bluuebunny/crossref_metadata_2025 huggingface dataset:
Variation in the Spectrum of New Mutations among Inbred Strains of Mice
Authors: López-Cortegano Eugenio , Chebib Jobran , Jonas Anika , Vock Anastasia , Künzel Sven , Tautz Diethard , Keightley Peter D
Published: August 2024

The mouse serves as a mammalian model for understanding the nature of variation from new mutations, a question that has both evolutionary and medical significance. Previous studies suggest that the rate of single-nucleotide mutations (SNMs) in mice is ∼50% of that in humans. However, information largely comes from studies involving the C57BL/6 strain, and there is little information from other mouse strains. Here, we study the mutations that accumulated in 59 mouse lines derived from four inbred strains that are commonly used in genetics and clinical research (BALB/cAnNRj, C57BL/6JRj, C3H/HeNRj, and FVB/NRj), maintained for eight to nine generations by brother–sister mating. By analyzing Illumina whole-genome sequencing data, we estimate that the average rate of new SNMs in mice is ∼μ = 6.7 × 10−9. However, there is substantial variation in the spectrum of SNMs among strains, so the burden from new mutations also varies among strains. For example, the FVB strain has a spectrum that is markedly skewed toward C→A transversions and is likely to experience a higher deleterious load than other strains, due to an increased frequency of nonsense mutations in glutamic acid codons. Finally, we observe substantial variation in the rate of new SNMs among DNA sequence contexts, CpG sites, and their adjacent nucleotides playing an important role.
Suppression of SMXL4 and SMXL5 confers enhanced thermotolerance through promoting HSFA2 transcription in Arabidopsis
Authors: Pan Yajie , Yu Bofan , Wei Xin , Qiu Yuping , Mao Xin , Liu Yuelin , Yan Wei , Linghu Qianyan , Li Wenyang , Guo Hongwei , Tang Zhonghua
Published: August 2024

Identifying the essential factors and underlying mechanisms regulating plant heat stress (HS) responses is crucial for mitigating the threat posed by HS on plant growth, development, distribution, and productivity. In this study, we found that the Arabidopsis (Arabidopsis thaliana) super-killer2 (ski2) dicer-like4 (dcl4) mutant, characterized by RNA processing defects and the accumulation of abundant 22-nt small interfering RNAs derived from protein-coding transcripts, displayed significantly increased expression levels of HS-responsive genes and enhanced thermotolerance. These traits primarily resulted from the suppression of SMAX1-LIKE4 (SMXL4) and SMXL5, which encode 2 putative transcriptional regulators that belong to the SMXL protein family. While smxl4 and smxl5 single mutants were similar to wild type, the smxl4 smxl5 double mutant displayed substantially heightened seedling thermotolerance. Further investigation demonstrated that SMXL4 and SMXL5 repressed the transcription of HEAT-SHOCK TRANSCRIPTION FACTOR A2 (HSFA2), encoding a master regulator of thermotolerance, independently of ethylene-response factor–associated amphiphilic repression motifs. Moreover, SMXL4 and SMXL5 interacted with HSFA1d and HSFA1e, central regulators sensing and transducing HS stimuli, and antagonistically affected their transactivation activity. In addition, HSFA2 directly bound to the SMXL4 and SMXL5 promoters, inducing their expression during recovery from HS. Collectively, our findings elucidate the role of the SMXL4/SMXL5–HSFA2 regulatory module in orchestrating plant thermotolerance under HS.
Can digital technology drive the integration of sports and health industries? Evidence from global businesses
Authors: Li Jiannan
Published: August 2024

The integration in sports and health industries is attracting increasing research attention, however, there is less empirical evidence about role of digital technology adoption in affecting the industrial integration. This article extends relevant research from intra-state to including cross-board cases by combing data of merger and acquisition (M&A) in global sports and health industries as well as the country-level digital adoption index. It is shown that the integration in sports and health industries is positively associated with the digital technology adoption that the country in which the acquiror firm is located. Thus, it is beneficial for policymakers to promote the digital technology use when aiming to encourage the spontaneous industrial integration in sports and health industries.
Changes of cerebral structure and perfusion in subtypes of systemic sclerosis: a brain magnetic resonance imaging study
Authors: Tong Xinyu , He Huilin , Xu Shihan , Shen Rui , Ning Zihan , Zeng Xiaofeng , Wang Qian , He Zuo-Xiang , Xu Dong , Zhao Xihai
Published: August 2024

Objectives

The characteristics of brain impairment in different subtypes of systemic sclerosis (SSc) (dcSSc, diffuse cutaneous SSc; lcSSc, limited cutaneous SSc) remain unclear. This study aimed to characterize cerebral structure and perfusion changes in different subtypes of SSc patients using magnetic resonance (MR) imaging.

Methods

Seventy SSc patients (46.0 ± 11.7 years, 62 females) and 30 healthy volunteers (44.8 ± 13.7 years, 24 females) were recruited and underwent brain MR imaging and Montreal Cognitive Assessment (MoCA) test. Gray matter (GM) volumes were measured using voxel-based morphometry analysis on T1-weighted images. Voxel-based and regional cerebral blood flow (CBF) was calculated on arterial spin labelling images. The cerebral structural and perfusion measurements by MR imaging were compared among dcSSc, lcSSc and healthy subjects using one-way ANOVA. The correlations between clinical characteristics and MR imaging measurements were also analysed.

