bluuebunny/crossref_metadata_2025 huggingface dataset:
ATF3 regulates CDC42 transcription and influences cytoskeleton remodeling, thus inhibiting the proliferation, migration and invasion of malignant skin melanoma cells
Authors: Niu Liang , Liu Shuo , Shen Jiuxiao , Chang Jin , Li Xiaojing , Zhang Ling
Published: November 2024

Cutaneous malignant melanoma (CMM) is one of the most aggressive and lethal types of skin cancer. Cytoskeletal remodeling is a key factor in the progression of CMM. Previous research has shown that activating transcription factor 3 (ATF3) inhibits metastasis in bladder cancer by regulating actin cytoskeleton remodeling through gelsolin. However, whether ATF3 plays a similar role in cytoskeletal remodeling in CMM cells remains unknown. Various gene and protein expression analyses were performed using techniques such as reverse transcription quantitative PCR, western blot, immunofluorescent staining, and immunohistochemical staining. CMM viability, migration, and invasion were examined through cell counting kit-8 and transwell assays. The interactions between cell division cycle 42 (CDC42) and ATF3 were investigated using chromatin immunoprecipitation and dual-luciferase reporter assays. CDC42 was upregulated in CMM tissues and cells. Cytoskeletal remodeling of CMM cells, as well as CMM cell proliferation, migration, and invasion, were inhibited by CDC42 or ATF3. ATF3 targeted the CDC42 promoter region to regulate its transcriptional activity. ATF3 suppresses cytoskeletal remodeling in CMM cells, thereby inhibiting CMM progression and metastasis through CDC42. This research may provide a foundation for using ATF3 as a therapeutic target for CMM.
Associations Among Problematic Internet Usage in Adolescents, Parental Internet Factors, and Parent-Adolescent Communication
Authors: Milkovich Libby Matile , Randell Kimberly A. , Sherman Ashley K. , Moreno Megan A.
Published: November 2024

Objective:

Adolescents with problematic internet use (PIU) have excessive, impulsive, or risky internet use that negatively affects social, physical, and functional outcomes. The role of parents in the prevention of adolescent PIU remains unclear. The purpose of this study was to evaluate possible association between adolescent PIU, parent PIU, and internet-related parenting factors.

Methods:

Adolescents aged 12 to 18 years and a parent were recruited through national Qualtrics panels for an online cross-sectional survey. Adolescents and parents completed the Problematic and Risky Internet Use Screening Scale-3 (PRIUSS-3) and Internet-Specific Parenting Practices (ISPP) scales for (1) internet content (ISPP-content) and (2) time on the internet (ISPP-time). Adolescents completed ISPP for quality of parent communication regarding internet use (ISPP-Quality). Bivariate analyses examined relationships between adolescent PIU, parent PIU, and ISPP.

Results:

In total, 4558 adolescents and 4568 parents completed surveys. Adolescent PIU prevalence was 69.9%. Parent PIU prevalence was 61.4%. Among parents with PIU, 87% had an adolescent with PIU compared with only 42% of parents without PIU (OR = 9.54, 95% CI: 8.24–11.05). More lenient content parenting practices and stricter time parenting practices were associated with increased likelihood of adolescent PIU. The quality of parent communication around the internet was lower for adolescents with PIU.

Conclusion:

Study findings suggest that coaching around positive parent-child relationships and healthy family internet use habits that include shared digital experiences may more effectively address PIU than enforcing child screen time limits.
The Research Progress: Cuproptosis and Copper Metabolism in Regulating Cardiovascular Diseases
Authors: Yanjuan Liu , Shuangyou Deng , Ying Wang , Xing Chen , Yue Chen , Zixuan Yu , Shumeng Zhang , Lingli Chen , Jie Li
Published: November 2024

Studies have shown an association between cardiovascular disease and abnormal copper metabolism. Cuproptosis is caused by the accumulation of copper in vivo, and is a newly identified form of cell death. It regulates cardiovascular diseases by affecting vascular endothelial function and myocardial energy metabolism through pathways such as oxidative stress, mitochondrial function, and gene expression. The treatment of copper accumulation in Traditional Chinese Medicine primarily involves heat-clearing and detoxification therapy, supplemented with diuretic therapy. In contrast, Western medicine mainly uses copper chelators. Flavonoids are common active ingredients used in the treatment of copper metabolism-related and cardiovascular diseases. In this article, we reviewed the relationship between copper metabolism, cuproptosis, and cardiovascular disease, providing novel strategies for preventing and treating cardiovascular disease; our ultimate aim is to encourage inspiration and contemplation among readers.
Feasibility study of a game-based virtual reality intervention for functional prosthesis use training: A preclinical assessment
Authors: Mu Jing , Garcia-Rosas Ricardo , Mayer Raphael Maria , Meise Daniel , Lavranos Jim , Graf Mark , Tan Ying , Oetomo Denny , Choong Peter
Published: November 2024

Objective:

This paper presents a preclinical feasibility study to investigate the efficacy of a game-based virtual reality (VR) intervention in the functional training of upper-limb prosthesis use.

Methods:

The study compared the skill of 2 able-bodied groups (intervention and control, 5 participants in each group) using a surface electromyography controlled self-experience prosthetic hand and wrist through the Box and Blocks Test (BBT). The Intervention Group followed the game-based VR intervention for 4 weeks and underwent real-life (RL) BBT assessments before and after the intervention using the self-experience prosthesis. The Control Group performed the RL BBT assessments 4 weeks apart with no VR intervention in between. As a follow-on study, the Control Group then underwent the VR intervention for further validation. The VR intervention consisted of 2 games designed to train the control and use of a surface electromyography–controlled prosthetic hand and an assessment (VR BBT). The VR intervention protocol included three 30-minute sessions per week over a period of 4 weeks.

