bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimistic and pessimistic cognitive judgement bias modulates the stress response and cancer progression in zebrafish
Authors: Espigares Felipe , Victoria Alvarado M. , Abad-Tortosa Diana , Varela Susana A. M. , Sobral Daniel , Faísca Pedro , Paixão Tiago , Oliveira Rui F. 
Published: May 2024

AbstractCognitive judgement bias in decision-making under ambiguity occurs both in animals and humans, with some individuals interpreting ambiguous stimulus as positive (optimism) and others as negative (pessimism). We hypothesize that judgement bias is a personality trait and that individuals with a pessimistic bias would be more reactive to stressors and therefore more susceptible to stress-related diseases than optimistic ones. Here, we show that zebrafish judgment bias is a consistent behavioral trait over time, and that pessimistic and optimistic fish express phenotype-specific neurogenomic responses to stress. Furthermore, both phenotypes show differential activation of the hypothalamic-pituitary-interrenal axis in response to chronic stress, suggesting that optimists have a lower stress reactivity. Accordingly, optimists seem to be more resilient to disease than pessimists, as shown by a lower tumorigenesis in a zebrafish melanoma line [Tg(mtifa:HRAS-GFP)]. Together these results indicate that judgement bias is paralleled by differences in the stress response with implications for disease resilience.
Zebrafish (Danio rerio) behavioral phenotypes not underscored by different gut microbiota
Authors: Ayayee Paul A. , Wong Ryan Y. 
Published: May 2024

AbstractDifferent animal behavioral phenotypes maintained and selectively bred over multiple generations may be underscored by dissimilar gut microbial community compositions or not have any significant dissimilarity in community composition. Operating within the microbiota-gut-brain axis framework, we anticipated differences in gut microbiome profiles between zebrafish (Danio rerio) selectively bred to display the bold and shy personality types. This would highlight gut microbe-mediated effects on host behavior. To this end, we amplified and sequenced a fragment of the 16S rRNA gene from the guts of bold and shy zebrafish individuals (n=10) via Miseq. We uncovered no significant difference in within-group microbial diversity nor between-group microbial community composition of the two behavioral phenotypes. Interestingly, though not statistically different, we determined that the gut microbial community of the bold phenotype was dominated byBurkholderiaceae, Micropepsaceae,andPropionibacteriaceae. In contrast, the shy phenotype was dominated byBeijerinckaceae, Pirelullacaeae, Rhizobiales_Incertis_Sedis, andRubinishaeraceae.The absence of any significant difference in gut microbiota profiles between the two phenotypes would suggest that in this species, there might exist a stable “core” gut microbiome, regardless of behavioral phenotypes, and or possibly, a limited role for the gut microbiota in modulating this selected-for host behavior. This is the first study to characterize the gut microbial community of distinct innate behavioral phenotypes of the zebrafish (that are not considered dysbiotic states) and not rely on antibiotic or probiotic treatments to induce changes in behavior. Such studies are crucial to our understanding of the modulating impacts of the gut microbiome on normative animal behavior.
Pathobiology of the autophagy-lysosomal pathway in the Huntington’s disease brain
Authors: Berg Martin J. , Veeranna  , Rosa Corrinne M. , Kumar Asok , Mohan Panaiyur S. , Stavrides Philip , Marchionini Deanna M. , Yang Dun-Sheng , Nixon Ralph A. 
Published: May 2024

