bluuebunny/crossref_metadata_2025 huggingface dataset:
Enterovirga aerilata sp. nov. and Knoellia koreensis sp. nov., isolated from an automobile air conditioning system
Authors: Lee Hyosun , Chaudhary Dhiraj Kumar , Kim Dong-Uk
Published: May 2024

Two strictly aerobic and rod-shaped bacteria, labelled as DB1703T and DB2414ST, were obtained from an automobile air conditioning system. Strain DB1703T was Gram-stain-negative, while strain DB2414ST was Gram-stain-positive. Both strains were catalase-positive and oxidase-negative. Strains DB1703T and DB2414ST were able to grow at 18–42 °C. Strain DB1703T grew within a NaCl range of 0–3 % and a pH range of 6.0–8.0; while strain DB2414ST grew at 0–1 % and pH 6.5–8.5. The phylogenetic and 16S rRNA gene sequence analysis indicated that strains DB1703T and DB2414ST belonged to the genera Enterovirga and Knoellia, respectively. Strain DB1703T showed the closest phylogenetic similarity to Enterovirga rhinocerotis YIM 100770T (94.8 %), whereas strain DB2414ST was most closely related to Knoellia remsis ATCC BAA-1496T (97.7 %). The genome sizes of strains DB1703T and DB2414ST were 4 652 148 and 4 282 418 bp, respectively, with DNA G+C contents of 68.8 and 70.5 mol%, respectively. Chemotaxonomic data showed Q-10 as the sole ubiquinone in DB1703T and ML-8 (H4) in DB2414ST. The predominant cellular fatty acid in DB1703T was summed feature 8 (C18 : 1
 ω7c and/or C18 : 1
 ω6c), whereas iso-C16 : 0, C17 : 1
 ω8c, and iso-C15 : 0 were dominant in DB2414ST. Overall, the polyphasic taxonomic comparisons showed that strains DB1703T and DB2414ST were distinct from their closest taxa and represent novel species within the genera Enterovirga and Knoellia, respectively. Accordingly, we propose the names Enterovirga aerilata sp. nov., with the type strain DB1703T (=KCTC 72724T=NBRC 114759T), and Knoellia koreensis sp. nov., with the type strain DB2414ST (=KCTC 49355T=NBRC 114620T).
Lutimonas zeaxanthinifaciens sp. nov., a zeaxanthin-producing marine bacterium isolated from coastal sediment
Authors: Jung Yoon-Hee , Kwon Yong Min , Chung Dawoon , Yu Woon-Jong , Choi Grace , Kim Tae Wan , Bae Seung Seob
Published: May 2024

A Gram-stain-negative, yellow-pigmented, strictly aerobic, non-flagellated, motile by gliding, rod-shaped bacterium, designated strain YSD2104T, was isolated from a coastal sediment sample collected from the southeastern part of the Yellow Sea. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain YSD2104T was closely related to three type strains, Lutimonas vermicola IMCC1616T (97.4 %), Lutimonas saemankumensis SMK-142T (96.9 %), and Lutimonas halocynthiae RSS3-C1T (96.8 %). Strain YSD2104T has a single circular chromosome of 3.54 Mbp with a DNA G+C content of 38.3 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strain YSD2104T and the three type strains (L. vermicola IMCC1616 T, L. saemankumensis SMK-142T, and L. halocynthiae RSS3-C1T) were 74.0, 86.2 and 73.6 %, and 17.9, 30.3 and 17.8 %, respectively. Growth was observed at 20–30 °C (optimum, 30 °C), at pH 6.5–8.5 (optimum, pH 7.0), and with NaCl concentrations of 1.5–3.5 % (optimum, 2.5 %). The major carotenoid was zeaxanthin, and flexirubin-type pigment was not produced. The major respiratory quinone was menaquinone-6. The major fatty acids (>10 %) were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1
 ω6c and/or C16 : 1
 ω7c), and summed feature 9 (iso-C17 : 1
 ω9c and/or 10-methyl C16 : 0). The major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid, two unidentified aminolipids, and eight unidentified lipids. Conclusively, based on this polyphasic approach, we classified strain YSD2104T (=KCTC 102008T=JCM 36287T) as representing a novel species of the genus Lutimonas and proposed the name Lutimonas zeaxanthinifaciens sp. nov.
Epithelial NSD2 maintains FMOs-mediated taurine biosynthesis to prevent intestinal barrier disruption
Authors: Xu Yue , Ma Chunxiao , Wang Ziyi , Feng Wenxin , Rao Hanyu , Zhang Wei , Liu Ningyuan , Aji Rebiguli , Meng Xiangjun , Gao Wei-Qiang , Li Li
Published: May 2024

Inflammatory bowel disease (IBD) poses a significant challenge due to its intricate pathogenesis. NSD2, a histone methyltransferase responsible for dimethylating histone 3 at lysine 36, is associated with transcriptional activation. However, the precise role of NSD2 in IBD remains unexplored. In this study, we discovered a downregulation of NSD2 in both the intestinal epithelial cells (IECs) of patients and the IBD mouse model. Deficiency of NSD2 in mouse IECs aggravated epithelial barrier disruption and inflammatory response in IBD. Mechanically, NSD2 loss downregulated H3K36me2 and FMO (taurine-synthesis enzyme) mRNA in IECs, resulting in decreased taurine biosynthesis in IECs. Importantly, supplementation with taurine significantly attenuated the symptoms of NSD2 deficiency-induced IBD. These data demonstrate that NSD2 plays a pivotal role in maintaining FMOs-mediated taurine biosynthesis to prevent intestinal inflammation. Our findings also underscore the importance of NSD2-H3K36me2-mediated taurine biosynthesis in maintaining intestinal mucosal barrier homeostasis.
Design, synthesis and cellular characterization of a new class of IPMK kinase inhibitors
Authors: Zhou Yubai , Chapagain Pratima , Desmarini Desmarini , Uredi Dilipkumar , Rameh Lucia E. , Djordjevic Julianne T. , Blind Raymond D. , Wang Xiaodong
Published: May 2024

