bluuebunny/crossref_metadata_2025 huggingface dataset:
Are clinics not affiliated with a Menopause Society Certified Practitioner more likely to offer guideline-nonconcordant treatment compared to clinics affiliated with a Menopause Society Certified Practitioner?
Authors: Marino Jean M. , Stanley Elizabeth E. , Ahrendt Hannah , Pope Rachel
Published: July 2024

Objective

To identify clinics in Ohio, Michigan, and Pennsylvania that advertise menopause treatment on their website and evaluate whether clinics not affiliated with a Menopause Society Certified Practitioner (MSCP) are more likely to offer guideline-nonconcordant treatment compared to clinics affiliated with an MSCP.

Methods

We performed an Internet search to identify clinics advertising on their website menopause treatment in Ohio, Michigan, and Pennsylvania. We checked clinic personnel against The Menopause Society directory of practitioners to determine if the clinic was affiliated with an MSCP.

Results

We identified 174 clinics (41% in OH, 28% in PA, and 31% in MI). Thirteen percent of clinics were affiliated with an MSCP. Clinics with an MSCP are significantly less likely to advertise hormone testing (primary outcome; odds ratio [OR], 0.11; 95% confidence interval, 0.02-0.39), compounded hormone therapy (OR, 0.06; 95% confidence interval, 0.001-0.41), and bioidentical hormone therapy (OR, 0.07; 95% confidence interval, 0.001-0.26), compared to clinics without an MSCP-affiliated clinics that are also less likely to advertise that hormone therapy will help maintain youth or help with weight loss.

Conclusions

Our pilot study has shown that in the states of Ohio, Michigan, and Pennsylvania, clinics with an MSCP were more likely to advertise on their website an adherence to The Menopause Society's guidelines and not advertise for compounded or bioidentical hormones, recommend hormone testing, or advertise hormones for a youthful appearance or weight loss.
Development and validation of a home quantitative sensory testing tool-kit to assess changes in sensory and pain processing: a study in healthy young adults
Authors: Ocay Don Daniel , Lobo Kimberly , Kim Angela , Halpin Meghan , Berde Charles B.
Published: July 2024

Quantitative sensory testing (QST) is a set of methods for quantifying somatosensory functioning. Limitations of laboratory-based QST (LQST) include high cost, complexity in training, lack of portability, and time requirements for testing. Translating QST to a home setting could facilitate future research and clinical care. The objective of this study was to develop a home QST (HQST) tool-kit that is cost-effective, easy to use, and detects changes in sensory and pain processing. Thirty-two young healthy adults underwent sensory testing on their nondominant forearm using standard in-person LQST, followed by “simulated HQST” using video guidance in a separate room from the investigator before and after application of either a lidocaine or capsaicin cream. We observed good agreement between HQST and LQST scores, with significant correlations observed between the pinprick, pressure, cold and heat measures (|ρ| range = 0.36-0.54). The participants rated the HQST protocol as highly acceptable and safe but can be improved in future implementations. Home QST was able to detect hypoesthesia to vibration after lidocaine cream application (P = 0.024, d = 0.502) and could detect hypoalgesia and hyperalgesia to pressure and heat pain sensitivity tests after application of lidocaine and capsaicin creams, respectively (P-value range = <0.001-0.036, d-value range = 0.563-0.901). Despite limitations, HQST tool-kits may become a cost-effective, convenient, and scalable approach for improving sensory profiling in clinical care and clinical research.
The roles of tertiary lymphoid structures in genitourinary cancers: molecular mechanisms, therapeutic strategies, and clinical applications
Authors: Yang Jie , Xiong Xingyu , Zheng Weitao , Xu Hang , Liao Xinyang , Wei Qiang , Yang Lu
Published: July 2024

The presence of tertiary lymphoid structures (TLSs) associated with distinct treatment efficacy and clinical prognosis has been identified in various cancer types. However, the mechanistic roles and clinical implications of TLSs in genitourinary (GU) cancers remain incompletely explored. Despite their potential role as predictive markers described in numerous studies, it is essential to comprehensively evaluate the characteristics of TLSs, including drivers of formation, structural foundation, cellular compositions, maturation stages, molecular features, and specific functionality to maximize their positive impacts on tumor-specific immunity. The unique contributions of these structures to cancer progression and biology have fueled interest in these structures as mediators of antitumor immunity. Emerging data are trying to explore the effects of therapeutic interventions targeting TLSs. Therefore, a better understanding of the molecular and phenotypic heterogeneity of TLSs may facilitate the development of TLSs-targeting therapeutic strategies to obtain optimal clinical benefits for GU cancers in the setting of immunotherapy. In this review, the authors focus on the phenotypic and functional heterogeneity of TLSs in cancer progression, current therapeutic interventions targeting TLSs and the clinical implications and therapeutic potential of TLSs in GU cancers.
Vitamin D Status and Cardiovascular Disease in College Athletes After SARS-CoV-2 Infection
Authors: Hollabaugh William L. , Hymel Alicia , Pennings Jacquelyn S. , Clark Daniel E. , Soslow Jonathan H. , Karpinos Ashley R.
Published: July 2024

Objective:

To evaluate the association between vitamin D status and CV disease after COVID-19 in college athletes.

Design:

Retrospective cohort study.

