bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Run-of-River Damming on Increasing Phytoplankton Biomass and Species Shift in a Large Amazonian River
Authors: Pineda Alfonso , Campos Beatriz Melissa , Zanon Felipe , Felicio Renata , Rodrigues Luzia C. 
Published: June 2024

AbstractRun-of-river (ROR) dams, often perceived as having minimal environmental impact, can induce significant hydrodynamic changes that alter aquatic ecosystems. We investigated the impacts of an ROR dam on the Madeira River, the largest Amazon tributary, focusing on phytoplankton communities, their ecological implications, and related environmental factors. Our study examined changes in biomass and environmental factors (using General Linear Mixed Models - GLMM), species composition (using PERMANOVA) before and after damming, in both the main channel and tributaries (N=549 samples). We also identified indicator species associated with different damming phases and regions through an indicator value analysis. The results showed that, following dam construction, the phytoplankton community changed in both the main channel and tributaries, with a shift from lotic diatoms to lentic phytoflagellates. This transition was likely facilitated by altered hydrodynamics and possibly influenced by the decomposition of flooded vegetation in the dam’s influence zone. The decomposition of this vegetation could explain both the observed increase in oxygen consumption and the subsequent rise in phytoflagellate biomass after damming. However, despite the overall increase in phytoplankton biomass, the values remained within oligotrophic to mesotrophic conditions, consistent with the low nutrient concentrations recorded. However, we caution that the dam-created hydrodynamic conditions are optimal for phytoplankton growth, potentially exacerbating nutrient-related issues in the future. We recommend proactive management strategies to prevent nutrient enrichment from activities such as agriculture and livestock in isolated Amazon areas affected by dams, thereby mitigating potential water quality degradation linked to increased phytoplankton biomass.
Coordinated Regulation of Renal Glucose Reabsorption and Gluconeogenesis by mTORC2 and Potassium
Authors: Demko John , Saha Bidisha , Takagi Enzo , Mannis Anna , Weber Robert , Pearce David 
Published: June 2024

ABSTRACTBackgroundThe kidney proximal tubule is uniquely responsible for reabsorption of filtered glucose and gluconeogenesis (GNG). Insulin stimulates glucose transport and suppresses GNG in the proximal tubule, however, the signaling mechanisms and coordinated regulation of these processes remain poorly understood. The kinase complex mTORC2 is critical for regulation of growth, metabolism, solute transport, and electrolyte homeostasis in response to a wide array of inputs. Here we examined its role in the regulation of renal glucose reabsorption and GNG.MethodsRictor, an essential component of mTORC2, was knocked out using the Pax8-LC1 system to generate inducible tubule specific Rictor knockout (TRKO) mice. These animals were subjected to fasting, refeeding, and variation in dietary K+. Metabolic parameters including glucose homeostasis and renal function were assessed in balance cages. Kidneys and livers were also harvested for molecular analysis of gluconeogenic enzymes, mTORC2-regulated targets, and plasma membrane glucose transporters.ResultsOn a normal chow diet, TRKO mice had marked glycosuria despite indistinguishable blood glucose relative to WT controls. Kidney plasma membrane showed lower SGLT2 and SGLT1 in the fed state, supporting reduced renal glucose reabsorption. Additional metabolic testing provided evidence for renal insulin resistance with elevated fasting insulin, impaired pyruvate tolerance, elevated hemoglobin A1c, and increased renal gluconeogenic enzymes in the fasted and fed states. These effects were correlated with reduced downstream phosphorylation of Akt and the transcription factor FOXO4, identifying a novel role of FOXO4 in the kidney. Interestingly, high dietary K+prevented glycosuria and excessive GNG in TRKO mice, despite persistent reduction in mTORC2 substrate phosphorylation.ConclusionRenal tubule mTORC2 is critical for coordinated regulation of sodium-glucose cotransport by SGLT2 and SGLT1 as well as renal GNG. Dietary K+promotes glucose reabsorption and suppresses GNG independently of insulin signaling and mTORC2, potentially providing an alternative signaling mechanism in states of insulin resistance.SIGNIFICANCE STATEMENTThe kidney contributes to regulation of blood glucose through reabsorption of filtered glucose and gluconeogenesis. This study shows that mTORC2 and dietary potassium coordinate the regulation of sodium-glucose cotransport and glucose production in the kidney via independent mechanisms. New insights into the regulation of these processes in the kidney offer promising implications for diabetes mellitus management and treatment.
Generation and initial characterization of in vivo knockout of tetherin/BST2 in chicken
Authors: Ungrová Lenka , Trefil Pavel , Plachý Jiří , Mucksová Jitka , Kalina Jiří , Reinišová Markéta , Härtle Sonja , Gáliková Eliška , Kučerová Dana , Krchlíková Veronika , Pečenka Vladimír , Karafiát Vít , Hejnar Jiří , Elleder Daniel 
Published: June 2024

