bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish
Authors: Rivera-Colón Angel G. , Rayamajhi Niraj , Minhas Bushra Fazal , Madrigal Giovanni , Bilyk Kevin T. , Yoon Veronica , Hüne Mathias , Gregory Susan , Cheng C.-H. Christina , Catchen Julian M. 
Published: August 2022

AbstractWhite-blooded Antarctic icefishes, a family within the adaptive radiation of Antarctic notothenioid fishes, are an example of extreme biological specialization to both the chronic cold of the Southern Ocean and life without hemoglobin. As a result, icefishes display derived physiology that limits them to the cold and highly oxygenated Antarctic waters. Against these constraints, remarkably one species, the pike icefishChampsocephalus esox, successfully colonized temperate South American waters. To study the genetic mechanisms underlying secondarily temperate adaptation in icefishes, we generated chromosome-level genome assemblies of bothC. esoxand its Antarctic sister species,Champsocephalus gunnari. TheC. esoxgenome is similar in structure and organization to that of its Antarctic congener; however, we observe evidence of chromosomal rearrangements coinciding with regions of elevated genetic divergence in pike icefish populations. We also find several key biological pathways under selection, including genes related to mitochondria and vision, highlighting candidates behind temperate adaptation inC. esox. Substantial antifreeze glycoprotein (AFGP) pseudogenization has occurred in the pike icefish, likely due to relaxed selection following ancestral escape from Antarctica. The canonicalAFGPlocus organization is conserved inC. esoxandC. gunnari, but both show a translocation of twoAFGPcopies to a separate locus, previously unobserved in cryonotothenioids. Altogether, the study of this secondarily temperate species provides an insight into the mechanisms underlying adaptation to ecologically disparate environments in this otherwise highly specialized group.
3rd-ChimeraMiner: A pipeline for integrated analysis of whole genome amplification generated chimeric sequences using long-read sequencing
Authors: Lu Na , Qiao Yi , An Pengfei , Luo Jiajian , Bi Changwei , Li Musheng , Lu Zuhong , Tu Jing 
Published: August 2022

AbstractMultiple displacement amplification (MDA) has become one of the most commonly used method of whole genome amplification (WGA) due to the high processivity, strand displacement capacity and high fidelity of the phi29 DNA polymerase, MDA generate vast amount of DNA with higher molecules weight (up to 100kb) and greater genome coverage. Along with the development of the sequencing platform, it is possible to sequence the MDA-amplified DNA molecules with over 20kb by long-read sequencing. However, one of the challenges is the formation of chimeras, which exist in all MDA products, and seriously interfere with the downstream analysis of the long-read sequencing data of MDA-amplified DNA. In this study, we constructed 3rd-ChimeraMiner, a chimera detection pipeline for analyzing the long-read sequencing of MDA products, recognizing chimeras, and integrating chimeras into the downstream analysis. Five sequencing data of MDA with different magnification fold were analyzed in here, the proportions of chimeras are much higher than that of next-generation sequencing reads and increase with the increase of magnification folds, ranging from 42% to over 76%. After comparing, 99.92% of recognized chimeras have been demonstrated not to exist in original genomes. After detecting chimeras by 3rd-ChimeraMiner, the full-length mapping ratio increased, means more PacBio data could be used in downstream analysis, and mean 97.77% inversions were removed after transferred chimeras into normal reads. 3rd-ChimeraMiner revealed efficiency and accuracy in discovering chimeras from long-read sequencing data of MDA, and is promising to be widely used in single-cell sequencing.
Long term maintenance of heterologous symbiont association in Acropora palmata on natural reefs
Authors: Elder Holland , Million Wyatt C. , Bartels Erich , Krediet Cory , Muller Erinn , Kenkel Carly D. 
Published: August 2022