Results:

A significantly larger improvement was shown in the BBT scores from the Intervention Group (mean 6.375) compared to the Control Group (1.5). The follow-on study further confirmed the result.

Conclusion:

The study demonstrated promising outcomes in the use of a game-based VR intervention for training functional prosthesis use, with participants showing significant improvements in prosthesis use skills measured with RL BBT. This motivates further development of VR interventions for prosthesis use training and their validation through clinical trials.
18F-FDG PET/CT Imaging of Cutaneous and Intramuscular Multiple Myeloma
Authors: Lippold Brandon , Jahromi Amin H.
Published: November 2024

Cutaneous manifestations of multiple myeloma are rare but, as with other extramedullary manifestations, carry a worse prognosis. We present the case of a 65-year-old man with immunoglobulin G κ multiple myeloma and prior autologous stem cell transplant. On subsequent therapy, he presented with multiple new cutaneous and subcutaneous left hip masses. Biopsy of these lesions revealed plasma cell neoplasm with anaplastic morphology, confirming progression of disease. He subsequently underwent radiation to these lesions with plans for chimeric antigen receptor T-cell therapy due to refractory disease.
Unusual Presentation of Oral DLBCL Resembling a Canine Fossa Abscess
Authors: Guzel Ceylan , Munevveroglu Sumer , Arar Elif Ezgi , Dasdan Hayrunisa
Published: November 2024

This report aims to describe a unique case of diffuse large B-cell lymphoma originating from the oral cavity, which presented with symptoms mimicking a canine fossa abscess. It emphasizes the importance of accurate differential diagnosis and appropriate treatment. A 64-year-old female patient visited the authors' clinic with a painful swelling in the left anterior region of the maxilla, persisting for 1 month. Initially, an abscess drainage procedure was performed, accompanied by extraction of the maxillary left canine and parenteral antibiotherapy. However, no improvement was observed during the follow-up appointment after 3 days. An incisional biopsy was then conducted under local anesthesia, leading to a histopathologic diagnosis of diffuse large B-cell lymphoma. The patient is currently under the care of the hematology department and receiving maintenance chemotherapy. Lymphomas occurring in the oral cavity are uncommon and may exhibit non-specific clinical features that resemble benign oral and dental conditions. Therefore, a comprehensive clinical evaluation is necessary to achieve an early and accurate diagnosis, with histopathologic examination being essential for suspicious lesions.
Impact of Nonalcoholic Fatty Liver Disease on Weight Loss Outcomes After One Anastomosis Gastric Bypass
Authors: Athar Rahmatullah , Shahsavan Masoumeh , Shahabi Shahab , Pazouki Abdolreza , Husain Farah A. , Kermansaravi Mohammad
Published: November 2024

Background:

Obesity-associated nonalcoholic fatty liver disease (NAFLD) is a significant cause of chronic liver disease. Our study sought to investigate preoperative NAFLD and the effect at 6 months and 2 years after surgery of one anastomosis gastric bypass (OAGB) and its development 6 months after surgery regarding weight loss outcomes.

Materials and Methods:

A retrospective cohort study was conducted on patients with severe obesity who underwent primary OAGB at Hazrat-e-Rasool Hospital between March 2020 and June 2021. Preoperative assessments included abdominal ultrasound (US) for NAFLD grading, weight, and biochemical blood tests. Follow-up examinations were performed at 10 days and 1, 3, 6, 9, 12, and 24 months postsurgery, with subsequent US examinations at the 6-month follow-up.

Results:

Two hundred thirty-one patients were included, with an average age of 40.3±10.5 years and a percentage of 78.4 women. Their mean weight and BMI were 131.2±26.8 and 48.8±8.5, respectively. Six-month grades of NAFLD showed that patients with grade 3 NAFLD had significantly lower TWL% compared with the lower grades. NAFLD grades improved in 72.3% of our patients, remained the same at 21.2%, and worsened at 6.5%. The 6-month TWL% was 28.4±4.3 in the no-change group, 28.4±5.3 for the improved group, and 25.2±14.6 in the worse group.

Conclusion:

The severity and progression of NAFLD can significantly impact weight loss outcomes post-OAGB, highlighting the importance of monitoring and managing NAFLD in patients undergoing bariatric surgery.
Dream of the Endless
Authors: Weant Kyle A. , Bailey Abby M.
Published: November 2024

Procedural sedation and analgesia (PSAA) is integral to facilitating painful and anxiety-inducing medical procedures in the emergency department (ED). Optimal PSAA enhances procedural success and improves both patient and provider satisfaction. The selection of appropriate sedative and analgesic agents, routes, and dosages, which depend on various patient- and procedure-specific factors is a complex process. Alternative routes of administration, such as intranasal, intramuscular, and oral, are all options, each with their own inherent benefits and limitations. It is important for providers to take into account patient-specific considerations, including age, medical history, body weight composition, and pregnancy, which can significantly impact PSAA effectiveness and safety. Implementation strategies targeted to minimize medication errors and optimize workflow are also important considerations in PSAA. By adopting a comprehensive and evidence-based approach, health care providers can navigate the intricacies of PSAA and ensure the best possible care for patients in the ED.
Pseudomonas machongensis sp. nov. and Stenotrophomonas capsici sp. nov., isolated from wilted pepper plants
Authors: Qiu Minghui , Li Yonglin , Liu Qingmei , Zhang Xiaohan , Huang Yulong , Guo Rui , Hu Ming , Zhou Jianuan , Zhou Xiaofan
Published: November 2024