AbstractAccumulated levels of mutant huntingtin protein (mHTT) and its fragments are considered contributors to the pathogenesis of Huntington’s disease (HD). Although lowering mHTT by stimulating autophagy has been considered a possible therapeutic strategy, the role and competence of autophagy-lysosomal pathway (ALP) during HD progression in the human disease remains largely unknown. Here, we used multiplex confocal and ultrastructural immunocytochemical analyses of ALP functional markers in relation to mHTT aggresome pathology in striatum and the less affected cortex of HD brains staged from HD2 to HD4 by Vonsattel neuropathological criteria compared to controls. Immunolabeling revealed the localization of HTT/mHTT in ALP vesicular compartments labeled by autophagy-related adaptor proteins p62/SQSTM1 and ubiquitin, and cathepsin D (CTSD) as well as HTT-positive inclusions. Although comparatively normal at HD2, neurons at later HD stages exhibited progressive enlargement and clustering of CTSD-immunoreactive autolysosomes/lysosomes and, ultrastructurally, autophagic vacuole/lipofuscin granules accumulated progressively, more prominently in striatum than cortex. These changes were accompanied by rises in levels of HTT/mHTT and p62/SQSTM1, particularly their fragments, in striatum but not in the cortex, and by increases of LAMP1 and LAMP2 RNA and LAMP1 protein. Importantly, no blockage in autophagosome formation and autophagosome-lysosome fusion was detected, thus pinpointing autophagy substrate clearance deficits as a basis for autophagic flux declines. The findings collectively suggest that upregulated lysosomal biogenesis and preserved proteolysis maintain autophagic clearance in early-stage HD, but failure at advanced stages contributes to progressive HTT build-up and potential neurotoxicity. These findings support the prospect that ALP stimulation applied at early disease stages, when clearance machinery is fully competent, may have therapeutic benefits in HD patients.
Enhancing lipid production in plant cells through high-throughput genome editing and phenotyping via a scalable automated pipeline
Authors: Dong Jia , Croslow Seth W. , Lane Stephan T. , Castro Daniel C. , Blanford Jantana , Zhou Shuaizhen , Park Kiyoul , Burgess Steven , Root Mike , Cahoon Edgar , Shanklin John , Sweedler Jonathan V. , Zhao Huimin , Hudson Matthew E. 
Published: May 2024

AbstractPlant bioengineering is a time-consuming and labor-intensive process, with no guarantee of achieving the desired trait. Here we report a fast, automated, scalable, high-throughput pipeline for plant bioengineering (FAST-PB). FAST-PB achieves gene cloning, genome editing, and product characterization by integrating automated biofoundry engineering of callus and protoplast cells with single cell matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). We first demonstrate that FAST-PB can streamline the Golden Gate cloning process, with the capacity to construct 96 vectors in parallel. To prove the concept, using FAST-PB, we first found that PEG2050 significantly increases transfection efficiency by over 45%. To validate the pipeline, we established a reporter-gene-free method for CRISPR editing via mutation ofHCF136, affecting cellular chlorophyll fluorescence. Next, we applied this pipeline for lipid production and found that diverse lipids were significantly enhanced up to sixfold through introducing multi-gene cassettes via CRISPR activation, and regenerated plant using this platform. Lastly, we harnessed FAST-PB to achieve high-throughput single-cell lipid profiling through the integration of MALDI-MS with the biofoundry, and differentiated engineered and unengineered cells using the single-cell lipidomics. These innovations massively increase the throughput of synthetic biology, genome editing, and metabolic engineering, and change what is possibly using single-cell metabolomics in plants.
Data Independent Acquisition to Inform the Development of Targeted Proteomics Assays Using a Triple Quadrupole Mass Spectrometer
Authors: Plubell Deanna L. , Huang Eric , Spencer Sandra E. , Poston Kathleen , Montine Thomas J. , MacCoss Michael J. 
Published: May 2024

ABSTRACTMass spectrometry based targeted proteomics methods provide sensitive and high-throughput analysis of selected proteins. To develop a targeted bottom-up proteomics assay, peptides must be evaluated as proxies for the measurement of a protein or proteoform in a biological matrix. Candidate peptide selection typically relies on predetermined biochemical properties, data from semi-stochastic sampling, or by empirical measurements. These strategies require extensive testing and method refinement due to the difficulties associated with prediction of peptide response in the biological matrix of interest. Gas-phase fractionated (GPF) narrow window data-independent acquisition (DIA) aids in the development of reproducible selected reaction monitoring (SRM) assays by providing matrix-specific information on peptide detectability and quantification by mass spectrometry. To demonstrate the suitability of DIA data for selecting peptide targets, we reimplement a portion of an existing assay to measure 98 Alzheimer’s disease proteins in cerebrospinal fluid (CSF). Peptides were selected from GPF-DIA based on signal intensity and reproducibility. The resulting SRM assay exhibits similar quantitative precision to published data, despite the inclusion of different peptides between the assays. This workflow enables development of new assays without additional up-front data acquisition, demonstrated here through generation of a separate assay for an unrelated set of proteins in CSF from the same dataset.
Time from treatment initiation to HIV viral suppression in public care facilities in Brazil: a nationwide linked databases cohort
Authors: Nemes Maria Ines Battistella , Sayuri Sato Ana Paula , Reis-Santos Barbara , Alves Ana Maroso , Parra do Nascimento Felipe , Agins Bruce 
Published: May 2024