Many genetic studies have established the kinase activity of inositol phosphate multikinase (IPMK) is required for the synthesis of higher-order inositol phosphate signaling molecules, the regulation of gene expression and control of the cell cycle. These genetic studies await orthogonal validation by specific IPMK inhibitors, but no such inhibitors have been synthesized. Here, we report complete chemical synthesis, cellular characterization, structure-activity relationships and rodent pharmacokinetics of a novel series of highly potent IPMK inhibitors. The first-generation compound1(UNC7437) decreased cellular proliferation and tritiated inositol phosphate levels in metabolically labeled human U251-MG glioblastoma cells. Compound1also regulated the transcriptome of these cells, selectively regulating genes that are enriched in cancer, inflammatory and viral infection pathways. Further optimization of compound 1 eventually led to compound15(UNC9750), which showed improved potency and pharmacokinetics in rodents. Compound15specifically inhibited cellular accumulation of InsP5, a direct product of IPMK kinase activity, while having no effect on InsP6levels, revealing a novel metabolic signature detected for the first time by rapid chemical attenuation of cellular IPMK activity. These studies designed, optimized and synthesized a new series of IPMK inhibitors, which reduces glioblastoma cell growth, induces a novel InsP5metabolic signature, and reveals novel aspects inositol phosphate cellular metabolism and signaling.
Modulatory Effects of IFN-γ and IL-22 on Inflammatory Signaling and Cellular Responses in Intestinal Epithelial Cells
Authors: Johnson Asia , Denning Timothy L.
Published: May 2024

Inflammatory bowel disease (IBD) continues to affect millions worldwide, with an increasing prevalence that highlights the urgent need for deeper understanding of its underlying immune mechanisms. The cytokine interactions, especially those mediated by cells from the TH1 and TH17 lymphocyte subsets, are crucial in orchestrating the immune landscape of IBD. TH1 cells are well known for producing TNF-α and IFNγ, which have been extensively studied for their roles in conjunction with each other within the context of IBD. TH17 cells secrete IL-22 and IL-17, with existing studies primarily focusing on IL-22’s interaction with IL-17 rather than its interplay with other cytokines such as IFNγ. Our study focuses on the co-stimulatory effects of IL-22 and IFNγ using organoids derived from mouse small intestines to model epithelial interactions. We found that IFNγ interferes with the capacity of IL-22 to up-regulate antimicrobial peptides, which is essential in mucosal defense. Additionally, higher concentrations of IL-22 enhance IFNγ’s ability to stimulate TNF-α gene expression and CXCL10 protein production, indicating a dose-dependent relationship. This co-stimulation also led to an increased rate of cell death, influenced partly by TNF-α. These findings suggest that IL-22, typically seen as an anti-inflammatory agent, can assume a pro-inflammatory role when combined with IFNγ, complicating its effects on epithelial cells. This study highlights the need to consider specific cytokine interactions in developing more effective IBD treatments.
Oviposition and vertical dispersal ofAedesspecies Meigen 1818 (Diptera: Culicidae) at different heights and seasonal periods in an urban forest fragment in Manaus, Amazonas, Brazil
Authors: Ribeiro da Silva William , Arcos Adriano Nobre , da Silva Ferreira Francisco Augusto , Soares-da-Silva Joelma , Pontes Grafe Oliveira , Navarro da Silva Mário Antônio , Roque Rosemary Aparecida , Zequi João Antonio Cyrino
Published: May 2024

Mosquitoes of the genusAedesstand out for their high susceptibility to several groups of arboviruses, especially those that cause dengue fever, Zika, and Chikungunya fever. However, aspects related to the vertical distribution of species in large urban centers are still poorly understood, therefore, this study aims to evaluate the dispersal and oviposition ofAedesat different height levels and seasonal periods. The study was developed in a tower with six floors located in an urban forest fragment, measuring 15.13 meters (m) high and 3.20 meters at the base. The following height ranges were considered: ground: 0 m; 1.20 m; 2.50 m; 3.60m; 4.90 m; 6m; 7.30m; 8.40m; 9.70 m; and 10.8 m. Three ovitraps were installed on each floor, separated by a distance of 1.50 m, totaling 30 for each sampling period. The ovitrap positivity index (OPI) and egg density index (EDI) were evaluated in order to monitorAedespopulations in different height ranges and also in different seasonal periods. The data demonstrated that lower heights show a greater abundance ofAedeseggs, however, this variable did not prove to be a limiting factor for mosquito colonization at the other heights evaluated. Furthermore, climatic factors, such as relative humidity have a positive influence (p<0.05) on the average number of eggs in the urban area of Manaus, especially during the dry period. These findings demonstrate that the vertical growth of urban centers can act positively tin increasing the density ofAedesand can influence the incidence of dengue and other arboviruses.
Pooled genetic screens identify breast cancer risk genes involved in evasion from T cell-mediated killing
Authors: Shi Wei , Luo Yi , Burrows Jacqueline M. , Black Debra , Civitarese Andrew , Perlaza-Jimenez Laura , Zhang Ping , Manning Murray , Tuano Natasha , Rentería Miguel E. , Xiao Christos , Tey Siok-Keen , Rosenbluh Joseph , Smith Corey , Chenevix-Trench Georgia , Beesley Jonathan
Published: May 2024

