bluuebunny/crossref_metadata_2025 huggingface dataset:
The Association Between Parity and Fecal Problems Differs by Urinary Status
Authors: Brinkman Lauret A.M. , Hierink G. Marije , Malmberg G.G. Alec , Lammers Rianne J.M. , Visser Ellen , van Eijndhoven Hugo W.F. , Trzpis Monika , Broens Paul M.A.
Published: November 2024

Importance

Urinary incontinence, fecal incontinence, and constipation frequently manifest and are risk factors for one another. Studies investigating the association between parity and fecal problems in urinary continent and urinary incontinent women are lacking.

Objectives

The aim of this study was to examine whether the association between parity and fecal problems differs in urinary continent and urinary incontinent women.

Study Design

This study was a cross-sectional, retrospective questionnaire-based study. The population was a representation of the general Dutch female population (n = 5,670), including nulliparous (n = 2,790) and parous women (n = 2,880). Data were collected using the Groningen Defecation and Fecal Continence questionnaire, addressing urinary and fecal problems according to validated criteria. Parametric test, χ2 test, Fisher exact test, and univariable and multivariable logistic regression analyses were used.

Results

Of the urinary incontinent women, 13.7% nulliparous and 6.3% parous women reported a combination of fecal incontinence with constipation. This made urinary incontinent nulliparous women 1.90 times more prone to have both fecal incontinence and constipation (P < 0.001), especially nulliparous women with stress urinary incontinence (odds ratio, 2.76; 95% confidence interval, 1.44–5.31; P = 0.002). In the urinary continent women, nulliparous women reported significantly more often fecal incontinence as a solitary problem than parous women (4.3% vs 2.5%; P = 0.016; odds ratio, 1.73; 95% confidence interval, 1.06–2.81; P = 0.028).

Conclusions

The association between parity and fecal problems is different in urinary continent and incontinent women. In urinary incontinent women, especially with stress urinary incontinence, nulliparous women experience more often the coexistence of fecal incontinence and constipation than parous women. In urinary continent women, nulliparous women had more frequently a solitary problem of fecal incontinence than parous women.
Dyadobacter helix sp. nov. and Dyadobacter linearis sp. nov., from drinking water
Authors: Lucena Teresa , Pujalte María J. , Arahal David R.
Published: November 2024

The purpose of this study is to better characterize and complete the classification of two bacterial strains, CECT 9275T and CECT 9623T, isolated from drinking water systems and affiliated to the genus Dyadobacter by partial 16S rRNA gene sequence comparison. Hence, we report here the phenotypic, genomic and phylogenetic characterization performed on these strains. Both strains grow on R2A agar forming mucous, bright yellow colonies, developing at 26 °C in 48 h. They produce flexirubin and are oxidase and catalase positive, mesophilic and non-halophilic. The cells of strain CECT 9275T are curved rods mainly associated in pairs, forming nearly closed rings or resembling the shape of the number three, to long spirals resembling a corkscrew. Its draft genome has an estimated size of 7.23 Mbp (G+C content 45.4%). Strain CECT 9623T appeared on wet mounts as straight rods, mostly in pairs, sometimes forming long filaments (up to 20 µm). Its draft genome is shorter, with an estimated size of 6.45 Mbp (G+C content is 46.1%). Overall genome relatedness indexes clearly define them as separate organisms, so based on all the data collected, we propose the species Dyadobacter helix sp. nov. with type strain AB1T (=CECT 9275T=LMG 32341T) and Dyadobacter linearis sp. nov. with type strain AB67T (=CECT 9623T=LMG 32342T).
Luteimonas flava sp. nov. and Aquilutibacter rugosus gen. nov., sp. nov., isolated from freshwater environments in China and re-examining the taxonomic status of genera Luteimonas and Lysobacter
Authors: Lu Huibin , Chen Li , Wang Yujing , Xing Peng , Wu Qinglong
Published: November 2024