AbstractObjectivesTo analyze the time between antiretroviral therapy (ART) initiation and the first HIV viral load (VL) test <40 copies—time to suppression (TS)—in a cohort of persons aged ≥15 years, between 2015-2018 in outpatient HIV care facilities of the Brazilian Unified Health System, as well as to analyze whether individual and facility characteristics accelerate or delay TS.MethodsThis was a cohort study with data from a linkage of national HIV databases, following a previously published procedure. Two types of variables were examined: individual-level (sex, age group, race/skin color, education, baseline CD4 cell count and VL, initial ART regimen, adherence, ART regimen change and number of VL tests until suppression) and facility-level (national and metropolitan region, caseload). Multilevel parametric accelerated failure time survival models were used. Fixed and random effects were analyzed through null, sociodemographic, combined sociodemographic and clinical, and facility-related variables, adjusted for the number of VL tests until suppression. Likelihood, interquartile range, and proportion of change in variance were used for comparisons.ResultsOf 132,540 participants, 89.4% (114,696) achieved viral suppression: 20.8% within three months, and 56.4% within six months. Median TS was 161 days, varying from 31 to 1,426 days, depending on the time interval between initiation and VL testing. Among those who had VL testing within 66 days, median TS was 55 days. All individual and facility-related variables were associated with TS, explaining the 16.2% and 13.2% variability, respectively.ConclusionsThis was the first Brazilian nationwide cohort to analyze TS. It is also one of the largest operational cohorts globally to assess healthcare facility characteristics. The findings indicated that both individual and facility-related characteristics contribute to TS. Strengthening VL monitoring should be included as part of a coordinated effort to improve the quality of care provided for people living with HIV/AIDS in Brazil.
Design nonrepetitive and diverse activity single-guide RNA by deep learning
Authors: Xia Yan , Liang Zeyu , Du Xiaowen , Cao Dengtian , Li Jing , Sun Lichao , Huo Yi-Xin , Guo Shuyuan 
Published: May 2024

AbstractMultiplex and precise control of the gene expression based on CRISPR/Cas9 is important to metabolic regulation in synthetic biology. However, employing single guide RNAs (sgRNAs) that possess repetitive DNA sequences and exhibit uniform activity could detrimentally affect the editing process, undermining both its stability and regulatory potential. In this study, we developed a deep generative model based on a decoder-only Transformer architecture (sgRNAGen) for thede novogeneration of a series of nonrepetitive and diverse sgRNAs with activity. To assess the quality of sgRNAs generated by sgRNAGen, we evaluated their activity by targeting essential genes, with the results indicating that 98% of the generated sgRNAs were active inBacillus subtilis. The generated sgRNAs were further validated for applications in single-gene editing, large fragment knockouts, and multiplex editing. Notably, the efficiency of knocking out long fragments up to 169.5 kb reached 100%, and targeting multiple sites allowed for the creation of strains with various combinations of mutations in a single editing. Furthermore, we developed a CRISPRi system utilizing the designed sgRNAs to regulate gene expression with desired strength and high precision. SgRNAGen offers a method for devising nonrepetitive and diverse activity sgRNAs, enhancing metabolic control and advancing applications within synthetic biology.TOC
Subtleties in Clathrin Heavy Chain Binding Boxes provide selectivity among Adaptor Proteins of Budding Yeast
Authors: Defelipe Lucas A. , Veith Katharina , Burastero Osvaldo , Kupriianova Tatiana , Bento Isabel , Skruzny Michal , Köbel Knut , Uetrecht Charlotte , Thuenauer Roland , García-Alai Maria M. 
Published: May 2024