Genome-wide association studies have identified more than 220 loci associated with breast cancer susceptibility. A major challenge is now to identify the effector genes with plausible functions in the context of breast cancer risk. We have previously performed pooled CRISPR screens to identify target genes at risk loci that drive cancer hallmarks including proliferation or modulating DNA damage response. We now extend these screens to identify genes involved in response to cytotoxic T lymphocyte (CTL) killing. We performed knockout and inhibition screens to identify genes that affect the response of the MCF7 human breast cancer cell line to CTL killing in anin vitroco-culture system. We identified 33 candidate risk genes associated with resistance or sensitisation to T cell-mediated killing. Using single gene perturbation, we showed that deletion of candidate risk genesIRF1, ATF7IP, CCDC170andCASP8induced resistance, while ablation ofCFLAR, CREBBP, andPRMT7sensitized cells to CTL killing. We used reporter assays to show that the risk-associated alleles at rs736801 and rs3769821 reduced transactivation of theIRF1andCASP8promoters, respectively. We showed that pharmacological inhibition of PRMT7 rendered breast cells sensitive to CTL killing andPRMT7levels were negatively correlated with CD8+ infiltration and patient survival in luminal A breast cancer patient cohorts. Our results demonstrate that phenotypic pooled CRISPR screens are a useful approach for high throughput functional follow-up of GWAS findings, identifying genes which alter immune responses to breast cancer which offer opportunities to enhance immunotherapy.
Understanding Antibody-Target Antigen Interactions and the Avidity Effect Using Mathematical Modelling
Authors: Heirene Luke A. , Byrne Helen M. , Gaffney Eamonn A. , Yates James W. T.
Published: May 2024

Background and Purpose

Immunotherapies are designed to exploit the immune system to target pathologies, for instance, but not exclusively, cancer. Monoclonal antibodies (mAbs) are an important class of immunotherapies that induce anti-tumour effects in numerous ways. Fundamental to the success of mAbs in cancer treatments are their interactions with target antigens. For example, binding multiple antigens, which increases binding affinity, termed the avidity effect, has been shown to impact treatment outcomes. However, there has been limited theoretical analysis addressing the impacts of antibody-antigen interactions on avidity, potency, and efficacy. Hence, our aim is to develop a mathematical model to develop insight on these impacts.

Experimental Approach

We analyse an ordinary differential equation model of bivalent, monospecific IgG antibodies binding to membrane bound antigens. We obtain equilibrium solutions of the model and conduct a global parameter sensitivity analysis to identify which antibody-antigen interactions impact quantities, such as antigen occupancy, that contribute to mAb potency and efficacy.

Key Results

We show that the ratio of antibody to antigen number impacts antigen occupancy, bound antibody number and whether an antibody can bind both its antigen-binding arms. A sensitivity analysis reveals that antigen occupancy and the ratio of bound antibody to total antigen number are sensitive to the antibody-antigen binding rates only for high antibody concentrations. We identify parameter ranges in which the avidity effect is predicted to be large for antigen occupancy and bound antibody numbers.

Conclusion and Implications

These results could be used in the preclinical development of mAb therapies by predicting conditions which enhance mAb potency, efficacy, and the avidity effect.
Multiple Unfolded Protein Response pathways cooperate to link cytosolic dsDNA release to Stimulator of Interferon Gene (STING) activation
Authors: Hu Tiancheng , Liu Yiping , Fleck Jeremy , King Cason , Schalk Elaine , Zhang Zhenyu , Mehle Andrew , Smith Judith A
Published: May 2024

The double-stranded DNA (dsDNA) sensor STING has been increasingly implicated in responses to “sterile” endogenous threats and pathogens without nominal DNA or cyclic di-nucleotide stimuli. Previous work showed an endoplasmic reticulum (ER) stress response, known as the unfolded protein response (UPR), activates STING. Herein, we sought to determine if ER stress generated a STING ligand, and to identify the UPR pathways involved. Induction of IFN-β expression following stimulation with the UPR inducer thapsigargin (TPG) or oxygen glucose deprivation required both STING and the dsDNA-sensing cyclic GMP-AMP synthase (cGAS). Furthermore, TPG increased cytosolic mitochondrial DNA, and immunofluorescence visualized dsDNA punctae in murine and human cells, providing a cGAS stimulus. N-acetylcysteine decreased IFN-β induction by TPG, implicating reactive oxygen species (ROS). However, mitoTEMPO, a mitochondrial oxidative stress inhibitor did not impact TPG-induced IFN. On the other hand, inhibiting the inositol requiring enzyme 1 (IRE1) ER stress sensor and its target transcription factor XBP1 decreased the generation of cytosolic dsDNA. iNOS upregulation was XBP1-dependent, and an iNOS inhibitor decreased cytosolic dsDNA and IFN-β, implicating ROS downstream of the IRE1-XBP1 pathway. Inhibition of the PKR-like ER kinase (PERK) pathway also attenuated cytoplasmic dsDNA release. The PERK-regulated apoptotic factor Bim was required for both dsDNA release and IFN-β mRNA induction. Finally, XBP1 and PERK pathways contributed to cytosolic dsDNA release and IFN-induction by the RNA virus, Vesicular Stomatitis Virus (VSV). Together, our findings suggest that ER stressors, including viral pathogens without nominal STING or cGAS ligands such as RNA viruses, trigger multiple canonical UPR pathways that cooperate to activate STING and downstream IFN-β via mitochondrial dsDNA release.
Targeting LxCxE cleft pocket of retinoblastoma protein in M2 macrophages inhibits ovarian cancer progression
Authors: Tcyganov Evgenii N. , Kwak Taekyoung , Yang Xue , Poli Adi Narayana Reddy , Hart Colin , Bhuniya Avishek , Cassel Joel , Kossenkov Andrew , Auslander Noam , Lu Lily , Sharma Paridhima , Mendoza Maria De Grecia Cauti , Zhigarev Dmitry , Cadungog Mark Gregory , Jean Stephanie , Chatterjee-Paer Sudeshna , Weiner David , Donthireddy Laxminarasimha , Bristow Bryan , Zhang Rugang , Tyurin Vladimir A. , Tyurina Yulia Y. , Bayir Hülya , Kagan Valerian E. , Salvino Joseph M. , Montaner Luis J.
Published: May 2024