Three Gram-stain-negative, aerobic, short rod-shaped and motile strains (FXH3WT, SHGZ20W and SMYT11WT) were isolated from freshwater environments in China. Comparisons based on the 16S rRNA gene sequences indicated that strains FXH3WT and SHGZ20W showed the highest 16S rRNA gene sequence similarity of about 99.6% to ‘Luteimonas cellulosilyticus’ MIC 1.5, and strain SMYT11WT showed the highest 16S rRNA gene sequence similarity of 99.8% to Luteimonas fraxinea D4P002T, respectively. Observing the phylogenetic trees reconstructed based on the 16S rRNA gene sequences, the species of genera Luteimonas and Lysobacter were not monophyletic and often mixed together. The further reconstructed phylogenomic tree and Genome Taxonomy Database also showed that the species of both genera were polyphyletic, implying that the current taxonomic status of the species of both genera was questionable. The calculated OrthoANIu, digital DNA–DNA hybridization and average amino acid sequence identity (AAI) values supported that strains FXH3WT and SHGZ20W should belong to the same novel species and strain SMYT11WT should also represent an independent novel species. Combining the AAI values and phylogenomic analyses, the species of genera Luteimonas and Lysobacter should be reassigned to 12 genera (Luteimonas, Lysobacter, Cognatiluteimonas, Noviluteimonas, Pseudoluteimonas, Solilutibacter, Agrilutibacter, Cognatilysobacter, Marilutibacter, Novilysobacter, Montanilutibacter and Aerolutibacter). The AAI values 69.5–76.0% were also proposed as the Lysobacteraceae-specific thresholds for genus delineation. Strain SMYT11WT should represent a novel species of the genus Luteimonas, for which the name Luteimonas flava sp. nov. (type strains SMYT11WT=GDMCC 1.4275T=KCTC 8304T) is proposed. Strains FXH3WT and SHGZ20W should represent a novel species of a new genus Aquilutibacter rugosus gen. nov., sp. nov. The type strain of the type species is FXH3WT (=GDMCC 1.4096T=KCTC 8154T).
Multi-stain modelling of histopathology slides for breast cancer prognosis prediction
Authors: Sharma Abhinav , Gustafsson Fredrik K. , Hartman Johan , Rantalainen Mattias
Published: November 2024

Background

Pathologic assessment of the established biomarkers using standard hematoxylin & eosin (H&E) and immunohistochemical (IHC) stained whole slide images (WSIs) is central in routine breast cancer diagnostics and contributes prognostic and predictive information that guides clinical decision-making. However, other than only aggregated protein-expression values from IHC WSIs, a spatial combination of histo-morphological information from IHC and H&E WSIs can potentially improve prognosis prediction in breast cancer patients. In this study, we aim to develop a deep learning-based risk-stratification method for breast cancer using routine H&E and IHC-stained histopathology WSIs from resected tumours.

Methods

This is a retrospective study including WSIs from surgical resected specimens from 945 patients from the South General Hospital in Stockholm. One H&E and four IHC (ER, PR, HER2, and Ki-67) stained sections were included from each patient, retrieved from the same tumour block. The IHC WSIs with the H&E WSI were registered, and corresponding images patches (tiles) were extracted for each image modality. Features from the registered tiles were extracted using two existing and publicly available histopathology foundation models (UNI and CONCH). Using the extracted features together with time-to-event data, we optimised an attention-based multiple instance learning (MIL) model using the Cox loss (negative partial log-likelihood loss) and recurrence-free survival (RFS) as the survival endpoint.

Results

Using cross-validation we observed a prognostic performance with a C-index of 0.65 (95%CI: 0.56 - 0.72) for the risk score prediction using only H&E WSIs and UNI as the tile-level feature extractor. Combinations of H&E with one or more IHC modalities were subsequently evaluated, with the highest performance observed in the model combining the H&E and PR WSI data and the model combining all the stains, obtaining a C-index of 0.72 (95% CI: 0.65 - 0.79) and 0.72 (95% CI: 0.64 - 0.79) respectively.