Two Gram-stain-negative, aerobic, rod-shaped, non-endospore-forming bacteria, designated as strain MH1T and MH2T, were isolated from branches of wilted pepper plants (Capsicum annuum) collected from a farmland in Machong town, Guangdong, China, and investigated using a polyphasic approach. MH1T grew at temperatures of 4–42 °C (optimum 28 °C), with 0–6.0 % (w/v) NaCl and at pH 4.0–10.0 (optimum pH 4.0). MH2T grew at temperatures of 4–42 °C (optimum 28 °C), with 0–6.0% (w/v) NaCl and at pH 4.0–10.0 (optimum pH 5.0). Analysis of the 16S rRNA gene sequence indicated that MH1T belongs to Stenotrophomonas and MH2T belongs to Pseudomonas. Genome-based phylogenetic analysis further established that MH1T shares the closest evolutionary relationships with Stenotrophomonas humi DSM 18929 and Stenotrophomonas terrae DSM 18941, and MH2T is sister to Pseudomonas wayambapalatensis RW3S1. Whole-genome comparisons between MH1T and known Stenotrophomonas species revealed average nucleotide identity (ANI) values up to 84.5%, as well as digital DNA–DNA hybridization (dDDH) values up to 28.3%, both substantially lower than the accepted thresholds for species delineation (ANI: 95%; dDDH: 70%). The ANI and dDDH values between MH2T and known Pseudomonas species were at most 94.6 and 59.2 %, respectively. Additional biochemical and physiological analyses further support that MH1T and MH2T represent a novel species in Stenotrophomonas and Pseudomonas, respectively. Notably, the differences in carbon source utilization could differentiate MH1T and its close relatives in Stenotrophomonas. The major fatty acids were iso-C15 : 0, iso-C16 : 0 and iso-C14 : 0 for MH1T and were C16 : 0, C18 : 1 ω7c/C18 : 1 ω6c (summed feature 8), C16 : 1 ω7c/C16 : 1 ω6c (summed feature 3) and C17 : 0 cyclo for MH2T. Therefore, we propose a new species Stenotrophomonas capsici sp. nov., with MH1T (=GDMCC 1.3749T=JCM 36317T) as the type strain, and a new species Pseudomonas machongensis sp. nov., with MH2T (=GDMCC 1.3750T=JCM 36318T) as the type strain. The MH1T genome has a size of 4.18 Mb and a GC-content of 67.19 mol%, while the MH2T genome has a size of 5.71 Mb and a GC-content of 63.12 mol%.
Microbe Profile: Candida glabrata – a master of deception
Authors: Granada Maria , Cook Emily , Sherlock Gavin , Rosenzweig Frank
Published: November 2024

Graphical abstract

Candida glabrata, an opportunistic fungal pathogen. (a) Unable to form hyphae, relies on tissue disruption to invade and disseminate host. (b) Calcofluor-white cells, 60X objective. (c) Colony morphology on YPD.
Quantitative MRI Measurements Capture Pancreatic Cancer and Stroma Reactions to New KRAS Inhibitor
Authors: Gupta Mamta , Choi Hoon , Kemp Samantha B , Furth Emma E , Pickup Stephen , Clendenin Cynthia , Orlen Margo , Rosen Mark , Liu Fang , Cao Quy , Stanger Ben Z. , Zhou Rong
Published: November 2024

In pancreatic ductal adenocarcinoma (PDAC), KRAS mutations drive both cancer cell growth and formation of a dense stroma. Small molecule KRAS inhibitors (KRASi) represent a breakthrough for PDAC treatment hence clinical tools that can assess early response, detect resistance and/or predict prolonged survival are desirable for management of patients undergoing KRASi therapy. We hypothesized that diffusion-weighted MRI (DWI) can detect cell death while dynamic contrast enhanced MRI (DCE) and magnetization transfer ratio (MTR) imaging are sensitive to tumor microenvironment changes, and these metrics shed insights into tumor size (standard care assessment) change induced by KRASi treatment. We tested this hypothesis in multiple preclinical PDAC models receiving MRTX1133, an investigational new drug specific for KRASG12Dmutation. Quantitative imaging markers corroborated by immunohistochemistry (IHC) revealed significant and profound changes related to cell death accompanied by changes in tumor cellularity, capillary perfusion /permeability and stromal matrix as early as 48h and day-7 after initiation of KRASi treatment, and greatly prolonged median survival over controls in a genetic engineered mouse model of PDAC (KPC). The MRI markers also captured distinct responses to KRASi therapy from PDAC tumors carrying KRASG12CversusKRASG12Dmutation. In tumors developed resistance to MRTX1133, the imaging markers exhibited a reversal from those of responding tumors. Our findings have established that multiparametric MRI provide biological insights including cell death, reduced cellularity and tumor microenvironment changes induced by KRASi treatment and set the stage for testing the utility of these clinically ready MRI methods in patients receiving KRASi therapy.

