bluuebunny/crossref_metadata_2025_split huggingface dataset:
Consumer-driven nutrient recycling of freshwater decapods: linking ecological theories and application in integrated multi-trophic aquaculture
Authors: Musin Gabriela E. , Torres Maria Victoria , Carvalho Débora A. 
Published: January 2022

AbstractThe Metabolic Theory of Ecology (MET) and the Ecological Stoichiometry Theory (EST) are central and complementary in the consumer-driven recycling conceptual basis. The comprehension of physiological processes of organisms at different levels of organizations is essential to explore and predict nutrient recycling behavior in different scenarios, and to design integrated productive systems that efficiently use the nutrient inputs through an adjusted mass balance. We fed with fish-feed three species of decapods from different families and with aquacultural potential to explore the animal-mediated nutrient dynamic and its applicability in productive systems. We tested whether physiological (body mass, body elemental content), ecological (diet), taxonomic and experimental (time of incubation) variables predicts N and P excretion rates and ratios across and within taxa. We also analysed body mass and body elemental content independently as predictors of N and P excretion of decapods across, among and within taxa. Finally, we verified if body content scales allometrically across and within taxa and if differed among taxa. Body mass and taxonomic identity predicted nutrient excretion rates both across and within taxa. When physiological variables were analysed independently, body size best predicted nutrient mineralization in both scales of analyses. Regarding body elemental content, only body P content scaled negatively with body mass across taxa. Results showed higher N-requirements and lower C:N of prawns than anomurans and crabs. The role of crustaceans as nutrient recyclers depends mainly on the species and body mass, and should be considered to select complementary species that efficiently use feed resources. Prawns need more protein in their feed and might be integrated with fish of higher N-requirements, while crabs and anomurans, with fish of lower N-requirements. Our study contributed to the background of MTE and EST through empirical data obtained from decapods and provided useful information to achieve more efficient aquaculture integration systems.
Meiotic pairing and double strand break formation along the heteromorphic threespine stickleback sex chromosomes
Authors: Nath Shivangi , Welch Lucille A. , Flanagan Mary K. , White Michael A. 
Published: January 2022

AbstractDouble strand break repair during meiosis is normally achieved using the homologous chromosome as a repair template. Heteromorphic sex chromosomes have reduced sequence homology with one another, presenting unique challenges to the repair of double strand breaks. Our understanding of how heteromorphic sex chromosomes behave during meiosis has been largely limited to the ancient sex chromosomes of mammals, where the X and Y differ markedly in overall structure and gene content. Consequently, pairing of the X and Y chromosomes is limited to a small pseudoautosomal region. It remains unclear how more recently evolved sex chromosomes, that share considerably more sequence homology with one another, pair and repair double strand breaks during meiosis. One possibility is barriers to pairing evolve rapidly. Alternatively, recently evolved sex chromosomes may exhibit pairing and double strand break repair that more closely resembles that of their autosomal ancestors. Here we use the recently evolved X and Y chromosomes of the threespine stickleback fish (Gasterosteus aculeatus) to study patterns of pairing and double stranded break formation using molecular cytogenetics. We found that the sex chromosomes of threespine stickleback fish do not pair exclusively in the pseudoautosomal region. Instead, the chromosomes fully pair in a non-homologous fashion. To achieve this, the X chromosome underwent synaptic adjustment during pachytene to match the axis length of the Y chromosome. Double strand break formation and repair rate also matched that of the autosomes. Our results highlight that recently evolved sex chromosomes exhibit meiotic behavior that is reminiscent of autosomes and argues for further work to identify the homologous templates that are used to repair double strand breaks on the X and Y chromosomes.
The Antimicrobial Activity of Pechuel-Loeschea leubnitziae Leaf Extract and its Effect on The Expression Level of Methicillin Resistant Staphylococcus Aureus and Candida albicans Virulence-Associated Genes
Authors: Muhongo Mariah Ndilimeke , Kangogo Mourine , Bii Christine 
Published: January 2022