Setting:

National College Athletic Association Division-I college athletes from a single academic institution.

Patients:

A total of 157 athletes (60 female; median age: 20 years) from 9 sports with a positive SARS-CoV-2 test, cardiac magnetic resonance imaging (CMR), and vitamin D level.

Independent Variables:

Serum 25-hydroxyvitamin D level (primary); age, sex (regression models).

Main Outcomes Measures:

Differences in age, sex, race, ethnicity, myocarditis, pericarditis, and CMR metrics by vitamin D status were analyzed. Regression models were used to assess the relationship between vitamin D status and CMR metrics accounting for age and sex.

Results:

Low vitamin D (LVD) was found in 33 (21.0%) of athletes, particularly Black males (P < 0.001). Athletes with LVD had higher biventricular and lower mid-ventricular extracellular volumes, but these differences were not significant when corrected for age and sex. Athletes with LVD had higher left ventricle (LV) mass (P < 0.001) and LV mass index (P = 0.001) independent of age and sex. Differences in global circumferential strain were noted but are likely clinically insignificant. Vitamin D status did not associate with myocarditis and pericarditis (P = 0.544).

Conclusions:

LVD is common in athletes, particularly in Black males. Although athletes with LVD had higher LV mass, cardiac function and tissue characterization did not differ by vitamin D status. Future studies are needed to determine if the differences in LV mass and LV mass index by vitamin D status are clinically significant. This study suggests that vitamin D status does not impact the development of myocarditis or pericarditis after COVID-19 infection.
Gender Diversity Among Reconstructive Microsurgery Studies Based on the Relative Citation Ratio
Authors: Falcon Dominick J. , Bustos Valeria P. , Mahmoud Amir-Ala , Lee Bernard T.
Published: July 2024

Background

Gender disparities in plastic surgery authorship have been previously described in the literature. The relative citation ratio (RCR) index is a new metric that normalizes citation rates for field and time, which can be utilized to compare authors. This study aims to evaluate differences in gender authorship in reconstructive microsurgery (RM) papers, as well as the impact of gender on the RCR index.

Methods

A PubMed query isolated RM studies between 2002 and 2020 across the 3 highest impact PS journals. Author names and RCR information were collected from NIH iCite. The likely gender was adjudicated by using NamSor-Software. Unpaired Wilcoxon rank-sum and chi-square tests were used to assess differences between groups.

Results

Of 1146 articles (2172 authors), there was a significant difference between the proportion of females as senior authors compared to first authors (P < 0.001). Overall, females represented 15.4% of all authors, 19.7% of first authors, and 11.3% of senior authors. Males had a significantly higher weighted RCR (P < 0.0001) and number of publications (P < 0.0001), which remained significant when stratified by first and senior author. Female authors collectively had a higher mean RCR (P = 0.008) and among first authors (P < 0.0001), with no significant difference among senior authors (P = 0.47).

Conclusion

A considerably greater number of males are publishing in reconstructive microsurgery compared to females, with significantly more males being senior authors compared to first authors. Males had higher weighted RCR scores and publications compared to females. This study suggests that equity in gender authorship within the field is yet to be achieved.
Representation of Racial Diversity on US Plastic Surgery Websites: A Cross-sectional Study
Authors: Escobar-Domingo Maria J. , Mahmoud Amir-Ala , Lee Daniela , Taritsa Iulianna , Foppiani Jose , Hernandez Alvarez Angelica , Schuster Kirsten , Lin Samuel J. , Lee Bernard T.
Published: July 2024

Background

The racial diversity portrayed in plastic and reconstructive surgery (PRS) media is an important indicator of an inclusive environment for potential patients. To evaluate the degree to which PRS websites demonstrate inclusivity, we assessed the racial composition of both patients and plastic surgeons depicted on the most visited academic and private PRS websites to determine the extent to which racial diversity is represented.

Methods

A cross-sectional study was conducted in September 2023. The 10 most visited websites in each state were identified. Sociodemographic characteristics including race and sex of patients and plastic surgeons, as well as the type of practice, were collected. Race was classified according to individuals' Fitzpatrick Phototypes into White and non-White. Differences in patient and surgeon representation were compared to the 2020 US Census and the 2020 ASPS demographics using χ2 tests. Subgroup analyses were conducted to identify differences by type of practice and region.

Results

We analyzed a total of 2,752 patients from 462 websites belonging to 930 plastic surgeons. PRS websites were predominantly from private practices (93%). Regarding patient representation, 92.6% were female, 7.4% were male, 87.6% were White, and 12.4% were non-White. The surgeon population on the studied webpages was 75.1% male, 92.1% White, and 7.8% non-White. Statistically significant differences were found in the patient population when compared to the 2020 national (P < 0.001) and regional (P < 0.001) US Census demographics and the 2020 ASPS Statistics Report (P < 0.001). Although minority representation was significantly higher on academic websites compared to private practice (22.9% vs. 12.1%; P = 0.007), both were significantly lower than the percentage of minority patients undergoing PRS.