Translational relevance

Emerging small molecule KRAS inhibitors (KRASi) represent a new class of therapy for PDAC. Clinical tools that can provide biological insights beyond tumor size change are desirable for management of patients under KRASi therapy. DWI and DCE are frequently applied MRI methods for assessing cancer treatment responses in clinical trials. Using multiple PDAC models, we examined whether DWI, DCE and MTR can enhance the standard care assessment (tumor size) to MRTX1133, a KARSi with investigational new drug (IND) status. Our data demonstrate the abilities of DWI, DCE and MTR derived imaging markers to detect the early (48h) cell death, pronounced stromal changes and development of resistance to KRASi. This study has high translational relevance by testing clinically ready MRI methods, an IND and a genetic engineered mouse model that recapitulates saline features of human PDAC.
Analysis of a hypomorphicmei-P26mutation reveals developmental control of CO patterning mechanisms
Authors: Berent Erica , Solomon Ally , Spencer Amanda P. , Bautista Oscar , Terry Joe , Ables Elizabeth T. , Crown Nicole
Published: November 2024

Female gametogenesis inDrosophilarequires both differentiation of germline stem cells and the unique cell cycle meiosis. Successful segregation of chromosomes into gametes during meiosis requires the formation of crossovers between homologous chromosomes. The frequency and distribution of crossovers is highly regulated at several levels, including formation of at least one obligate crossover per pair of homologs, crossover interference that keeps crossovers farther apart than expected by chance, and suppression of crossovers in and near the centromere. To achieve crossover patterning, a meiosis specific version of homologous recombination is used to repair programmed double-stranded breaks, and inDrosophila melanogaster, this recombination pathway requires the putative double Holliday junction resolvase MEI-9. Despite our understanding of crossover patterning mechanisms at the phenomenological level, how crossover patterning mechanisms are developmentally controlled in the context of germ cell differentiation is unknown. Here, we take advantage of a hypomorphic mutation inmei-P26,a gene previously associated with regulation of both germ cell mitoses and meiotic induction. We confirm thatmei-P261mutants show extended expression of mitotic cell cycle markers but rarely completely block differentiation, indicating that the mitotic cell cycle is mis-regulated. In this developmentally delayed context, we show thatmei-P261mutants enter meiosis and complete the earliest stages of prophase, including loading of synaptonemal complex proteins onto the centromere and initial loading onto the arms. Most nuclei do not progress past this to make full length synaptonemal complex, yet meiotic double-strand breaks are induced and crossovers form. However, while these crossovers require MEI-9 and exhibit crossover assurance, the centromere effect and interference are lost. We suggest a model where entry into zygotene of prophase is enough to commit pro-oocytes to using the meiotic homologous recombination machinery and thus ensuring crossover assurance, but that full length synaptonemal complex assembly is required for crossover interference.
Extraordinary physiology of polyphosphate-accumulatingBeggiatoamats suggests a key role for phosphate buffering in marine sediments
Authors: Iakovchuk Nadezhda , Fabian Jenny , Dellwig Olaf , Hassenrück Christiane , Schulz-Vogt Heide N.
Published: November 2024

Filamentous sulfide-oxidizingBeggiatoaspp. are widespread in marine coastal environments and can achieve significant biomass because of their substantial size. Their ability to store phosphates in the polymerized form of polyphosphates makes them potentially key players in altering the phosphorus (P) cycle at the sediment-water interface. This study examined phosphate uptake and polyphosphate formation in a P starved culture of theBeggiatoasp. 35Flor strain. Remarkably, even after severe P starvation over five generations, the survival of the cultures was 46%, demonstrating considerable plasticity to different levels of phosphate availability. Under these P-depleted conditions, 23% of filaments still contained polyphosphates, underscoring its critical role in their metabolism. Upon reintroduction of phosphate to starved cultures, an extremely rapid phosphate uptake was observed within the first 10 minutes, with rates reaching up to 298 mmol P g-1protein d-1, which is significantly higher than values previously described in the literature for similar-sized organisms. The high phosphate uptake capacity ofBeggiatoaspp., estimated at 0.6 – 6 mmol m-2d-1for typical densities of filaments in coastal sediments, suggests that these bacteria may play an important role in buffering the phosphate flux in these environments. Thereby, they reduce primary production and subsequent oxygen consumption by other organisms, creating a negative feedback loop that helps maintain ecosystem stability.

Importance

Sulfide-oxidizing bacteria of the genusBeggiatoaoccur ubiquitously in marine coastal sediments and have a large potential to influence phosphate fluxes at the sediment-water interface owing to their ability to accumulate polyphosphate and their large size. However, the extent to which these bacteria can contribute to phosphorus (P) sequestration or release remains poorly assessed. The importance of this study lies in demonstrating the unusual flexibility in adaptation of theBeggiatoasp. 35Flor strain to varying P availability, including extreme P starvation, and its capacity to rapidly uptake and store available phosphate in the form of polyphosphate. When considered at a global scale, these physiological traits could lead to P retention in shallow coastal waters, which, in turn, profoundly impacts ecological stability and ecosystem functioning.
Sequence-Dependent Liquid Crystalline Ordering of Gapped DNA
Authors: Kodikara Sineth G. , Gleeson James , Jakli Antal , Sprunt Samuel , Balci Hamza
Published: November 2024

We investigate the impact of poly-adenine (poly-A) sequences on the type and stability of liquid crystalline (LC) phases formed by concentrated solutions of gapped DNA (two duplex arms bridged by a flexible single strand) using synchrotron small angle X-ray scattering and polarizing optical microscopy. While samples with mixed sequence form layered (smectic) phases, poly-A samples demonstrate a columnar phase at lower temperatures (5-35 °C), not previously observed in GDNA samples, and a smectic-B phase of exceptional stability at higher temperatures (35-65 °C). We present a model that connects formation of these LC phases with the unique characteristics of poly-A sequences, which manifest in various biological contexts, including DNA condensation and nucleosome formation.
Unravelling the bottom-up and top-down control of a worldwide chestnut tree pest invader through integrative ecological genomics
Authors: Zitoun Jean-Loup , Rousseau Raphaël , Bertrand Joris , Toulza Eve , Rosalie Martin , Gourbière Sébastien
Published: November 2024