Results

The dcSSc patients exhibited a significant reduction in GM volume in the para-hippocampal region (cluster P < 0.01, FWE corrected) compared with healthy volunteers. Whereas SSc patients, particularly lcSSc patients, showed elevated CBF in cerebellum, insula, cerebral cortex and subcortical structures (regional analyses: all P < 0.05; voxel-based analyses: cluster P < 0.01, FWE corrected). Furthermore, clinical characteristics of modified Rodnan skin score (mRSS) (r value ranged from −0.29 to −0.45), MoCA scores (r = 0.40) and anti-nuclear antibody (ANA) positivity (r = −0.33) were significantly associated with CBF in some regions (all P < 0.05).

Conclusion

The manifestations of brain involvement vary among different subtypes of SSc. In addition, severe skin sclerosis may indicate higher risk of brain involvement in SSc patients.
Escin induces cell death in human skin melanoma cells through apoptotic mechanisms
Authors: Vejselova Sezer Canan
Published: August 2024

Natural products based on their significant anti-cancer potencies have been used in cancer treatment. A natural blend of triterpenoid saponins derived from the horse chestnut (Aesculus hippocastanum L.), has been investigated in various diseases based on its main active ingredient escin. Herein, we examined the potential antiproliferative, proapoptotic, and cytotoxic activities of escin on human skin melanoma (CHL-1) cells. Cytotoxicity of escin was determined by MTT assay. Morphological changes were detected by confocal microscopy and ultrastructural changes by transmission electron microscopy studies. Phosphatidylserine translocation assay, Bcl-2 activation assessment, and oxidative stress analysis were used to determine the cell death mode of the cells. The results showed that escin reduced cell viability in a dose-dependent manner within 24 h of exposure and was highly cytotoxic at lower concentrations (IC50 value 6 μg/mL). Escin inactivated Bcl-2 signaling and triggered apoptosis by increasing the reactive oxygen species and by causing morphological and ultrastructural changes that implicate to the proapoptotic activity. Escin has been found to exert high potential for an anti-cancer drug following further in vitro and in vivo investigations.
Stronger Together: Group Self-Care Goal-Setting to Support Graduate Nursing Students’ Resilience, Wellness, and Manage Burnout
Authors: Phillips Kathryn E. , Corcoran Karen J.
Published: August 2024

Graduate students are faced with many stressors, including school, work, and home roles. They may not have the self-care skills and support to manage the increased stress from school. Self-care goal setting check-ins were implemented in a graduate course to support students’ stress management. Student resilience levels, wellness, and burnout were moderate. Students indicated the check-ins were helpful, yet still found challenges in completing self-care. They also stated less assignments and integrating more wellness into the curriculum would be helpful in supporting their self-care goals. Nursing educators can impact student wellness by providing skills and support in the curriculum.
Restoring Psychiatric Mental Health APRN Roles: A Report of Innovations in Workforce Development Design Supported by Salutogenic Solutions and an Enduring Educational Frame, Part One
Authors: Libster Martha M. , Evers Leslie
Published: August 2024

BACKGROUND

The change from a clinical nurse specialist to nurse practitioner model has significantly affected graduate education and practice because of emphasis on the dominant biomedical prescriber role, marginalizing the nurse-psychotherapy and consultation-liaison roles fundamental to quality psychiatric advanced practice nursing practice.

AIM/METHOD

We report on a four-year Workforce Development Project supported by an academic-practice partnership to restore formation and skill building of the marginalized roles. Part One focuses on program design, the curriculum for nine specialty courses, and the teaching and learning community approach that promotes engagement, faculty commitment, and preceptor recruitment and retention; the creative faculty staffing model is described.

RESULTS

The educational frame described includes highlights of teaching/learning strategies drawn from the history of professional formation curriculum rooted in salutogenesis and belonging science, existentialism, solution-focused therapy, modeling and role modeling theory, and Peplau’s Interpersonal Relations.

CONCLUSION

There is significant interest and commitment to learning the nurse-psychotherapist and consultation-liaison roles.
Retrospective Analysis of Fibromyalgia
Authors: Lahat-Birka Noa , Boussi-Gross Rahav , Ben Ari Amichai , Efrati Shai , Ben-David Shiri
Published: August 2024

Objectives:

This study aimed to explore the diverse etiological factors associated with fibromyalgia (FM), including trauma, stress, infections, and head injuries, and investigate their potential correlation with FM severeness manifestation, aiming to discern FM subgroups.

Methods:

The study was a retrospective analysis, conducted with data of 182 FM patients. Each patient’s medical history was analyzed to identify a primary etiological event preceding FM. Following this, correlations were examined between each etiology group and different measurements, such as the impact of FM on overall function, widespread pain, depression, anxiety, and cognitive impairments. Cluster analysis was conducted to distinguish between groups of symptoms and functioning.

Results:

Contrary to the initial hypothesis, no direct association between a specific trigger and symptom manifestation was identified. However, cluster analyses revealed 2 distinct profiles based on symptom severity. Emotional trauma emerged as a potential contributor to heightened symptom severity, impacting overall function and cognitive abilities.