Conclusions

This study illuminates racial disparities in the representation of racial groups among patients and plastic surgeons in the most frequented plastic surgery websites. Moreover, it underscores the imperative to bolster racial diversity within the digital content of both private and academic PRS websites. Greater racial representation can foster a more inclusive perception of the plastic surgery field, which may potentially broaden access to care and enrich the professional landscape.
Sedimentary biomarkers and bone specimens reveal a history of prehistoric occupation on Somerset Island (Arctic Canada)
Authors: Gallant Lauren R. , Hargan Kathryn E. , Kimpe Linda E. , Michelutti Neal , Grooms Christopher , Savelle James M. , Smol John P. , Blais Jules M.
Published: July 2024

Archaeological studies of pre-historic Arctic cultures are often limited to artefacts and architecture; such records may be incomplete and often do not provide a continuous record of past occupation. Here, we used lake sediment archives to supplement archaeological evidence to explore the history of Thule and Dorset populations on Somerset Island, Nunavut (Canada). We examined biomarkers in dated sediment cores from two ponds adjacent to abandoned Thule settlements (PaJs-3 and PaJs-13) and compared these to sediment cores from two ponds without past human occupation. Coprostanol and epicoprostanol, δ
15
N measurements, sedimentary chlorophyll
a
and the ratio of diatom valves to chrysophyte cysts were elevated in the dated sediment profiles at both sites during Thule and Dorset occupations. Periods of pronounced human impact during the Thule occupation of the site were corroborated by
14
C-dated caribou bones found at both sites that identified intense caribou hunting between
ca
1185 and 1510 CE. Notably, these sediment core data show evidence of the Dorset occupation from
ca
200 to 500 CE at sites where archaeological evidence was heretofore lacking. We highlight the utility of lake sediments in assisting archaeological studies to better establish the timings, peak occupations and even lifestyle practices of the Dorset and Thule Arctic peoples.
Coevolution between eggs and sperm of insects
Authors: Soulsbury Carl D. , Iossa Graziella
Published: July 2024

Sexual selection is known to play a major role in the evolution of insect sperm size, whereas natural selection is thought to be a major driver of insect egg size. Despite these differing forms of selection operating, it is possible coevolution between male and female gametes can occur owing to their vital interactions during fertilization. We tested egg–sperm coevolution in insects and found that longer sperm correlated to longer and wider eggs. Moreover, the size of the entry point of sperm into insect eggs (micropyles), was positively related to the diameter of sperm, on average being approximately three times the diameter of the sperm. This suggests a function in reducing and channelling sperm entry, but potentially still leaving space for movement. Our work suggests that greater attention needs to be paid to egg–sperm interactions prior to the point of fertilization as they may influence the evolution of gametes.
Correlated evolution of conspicuous colouration and burrowing in crayfish
Authors: Graham Zackary A. , Padilla Perez Dylan J.
Published: July 2024

Conspicuous colours have fascinated biologists for centuries, leading to research on the evolution and functional significance of colour traits. In many cases, research suggests that conspicuous colours are adaptive and serve a function in sexual or aposematic signalling. In other cases, a lack of evidence for the adaptive value of conspicuous colours garners interest from biologists, such as when organisms that live underground and are rarely exposed to the surface are nevertheless colourful. Here, we use phylogenetic comparative methods to investigate colour evolution throughout freshwater crayfishes that vary in burrowing ability. Within the taxa we analysed, conspicuous colours have evolved independently over 50 times, and these colours are more common in semi-terrestrial crayfishes that construct extensive burrows. The intuitive but not evolutionarily justified assumption when presented with these results is to assume that these colours are adaptive. But contrary to this intuition, we discuss the hypothesis that colouration in crayfish is neutral. Supporting these ideas, the small population sizes and reduced gene flow within semi-terrestrial burrowing crayfishes may lead to the fixation of colour-phenotype mutations. Overall, our work brings into question the traditional view of animal colouration as a perfectly adapted phenotype.
Antifungal activity of propafenone on Candida spp. strains: interaction with antifungals and possible mechanism of action
Authors: Barbosa Amanda Dias , Leitão Amanda Cavalcante , de Oliveira Leilson Carvalho , Rodrigues Daniel Sampaio , de Farias Cabral Vitória Pessoa , Moreira Lara Elloyse Almeida , Silveira Maria Janielly Castelo Branco , Barbosa Sarah Alves , de Souza Beatriz Oliveira , Sá Lívia Gurgel do Amaral Valente , de Andrade Neto João Batista , Cavalcanti Bruno Coelho , Magalhães Islay Lima , de Moraes Manoel Odorico , Júnior Hélio Vitoriano Nobre , da Silva Cecília Rocha
Published: July 2024

Introduction. The development of new antifungal drugs has become a global priority, given the increasing cases of fungal diseases together with the rising resistance to available antifungal drugs. In this scenario, drug repositioning has emerged as an alternative for such development, with advantages such as reduced research time and costs.

Gap statement. Propafenone is an antiarrhythmic drug whose antifungal activity is poorly described, being a good candidate for further study.

Aim. This study aims to evaluate propafenone activity against different species of Candida spp. to evaluate its combination with standard antifungals, as well as its possible action mechanism.

Methodology. To this end, we carried out tests against strains of Candida albicans, Candida auris, Candida parapsilosis, Candida tropicalis, Candida glabrata and Candida krusei based on the evaluation of the MIC, minimum fungicidal concentration and tolerance level, along with checkerboard and flow cytometry tests with clinical strains and cell structure analysis by scanning electron microscopy (SEM).