AbstractThe sensitivity of reef-building coral to elevated temperature is a function of their symbiosis with dinoflagellate algae in the family Symbiodiniaceae. Changes in the composition of the endosymbiont community in response to thermal stress can increase coral thermal tolerance. Consequently, this mechanism is being investigated as a human-assisted intervention for rapid acclimation of coral in the face of climate change. Successful establishment of novel symbioses that increase coral thermal tolerance have been demonstrated in laboratory conditions; however, it is unclear how long these heterologous relationships persist in nature. Here, we show that Acropora palmata can form a novel symbiosis with Durusdinium spp. when reared in land-based aquaria. We tested the stability of this heterologous relationship by outplanting clonal replicates (ramets) of five A. palmata host genotypes to natural reefs in the lower Florida Keys. Amplicon sequencing analysis of ITS2-type profiles revealed that the majority of surviving ramets remained dominated by Durusdinium spp. two years after transplantation. However, 15% of ramets, including representatives of all genotypes, did exhibit some degree of symbiont shuffling or switching at six of eight sites, including complete takeover by site-specific strains of the native symbiont, Symbiodinium fitti. The predominant long-term stability of the novel symbiosis supports the potential effectiveness of symbiont modification as a management tool. However, the finding that 6–7 year-old coral can alter symbiont community composition in the absence of bleaching indicates that Symbiodiniaceae communities are indeed capable of greater flexibility under ambient conditions.
Temporal structure of two call types produced by competing male cicadas
Authors: Ishimaru Takahiro , Aihara Ikkyu 
Published: August 2022

AbstractMale cicadas vocalize sounds to attract conspecific females. The acoustic traits of calls vary significantly among species and show unique temporal and spectral patterns that dynamically change, even in the same bout. While the calling behavior of a single cicada has been quantified for many species, the acoustic interaction between multiple cicadas and the usage of different call types have not been well studied. In this study, we examined the interaction between male cicadas (Meimuna opalifera) that utilize two types of calls. First, we caught two cicadas in their natural habitat and recorded their calls in the laboratory. Second, we detected the calls of each cicada and classified them into two types: Type I calls with a short duration and high repetition rate and Type II calls with a longer duration and low repetition rate. The analysis of the chorus structure demonstrated that the cicadas vocalized a Type II call immediately after another cicada vocalized a Type I call. Furthermore, we tested the hypothesis that such a timing strategy allowed the cicadas to effectively mask the calls of their competitors. Specifically, we conducted a numerical simulation randomizing the onsets of calls and compared the masking performance with empirical data, which did not support our hypothesis. This study highlights the well-organized structure of cicada calls, even in the choruses with multiple call types, and indicates these calls have a function other than male-male acoustic interaction that requires further investigation.Summary statementMale cicadas (Meimuna opalifera) produce two types of calls by synchronizing their temporal structure and switching call types when positioned close together.
Genetic Association of LDHA Variant g.2582481G>A with Racing Performance of Pakistani Pigeons
Authors: Saif Rashid , Zafar Muhammad Osama , Raza Muhammad Hassan 
Published: August 2022

AbstractPigeons are being used as a means of communication back in history due to their efficient flight stamina, navigational (homing) ability and endurance to harsh weather conditions. Due to these distinctive characteristics, pigeon racing and rearing has become a popular sport and hobby throughout the world, predominantly in Pakistan. The genetic tendency of LDHA gene in pigeons should be considered for understanding racing ability. The present study aimed to examine the genetic association of LDHA variant g.2582481G>A with racing performance in Pakistani pigeons. Our results demonstrated that 55% of the pigeon’s population was homozygous wild-type (G/G), 37.5% was heterozygous (G/A) and the remaining 7.5% was homozygous-mutant (A/A) at this locus. Furthermore, alternative allele frequencies within the best and low-performing cohorts of pigeons were 0.45 and 0.075 respectively. Furthermore, the Chi-Square association test was applied using PLINK data analysis toolset which showed a significant p-value of 1.381×10-4 with odds ratio (OR) of 10.09. Consequently, Pakistani pigeon population suggests a significant association of g.2582481G>A with racing performance similar to the other pigeon population of the world.
The Translation Initiation Factor Homolog,eif4e1c, Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration
Authors: Rao Anupama , Lyu Baken , Jahan Ishrat , Lubertozzi Anna , Zhou Gao , Tedeschi Frank , Jankowsky Eckhard , Kang Junsu , Carstens Bryan , Poss Ken , Baskin Kedryn , Goldman Joseph Aaron 
Published: August 2022

