bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in Iris Stiffness and Permeability in Primary Angle Closure Glaucoma
Authors: Panda Satish K. , Tan Royston K. Y. , Tun Tin A. , Buist Martin L. , Nongpiur Monisha , Baskaran Mani , Aung Tin , Girard Michaël J. A. 
Published: May 2021

AbstractPurposeTo evaluate the biomechanical properties of the iris by evaluating iris movement during pupil constriction and to compare such properties between healthy and primary angle-closure glaucoma (PACG) subjects.MethodsA total of 140 subjects were recruited for this study. In a dark room, the anterior segments of one eye per subject were scanned using anterior segment optical coherence tomography (AS-OCT, SS-1000 CASIA, Tomey Corporation, Nagoya, Japan) imaging during induced pupil constriction with an external white light source of 1700 lux. Using a custom segmentation code, we automatically isolated the iris segments from the AS-OCT images, which were then discretized and transformed into a three-dimensional point cloud. For each iris, a finite element (FE) mesh was constructed from the point cloud, and an inverse FE simulation was performed to match the clinically observed iris constriction in the AS-OCT images. Through this optimization process, we were able to identify the elastic modulus and permeability of each iris.ResultsFor all 140 subjects (95 healthy and 45 PACG of Indian/Chinese ethnicity, Age: 60.2±8.7 for PACG subjects and 57.7±10.1 for healthy subjects), the simulated deformation pattern of the iris during pupil constriction matched well with OCT images. We found that the iris stiffness was higher in PACG than in healthy controls (24.5±8.4 kPa vs 17.1±6.6 kPa with 40 kPa of active stress specified in the sphincter region;p< 0.001), whereas iris permeability was lower (0.41±0.2 mm2/kPa.s vs 0.55±0.2 mm2/kPa.s;p= 0.142).ConclusionThis study suggests that the biomechanical properties of the iris in PACG are different from those in healthy controls. An improved understanding of the biomechanical behavior of the iris may have implications for the understanding and management of angle-closure glaucoma.
Vacuole-specific lipid release for tracking intracellular lipid metabolism and transport inSaccharomyces cerevisiae
Authors: Girik Vladimir , Feng Suihan , Hariri Hanaa , Henne W Mike , Riezman Howard 
Published: May 2021

ABSTRACTLipid metabolism is spatiotemporally regulated within cells, yet intervention into lipid functions at subcellular resolution remains difficult. Here we report a method that enables site-specific release of sphingolipids and cholesterol inside the vacuole inSaccharomyces cerevisiae. Using this approach, we monitored real-time sphingolipid metabolic flux out of the vacuole by mass spectrometry and found that the ER-vacuole tethering protein Mdm1 facilitated the metabolism of sphingoid bases into ceramides. In addition, we showed that cholesterol, once delivered into yeast using our method, could restore cell proliferation induced by ergosterol deprivation, overcoming the previously described sterol-uptake barrier under aerobic conditions. Together, these data define a new way to study intracellular lipid metabolism and transport from the vacuole in yeast.
Generation of lineage-resolved complete metagenome-assembled genomes by precision phasing
Authors: Bickhart Derek M. , Kolmogorov Mikhail , Tseng Elizabeth , Portik Daniel M. , Korobeynikov Anton , Tolstoganov Ivan , Uritskiy Gherman , Liachko Ivan , Sullivan Shawn T. , Shin Sung Bong , Zorea Alvah , Andreu Victòria Pascal , Panke-Buisse Kevin , Medema Marnix H. , Mizrahi Itzik , Pevzner Pavel A. , Smith Timothy P.L. 
Published: May 2021