Abstract

Ovarian cancer remains a major health threat with limited treatment options available. It is characterized by immunosuppressive tumor microenvironment (TME) maintained by tumor- associated macrophages (TAMs) hindering anti-tumor responses and immunotherapy efficacy. Here we show that targeting retinoblastoma protein (Rb) by disruption of its LxCxE cleft pocket, causes cell death in TAMs by induction of ER stress, p53 and mitochondria-related cell death pathways. A reduction of pro-tumor RbhighM2-type macrophages from TME in vivo enhanced T cell infiltration and inhibited cancer progression. We demonstrate an increased Rb expression in TAMs in women with ovarian cancer is associated with poorer prognosis. Ex vivo, we show analogous cell death induction by therapeutic Rb targeting in TAMs in post-surgery ascites from ovarian cancer patients. Overall, our data elucidates therapeutic targeting of the Rb LxCxE cleft pocket as a novel promising approach for ovarian cancer treatment through depletion of TAMs and re-shaping TME immune landscape.

Statement of significance

Currently, targeting immunosuppressive myeloid cells in ovarian cancer microenvironment is the first priority need to enable successful immunotherapy, but no effective solutions are clinically available. We show that targeting LxCxE cleft pocket of Retinoblastoma protein unexpectedly induces preferential cell death in M2 tumor-associated macrophages. Depletion of immunosuppressive M2 tumor-associated macrophages reshapes tumor microenvironment, enhances anti-tumor T cell responses, and inhibits ovarian cancer. Thus, we identify a novel paradoxical function of Retinoblastoma protein in regulating macrophage viability as well as a promising target to enhance immunotherapy efficacy in ovarian cancer.
Personalized transcriptome signatures in a cardiomyopathy stem cell biobank
Authors: Monte Emma , Furihata Takaaki , Wang Guangwen , Perea-Gil Isaac , Wei Eric , Chaib Hassan , Nair Ramesh , Guevara Julio Vicente , Mares Rene , Cheng Xun , Zhuge Yan , Black Katelyn , Serrano Ricardo , Dagan-Rosenfeld Orit , Maguire Peter , Mercola Mark , Karakikes Ioannis , Wu Joseph C. , Snyder Michael P.
Published: May 2024

BACKGROUND

There is growing evidence that pathogenic mutations do not fully explain hypertrophic (HCM) or dilated (DCM) cardiomyopathy phenotypes. We hypothesized that if a patient’s genetic background was influencing cardiomyopathy this should be detectable as signatures in gene expression. We built a cardiomyopathy biobank resource for interrogating personalized genotype phenotype relationships in human cell lines.

METHODS

We recruited 308 diseased and control patients for our cardiomyopathy stem cell biobank. We successfully reprogrammed PBMCs (peripheral blood mononuclear cells) into induced pluripotent stem cells (iPSCs) for 300 donors. These iPSCs underwent whole genome sequencing and were differentiated into cardiomyocytes for RNA-seq. In addition to annotating pathogenic variants, mutation burden in a panel of cardiomyopathy genes was assessed for correlation with echocardiogram measurements. Line-specific co-expression networks were inferred to evaluate transcriptomic subtypes. Drug treatment targeted the sarcomere, either by activation with omecamtiv mecarbil or inhibition with mavacamten, to alter contractility.

RESULTS

We generated an iPSC biobank from 300 donors, which included 101 individuals with HCM and 88 with DCM. Whole genome sequencing of 299 iPSC lines identified 78 unique pathogenic or likely pathogenic mutations in the diseased lines. Notably, only DCM lines lacking a known pathogenic or likely pathogenic mutation replicated a finding in the literature for greater nonsynonymous SNV mutation burden in 102 cardiomyopathy genes to correlate with lower left ventricular ejection fraction in DCM. We analyzed RNA-sequencing data from iPSC-derived cardiomyocytes for 102 donors. Inferred personalized co-expression networks revealed two transcriptional subtypes of HCM. The first subtype exhibited concerted activation of the co-expression network, with the degree of activation reflective of the disease severity of the donor. In contrast, the second HCM subtype and the entire DCM cohort exhibited partial activation of the respective disease network, with the strength of specific gene by gene relationships dependent on the iPSC-derived cardiomyocyte line. ADCY5was the largest hubnode in both the HCM and DCM networks and partially corrected in response to drug treatment.