Discussion:

Emotional trauma and stress are crucial factors exacerbating FM symptoms, highlighting the importance of managing these elements in FM patients. This study underscores the complexity of FM, necessitating a nuanced understanding of its etiology and symptomatology. We recommend a multidisciplinary treatment approach that includes assessing and addressing chronic stress and trauma and incorporating stress management interventions to improve patient outcomes.
Magnesium lithospermate B enhances the potential of human-induced pluripotent stem cell-derived cardiomyocytes for myocardial repair
Authors: Fan Chengming , Qin Kele , Iroegbu Chukwuemeka Daniel , Xiang Kun , Gong Yibo , Guan Qing , Wang Wenxiang , Peng Jun , Guo Jianjun , Wu Xun , Yang Jinfu
Published: August 2024

Background:

We previously reported that activation of the cell cycle in human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) enhances their remuscularization capacity after human cardiac muscle patch transplantation in infarcted mouse hearts. Herein, we sought to identify the effect of magnesium lithospermate B (MLB) on hiPSC-CMs during myocardial repair using a myocardial infarction (MI) mouse model.

Methods:

In C57BL/6 mice, MI was surgically induced by ligating the left anterior descending coronary artery. The mice were randomly divided into five groups (n = 10 per group); a MI group (treated with phosphate-buffered saline only), a hiPSC-CMs group, a MLB group, a hiPSC-CMs + MLB group, and a Sham operation group. Cardiac function and MLB therapeutic efficacy were evaluated by echocardiography and histochemical staining 4 weeks after surgery. To identify the associated mechanism, nuclear factor (NF)-κB p65 and intercellular cell adhesion molecule-1 (ICAM1) signals, cell adhesion ability, generation of reactive oxygen species, and rates of apoptosis were detected in human umbilical vein endothelial cells (HUVECs) and hiPSC-CMs.

Results:

After 4 weeks of transplantation, the number of cells that engrafted in the hiPSC-CMs + MLB group was about five times higher than those in the hiPSC-CMs group. Additionally, MLB treatment significantly reduced tohoku hospital pediatrics-1 (THP-1) cell adhesion, ICAM1 expression, NF-κB nuclear translocation, reactive oxygen species production, NF-κB p65 phosphorylation, and cell apoptosis in HUVECs cultured under hypoxia. Similarly, treatment with MLB significantly inhibited the apoptosis of hiPSC-CMs via enhancing signal transducer and activator of transcription 3 (STAT3) phosphorylation and B-cell lymphoma-2 (BCL2) expression, promoting STAT3 nuclear translocation, and downregulating BCL2-Associated X, dual specificity phosphatase 2 (DUSP2), and cleaved-caspase-3 expression under hypoxia. Furthermore, MLB significantly suppressed the production of malondialdehyde and lactate dehydrogenase and the reduction in glutathione content induced by hypoxia in both HUVECs and hiPSC-CMs in vitro.

Conclusions:

MLB significantly enhanced the potential of hiPSC-CMs in repairing injured myocardium by improving endothelial cell function via the NF-κB/ICAM1 pathway and inhibiting hiPSC-CMs apoptosis via the DUSP2/STAT3 pathway.
The reduced function allele SLCO1B1 c.521T>C is of no practical relevance for the renal graft function over the first post-transplant year in patients treated with mycophenolic acid
Authors: Nađ Škegro Sandra , Penezić Luka , Šimičević Livija , Hudolin Tvrtko , Kaštelan Željko , Božina Nada , Trkulja Vladimir
Published: August 2024

Objective

It is unclear whether renal transplant recipients treated with mycophenolic acid (MPA) who carry the reduced-function allele at polymorphism SLCO1B1 c.521T>C differ from their wild-type peers regarding renal outcomes and tolerability. We aimed to estimate the effect of this polymorphism on the graft function (estimated glomerular filtration rate, eGFR) over the first 12 post-transplant months in patients on MPA-based maintenance immunosuppression.

Methods

In a 12-month observational cohort study, consecutive adult patients were repeatedly assessed for eGFR. The SLCO1B1 c.521C>T variant allele carriers (exposed) and wild-type subjects (controls) were balanced on a range of demographic, medical, and genetic variables at baseline, and eGFR trajectory was estimated with further adjustment for time-varying covariates. A subset of patients were assessed for exposure to MPA 5–7 days after the transplantation.

Results

The adjusted eGFR slopes from day 1 to day 28 (daily), and from day 28 to day 365 (monthly) were practically identical in exposed (n = 86) and control (n = 168) patients [geometric means ratios (GMR) = 0.99, 95% confidence interval (CI) = 0.92–1.06 and GMR = 0.98, 0.94–1.01, respectively]. The rates of adverse renal outcomes and possible MPA-related adverse effects were low, and similar in exposed and controls [rate ratios (RR) = 0.94, 0.49–1.84 and RR = 1.08, 0.74–1.58, respectively]. The pharmacokinetic analysis did not signal meaningful differences regarding exposure to MPA, overall (exposed n = 23, control n = 45), if cotreated with cyclosporine (n = 17 vs. n = 26) or with tacrolimus (n = 8 vs. n = 17).

Conclusions

In patients treated with MPA, variant allele SLCO1B1 c.521T>C appears of no practical relevance regarding the 12-month renal graft function, MPA safety and exposure to MPA at early steady-state.
Neutrophil extracellular traps induce intrahepatic thrombotic tendency and liver damage in cholestatic liver disease
Authors: Yu Muxin , Li Xiaowen , Xu Long , Zheng Chuwei , Pan Weiwei , Chen Hui , Liu Xiaoyu , Zhang Xianshan , Zhang Jinming
Published: August 2024

Background:

Cholestatic liver diseases induce local and systemic hypercoagulation, with neutrophil extracellular traps (NETs) serving as major drivers. These NETs have been linked to decreased liver function in patients with obstructive jaundice. However, the impact of NETs on liver hypercoagulation in cholestatic liver disease remains unknown.

