardiac architecture and mechanics in toto. However, segmentation of the cardiac trabecular network to quantify cardiac injury remains a challenge. We hereby employed “subspace approximation with augmented kernels (Saak) transform” for accurate and efficient quantification of the light-sheet image stacks following chemotherapy-treatment. We established a machine learning framework with augmented kernels based on the Karhunen-Loeve Transform (KLT) to preserve linearity and reversibility of rectification. The Saak transform-based machine learning enhances computational efficiency and obviates iterative optimization of cost function needed for neural networks, minimizing the number of training data sets to three 2-D slices for segmentation in our scenario. The integration of forward and inverse Saak transforms serves as a light-weight module to filter adversarial perturbations and reconstruct estimated images, salvaging robustness of existing classification methods. The accuracy and robustness of the Saak transform are evident following the tests of dice similarity coefficients and various adversary perturbation algorithms, respectively. The addition of edge detection further allows for quantifying the surface area to volume ratio (SVR) of the myocardium in response to chemotherapy-induced cardiac remodeling. The combination of Saak transform, random forest, and edge detection augments segmentation efficiency by 20-fold as compared to manual processing; thus, establishing a robust framework for post light-sheet imaging processing, creating a data-driven machine learning for 3-D quantification of cardiac ultra-structure.
Further Exploration of the SAR of Imidazoquinolines; Identification of Potent C7 Substituted Imidazoquinolines
Authors: Hunt Jordan R. , Kleindl Peter A. , Moulder K. Ryan , Prisinzano Thomas E. , Forrest M. Laird
Published: October 2019

Small molecule agonists of TLR7/8, such as imidazoquinolines, are validated agonists for the treatment of cancer and for use in vaccine adjuvants. Imidazoquinolines have been extensively modified to understand the structure-activity relationship (SAR) at the N1- and C2-positions resulting in the clinical drug imiquimod, resiquimod, and several other highly potent analogues. However, the SAR of the aryl ring has not been fully elucidated in the literature. This initial study examines the SAR of C7-substituted imidazoquinolines. These compounds not only demonstrated that TLR7/8 tolerate changes at the C7 position but can increase potency and change their cytokine profiles. The most notable TLR7/8 agonists developed from this study 5, 8, and 14 which are up to 4-fold and 2-fold more active than resiquimod for TLR8 and/or TLR7, respectively, and up to 100-fold more active than the FDA approved imiquimod for TLR7.
Live imaging-assisted domain-specific CRISPR genome editing at single cell resolution in plants
Authors: Li Ting , Yan An , Meyerowitz Elliot M.
Published: October 2019

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) technology has been widely used for genome engineering in a wide range of organisms1, but much of the development of CRISPR-based genome editing has been aimed toward improving its efficiency and accuracy, so as to obtain genetic materials carrying known and stably heritable genome modifications. Precise spatiotemporal control over genome editing technology at cell type resolution is a key challenge for gene function studies. Some tissue-specific CRISPR genome editing methods relying on phenotypic characterization and fluorescent immune-staining techniques have been developed for biomedical research and gene therapy, they function by spatially controlling expression of Cas9 2. Recent work establishes the presence and location of mutational events at a single cell level in Arabidopsis roots and stomata3,4. Here we present an efficient domain-specific CRISPR-Cas9 system combined with a high resolution live-imaging based screening strategy, applied in the shoot apical meristem of Arabidopsis thaliana. Using the system we investigate PIN-FORMED1 (PIN1) protein functions in tissue morphogenesis and PIN1 mechanical stress response in a cell layer-specific fashion. We find that reported failure to generate new primordia in epidermal PIN1 knockout SAMs is due to a reduction in mechanical stress differences in the sub-epidermal layer. The methods described are applicable to spatial-temporal gene manipulation in plants.
Genome Elimination Mediated by Gene Expression from a Selfish Chromosome
Authors: Benetta Elena Dalla , Antoshechkin Igor , Yang Ting , Nguyen Hoa Quang My , Ferree Patrick M. , Akbari Omar S.
Published: October 2019