Results. The results showed that propafenone has a 50% MIC ranging from 32 to 256 µg ml−1, with fungicidal activity and positive interactions with itraconazole in 83.3% of the strains evaluated. The effects of the treatments observed by SEM were extensive damage to the cell structure, while flow cytometry revealed the apoptotic potential of propafenone against Candida spp.

Conclusion. Taken together, these results indicate that propafenone has the potential for repositioning as an antifungal drug.
Control of Modular Tissue Flows Shaping the Embryo in Avian Gastrulation
Authors: Serrano Nájera Guillermo , Plum Alex M. , Steventon Ben , Weijer Cornelis J. , Serra Mattia
Published: July 2024

Avian gastrulation requires coordinated flows of thousands of cells to form the body plan. We quantified these flows using their fundamental kinematic units: one attractor and two repellers constituting its Dynamic Morphoskeleton (DM). We have also elucidated the mechanistic origin of the attractor, marking the primitive streak (PS), and controlled its shape, inducing gastrulation flows in the chick embryo that are typical of other vertebrates. However, the origins of repellers and dynamic embryo shape remain unclear. Here, we address these questions using active matter physics and experiments. Repeller 1, separating the embryo proper (EP) from extraembryonic (EE) tissues, arises from the tug-of-war between EE epiboly and EP isotropic myosin-induced active stress. Repeller 2, bisecting the anterior and posterior PS and associated with embryo shape change, arises from anisotropic myosin-induced active intercalation in the mesendoderm. Combining mechanical confinement with inhibition of mesendoderm induction, we eliminated either one or both repellers, as predicted by our model. Our results reveal a remarkable modularity of avian gastrulation flows delineated by the DM, uncovering the mechanistic roles of EE epiboly, EP active constriction, mesendoderm intercalation and ingression. These findings offer a new perspective for deconstructing morphogenetic flows, uncovering their modular origin, and aiding synthetic morphogenesis.
stormTB: A web-based simulator of a murine minimal-PBPK model for anti-tuberculosis treatments
Authors: Visintainer Roberto , Fochesato Anna , Boaretti Daniele , Giampiccolo Stefano , Watson Shayne , Levi Micha , Reali Federico , Marchetti Luca
Published: July 2024

Introduction

Tuberculosis (TB) poses a significant threat to global health, with millions of new infections and approximately one million deaths annually. Various modeling efforts have emerged, offering tailored data-driven and physiologically-based solutions for novel and historical compounds. However, this diverse modeling panorama may lack consistency, limiting result comparability. Drug-specific models are often tied to commercial software and developed on various platforms and languages, potentially hindering access and complicating the comparison of different compounds.

Methods

This work introduces stormTB: SimulaTOr of a muRine Minimal-pbpk model for anti-TB drugs. It is a web-based interface for our minimal physiologically based pharmacokinetic (mPBPK) platform, designed to simulate custom treatment scenarios for tuberculosis in murine models. The app facilitates visual comparisons of pharmacokinetic profiles, aiding in assessing drug-dose combinations.

Results

The mPBPK model, supporting 11 anti-TB drugs, offers a unified perspective, overcoming the potential inconsistencies arising from diverse modeling efforts. The app, publicly accessible, provides a user-friendly environment for researchers to conduct what-if analyses and contribute to collective TB eradication efforts. The tool generates comprehensive visualizations of drug concentration profiles and pharmacokinetic/pharmacodynamic indices for TB-relevant tissues, empowering researchers in the quest for more effective TB treatments. stormTB is freely available at the link:https://apps.cosbi.eu/stormTB.
Structurally targeted mutagenesis identifies key residues supporting α-synuclein misfolding in multiple system atrophy
Authors: Reis Patricia M. , Holec Sara A. M. , Ezeiruaku Chimere , Frost Matthew P. , Brown Christine K. , Liu Samantha L. , Olson Steven H. , Woerman Amanda L.
Published: July 2024

Multiple system atrophy (MSA) and Parkinson’s disease (PD) are caused by misfolded α-synuclein spreading throughout the central nervous system. While familial PD is linked to several point mutations in α-synuclein, there are no known mutations associated with MSA. Our previous work investigating differences in α-synuclein misfolding between the two disorders showed that the familial PD mutation E46K inhibits replication of MSA prions bothin vitroandin vivo, providing key evidence to support the hypothesis that α-synuclein adopts unique strains in patients. Here, to further interrogate α-synuclein misfolding, we engineered a panel of cell lines harboring both PD-linked and novel mutations designed to identify key residues that facilitate α-synuclein misfolding in MSA. These data were paired within silicoanalyses using Maestro software to predict the effect of each mutation on the ability of α-synuclein to misfold into one of the reported MSA cryo-electron microscopy conformations. In many cases, our modeling accurately identified mutations that facilitated or inhibited MSA replication. However, Maestro was occasionally unable to predict the effect of a mutation on MSA propagationin vitro, demonstrating the challenge of using computational tools to investigate intrinsically disordered proteins. Finally, we used our cellular models to determine the mechanism underlying the E46K-driven inhibition of MSA replication, finding that the E46/K80 salt bridge is necessary to support α-synuclein misfolding. Overall, our studies use a structure-based approach to investigate α-synuclein misfolding, resulting in the creation of a powerful panel of cell lines that can be used to interrogate MSA strain biology.
Mutation of phosphatidate phosphohydrolase genes confers broad-spectrum disease resistance in plants
Authors: Gong Qiuwen , Sha Gan , Han Xinyu , Guo Zhenhua , Yang Lei , Yang Wei , Tan Ronglei , Chen Guang , Li Yufei , Shen Xin , Xie Kabin , Cai Guangqin , Hu Honghong , Luo Jie , Li Qiang , Li Guotian
Published: July 2024

