bluuebunny/crossref_metadata_2025 huggingface dataset:
Persistent and De Novo Stress Urinary Incontinence After Minimally Invasive Sacrocolpopexy
Authors: Sinha Annika , Yao Meng , Ferrando Cecile A.
Published: January 2024

Importance

Data on stress urinary incontinence (SUI) after minimally invasive sacrocolpopexy (SCP) with or without midurethral sling placement are limited.

Objective

The aim of the study was to determine the incidence of SUI after minimally invasive sacrocolpopexy.

Study Design

This was a secondary analysis of 2 randomized clinical trials of participants undergoing SCP. Participants completed symptom assessment and urodynamic testing. Participants underwent SCP with or without midurethral sling placement. Preoperatively, participants were defined as having symptomatic SUI, occult SUI, or no SUI. Participants completed the Pelvic Floor Distress Inventory-20 at 6 and 12 months postoperatively and were categorized as having persistent SUI in the setting of symptomatic or occult SUI or de novo SUI.

Results

Eighty-one participants were included. Sixty-one participants met inclusion criteria for the persistent SUI analysis: 42 participants with symptomatic SUI and 19 participants with occult SUI. There were 20 participants in the de novo SUI group. The overall incidence of persistent SUI was 26.2% (95% confidence interval [CI], 15.8%–39.1%) with 33.3% (95% CI, 19.6%–49.6%) of symptomatic and 10.5% (95% CI, 1.5%–33.1%) of occult participants. Bothersome symptoms were defined as “moderately” or “quite a bit” bothered postoperatively. Of participants with symptomatic SUI, 14.3% participants were bothered and no participants underwent retreatment. No patient with occult SUI was bothered; however, 1 patient underwent retreatment. The incidence of de novo SUI was 45% (95% CI, 23.1%–68.5%). No patient in the de novo SUI group was bothered or underwent SUI treatment.

Conclusions

Approximately 1 in 4 participants reported persistent SUI. Almost 50% reported de novo SUI. However, few participants were bothered or underwent treatment.
Azospirillum isscasi sp. nov., a bacterium isolated from rhizosphere soil of rice
Authors: Wang Hui , Jin Haiyang , Chen Zhe , Li Wenjun , Ma Jing , Hu Tianlong , Liu Qi , Zhang Yanhui , Lin Xingwu , Xie Zubin
Published: January 2024

A Gram-negative and rod-shaped bacterium, designated C340-1T, was isolated and screened from paddy soil in Zhongshan County, Guangxi Province, PR China. This strain grew at 20–42 °C (optimum, 37 °C), pH 5.0–9.0 (optimum, pH 7.0) and 0–4 % (w/v) NaCl (optimum, 0–1 %) on Reasoner's 2A medium. The strain could fix atmospheric nitrogen and acetylene reduction activity was recorded up to 120.26 nmol ethylene h–1 (mg protein)–1. Q-10 was the only isoprenoid quinone component; phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid and an unidentified polar lipid were the major polar lipids. Summed feature 8 (C18 : 1
 ω7c and/or C18 : 1
 ω6c) and summed feature 3 (C16 : 1
 ω7c and/or C16 : 1
 ω6c) were the primary cellular fatty acids. The genome of strain C340-1T was 6.18 Mb, and the G+C content was 69.0 mol%. Phylogenetic tree analysis based on 16S rRNA gene and 92 core genes showed that strain C340-1T was closely related to and clustered with the type strains

Azospirillum brasilense

JCM 1224T, Azospirillum argentinense Az39T,

Azospirillum baldaniorum

Sp245T and

Azospirillum formosense

JCM 17639T. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA–DNA hybridization (dDDH) values between strain C340-1T and the closely related type strains mentioned above were significantly lower than the threshold values for species classification (95–96 %, 95–96 % and 70 %, respectively). Based on phylogenetic, genomic, phenotypic, physiological and biochemical data, we have reason to believe that C340-1T represents a new species of the genus

Azospirillum

, for which the name Azospirillum isscasi sp. nov. is proposed. The type strain is C340-1T(=CCTCC AB 2023105T=KCTC 8126T).
Genomic and clinical characteristics of campylobacteriosis in Australia
Authors: Cribb Danielle M. , Moffatt Cameron R. M. , Wallace Rhiannon L. , McLure Angus T. , Bulach Dieter , Jennison Amy V. , French Nigel , Valcanis Mary , Glass Kathryn , Kirk Martyn D.
Published: January 2024

Campylobacter

spp. are a common cause of bacterial gastroenteritis in Australia, primarily acquired from contaminated meat. We investigated the relationship between genomic virulence characteristics and the severity of campylobacteriosis, hospitalisation, and other host factors.

We recruited 571 campylobacteriosis cases from three Australian states and territories (2018–2019). We collected demographic, health status, risk factors, and self-reported disease data. We whole genome sequenced 422

C

.

jejuni

and 84

C

.

coli

case isolates along with 616 retail meat isolates. We classified case illness severity using a modified Vesikari scoring system, performed phylogenomic analysis, and explored risk factors for hospitalisation and illness severity.

On average, cases experienced a 7.5 day diarrhoeal illness with additional symptoms including stomach cramps (87.1 %), fever (75.6 %), and nausea (72.0 %). Cases aged ≥75 years had milder symptoms, lower Vesikari scores, and higher odds of hospitalisation compared to younger cases. Chronic gastrointestinal illnesses also increased odds of hospitalisation. We observed significant diversity among isolates, with 65

C

.

jejuni

and 21

C

.

coli

sequence types. Antimicrobial resistance genes were detected in 20.4 % of isolates, but multidrug resistance was rare (0.04 %). Key virulence genes such as cdtABC (

C. jejuni

) and cadF were prevalent (>90 % presence) but did not correlate with disease severity or hospitalisation. However, certain genes (e.g. fliK, Cj1136, and Cj1138) appeared to distinguish human

C. jejuni

cases from food source isolates.