Numerous plants and animals harbor selfish B chromosomes that “drive,” or transmit themselves at higher-than-Mendelian frequencies, despite long-term fitness costs to the organism. Currently it is unknown how B chromosome drive is mediated, and whether B-gene expression plays a role. We used modern sequencing technologies to analyze the fine-scale sequence composition and expression of Paternal Sex Ratio (PSR), a B chromosome in the jewel waspNasonia vitripennis. PSR causes female-to-male conversion by destroying the sperm’s hereditary material in young embryos in order to drive. Using RNA interference, we show that testis-specific expression of a PSR-linked gene, namedhaploidizer, facilitates this genome elimination-and-sex conversion effect.Haploidizershares homology with a gene inCandidatus cardinium, a bacterial symbiont that also induces genome elimination in its insect host.

One Sentence Summary

haploidizermediates B chromosome drive
The genetics of male pheromone preference difference betweenDrosophila melanogasterandD. simulans
Authors: Shahandeh Michael P. , Pischedda Alison , Rodriguez Jason M. , Turner Thomas L.
Published: October 2019

Species of flies in the genusDrosophiladiffer dramatically in their preferences for mates, but little is known about the genetic or neurological underpinnings of this evolution. Recent advances have been made to our understanding of one case: pheromone preference evolution between the speciesD. melanogasterandD. simulans. Males of both species are very sensitive to the pheromone 7,11-HD that is present only on the cuticle of femaleD. melanogaster. In one species this cue activates courtship, and in the other it represses it. This change in valence was recently shown to result from the modification of central processing neurons, rather than changes in peripherally expressed receptors, but nothing is known about the genetic changes that are responsible. In the current study, we show that a 1.35 Mb locus on the X chromosome has a major effect on male 7,11-HD preference. Unfortunately, when this locus is divided, the effect is largely lost. We instead attempt to filter the 159 genes within this region using our newfound understanding of the neuronal underpinnings of this phenotype to identify and test candidate genes. We present the results of these tests, and discuss the difficulty of identifying the genetic architecture of behavioral traits and the potential of connecting these genetic changes to the neuronal modifications that elicit different behaviors.
Investigating the Influence of the Brain-Derived Neurotrophic Factor Val66Met Single Nucleotide Polymorphism on Familiarity and Recollection Event-Related Potentials
Authors: McKay Nicole S. , Moreau David , Corballis Paul M. , Kirk Ian J.
Published: October 2019

The Val66Met single nucleotide polymorphism (SNP) has previously been reported to impact performance on recognition memory tasks. Whether the two subprocesses of recognition—familiarity and recollection—are differentially impacted by the Val66Met SNP remains unknown. Using event-related potentials (ERPs) recorded during a source memory task, we attempted to dissociate these two subprocesses. Behaviourally, we used participants’ scores on an item-recognition subtask as a measure of familiarity, and participants’ scores on a source-recognition subtask as a measure of recollection. Our findings reveal that Val/Val individuals outperform Met allele carriers on the item-but not the source-recognition task. Electrophysiologically, we were interested in the N400, an early frontal component previously linked to familiarity, and the late positive complex (LPC), a posterior component linked to recollection. We found evidence for Val/Val individuals having larger amplitudes of the LPC compared to Met allele carriers, and evidence for no difference in the N400 amplitudes of these groups. Based on the lack of dissociation between familiarity- and recollection-specific ERPs at the LPC time window, we argue that our behavioural and ERP results might reflect better item-recognition for Val/Val individuals compared to Met allele carriers. We further suggest that both these results reflect differences related to familiarity, rather than recollection.
Human hepatic tryptophan 2,3-dioxygenase ubiquitin-dependent protein degradation: The critical role of its exosite as the molecular lynchpin of its substrate-mediated protein stabilization
Authors: Kim Sung-Mi , Liu Yi , Wang YongQiang , Karkashon Shay , Lewis-Ballester Ariel , Yeh Syun-Ru , Correia Maria Almira
Published: October 2019

