bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using genetically encoded heme sensors to probe the mechanisms of heme uptake and homeostasis inCandida albicans
Authors: Weissman Ziva , Pinsky Mariel , Donegan Rebecca K. , Reddi Amit R. , Kornitzer Daniel 
Published: July 2020

ABSTRACTCandida albicansis a major fungal pathogen that can utilize hemin and hemoglobin as iron sources in the iron-scarce host environment. WhileC. albicansis a heme prototroph, we show here that it can also efficiently utilize external heme as a cellular heme source. Using genetically encoded ratiometric fluorescent heme sensors, we show that heme extracted from hemoglobin and free hemin enter the cells with different kinetics. Heme supplied as hemoglobin is taken up via the CFEM (Common in Fungal Extracellular Membrane) hemophore cascade, and reaches the cytoplasm over several hours, whereas entry of free hemin via CFEM-dependent and independent pathways is much faster, less than an hour. To prevent an influx of extracellular heme from reaching toxic levels in the cytoplasm, the cells deploy Hmx1, a heme oxygenase. Hmx1 was previously suggested to be involved in utilization of hemoglobin and hemin as iron sources, but we find that it is primarily required to prevent heme toxicity. Taken together, the combination of novel heme sensors with genetic analysis revealed new details of the fungal mechanisms of heme import and homeostasis, necessary to balance the uses of heme as essential cofactor and potential iron source against its toxicity.
Fluffy feathers: how neoptile feathers contribute to camouflage in precocial chicks
Authors: Rohr Veronika A. , Volkmer Tamara , Metzler Dirk , Küpper Clemens 
Published: July 2020

AbstractCamouflage is a widespread strategy to increase survival. The plumage of precocial chicks often contains elements of disruptive colouration and background matching to enhance concealment. Chick plumage also features fringed feathers as appendages that may contribute to camouflage. Here, we examine whether and how neoptile feathers conceal the outline of chicks. We first conducted a digital experiment to test two potential mechanisms for outline diffusion through appendages: 1) edge intensity reduction and 2) luminance transition. Local Edge Intensity Analysis (LEIA) showed that appendages decreased edge intensity and a mean luminance comparison revealed that the appendages created an intermediate transition zone to conceal the object’s outline. The outline was most diffused through an intermediate number of interspersed thin appendages. Increased appendage thickness resulted in fewer appendages improving camouflage, whereas increased transparency required more appendages for best concealment. For edge intensity, the outline diffusion was strongest for a vision system with low spatial acuity, which is characteristic of many mammalian predators. We then analysed photographs of young snowy plover (Charadrius nivosus) chicks to examine whether neoptile feathers increase outline concealment in a natural setting. Consistent with better camouflage, the outline of digitally cropped chicks with protruding feathers showed lower edge intensities than the outline of chicks cropped without those feathers. However, the observed mean luminance changes were not consistent with better concealment. Taken together, our results suggest that thin skin appendages such as neoptile feathers improve camouflage. As skin appendages are widespread, this mechanism may apply to a large variety of organisms.
Structure of voltage-modulated sodium-selective NALCN-FAM155A channel complex
Authors: Kang Yunlu , Wu Jing-Xiang , Chen Lei 
Published: July 2020

AbstractResting membrane potential determines the excitability of the cell and is essential for the cellular electrical activities. NALCN channel mediates sodium leak currents, which positively tune the resting membrane potential towards depolarization. NALCN channel is involved in many important neurological processes and is implicated in a spectrum of neurodevelopmental diseases. Despite its functional importance, the mechanisms of ion permeation and voltage-modulation for NALCN channel remain elusive. Here, we report the cryo-EM structure of rat NALCN and mouse FAM155A complex to 2.7 Å resolution. The structure reveals detailed interactions between NALCN and extracellular cysteine-rich domain of FAM155A. The non-canonical architecture of NALCN selectivity filter dictates its sodium selectivity and calcium block. The asymmetric arrangement of two functional voltage-sensors confers the modulation by membrane potential. Moreover, mutations found in human diseases were mapped to the domain-domain interfaces or the pore domain of NALCN, intuitively suggesting their pathological mechanisms.
Practical Design and Implementation of Animal Movements Tracking System for Neuroscience Trials
Authors: Sorkhabi Majid Memarian 
Published: July 2020