Conclusion

Multiple stain modalities are used in routine breast cancer pathology, but has not been considered together for prognostic modelling. The results in this study suggests that models combining morphological features extracted by histopathology foundation models across multiple stain modalities can improve prognostic risk-stratification performance compared to single-modality models.
Transforming diagnostic capacity by syndromic infection testing for remote isolated communities
Authors: Dryden Matthew , Lee John , Toplass Janice , Cortes Nicholas , Russo Del Piano Fabio , Skerritt Tiffanie , St.Hill Mykala A S. , Crowie Chester , Benjamin Geoffrey , Siebs Arlene A S. , Smellie Jonathan , Hardy Bill , Duncan Everette S. , Wright Natalie
Published: November 2024

Objective

Many of the UK overseas territories are small with limited microbiological diagnostic capacity for pathogens and antimicrobial resistance detection. The Covid-19 pandemic highlighted the particular vulnerability of these territories for the emergence of novel infections and antimicrobial resistance.

Methods

The UKHSA program with its territory partners implemented rapid automated syndromic molecular diagnostics (RASM), aiming to improve diagnostic capacity. Local laboratory staff were trained in the use of the diagnostics, and guidance was provided to clinicians for requesting tests. Syndromic diagnoses included enteric, respiratory, bloodstream, neurological infection, and antibiotic resistance mechanisms. Data on diagnostic capacity, turnaround times and clinical impact were collected from records before and after implementation of RASM.

Results

Turnaround time for results went from an average 14 days to 1 day, and often much shorter. Previously undiagnosed conditions, could now be identified to the microbiological level rapidly in territory, allowing appropriate specific clinical management, infection prevention, improved antimicrobial stewardship and rapid public health response. This technology is simple to operate and maintain with little scope for user error. The speed of microbiological diagnosis for patient management and public health detection and response was greatly enhanced.

Conclusion

Rapid microbiological diagnosis on site transformed patient management, the timely investigation and management of outbreaks and clusters, accurate surveillance and antimicrobial stewardship. Targeted RASM is cost effective, reducing the requirement for highly trained scientific staff and expensive logistics around rapid transport to reference laboratories. This innovation improves clinical care and strengthens local preparedness in communicable disease and public health response.
Top-Down Effects on Translucency Perception in Relation to Shape Cues
Authors: Nagai Takehiro , Kiyokawa Hiroaki , Kim Juno
Published: November 2024

0.

It is well established that object shape perception significantly influences the perception of translucency. However, how object shape cues such as motion and binocular disparity affect the perception of translucency in rich environments, like virtual reality or real visual environments, remains unclear. This study aims to psychophysically measure the extent to which multiple object shape cues influence the perception of translucency. Additionally, we examined whether top-down factors, such as changes in cognitive attitude caused by the sequence of experiments, affect translucency perception. The results revealed that while motion and binocular disparity enhance translucency perception, this effect is confined to situations where shape cues are poor. Moreover, the effect became particularly pronounced when the experiments began with weak specular reflection stimuli, followed by the experiments using stimuli with specular reflection. In the case of translucent objects without specular reflection, strong shape information cannot be derived solely from shading patterns. These findings thus suggest that top-down factors related to shape modulate the influence of shape cues on translucency perception.
High-resolution Cryo-EM visualises hydrated type I and IV pilus structures from enterotoxigenicEscherichia coli
Authors: Kawahara Kazuki , Oki Hiroya , Iimori Minato , Muramoto Ryuki , Imai Tomoya , Gerle Christoph , Shigematsu Hideki , Matsuda Shigeaki , Iida Tetsuya , Nakamura Shota
Published: November 2024

To efficiently colonise intestinal epithelium, enteric pathogens utilise a wide variety of pilus filaments, including those synthesised by the chaperone–usher or type IV pilus assembly pathway. Despite the importance of these filaments as potential drug and vaccine targets, their large size and dynamic nature present challenges for atomic-resolution structural determination. Here, we used cryo-electron microscopy (cryo-EM) and whole genome sequencing to identify and determine the structures of type I and IV pili expressed in enterotoxigenicEscherichia coli. The well-defined cryo-EM maps at resolutions of 2.20 and 1.78 Å for Type I and Type IV pilus, respectively, facilitatedde novostructural modelling for these filaments, revealing side chain structures in detail. Further, we resolved thousands of hydrated water molecules around and within the inner core of the filaments, functioning as a buffer to stabilise the otherwise metastable subunit assembly. The high-resolution structures offer novel insights into the subunit–subunit interactions, providing important clues to understand pilus assembly, stability, and flexibility.
Versatile and Portable Cas12a-mediated Detection of Antibiotic Resistance Markers
Authors: Vargas-Reyes Maryhory , Alcántara Roberto , Alfonsi Soraya , Peñaranda Katherin , Petrelli Dezemona , Spurio Roberto , Pajuelo Monica J. , Milon Pohl
Published: November 2024