Biological invasions have become a major threat to all agro-ecosystems. Estimating the bottom-up and top-down forces controlling the spread of invasive insects is a key challenge to lessen their burden on crops, forestry, and biodiversity. We combined ecological, metabarcoding and population genomics analyses with an integrative modelling of the invasion of a global insect pest to identify the impacts of its chestnut tree resource, natural enemies and biological control agent in Eastern Pyrenees. The host tree frequency and genomic variation associated with common resistance pathways had effects 4-10 times greater than the native hyperparasite community on the pest’s invasion potential (R0). The >90% field rates of hyperparasitism by the control agent and the associated 80% reduction in pest infestation are likely to be deceptive as our modelling consistently predicts their long-term coexistence with periodic re-emergences. Such a persistent ‘co-invasion’ scenario calls for a thorough assessment of the impact of these global pest and control agent on natural forest ecosystems.
FAK inhibition suppresses breast cancer progression via DNA methylation-mediated DAB2 gene reactivation
Authors: Murphy James M. , Jeong Kyuho , Ahn Eun-Young Erin , Lim Ssang-Taek Steve
Published: November 2024

Epigenetic silencing of tumor suppressor genes is one of the main drivers of tumor progression. Without these tumor suppressors to reduce proliferation, tumor cells proliferate unchecked. Focal adhesion kinase (FAK) is a tyrosine kinase which is often upregulated in various tumors and promotes cell proliferation and migration. Recent studies have demonstrated that pharmacological or genetic FAK inhibition can reduce suppressive DNA methylation in vascular cells. Mechanistically, this is through nuclear FAK-mediated ubiquitination and proteasomal degradation of DNA methyltransferase 3A (DNMT3A). Treatment of breast cancer cell lines with FAK inhibitor (FAK-I) was able to reduce both FAK activity and DNMT3A protein expression. Further, global DNA methylation was reduced in breast cancer cell lines treated with FAK-I. This decrease in DNA methylation was correlated with decreased cell proliferation. We further showed that FAK-I reduced DNMT3A expression in breast cancer cells and that treatment with the proteasome inhibitor MG132 prevented loss of DNTM3A protein stability. To identify how FAK-I and DNMT3A loss could reduce breast cancer cell growth we compared RNA sequencing data from breast cancer cells treated with or without FAK-I or in shRNA DNMT3A knockdown. We have identified a potential tumor suppressor, DAB2, as being regulated by the nuclear FAK-DNMT3A axis. DAB2 is often downregulated in cancers and has been shown to play a vital role in switching TGFβ signaling from proliferative to apoptotic by altering TGFβRI binding partners. Immunoblotting and immunostaining indeed revealed that FAK-I and shDNMT3A could induce DAB2 protein expression. Further, FAK-I treatment showed efficacy in reducing tumor growth in vivo using the murine 4T1 tumor model. Immunostaining of 4T1 tumors showed FAK-I decreased DNMT3A, DNA methylation (5-methylcytosine, 5-mC), and increased DAB2 expression. Taken together, these data suggest that nuclear FAK-mediated regulation of DNMT3A can alter the epigenetic landscape and induce tumor suppressor gene expression.
Ascitic fluid protects against ferroptosis and enables the peritoneal spread of ovarian cancer
Authors: Setayeshpour Yasaman , Chen Ssu-Yu , Dayanidhi Divya L. , Lee Yunji , Federico Chiara , Aristizabal-Henao Juan J. , Wu Jianli , Lin Chao-Chieh , Mestre Alexander A. , Kiebish Michael A. , Berchuck Andrew , Hsu David S. , Huang Zhiqing , Murphy Susan K. , Chi Jen-Tsan
Published: November 2024

One of the most common sites of metastasis in ovarian cancer (OVCA) is the peritoneum. Often, this spread is accompanied by the accumulation of a fluid called ascites in the peritoneal cavity. Despite its common occurrence in metastatic OVCA patients, ascites and its influence on the peritoneal spread of OVCA are poorly understood. Interestingly, OVCA cells are vulnerable to ferroptosis, a type of cell death caused by lipid peroxidation. Hence, how these ferroptosis-sensitive OVCA cells persist in their spread to the peritoneum remains unknown. Here, we show that ascites robustly protects OVCA cells and patient-derived organoids against ferroptosis and enhances the peritoneal spread of OVCA cells in mice. Mechanistically, ascites downregulates the mitochondrial enzyme, 3-hydroxy-3-methylglutaryl-CoA synthase 2 (HMGCS2), which contributes to an increase in lipid droplets. Additionally, upon ferroptosis induction, ascites represses the upregulation of the transferrin receptor,TFRC, thereby decreasing cellular labile iron levels. Furthermore, we show that lipid-lowering fibrates reverse cellular changes induced by ascites, and they attenuate the peritoneal spread of OVCA cells in mice. Our findings implicate the importance of ascites in ferroptosis protection and the peritoneal spread of OVCA, and they suggest that targeting the ferroptosis protection by ascites may present a novel therapeutic approach to limit OVCA metastasis.
Th1 cells are critical tissue organizers of myeloid-rich perivascular activation niches
Authors: Bala Noor , McGurk Alexander , Carter Evan M. , Sidhu Ikjot , Niak Shruti , Leddon Scott A. , Fowell Deborah J.
Published: November 2024

Aggregating immune cells within perivascular niches (PVN) can regulate tissue immunity in infection, autoimmunity and cancer. How cells are assembled at PVNs and the activation signals imparted within remain unclear. Here, we integrate dynamic time-resolvedin vivoimaging with a novel spatially-resolved platform for microanatomical interrogation of transcriptome, immune phenotype and inflammatory mediators in skin PVNs. We uncover a complex positive-feedback loop within CXCL10+PVNs that regulates myeloid and Th1 cell positioning for exchange of critical signals for Th1 activation. Th1 cells spend ∼24h in the PVN, receiving initial peripheral activation signals, before redeploying to the inflamed dermal parenchyma. Niche-enriched, CCR2-dependent myeloid cells were critical for Th1 IFNγ-production. In turn, PVN instructional signals enabled Th1s to orchestrate PVN assembly by CXCR2-dependent intra-tissue myeloid cell aggregation. The results reveal a critical tissue organizing role for Th1s, gained rapidly on tissue entry, that could be exploited to boost regional immunity.