Campylobacteriosis generally presents similarly across cases, though some are more severe. Genotypic virulence factors identified in the literature to-date do not predict disease severity but may differentiate human

C. jejuni

cases from food source isolates. Host factors like age and comorbidities have a greater influence on health outcomes than virulence factors.
A precision medicine approach forHCN1Developmental and Epileptic Encephalopathy
Authors: Bleakley Lauren E. , McKenzie Chaseley E. , Zhao Da , Soh Ming S. , Spyrou James , Forster Ian C. , Bui Bang V. , Reid Christopher A.
Published: January 2024

Pathogenic variants inHCN1causing cation leak result in a severe developmental and epileptic encephalopathy (DEE). Current treatment options for patients withHCN1-DEE are limited and are insufficient to fully address both the seizures and clinical comorbidities of this disorder.

Org 34167 is a brain penetrant broad-spectrum HCN channel inhibitor that has completed phase I clinical trials. We used a range of assays at molecular, cellular, network and behavioural levels to explore the potential of Org 34167 as a precision medicine forHCN1-DEE.

Org 34167 restored the voltage sensitivity of the DEE HCN1M305Lmutated channel, significantly reducing cation leak. It also restored Ih-mediated ‘sag’, hyperpolarised the resting membrane potential and reduced firing of layer V neurons from the Hcn1M294Lmouse model ofHCN1-DEE, which was engineered based on the HCN1M305Lpathogenic variant. Additionally, Org 34167 reduced neuronal epileptiform activity and restored retinal light sensitivity in these mice, suggesting it may improve both seizures and other clinical comorbidities. However, Org 34167-mediated tremors were noted at therapeutic doses. Org 34167 was also effective at reducing cation leak caused by five additionalHCN1pathogenic variants, suggesting broader utility.

Overall, these data demonstrate that a small molecule HCN inhibitor can restore channel and consequent physiological functions, positioning it as a promising precision therapeutic approach forHCN1-DEE.
Numerical modeling of senile plaque development under conditions of limited diffusivity of amyloid-β monomers
Authors: Kuznetsov Andrey V.
Published: January 2024

This paper introduces a method to simulate the progression of senile plaques, focusing on scenarios where concentrations of amyloid beta (Aβ) monomers and aggregates vary between neurons. Extracellular variations in these concentrations may arise due to limited diffusivity of Aβ monomers and a high rate of Aβ monomer production at lipid membranes, requiring a substantial concentration gradient for diffusion-driven transport of Aβ monomers. The dimensionless formulation of the model is presented, identifying four key dimensionless parameters governing the solutions for Aβ monomer and aggregate concentrations, as well as the radius of a growing Aβ plaque within the control volume. These parameters include the dimensionless diffusivity of Aβ monomers, the dimensionless rate of Aβ monomer production, and the dimensionless half-lives of Aβ monomers and aggregates. A dimensionless parameter is introduced to assess the validity of the lumped capacitance approximation. An approximate solution is derived for the scenario involving large diffusivity of Aβ monomers and dysfunctional protein degradation machinery, resulting in infinitely long half-lives for Aβ monomers and aggregates. In this scenario, the concentrations of Aβ aggregates and the radius of the Aβ plaque depend solely on a single dimensionless parameter that characterizes the rate of Aβ monomer production. According to the approximate solution, the concentration of Aβ aggregates is linearly dependent on the rate of monomer production, and the radius of an Aβ plaque is directly proportional to the cube root of the rate of monomer production. However, when departing from the conditions of the approximate solution (e.g., finite half-lives), the concentrations of Aβ monomers and aggregates, along with the plaque radius, exhibit complex dependencies on all four dimensionless parameters. For instance, under physiological half-life conditions, the plaque radius reaches a maximum value and stabilizes thereafter.
RhoA activation promotes glucose uptake to elevate proliferation in MAPK inhibitor resistant melanoma cells
Authors: Murali Vasanth Siruvallur , Rajendran Divya , Isogai Tadamoto , DeBerardinis Ralph J. , Danuser Gaudenz
Published: January 2024

Cutaneous melanomas harboring a B-RafV600Emutation are treated with immune check point inhibitors or kinase inhibitor combination therapies relying on MAPK inhibitors (MAPKi) Dabrafenib and Trametinib (Curti and Faries, 2021). However, cells become resistant to treatments over the timespan of a few months. Resistance to MAPKi has been associated with adoption of an aggressive amoeboid phenotype characterized by elevated RhoA signaling, enhanced contractility and thick cortical filamentous actin (F-actin) structures (Kim et al., 2016; Misek et al., 2020). Targeting active RhoA through Rho-kinase (ROCK) inhibitors, either alone or in combination with immunotherapies, reverts MAPKi-resistance (Misek et al., 2020; Orgaz et al., 2020). Yet, the mechanisms for this behavior remain largely unknown. Given our recent findings of cytoskeleton’s role in cancer cell proliferation (Mohan et al., 2019), survival (Weems et al., 2023), and metabolism (Park et al., 2020), we explored possibilities by which RhoA-driven changes in cytoskeleton structure may confer resistance. We confirmed elevated activation of RhoA in a panel of MAPKi-resistant melanoma cell lines, leading to a marked increase in the presence of contractile F-actin bundles. Moreover, these cells had increased glucose uptake and glycolysis, a phenotype disrupted by pharmacological perturbation of ROCK. However, glycolysis was unaffected by disruption of F-actin bundles, indicating that glycolytic stimulation in MAPKi-resistant melanoma is independent of F-actin organization. Instead, our findings highlight a mechanism in which elevated RhoA signaling activates ROCK, leading to the activation of insulin receptor substrate 1 (IRS1) and P85 of the PI3K pathway, which promotes cell surface expression of GLUT1 and elevated glucose uptake. Application of ROCK inhibitor GSK269962A results in reduced glucose uptake and glycolysis, thus impeding cell proliferation. Our study adds a mechanism to the proposed use of ROCK inhibitors for long-term treatments on MAPKi-resistant melanomas.
Functional profiling of the male gametophyte-specific promoter fragment ofArabidopsis PIRL6gene and prediction ofcis-regulatory elements
Authors: Ajith T.G. , Shah Jasmine M.
Published: January 2024