ABSTRACTTetherin/BST2 is an antiviral restriction factor initially described in mammals. It is active against multiple enveloped viruses at the budding phase, where it is able to physically link the budding virions to the virus-producing cell. We and others have previously identified tetherin orthologs in birds, and characterized the antiviral activity and interferon-inducibility of chicken tetherin. In this work, we have generated anin vivomodel of tetherin absence in chicken by CRISPR/Cas9 modification of chicken primordial germ cells (PGC). The modified PGCs were transplanted into roosters with suppressed endogenous spermatogenesis, and transgenic (tetherin knockout) progeny was obtained by further crosses. The viability and phenotype of tetherin knockout animals did not differ from wild type chicken. In more detailed investigation, flow cytometry based differential white blood cell count revealed an increased number of heterophils in tetherin knockouts. Upon challenge with avian sarcoma and leukosis virus (ASLV), a prototypic avian retrovirus, we detected increase in viremia at days 6 and 13 post infection in tetherin knockout animals. The increased virus susceptibility is consistent with absence of antiviral tetherin. In summary, we introduce a newin vivoknockout model of chicken antiviral gene tetherin. These animals can be used in further characterizations of avian antiviral defenses and also to define thus far unknown physiological effects of tetherin in birds.
Selection of Fluorinated Aptamer Targeting RNA Element with Different Chirality
Authors: Dantsu Yuliya , Zhang Ying , Zhang Wen 
Published: June 2024

ABSTRACTThe development of RNA aptamers with high specificity and affinity for target molecules is a critical advancement in the field of therapeutic and diagnostic applications. This study presents the selection of a 2’-fluoro modified mirror-image RNA aptamer through thein vitroSELEX process. Using a random RNA library, we performed iterative rounds of selection and amplification to enrich aptamers that bind specifically to the viral frameshift element which contains the opposite chirality. The unnatural chirality of the aptamer improved its enzymatic stability, and the incorporation of 2’-fluoro modifications was crucial in enhancing the binding affinity of the aptamers. After nine rounds of SELEX, the enriched RNA pool was sequenced and analyzed, revealing the dominant aptamer sequences. The selected 2’-fluoro modified mirror-image RNA aptamer demonstrated a dissociation constant of approximately 1.6 μM, indicating moderate binding affinity with the target and exceptional stability against nuclease degradation. Our findings highlight the potential of 2’-fluoro modified mirror-image RNA aptamers in enhancing the stability and utility of RNA-based therapeutics and diagnostics, paving the way for future applications in diverse biomedical fields.
Resolving the three-dimensional interactome of Human Accelerated Regions during human and chimpanzee neurodevelopment
Authors: Pal Atreyo , Noble Mark A. , Morales Matheo , Pal Richik , Baumgartner Marybeth , Yang Je Won , Yim Kristina M. , Uebbing Severin , Noonan James P. 
Published: June 2024

AbstractHuman Accelerated Regions (HARs) are highly conserved across species but exhibit a significant excess of human-specific sequence changes, suggesting they may have gained novel functions in human evolution. HARs include transcriptional enhancers with human-specific activity and have been implicated in the evolution of the human brain. However, our understanding of how HARs contributed to uniquely human features of the brain is hindered by a lack of insight into the genes and pathways that HARs regulate. It is unclear whether HARs acted by altering the expression of gene targets conserved between HARs and their chimpanzee orthologs or by gaining new gene targets in human, a mechanism termed enhancer hijacking. We generated a high-resolution map of chromatin interactions for 1,590 HARs and their orthologs in human and chimpanzee neural stem cells (NSCs) to comprehensively identify gene targets in both species. HARs and their chimpanzee orthologs targeted a conserved set of 2,963 genes enriched for neurodevelopmental processes including neurogenesis and synaptic transmission. Changes in HAR enhancer activity were correlated with changes in conserved gene target expression. Conserved targets were enriched among genes differentially expressed between human and chimpanzee NSCs or between human and non-human primate developing and adult brain. Species-specific HAR gene targets did not converge on known biological functions and were not significantly enriched among differentially expressed genes, suggesting that HARs did not alter gene expression via enhancer hijacking. HAR gene targets, including differentially expressed targets, also showed cell type-specific expression patterns in the developing human brain, including outer radial glia, which are hypothesized to contribute to human cortical expansion. Our findings support that HARs influenced human brain evolution by altering the expression of conserved gene targets and provide the means to functionally link HARs with novel human brain features.
Broad-scale phenotyping in Arabidopsis reveals varied involvement of RNA interference across diverse plant-microbe interactions
Authors: Ruf Alessa , Thieron Hannah , Nasfi Sabrine , Lederer Bernhard , Fricke Sebastian , Adeshara Trusha , Postma Johannes , Blumenkamp Patrick , Kwon Seomun , Brinkrolf Karina , Feldbrügge Michael , Goesmann Alexander , Kehr Julia , Steinbrenner Jens , Šečić Ena , Göhre Vera , Weiberg Arne , Kogel Karl-Heinz , Panstruga Ralph , Robatzek Silke 
Published: June 2024