Methods:

We utilized bile duct ligation to create experimental mice and analyzed NETs formation in the liver. Fibrin deposition, tissue factor expression, and inflammation in the liver were visualized through western blot and immunohistochemical techniques. LSECs were incubated with isolated NETs, and we detected endothelial procoagulant activity using coagulation protein production assays and measuring endothelial permeability. In both in vivo and in vitro settings, DNase I was applied to clarify the effect of NETs on intrahepatic hypercoagulability, hepatotoxicity, LSEC, and macrophage activation or injury.

Results:

Bile duct ligation mice exhibited significantly increased levels of NETs in liver tissue, accompanied by neutrophil infiltration, tissue necrosis, fibrin deposition, and thrombophilia compared to sham mice. Notably, NETs resulted in phosphatidylserine and tissue factor exposure on LSEC, enhancing coagulation Factor Xa and thrombin production. The enhanced procoagulant activity could be reversed by degrading NETs with DNase I. Additionally, NETs-induced permeability changes in LSECs, characterized by increased VE-cadherin expression and F-actin retraction, which could be rescued by DNase I. Meanwhile, NET formation is associated with KC activation and the formation of inflammatory factors.

Conclusions:

NETs promote intrahepatic activation of coagulation and inflammation, leading to liver tissue injury. Strategies targeting NET formation may offer a potential therapeutic approach for treating cholestatic liver disease.
Suicidal Ideation and Behaviors Among LGBTQ+ Adolescents and Young Adults Who Have Experienced Sexual Violence: A Scoping Review of the Literature
Authors: Allen Larissa , Zelazny Jamie
Published: August 2024

Introduction

The relationship between sexual violence (SV) experiences and suicidal ideation (SI) is known. However, when applied to lesbian, gay, bisexual, transgender, queer, and more (LGBTQ+) populations, the impact that experiences with SV have on the severity and magnitude of SI continues to be explored. A scoping review of the literature was conducted to summarize the current literature related to SI experienced by LGBTQ+ adolescents and young adults (AYAs) who have experienced SV.

Methods

Studies were found by searching electronic databases. To be included in the review, the study must have (a) been written in the English language, (b) been conducted in the United States, (c) presented empirical data, (d) been exclusively focused on LGBTQ+ AYAs, (e) focused on experiences with SV or have analyses separate from other types of violence, and (f) investigated suicidality as an outcome. All relevant studies published to date were included. Forty-one articles were retrieved for full-text review, of which five were determined to meet eligibility.

Results

LGBTQ+ AYAs were significantly associated with increased rates of SI compared with their cisgender heterosexual peers. LGBTQ+ AYAs were also associated with higher rates of SV victimization, ranging from intimate partner violence to previous child sexual abuse. Higher rates of depression were also associated with the population studied in each included article.

Conclusion

The relationship between SV and SI in this population is not well studied, as highlighted through this completed review. Targeting this knowledge gap through future research can lead to intervention development for this population niche.
Antimicrobial resistantSalmonellaspp. circulating in antibiotic-free organic pig farms of northern-Thailand
Authors: Tadee Pakpoom , Patchanee Prapas , Pascoe Ben , Sheppard Samuel K. , Meunsene Dethaloun , Tadee Phacharaporn
Published: August 2024

We investigated the prevalence ofSalmonellacirculating in local organic pig farms in northern Thailand and typed isolated clones to better understand the population structure of the underlyingSalmonellacontamination. In total, 112 samples from 11 organic pig farms were processed from October to December 2018.Salmonellawere detected in 9 farms with an overall prevalence of 25.0% (28/112). Prevalence detected in fecal, feeder, and boot swab samples was found to be 32.7% (17/53), 17.7% (6/34), and 20.0% (5/25), respectively. Of the 28 positive strains, SevenSalmonellaserotypes were identified, withS. Rissen being the most common (15/28; 53.6%). 89.3% (25/28), 78.6% (22/28) and 71.4% (20/28) of isolatedSalmonellawere resisted against tetracycline, ampicillin, and sulfamethoxazole-trimethoprim, respectively. From multilocus sequence typing (MLST) analysis, the phylogenetic tree suggests dissemination of specific clones within herds that share routes of pig transportation and point mutations in housekeeping genes within herds. A minimum spanning tree (MST) revealed thatSalmonellacontamination in organic pig farming is possibly linked with conventional farming. Based on the own results, strictly highly organic practices provide a safe alternative enhancing domestic consumer trust and improve public health safety.
Molecular and functional basis of a novel Amazonian Dark Earth Esterase 1 (Ade1) with hysteresis behavior and quorum-quenching activity
Authors: Vinces Tania Churasacari , Souza Anacleto Silva de , Carvalho Cecília F. , Teixeira Raphael D. , Bismara Beatriz Aparecida Passos , Vicente Elisabete J. , Pereira José O. , Souza Robson Francisco de , Yonamine Mauricio , Marana Sandro Roberto , Farah Chuck Shaker , Guzzo Cristiane R.
Published: August 2024

Amazon Dark Earth (ADE) soil is rich in organic compounds and its fertility has been associated with a high diversity of microorganisms. Herein, we investigate the biochemical and functional features of a novel esterase, Ade1, obtained from a metagenomic library of Amazonian Dark Earth soils of the Amazonian Rainforest, in Brazil. The esterases cleave ester bonds to form a carboxylic and an alcohol group. Esterases and lipases are enzymes found in almost all living organisms, demonstrating their biological relevance. We reported that Ade1 belongs to an α/β-hydrolase superfamily. We suggest that Ade1 is a moonlighting enzyme with hysteresis behavior and quorum-quenching activity, which may play a key role in the metabolism of a Gram-negative proteobacteria. In addition, molecular dynamics simulations reveal that the hysteresis behavior is directly associated with structural properties of the cap domain. Our findings reveal details of the molecular basis, catalytic and structural mechanisms of a novel α/β-hydrolase, which may be applied to other esterases of biotechnological, food, and/or pharmaceutical interest.