Gametophyte-specific promoters drive the expression of genes in male and/or female gametophytes. These have applications in breeding experiments, gene function identification, developmental biology-related studies, and off-lately in genome editing also. ThePlant Intracellular Ras-group Leucine-Rich-Repeat6 (PIRL6) gene is known to be necessary for male and female gametogenesis. Using theGUS-based deletion analysis, we have identified thePIRL6promoter length that is essential for exclusive expression in the male gametophyte ofArabidopsis thaliana.We studied the strength of various lengths ofPIRL6promoters in different tissues, by GUS expression quantification. The male-gametophyte-specific promoter segment (PA1) exhibited stronger expression in mature anthers than the younger ones. We identified 50 other genes that co-expressed withPIRL6inArabidopsisusing the Expression Angler tool. Gene ontology (GO) analysis shows that these 51 co-expressing genes were predominantly involved in cell differentiation. By comparing the promoter sequences of these 51 genes, the presence of three over-represented known motifs, POLLEN1LELAT52, ACGTATERD1 and CIACADIANLELHC was identified. We could also predict the presence of three novelcis-regulatory elements in the co-expressing gene network using the MEME suite tool. Additionally, we confirmed the functionality of the ABRE and P-box elements present inPIRL6promoter using the tobacco leaf transient assay. Thus, we cloned and functionally confirmed the promoter region ofPIRL6required for male gametophyte-specific expression, compared this promoter with those of 50 other co-expressed genes and predicted their functions, and analyzed theircisregulatory regions and predicted three novel motifs also.

Key message

A pollen-specific promoter fragment ofPIRL6was functionally characterized usingGUS-based deletion analysis. Fifty other co-expressed genes were compared and novelcis-regulatory elements were predicted. Two hormone-responsive elements in thePIRL6promoter were found to influence theGUSexpression. PA1 promoter can be used in experiments that require male gametophyte-specific expression of genes.
The decision of male medaka to mate or fight depends on two complementary androgen signaling pathways
Authors: Nishiike Yuji , Okubo Kataaki
Published: January 2024

Adult male animals typically court and attempt to mate with females, while attacking other males. Emerging evidence from mice indicates that neurons expressing the estrogen receptor ESR1 in behaviorally relevant brain regions play a central role in mediating these mutually exclusive behavioral responses to conspecifics. However, the findings in mice are unlikely to apply to most other vertebrates, where androgens — rather than estrogens — have been implicated in male behaviors. Here we report that male medaka (Oryzias latipes) lacking one of the two androgen receptor subtypes (Ara) are less aggressive toward other males and instead actively court them, while those lacking the other subtype (Arb) are less motivated to mate with females and conversely attack them. These findings indicate that, in male medaka, the Ara- and Arb-mediated androgen signaling pathways facilitate appropriate behavioral responses, while simultaneously suppressing inappropriate responses, to males and females, respectively. Notably, males lacking either receptor retain the ability to discriminate the sex of conspecifics, suggesting a defect in the subsequent decision-making process to mate or fight. We further show that Ara and Arb are expressed in intermingled but largely distinct populations of neurons, and stimulate the expression of different behaviorally relevant genes including galanin and vasotocin, respectively. Collectively, our results demonstrate that male teleosts make adaptive decisions to mate or fight as a result of the activation of one of two complementary androgen signaling pathways, depending on the sex of the conspecific that they encounter.
Internal regulation between constitutively expressed T cell coinhibitory receptors BTLA and CD5 and tolerance in recent thymic emigrants
Authors: Adegoke Adeolu O. , Thangavelu Govindarajan , Chou Ting-Fang , Petersen Marcos , Kakugawa Kiyokazu , May Julia F. , Joannou Kevin , Wang Qingyang , Ellestad Kristofor K. , Boon Louis , Bretscher Peter A. , Cheroutre Hilde , Kronenberg Mitchell , Baldwin Troy A. , Anderson Colin C.
Published: January 2024