Antimicrobial resistance (AMR) is a global public health problem particularly accentuated in low-and middle-income countries, largely due to a lack of access to sanitation and hygiene, lack of awareness and knowledge, and the inadequacy of molecular laboratories for timely and accurate surveillance programs. This study introduces a versatile molecular detection toolbox (C12a) for antibiotic resistance gene markers using CRISPR/Cas12a coupled to PCR. Our toolbox can detect less than 3×10-7ng of DNA (100 attoMolar) or 102CFU/mL. High concordance was observed when comparing the C12a toolbox with sequenced genomes and antibiotic susceptibility tests for theblaCTX-M-15andfloRantibiotic resistance genes (ARGs), which confer resistance to cefotaxime and other β- lactams, and amphenicols, respectively. C12aINT, designed to detect the Integrase 1 gene, confirmed a high prevalence of the integrase/integron system inE. colicontaining multiple ARGs. The C12a toolbox was tested across a wide range of laboratory infrastructure including a portable setup. When combined with lateral flow assays (LFA), C12a exhibited competitive performance, making it a promising solution for on-site ARG detection. Altogether, this work presents a collection of molecular tools (primers, crRNAs, probes) and validated assays for rapid, versatile, and portable detection of antibiotic resistance markers, highlighting the C12a toolbox potential for applications in surveillance and ARG identification in clinical and environmental settings.
Microstructural Brain Changes in Buerger’s Disease and Smokers: A Case-Control Study Using Diffusion Tensor Imaging
Authors: Asadollahi Shahir Ali Asghar , Gharib Mohammad Hadi , Shahali Ramsheh Maryam , Zahedpasha Reza , Razman Asma , Omidi Abdollah , Kharazm Pezhman , Ghaderi Amir , Ghorbani Somayeh , Hashemian Shervin-sadat
Published: November 2024

Aim

Thromboangiitis Obliterans (TAO), or Buerger’s disease, affects peripheral vessels and is linked to smoking. This Diffusion tensor imaging tractography (DTI) study examines brain function changes in TAO patients compared to healthy smokers and non-smokers, aiming to reveal neurological implications beyond the known peripheral effects.

Methods

The case-control study involved 50 participants aged 27-56 in northeast Iran, including TAO patients, healthy smokers, and non-smoking controls. MRI scans with DTI were conducted to assess 21 brain tracts for fractional anisotropy (FA) and apparent diffusion coefficient (ADC).

Results

Significant differences in brain tract integrity were observed among the groups. TAO patients showed lower FA values in the minor forceps compared to healthy smokers, while smokers had higher FA values than non-smoking controls. ADC values were notably higher in TAO patients across several tracts, including corticospinal tracts, fornix tracts, arcuate fasciculus, and inferior longitudinal fasciculus, compared to both healthy smokers and controls.

Conclusion

The study highlights distinct brain tract alterations in TAO patients and suggests potential neurological consequences associated with the disease and smoking habits. DTI proves valuable in understanding microstructural brain changes and could serve as a diagnostic tool for evaluating smoking-related neurologic complications, providing insights into TAO’s impact beyond peripheral vessels.

Key Points

Advanced MRI techniques, particularly DTI, reveal significant differences in fractional anisotropy (FA) and apparent diffusion coefficient (ADC) in the brains of individuals with Buerger’s disease and smokers.

Notable ADC variations in corticospinal and fornix tracts are observed between Buerger’s patients, smokers, and non-smokers.