Hepatic tryptophan 2,3-dioxygenase (TDO) is a cytoplasmic homotetrameric hemoprotein and the rate-limiting enzyme in the irreversible degradation of the essential amino acidL-tryptophan (L-Trp) to N-formylkynurenine, thus controlling the flux ofL-Trp into its serotonergic and kynureninic/NAD pathways. TDO has long been recognized to be substrate-inducible via protein stabilization, but the molecular mechanism of this stabilization has remained elusive. Recent elucidation of human TDO (hTDO) crystal structure has identified a high-affinity (Kd ≈ 0.5 μM) Trp-binding exosite in each of its 4 monomeric subunits. Mutation of the Glu105, Trp208and Arg211comprising this exosite not only abolished the high-affinityL-Trp binding, but also accelerated the ubiquitin-dependent proteasomal degradation of hTDO. We have further characterized this hTDO degradation by documenting that its ubiquitination by gp78/AMFR and CHIP E2/E3 ligase complexes occurs on external Lys-residues within or vicinal to acidic Asp/Glu and phosphorylated pSer/pThr (DEpSpT)-clusters. Furthermore, we have identified the unstructured hTDO N- and C-termini as imparting relatively high proteolytic instability, as their deletion (ΔNC) markedly prolonged hTDO t1/2. Additionally, although previous studies reported that upon hepatic heme-depletion, the heme-free apoTDO turns over with a t1/2≈ 2.2 h relative to the t1/2of 7.7 h of holoTDO, mutating the axial heme-ligating His328to Ala has the opposite effect of prolonging hTDO t1/2. Most importantly, introducing the exosite mutation into the ΔNC-deleted or H328A-mutant completely abolished their prolonged half-lives irrespective ofL-Trp presence or absence, thereby revealing that the exosite is the molecular lynchpin that definesL-Trp-mediated TDO induction via protein stabilization.
Theory of neural coding predicts an upper bound on estimates of memory variability
Authors: Taylor Robert , Bays Paul M
Published: October 2019

Observers reproducing elementary visual features from memory after a short delay produce errors consistent with the encoding-decoding properties of neural populations. While inspired by electrophysiological observations of sensory neurons in cortex, the population coding account of these errors is based on a mathematical idealization of neural response functions that abstracts away most of the heterogeneity and complexity of real neuronal populations. Here we examine a more physiologically grounded model based on the tuning of a large set of neurons recorded in macaque V1, and show that key predictions of the idealized model are preserved. Both models predict long-tailed distributions of error when memory resources are taxed, as observed empirically in behavioral experiments and commonly approximated with a mixture of normal and uniform error components. Specifically, for an idealized homogeneous neural population, the width of the fitted normal distribution cannot exceed the average tuning width of the component neurons, and this also holds to a good approximation for more biologically realistic populations. Examining eight published studies of orientation recall, we find a consistent pattern of results suggestive of a median tuning width of approximately 20 degrees, which compares well with neurophysiological observations. The finding that estimates of variability obtained by the normal-plus-uniform mixture method are bounded from above leads us to reevaluate previous studies that interpreted a saturation in width of the normal component as evidence for fundamental limits on the precision of perception, working memory and long-term memory.
Two XMAP215/TOG microtubule polymerases, Alp14 and Dis1, play non-exchangeable, distinct roles in microtubule organisation in fission yeast
Authors: Yukawa Masashi , Kawakami Tomoki , Pinder Corinne , Toda Takashi
Published: October 2019

Proper bipolar spindle assembly underlies accurate chromosome segregation. A cohort of microtubule-associated proteins orchestrates spindle microtubule formation in a spatiotemporally coordinated manner. Among them, the conserved XMAP215/TOG family of microtubule polymerase plays a central role in spindle assembly. In fission yeast, two XMAP215/TOG members, Alp14 and Dis1, share essential roles in cell viability; however how these two proteins functionally collaborate remains undetermined. Here we show the functional interplay and specification of Alp14 and Dis1. Creation of new mutant alleles of alp14, which display temperature sensitivity in the absence of Dis1, enabled us to conduct detailed analyses of a double mutant. We have found that simultaneous inactivation of Alp14 and Dis1 results in early mitotic arrest with very short, fragile spindles. Intriguingly, these cells often undergo spindle collapse, leading to a lethal “cut” phenotype. By implementing an artificial targetting system, we have shown that Alp14 and Dis1 are not functionally exchangeable and as such are not merely redundant paralogues. Intriguingly, while Alp14 promotes microtubule nucleation, Dis1 does not. Our results uncover that the intrinsic specification, not the spatial regulation, between Alp14 and Dis1 underlies the collaborative actions of these two XMAP215/TOG members in mitotic progression, spindle integrity and genome stability.
Heart rate variability as an indicator of autonomic nervous system disturbance in tetanus
Authors: Duong Ha Thi Hai , Abebe Tadesse Girmaw , Nhat Phung Tran Huy , Van Hao Nguyen , Prince John , Duong Tran Duc , Trung Kien Trịnh , Van Tan Le , Pugh Chris , Loan Huynh Thi , Van Vinh Chau Nguyen , Minh Yen Lam , Zhu Tingting , Clifton David , Thwaites Louise
Published: October 2019