Several coinhibitory receptors are upregulated upon activation, whereas a small number of coinhibitory receptors are expressed constitutively by naive T cells. The relationship between constitutively expressed coinhibitors is unknown. We found an inverse relationship between two constitutively expressed coinhibitors, CD5 and BTLA; BTLA expression was low in the thymus and high in the periphery, corresponding respectively with high and low CD5 expression. Germline or induced deletion ofBtlain somatic cells demonstrated a causal relationship between BTLA expression and CD5 levels in T cells of central and peripheral lymphoid tissues. The effect of BTLA on CD5 expression on thymic and peripheral CD4 T cells was due to BTLA signaling, rather than signaling by its ligand, the herpes virus mediator (HVEM). Regulation was maintained in mice with a non-signaling HVEM mutant but was lost inTnfrsf14−/−(Hvem−/−) mice. Increased CD5 levels have been positively associated with increased recognition of self-peptide MHC complexes. Thus, control of CD5 expression by BTLA signals early in T cell ontogeny suggested that BTLA might be important for establishing self-tolerance in newly generated T cells. Consistent with this concept, we found that BTLA, as well as the inducible coinhibitor PD-1, were needed post thymic selection in recent thymic emigrants (RTE) to establish self-tolerance. RTE lacking BTLA caused a multiorgan autoimmune disease whose development required CD4 T cells and MHC class II. Together, our findings identify a negative regulatory pathway allowing constitutively expressed coinhibitory receptors to calibrate their expression in thymic T cell differentiation. Expression of constitutive and induced coinhibitory receptors is needed to establish tolerance in the periphery for RTE.
Whole-cortex simulation reveals spatiotemporal patterns emerging from the interplay of network connectivity and intracellular dynamics
Authors: Sun Guanhua , Hazelden James , Kim Ruby , Forger Daniel
Published: January 2024

Recent advances in Graphics Processing Unit (GPU) computing have allowed for computational models of whole-brain activity at unprecedented scales. In this work, we use desktop computers to build and simulate a whole-cortex mouse brain model using Hodgkin-Huxley type models for all the most active neurons in the mouse cortex. We compare the model dynamics over different types of connectivity, ranging from uniform random to realistic connectivity derived from experimental data on cell positions and the Allen Brain Atlas. By changing the external drive and coupling strength of neurons in the network, we can produce a wide range of oscillations in the gamma through delta bands. While the global mean-field behaviors of different connectivities share some similarities, an experimentally determined hierarchical connectivity allows for complex, heterogeneous behaviors typically seen in EEG recordings that are not observed in networks with nearest neighbors or uniform coupling. Moreover, our simulations reveal a wide range of spatiotemporal patterns, such as rotational or planar traveling waves, that are observed in experiments. Different traveling waves are observed with different connectivity and coupling strengths on the same connectivity. Our simulations show that many cortical behaviors emerge at scale with the full complexity of the network structure and ionic dynamics. We also provide a computational framework to explore these cortex- wide behaviors further.
Deubiquitinating enzyme mutagenesis screens identify a USP43 driven HIF-1 transcriptional response
Authors: Pauzaite Tekle , Wit Niek , Seear Rachel V , Nathan James A
Published: January 2024

The ubiquitination and proteasome-mediated degradation of Hypoxia Inducible Factors (HIFs) is central to metazoan oxygen-sensing, but the involvement of deubiquitinating enzymes (DUBs) in HIF signalling is less clear. Here, using a bespoke DUBs sgRNA library we conduct CRISPR/Cas9 mutagenesis screens to determine how DUBs are involved in HIF signalling. Alongside defining DUBs involved in HIF activation or suppression, we identify USP43 as a DUB required for efficient activation of a HIF response. USP43 is hypoxia regulated and selectively associates with the HIF-1α isoform, and while USP43 does not alter HIF-1α stability, it facilitates HIF-1 nuclear accumulation and binding to its target genes. Mechanistically, USP43 associates with 14-3-3 proteins in a hypoxia and phosphorylation dependent manner to increase the nuclear pool of HIF-1. Together, our results unveil the DUB landscape in HIF signalling, and highlight the multifunctionality of DUBs, illustrating that they can provide important signalling functions alongside their catalytic roles.
Flap endonuclease Substrate Interactions studied using Dynamic Single-Molecule Atomic Force Microscopy
Authors: Verma Vinny , Brudenell Emma L. , Cussons Sophie , Phipps Janine , Kong Su Chii , Sayers Jon R. , Hobbs Jamie K.
Published: January 2024

Flap endonucleases (FENs) recognise and cleave DNA substrates containing a 5’-single-strand (ss) of nucleic acid branching off a double-stranded (ds) DNA to yield a nicked duplex during DNA replication. Dynamic Atomic Force Microscopy of an inactive FEN mutant complexed with branched DNA revealed mobilisation of immobilised DNA, indicating that protein interaction affected substrate conformation and disrupted the forces that anchored it to the poly-L-ornithine -treated mica surface. Enzymatically-active FEN was seen intermittently binding DNA, altering its conformation and cleaving the ssDNA branch. We developed a method using motion tracking for quantifying the movement of DNA sections, by visually segmenting DNA and tracking each segment to recognise the DNA sections most affected by the protein. It was found that whilst bound, FEN caused localised DNA bending, and changes in DNA shape were witnessed in the short time span of the protein’s appearance close to the nucleic acid, followed by protein adsorption on the mica surface. The results provide the first dynamic observations of FEN-DNA interaction. FEN initially binds to the dsDNA, slides to find the ds/ssDNA junction, and the 5’ ssDNA likely threads through a hole in the enzyme which leads to enzymatic hydrolysis of the branched substrate.
Iron deficiency in people with obesity drives defective Natural Killer cell mitochondrial fitness and function
Authors: De Barra Conor , Ryan Eimear , Sugrue Michelle , Ryan Odhran , Lynn Evelyn , Heneghan Helen M. , McCarthy Cormac , Moynagh Paul N. , Sinclair Linda V. , Jones Nicholas , Hogan Andrew E. , O’Shea Donal
Published: January 2024