CONCLUSIONS

We have a established a stem cell biobank for studying cardiomyopathy. Our analysis supports the hypothesis the genetic background influences pathologic gene expression programs and support a role forADCY5in cardiomyopathy.
Tendon-associated gene expression precedes osteogenesis in mid-palatal suture establishment
Authors: Roth Daniela M. , Oliver Piña Jeremie , Raju Resmi , Iben James , Faucz Fabio R. , Makareeva Elena , Leikin Sergey , Graf Daniel , D’Souza Rena N.
Published: May 2024

Orthodontic maxillary expansion relies on intrinsic mid-palatal suture mechanobiology to induce guided osteogenesis, yet establishment of the mid-palatal suture within the continuous secondary palate and causes of maxillary insufficiency remain poorly understood. In contrast, advances in cranial suture research hold promise to improve surgical repair of prematurely fused cranial sutures in craniosynostosis to potentially restore the obliterated signaling environment and ensure continual success of the intervention. We hypothesized that mid-palatal suture establishment is governed by shared principles with calvarial sutures and involves functional linkage between expanding primary ossification centres with the midline mesenchyme. We characterized establishment of the mid-palatal suture from late embryonic to early postnatal timepoints. Suture establishment was visualized using histological techniques and multimodal transcriptomics. We identified that mid-palatal suture formation depends on a spatiotemporally controlled signalling milieu in which tendon-associated genes play a significant role. We mapped relationships between extracellular matrix-encoding gene expression, tenocyte markers, and novel suture patency candidate genes. We identified similar expression patterns in FaceBase-deposited scRNA-seq datasets from cranial sutures. These findings demonstrate shared biological principles for suture establishment, providing further avenues for future development and understanding of maxillofacial interventions.
Natural selection and evolution of mitochondrial genome in terrestrial and aquatic turbellarians
Authors: Li Rong , Feng Hui , Cao Pinglin , Wang Jianxing
Published: May 2024

Mitochondrial energy metabolism may be directly influenced by natural selection pressures in response to the energy demands of an organism’s specific ecological niche. Here, we hypothesized that the mitochondrial genome of turbellarian animals was influenced by the metabolic requirements of various habitats We used selection pressure and phylogenetic independent contrasts (PIC) analyses to detect the selection pressure of protein-coding genes in the mitochondrial genome of turbellarian living in aquatic and terrestrial habitats. The results indicated turbellarians in aquatic habitats experienced greater selection pressure, resulting in the evolution of several genes at a lower ω value compared to their terrestrial counterparts. The NAD4 was identified as having positive selection sites in all site models analyzed. Among all genes, the equilibrium constant (ionization of COOH) was the most frequently detected amino acid characteristic with significant positive selection changes, followed by hydropathy and molecular volume. The equilibrium constant (ionization of COOH) was found to be the amino acid characteristic with the greatest magnitude of change in NAD4. This suggests that it plays a crucial role in the adaptive evolution of turbellarians to varying habitats. The study found a significant positive correlation (R = 0.61, p < 0.05) between the ω value of turbellarian and their habitats by PIC analysis. These findings shed light on the adaptive evolution of turbellarian mtDNAs and their influence on the oxidative phosphorylation molecular mechanism.

0.

Significance statement

The adaptive evolution of mitochondrial genes is closely related to environmental temperature, high energy metabolism demand, altitude, and oxygen availability. Mitochondrial energy metabolism may be directly influenced by natural selection pressures in response to the energy demands of an organism’s specific ecological niche. Here, we investigated the evolution of mtDNA PCGs in turbellarians across different habitats, and identified purifying selection as the main evolutionary pattern of the turbellarian mitochondrial genome. Additionally, we found that NAD4 played an important role in the adaptive evolution of turbellarians to different habitats.
N-acetylcysteine as a treatment for substance use cravings: A meta-analysis
Authors: Winterlind Emma L. , Malone Samantha G. , Setzer Michael R. , Murphy Mikela A. , Saunders David , Gray Joshua C.
Published: May 2024

N-acetylcysteine (NAC) may serve as a novel pharmacotherapy for substance use and substance craving in individuals with substance use disorders (SUDs), possibly through its potential to regulate glutamate. Though prior meta-analyses generally support NAC’s efficacy in reducing symptoms of craving, individual trials have found mixed results. The aims of the this updated meta-analysis were to (1) examine the efficacy of NAC in treating symptoms of craving in individuals with a SUD and (2) explore subgroup differences, risk of bias, and publication bias across trials. Database searches of PubMed, Cochrane Library, andClinicalTrials.govwere conducted in June and July of 2023 to identify relevant randomized control trials (RCTs). The meta-analysis consisted of 9 trials which analyzed data from a total of 623 participants. The most targeted substance in the clinical trials was alcohol (3/9; 33.3%), followed by tobacco (2/9; 22.2%) and multiple substances (2/9; 22.2%). Meta-analysis, subgroup analyses, and leave-one-out analyses were conducted to examine treatment effect on craving symptoms and adverse events (AEs). Risk of bias assessments, Egger’s tests, and funnel plot tests were conducted to examine risk of bias and publication bias. NAC did not significantly outperform placebo in reducing symptoms of craving in the meta-analysis (SMD = 0.189, 95% CI = -0.015 - 0.393). Heterogeneity was very high in the meta-analysis (99.26%), indicating that findings may have been influenced by clinical or methodological differences in the study protocols. Additionally, results indicate that there may be publication bias present. Overall, our findings are contrary to those of prior meta-analyses, suggesting limited impact of NAC on substance craving. However, the high heterogeneity and presence of publication bias identified warrants cautious interpretation of the meta-analytic outcomes.
Data-driven neuroanatomical subtypes of primary progressive aphasia
Authors: Taylor Beatrice , Bocchetta Martina , Shand Cameron , Todd Emily G , Chokesuwattanaskul Anthipa , Crutch Sebastian J , Warren Jason D , Hardy Chris JD , Rohrer Jonathan D , Oxtoby Neil P
Published: May 2024