ABSTRACTThe complete halt in the synthesis of new effective antimicrobial compounds is a global concern. Pathogenic microorganisms’ virulence mechanisms seem to have a significant impact on their pathogenesis. The purpose of this study was to examine the antimicrobial activity of the ethanol and methanol fractions of Pechuel-Loeschea leubnitziae leaf extract, as well as its effect on the expression level of virulence-associated genes.The extract’s fractions were evaluated for antimicrobial activity against Escherichia coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853, Klebsiella pneumoniae (clinical), Methicillin-resistant Staphylococcus aureus, and Candida albicans ATCC 90029. The test organism’s antibiogram pattern was determined. The extracts’ attenuation effect on the target genes of the susceptible organisms was investigated employing relative quantification using RT-qPCR. The test organism’s antibiogram pattern revealed that it was drug-resistant, intermediate, and sensitive. The extracts tested positive for antimicrobial activity against Methicillin-resistant Staphylococcus aureus and Candida albicans ATCC 90029, with zones of inhibition varying from 20.33 to 29 mm. The lowest recorded MIC value was 4.688 mg/ml, while the highest was 37.5 mg/ml. In contrast to the methanol extract, the ethanol extract had a cidal action at a lower dose. The ethanol extract’s Sub-MIC (18.25 mg/ml) merely reduced the expression of the hly gene in MRSA. The MRSA virulence genes were not suppressed by the sub-MIC of methanol extract (18.25 mg/ml). Notably, the expression of als1, pbl1, and sap1 in Candida albicans ATCC 90029 was significantly attenuated when exposed to sub-MICs of ethanol extract (2,344 mg/ml) and methanol extract (9.375 mg/ml). Per the findings of this research, the leaves of P. leubnitziae could be a source of an effective antimicrobial agent in the therapy of MRSA/Candida-related disorders.
Skeletal muscle regeneration is altered in the R6/2 mouse model of Huntington’s disease
Authors: Hoque Sanzana , Sjögren Marie , Allamand Valérie , Gawlik Kinga , Franke Naomi , Durbeej Madeleine , Björkqvist Maria , Soylu-Kucharz Rana 
Published: January 2022

AbstractHuntington’s disease (HD) is caused by CAG repeat expansion in the huntingtin (HTT) gene. Skeletal muscle wasting alongside central pathology is a well-recognized phenomenon seen in patients with HD and HD mouse models. HD muscle atrophy progresses with disease and affects prognosis and quality of life. Satellite cells, progenitors of mature skeletal muscle fibers, are essential for proliferation, differentiation, and repair of muscle tissue in response to muscle injury or exercise.In this study, we aim to investigate the effect of mutant HTT on the differentiation and regeneration capacity of HD muscle by employing in vitro mononuclear skeletal muscle cell isolation and in vivo acute muscle damage model in R6/2 mice.We found that, similar to R6/2 adult mice, neonatal R6/2 mice also exhibit a significant reduction in myofiber width and morphological changes in gastrocnemius and soleus muscles compared to WT mice. Cardiotoxin (CTX)-induced acute muscle damage in R6/2 and WT mice showed that the Pax7+ satellite cell pool was dampened in R6/2 mice at 4 weeks post-injection, and R6/2 mice exhibited an altered inflammatory profile in response to acute damage.Our results suggest that, in addition to the mutant HTT degenerative effects in mature muscle fibers, expression of mutant HTT in satellite cells might alter developmental and regenerative processes to contribute to the progressive muscle mass loss in HD. Taken together, the results presented here encourage further studies evaluating the underlying mechanisms of satellite cell dysfunction in HD mouse models.
Pan-genomic analysis of transcriptional modules acrossSalmonellaTyphimurium reveals the regulatory landscape of different strains
Authors: Yuan Yuan , Seif Yara , Rychel Kevin , Yoo Reo , Chauhan Siddharth , Poudel Saugat , Al-bulushi Tahani , Palsson Bernhard O. , Sastry Anand 
Published: January 2022