AbstractMicrobial communities in many environments include distinct lineages of closely related organisms which have proved challenging to separate in metagenomic assembly, preventing generation of complete metagenome-assembled genomes (MAGs). The advent of long and accurate HiFi reads presents a possible means to address this challenge by generating complete MAGs for nearly all sufficiently abundant bacterial genomes in a microbial community. We present a metagenomic HiFi assembly of a complex microbial community from sheep fecal material that resulted in 428 high-quality MAGs from a single sample, the highest resolution achieved with metagenomic deconvolution to date. We applied a computational approach to separate distinct haplotype lineages and identified haplotypes of hundreds of variants across hundreds of kilobases of genomic sequence. Analysis of these haplotypes revealed 220 lineage-resolved complete MAGs, including 44 in single circular contigs, and demonstrated improvement in overall assembly compared to error-prone long reads. We report the characterization of multiple, closely-related microbes within a sample with potential to improve precision in assigning mobile genetic elements to host genomes within complex microbial communities.
Comparative Morphometric Analysis Of Captive Jaguars Vs. Wild Jaguars (Panthera onca) In Venezuela
Authors: Cañizales Israel 
Published: May 2021

ABSTRACTIn Venezuela the oldest, although anecdotical, record known of a captive jaguar is a male in the city of Maracay between 1918 and 1935. Body measurements were made on 22 jaguars kept in Venezuelan zoos between 1996 and 2009 to provide data on external morphometrics and compare with the measurements of 25 free-living animals, published by Hoogesteijn and Mondolfi (1992) and determine whether there are significant differences in the morphology between sexes of captive and free-living animals. The evaluation of morphometric variation was focused on three body measurements and body weight: Head-and-body length (HBL) and Tail length (Tl). Total body length (TBL) was calculated by adding HBL and Tl. Body weight (BW) was determined using a clock scale to the nearest gramme/kilogram. To determine the values all animals were anesthetized. The sexes were analyzed separately. All data were used for the calculation of descriptive statistics. Student t-tests were used with a significance level α 0.05 to establish if there is a significant difference between the measurements and weights of the sexes. The TBL and HBL in captive males were observed to be 8.78% and 12.13%, respectively, less than that of free-living males. A principal components analysis made it possible to assess the variability between HBL, TBL, and BW between sexes and between free-living/wild and captive animals. This study showed no significant differences in the BW of captives and wild females. Some captive males’ jaguars in this study may be thinner than normal, because of their diet and others may be fatter because of the lack of physical activity imposed by captivity. Body mass index (BMI) was used to contrast the difference in the average mass of each sex in both captive and free-living animals. Simple linear regressions and correlation coefficients were used to determine the relationship between body mass and male/female size. According to correlation coefficients, the change in weight that can be attributed to the ratio of weight to body length is 8.55 % for males and 9.83 % for females.
A Discriminative Characterization of Heschl’s Gyrus Morphology using Spectral Graph Features
Authors: Maghsadhagh Sevil , Dalboni da Rocha Josué L. , Benner Jan , Schneider Peter , Golestani Narly , Behjat Hamid 
Published: May 2021

AbstractHeschl’s Gyrus (HG), which hosts the primary auditory cortex, exhibits large variability not only in size but also in its gyrification patterns, within (i.e., between hemispheres) and between individuals. Conventional structural measures such as volume, surface area and thickness do not capture the full morphological complexity of HG, in particular, with regards to its shape. We present a method for characterizing the morphology of HG in terms of Laplacian eigenmodes of surface-based and volume-based graph representations of its structure, and derive a set of spectral graph features that can be used to discriminate HG subtypes. We applied this method to a dataset of 177 adults previously shown to display considerable variability in the shape of their HG, including data from amateur and professional musicians, as well as non-musicians. Results show the superiority of the proposed spectral graph features over conventional ones in differentiating HG subtypes, in particular, single HG versus Common Stem Duplications (CSDs). We anticipate the proposed shape features to be found beneficial in the domains of language, music and associated pathologies, in which variability of HG morphology has previously been established.
AZBA: A 3D Adult Zebrafish Brain Atlas for the Digital Age
Authors: Kenney Justin W. , Steadman Patrick E. , Young Olivia , Shi Meng Ting , Polanco Maris , Dubaishi Saba , Covert Kristopher , Mueller Thomas , Frankland Paul W. 
Published: May 2021