ABSTRACTRNA interference (RNAi) is a crucial mechanism that can contribute to immunity against infectious microbes through the action of DICER-LIKE (DCL) and ARGONAUTE (AGO) proteins. In the case of the fungal pathogenBotrytis cinereaand the oomyceteHyaloperonospora arabidopsidis, plant DCL and AGO proteins have proven roles as negative regulators of immunity, suggesting functional specialization of these proteins. To address this aspect in a broader taxonomic context, we characterized the colonization pattern of an informative set ofDCLandAGOloss-of-function mutants inArabidopsis thalianaupon infection with a panel of pathogenic microbes with different lifestyles, and a fungal mutualist. Our results revealed that AGO1 and AGO4 function as positive regulators of immunity to a bacterial and a fungal pathogen, respectively. Additionally, AGO2 and AGO10 positively modulated the colonization by a fungal mutualist. Therefore, analysing the role of RNAi across a broader range of plant-microbe interactions has identified previously unknown functions for AGO proteins. For some pathogen interactions, however, all tested mutants exhibited wild type-like infection phenotypes, suggesting that the roles of AGO and DCL proteins in these interactions may be more complex to elucidate.
Process Mining/Deep Learning Model to Predict Mortality in Coronary Artery Disease Patients
Authors: Ashrafi Negin , Abdollahi Armin , Placencia Greg , Pishgar Maryam 
Published: June 2024

AbstractPatients with Coronary Artery Disease (CAD) are at high risk of death. CAD is the third leading cause of mortality worldwide. However, there is a lack of research concerning CAD patient mortality prediction; thus, more accurate prediction modeling is needed to predict the mortality of patients diagnosed with CAD. This paper demonstrates performance improvements in predicting the mortality of CAD patients. The proposed framework is a modification of the work used for the prediction of 30-day readmission for ICU patients with heart failure. Our framework demonstrates better performance with an Area Under the ROC Curve (AUC) score of 0.871 for the Neural Network (NN) model compared to traditional baseline machine learning models that we developed. Our framework uses the medical history of patients, the time related to the variables, and patients’ demographic information for prediction. This framework has the potential to be used by medical teams to make more accurate decisions for treatment and care for patients with CAD, increasing their life expectancy.
Simultaneous enumeration of yeast and bacterial cells in the context of industrial bioprocesses
Authors: Martins Carolina Teixeira , Jacobus Ana Paula , Conceição Renilson , Barbin Douglas Fernandes. , Bolini Helena , Gombert Andreas Karoly 
Published: June 2024