Phosphatidic acid (PA) is considered as a second messenger that interacts with protein kinases, phosphatases and NADPH oxidases, amplifying the signal to initiate plant defense signaling responses (Li and Wang, 2019). In rice, mutation ofRBL1causes the accumulation of PA, enhancing multipathogen resistance (Sha et al., 2023). In our previous study, we attempted to rescuerbl1mutant by overexpressing phosphatidate phosphohydrolase (PAH) genes. However, overexpression ofPAH2reduced the PA level but did not affect the disease resistance, which made us to reconsider the importance of PA andPAHin rice immunity. Here, we identified that mutation ofPAHscaused PA accumulation and enhanced multipathogen resistance in rice andArabidopsis.
Developing peptide-based fusion inhibitors as an antiviral strategy utilizing Coronin 1 as a template
Authors: Panda Manbit Shubhadarsi , Qazi Bushra , Vishwakarma Vaishali , Pattnaik Gourab Prasad , Haldar Sourav , Chakraborty Hirak
Published: July 2024

Enveloped viruses can enter the host cells by endocytosis and subsequently fuse with the endosomal membranes, or fuse with the plasma membrane at the cell surface. The crucial stage of viral infection, regardless of the route taken to enter the host cell, is membrane fusion. The present work aims to develop a peptide-based fusion inhibitor that prevents membrane fusion by modifying the properties of the participating membranes, without targeting a protein. This would allow us to develop a fusion inhibitor that might work against a larger spectrum of enveloped viruses as it does not target any specific viral fusion protein. With this goal, we have designed a novel peptide by modifying a native sequence derived from coronin 1, a phagosomal protein, that helps to avoid lysosomal degradation of mycobacterium-loaded phagosomes. The designed peptide, mTG-23, inhibits ~ 30- 40% fusion between small unilamellar vesicles containing varying amounts of cholesterol by modulating the biophysical properties of the participating bilayers. As a proof of principle, we have further demonstrated that the mTG-23 inhibits Influenza A virus infection in A549 and MDCK cells (with~ EC50 of 20.45 μand 21.45 μ, respectively), where viral envelope and endosomal membrane fusion is a crucial step. Through a gamut of biophysical and biochemical methods, we surmise that mTG-23 inhibits viral infection by inhibiting viral envelope and endosomal membrane fusion. We envisage that the proposed antiviral strategy can be extended to other viruses that employ a similar modus operandi, providing a novel pan-antiviral approach.
Loss of conserved noncoding elements likely shaped the evolution of regressed phenotypes in cavefish
Authors: Lal Mohan , Bhattacharya Jui , Sandhu Kuljeet Singh
Published: July 2024

The Mexican cavefish, Astyanaxmexicanus, is a captivating model for probing cave adaptations, showcasing pronounced divergence in traits like vision, brain morphology, behaviour, pigmentation, and hypoxia tolerance compared to its surface-dwelling counterpart. Very few protein-coding variants are identified in cave-morphs, and the vast phenotypic gap between the two morphs remains inadequately explained. We investigated the noncoding genomes of teleosts and found that 3,343 conserved non-coding elements (CNEs) were independently lost in cave-morphs. These CNEs, confirmed in Zebrafish, displayed enhancer-associated histone modifications, possessed binding sites of neuronal transcription factors and interacted with cognate genes through chromatin loops. Genes crucial for eye and nervous system development were located adjacent to CNEs lost in cave morphs. Notably, these flanking genes were gradually downregulated during embryonic development of cave-morphs, contrasting with surface morphs. These insights underscore how compromised developmental pathways, stemming from the loss of distal regulatory elements, contribute to the regression of phenotypes in cave morphs.

Article Summary

Despite availability of genome sequences and allied datasets, the genetic underpinning of regressed traits of cavefish remains enigmatic. By aligning the genome sequences of teleosts, we identified thousands of noncoding elements specifically lost in cavefish, exhibited enhancer-associated hallmarks, and were enriched with the binding sites of neuronal transcription factors. Their cognate genes were associated with eye and nervous system development, and exhibited developmental downregulation in cavefish. This study highlights how the loss of regulatory elements impacted the cavefish evolution and adaptation.
BacTermFinder: A Comprehensive and General Bacterial Terminator Finder using a CNN Ensemble
Authors: Taheri Ghahfarokhi Seyed Mohammad Amin , Peña-Castillo Lourdes
Published: July 2024