AbstractThe eIF4E family of translation initiation factors bind 5’ methylated caps and act as the limiting-step for mRNA translation. The canonical eIF4E1A is required for cell viability, yet other related eIF4E families exist and are utilized in specific contexts or tissues. Here, we describe a family called Eif4e1c for which we find roles during heart development and regeneration in zebrafish. The Eif4e1c family is present in all aquatic vertebrates but is lost in all terrestrial species. A core group of amino acids shared over 500 million years of evolution forms an interface along the protein surface, suggesting Eif4e1c functions in a novel pathway. Deletion ofeif4e1cin zebrafish caused growth deficits and impaired survival in juveniles. Mutants surviving to adulthood had fewer cardiomyocytes and reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Althougheif4e1cis broadly expressed, its disruption had most notable impact on the heart and at juvenile stages. Our findings reveal context-dependent requirements for translation initiation regulators during heart regeneration.
Morphological Subprofile Analysis for Bioactivity Annotation of Small Molecules
Authors: Pahl Axel , Schölermann Beate , Rusch Marion , Dow Mark , Hedberg Christian , Nelson Adam , Sievers Sonja , Waldmann Herbert , Ziegler Slava 
Published: August 2022

AbstractFast prediction of mode of action for bioactive compounds would immensely foster bioactivity annotation in compound collections and may early on reveal off-targets in chemical biology research and drug discovery. A variety of target-based assays is available for addressing the modulation of druggable proteins. However, they cannot precisely predict how a compound would influence cellular processes due to polypharmacology. Furthermore, non-protein targets are often not considered. Morphological profiling, e.g., using the Cell Painting assay that monitors hundreds of morphological features upon compound perturbation and staining of cellular components, offers a fast, unbiased assessment of compound activity on various targets and cellular processes in one single experiment. However, due to incomplete bioactivity annotation and unknown activities of reference (landmark) compounds, prediction of bioactivity is not straightforward. Here we introduce the concept of subprofile analysis to map the mode of action for both reference and unexplored compounds. We defined mode-of-action clusters for a group of reference compounds and extracted cluster subprofiles that contain only a subset of morphological features (i.e., subprofiles) to represent a consensus profile. Subprofile analysis allows for assignment of compounds to, currently, ten different targets or modes of action in one single assay and bypasses the need of exploring all biosimilar reference compounds for the generation of target hypothesis. This approach will enable rapid bioactivity annotation of compound collections, particularly of uncharacterized small molecules, and will be extended to further bioactivity clusters in future. The data is public accessible viahttps://github.com/mpimp-comas/2022_pahl_ziegler_subprofilesand the web app toolhttp://cpcse.pythonanywhere.com/.
Outer membrane utilisomes mediate oligosaccharide uptake in gut Bacteroidetes
Authors: White Joshua B. R. , Silale Augustinas , Feasey Matthew , Heunis Tiaan , Zhu Yiling , Zheng Hong , Gajbhiye Akshada , Firbank Susan , Baslé Arnaud , Trost Matthias , Bolam David N. , Ranson Neil A. , van den Berg Bert 
Published: August 2022

AbstractBacteroidetes are abundant members of the human microbiota, with species occupying the distal gut capable of utilising a myriad of diet- and host-derived glycans. Transport of glycans across the outer membrane (OM) of these bacteria is mediated by SusCD protein complexes, comprising a membrane-embedded barrel and a lipoprotein lid, that are thought to operate via a ‘pedal-bin’ mechanism in which the lids open and close to facilitate substrate binding. However, additional cell surface-exposed lipoproteins, namely surface glycan binding proteins and glycoside hydrolases, play critical roles in the capture and processing of large glycan chains into transport-competent substrates. Despite constituting a crucial mechanism of nutrient acquisition by our colonic microbiota, the interactions between these components in the OM are poorly understood. Here we show that for the levan and dextran utilisation systems of Bacteroides thetaiotaomicron, the additional OM components assemble on the core SusCD transporter, forming stable glycan utilising machines which we term ‘utilisomes’. Single particle electron cryogenic electron microscopy (cryo-EM) structures in the absence and presence of substrate reveal concerted conformational changes that rationalise the role of each component for efficient nutrient capture, as well as providing a direct demonstration of the pedal bin mechanism of substrate capture in the intact utilisome.
Clonal evolution during metastatic spread in high-risk neuroblastoma
Authors: Gundem Gunes , Levine Max F. , Roberts Stephen S. , Cheung Irene Y , Medina-Martínez Juan S. , Feng Yi , Arango-Ossa Juan E. , Chadoutaud Loic , Rita Mathieu , Asimomitis Georgios , Zhou Joe , You Daoqi , Bouvier Nancy , Spitzer Barbara , Solit David B. , Cruz Dela Filemon , LaQuaglia Michael P. , Kushner Brian H. , Modak Shakeel , Shukla Neerav , Iacobuzio-Donahue Christine A. , Kung Andrew L. , Cheung Nai-Kong V. , Papaemmanuil Elli 
Published: August 2022