AbstractClathrin, forming the triskelion network, orchestrates highly regulated cellular processes facilitating cargo internalization and trafficking in eukaryotes, with its N-terminal domain (NTD) pivotal for adaptor protein (AP) interactions. The NTD contains up to four AP-binding sites, and their roles in preferential occupancy by APs have not been addressed. Here, employing a combination of integrative biophysical and structural approaches together within vivofunctional experiments, we investigated the binding hierarchy and selectivity of adaptors for clathrin, aiming to understand the evolutionary conservation of redundant APs and their specialized roles in endocytosis and cellular trafficking mechanisms. We found that yeast epsin Ent5 displayed the highest affinity for clathrin, indicating its significant role in cellular trafficking processes. Epsins Ent1 and Ent2, which are crucial for endocytosis but described to have redundant functions, revealed distinct binding patterns; Ent1 demonstrated stronger interactions with clathrin than Ent2, explaining its functional divergence towards actin binding. Despite both having actin anchoring domains, since Ent1 is actually more stably recruited by clathrin, it would provide a better actin anchoring function. These results offer molecular insights into AP selectivity, suggesting they competitively bind clathrin while also targeting different clathrin sites.
2’-Fucosyllactose Inhibits Human Norovirus Replication in Human Intestinal Enteroids
Authors: Patil Ketki , Ayyar B. Vijayalakshmi , Neill Frederick H. , Bode Lars , Estes Mary K. , Atmar Robert L. , Ramani Sasirekha 
Published: May 2024

ABSTRACTHuman noroviruses (HuNoVs) are the leading cause of acute gastroenteritis worldwide. Currently, there are no targeted antivirals for the treatment of HuNoV infection. Histo-blood group antigens (HBGAs) on the intestinal epithelium are cellular attachment factors for HuNoVs; molecules that block the binding of HuNoVs to HBGAs thus have the potential to be developed as antivirals. Human milk oligosaccharides (HMOs) are glycans in human milk with structures analogous to HBGAs. HMOs have been shown to act as decoy receptors to prevent the attachment of multiple enteric pathogens to host cells. Previous X-ray crystallography studies have demonstrated the binding of HMO 2’-fucosyllactose (2’FL) in the same pocket as HBGAs for some HuNoV strains. We evaluated the effect of 2’FL on the replication of a globally dominant GII.4 Sydney [P16] HuNoV strain using human intestinal enteroids (HIEs) from adults and children. A significant reduction in GII.4 Sydney [P16] replication was seen in duodenal and jejunal HIEs from multiple adult donors, all segments of the small intestine from an adult organ donor and in two pediatric duodenal HIEs. However, 2’FL did not inhibit HuNoV replication in two infant jejunal HIEs that had significantly lower expression of α1-2-fucosylated glycans. 2’FL can be synthesized in large scale, and safety and tolerance have been assessed previously. Our data suggest that 2’FL has the potential to be developed as a therapeutic for HuNoV gastroenteritis.IMPORTANCEHuman noroviruses infect the gastrointestinal tract and are a leading cause of acute gastroenteritis worldwide. Common symptoms of norovirus include diarrhea, vomiting and stomach cramps. Virus shedding and symptoms are prolonged and debilitating in immunocompromised patients. Currently, there are no approved vaccines or targeted antivirals for treating human norovirus infection. Human intestinal enteroids derived from intestinal stem cells allow the successful replication of norovirus in the laboratory and can be used as a physiologically relevant model system to evaluate antivirals. We discovered that 2’fucosyllactose (2’FL), an oligosaccharide naturally occurring in human milk, inhibits norovirus replication in HIEs from multiple donors and thus has the potential to be developed as a therapeutic for human norovirus. These findings have high translational potential since 2’FL from several manufacturers have GRAS (generally recognized as safe) status and can be synthesized on a large scale for immediate application.
Cognitive Computational Model Reveals Repetition Bias in a Sequential Decision-Making Task
Authors: Legler Eric , Rivera Darío Cuevas , Schwöbel Sarah , Wagner Ben J. , Kiebel Stefan 
Published: May 2024

AbstractHumans tend to repeat past actions due to rewarding outcomes. Recent computational models propose that the probability of selecting a specific action is also, in part, based on how often this action was selected before, independent of previous outcomes or reward. However, these new models so far lack empirical support. Here, we present evidence of a repetition bias using a novel sequential decision-making task and computational modeling to reveal the influence of choice frequency on human value-based choices. Specifically, we find that value-based decisions can be best explained by concurrent influence of both goal-directed reward seeking and a repetition bias. We also show that participants differ substantially in their repetition bias strength, and relate these measures to task performance. The new task enables a novel way to measure the influence of choice repetition on decision-making. These findings can serve as a basis for further experimental studies on the interplay between rewards and choice history in human decision-making.
The Chemokine Receptor CCR8 is Not a High-affinity Receptor for the Human Chemokine CCL18
Authors: Hussain Khansa , Lim Herman D. , Devkota Shankar Raj , Kemp-Harper Barbara K. , Lane J. Robert , Canals Meritxell , Pease James E. , Stone Martin J. 
Published: May 2024