Natural killer (NK) cells are a population of innate effector lymphocytes, involved in host-defences against viral infections and cancer. Upon activation, NK cells can produce a milieu of cytotoxic molecules and cytokines, which can directly target infected and transformed cells, but also amplify an immune response. Metabolic rewiring underpins NK cell effector functionality, providing the required signals, energy and biointermediates to support their immune responses. Obesity is associated with significant defects in the functionality of human NK cells, especially in the periphery. Dysregulated cellular metabolism has been demonstrated to be a major mechanistic driver of the reported defects. However, how obesity links to defective NK cell metabolism and functionality remains unclear. Iron deficiency is a common co-morbidity in people living with obesity (PWO). Recent studies have highlighted the importance for iron in host immunity, with murine models of iron deficiency resulting in defective cellular metabolism and function. We hypothesized that obesity-driven iron deficiency might underpin the reported defects in NK cells. Our data demonstrates that in response to cytokine stimulation, healthy human NK cells utilize iron to support their metabolic activity and cytokine responses. In a cohort of PWO, we demonstrate alterations in NK cell metabolism, mitochondrial fitness and cytokine production. Furthermore, upon stratification into PWO with normal iron status versus low iron status, we show the observed obesity-related defects in NK cell metabolism, mitochondrial fitness and cytokine production are concentrated in the PWO with low-iron status. Collectively, our data highlights the importance of iron for human NK cell responses and provides evidence that obesity-driven defects in NK cell metabolism and function are linked in part to altered iron availability.
Evidence for compensatory evolution within pleiotropic regulatory elements
Authors: Kliesmete Zane , Orchard Peter , Lee Victor Yan Kin , Geuder Johanna , Krauß Simon M. , Ohnuki Mari , Jocher Jessica , Vieth Beate , Enard Wolfgang , Hellmann Ines
Published: January 2024

Pleiotropy, measured as expression breadth across tissues, is one of the best predictors for protein sequence and expression conservation. In this study, we investigated its effect on the evolution of cis-regulatory elements (CREs). To this end, we carefully reanalyzed the Epigenomics Roadmap data for nine fetal tissues, assigning a measure of pleiotropic degree to nearly half a million CREs. To assess the functional conservation of CREs, we generated ATAC-seq and RNA-seq data from humans and macaques. We found that more pleiotropic CREs exhibit greater conservation in accessibility, and the mRNA expression levels of the associated genes are more conserved. This trend of higher conservation for higher degrees of pleiotropy persists when analyzing the transcription factor binding repertoire. In contrast, simple DNA sequence conservation of orthologous sites between species tends to be even lower for pleiotropic CREs than for species-specific CREs. Combining various lines of evidence, we suggest that the lack of sequence conservation for functionally conserved pleiotropic elements is due to compensatory evolution within these large pleiotropic CREs. Furthermore, for less pleiotropic CREs, we find an indication of compensation across CREs. This suggests that pleiotropy is also a good predictor for the functional conservation of CREs, but this is not reflected in the sequence conservation for pleiotropic CREs.
Pangenome reconstruction in rats enhances genotype-phenotype mapping and novel variant discovery
Authors: Villani Flavia , Guarracino Andrea , Ward Rachel R , Green Tomomi , Emms Madeleine , Pravenec Michal , Prins Pjotr , Garrison Erik , Williams Robert W. , Chen Hao , Colonna Vincenza
Published: January 2024

The HXB/BXH family of recombinant inbred rat strains is a unique genetic resource that has been extensively phenotyped over 25 years, resulting in a vast dataset of quantitative molecular and physiological phenotypes. We built a pangenome graph from 10x Genomics Linked-Read data for 31 recombinant inbred rats to study genetic variation and association mapping. The pangenome includes 0.2Gb of sequence that is not present the reference mRatBN7.2, confirming the capture of substantial additional variation. We validated variants in challenging regions, including complex structural variants resolving into multiple haplotypes. Phenome-wide association analysis of validated SNPs uncovered variants associated with glucose/insulin levels and hippocampal gene expression. We propose an interaction betweenPirl1l1, chromogranin expression,TNF-αlevels, and insulin regulation. This study demonstrates the utility of linked-read pangenomes for comprehensive variant detection and mapping phenotypic diversity in a widely used rat genetic reference panel.
Generation of Systemic Chimeras via Rabbit Induced Pluripotent Stem Cells Reprogrammed with KLF2, ERAS, and PRMT6
Authors: Perold Florence , Pham Hong-Thu , Pijoff Yannicke , Doerflinger Nathalie , Rival-Gervier Sylvie , Moulin Anaïs , Jouneau Luc , Pain Bertrand , Joly Thierry , Duranthon Véronique , Afanassieff Marielle , Savatier Pierre , Beaujean Nathalie
Published: January 2024

Little is known about the molecular underpinnings of pluripotent stem cells’ (PSCs) ability to colonize the epiblast of preimplantation embryos and generate chimeras. In our study, using rabbit PSCs as a model system, we conducted unbiased screening of a cDNA library that encodes a panel of 36 pluripotency factors. From this screening, we identified KLF2, ERAS and PRMT6, whose overexpression confers the ability for self-renewal in a KOSR/FGF2-free culture medium supplemented with LIF, activin A, PKC and WNT inhibitors. The reprogrammed cells acquired transcriptomic and epigenetic features of naive pluripotency, including the reactivation of the 2ndX-chromosome. Leveraging these PSC lines, we determined the transcriptomic signature of embryonic colonization-competence, demonstrating transcriptional repression of genes involved in MAPK, WNT, HIPPO, and EPH signaling pathways, alongside the activation of genes involved in amino-acid metabolism, NF-kB signaling, and p53 pathway. Remarkably, a subset of reprogrammed cells, expressing CD75 at a high level, gained the ability to produce chimeric fetuses with a high contribution from PSCs in all lineages.
Cross-Domain Text Mining of Pathophysiological Processes Associated with Diabetic Kidney Disease
Authors: Patidar Krutika , Deng Jennifer H. , Mitchell Cassie S. , Ford Versypt Ashlee N.
Published: January 2024