AbstractZebrafish have made significant contributions to our understanding of the vertebrate brain and the neural basis of behavior, earning a place as one of the most widely used model organisms in neuroscience. Their appeal arises from the marriage of low cost, early life transparency, and ease of genetic manipulation with a behavioral repertoire that becomes more sophisticated as animals transition from larvae to adults. To further enhance the use of adult zebrafish, we created the first fully segmented three-dimensional digitaladultzebrafishbrainatlas (AZBA). AZBA was built by combining tissue clearing, light-sheet fluorescence microscopy, and three-dimensional image registration of nuclear and antibody stains. These images were used to guide segmentation of the atlas into over 200 neuroanatomical regions comprising the entirety of the adult zebrafish brain. As an open source, onlineazba.wayne.edu), updatable digital resource, AZBA will significantly enhance the use of adult zebrafish in furthering our understanding of vertebrate brain function in both health and disease.
The Hypoxia Response Pathway Promotes PEP Carboxykinase Expression And Gluconeogenesis
Authors: Vora Mehul , Pyonteck Stephanie M. , Matlack Tarmie L. , Prashar Aparna , Kane Nanci S. , Shah Premal , Rongo Christopher 
Published: May 2021

ABSTRACTActively dividing cells, including some cancers, rely on aerobic glycolysis rather than oxidative phosphorylation to generate energy, a phenomenon termed “the Warburg effect1.” Constitutive activation of the Hypoxia Inducible Factor (HIF-1), a transcription factor known for mediating an adaptive response to oxygen deprivation (hypoxia), is a hallmark of the Warburg effect2. HIF-1 is thought to promote glycolysis and suppress oxidative phosphorylation. Here, we show instead that HIF-1 can promote gluconeogenesis. Using a multiomics approach, we determined the genomic, transcriptomic, and metabolomic landscapes regulated by constitutively active HIF-1 inC. elegans. We performed RNA-seq and ChIP-seq under aerobic conditions in mutants lacking EGL-9, a key negative regulator of HIF-1, and then integrated these approaches to identify over a hundred genes directly and functionally upregulated by HIF-1. We show that HIF-1 directly promotes the expression of PCK-1, a PEP carboxykinase that is a rate-limiting mediator of gluconeogenesis3. This activation of PCK-1 by HIF-1 promotes survival in response to both oxidative and hypoxic stress. Our work is the first to identify functional direct targets of HIF-1in vivo, and it describes the first complete metabolome induced by constitutive HIF-1 activation in any organism.
Biphasic Control of Cell Expansion by Auxin Coordinates Etiolated Seedling Development
Authors: Du Minmin , Daher Firas Bou , Liu Yuanyuan , Steward Andrew , Tillmann Molly , Zhang Xiaoyue , Wong Jeh Haur , Ren Hong , Cohen Jerry D. , Li Chuanyou , Gray William M. 
Published: May 2021

AbstractSeedling emergence is critical for food security. It requires rapid hypocotyl elongation and apical hook formation, both of which are mediated by regulated cell expansion. How these events are coordinated in etiolated seedlings is unclear. Here, we show that biphasic control of cell expansion by the phytohormone auxin underlies this process. Shortly after germination, high auxin levels restrain elongation. This provides a temporal window for apical hook formation, involving a gravity-induced auxin maximum on the eventual concave side of the hook, triggering PP2C.D1controlled asymmetrical H+-ATPase activity, resulting in differential cell elongation. Subsequently, auxin concentrations decline acropetally and switch from restraining to promoting elongation, driving hypocotyl elongation. Our findings elucidate how differential auxin concentrations throughout the hypocotyl coordinate etiolated development, leading to successful soil emergence.One-Sentence SummaryAuxin concentration-dependent cell expansion coordinates hypocotyl elongation and apical hook development for soil emergence.
Cellular Bases of Olfactory Circuit Assembly Revealed by Systematic Time-lapse Imaging
Authors: Li Tongchao , Fu Tian-Ming , Li Hongjie , Xie Qijing , Luginbuhl David J. , Betzig Eric , Luo Liqun 
Published: May 2021