A terminator is a DNA region that ends the transcription process. Currently, multiple computational tools are available for predicting bacterial terminators. However, these methods are specialized for certain bacteria or terminator type (i.e., intrinsic or factor-dependent). In this work, we developed BacTermFinder using an ensemble of Convolutional Neural Networks (CNNs) receiving as input four different representations of terminator sequences. To develop BacTermFinder, we collected roughly 41k bacterial terminators (intrinsic and factor-dependent) of 22 species with varying GC-content (from 28% to 71%) from published studies that used RNA-seq technologies. We evaluated BacTermFinder’s performance on terminators of five bacterial species (not used for training BacTermFinder) and two archaeal species. BacTermFinder’s performance was compared with that of four other bacterial terminator prediction tools. Based on our results, BacTermFinder outperforms all other four approaches in terms of average recall without increasing the number of false positives. Moreover, BacTermFinder identifies both types of terminators (intrinsic and factor-dependent) and generalizes to archaeal terminators. Additionally, we visualized the saliency map of the CNNs to gain insights on terminator motif per species. BacTermFinder is publicly available athttps://github.com/BioinformaticsLabAtMUN/BacTermFinder.
Independent genetic mapping experiments identify diverse molecular determinants of host adaptation in a generalist herbivore
Authors: Villacis-Perez Ernesto , Graeve Femke De , Beer Berdien De , Alshami Seham Ali , de Jong Rick , Meyer Tim De , Leeuwen Thomas Van
Published: July 2024

Interactions between plants and herbivores promote evolutionary change. Studying the evolution of herbivore mechanisms aimed to cope with diUerent host plant species is a critical intersection between evolutionary biology and sustainable pest management. Generalist herbivores are of particular interest, as hybridization between genetically distinct populations can increase the standing genetic variation and therefore the adaptive potential of the species.Tetranychus urticaeis a generalist arthropod known for its adaptive potential, evidenced in its immense host range and ability to develop metabolic resistance to xenobiotics. However, the molecular underpinnings associated with the potential of host adaptation and the consequences of host adaptation in this and many other pests remain elusive. Here, we use two independent, empirical approaches to identify and map the genetic basis of host plant performance and adaptation in genetically distinct populations ofT. urticae. In the first approach, we subject a genetically diverse mite population to tomato selection and map genomic regions linked to the phenotypic evolution of increased reproductive performance. In the second approach, we map genomic regions responsible for performance on tomato by comparing the genomes of pooled individuals from a F2 backcross between populations with high and low reproductive performance. Both approaches revealed specific and shared genomic regions associated with host plant performance and adaptation and key candidate genes were identified. Our findings highlight the power of spider mite genetic approaches to identify the complex genetic basis of host adaptation in a generalist herbivore.
Soil microbial responses to multiple global change factors as assessed by metagenomics
Authors: Rodríguez del Río Álvaro , Rillig Matthias C.
Published: July 2024

Anthropogenic activities impose multiple concurrent pressures on soil ecosystems at a global scale, but the response of soil microbes to multiple concurrent global change (GC) factors is poorly understood. Here, we applied 10 GC treatments individually and in random combinations of 8 factors to soil samples, and monitored their bacterial and viral composition by metagenomic analysis. The application of multiple GC factors selects for particular prokaryotic and viral communities different from the effects of any individual factor, favoring, for instance, potentially pathogenic unknown mycobacteria and novel viruses. At the functional level, multiple GC factors select for sessile and non-biofilm-forming bacteria which are metabolically diverse and show a high load of antibiotic resistance genes. Finally, we show that novel genes are also relevant for understanding microbial response to GC. Our study indicates that multiple GC factors impose directional selective pressures on soil prokaryotes and viruses not observed at the individual GC factor level, and improves our understanding of how GC interactions shape microbial communities.
Targeting prostate cancer by new bispecific monocyte engager directed to prostate-specific membrane antigen
Authors: Das Gargi , Ptacek Jakub , Havlinova Barbora , Nedvedova Jana , Barinka Cyril , Novakova Zora
Published: July 2024

Prostate cancer (PCa) ranks as the second leading cause of cancer-related deaths among men in the United States. Prostate-specific membrane antigen (PSMA) represents a well-established biomarker of PCa and its levels correlate positively with the disease progression, culminating at the stage of metastatic castration-resistant prostate cancer. Due to its tissue-specific expression and cell surface localization, PSMA shows superior potential for precise imaging and therapy of PCa. Antibody-based immunotherapy targeting PSMA offers the promise of selectively engaging the host immune system with minimal off-target effects.

Here we report on the design, expression, purification, and characterization of a bispecific engager, termed 5D3-CP33, that efficiently recruits macrophages to the vicinity of PSMA-positive cancer cells mediating PCa death. The engager was engineered by fusing the anti-PSMA 5D3 antibody fragment to a cyclic peptide 33 (CP33) selectively binding the Fc gamma receptor I (FcγRI/CD64) on the surface of phagocytes. Functional parts of 5D3-CP33 engager revealed nanomolar affinity for PSMA and FcγRI/CD64 with dissociation constants of KD= 3 nM and KD= 140 nM, respectively. At a concentration as low as 0.3 nM, the engager was found to trigger production of reactive oxygen species by U937 monocytic cells in the presence of PSMA-positive cells. Moreover, flow cytometry analysis demonstrated antibody-dependent cell-mediated phagocytosis of PSMA-positive cancer cells by U937 monocytes when exposed to 0.1 nM 5D3-CP33. Our findings illustrate that 5D3-CP33 effectively and specifically activates monocytes upon PSMA-positive target engagement, resulting in the elimination of tumor cells. The 5D3-CP33 engager can thus serve as a promising lead for the development of new immunotherapy tools for the efficient treatment of PCa.
Uncertainty-Aware Traction Force Microscopy
Authors: Kandasamy Adithan , Yeh Yi-Ting , Serrano Ricardo , Mercola Mark , del Álamo Juan C.
Published: July 2024