Abstract Figure
Methylation of Dual Specificity Phosphatase 4 Controls Cell Differentiation
Authors: Su Hairui , Jiang Ming , Senevirathne Chamara , Aluri Srinivas , Zhang Tuo , Guo Han , Xavier-Ferrucio Juliana , Jin Shuiling , Tran Ngoc-Tung , Liu Szu-Mam , Sun Chiao-Wang , Zhu Yongxia , Zhao Qing , Chen Yuling , Cable LouAnn , Shen Yudao , Liu Jing , Qu Cheng-Kui , Han Xiaosi , Klug Christopher A. , Bhatia Ravi , Chen Yabing , Nimer Stephen D. , Zheng Y. George , Iancu-Rubin Camelia , Jin Jian , Deng Haiteng , Krause Diane S. , Xiang Jenny , Verma Amit , Luo Minkui , Zhao Xinyang
Published: August 2024

A collection of signaling and epigenetic events needs to be orchestrated for normal development of hematopoietic lineages. While mitogen-activated protein (MAP) kinases (MAPKs) and multiple epigenetic modulators have been implicated in the megakaryocytic (Mk) cell differentiation, the underlying molecular mechanisms of signaling-epigenetic crosstalk remain unclear. MAPKs are in general inactivated by dual specificity phosphatases (DUSPs), whose activities are tightly regulated by various posttranslational modifications. Using knockdown screening and single-cell transcriptional analysis, we determined that DUSP4 is the phosphatase that inactivates p38 MAPK in hematopoietic cells and serves as a key regulator to promote Mk differentiation. With the nextgeneration Bioorthogonal Profiling of Protein Methylation technology for live cells, we identified DUSP4 as a PRMT1 substrate. Mechanistically, PRMT1-mediated Arg351 methylation of DUSP4 triggers its ubiquitinylation by HUWE1 (an E3 ligase) and then degradation, which results in p38 MAPK activation and inhibition of Mk differentiationin vitroandin vivo. Interestingly, the mechanistic axis of the DUSP4 degradation and p38 activation is also associated with a transcriptional signature of immune activation and thus argues immunological roles of Mk cells. Collectively, these results demonstrate a critical role of PRMT1-mediated posttranslational modification of DUSP4 in regulation of Mk differentiation and maturation. In the context of thrombocytopenia observed in myelodysplastic syndromes (MDS), we demonstrated that high levels of p38 MAPK and PRMT1 are associated with low platelet counts and adverse prognosis, while pharmacological inhibition of p38 MAPK or PRMT1 stimulates megakaryopoiesis in MDS samples. These findings provide novel mechanistic insights into the role of the PRMT1-DUSP4-p38 axis on Mk differentiation and present a targeting strategy for treatment of thrombocytopenia associated with myeloid malignancies such as MDS.
Major threats to a migratory raptor vary geographically along the eastern Mediterranean flyway
Authors: Oppel Steffen , Arkumarev Volen , Bakari Samuel , Dobrev Vladimir , Saravia Victoria , Adefolu Solomon , Sözüer Lale Aktay , Apeverga Paul Tersoo , Arslan Şafak , Barshep Yahkat , Bino Taulant , Bounas Anastasios , Çetin Turan , Dayyoub Maher , Dobrev Dobromir , Duro Klea , El-Moghrabi Laith , ElSafoury Hana , Endris Ahmed , Asswad Nabegh Ghazal , Harry Junior Hanson , Ivande Sam T , Jbour Sharif , Kapsalis Eleftherios , Kret Elzbieta , Mahamued Bruktawit A , Manu Shiiwua A , Mengistu Solomon , Moussa Zabeirou Abdoul Razack , Muhammad Sulaiman Inuwa , Nakev Slave , Ngari Alex , Onoja Joseph , Osta Maher , Özuslu Serdar , Petrovski Nenad , Popgeorgiev Georgi , Pourchier Cloé , Ruffo Alazar , Shobrak Mohammed , Sidiropoulos Lavrentis , Skartsi Theodora , Sözüer Özgün , Stara Kalliopi , Tesfaye Million , Topi Mirjan , Vavylis Dimitrios , Velevski Metodija , Vorpsi Zydjon , Wondafrash Mengistu , Xeka Erald , Yeniyurt Can , Yordanov Emil , Nikolov Stoyan C
Published: August 2024