AbstractBackgroundThe nervous system functions of an animal are predominantly reflected in the behaviour and the movement, therefore the movement-related data and measuring behavior quantitatively are crucial for behavioural analyses. The animal movement is traditionally recorded, and human observers follow the animal behaviours; if they recognize a certain behaviour pattern, they will note it manually, which may suffer from observer fatigue or drift.ObjectiveAutomating behavioural observations with computer-vision algorithms are becoming essential equipment to the brain function characterization in neuroscience trials. In this study, the proposed tracking module is eligible to measure the locomotor behaviour (such as speed, distance, turning) over longer time periods that the operator is unable to precisely evaluate. For this aim, a novel animal cage is designed and implemented to track the animal movement. The frames received from the camera are analyzed by the 2D bior 3.7 Wavelet transform and SURF feature points.ResultsImplemented video tracking device can report the location, duration, speed, frequency and latency of each behavior of an animal. Validation tests were conducted on the auditory stimulation trial and the magnetic stimulation treatment of hemi-Parkinsonian rats.Conclusion/ SignificanceThe proposed toolkit can provide qualitative and quantitative data on animal behaviour in an automated fashion, and precisely summarize an animal’s movement at an arbitrary time and allows operators to analyse movement patterns without requiring to check full records for every experiment.
ClpAP proteolysis does not require rotation of the ClpA unfoldase relative to ClpP
Authors: Kim Sora , Zuromski Kristin L , Bell Tristan A , Sauer Robert T , Baker Tania A 
Published: July 2020

AbstractAAA+ proteases, which perform regulated protein degradation in all kingdoms of life, consist of a hexameric AAA+ unfoldase/translocase in complex with a self-compartmentalized peptidase. Based on asymmetric features of cryo-EM structures and a sequential hand-over-hand model of substrate translocation, recent publications have proposed that the AAA+ unfoldases ClpA and ClpX must rotate with respect to their partner peptidase ClpP to allow function. Here, we test this model by covalently crosslinking ClpA to ClpP to prevent rotation. We find that crosslinked ClpAP omplexes unfold, translocate, and degrade protein substrates, albeit modestly slower han uncrosslinked enzyme controls. Rotation of ClpA with respect to ClpP therefore is ot required for ClpAP protease activity, although some flexibility in how the AAA+ ring ocks on ClpP may be necessary for optimal function.
Bioremediation Potential of Select Bacterial Species for the Neonicotinoid Insecticides, Thiamethoxam and Imidacloprid
Authors: Zamule Stephanie M. , Dupre Cassandra , Mendola Meghan , Widmer Julia , Shebert Jane , Roote Carol E. , Das Padmini 
Published: July 2020

AbstractThe neonicotinoid insecticides, including thiamethoxam (THM) and imidacloprid (IMI), have become increasingly favored in the past decade due to their specificity as insect neurotoxicants. However, neonicotinoids have been implicated as a potential contributing factor in Colony Collapse Disorder (CCD), the widespread disappearance of honey bees, which affects produce production on a global scale. The environmental persistence of neonicotinoids underscores the importance of developing a sustainable, ecologically-friendly remediation technique to remove residual insecticides from the environment. The present study characterizes the neonicotinoid bioremediation potential of six bacterial species:Pseudomonas fluorescens, Pseudomonas putida, Pseudomonas aeruginosa, Alcaligenes faecalis, Escherichia coli, andStreptococcus lactis. In Phase I, we evaluated the utilization of IMI or THM as the sole carbon or nitrogen source byP. fluorescens, P. putida, andP. aeruginosa. All three species were better able to utilize THM over IMI as their sole carbon or nitrogen source, and better growth was noted when THM was used as the sole nitrogen source compared to the sole carbon source. Thus, further studies proceeded with THM only. In Phase II, we assessed the kinetics of THM removal from aqueous media by the six species. Significant (p<0.0001) reductions in 70 mg/L THM concentration were observed forP. fluorescens(67%),P. putida(65%),P. aeruginosa(52%), andA. faecalis(39%) over the 24-day study period, and forE. coli(60%) andS. lactis(12%) over the 14-day study period. The amount of time required to remove 50% of the THM in the media (T50) was: 12 days (d) (E. coli), 18 d (P. fluorescens), 19 d (P. putida), and 23 d (P. aeruginosa). NeitherA. faecalisnorS. lactisachieved 50% removal during the study periods. The THM removal by all species followed a first-order kinetic reaction and half-lives were calculated accordingly. HPLC chromatograms ofP. fluorescens, P. putida, andE. colicultures revealed that as the area of the THM peak decreased over time, the area of an unidentified metabolite peak increased. In Phase II, we sought to characterize this metabolite and the overall metabolic efficiency of these three species. Maximal THM removal occurred at 30°C for all bacterial species assessed. Identification of the metabolite is currently underway, which will allow determination of whether the metabolite is less toxic than the parent compound, a prerequisite for this remediation technique to be viable. If the metabolite is found to be less hazardous than THM, further testing will follow to evaluate the use of this bioremediation technique in the field.
Species richness, geographical affinities, and activity patterns of mammals in premontane Andean forests of the Magdalena river basin of Colombia
Authors: Torres Diego A. , Rojas Abel Eduardo 
Published: July 2020