Autonomic nervous system dysfunction (ANSD) is a significant cause of mortality in tetanus. Currently diagnosis relies on non-specific clinical signs. Heart rate variability (HRV) may indicate underlying autonomic nervous system activity and represents a potentially valuable non-invasive tool for ANSD diagnosis in tetanus. HRV was measured from 3 5-minute ECG recordings during a 24-hour period in a cohort patients with severe tetanus, all receiving mechanical ventilation. HRV measurements from all subjects - 5 with ANSD (Ablett Grade 4) and 4 patients without ANSD (Ablett Grade 3) - showed HRV was lower than reported ranges for healthy individuals. Comparing different severities of tetanus, raw data for both time and frequency measurements of HRV were reduced in those with ANSD compared to those without. Differences were statistically significant in all except root mean square standard deviation RMSSD (p=0.07) indicating HRV may be a valuable tool in ANSD diagnosis.
Skilled strategies of release parameters for accurate free-throw shooting in the presence of motor noise
Authors: Nakano Nobuyasu , Inaba Yuki , Fukashiro Senshi , Yoshioka Shinsuke
Published: October 2019

How humans execute accurate movement in the presence of motor noise is a key problem in the field of biomechanics and motor control that limits the performance improvement in daily or sporting activities. The aim of this study was to clarify the strategy of basketball players during free-throw shooting. Two possible hypotheses were examined: the players minimize the release speed to decrease signal-dependent noise or the players maximize the shot success probability by accounting for their variability. Eight collegiate players and one professional player participated in this study by attempting shots from the free-throw line using a motion capture system. The solution manifold consisting of ball parameters at release was calculated and the optimal strategy was simulated by considering ball parameter variability; this result was compared with the actual data. Our results showed that participants selected the solution of near-minimum release speed. The deviation of the measured release angle from the minimum-speed angle was close to zero (2.8 ± 3.1°). However, an increase in speed-dependent noise did not have a significant influence on the ball landing position through simulation. Additionally, the effect of release angle error on the ball landing position was minimum when using the minimum speed strategy. Therefore, the players minimize the release speed to minimize the effect of the release error on performance, instead of minimizing the speed-dependent noise itself. In other words, the strategy is “near-minimum-speed strategy” as well as “minimum-error-propagation strategy”. These findings will be important for understanding how sports experts deal with intrinsic noise to improve performance.
Genetic and physical interaction of Drosophila Ino80 with Polycomb Responsive Element
Authors: Ghasemi Mohsen , Maini Jayant , Jain Shruti , Dasari Vasanthi , Mishra Rakesh , Brahmachari Vani
Published: October 2019

The chromatin remodeling protein, dIno80 (DrosophilaIno80) regulates homeotic genes. We show that Ino80, along with Trx and ETP (Enhancer of Trithorax and Polycomb) proteins, interacts with two Polycomb/Trithorax Responsive Elements (PRE/TRE),iab-7andbxd PREin flies and the larval imaginal discs. In S2 cells, dIno80 localizes to the endogenousiab-7andbxd-PREs. The localization of Ino80 and Pleiohomeotic (Pho) at the PRE is sensitive to the cellular abundance of each other; when levels ofIno80are limiting, there is increased Pho enrichment, andPhoknock-down leads to increased enrichment of Ino80. We demonstrate that over-expression of dIno80 rescues the pupal lethality inpleiohomeotic(pho) deficient flies, which suggests that dIno80 has a role in cellular memory. The apparent competition between Pho and Ino80 for binding at the PRE indicates that Ino80 may act as a potential recruiter of the regulatory complex in addition to being a chromatin remodeler.