AbstractSalmonella entericaTyphimurium is a serious pathogen that is involved in human nontyphoidal infections. Tackling Typhimurium infections is difficult due to the species’ dynamic adaptation to its environment, which is dictated by a complex transcriptional regulatory network (TRN). While traditional biomolecular methods provide characterizations of specific regulators, it is laborious to construct the global TRN structure from this bottom-up approach. Here, we used a machine learning technique to understand the transcriptional signatures ofS. entericaTyphimurium from the top down, as a whole and in individual strains. Furthermore, we conducted cross-strain comparison of 6 strains in serovar Typhimurium to investigate similarities and differences in their TRNs with pan-genomic analysis. By decomposing all the publicly available RNA-Seq data of Typhimurium with independent component analysis (ICA), we obtained over 400 independently modulated sets of genes, called iModulons. Through analysis of these iModulons, we 1) discover three transport iModulons linked to antibiotic resistance, 2) describe concerted responses to cationic antimicrobial peptides (CAMPs), 3) uncover evidence towards new regulons, and 4) identify two iModulons linked to bile responses in strain ST4/74. We extend this analysis across the pan-genome to show that strain-specific iModulons 5) reveal different genetic signatures in pathogenicity islands that explain phenotypes and 6) capture the activity of different phages in the studied strains. Using all high-quality publicly-available RNA-Seq data to date, we present a comprehensive, data-driven Typhimurium TRN. It is conceivable that with more high-quality datasets from more strains, the approach used in this study will continue to guide our investigation in understanding the pan-transcriptome of Typhimurium. Interactive dashboards for all gene modules in this project are available athttps://imodulondb.org/under the “SalmonellaTyphimurium” page to enable browsing for interested researchers.
Canonical Wnt Signaling Induces Focal Adhesion and Integrin Beta-1 Endocytosis
Authors: Tejeda-Muñoz Nydia , Morselli Marco , Moriyama Yuki , Sheladiya Pooja , Pellegrini Matteo , De Robertis Edward M. 
Published: January 2022

AbstractDuring canonical Wnt signaling, the Lrp6 and Frizzled co-receptors bind to the Wnt growth factor and the complex is endocytosed and sequestered together with Glycogen Synthase Kinase 3 (GSK3), Dishevelled (Dvl), and Axin inside the intraluminal vesicles of late endosomes, known as multivesicular bodies (MVBs). Here we present experiments showing that Wnt causes the endocytosis of focal adhesion (FA) proteins and depletion of Integrin β 1 (ITGβ1) from the cell surface. FAs and integrins link the cytoskeleton to the extracellular matrix. Wnt-induced endocytosis caused ITGβ1 depletion from the plasma membrane and was accompanied by striking changes in the actin cytoskeleton. In situ protease protection assays in cultured cells showed that ITGβ1 was sequestered within membrane-bounded organelles that corresponded to Wnt-induced MVBs containing GSK3 and FA-associated proteins. An in vivo model using Xenopus embryos dorsalized by Wnt8 mRNA showed that ITGβ1 depletion decreased Wnt signaling. The finding of a crosstalk between two mayor signaling pathways, canonical Wnt and focal adhesions, should be relevant to human cancer and cell biology.
Hemagglutinin stability determines influenza A virus susceptibility to a broad-spectrum fusion inhibitor Arbidol
Authors: Zhenyu Li , Tian Li , Meisui Liu , Tijana Ivanovic 
Published: January 2022