AbstractThe Magdalena river basin is home to more than half of Colombia’s human population, and consequently the basin also harbors their economic activities. These activities have generated high deforestation rates and negative pressures on natural resources. With such a scenario of forest loss it is imperative to assess the state of the biodiversity and its conservation. Here, during six years we assessed the mammalian species richness and abundance in premontane forests of Caldas department in the Magdalena river basin. We also presented additional information on the activity patterns and geographical affinities of this fauna. We recorded 100 species of mammals with the Chiroptera as the richest order, followed by Rodentia. Most of the species are common and are not under risk of extinction; however, it is important to highlight the presence of six endemic species, three vulnerable species and one endangered species (white-footed tamarin). The mammalian fauna of this region is similar to other lowland localities in the Neotropics, and less similar to highland localities, including the nearby ones. Specifically, this fauna is most similar to lowland Tolima, and the Caribbean region of Colombia, Venezuela and Costa Rica; however, when we accounted only for bat fauna, it was more similar to the Caribbean and Pacific regions of Colombia. To secure the long-term persistence of these species we recommend maintenance of the current corridors such as riparian forests and living fences and an increase in the forested area.
Fungal zygote survival and ploidy maintenance rely on cell cycle-dependent and independent mating blocks
Authors: Vještica Aleksandar , Bérard Melvin , Liu Gaowen , Merlini Laura , Nkosi Pedro Junior , Martin Sophie G 
Published: July 2020

AbstractTo ensure genome stability, sexually reproducing organisms require that mating brings together exactly two haploid gametes and that meiosis occurs only in diploid zygotes. In the fission yeastSchizosaccharomyces pombe, fertilization triggers the Mei3-Pat1-Mei2 signaling cascade, which represses subsequent mating and initiates meiosis. Here, we establish a degron system to specifically degrade proteins post-fusion and demonstrate that mating blocks not only safeguard zygote ploidy but also prevent lysis caused by aberrant fusion attempts. Using long-term imaging and flow-cytometry approaches, we identify previously unrecognized and independent roles for Mei3 and Mei2 in zygotes. We show that Mei3 promotes premeiotic S-phase independently of Mei2 and that cell cycle progression is both necessary and sufficient to reduce zygotic mating behaviors. Mei2 imposes the meiotic program and promotes the meiotic cycle, but also blocks mating behaviors independently of Mei3 and cell cycle progression. Thus, we find that fungi preserve zygote ploidy and survival by at least two mechanisms where the zygotic fate imposed by Mei2 and the cell cycle re-entry triggered by Mei3 synergize to prevent zygotic mating.
Modeling the complete kinetics of coxsackievirus B3 reveals human determinants of host-cell feedback
Authors: Lopacinski Aaron B. , Sweatt Andrew J. , Smolko Christian M. , Gray-Gaillard Elise , Borgman Cheryl A. , Shah Millie , Janes Kevin A. 
Published: July 2020