Millions of large soaring birds migrate from the Palaearctic to Africa every year, and follow distinct flyways around the Mediterranean Sea. While there is conservation concern for many long-distance migratory bird populations, the magnitude and geographic range of threats affecting birds along flyways are poorly known, which complicates efficient mitigation. We used an endangered soaring migrant, the Egyptian VultureNeophron percnopterus, as an example species to assess important threats in 13 countries along the eastern Mediterranean flyway. We tracked 71 birds using satellite telemetry to quantify mortalities, surveyed 4198 km of powerlines to detect dead birds, conducted 910 interviews to quantify the prevalence of poison use, and assessed the magnitude of direct persecution by surveying markets and hunters. We lost 44 birds (50% in Europe and the Mediterranean Sea, 16% in the Middle East, and 34% in Africa), and mortality causes varied geographically. Inadvertent poisoning resulting from rural stakeholders targeting predators occurred along most of the flyway. On the breeding grounds in eastern Europe, poisoning and collision and electrocution continue to be major threats. Electrocution on small and poorly designed electricity pylons was most severe in Turkey, Ethiopia and Saudi Arabia, while direct persecution to meet market demands for belief-based use of vulture products appears to be the largest threat in Nigeria and Niger. Illegal direct persecution for leisure is a major threat in the Middle East and Egypt. Although our work cannot quantitatively estimate which of the identified threats has the greatest demographic impact on Egyptian Vultures, none of threats are species-specific and are therefore relevant for many other migratory birds. Our assessment highlights the key threats per country that range states need to address to meet their obligations under the Convention of Migratory Species to protect migratory birds.
Inhibitory control, personality, and manipulated ecological conditions influence foraging plasticity in the great tit
Authors: Coomes Jenny R. , Davidson Gabrielle L. , Reichert Michael S. , Kulahci Ipek G. , Troisi Camille A. , Quinn John L.
Published: August 2024

Organisms are consistently under selection to respond effectively to a diversity of, sometimes rapid, changes in their environment. Behavioural plasticity can allow individuals to do so instantaneously, but why individuals vary in this respect is poorly understood. Although personality and cognitive traits are often hypothesised to influence plasticity, the effects reported are highly inconsistent, which we hypothesise is because ecological context is usually not considered.

Here we explore the roles of individual cognitive and personality variation – assayed using standard tasks for inhibitory control, a measure of self-control, and ‘reactive-proactive’ personality axis (RPPA), respectively – in driving foraging plasticity, and asked how these effects varied across two experimentally manipulated ecological contexts: food value and predation risk.

After great tits (Parus major) had initially been trained to retrieve high value food hidden in sand, they were then simultaneously offered the hidden food and an alternative food choice on the surface, that was either high or low value. Their choices were further examined under high and low perceived predation risk treatments. Individuals’ choices were classified in terms of whether they continued to forage on the hidden but familiar food source, or instead switched to the new visible food source. We defined the latter option as the plastic response.

Our assays captured consistent differences among individuals in foraging behaviour. Both inhibitory control and exploration influenced whether birds switched from the familiar but hidden food source to the new alternative visible food on the surface. These effects depended on the relative value of the food items available and on the perceived level of predation risk, but also on the time scale over which the response was measured.

Our results demonstrate how an executive cognitive function and one specific personality axis can simultaneously influence plasticity in a key functional behaviour. That their effects on foraging were primarily observed as interactions with food value or predation risk treatments also suggest that the population level consequences of behavioural mechanisms, such as these, may only be revealed across key ecological conditions or gradients.
Prospective modelling of operational offshore windfarms on the distribution of marine megafauna in the southern North Sea
Authors: Virgili Auriane , Laran Sophie , Authier Matthieu , Doremus Ghislain , Van Canneyt Olivier , Spitz Jérôme
Published: August 2024

Intense development of Offshore Wind Farms (OFWs) has occurred in the North Sea with several more farms planned for the near future. These OFWs pose a threat to marine megafauna stressing the need to mitigate the impact of human activities. To help mitigating impacts, the Before After Gradient (BAG) design was proposed. We thus explored the use of the BAG method on megafauna sightings recorded at different distances from wind farms in the southern North Sea. We predicted intra-annual variability in species distribution, then correlated species distribution with the presence of operational OFWs and investigated the potential impact the operation of prospective OFWs may have on species distribution. Three patterns of intra-annual variability were predicted: species present most abundantly in spring, in winter or all year-round. We recommend that future OFW constructions be planned in summer and early fall to minimise impact on cetaceans and that offshore areas off northern France and Belgium be avoided to minimise impact on seabirds. Our prospective analysis predicted an increased or a decreased density with the operation of prospective OFWs. Prospective approaches, using e.g. a BAG design, are paramount to inform species conservation as they can forecast the likely responses of megafauna to anthropogenic disturbances.
Optimizing reduction of Western blotting analytical variations: use of replicate test samples, multiple normalization methods, and sample loading positions
Authors: Rees Phyllis A. , Lowy R. Joel
Published: August 2024

Western blot (WB) analysis is widely used, but obtaining consistent results can be problematic, particularly if all the treatments cannot be placed on one gel. Sources of variation were investigated by analyzing a set of samples which should produce statistically identical results, an approach commonly applied to analytical instruments. Test samples were lysates from RAW 264.7 murine macrophages treated with LPS to activate MAPK and NF-kB signaling targets. The resulting WB were probed for p-ERK, ERK, IkBβ and non-target protein levels. The first test set (Set 1) was a pooled cell lysate and the second (Set 2) four independently prepared lysates.