HIGHLIGHTS

Perivascular niche (PVN): myeloid hubs in inflamed mouse and healthy human skin

Th1 cells enter, get activated, and leave the PVN within first 24h of tissue entry

Antigen-specific signals in the PVN promote the tissue organizing functions of Th1s

Th1 cells assemble the PVN via CXCR2-dependent myeloid cell aggregation
Leg immobilization and subsequent recovery resistance training affect skeletal muscle angiogenesis related markers in young healthy adults regardless of prior resistance training experience
Authors: McIntosh Mason C. , Michel J. Max , Godwin Joshua S. , Plotkin Daniel L. , Anglin Derick A. , Mattingly Madison L. , Agyin-Birikorang Anthony , Kontos Nicholas J. , Baweja Harsimran S. , Stock Matt S. , Mobley C. Brooks , Roberts Michael D.
Published: November 2024

We recently reported that resistance trained (T, n=10) and untrained (UT, n=11) young adults experience vastus lateralis (VL) muscle atrophy following two weeks of disuse, and 8 weeks of recovery resistance training (RT) promotes VL hypertrophy in both participant cohorts. However, angiogenesis targets and muscle capillary number were not examined and currently no human studies that have sought to determine if disuse followed by recovery RT affects these outcomes. Thus, we examined whether disuse and/or recovery RT affected these outcomes. All participants underwent two weeks of left leg immobilization using locking leg braces and crutches followed by eight weeks (3d/week) of knee extensor focused progressive RT. VL biopsies were obtained at baseline (PRE), immediately after disuse (MID), and after RT (POST). Western blotting was used to assay angiogenesis markers and immunohistochemistry was performed in 16/21 participants to determine type I and II muscle fiber capillary number. Significant main effects of time (p<0.05) were observed for protein levels of VEGF (MID<POST), VEGFR2 (PRE&MID<POST), TSP-1 (PRE<POST), TIMP1 (MID<POST), phosphorylated/pan eNOS (Ser1177) (POST<PRE), and pan eNOS (PRE<POST). VEGFR2 exhibited a training status*time (p=0.018), but no differences existed between T and UT at any time point. A significant main effect of time was observed for type II fiber capillary number (PRE<POST), and type II fiber cross-sectional area (fCSA) increased from MID to POST (+25%, p<0.001) and PRE to POST (+20%, p=0.019). No significant correlations exist for percentage changes in type II fiber capillary number and type II fCSA from PRE-to-MID (r= 0.020), MID-to-POST (r= 0.392), or PRE-to-POST (r= −0.120) across all participants (p>0.100). Although disuse and recovery RT affect skeletal muscle angiogenesis-related protein targets, prior training history does not differentially affect these outcomes.

NEW AND NOTEWORTHY

This is the first study to examine how limb immobilization and recovery resistance training affect molecular outcomes related to angiogenesis in younger adults with or without a prior training history. Regardless of resistance training history, the molecular responses are largely similar between participant cohorts and is suggestive of a reduced (pre-mid) and increased (mid-post) angiogenic response, with disuse and subsequent recovery resistance training.
Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes
Authors: Aroney Samuel T. N. , Newell Rhys J. P. , Tyson Gene W. , Woodcroft Ben J.
Published: November 2024

Recovery of microbial genomes from metagenomic datasets has provided genomic representation for hundreds of thousands of species from diverse biomes. However, low abundance microorganisms are often missed due to insufficient genomic coverage. Here we present Bin Chicken, an algorithm which substantially improves genome recovery through automated, targeted selection of metagenomes for coassembly based on shared marker gene sequences derived from raw reads. Marker gene sequences that are divergent from known reference genomes can be further prioritised, providing an efficient means of recovering highly novel genomes. Applying Bin Chicken to public metagenomes and coassembling 800 sample-groups recovered 77,562 microbial genomes, including the first genomic representatives of 6 phyla, 41 classes, and 24,028 species. These genomes expand the genomic tree of life and uncover a wealth of novel microbial lineages for further research.
Bridging the Python Training Gap for Bioscientists in Brazil: Improvements and Challenges
Authors: Crestana Gustavo Schiavone , da Silva Batista Ubiratan , Gonçalves Funnicelli Michelli Inácio , Braga Larissa Graciano , Zuvanov Luíza , Bizarria Rodolfo , de Sousa Raissa Melo , Narciso Ferreira Pedro Henrique , Winck Flavia Vischi , Alves Margarido Gabriel Rodrigues , de Mello Varani Alessandro , Riaño-Pachón Diego Mauricio , Corrêa dos Santos Renato Augusto
Published: November 2024