SUMMARYComplete kinetic models are pervasive in chemistry but lacking in biological systems. We encoded the complete kinetics of infection for coxsackievirus B3 (CVB3), a compact and fast-acting RNA virus. The kinetics are built from detailed modules for viral binding–delivery, translation–replication, and encapsidation. Specific module activities are dampened by the type I interferon response to viral double-stranded RNAs (dsRNAs), which is itself disrupted by viral proteinases. The validated kinetics uncovered that cleavability of the dsRNA transducer mitochondrial antiviral signaling protein (MAVS) becomes a stronger determinant of viral outcomes when cells receive supplemental interferon after infection. Cleavability is naturally altered in humans by a common MAVS polymorphism, which removes a proteinase-targeted site but paradoxically elevates CVB3 infectivity. These observations are reconciled with a simple nonlinear model of MAVS regulation. Modeling complete kinetics is an attainable goal for small, rapidly infecting viruses and perhaps viral pathogens more broadly.
The direct regulation ofAalbdsxonAalVgRis indispensable for ovarian development inAedes albopictus
Authors: Jin Binbin , Zhao Yijie , Liu Peiwen , Sun Yan , Li Xiaocong , Zhang Xin , Chen Xiao-Guang , Gu Jinbao 
Published: July 2020

AbstractBACKGROUNDAedes albopictusis an important vector with an extensive worldwide distribution. Only female mosquitoes play a significant role in the transmission of pathogens.Doublesex(dsx) is a central nexus gene in the insect somatic sex determination hierarchy.RESULTSIn this study, we characterized the full-length sex-specific splicing forms of theAe. albopictus dsxgene (Aalbdsx). Then, we identified 15 direct target genes of DSX in adult females using digital gene expression (DGE) combined with qPCR following a chromatin immunoprecipitation assay (ChIP) with specific DSX antibodies. The knockdown ofAalbdsxsuppressed ovarian development, and the transcript levels of theAalbdsxtargetvitellogenin receptor(VgR) gene decreased, whereasvitellogenin(Vg) expression showed an increase in the fat body. Genes in the majorVgregulatory pathway were also upregulated. Our results suggest that the effects ofAalbdsxRNAi on ovarian development are exerted mainly viaVgRrather thanVg.CONCLUSIONThe results of our study not only provide a reference for the further elucidation of the sex determination cascade and comparative analyses ofdsxtarget interactions in mosquitoes but also reveal potential molecular targets for application to the development of sterile male mosquitoes to be released for vector control.
Inducing Human Retinal Pigment Epithelium-like Cells from Somatic Tissue
Authors: Woogeng Ivo Ngundu , Abugessaisa Imad , Tachibana Akihiro , Sahara Yoshiki , Hon Chung-Chau , Hasegawa Akira , Kaczkowski Bogumil , Sakai Noriko , Nishida Mitsuhiro , Hu Haiming , Sanyal Hashimita , Sho Junki , Kasukawa Takeya , Takasato Minoru , Carninci Piero , Maeda Akiko , Mandai Michiko , Arner Erik , Takahashi Masayo , Kime Cody 
Published: July 2020

SUMMARYRegenerative medicine relies on basic research to find safe and useful outcomes that are only practical when cost-effective. The human eyeball requires the retinal pigment epithelium (RPE) for support and maintenance that interfaces the neural retina and the choroid at large. Nearly 200 million people suffer from age-related macular degeneration (AMD), a blinding multifactor genetic disease among other retinal pathologies related to RPE degradation. Recently, autologous pluripotent stem cell-derived RPE cells were prohibitively expensive due totime,therefore we developed a new simplified cell reprogramming system. We stably induced RPE-like cells (iRPE) from human fibroblasts by conditional overexpression of broad plasticity and lineage-specific pioneering transcription factors. iRPE cells showed features of modern RPE benchmarks and significantin-vivointegration in transplanted chimeric hosts. Herein, we detail the iRPE system with comprehensive modern single-cell RNA (scRNA) sequencing profiling to interpret and characterize its best cells. We anticipate that our system may enable robust retinal cell induction for regenerative medicine research and affordable autologous human RPE tissue for cell therapy.
Connecting the stimuli-responsive rheology of biopolymer hydrogels to underlying hydrogen-bonding interactions
Authors: Giubertoni Giulia , Burla Federica , Bakker Huib J. , Koenderink Gijsje H. 
Published: July 2020