Author Summary

The null mutants of Pho and dIno80 show lethality at different stages of development in the fly, implying that they may function independent of each other. The observation that Pho-lethality can be rescued by overexpression of dIno80 with significant penetrance and that Ino80 has its own DNA binding domain, led us to predict that Ino80 may have Pho-independent functions, perhaps through non-canonical complexes. In the current study, we show that dIno80 interacts withbxdandiab-7PRE in cooperation with Polycomb and Trithorax proteins and regulate the homeotic genes. The effect of knock-down or mutation of dIno80 results in altered phenotype in adult flies and rescue of Lac-Z expression in imaginal discs, in parallel with similar effect of Pho mutation or knock-down. We provide evidence of direct interaction of dIno80 withiab7-andbxd-PRE using chromatin immunoprecipitation. The dIno80 localization in and around the PRE sequence was enhanced in the absence of Pho, indicating competition between Pho and dIno80 for binding at the PRE.
Methodological considerations on selection of stable reference genes for RT-qPCR in the neonatal rat brain in hypoxia and hypothermia
Authors: Bustelo M. , Bruno M.A. , Loidl C.F. , Steinbusch H.W.M. , Gavilanes A.W.D. , van den Hove D.L.A.
Published: October 2019

Real-time reverse transcription PCR (qPCR) normalized to an internal reference gene (RG), is a frequently used method for quantifying gene expression changes in neuroscience. Although RG expression is assumed to be constantly independent of physiological or experimental conditions, several studies have shown that commonly used RGs are not expressed stably. The use of unstable RGs has a profound effect on the conclusions drawn from studies on gene expression, and almost universally results in spurious estimation of target gene expression. Approaches aimed at selecting and validating RGs often make use of different statistical methods, which may lead to conflicting results. The present study evaluates the expression of 5 candidate RGs (Actb,Pgk1,Sdha,Gapdh,Rnu6b) as a function of hypoxia exposure and hypothermic treatment in the neonatal rat cerebral cortex –in order to identify RGs that are stably expressed under these experimental conditions– and compares several statistical approaches that have been proposed to validate RGs. In doing so, we first analyzed the RG ranking stability proposed by several widely used statistical methods and related tools, i.e. the Coefficient of Variation (CV) analysis, GeNorm, NormFinder, BestKeeper, and the ΔCt method. Subsequently, we compared RG expression patterns between the various experimental groups. We found that these statistical methods, next to producing different rankings per se, all ranked RGs displaying significant differences in expression levels between groups as the most stable RG. As a consequence, when assessing the impact of RG selection on target gene expression quantification, substantial differences in target gene expression profiles were observed. As such, by assessing mRNA expression profiles within the neonatal rat brain cortex in hypoxia and hypothermia as a showcase, this study underlines the importance of further validating RGs for each new experimental paradigm considering the limitations of each selection method.
Regional Disparities of Antenatal Care Utilization in Indonesia
Authors: Laksono Agung Dwi , Rukmini Rukmini , Wulandari Ratna Dwi
Published: October 2019

Introduction

The main strategy for decreasing maternal morbidity and mortality with antenatal care (ANC). ANC aims to monitor and maintain the health and safety of the mother and fetus, detect all complications of pregnancy and take the necessary actions, respond to complaints, prepare for birth, and promote healthy living behavior. The study aims to analyze inter-regional disparities in ≥4 ANC visits during pregnancy in Indonesia.

Methods

Data sources from 2017 Indonesian Demographic and Health Survey (IDHS). With an analysis unit of women aged 15-49 years old, a sample of 15,351 women was obtained. Besides ANC as the dependent variable, other variables analyzed were place of residence, age, husband/partner, education, parity, wealth status, and health insurance. Analysis using Binary Logistic Regression for the final test to determine disparity.