Diabetic kidney disease (DKD) remains a significant burden on the healthcare system and is the leading cause of end-stage renal disease worldwide. The pathophysiology of DKD is multifactorial and characterized by various early signs of metabolic impairment, inflammatory biomarkers, and complex pathways that lead to progressive kidney damage. New treatment prospects rely on a comprehensive understanding of disease pathology. The study aimed to identify signaling drivers and pathways that modulate glomerular endothelial dysfunction in DKD via cross-domain text mining with SemNet 2.0. The open-source literature-based discovery approach, SemNet 2.0, leverages the power of text mining 33+ million PubMed articles to provide integrative insight into multiscalar and multifactorial pathophysiology. A set of identified relevant genes and proteins that regulate different pathological events associated with DKD were analyzed and ranked using normalized mean HeteSim scores. High-ranking genes and proteins intersecting three domains—DKD, immune response, and glomerular endothelial cells—were analyzed. The top 10% of ranked concepts mapped to the following biological functions: angiotensin, apoptosis, cell-cell function, cell adhesion, chemotaxis, growth factor signaling, vascular permeability, nitric oxide response, oxidative stress, cytokine response, macrophage signaling, NFκB factor activity, TLR signaling, glucose metabolism, inflammatory response, ERK/MAPK signaling, JAK/STAT signaling, T-cell mediated response, WNT signaling, renin angiotensin system, and NADPH response. High-ranking genes and proteins were used to generate a protein-protein interaction network. This comprehensive analysis identified testable hypotheses for interactions or molecules involved with dysregulated signaling in DKD, which can be further studied through biochemical network models.
Acanthella acutaMitochondrial DNA: Linear Architecture and Other Unique Features
Authors: Ahmed Momin , Kayal Ehsan , Lavrov Dennis V.
Published: January 2024

WhileAcanthella acuta(Schmidt 1862), a common demosponge found in the Mediterranean Sea and Atlantic Ocean, is — morphologically — little distinguishable from other sponges, its mitochondrial DNA (mtDNA) is unique within the class. In contrast to all other studied demosponges,A. acutamtDNA appears to be linear and displays several unusual features: inverted terminal repeats, group II introns in three mt-genes, and two unique ORFs. One of the ORFs (ORF1535) combines a DNA-polymerase domain with a DNA-directed RNA-polymerase domain, while the second bears no discernable similarity to any reported sequences. The group II intron within thecox2gene is the first such intron reported in an animal. Our phylogenetic analyses indicate that thecox1intron is related to similar introns found in other demosponges, while thecox2intron is likely not of animal origin. The two domains found withinORF1535do not share a common origin and, along with thecox2intron, were likely acquired by horizontal transfer. The findings of this paper open new avenues of exploration in the understanding of mtDNA linearization within Metazoa.

Significance

The transition from circular to linear mtDNA architecture is a rare and poorly understood phenomenon in animals. In addition, the few lineages that made this transition (Medusozoa, Calcarea, and Isopoda), adopted linear mt-DNA architecture early in their history, making it difficult to reconstruct the underlying events. The identification of linear mtDNA inAcanthella acutanot only provides an independent example of the origin of linear mtDNA architectures in animals but also an opportunity to investigate its evolution at a much shorter evolutionary time. In particular, the conservation of circular mtDNA in other studied species within the family Dictyonellidae highlights the need to investigate other species in the genusAcanthella, to better understand mtDNA linearization inA. acuta.
Elongasome core proteins and class A PBP1a display zonal, processive movement at the midcell ofStreptococcus pneumoniae
Authors: Perez Amilcar J. , Lamanna Melissa M. , Bruce Kevin E. , Touraev Marc A. , Page Julia E. , Shaw Sidney L. , Tsui Ho-Ching Tiffany , Winkler Malcolm E.
Published: January 2024

Ovoid-shaped bacteria, such asStreptococcus pneumoniae(pneumococcus), have two spatially separated peptidoglycan (PG) synthase nanomachines that locate zonally to the midcell of dividing cells. The septal PG synthase bPBP2x:FtsW closes the septum of dividing pneumococcal cells, whereas the elongasome located on the outer edge of the septal annulus synthesizes peripheral PG outward. We showed previously by sm-TIRFm that the septal PG synthase moves circumferentially at midcell, driven by PG synthesis and not by FtsZ treadmilling. The pneumococcal elongasome consists of the PG synthase bPBP2b:RodA, regulators MreC, MreD, and RodZ, but not MreB, and genetically associated proteins Class A aPBP1a and muramidase MpgA. Given its zonal location separate from FtsZ, it was of considerable interest to determine the dynamics of proteins in the pneumococcal elongasome. We found that bPBP2b, RodA, and MreC move circumferentially with the same velocities and durations at midcell, driven by PG synthesis. However, outside of the midcell zone, the majority of these elongasome proteins move diffusively over the entire surface of cells. Depletion of MreC resulted in loss of circumferential movement of bPBP2b, and bPBP2b and RodA require each other for localization and circumferential movement. Notably, a fraction of aPBP1a molecules also moved circumferentially at midcell with velocities similar to those of components of the core elongasome, but for shorter durations. Other aPBP1a molecules were static at midcell or diffusing over cell bodies. Last, MpgA displayed non-processive, subdiffusive motion that was largely confined to the midcell region and less frequently detected over the cell body.