The primary progressive aphasias are rare, language-led dementias, with three main variants: semantic, non-fluent/agrammatic, and logopenic. Whilst semantic variant has a clear neuroanatomical profile, the non-fluent/agrammatic and logopenic variants are difficult to discriminate from neuroimaging. Previous phenotype-driven studies have characterised neuroanatomical profiles of each variant on MRI. In this work we used a machine learning algorithm known as SuStaIn to discover data-driven neuroanatomical “subtype” progression profiles and performed an in-depth subtype–phenotype analysis to characterise the heterogeneity of primary progressive aphasia.

Our study included 270 participants with primary progressive aphasia seen for research in the UCL Queen Square Institute of Neurology Dementia Research Centre, with follow-up scans available for 137 participants. This dataset included individuals diagnosed with all three main variants (semantic: n=94, non-fluent/agrammatic: n=109, logopenic: n=51) as well as individuals with un-specified primary progressive aphasia (n=16). A data set of 66 patients (semantic n=37, non-fluent/agrammatic: n=29) from the ALLFTD North American cohort study, was used to validate our results. MRI scans were segmented and SuStaIn was employed on 19 regions of interest to identify neuroanatomical profiles independent of the diagnosis. We assessed the assignment of subtypes and stages, as well as their longitudinal consistency.

We discovered four neuroanatomical subtypes of primary progressive aphasia, labelled S1, S2, S3, S4, exhibiting robustness to statistical scrutiny. S1 correlated strongly with semantic variant, while S2, S3, and S4 showed mixed associations with the logopenic and non-fluent/agrammatic variants. Notably, S3 displayed a neuroanatomical signature akin to a logopenic only signature, yet a significant proportion of logopenic cases were allocated to S2. The non-fluent/agrammatic variant demonstrated diverse associations with S2, S3, and S4. No clear relationship emerged between any of the neuroanatomical subtypes and the unspecified cases. At first follow up 84% of patients subtype assignment was stable, and 91.9% of patients stage assignment was stable. The ALLFTD dataset validated the findings.

Our study, leveraging machine learning on a large primary progressive aphasia dataset, delineated four distinct neuroanatomical patterns. The identification of multiple profiles within the logopenic and non-fluent/agrammatic variants, alongside intra-phenotypic overlap, supports recent conceptualisations of primary progressive aphasia as a spectrum of disorders rather than discrete entities. Understanding the multifaceted profiles of the disease, encompassing neuroanatomical, molecular, clinical, and cognitive dimensions, holds potential implications for clinical decision support.
Persistent lung inflammation and alveolar-bronchiolization due to Notch signaling dysregulation in SARS-CoV-2 infected hamster
Authors: Li Can , Xiao Na , Song Wenchen , Lam Alvin Hiu-Chung , Liu Feifei , Cui Xinrui , Ye Zhanhong , Chen Yanxia , Ren Peidi , Cai Jianpiao , Lee Andrew Chak-Yiu , Chen Honglin , Ou Zhihua , Chan Jasper Fuk-Woo , Yuen Kwok-Yung , Chu Hin , Zhang Anna Jin-Xia
Published: May 2024

Long COVID or Post-acute sequalae of COVID-19 (PASC) defines the persistent signs, symptoms, and conditions long after initial SARS-CoV-2 infection which affecting over 10% of COVID-19 patients, with 40% of them affecting respiratory system. The lung histopathological changes and underlying mechanism remain elusive. Here we systemically investigate histopathological and transcriptional changes at 7, 14, 42, 84 and 120 days-post-SARS-CoV-2-infection (dpi) in hamster. We demonstrate persistent viral residues, chronic inflammatory and fibrotic changes from 42dpi to 120dpi. The most prominent lung histopathological lesion is multifocal alveolar-bronchiolization observed in every animal from 14dpi until 120dpi. However, none of the above are observed in hamsters recovered from influenza A infection. We show airway progenitor CK14+ basal cells actively proliferate, differentiate into SCGB1A+ club cell or Tubulin+ ciliated cells, leading to alveolar-bronchiolization. Most importantly, Notch pathway is persistently upregulated. Intensive Notch3 and Hes1 protein expression are detected in alveolar-bronchiolization foci, suggesting the association of sustained Notch signaling with dysregulated lung regeneration. Lung spatial transcriptomics show upregulation of genes positively regulating Notch signaling is spatially overlapping with alveolar-bronchiolization region. To be noted, significant upregulation of tumor-related genes was detected in abnormal bronchiolization region by spatial transcriptomics analysis, indicating possible risk of lung carcinoma. Collectively, our data suggests SARS-CoV-2 infection caused chronic inflammatory and fibrotic tissue damages in hamster lung, sustained upregulation of Notch pathway signaling contributed to the dysregulated lung regeneration and CK14+ basal cells-driven alveolar-bronchiolization. The study provides important information for potential therapeutic approaches and probable long-term surveillance of malignancy in PASC management.
Residues Neighboring an SH3-Binding Motif Participate in the InteractionIn Vivo
Authors: Jordan David F. , Dubé Alexandre K. , Dionne Ugo , Bradley David , Landry Christian R.
Published: May 2024