ABSTRACTNeural circuit assembly features simultaneous targeting of numerous neuronal processes from constituent neuron types, yet the dynamics is poorly understood. Here, we use theDrosophilaolfactory circuit to investigate dynamic cellular processes by which olfactory receptor neurons (ORNs) target axons precisely to specific glomeruli in the ipsi- and contralateral antennal lobes. Time-lapse imaging of individual axons from 28 ORN types revealed a rich diversity in extension speed, innervation timing, and ipsilateral branch locations, and identified that ipsilateral targeting occurs via stabilization of transient interstitial branches. Fast imaging using adaptive optics- corrected lattice light-sheet microscopy showed that upon approaching target, many ORN types exhibit “exploring branches” consisted of parallel microtubule-based terminal branches emanating from an F-actin-rich hub. Antennal nerve ablations uncovered essential roles for bilateral interactions in contralateral target selection, and for ORN axons to facilitate dendritic refinement of postsynaptic partner neurons. Altogether, these observations provide cellular bases for wiring specificity establishment.
Visualization of Arabidopsis root system architecture in 3D by refraction-contrast X-ray micro-computed tomography
Authors: Kurogane Tomofumi , Tamaoki Daisuke , Yano Sachiko , Tanigaki Fumiaki , Shimazu Toru , Kasahara Haruo , Yamauchi Daisuke , Uesugi Kentaro , Hoshino Masato , Kamisaka Seiichiro , Mineyuki Yoshinobu , Karahara Ichirou 
Published: May 2021

AbstractPlant roots change their morphological traits in order to adapt themselves to different environmental conditions, resulting in alteration of the root system architecture. To understand this mechanism, it is essential to visualize morphology of the entire root system. To reveal effects of long-term alteration of gravity environment on root system development, we have performed an experiment in the International Space Station using Arabidopsis (Arabidopsis thaliana(L.) Heynh.) plants and obtained dried root systems grown in rockwool slabs (mineral wool substrate). X-ray computer tomography (CT) technique using an industrial X-ray scanner has been introduced for the purpose to visualize root system architecture of crop species grown in soil in 3D non-invasively. In the case of the present study, however, root system of Arabidopsis is composed of finer roots compared with typical crop plants and rockwool is also composed of fibers having similar dimension to that of the roots. A higher spatial resolution imaging method is required for distinguishing roots from rockwool. Therefore, in the present study, we tested refraction-contrast X-ray micro-CT using coherent X-ray optics available at the beamline BL20B2 of the synchrotron radiation facility SPring-8. Using this technique, both the primary and the secondary roots were successfully identified in the tomographic slices, clearly distinguished from the individual rockwool fibers and resulting in successful tracing of these roots from their basal regions. This newly-developed technique should contribute to elucidate the effect of microgravity on Arabidopsis root system architecture in space.
The human innate immune protein calprotectin elicits a multi-metal starvation response inPseudomonas aeruginosa
Authors: Nelson Cassandra E. , Huang Weilang , Zygiel Emily M. , Nolan Elizabeth M. , Kane Maureen A. , Oglesby Amanda G. 
Published: May 2021