ABSTRACTThe primate-specific chemokine CCL18 is a potent chemoattractant for T cells and is expressed at elevated levels in several inflammatory diseases. However, the cognate receptor for CCL18 remains unconfirmed. Here, we describe attempts to validate a previous report that the chemokine receptor CCR8 is the human CCL18 receptor (Islam et al.J Exp Med.2013,210:1889-98). Two mouse pre-B cell lines (4DE4 and L1.2) exogenously expressing CCR8 exhibited robust migration in response to the known CCR8 ligand CCL1 but not to CCL18. Similarly, CCL1 but not CCL18 induced internalization of CCR8 on 4DE4 cells. CCR8 expressed on Chinese hamster ovarian (CHO) cells mediated robust G protein activation, inhibition of cAMP synthesis and β-arrestin2 recruitment in response to CCL1 but not CCL18. Several N- and C-terminal variants of CCL18 also failed to stimulate CCR8 activation. On the other hand, and as previously reported, CCL18 inhibited CCL11-stimulated migration of 4DE4 cells expressing the receptor CCR3. These data suggest that CCR8, at least in the absence of unidentified cofactors, does not function as a high affinity receptor for CCL18.
Ohmic analogies and metaphorical circuits: Vascular partitioning of leaf air spaces and stomatal patchiness can create apparent undersaturation and gradient inversion
Authors: Rockwell Fulton E. 
Published: May 2024

SummaryRationaleAnalyses of leaf gas exchange rely on an Ohmic analogy that arrays single stomatal, internal air space, and mesophyll conductances in series. Such models underlie inferences of mesophyll conductance and the relative humidity of leaf airspaces, reported to fall as low as 80%. An unresolved question is whether such Ohmic models are biased with respect to real leaves, whose internal air spaces are chambered at various scales by vasculature.DescriptionTo test whether undersaturation could emerge from modeling artifacts, we compared Ohmic model estimates with true parameter values for a chambered leaf with varying distributions and magnitudes of leaf surface conductance (“patchiness”).Key ResultsDistributions of surface conductance can create large biases in gas exchange calculations. Both apparent unsaturation and internalCO2gradient inversion can be produced by the evolution of particular distributions of stomatal apertures consistent with a decrease in surface conductance, as might occur under increasing vapor pressure deficit.Main conclusionIn gas exchange experiments, the behaviors of derived quantities defined by simple Ohmic models are highly sensitive to the true partitioning of flux and stomatal apertures across leaf surfaces. We need new methods to disentangle model artifacts from real biological responses.
Arginine impacts aggregation, biofilm formation, and antibiotic susceptibility inEnterococcus faecalis
Authors: Snell Alex , Manias Dawn A. , Elbehery Reham R. , Dunny Gary M. , Willett Julia L. E. 
Published: May 2024

AbstractEnterococcus faecalisis a commensal bacterium in the gastrointestinal tract (GIT) of humans and other organisms.E. faecalisalso causes infections in root canals, wounds, the urinary tract, and on heart valves.E. faecalismetabolizes arginine through the arginine deiminase (ADI) pathway, which converts arginine to ornithine and releases ATP, ammonia, and CO2.E. faecalisarginine metabolism also affects virulence of other pathogens during co-culture.E. faecalismay encounter elevated levels of arginine in the GIT or the oral cavity, where arginine is used as a dental therapeutic. Little is known about howE. faecalisresponds to growth in arginine in the absence of other bacteria. To address this, we used RNAseq and additional assays to measure growth, gene expression, and biofilm formation inE. faecalisOG1RF grown in arginine. We demonstrate that arginine decreasesE. faecalisbiofilm production and causes widespread differential expression of genes related to metabolism, quorum sensing, and polysaccharide synthesis. Growth in arginine also increases aggregation ofE. faecalisand promotes decreased susceptibility to the antibiotics ampicillin and ceftriaxone. This work provides a platform for understanding of how the presence of arginine in biological niches affectsE. faecalisphysiology and virulence of surrounding microbes.