AbstractUnderstanding mechanisms of resistance to antiviral inhibitors can reveal nuanced features of targeted viral mechanisms and, in turn, lead to improved strategies for inhibitor design. Arbidol is a broad-spectrum antiviral which binds to and prevents the fusion-associated conformational changes in the trimeric influenza hemagglutinin (HA). The rate-limiting step during HA-mediated membrane fusion is the release of the hydrophobic fusion peptides from a conserved pocket on HA. Here, we investigated how destabilizing or stabilizing mutations in or near the fusion peptide affect viral sensitivity to Arbidol. The degree of sensitivity was proportional to the extent of fusion peptide stability on the pre-fusion HA: stabilized mutants were more sensitive, and destabilized ones resistant to Arbidol. Single-virion membrane fusion experiments for representative Wild Type and mutant viruses demonstrated that resistance is a direct consequence of fusion-peptide destabilization not dependent on reduced Arbidol binding to HA at neutral pH. Our results support the model whereby the probability of individual HAs extending to engage the target membrane is determined by the composite of two critical forces: a ‘tug’ on the fusion peptide by the extension of the central coiled-coil on HA, and the key interactions stabilizing fusion peptide in the pre-fusion pocket. Arbidol increases the free-energy penalty for coiled-coil extension, but destabilizing mutations decrease the free-energy cost for fusion peptide release, accounting for the observed resistance. Our findings have broad implications for fusion-inhibitor design, viral mechanisms of resistance, and our basic understanding of HA-mediated membrane fusion.
Efficient enrichment of synchronized mouse spermatocytes suitable for genome-wide analysis
Authors: Carbajal Agustin , Gryniuk Irma , de Castro Rodrigo O. , Pezza Roberto J. 
Published: January 2022

SummaryChromatin-based mechanisms regulating developmental transitions during meiosis are fundamental but understudied aspects of male gametogenesis. Indeed, chromatin undergoes extensive remodeling during meiosis, leading to specific patterns of gene expression and chromosome organization, which ultimately controls fundamental meiotic processes such as recombination and homologous chromo-some associations. Recent game-changing advances have been made by analysis of chromatin binding sites of meiotic specific proteins genome-wide in mouse spermatocytes. However, further progress is still highly dependent on the reliable isolation of sufficient quantities of spermatocytes at specific stages of prophase I. Here, we describe a combination of methodologies adapted for rapid and reliable isolation of synchronized fixed mouse spermatocytes. We show that chromatin isolated from these cells can be used to study chromatin binding sites by ChIP-seq. High quality data we obtained from INO80 ChIP-seq in zygotene cells was used for functional analysis of chromatin binding sites.
cpSRP43 is both highly flexible and stable: Structural insights using a combined experimental and computational approach
Authors: Benton Mitchell , Furr Mercede , Kumar Vivek Govind , Gao Feng , Heyes Colin David , Suresh Kumar Thallapuranam Krishnaswamy , Moradi Mahmoud 
Published: January 2022

AbstractThe novel multidomain protein, cpSRP43, is a unique subunit of the post-translational chloroplast signal recognition particle (cpSRP) targeting pathway in higher plants. The cpSRP pathway is responsible for targeting and insertion of light-harvesting chlorophyll a/b binding proteins (LHCPs) to the thylakoid membrane. Nuclear-encoded LHCPs are synthesized in the cytoplasm then imported into the chloroplast. Upon emergence into the stroma, LHCPs form a soluble transit complex with the cpSRP heterodimer, which is composed of cpSRP43 and cpSRP54, a 54 kDa subunit homologous to the universally conserved GTPase in cytosolic SRP pathways. cpSRP43 is irreplaceable as a chaperone to LHCPs in their translocation to the thylakoid membrane and remarkable in its ability to dissolve aggregates of LHCPs without the need for external energy input. In previous studies, cpSRP43 has demonstrated significant flexibility and interdomain dynamics. However, the high flexibility and structural dynamics of cpSRP43 is yet unexplained by current crystal structures of cpSRP43. This is due, in part, to the fact that free full length cpSRP43 is so flexible that it is unable to crystalize. In this study, we explore the structural stability of cpSRP43 under different conditions using various biophysical techniques and find that this protein is concurrently highly stable and flexible. This conclusion is interesting considering that stable proteins typically possess a non-dynamic structure. Molecular dynamics (MD) simulations which correlated with data from biophysical experimentation were used to explain the basis of the extraordinary stability of cpSRP43. This combination of biophysical data and microsecond-level MD simulations allows us to obtain a detailed perspective of the conformational landscape of these proteins.
Application of the Logistic Model to the COVID-19 Pandemic in South Africa and the United States: Correlations and Predictions
Authors: Roberts David H. 
Published: January 2022