Traction Force Microscopy (TFM) is a versatile tool to quantify cell-exerted forces by imaging and tracking fiduciary markers embedded in elastic substrates. The computations involved in TFM are ill-conditioned, and data smoothing or regularization is required to avoid overfitting the noise in the tracked substrate displacements. Most TFM calculations depend critically on the heuristic selection of regularization (hyper)parameters affecting the balance between overfitting and smoothing. However, TFM methods rarely estimate or account for measurement errors in substrate deformation to adjust the regularization level accordingly. Moreover, there is a lack of tools to quantify how these errors propagate to the recovered traction stresses. These limitations make it difficult to interpret TFM readouts and hinder comparing different experiments. This manuscript presents an uncertainty-aware TFM technique that estimates the variability in the magnitude and direction of the traction stress vector recovered at each point in space and time of each experiment. In this technique, substrate deformation and its uncertainty are quantified using a non-parametric bootstrap PIV method by resampling the microscopy image pixels (PIV-UQ). This information is passed to a hierarchical Bayesian framework that automatically selects its hyperparameters to perform spatially adaptive regularization conditioned on image quality and propagates the uncertainty to the traction stress readouts (TFM-UQ). We validate the performance of PIV-UQ and TFM-UQ using synthetic datasets with prescribed image quality variations and demonstrate the application of PIV-UQ and TFM-UQ to experimental datasets. These studies show that TFM-UQ locally adapts the level of smoothing, outperforming traditional regularization methods. They also illustrate how uncertainty-aware TFM tools can be used to objectively choose key image analysis parameters like PIV-UQ interrogation window size. We anticipate that these tools will allow for decoupling biological heterogeneity from measurement variability and facilitate automating the analysis of large datasets by parameter-free, input data-based regularization.
scTail: precise polyadenylation site detection and its alternative usage analysis from reads 1 preserved 3’ scRNA-seq data
Authors: Hou Ruiyan , Huang Yuanhua
Published: July 2024

Three-prime single-cell RNA-seq (scRNA-seq) has been widely employed to dissect the variability of cellular transcriptomes, while only the cDNAs on reads 2 are routinely used, including to analyze polyadenylation sites (PAS). However, despite of high sequencing noise, we found the cDNAs on reads 1 are highly informative in precisely detecting PAS. Here, we further develop a computational method, scTail, to identify PAS using reads 1 and quantify its expression leveraging reads 2, which enables effective detection of alternative PAS usage (PAU). When compared with other methods, scTail detects PAS more sensitively and precisely. With various experimental data sets, we demonstrated that the combination usage of scTail and BRIE2 can discover differential alternative PAS usage in various biological processes including cell types in human intestinal, disease status of esophageal squamous cell carcinoma, and time point of mouse forelimb histogenesis, revealing critical insights in PAS regulations.
Cell segmentation without annotation by unsupervised domain adaptation based on cooperative self-learning
Authors: Miyaki Shintaro , Nishimoto Shori , Tokuoka Yuta , Yamada Takahiro G , Morikura Takashi , Funahashi Akira
Published: July 2024

Cell segmentation, which extracts cells from microscopic images, is essential for quantitative evaluation of cell morphology. Recently, supervised deep-learning-based models have been shown to achieve highly accurate segmentation. However, the performance of these supervised models is often degraded when the models infer unknown cell types that are not included in the train dataset. One approach to overcoming the performance degradation is acquiring new annotated data for each cell type. However, constructing datasets for all cell types is not feasible because labeling every single pixel, rather than each image, is required in the segmentation task. Learning methods that can achieve highly accurate segmentation without annotation is strongly required.

Here, we developed a cell segmentation method based on unsupervised domain adaptation with cooperative self-learning (CULPICO: Cooperative Unsupervised Learning for PIxel-wise COloring). The proposed method consists of two independent segmentation models and a mutual exchange mechanism of inference data. For the data with labels, the models are trained through supervised learning. For the data without labels, the models infer a label probability at each pixel and generate a pseudo-label as unsupervised learning. The pseudo-labels created by each model are mutually used as ground-truth in the other model. Loss function is corrected by considering pixel-level discrepancies between the label probabilities inferred by the two models. The proposed method, despite being an unsupervised learning method, can segment the unknown cell types without labels with an accuracy comparable to supervised learning models. Our method, which could solve the performance degradation problem without constructing new datasets, is expected to accelerate life science by reducing the cost of extracting quantitative biological knowledge.
Exercise and disease state influence the beneficial effects of Fn14-depletion on survival and muscle pathology in theSOD1G93Aamyotrophic lateral sclerosis (ALS) mouse model
Authors: Hazell Gareth , Ahlskog Nina , Sutton Emma R , Okoh Magnus , Hoolachan Joseph M , Scaife Taylor , Iqbal Sara , McCallion Eve , Bhomra Amarjit , Kordala Anna J , Scamps Frederique , Raoul Cedric , Wood Matthew JA , Bowerman Melissa
Published: July 2024

Background

Amyotrophic lateral sclerosis (ALS) is a devastating and incurable neurodegenerative disease. Accumulating evidence strongly suggests that intrinsic muscle defects exist and contribute to disease progression, including imbalances in whole-body metabolic homeostasis. We have previously reported that tumour necrosis factor (TNF)-like weak inducer of apoptosis (TWEAK) and fibroblast growth factor inducible 14 (Fn14) are significantly upregulated in skeletal muscle of theSOD1G93AALS mouse model. While antagonising TWEAK did not impact survival, we did observe positive effects in skeletal muscle. Given that Fn14 has been proposed as the main effector of the TWEAK/Fn14 activity and that Fn14 can act independently from TWEAK in muscle, we suggest that manipulating Fn14 instead of TWEAK in theSOD1G93AALS mice could lead to differential and potentially improved benefits.