SIGNIFICANCE

This paper reports three types of single-molecule motions of PG synthesis proteins in the ovoid-shaped, pathogenic bacteriumStreptococcus pneumoniae, not reported previously in other bacteria. The core elongasome exhibits zonal, circumferential motion in the absence of MreB filaments, independent of FtsZ treadmilling or the processive movement of the septal PG synthase. Class A aPBP1a also moves processively at midcell, but is not a persistent component of the core elongasome. These types of motions have implications for the functions of these PG synthases and indicate that processive motion in pneumococcus follows spatially separate tracks, possibly reflective of PG structure. In contrast, the MpgA muramidase displays a different kind of subdiffusive motion that is largely confined to midcell by an unknown mechanism.
Effects of different feeding methods on serum biochemical indexes, metabolic indexes, immune indexes, and intestinal microorganisms of Nanjiang yellow goats
Authors: Luo Yangyang , Anwar Asma , Pan Cheng , Shi Hengbo , Mustafa Shehr Bano , Chen Yu , Zhang Zhenzhen , Li Jingjing , Zhu Jiangjiang , Zhao Wangsheng
Published: January 2024

The intestinal microbiota significantly influences the intake, storage, and absorption of nutrients in animals, thereby greatly impacting the growth and development of the animals. Factors such as diet, animal breed, growth stage, and feeding methods may affect variations in the composition of the intestinal microbiota. However, research on the variations in the intestinal microbiota and metabolites of Nanjiang Yellow goats under different feeding methods is still unclear. We measured various serum biochemical indicators and immune biochemical indicators and found that the triglyceride (TC) content in the grazing group (the FMMF) was significantly lower than in the barn-feeding group (the SSMF) (P<0.05). Serum levels of immunoglobulin A (IgA), immunoglobulin G (IgG), and immunoglobulin G (IgM) were higher in the FMMF group. At the phylum level, the most abundant bacteria wereFirmicutes, Bacteroidota, andVerrucomicrobiota. At the genus level, the most abundant microbial groups wereChristensenellaceae_R-7_group, UCG-005, andRikenellaceae_RC9_gut_group. Differential metabolite enrichment analysis through KEGG pathways revealed that the most remarkably enriched pathway was “Metabolic pathways,” including Steroid hormone biosynthesis and Arachidonic acid metabolism, among others. Analyzed by multi-omics association, we identified notably different microbial features correlated with immune indicators and metabolites after different feeding methods. We observed a significant negative correlation (P<0.05) between the concentrations of serum immune factors interleukin-2 (IL-2), interleukin-4 (IL-4), andg__probable_genus_10. The concentration of IgM in serum showed a highly significant positive correlation (P<0.01) with the relative abundance ofg__Erysipelatoclostridiumin the intestine. Interestingly, most differential metabolites were significantly associated with intestinal microbiota. This experiment indicates that different feeding methods may influence the diversity and relative abundance of the intestinal microbiota in Nanjiang Yellow goats. The intestinal microbiota is correlated with immune indicators and metabolism, and regulating the diversity and relative abundance of the intestinal microbiota can be a way to adjust metabolism, thereby promoting the healthy growth of the Nanjiang Yellow goats.
Analysis of Dental Tissues Density in Healthy Children Based on Radiological Data
Authors: Aleksei Reshetnikov , Natalia Shaikhattarova , Margarita Mazurok , Nadezhda Kasatkina
Published: January 2024

Introduction

The information about the Hounsfield range values for healthy tooth tissues could become an additional tool in assessing dental health and could be used, among other data, for subsequent machine learning.

Aim

The aim of our study was to determine dental tissues density values in Hounsfield units.

Materials and Methods

The total selection included 36 healthy children (21 girls and 15 boys) with an age range of 6-10 to 11-15 years at the time of the study. The analysis of 320 teeth’s tissue density was carried out. The data were expressed as a mean and standard deviation. The significance was determined using the Student’s t-test. P-values less than 0.05 were considered significant.

Results

Analysis of the data showed that the tissues of healthy teeth in children have different density ranges. Enamel: 2954.69±223.77 HU - 2071.00±222.86 HU; dentin: 1899.23±145.94 HU - 1323.10±201.67 HU; pulp: 420.29±196.47 HU -183.63±97.59 HU. No gender differences concerning the density of dental tissues were reliably identified.

Conclusion

The evaluation of Hounsfield values for dental tissues can be used as an objective method for assessing their density. If the determined density values of the enamel, dentin, and pulp of the tooth do not correspond to the range of values for healthy tooth tissues, it may indicate a pathology.

Key Messages

Studying the range of healthy and diseased dental tissues using Hounsfield scores, as well as standardizing studies, can help clinicians improve screening accuracy and optimize follow-up of the effectiveness of preventive and therapeutic interventions in the future.
Transient RNA structures underlie highly pathogenic avian influenza virus genesis
Authors: Funk Mathis , Spronken Monique I. , Bestebroer Theo M. , de Bruin Anja C.M. , Gultyaev Alexander P. , Fouchier Ron A.M. , te Velthuis Aartjan J.W. , Richard Mathilde
Published: January 2024