ABSTRACTWe apply the logistic model to the four waves of COVID-19 taking place in South Africa over the period 3 January 2020 through 14 January 2022. We show that this model provides an excellent fit to the time history of three of the four waves. We then derive a theoretical correlation between the growth rate of each wave and its duration, and demonstrate that it is well obeyed by the South African data.We then turn to the data for the United States. As shown by Roberts (2020a, 2020b), the logistic model provides only a marginal fit to the early data. Here we break the data into six “waves,” and treat each one separately. Five of the six can be analyzed, and we present full results. We then ask if these data provide a way to predict the length of the ongoing Omicron wave in the US (commonly called “wave 4,” but the sixth wave as we have broken the data up). Comparison of these data to those from South Africa, and internal evaluation of the US data, suggest that this current wave will peak about 18 January 2022, and will be substantially over by about 11 February 2022. The total number of infected persons by the time that the Omicron wave is completely over is projected be between 22 and 24 million.
Human endothelial cells display a rapid and fluid flow dependent tensional stress increase in response to tumor necrosis factor-α
Authors: Brandt Matthias , Gerke Volker , Betz Timo 
Published: January 2022

AbstractAs endothelial cells form the inner layer of blood vessels they display the first barrier to interstitial tissues, which results in a crucial role for inflammation. On the global, systemic level an important element of the complex process controlling the inflammatory response is the release of the cytokine tumor necrosis factor-α (TNF-α). While other pro-inflammatory agents like thrombin or histamine are known to induce acute but transient changes in endothelial cells which have been well studied biologically as well as mechanically, TNF-α is primarily known for its sustained effects on permeability and leukocyte recruitment. These functions are associated with transcriptional changes that take place on the timescale of hours and days. Here we show that already 4 minutes after the addition of TNF-α onto monolayers of human umbilical vein endothelial cells, a striking rise in mechanical substrate traction force and internal monolayer tension can be recorded. As expected, the traction forces act primarily at the boundary of the monolayer. While the traction forces increase monotonically during the initial cellular response, we find that the internal monolayer tension displays a rapid peak that can be abolished when applying a shear flow to the cells. The increased internal monolayer tension may provide a mechanical signal for the cells to prepare for the recruitment of leukocytes, additionally to the well studied biochemical response.
Enhanced food motivation in obese mice is controlled by D1R expressing spiny projection neurons in the nucleus accumbens
Authors: Matikainen-Ankney Bridget A , Legaria Alex A , Vachez Yvan M , Murphy Caitlin A , Pan Yiyan , Schaefer Robert F , McGrath Quinlan J , Wang Justin G , Bluitt Maya N , Norris Aaron J , Creed Meaghan C , Kravitz Alexxai V 
Published: January 2022

AbstractObesity is a chronic relapsing disorder that is caused by an excess of caloric intake relative to energy expenditure. In addition to homeostatic feeding mechanisms, there is growing recognition of the involvement of food reward and motivation in the development of obesity. However, it remains unclear how brain circuits that control food reward and motivation are altered in obese animals. Here, we tested the hypothesis that signaling through pro-motivational circuits in the core of the nucleus accumbens (NAc) is enhanced in the obese state, leading to invigoration of food seeking. Using a novel behavioral assay that quantifies physical work during food seeking, we confirmed that obese mice work harder than lean mice to obtain food, consistent with an increase in the relative reinforcing value of food in the obese state. To explain this behavioral finding, we recorded neural activity in the NAc core with bothin vivoelectrophysiology and cell-type specific calcium fiber photometry. Here we observed greater activation of D1-receptor expressing NAc spiny projection neurons (NAc D1SPNs) during food seeking in obese mice relative to lean mice. Withex vivoslice physiology we identified both pre- and post-synaptic mechanisms that contribute to this enhancement in NAc D1SPNactivity in obese mice. Finally, blocking synaptic transmission from D1SPNsdecreased physical work during food seeking and attenuated high-fat diet-induced weight gain. These experiments demonstrate that obesity is associated with a selective increase in the activity of D1SPNsduring food seeking, which enhances the vigor of food seeking. This work also establishes the necessity of D1SPNsin the development of diet-induced obesity, establishing these neurons as a potential therapeutic target for preventing obesity.