AbstractMany biopolymer hydrogels are environmentally responsive because they are held together by physical associations that depend on pH and temperature. Here we investigate how the pH and temperature response of the rheology of hyaluronan hydrogels is connected to the underlying molecular interactions. Hyaluronan is an essential structural biopolymer in the human body with many applications in biomedicine. Using two-dimensional infrared (2DIR) spectroscopy, we show that hyaluronan chains become connected by hydrogen bonds when the pH is changed from 7.0 to 2.5, and that the bond density at pH 2.5 is independent of temperature. Temperature-dependent rheology measurements show that due to this hydrogen bonding the stress relaxation at pH 2.5 is strongly slowed down in comparison to pH 7.0, consistent with the sticky reptation model of associative polymers. From the flow activation energy we conclude that each polymer is crosslinked by multiple (5-15) hydrogen bonds to others, causing slow macroscopic stress relaxation, despite the short time scale of breaking and reformation of each individual hydrogen bond. Our findings can aid the design of stimuli-responsive hydrogels with tailored viscoelastic properties for biomedical applications.
Single-cell transcriptomics of theDrosophilawing disc reveals instructive epithelium-to-myoblast interactions
Authors: Everetts Nicholas J. , Worley Melanie I. , Yasutomi Riku , Yosef Nir , Hariharan Iswar K. 
Published: July 2020

AbstractIn both vertebrates and invertebrates, generating a functional appendage requires interactions between ectoderm-derived epithelia and mesoderm-derived cells. To investigate such interactions, we used single-cell transcriptomics to generate a cell atlas of theDrosophilawing disc at two time points during development. Using these data, we investigate gene expression using a multi-layered model of the wing disc and catalogued ligand-receptor pairs that could mediate signaling between epithelial cells and adult muscle precursors (AMPs). We found that localized expression of the FGF ligands, Thisbe and Pyramus, in the disc epithelium regulates the number and location of the AMPs. In addition, Hedgehog ligand from the epithelium activates a specific transcriptional program within adjacent AMP cells, which is critical for proper formation of a subset of the direct flight muscles. More generally, our annotated atlas provides a global view of potential cell-cell interactions between subpopulations of epithelial and myogenic cells.
Structural and biochemical characterization of a glutathione transferase from the citrus canker pathogenXanthomonas
Authors: Hilario Eduardo , De Keyser Sawyer , Fan Li 
Published: July 2020

The genusXanthomonascomprises several cosmopolitan plant-pathogenic bacteria that affect more than 400 plant species, most of which are of economic interest. Citrus canker is a bacterial disease that affects citrus species, reducing fruit yield and quality, and is caused by the bacteriumXanthomonas citrisubsp.citri(Xac). The Xac3819 gene, which has previously been reported to be important for citrus canker infection, encodes an uncharacterized glutathioneS-transferase (GST) of 207 amino-acid residues in length (XacGST). Bacterial GSTs are implicated in a variety of metabolic processes such as protection against chemical and oxidative stresses. XacGST shares high sequence identity (45%) with the GstB dehalogenase fromEscherichia coliO6:H1 strain CFT073 (EcGstB). Here, XacGST is reported to be able to conjugate glutathione (GSH) with bromoacetate with aKmof 6.67 ± 0.77 mM, akcatof 42.69 ± 0.32 s−1and a kcat/Kmof 6.40 ± 0.72 mM−1 s−1under a saturated GSH concentration (3.6 mM). These values are comparable to those previously reported for EcGstB. In addition, crystal structures of XacGST were determined in the apo form (PDB entry 6nxv) and in a GSH-bound complex (PDB entry 6nv6). XacGST has a canonical GST-like fold with a conserved serine residue (Ser12) at the GSH-binding site near the N-terminus, indicating XacGST to be a serine-type GST that probably belongs to the theta-class GSTs. GSH binding stabilizes a loop of about 20 residues containing a helix that is disordered in the apo XacGST structure.