Highly pathogenic avian influenza viruses (HPAIVs) cause severe disease and high fatality in poultry1. They emerge exclusively from H5 and H7 low pathogenic avian influenza viruses (LPAIVs)2. Although insertion of a furin-cleavable multibasic cleavage site (MBCS) in the hemagglutinin gene was identified decades ago as the genetic basis for LPAIV-to-HPAIV transition3,4, the exact mechanisms underlying said insertion have remained unknown. Here we used an innovative combination of bioinformatic models to predict RNA structures forming around the influenza virus RNA polymerase during replication, and circular sequencing5to reliably detect nucleotide insertions. We show that transient H5 hemagglutinin RNA structures predicted to trap the polymerase on purine-rich sequences drive nucleotide insertions characteristic of MBCSs, providing the first strong empirical evidence of RNA structure involvement in MBCS acquisition. Insertion frequencies at the H5 cleavage site were strongly affected by substitutions in flanking genomic regions altering predicted transient RNA structures. Introduction of H5-like cleavage site sequences and structures into an H6 hemagglutinin resulted in MBCS-yielding insertions never observed before in H6 viruses. Our results demonstrate that nucleotide insertions that underlie H5 HPAIV emergence result from a previously unknown RNA-structure-driven diversity-generating mechanism, which could be shared with other RNA viruses.
Development of Int-Plex@ binary memory switch system: plant genome modulation driven by large serine-integrases
Authors: de Oliveira Marco Antônio , Lima Rayane Nunes , Florentino Lilian Hasegawa , Severo de Almeida Mariana Martins , Melo Fernando Lucas , Bonnet Raquel Vasquez , Lacorte Cristiano , Rech Elibio
Published: January 2024

The comprehension of virus-host interactions has allowed numerous advances in developing biotechnological methodologies for plant genome editions, constituting a promising path for plant genetic engineering. Among these advancements, phage- encoded large serine-integrases have emerged as noteworthy tools to modulate plant metabolic pathways by inserting, excising, or inverting DNA stretches in a reversible and specific way. The present work shows the foundation of the Int-Plex@ (INTegrase PLant EXpression) binary memory switch system, which consists of the application of four distinct orthogonal prophage large serine-integrases (Int) (BxB1, phiC31, Int13, and Int9) as an input trigger mechanism for the inversion or excision of genomic DNA. The memory genetic switch is divided into the excision module and the inversion module. The excision module is activated by BxB1 or phiC31 enzymes (input). In this case, the DNA sequence flanked by its attachment sites is excised from the genome (output). The inversion module is activated by Int9 or Int13 (input). The invertedmgfgene sequence is flipped to its functional coding sequence, and the switch output is mGFP. Moreover, prokaryotic-based cell-freein vitrotranscription-translation reactions (TxTl) were used as a fast platform for testing IntsattB/P in tandemsite activity. Furthermore different plasmid delivery strategies for plant cell Int heterologous expression were tested: leaf tissue agroinfiltration ofAgrobacterium tumefacienstransformed with binary plasmids and a biolistic system. After each treatment, the edited genomic DNA sequences were amplified and verified by Sanger and Nanopore sequencing. Despite the challenges of using Ints, the potential benefits are significant and deserve deeper exploration and development. The Int-Plex@ binary genome memory switch system can be applied to produce genetic circuits combined with omics tools and sgRNAs to engineer and modulate plant metabolic pathways temporally and reversibly.
A robust set of qPCR methods to evaluate adulteration in major spices and herbs
Authors: Behr Marc , Garlant Linda , Pietretti Danilo , Pellegrin Clément , Lievens Antoon , Boix Sanfeliu Ana , Maquet Alain , Alvarellos Lourdes
Published: January 2024

Spices and herbs are used in multiple forms by consumers and companies related to food or pharmaceuticals. Their intricate supply chains, high prices and limited productions make them susceptible to deceptive practises. However, robust methodology to detect multiple adulterants is still rarely available, preventing national control laboratories from enforcing European and national regulations.

This article presents qPCR methods developed to identify adulterants in six commonly consumed spices and herbs, namely paprika, turmeric, saffron, cumin, oregano and black pepper. Each genuine sample was blended with the top five adulterants identified in the European Union-wide coordinated control plan on herbs and spices and existing literature. These SYBR™ Green qPCR methods enable specific detection of adulterants, and their sensitivities allow to differentiate inadvertent contamination from deliberate adulteration. Methods performances were evaluated both in binary mixtures and with complex adulteration pattern, validating their effectiveness in safeguarding the authenticity of these high values commodities.

Highlights

Authenticity of spices and herbs is at high risk of fraudulent malpractices.

We provide specific qPCR methods to detect prevalent adulterants.

Trueness of each method was systematically assessed.

Sensitivity of methods meet ISO requirements for purity assessment.

Methods versatility is evaluated with multi-adulterated samples.
Dual DNA/RNA-binding factor regulates dynamics of hnRNP splicing condensates
Authors: Ray Mukulika , Zaborowsky Julia , Mahableshwarkar Pranav , Vaidyanathan Smriti , Shum Jasmine , Viswanathan Renjith , Huang Annie , Wang Szu-Huan , Johnson Victoria , Wake Noah , Conard Ashley M. , Conicella Alexander E. , Puterbaugh Ryan , Fawzi Nicolas L. , Larschan Erica
Published: January 2024

Despite decades of research, mechanisms by which co-transcriptional alternative splicing events are targeted to the correct genomic locations to drive cell fate decisions remain unknown. By combining structural and molecular approaches, we define a new mechanism by which an essential transcription factor (TF) targets co-transcriptional splicing through physical and functional interaction with RNA and RNA binding proteins (RBPs). We show that an essential TF co-transcriptionally regulates sex-specific alternative splicing by directly interacting with a subset of target RNAs on chromatin and modulating the dynamics of hnRNPA2 homolog nuclear splicing condensates.