The rapid evolution of high-throughput technologies in biosciences has generated diverse and voluminous datasets, requiring bioscientists to develop data manipulation and analysis skills. Python, known for its versatility and powerful libraries, has become a crucial tool for managing these datasets. However, there is a significant lack of programming training for bioscientists in many countries. To address this knowledge gap among scientists in Brazil, the Brazilian Python Workshop for Biological Data was introduced several years ago, focusing on basic programming concepts and data handling techniques using popular Python libraries. Despite the progress and positive feedback from earlier editions, challenges persisted, necessitating continuous adaptation and improvement to meet the evolving needs of bioscientists.This work describes the advancements made in the 2021 and 2022 editions of the workshop and discusses new suggestions for its ongoing enhancement. Key innovations were introduced in the workshop structure and coordination, including the creation of new committees and the establishment of a code of conduct. Feedback forms were updated to enable real-time adjustments during the event, improving its overall effectiveness. The workshop also expanded its reach by increasing geographical diversity among participants. New didactic strategies, such as pair-teaching, code clubs, and the integration of information and communication technologies (ICTs), were implemented to enhance learning outcomes. Programming best practices and scientific reproducibility were emphasized through talks and hands-on activities, guided by PEP8 conventions. Furthermore, efforts to enhance scientific dissemination were intensified, with an increased presence on social media and participation in international scientific events and communication networks. Finally, we present updated recommendations for students, researchers, and educators interested in organizing and promoting similar events, building on those previously described.
Pathogenicity determinant protein E is aFrancisellatype VI secretion system effector protein that modulates host death
Authors: Adams Nicole , Hulvey Danielle , Khalid Nimra , Burne Alexandra , Brown Mary B. , Eshraghi Aria
Published: November 2024

Francisella tularensisis a highly pathogenic Gram-negative intracellular bacterial pathogen and the etiologic agent of tularemia, a fatal zoonotic disease that poses a threat to global public health.F. tularensisvirulence is mediated by genes on theFrancisellapathogenicity island (FPI), which encodes a unique contractile secretion apparatus with functional and structural similarity to bacterial type VI secretion systems (T6SSs). T6SSs can inject effector proteins into host cells to facilitate invasion, intracellular proliferation, and pathogenesis; however, the identity and function ofFrancisellaeffectors are still unclear. In this study, we measured T6SS activity in a series of FPI deletion mutants to identify genes that are required for core apparatus activity. We found that Pathogenicity Determinant Protein E (PdpE) is not required for secretion of T6SS substrates or intramacrophage growth. Instead, PdpE forms a complex with another T6SS-secreted effector, PdpC, and limits death of infected host cells by attenuating the macrophage type I interferon response. Importantly, a ΔpdpEmutant more rapidly induces death in an established invertebratein vivomodel forFrancisellainfection. These data define the role of a previously uncharacterized substrate of theFrancisellaT6SS and provide new insights into host-Francisellainteraction.
Saccharibacteria deploy two distinct Type IV pili, driving episymbiosis, host competition, and twitching motility
Authors: Grossman Alex S. , Lei Lei , Botting Jack M. , Liu Jett , Nahar Nusrat , Souza João Gabriel S. , Liu Jun , McLean Jeffrey S. , He Xuesong , Bor Batbileg
Published: November 2024

All cultivated Patescibacteria, or CPR, exist as obligate episymbionts on other microbes. Despite being ubiquitous in mammals and environmentally, molecular mechanisms of host identification and binding amongst ultrasmall bacterial episymbionts are largely unknown. Type 4 pili (T4P) are well conserved in this group and predicted to facilitate symbiotic interactions. To test this, we targeted T4P pilin genes in SaccharibacteriaNanosynbacter lyticusstrain TM7x to assess their essentiality and roles in symbiosis. Our results revealed thatN. lyticusassembles two distinct T4P, a non-essential thin pili that has the smallest diameter of any T4P and contributes to host-binding, episymbiont growth, and competitive fitness relative to other Saccharibacteria, and an essential thick pili whose functions include twitching motility. Identification of lectin-like minor pilins and modification of host cell walls suggest glycan binding mechanisms. Collectively our findings demonstrate that Saccharibacteria encode unique extracellular pili that are vital mediators of their underexplored episymbiotic lifestyle.
Sirt5 preserves cardiac function in ischemia-reperfusion injury by inhibiting ANT2 lactylation
Authors: Li Simeng , Shen Siman , Hong Yongfang , Ding Kun , Chen Suyun , Chen Jianning , Wang Changsen , Wen Yaofeng , Mo Guixi , Yu Lili , Shi De-Li , Zhang Liangqing
Published: November 2024

Myocardial ischemia-reperfusion (IR) injury is the most common type of heart disease. IR-disrupted mitochondrial homeostasis affects heart energy metabolism and function, but the mechanism remains poorly understood. Here we report a cardioprotective role of the mitochondrial protein Sirt5 in a mouse model of cardiac IR injury. The down-regulation of Sirt5 in IR-injured heart is associated with an increased protein lactylation and impaired mitochondrial function. Overexpression ofSirt5alleviates, whereas conditional knockout ofSirt5aggravates, mitochondrial damage and cardiac injury. Mechanistically, Sirt5 interacts with the inner mitochondrial membrane protein adenine nucleotide translocase 2 (ANT2), inhibiting its lysine lactylation to promote its association with the outer mitochondrial membrane protein voltage-dependent anion-selective channel 1 (VDAC1). Lactylation-resistant ANT2 efficiently complexes with VDAC1 and improves cardiac function after injury. Therefore, we uncover a Sirt5-regulated interaction of ANT2 and VDAC1 in maintaining mitochondrial homeostasis, highlighting the potential of targeting ANT2 lactylation as a therapeutic strategy in the treatment of cardiac injury.