AbstractIn scenarios where yeast and bacterial cells coexist, e.g. the food and bioethanol industries, it would be of interest to simultaneously quantify the concentrations of both cell types, since traditional methods used to determine these concentrations individually take more time and resources. Here, we compared different methods for quantifying the fuel ethanolSaccharomyces cerevisiaePE-2 yeast strain and cells from the probioticLactiplantibacillus plantarumstrain in microbial suspensions. Individual suspensions were prepared (∼107, yeast cells/mL or ∼109, bacterial cells/mL) and mixed in 1:1 or 100:1 yeast-to-bacteria ratios, covering the range typically encountered in sugarcane biorefineries. The following methods were used: bright field microscopy, manual and automatic Spread-plate and Drop-plate counting, flow cytometry (at 1:1 and 100:1 ratios), and a Coulter counter (at 1:1 and 100:1 ratios). By subjecting the same mixed cell suspension to each technique, we observed that for yeast cell counts in the mixture (1:1 and 100:1 ratios), flow cytometry, the Coulter counter, and both Spread-plate options (manual and automatic CFU counting) yielded statistically similar results, while the Drop-plate and microscopy-based methods gave statistically different results. For bacterial cell quantification, the microscopy-based method, Drop-plate, and both Spread-plate plating options and flow cytometry (1:1 ratio) produced no significantly different results (P>0.05). In contrast, the Coulter counter (1:1 ratio) and flow cytometry (100:1 ratio) presented results statistically different (P<0.05). Additionally, quantifying bacterial cells in a mixed suspension at a 100:1 ratio wasn’t possible due to an observed overlap between yeast cell debris and bacterial cells. The results from this work indicate that each method has limitations, advantages, and disadvantages, meaning that the best option will always depend on the application. We present a comparison of the techniques, in terms of time-to-results, cost of analysis and equipment, range of detectable cell/particle diameters, adequacy for simultaneous enumeration, and general pros and cons.Graphical AbstractThis study compares methods for simultaneously quantifying yeast and bacterial cells in a mixed sample, highlighting that in different cell proportions, some methods cannot quantify both cell types and present distinct advantages and limitations regarding time, cost, and precision.
Purkinje Cell-specific Deficiency in SEL1L-HRD1 Endoplasmic Reticulum-Associated Degradation Causes Progressive Cerebellar Ataxia in Mice
Authors: Torres Mauricio , Wang Hui , Pederson Brent , Lin Liangguang Leo , Wang Huilun H. , Bugarin-Lapuz Amara , Zhao Zhen , Qi Ling 
Published: June 2024

ABSTRACTRecent studies have identified multiple genetic variants of SEL1L-HRD1 ER-associated degradation (ERAD) in humans with neurodevelopmental disorders and locomotor dysfunctions, including ataxia. However, the relevance and importance of SEL1L-HRD1 ERAD in the pathogenesis of ataxia remain unexplored. Here we show that SEL1L deficiency in Purkinje cells leads to early-onset progressive cerebellar ataxia with progressive loss of Purkinje cells with age. Mice with Purkinje cell-specific deletion of SEL1L (Sel1LPcp2Cre) exhibit motor dysfunction beginning around 9 weeks of age. Transmission electron microscopy (TEM) analysis reveals dilated ER and fragmented nuclei in Purkinje cells of adultSel1LPcp2Cremice, indicative of altered ER homeostasis and cell death. Lastly, loss of Purkinje cells is associated with a secondary neurodegeneration of granular cells, as well as robust activation of astrocytes and proliferation of microglia, in the cerebellum ofSel1LPcp2Cremice. These data demonstrate the pathophysiological importance of SEL1L-HRD1 ERAD in Purkinje cells in the pathogenesis of cerebellar ataxia.One-sentence summarySEL1L-HRD1 ERAD is indispensable for Purkinje cell function and cerebellar ataxia pathogenesis in mice.
The Enterococcal Polysaccharide Antigen: from structure to biosynthesis and function
Authors: Davis Jessica L , Norwood Joshua S , Smith Robert E , O’Dea Finn , Chellappa Krishna , Rowe Michelle L , Williamson Mike P , Stafford Graham P , Vinogradov Evguenii , Maes Emmanuel , Guérardel Yann , Mesnage Stéphane 
Published: June 2024

AbstractL-Rhamnose-containing polysaccharides are produced by Streptococci and Enterococci. They define Lancefield serotypes and represent promising candidates for the design of glycoconjugate vaccines. The Enterococcal Polysaccharide Antigen produced by the opportunistic pathogenEnterococcus faecalisplays a critical role in normal growth, division, biofilm formation, antimicrobial resistance, phage susceptibility, and innate immune evasion. Despite the critical role of this polymer forE. faecalisphysiology and host-pathogen interactions, little information is available on its structure and biosynthesis. Here, we elucidate the structure of the intact EPA produced byE. faecalisOG1RF. We report the structure of the linkage unit, revealing an unprecedented complexity of the rhamnose backbone and decorations. Finally, we explore the impact of several EPA structural modifications on innate immune evasion and recognition by bacteriophages. This work represents a first step towards the functional characterisation of EPA for the rational design of therapeutic strategies against a group of important pathogens.
A detailed analysis of 16S rRNA gene sequencing and conventional PCR-based testing for the diagnosis of bacterial pathogens and discovery of novel bacteria
Authors: Li Mei-Na , Wang Ting , Wang Nan , Han Qiang , You Xue-Ming , Zhang Shuai , Zhang Cui-Cui , Shi Yong-Qiang , Qiao Pei-Zhuang , Man Cheng-Lian , Feng Teng , Li Yue-Yue , Zhu Zhuang , Quan Ke-Ji , Xu Teng-Lin , Zhang George Fei 
Published: June 2024