Analytical replicate data were generated by using multiple WB. Different normalization methods and sample groupings were applied to the density values and the resulting coefficients of variation (CV) and ratios of maximal to minimal values (Max/Min) were compared. Ideally, as the samples were identical (Set 1), or nearly so (Set 2), CVs would be 0 and the Max/Min 1. Results showed the raw density data variance was composed of variability between gel lanes and between gels; but only between gels after applying normalization calculations. CV and Max/Min were 30-70% and 1.5 for raw data, respectively. Common normalization methods, total lane protein, % Control, and p-ERK/ERK ratios, did not have the lowest CVs or Max/Min values. Some of these methods were counterproductive, greatly increasing CV and Max/Min. The best normalization methods resulted in CV and Max/Min value, as low as 5-10% and 1.1, respectively, but more typically 20-25% and 1.2. Application of these methods should allow reliable interpretation of complex experiments that require samples to be placed on multiple gels to provide results, even if fold changes in the target proteins are relatively modest.
Integrative analysis of patient-derived tumoroids and ex vivo organoid modeling of ARID1A loss in bladder cancer reveals therapeutic molecular targets
Authors: Scholtes Mathijs Pieter , Akbarzadeh Maryam , Nakauma-Gonzales J. Alberto , Galaras Alexandros , Bazrafshan Ameneh , Torenvliet Bram , Beikmohammadi Leila , Lozovanu Valeria , Romal Shahla , Moulos Panagiotis , Kan Tsung Wai , Algoe Mahesh , van Royen Martin E. , Sachetti Andrea , van den Bosch Thierry P.P. , Eussen Bert , de Klein Annelies , van Leenders Geert J.L.H. , Boormans Joost L. , Hatzis Pantelis , Palstra Robert-Jan , Zuiverloon Tahlita C.M. , Mahmoudi Tokameh
Published: August 2024

Somatic mutations in ARID1A (AT-rich interactive domain-containing protein 1A) are present in approximately 25% of bladder cancers (BC) and are associated with poor prognosis. With a view to discover effective treatment options for ARID1A-deficient BC patients, we set out to identify targetable effectors dysregulated consequent to ARID1A deficiency. Integrative analyses of ARID1A depletion in normal organoids and data mining in publicly available datasets revealed upregulation of DNA repair and cell cycle-associated genes consequent to loss of ARID1A and identified CHEK1 (Checkpoint kinase 1) and chromosomal passenger complex member BIRC5 (Baculoviral IAP Repeat Containing 5) as therapeutically drug-able candidate molecular effectors. Ex vivo treatment of patient-derived BC tumoroids with clinically advanced small molecule inhibitors targeting CHEK1 or BIRC5 was associated with increased DNA damage signalling and apoptosis, and selectively induced cell death in tumoroids lacking ARID1A protein expression. Thus, integrating public datasets with patient-derived organoid modelling and ex-vivo drug testing can uncover key molecular effectors and mechanisms of oncogenic transformation, potentially leading to novel therapeutic strategies. Our data point to ARID1A protein expression as a suitable candidate biomarker for the selection of BC patients responsive to therapies targeting BIRC5 and CHEK1.
Resveratrol targets G-quadruplexes to exert its pharmacological effects
Authors: Soriano-Lerma Ana , Sánchez-Martín Victoria , Murciano-Calles Javier , Ortiz-González Matilde , Tello-López María J , Pérez-Carrasco Virginia , Linde-Rodríguez Ángel , Ramírez-Macías Inmaculada , Gómez-Pìnto Irene , López-Aliaga Inmaculada , Soriano Miguel , Garcia Salcedo Jose A.
Published: August 2024

Resveratrol (RSV) is one of the most studied and used biomolecules, for which many pharmacological effects targeting multiple tissues have been described. However, a common underlying mechanism driving its full pharmacological activity has not been elucidated to date. G-quadruplexes (G4s) are non-canonical nucleic acid structures found in promoters and involved in controlling gene transcription. This study demonstrates a G4-dependent mode of action for RSV, explaining its multi-target traits. RSV was shown to stabilise cellular G4s, which accumulate around double strand breaks (DSBs) in the promoters of differentially expressed genes (DEGs). G4 targeting triggers DNA damage and controls gene expression. Unravelling the main mode of action of RSV will be helpful to improve its therapeutic potential in a wide variety of health scenarios.
Identification of Disease-relevant, Sex-based Proteomic Differences in iPSC-derived Vascular Smooth Muscle
Authors: Ariyasinghe Nethika R. , Gupta Divya , Escopete Sean , Stotland Aleksandr B. , Sundararaman Niveda , Ngu Ben , Dabke Kruttika , Rai Deepika , McCarthy Liam , Santos Roberta S. , McCain Megan L. , Sareen Dhruv , Parker Sarah J.
Published: August 2024

The prevalence of cardiovascular disease varies with sex, and the impact of intrinsic sex-based differences on vasculature is not well understood. Animal models can provide important insight into some aspects of human biology, however not all discoveries in animal systems translate well to humans. To explore the impact of chromosomal sex on proteomic phenotypes, we used iPSC-derived vascular smooth muscle cells from healthy donors of both sexes to identify sex-based proteomic differences and their possible effects on cardiovascular pathophysiology. Our analysis confirmed that differentiated cells have a proteomic profile more similar to healthy primary aortic smooth muscle than iPSCs. We also identified sex-based differences in iPSC- derived vascular smooth muscle in pathways related to ATP binding, glycogen metabolic process, and cadherin binding as well as multiple proteins relevant to cardiovascular pathophysiology and disease. Additionally, we explored the role of autosomal and sex chromosomes in protein regulation, identifying that proteins on autosomal chromosomes also show sex-based regulation that may affect the protein expression of proteins from autosomal chromosomes. This work supports the biological relevance of iPSC-derived vascular smooth muscle cells as a model for disease, and further exploration of the pathways identified here can lead to the discovery of sex-specific pharmacological targets for cardiovascular disease.