Results

All regions show a gap with the Papua region as a reference, except the Maluku region which was not significant shows differences in the use of ANC compared to the Papua. Women in the Nusa Tenggara have 4,365 chances of making ≥4 ANC visits compared to the Papua region. Women in Java-Bali have 3,607 times more chances to make ≥4 ANC visits than women in the Papua region. Women in Sumatra have 1,370 chances of making ≥4 ANC visits compared to women in the Papua region. Women in Kalimantan have 2.232 times made ≥4 ANC visits compared to women in the Papua region. Women in Sulawesi have 1,980 times more than AN4 ANC visits compared to women in the Papua region. In addition to the region category, other variables found to contribute to the predictor were age, husband/partner, education, parity, wealth and insurance.

Conclusion

There were disparities between regions in the ANC utilization in Indonesia.
Education influences knowledge about environmental issues in Washington, DC, USA
Authors: Richardson Matthew L. , Milton Ashley D. , Harrison Elgloria
Published: October 2019

We predicted that demographic differences in Washington, DC’s population would influence people’s knowledge and perceptions about the interconnectedness of natural resources, climate change, economics, and socio-cultural well-being, so we conducted surveys over three years to test that prediction. We collected demographic data from 455 participants and asked them 26 questions/statements related to natural resources, climate change, economics, and health. We selected education as the focal demographic category and participants were categorized based on their level of educational attainment: 1) completion of high school or less (hereafter “high school”); 2) some trade school or university education beyond high school up to and including completion of a trade school, two-, or four-year degree (hereafter “post-high school”); and 3) completion of a Master’s, professional, or doctoral degree (hereafter “advanced education”). Answers to 14 of the 26 survey questions were dissimilar across educational groups. People with advanced education reported the highest connection with the natural community and were more likely to report that their personal welfare depended on the natural community. Participants in the high school group were more likely to believe that humans do not have much influence on natural resources and placed more trust in technology and human achievements to control nature and ensure that earth will not become unlivable. Compared to those with education beyond high school, those with a high school education were more likely to express an interest in local environmental concerns over global, jobs over natural resources, and effects of degraded local natural resources on income, health, and the environment instead of on cultural/social practices, neighborhood aesthetics, and recreation. The results suggest ways in which educational information and engagement in environmental issues should be targeted for stakeholders of different educational background in order to increase knowledge and build effective partnerships that find solutions for environmental problems.
Adhesion-free cell migration by topography-based force transduction
Authors: Reversat Anne , Merrin Jack , Hauschild Robert , de Vries Ingrid , Piel Matthieu , Callan-Jones Andrew , Voituriez Raphael , Sixt Michael
Published: October 2019

Eukaryotic cells migrate by coupling the intracellular force of the actin cytoskeleton to the environment. While force-coupling is usually mediated by transmembrane adhesion receptors, especially these of the integrin family, amoeboid cells like leukocytes can migrate extremely fast despite very low adhesive forces1. We show that leukocytes cannot only migrate under low adhesion but indeed can transduce forces in the complete absence of transmembrane force coupling. When confined within three-dimensional environments, they use the topographic features of the substrate to propel themselves. Here, the retrograde flow of the actin cytoskeleton follows the texture of the substrate, creating shear forces sufficient to drive deformations towards the back of the cell. Notably, adhesion dependent and adhesion independent migration are not exclusive but rather variants of the same principle of coupling retrograde actin flow to the environment and thus can potentially operate simultaneously. As adhesion free migration is independent of the chemical composition of the environment it renders cells completely autonomous in their locomotive behavior.
Deep Generative Models for Detecting Differential Expression in Single Cells
Authors: Boyeau Pierre , Lopez Romain , Regier Jeffrey , Gayoso Adam , Jordan Michael I. , Yosef Nir
Published: October 2019

Detecting differentially expressed genes is important for characterizing subpopulations of cells. However, in scRNA-seq data, nuisance variation due to technical factors like sequencing depth and RNA capture efficiency obscures the underlying biological signal. First, we show that deep generative models, which combined Bayesian statistics and deep neural networks, better estimate the log-fold-change in gene expression levels between subpopulations of cells. Second, we use Bayesian decision theory to detect differentially expressed genes while controlling the false discovery rate. Our experiments on simulated and real datasets show that our approach out-performs state-of-the-art DE frameworks. Finally, we introduce a technique for improving the posterior approximation, and show that it also improves differential expression performance.