In signaling networks, protein-protein interactions are often mediated by modular domains that bind short linear motifs. The motifs’ sequences affect many factors, among them affinity and specificity, or the ability to bind strongly and to bind the appropriate partners. Using Deep Mutational Scanning to create a mutant library, and protein complementation assays to measure protein-protein interactions, we determined thein vivobinding strength of a library of mutants of a binding motif on the MAP kinase kinase Pbs2, which binds the SH3 domain of the osmosensor protein Sho1 inSaccharomyces cerevisiae. These measurements were made using the full-length endogenous proteins, in their native cellular environment. We find that along with residues within the canonical motif, many mutations in the residues neighboring the motif also modulate binding strength. Interestingly, all Pbs2 mutations which increase affinity are situated outside of the Pbs2 region that interacts with the canonical SH3 binding pocket, suggesting that other surfaces on Sho1 contribute to binding. We use predicted structures to hypothesize a model of binding which involves residues neighboring the canonical Pbs2 motif binding outside of the canonical SH3 binding pocket. We compared this predicted structure with known structures of SH3 domains binding peptides through residues outside of the motif, and put forth possible mechanisms through which Pbs2 can bind specifically to Sho1. We propose that for certain SH3 domain-motif pairs, affinity and specificity are determined by a broader range of sequences than what has previously been considered, potentially allowing easier differentiation between otherwise similar partners.

Protein-protein interactions are often mediated by a binding domain on one protein and a short disordered binding motif on another protein. We measured the binding strength of a mutant library of a binding motif situated in the yeast protein Pbs2 to the SH3 domain of Sho1. Many mutations in the residues neighboring the binding motif affect binding. A protein structure prediction of the interaction partners shows that residues neighboring the motif bind residues outside the known binding pocket on the SH3 domain. The Sho1-Pbs2 interaction differs enough from other known SH3-motif pairs to allow specific binding.
Effect of 2,4-Dinitrophenol Against Multidrug-Resistant Bacteria
Authors: Víctor Hugo Pérez Carrillo , Ángel Alfredo Nuñez Vázquez , Raquel Ortega Muñoz , Juan Carlos Jiménez-Castellanos , Jesús Fernando Montiel Aguirre
Published: May 2024

Multidrug-resistant bacteria have become very important in recent decades due to the health problems they cause. Different mechanisms of resistance in bacteria have been identified among which are efflux pumps. It is believed that chemical compounds such as 2,4-dinitrophenol (2,4-DNP) can inhibit efflux pumps which normally participate in detoxifying cells. In the present work antibiotic multiresistant cells were isolated. Resistance of these bacteria to different antibiotics was tested by the Kirby-Bauer method and ethidium bromide tolerance. It was assumed that they showed overexpression of efflux pumps. The effect of 2,4-DNP was tested and the antibiotic resistance and growth of the cells were measured. Although a strong inhibition effect by 2,4-DNP was observed, an unexpected variation in MICs among the samples suggests that 2,4DNP has a more complex effect on bacteria than originally assumed.
H2A.Z chaperones converge on E2F target genes for melanoma cell proliferation
Authors: Jostes Sina , Vardabasso Chiara , Dong Joanna , Carcamo Saul , Singh Rajendra , Phelps Robert , Meadows Austin , Grossi Elena , Hasson Dan , Bernstein Emily
Published: May 2024

High levels of H2A.Z promote melanoma cell proliferation and correlate with poor prognosis. However, the role of the two distinct H2A.Z histone chaperone complexes SRCAP and P400–TIP60 in melanoma remains unclear. Here, we show that individual subunit depletion ofSRCAP,P400, andVPS72(YL1) results in not only the loss of H2A.Z deposition into chromatin but also a reduction of H4 acetylation in melanoma cells. This loss of H4 acetylation is particularly found at the promoters of cell cycle genes directly bound by H2A.Z and its chaperones, suggesting a coordinated regulation between H2A.Z deposition and H4 acetylation to promote their expression. Knockdown of each of the three subunits downregulates E2F1 and its targets, resulting in a cell cycle arrest akin to H2A.Z depletion. However, unlike H2A.Z deficiency, loss of the shared H2A.Z chaperone subunit YL1 induces apoptosis. Furthermore, YL1 is overexpressed in melanoma tissues, and its upregulation is associated with poor patient outcome. Together, these findings provide a rationale for future targeting of H2A.Z chaperones as an epigenetic strategy for melanoma treatment.
GFP and FAP imaging of neuropeptide release inDrosophila
Authors: Levitan Edwin S. , Bulgari Dinara , Klose Markus K.
Published: May 2024

Genetics inDrosophilahave revealed the role of neuropeptides in development and behavior. However, determining when and where neuropeptides are released has been challenging. Furthermore, the cell biology underlying neuropeptide release has largely been unexplored. Thus, it has not been possible to determine whether changes in neuropeptide immunofluorescence reflect traffic and/or release, and in neurons where such changes are not detectable, conclusions about neuropeptide release have been formulated based on the assumption that electrical and Ca2+recordings are accurate and quantitative predictors of release. Recently, the advent of optical detection of neuropeptides tagged with fluorescent proteins and fluorogen-activating proteins (FAPs) has made it feasible to directly image vesicle traffic and exocytosis that mediates neuropeptide release in peripheral synapses and in the brain. In fact, these approaches have led to the discovery of unexpected insights concerning neuropeptide release. Here procedures are presented for optimizing fluorescence imaging of neuropeptides tagged with green fluorescent protein or a FAP.
Wallerian Degeneration and Clearance of Olfactory Receptor Neuron Axons followingDrosophilaAntennal Transection
Authors: Waller Thomas J. , Smithson Laura J. , Collins Catherine A.
Published: May 2024