AbstractHigh-risk neuroblastoma is generally metastatic and often lethal. Using genomic profiling of 470 sequential and spatially separated samples from 283 patients, we characterize subtype-specific genetic evolutionary trajectories from diagnosis, through progression and end-stage metastatic disease. Clonal tracing timed disease initiation to embryogenesis. Continuous acquisition of structural variants at disease defining loci (MYCN, TERT, MDM2-CDK4) followed by convergent evolution of mutations targeting shared pathways emerged as the predominant feature of progression. At diagnosis metastatic clones were already established at distant sites where they could stay dormant, only to cause relapses years later and spread via metastasis-to-metastasis and polyclonal seeding after therapy.
Not all seed transfer zones are created equal: Using fire history to identify seed needs in the Cold Deserts of the Western US
Authors: Barga Sarah C. , Kilkenny Francis F , Jensen Scott , Kulpa Sarah M. , Agneray Alison C. , Leger Elizabeth A. 
Published: August 2022

ABSTRACTRestoration planning requires a reliable seed supply, yet many projects occur in response to unplanned events. Identifying regions of greater risk could help guide seed procurement. Using fire perimeters (2000–2019), we investigated differences in fire occurrence (frequency, area burned, percent of area burned) among seed transfer zones within Cold Deserts of the US. We considered both provisional seed transfer zones (PSTZs), created using climate and stratified by ecoregion, and empirical seed transfer zones (ESTZs) for two species commonly used in restoration. Finally, we present a case study on fire occurrence within Northern Basin and Range greater sage-grouse Priority Areas for Conservation (PACs). Historic fire was effective for prioritizing seed zones: 23 of 132 PSTZs burned every year, and, within each ecoregion, two PSTZs comprised ≧ 50% of the total area burned across all years. Similarly, fire disproportionately occurred in some ESTZs; in the Northern Basin and Range, one (Artemisia tridentata- 83%) or two zones (Pseudoroegneria spicata- 65%) made up a majority of total area burned. Fire occurrence within PACs largely reflected the PSTZ and ESTZ priorities found for the ecoregion, with small exceptions. Imperiled PSTZs (high proportion burned) in PACs largely reflected the patterns found across the ecoregion, while imperiled ESTZs departed from ecoregional patterns. Considering historic disturbance can focus seed procurement efforts on regions that encounter regular disturbance, experience large disturbances, or have particular conservation value. This information can guide seed production, purchase, and storage, create more certainty for growers and managers, and ultimately increase restoration success.IMPLICATIONS FOR PRACTICEAvailable data on past disturbance patterns may inform strategies for prioritizing seed procurement decisions, especially as geospatial information becomes more widely availableThe methods presented here illustrate an approach for using historic disturbance data to identify regions that are of greatest need for seed collection and conservation, using seed transfer zones within US Cold Desert ecoregions as an exampleIdentifying regions that experience disturbance over large areas or are likely to be imperiled due to disturbance at a high proportion can guide the collection and conservation of plant materials and better align available plant material with future restoration needs
The role of calcium, Akt and ERK signaling in cadmium-induced hair cell death
Authors: Galdieri Jennifer , Adams Chloe , Padilla María , Stawicki Tamara M. 
Published: August 2022