AbstractTo combat infections, the mammalian host limits availability of essential transition metals such as iron (Fe), zinc (Zn), and manganese (Mn) in a strategy termed “nutritional immunity”. The innate immune protein calprotectin (CP) contributes to nutritional immunity by sequestering these metals to exert antimicrobial activity against a broad range of microbial pathogens. One such pathogen isPseudomonas aeruginosa, which causes opportunistic infections in vulnerable populations including individuals with cystic fibrosis. CP was previously shown to withhold Fe(II) and Zn(II) fromP. aeruginosaand induce Fe- and Zn-starvation responses in this pathogen. In this work, we performed quantitative, label-free proteomics to further elucidate how CP impacts metal homeostasis pathways inP. aeruginosa. We report that CP induces an incomplete Fe-starvation response, as many Fe-containing proteins that are repressed by Fe limitation are not affected by CP treatment. The Zn-starvation response elicited by CP seems to be more complete than the Fe-starvation response and includes increases in Zn transporters and Zn-independent proteins. CP also induces the expression of membrane-modifying proteins, and metal-depletion studies indicate this response results from the sequestration of multiple metals. Moreover, the increased expression of membrane-modifying enzymes upon CP treatment correlates with increased resistance to polymyxin B. Thus, response ofP. aeruginosato CP treatment includes both single and multi-metal starvation responses and includes many factors related to virulence potential, broadening our understanding of this pathogen’s interaction with the host.ImportanceTransition metals are critical for growth and infection by all pathogens, and the innate immune system withholds these metals from pathogens to limit their growth in a strategy termed “nutritional immunity”. While multi-metal depletion by the host is appreciated, the majority of metal depletion studies have focused on individual metald. Here we use the innate immune protein calprotectin (CP), which complexes with several metals including iron (Fe), zinc (Zn), and manganese (Mn), and the opportunistic pathogenPseudomonas aeruginosato investigate multi-metal starvation. Using an unbiased label-free proteomics response, we demonstrate that multi-metal withholding by CP induces a regulatory response that is not merely additive of individual metal starvation responses, including the induction of Lipid A modification enzymes.
The dengue virus NS1 protein conveys pro-inflammatory signals by docking onto human high-density lipoproteins
Authors: Benfrid Souheyla , Park Kyu-Ho , Dellarole Mariano , Voss James E. , Tamietti Carole , Pehau-Arnaudet Gérard , Raynal Bertrand , Brûlé Sébastien , England Patrick , Zhang Xiaokang , Mikhailova Anastassia , Ungeheuer Marie-Noëlle , Petres Stéphane , Biering Scott B. , Harris Eva , Sakunthabaï Anavaj , Buchy Philippe , Duong Veasna , Dussart Philippe , Coulibaly Fasséli , Bontems François , Rey Félix A. , Flamand Marie 
Published: May 2021

ABSTRACTThe nonstructural NS1 protein is a virulence factor secreted by dengue virus (DENV)-infected cells. NS1 is known to alter the complement system, activate immune cells and perturb endothelial barriers. Here we show that pro-inflammatory signals are triggered by a high affinity complex formed between NS1 and human high-density lipoproteins (HDL). Electron microscopy images of the NS1-HDL complexes show spherical HDL particles with rod-shaped NS1 protrusions on their surface. These complexes are readily detectable in the plasma of hospitalized dengue patients using anti-apolipoprotein A-I (ApoA-I) antibodies specific of the HDL moiety. The functional reprogramming of HDL particles by the NS1 protein as a means to exacerbate systemic inflammation during DENV infection provides a new paradigm linking the human lipoprotein network to dengue pathogenesis.
Endoplasmic reticulum-targeting but not translation is required for mRNA balancing in trypanosomes
Authors: Aroko Erick O , Soale Majeed Bakari , Batram Christopher , Jones Nicola G , Engstler Markus 
Published: May 2021

AbstractThe cell surface of bloodstream form African trypanosomes is covered by a dense coat of immunogenic variant surface glycoproteins (VSGs). By continuously changing the expressed VSG antigen, the parasites can survive the host’s immune response. TheVSGis highly expressed inTrypanosoma brucei, accounting for approximately 10 – 20% of total mRNA. Depletion ofVSGmRNA is lethal, and a counterbalancing of the mRNA levels occurs when two or moreVSGsare simultaneously expressed. How the VSG expression levels are regulated is unknown. Here, by using inducible and constitutive systems for ectopic VSG expression, we have discovered that (i) the endogenousVSGmRNA level is downregulated only when the ectopicVSGis targeted to the ER, (ii) VSG translation is dispensable and in fact, (iii) the regulation ofVSGmRNA levels does not depend on aVSGopen reading frame. We propose that feedback elicited at the ER regulates theVSGmRNA amounts to avoid overshooting the secretory pathway capacity. In this way, VSG expression is quantitatively and qualitatively fine-tuned. Balancing the overall number of ER-targeted mRNAs could well be a general mechanism in cell biology. The trypanosome system with just one dominant mRNA species provides a versatile model for studying this phenomenon.