Neurons extend their axons and dendrites over long distances and rely on evolutionarily conserved mechanisms to maintain the cellular structure and function of neurites at a distance from their cell body. Neurites that lose connection with their cell body following damage or stressors to their cytoskeleton undergo a programmed self-destruction process akin to apoptosis but using different cellular machinery, termed Wallerian degeneration. While first described for vertebrate axons by Augustus Waller in 1850, key discoveries of the enzymes that regulate Wallerian degeneration were made through forward genetic screens inDrosophila melanogaster. Powerful techniques for genetic manipulation and visualization of single neurons combined with simple methods for introducing axotomy (neuron severing) to certain neuron types inDrosophilahave enabled the discovery and study of the cellular machinery responsible for Wallerian degeneration, in addition to mechanisms that enable clearance of the resulting debris. This protocol describes how to study the degeneration and clearance of axons from olfactory receptor neurons (ORNs). These peripheral neurons reside in the antennae and project axons to olfactory glomeruli of the anterior brain. Simple and nonlethal removal of antennae from adult flies causes axotomy of ORNs, and the fate of the injured axons can be readily visualized in a whole-mount dissected brain. This assay takes advantage of well-characterized genetic methods to robustly and specifically label subsets of ORNs. This method of neurite labeling and axotomy was the first axon injury paradigm to be developed in flies and is still regularly used due to its simplicity to perform, dissect, image, and analyze.
Immobilizing Second-InstarDrosophilaLarvae for Imaging and Surgery Using the Larva Chip
Authors: Smithson Laura J. , Waller Thomas J. , Collins Catherine A.
Published: May 2024

The simple body plan and semitranslucent cuticle of theDrosophilalarva allow for imaging of structures close to the body wall within intact animals. These include sensory neurons, muscles, neuromuscular junctions, and some regions of the segmental nerve. However, imaging within an intact larva requires a strategy to immobilize the animal in a position that presents the structures within the working distance of the microscope objective. Although various methods have been implemented forDrosophilalarvae, this protocol describes a simple and noninvasive method that makes use of the polydimethylsiloxane (PDMS) larva chip. This larva chip immobilizes animals without the use of anesthetics or changes in temperature, which alter neuronal physiology, making it suitable for calcium imaging of endogenous activity in live animals. The membrane is air-permeable. Animals robustly survive short periods of immobilization (up to 30 min) and can even survive longer time periods. Since animals recover well after the procedure, the same animal can be reimaged multiple times. This makes the method amenable to manipulations such as laser microsurgery, photobleaching, and photoconversion followed by imaging of outcomes of these manipulations over time.
Study of Axonal Injury and Degeneration inDrosophila
Authors: Waller Thomas J. , Smithson Laura J. , Collins Catherine A.
Published: May 2024

A fundamental feature of nervous systems is a highly specified synaptic connectivity between cells and the ability to adaptively change this connectivity through plasticity mechanisms. Plasticity mechanisms are highly relevant for responding to nervous system damage, and studies using nervous system injury paradigms inDrosophila(as well as other model organisms) have revealed conserved molecular pathways that are triggered by axon damage. Simple assays that introduce injuries to axons in either adult flies or larvae have proven to be particularly powerful for uncovering mechanisms of axonal degeneration and clearance. They have also been used to reveal requirements for regrowth of axons and dendrites, as well as signaling pathways that regulate cellular responses to nerve injury. Here we review commonly used and simple to carry out techniques that enable experimenters to study responses to axonal damage in either adult flies (following antennal transection) or larvae (following nerve crush to segmental nerves). Because axons and dendrites in the larval peripheral nervous system can be readily visualized through the translucent cuticle, another versatile method to probe injury responses is to focus high-energy laser light to a small and specific location in the animal. We therefore discuss a method for immobilizing intact larvae for imaging through the cuticle to carry out injury by pulse dye laser, which can be used to generate many different kinds of injuries and directed ablations within intact larvae. These techniques, combined with powerful genetic tools inDrosophila, make the fruit fly an excellent model system for studying the effects of injury and the mechanisms of axon degeneration, synapse plasticity, and immune response.
Quantifying Nitrogen Uptake Rates of Maize Roots Using Stable Isotopes
Authors: Ishaya Findimila Dio , Rasmussen Amanda
Published: May 2024

Nitrogen is an essential element for plant growth and development; however, application of nitrogen (N)-based fertilizers comes with a high environmental cost. This includes the energy required for production, volatilization from fields, and runoff or leaching to waterways triggering algal blooms. As such, a key goal in plant breeding programs is to develop varieties that maintain yield while requiring less fertilization. Central to this goal is understanding how roots take up nitrogen and finding traits that represent improvements in the net uptake. Maize, one of the most widely produced crops in the world, has seminal, crown, and brace root types, each under independent developmental control. Recent evidence suggests that these independent developmental patterns may result in different nutrient uptake characteristics. As such, understanding the uptake dynamics of each root type under different environmental conditions is an essential aspect for the selection of new maize varieties. A key method for tracking nitrogen uptake is the use of the15N stable isotope, which is naturally less abundant than the main14N isotope. This method involves replacing the14N in nutrient solutions with15N, exogenously providing it to the plant tissues (roots in this case), and then measuring the15N content of the tissues after a fixed amount of time. Here, we provide a brief overview of nitrogen uptake and remobilization in maize, and discuss current techniques for measuring nutrient uptake, with a focus on methods using stable isotopes of nitrogen.