ABSTRACTExposure to heavy metals has been shown to cause damage to a variety of different tissues and cell types including hair cells, the sensory cells of our inner ears responsible for hearing and balance. Elevated levels of one such metal, cadmium, have been associated with hearing loss and shown to cause hair cell death in multiple experimental models. While the mechanisms of cadmium-induced cell death have been extensively studied in other cell types they remain relatively unknown in hair cells. We have found that calcium signaling, which is known to play a role in cadmium-induced cell death in other cell types through calmodulin and CaMKII activation as well as IP3 receptor and mitochondrial calcium uniporter mediated calcium flow, does not appear to play a significant role in cadmium-induced hair cell death. While calmodulin inhibition can partially protect hair cells this may be due to impacts on mechanotransduction activity. Removal of extracellular calcium, and inhibiting CaMKII, the IP3 receptor and the mitochondrial calcium uniporter all failed to protect against cadmium-induced hair cell death. We also found cadmium treatment increased pAkt levels in hair cells and pERK levels in supporting cells. This activation may be protective as inhibiting these pathways enhances cadmium-induced hair cell death rather than protecting cells. Thus cadmium-induced hair cell death appears distinct from cadmium-induced cell death in other cell types where calcium, Akt and ERK signaling all promote cell death.
Single-cell analysis of non-alcoholic fatty livers identifies a role for the constitutive androstane receptor
Authors: Coassolo Laetitia , Liu Tianyun , Jung Yunshin , Taylor Nikki P. , Zhao Meng , Charville Gregory W. , Nissen Silas Boye , Yki-Jarvinen Hannele , Altman Russ , Svensson Katrin J. 
Published: August 2022

ABSTRACTNon-alcoholic fatty liver disease is a heterogeneous disease with unclear underlying molecular mechanisms. While several genetic risk factors have been identified, the cellular and molecular heterogeneity associated with the development of hepatic steatosis are still not fully understood. Here, we perform single-cell RNA sequencing of hepatocytes and hepatic nonparenchymal cells to map the lipid signatures in mice with non-alcoholic fatty liver disease (NAFLD). We uncover previously unidentified clusters of hepatocytes characterized by either high or low srebp1 expression with unique molecular signatures of lipid synthesis. We find that NAFLD livers have elevated expression of the constitutive androstane receptor (CAR), a gene previously associated with lipid synthesis. Furthermore, nuclear expression of CAR positively correlates with steatohepatitis in humans. These findings demonstrate significant cellular differences in lipid signatures and identify a gene with a high likelihood of being linked to hepatic steatosis in humans.
Wenzhou shrimp virus 8 (WzSV8) detection by unique inclusions in shrimp hepatopancreatic E-cells and by RT-PCR
Authors: Srisala Jiraporn , Thaiue Dararat , Saguanrut Piyachat , Taengchaiyaphum Suparat , Flegel Timothy W. , Sritunyalucksana Kallaya 
Published: August 2022

AbstractThe genome sequence of Wenzhou shrimp virus 8 (WzSV8) (GenBank recordKX883984.1) was described in 2015 from wide screening for RNA viruses in aquatic animals. A closely related sequence (GenBank recordOK662577.1) from the whiteleg shrimpPenaeus vannameiwas deposited in 2021 under the name Penaeus vannamei picornavirus (PvPV). In 2022 another closely related sequence (GenBank accession:OP265432) was submitted under the name Penaeus vannamei solinvivirus (PvSV). In 2021, prior to the publication of PvPV and PvSV, we used an RT-PCR method devised from the sequence of KX883984.1 (described herein) to screen for WzSV8 in specimens of cultivated shrimp. Samples that gave positive RT-PCR results were subsequently tested byin situhybridization (ISH) analysis to identify virus target tissues. Several tissues gave positive ISH results within morphologically normal nuclei. Thus, these tissues were of no use for diagnosis of WzSV8 by normal histological analysis. However, unique basophilic, cytoplasmic inclusions within vacuoles in the hepatopancreatic E-cells were also found in the same WzSV8-positive shrimp specimens, sometimes accompanied by a smaller eosinophilic inclusion. We call these Lightner double Inclusions (LDI) that can be considered pathognomonic for diagnosis of WzSV8 infection when detected using the light microscope. Although no current proof of WzSV8 is the cause of disease, it is important to investigate new viruses and related tissue anomalies, even from normal cultivated shrimp, to determine whether they may have any relationship to significant negative effects on the production of cultivated shrimp.