Methods

We thus investigated the contribution of Fn14 to disease phenotypes in theSOD1G93AALS mice. To do so, Fn14 knockout mice (Fn14-/-) were crossed onto theSOD1G93Abackground to generateSOD1G93A;Fn14-/-mice. Investigations were performed on both unexercised and exercised (rotarod and/or grid test) animals (wild type (WT),Fn14-/-,SOD1G93AandSOD1G93A;Fn14-/-).

Results

Here, we firstly confirm that the TWEAK/Fn14 pathway is dysregulated in skeletal muscle ofSOD1G93Amice. We then show that Fn14-depletedSOD1G93Amice display an increased lifespan and decreased muscle pathology, without an impact on motor function, and that this is dependent on exposure to exercise. Indeed, we observe that endurance (rotarod) and resistance (grid test) exercises influence the positive effects of Fn14 deletion on survival and muscle phenotypes inSOD1G93Amice, which may be further influenced by genotype and disease state.

Conclusions

Our study provides further insights on the different roles of the TWEAK/Fn14 pathway in pathological skeletal muscle and how they can be influenced by age, disease and metabolic state. This is particularly relevant in the ALS field, where combinatorial therapies that include exercise regimens are currently being explored. As such, a better understanding and consideration of the interactions between treatments, muscle metabolism and exercise will be of importance in future studies.
Potato cultivars use different root physiological and molecular mechanisms to acclimate to salt stress
Authors: Nicolas Michael , Bouma Jort , Venema Jan Henk , van der Schoot Hanneke , Verstappen Francel , de Zeeuw Thijs , Langedijk Sanne E. , Boer Damian , Bucher Johan , Staal Marten , Krom Ben , Elzenga J. Theo M. , Visser Richard G.F. , Testerink Christa , Karlova Rumyana
Published: July 2024

Soil salinity induces osmotic stress and ion toxicity in plants, detrimentally affecting their growth and development. Potato (Solanum tuberosum) faces yield reductions due to salt stress. The mechanisms of salt stress resilience, especially in adventitious roots, remain unknown.

We investigated the resilience of three potato cultivars - Desirée, Innovator, and Mozart - by studying their physiological and transcriptomic responses to salt stress.

Our findings reveal that under salt stress, the growth of stolons and stolon node roots is similarly reduced unlike tubers, even though they are physically connected. Surprisingly, tubers accumulate Cl-but not Na+under salt stress, suggesting an active Na+exclusion mechanism. Innovator showed the lowest suberin and lignin deposition before salt stress and higher K+leakage, leading to a stronger initial stress response with high ABA content and a distinct transcriptomic pattern. Nevertheless, Innovator was the most resilient, displaying lower growth, salt-tolerance index and tuber yield reduction. Transcriptomic analysis revealed several K+/Na+channel genes which might regulate ions homeostasis during salt stress, in particular in Innovator.

Altogether, we conclude that acclimation ability, rather than initial protection of roots against salt, prevails in long term salt-stress resilience of potato.
Structural insights into thein situassembly of clustered protocadherin γB4
Authors: Zhang Ze , Chen Fabao , Zhang Zihan , Guo Luqiang , Feng Tingting , Fang Zhen , Xin Lihui , Yu Yang , Hu Hongyu , He Yongning
Published: July 2024

Clustered protocadherins (cPcdhs) belong to the cadherin superfamily and play important roles in neural development. cPcdhs can mediate homophilic adhesion and lead to self-avoidance and tiling by giving neurons specific identities in vertebrates. Structures and functions of cPcdhs have been studied extensively in the past decades, but the mechanisms behind the functions have not been fully understood. Here we investigate thein situassembly of cPcdh-γB4, a member in the γ subfamily of cPcdhs, by electron tomography and find that the full length cPcdh-γB4 does not show regular organization at the adhesion interfaces. By contrast, cPcdh-γB4 lacking the intracellular domain can generate an ordered zigzag pattern between cells and thecisinteracting mode is different from the crystal packing of the ectodomain. We also identify the residues on the ectodomain that might be important for the zigzag pattern formation by mutagenesis. Furthermore, truncation mutants of the intracellular domain of cPcdh-γB4 reveal different assembly patterns between cell membranes, suggesting that the intracellular domain plays a crucial role in the intermembrane organization of cPcdh-γB4. Taken together, these results suggest both ectodomain and intracellular domain regulate thein situassembly of cPcdh-γB4 at the adhesion interfaces, thereby providing mechanistic insights into the functional roles of cPcdhs during neuronal wiring.