Significance

In this work, we have differentiated 4 male and 4 female iPSC lines into vascular smooth muscle cells, giving us the ability to identify statistically-significant sex-specific proteomic markers that are relevant to cardiovascular disease risk (such as PCK2, MTOR, IGFBP2, PTGR2, and SULTE1).
Accelerated enzyme engineering by machine-learning guided cell-free expression
Authors: Landwehr Grant M , Bogart Jonathan W , Magalhaes Carol , Hammarlund Eric , Karim Ashty S , Jewett Michael C
Published: August 2024

Enzyme engineering is limited by the challenge of rapidly generating and using large datasets of sequence-function relationships for predictive design. To address this challenge, we developed a machine learning (ML)-guided platform that integrates cell-free DNA assembly, cell-free gene expression, and functional assays to rapidly map fitness landscapes across protein sequence space and optimize enzymes for multiple, distinct chemical reactions. We applied this platform to engineer amide synthetases by evaluating substrate preference for 1,217 enzyme variants in 10,953 unique reactions. We used these data to build augmented ridge regression ML models for predicting amide synthetase variants capable of making 9 small molecule pharmaceuticals. Our ML-guided, cell-free framework promises to accelerate enzyme engineering by enabling iterative exploration of protein sequence space to build specialized biocatalysts in parallel.
Genetic diversity and antimicrobial resistance ofCampylobacter jejuniisolates from Gambian children under five with moderate-to-severe diarrhoea and healthy Controls
Authors: Betts Modupeh , Dione Michel , Ikumapayi Usman Nurudeen , Senghore Madikay , Lamin Modou , Foster-Nyarko Ebenezer , Jaffali James , Panchalingam Sandra , Nataro James P , Kotloff Karen L , Levine Myron M , Saha Debasish , Hossain Jahangir , Kwambana-Adams Brenda , Antonio Martin
Published: August 2024

Introduction

Campylobacteris a leading cause of bacterial gastroenteritis globally, but its molecular epidemiology remains poorly understood in sub-Saharan Africa. This study investigates the genotypic population structure ofCampylobacter jejuniisolates from children with moderate-to-severe diarrhoea (MSD) and healthy controls in The Gambia. Additionally, we determined the antimicrobial susceptibility levels of the isolates.

Methods

As part of the Global Enteric Multicenter Study (GEMS) in The Gambia, a total of 49C. jejuniisolates were collected from the stools of children under 5 years old, including 22 with MSD and 27 healthy controls. These isolates were subjected to multilocus sequence typing (MLST) and antimicrobial susceptibility testing using the disc-diffusion method.

Results

TheC. jejuniisolates belonged to 22 sequence types (STs), ten of which were novel. The most common STs were ST-353 (19.1%, 9/47), ST-7784 (12.7%, 6/47), and ST-1038 (10.6%, 5/47). All isolates were fully susceptible to erythromycin, tetracycline, gentamicin and chloramphenicol, with two isolates (4.4%, 2/45) resistant to ciprofloxacin and nalidixic acid. Antimicrobial resistance or intermediate susceptibility to trimethoprim-sulfamethoxazole, cefotaxime and ampicillin was observed in 91.1% (41/45), 90.9% (40/44), and 44.4% (20/45) of the isolates, respectively. There was no strong evidence linkingC. jejuniantimicrobial susceptibility or MLST genotype to MSD status.

Conclusion

This study provides the first overview of the high genotypic diversity of humanC. jejuniisolates in The Gambia and reveals low-level resistance among the isolates to antibiotics commonly used to treat campylobacteriosis. The study contributes to understanding the epidemiology and resistance patterns ofC. jejuniin this region.
Quantitative Microscopy in Medicine
Authors: Matov Alexandre , Modiri Shayan
Published: August 2024

Introduction

Methods for personalizing medical treatment are the focal point of contemporary biomedical research. In cancer care, we can analyze the effects of therapies at the level of individual cells. Quantitative characterization of treatment efficacy and evaluation of why some individuals respond to specific regimens, whereas others do not, requires additional approaches to genetic sequencing at single time points. Methods for the analysis of changes in phenotype, such asin vivoandex vivomorphology and localization of cellular proteins and organelles can provide important insights into patient treatment options.

Methods

Novel therapies are needed to extend survival in metastatic castration-resistant prostate cancer (mCRPC). Prostate-specific membrane antigen (PSMA), a cell surface glycoprotein that is commonly overexpressed by prostate cancer (PC) cells relative to normal prostate cells, provides a validated target.

Results

We developed a software for image analysis designed to identify PSMA expression on the surface of epithelial cells in order to extract prognostic metrics. In addition, our software can deliver predictive information and inform clinicians regarding the efficacy of PC therapy. We can envisage additional applications of our software system, beyond PC, as PSMA is expressed in a variety of tissues. Our method is based on image denoising, topologic partitioning, and edge detection. These three steps allow to segment the area of each PSMA spot in an image of a coverslip with epithelial cells.

Conclusions

Our objective has been to present the community with an integrated, easy to use by all, tool for resolving the complex cellular organization and it is our goal to have such software system approved for use in the clinical practice.