AbstractThis study represents the first analysis of the bacterial community in chickens affected by swollen head syndrome, utilizing 16S rRNA gene sequencing. Samples were obtained from clinical laying chickens and were examined for the presence ofAvibacterium paragallinarum(APG) andOrnithobacterium rhinotracheale(ORT) using conventional polymerase chain reaction (PCR). From the samples, five APG-positive (APG) and APG-negative (N-APG) samples were chosen, along with five specific pathogen-free chickens, for 16S rRNA gene sequencing. Results showed that APG and ORT were widely detected in the chicken samples with swollen head syndrome (SHS, 9/10), while APG was detected in all five specific pathogen-free (SPF) samples. In contrast, conventional PCR sensitivity was found to be inadequate for diagnosis, with only 35.7% (5/14) and 11.1% (1/9) sensitivity for APG and ORT, respectively, based on 16S rRNA gene sequencing data. Furthermore, 16S rRNA gene sequencing was able to quantify the bacteria in the samples, revealing that the relative abundance of APG in the APG group ranged from 2.7% to 81.3%, while the relative abundance of APG in the N-APG group ranged from 0.1% to 21.0%. Notably, a low level of APG was also detected in all 5 SPF samples. The study also identified a significant number of animal and human common bacterial pathogens, including but not limited toGallibacterium anatis,Riemerella columbina,Enterococcus cecorum, Mycoplasma synoviae,Helicobacter hepaticus, andStaphylococcus lentus. In conclusion, 16S rRNA gene sequencing is a valuable tool for bacterial pathogen diagnosis and the discovery of novel bacterial pathogens, while conventional PCR is not reliable for diagnosis.
Identification of novel broad host-range promoter sequences functional in diversePseudomonadotaby a promoter-trap approach
Authors: Roldán Diego M. , Amarelle Vanesa 
Published: June 2024

AbstractFinding novel promoter sequences is a cornerstone of synthetic biology. To contribute to the expanding catalog of biological parts, we employed a promoter-trap approach to identify novel sequences within an Antarctic microbial community that act as broad host-range promoters functional in diversePseudomonadota. UsingPseudomonas putidaKT2440 as host, we generated a library comprising approximately 2,000 clones resulting in the identification of thirteen functional promoter sequences, thereby expanding the genetic toolkit available for this chassis. Some of the discovered promoter sequences prove to be broad host-range as they drove gene expression not only inP. putidaKT2440 but also inEscherichia coliDH5α,Cupriavidus taiwanensisR1T,Paraburkholderia phymatumSTM 815T,Ensifer meliloti1021, and an indigenous Antarctic bacterium,Pseudomonassp. UYIF39. Our findings enrich the existing catalog of biological parts, offering a repertoire of broad host-range promoter sequences that exhibit functionality across diverse members of the phylumPseudomonadota,proving Antarctic microbial community as a valuable resource for prospecting new biological parts for synthetic biology.
Predictive and Experimental Motif Interaction Analysis Identifies Functions of the WNK-OSR1/SPAK Pathway
Authors: Taylor Clinton A , Jung Ji-Ung , Kankanamalage Sachith Gallolu , Li Justin , Grzemska Magdalena , Jaykumar Ankita B. , Earnest Svetlana , Stippec Steve , Saha Purbita , Sauceda Eustolia , Cobb Melanie H. 
Published: June 2024

ABSTRACTThe WNK-OSR1/SPAK protein kinase signaling pathway regulates ion homeostasis and cell volume, but its other functions are poorly understood. To uncover undefined signaling functions of the pathway we analyzed the binding specificity of the conserved C-terminal (CCT) domains of OSR1 and SPAK to find all possible interaction motifs in human proteins. These kinases bind the core consensus sequences R-F-x-V/I and R-x-F-x-V/I. Motifs were ranked based on sequence, conservation, cellular localization, and solvent accessibility. Out of nearly 3,700 motifs identified, 90% of previously published motifs were within the top 2% of those predicted. Selected candidates (TSC22D1, CAVIN1, ATG9A, NOS3, ARHGEF5) were tested. Upstream kinases WNKs 1-4 and their close relatives, the pseudokinases NRBP1/2, contain CCT-like domains as well. We identified additional distinct motif variants lacking the conserved arginine previously thought to be required, and found that the NRBP1 CCT-like domain binds TSC22D1 via the same motif as OSR1 and SPAK. Our results further highlight the rich and diverse functionality of CCT and CCT-like domains in connecting WNK signaling to cellular processes.