Teaser

Sirt5 promotes the interaction of mitochondrial proteins to protect mitochondrial homeostasis and improve heart function in ischemia-reperfusion injury.
Revealing the Ultrastructure of LiveCandida albicansusing Stimulated Emission Depletion Microscopy
Authors: Baxter Katherine J. , Rooney Liam M. , Foylan Shannan , Gould Gwyn W. , McConnell G.
Published: November 2024

Candida albicans, a commensal fungal pathogen, is a major cause of opportunistic infections in immunocompromised individuals. Understanding its cellular structures and pathogenic mechanisms is critical for developing targeted antifungal therapies. Stimulated emission depletion (STED) microscopy enables nanoscale visualization of cellular components, surpassing the diffraction limit of conventional light microscopy. In this study, we employed STED microscopy to investigate the ultrastructural organization ofC. albicansin live specimens. We showed that dyes commonly used in STED microscopy of mammalian cells are ineffective for the study ofC. albicans, and we showed the utility of Nile Red staining for visualising the organisation of dynamic cellular components, including tracking of lipid droplets, using time-lapse recording in experiments exceeding 12 hours. STED microscopy offered more than a two-fold improvement in resolution compared to confocal laser scanning microscopy applied to the same specimens with negligible photobleaching. This study demonstrates the utility of STED microscopy in advancing our understanding ofC. albicansbiology at the nanoscale, providing a platform for future investigations into fungal pathogenicity and antifungal development.

GRAPHICAL ABSTRACT

We present an optimised fluorescence staining method for super-resolution live-cell imaging ofCandida albicans, using Stimulated Emission Depletion (STED) microscopy to resolve and track sub-cellular structures. We compare the performance of conventional confocal laser scanning microscopy (CLSM) to STED imaging, providing a three-fold resolution improvement beyond the diffraction limit. Finally, we perform live cell tracking to visualise and quantify the trajectories of multiple sub-diffraction limit-sized objects over a period of 12 hours, demonstrating the potential for live-cell STED imaging ofCandidato visualise key processes involved in pathogenesis, drug resistance and infection.
HsbA represses stationary phase biofilm formation inPseudomonas putida
Authors: Pulido-Sánchez Marta , Montero-Beltrán Elisa , López-Sánchez Aroa , Govantes Fernando
Published: November 2024

Pseudomonas putidabiofilm growth is associated to nutrient-sufficient conditions and biofilm dispersal is induced by nutrient starvation, signaled by the stringent response-associated nucleotide alarmone (p)ppGpp. We have used transcriptomic analysis to show that (p)ppGpp regulates thehsbAR-hptBgene cluster, encoding components of a phosphorelay pathway and an anti-α factor antagonist, andcfcR, encoding a response regulator with diguanylate cyclase (DGC) activity. Transcription ofhsbAR-hptBandcfcRis RpoS-dependent and induced by stationary phase and the stringent response. A ΔhsbAmutant resumed biofilm formation after dispersal in late stationary phase, stimulated liquid-air biofilm formation and increased Congo Red adsorption. All these phenotypes were traced down to increased c-di-GMP levels in stationary phase dependent on the activity of CfcR and its cognate sensor kinase, CfcA. HsbA was reversibly phosphorylated by the combined action of HptB and HsbR HsbA phosphorylation conditioned its interaction with CfcR and CfcA and the intracellular distribution of the three proteins, but did not greatly influence biofilm regulation. Our results support a model in which HsbA forms a complex with CfcR to inhibit its DGC activity regardless of its phosphorylation state. Upon HsbA dephosphorylation, this complex is recruited to the cell membrane by CfcA to strengthen the inhibitory effect. This system contributes to biofilm dispersal by denying biofilm formation, but allows quick onset ofde novobiofilm formation in response to physiological cues that release HsbA inhibition to restore CfcR DGC activity.
Evaluating bacteriophage impact on gut microbiome composition in broad-nosed pipefish (Syngnathus typhle)
Authors: Parker Jamie , Marten Silke-Mareike , Rajkov Jelena , Theising Franziska I. , Dubin Arseny , Roth Olivia
Published: November 2024

Bacteriophages play a crucial role in shaping microbial community dynamics in marine systems and have the potential to stimulate surges in pathogenic bacteria facilitating disease outbreaks. Notwithstanding, bacteriophages also serve as valuable biocontrol agents, underscoring their huge potential for aquaculture therapy treatments. Insights into the intricate tripartite interplay upon an infection with a virulent bacterium, its specific phages and the eukaryotic microbiome could improve our understanding of how bacteria-phage interactions behave in a natural microbial system. This investigation assessed the influence of a virulentVibrio alginolyticus(K01M1) infection, in tandem with lytic (фSt2) and filamentous (фK04M1)Vibrio-specific phages, on the broad-nosed pipefish (Syngnathus typhle) gut microbiome using 16S rRNA amplicon sequencing and non-intrusive gastric swabbing. Microbial communities and diversity metrics were not permanently impacted byVibrioand phage introductions, while the different infection regimes shapedVibrio-specific dynamics. In the filamentous phage andVibrio-only treatments,V. alginolyticusabundances spiked 12 hours post-ingestion. In contrast,V. alginolyticusnumbers in the lytic phage and control treatment were significantly reduced, suggesting phage activity and specific elimination of the introduced bacteria. Assisted by relative true-gut tissue samples, a newly implemented non-intrusive swabbing method was successful at discerning the activity of two contrasting phages and supports previous work that encourages the use of фSt2 in bacteriophage treatments. IdentifyingVibrio-specific phages with similar positive characteristics could be beneficial for the aquaculture trade, which is currently heavily impacted by the antibiotic crisis.