FA values in the superior longitudinal fasciculus and the minor and major forceps significantly differ among Buerger’s patients, smokers, and controls, highlighting microstructural brain alterations.
Highway paving dramatically increased dengue transmission in the Amazon
Authors: Singleton Alyson L. , Lescano Andres G. , MacDonald Andrew J. , Mandle Lisa , Sipin Terrell J. , Martel Kevin S. , Munayco César V. , Carrera Esteban D. R. , Choque Gustavo A. , Bautista Ana S. M. , Luby Stephen P. , Mordecai Erin A.
Published: November 2024

Human mobility drives the spread of many infectious diseases, yet the health impacts of changes in mobility due to new infrastructure development are poorly understood and currently not accounted for in impact assessments. We take a novel quasi-experimental approach to identifying the link between mobility and infectious disease, leveraging historical road upgrades as a proxy for regional human mobility changes. We analyzed how highway paving altered transmission of dengue—a high-burden mosquito-borne disease—via changes in human movement in the Madre de Dios region of Peru. The paving of the Interoceanic Highway through a formerly isolated region of the Amazon in 2009 provided a unique opportunity to quantify the causal impact of road paving on disease transmission. To uncover this relationship, we compared dengue incidence data from healthcare facilities in Madre de Dios near to versus far from the newly paved highway before and after paving, while controlling for observable and unobservable confounding variables (a difference-in-differences causal inference approach). We found that the paving of the highway caused at least an additional 9,826 (95% CI: 8,562–10,684) dengue cases since paving, accounting for 45.2% (95% CI: 39.4%–49.2%) of all dengue cases recorded in the region post highway paving (2009–2022). Our findings demonstrate the impact that infrastructure can have on dengue transmission, likely via its effects on human mobility. As a result, we advocate for future road construction plans in tropical regions to account for potential increases in dengue transmission during impact assessments.

Significance statement

Large-scale infrastructure projects are critical for meeting global development goals, but they can also have unintended consequences for local human and environmental health. More evidence attributing human health effects to infrastructure projects is needed to understand how to mitigate these negative health impacts. Our study contributes to this body of knowledge, attributing nearly half of recent dengue cases in Madre de Dios, Peru to the paving of the Interoceanic Highway through the region in 2009. Our results demonstrate the impact that highway construction can have on human health and call for future infrastructure projects through tropical forests to consider infectious disease outcomes in their impact assessments.
Precision-cut lung slices in air-liquid interface (PCLS-ALI): A novelex-vivomodel for the study of Pulmonary Aspergillosis
Authors: Gonzales-Huerta LE , Williams TJ , Aljohani R , Robertson BD , Evans CA , Armstrong-James DPH
Published: November 2024

Pulmonary Aspergillosis is a respiratory infection with a high mortality rate, which affects patients with immunosuppression or structural lung defects. Antifungal treatment options are few and many have narrow therapeutic margins and potentially serious side effects. In recent years, there are growing numbers of reports of antifungal resistance. Thus, there is an urgent need for effective models to study fungal pathogenesis and test antifungal therapies in the respiratory system. Here, we present a novelex-vivomodel using precision-cut lung slices in an air-liquid interface platform to evaluate lung tissue responses to fungal infection and antifungal treatment. Readouts assessed were lactate dehydrogenase for tissue damage, release of inflammatory cytokines (TNF-α, IL-1β, CXCL1), and histology for confirmation of hyphal invasion. Overall, the PCLS-ALI model is a promising approach for understanding lung tissue responses to fungal infections, which fulfils the reduction and refinement components of the 3Rs guiding principles for ethical use of experimental animals.
TEAD-targeting small molecules induce a cofactor switch to regulate the Hippo pathway
Authors: Guarnaccia Alissa D. , Hagenbeek Thijs J. , Lee Wendy , Kljavin Noelyn , Choi Meena , Ulas Gözde , Kameswaran Vasumathi , Le Daniel , Paul Sayantanee , Vaidya Samir , Zbieg Jason R. , Crawford James J. , Daniel Bence , Dey Anwesha , Lill Jennie R.
Published: November 2024

TEAD proteins are the main transcriptional effectors of the Hippo signaling pathway and a pharmacological target in oncology. Most TEAD-targeting small molecules act by disrupting interaction with the oncogenic transcriptional activators YAP and TAZ. Here, we describe an alternative mechanism for TEAD lipid pocket binding molecules. We report that select sulfonamide-containing compounds promote TEAD interaction with the transcriptional repressor VGLL4 to induce a small molecule-mediated cofactor switch from YAP to VGLL4. Chemically induced VGLL4–TEAD complexes counteract YAP activity at chromatin to repress pro-growth gene networks, including genes involved in cellular proliferation and mechanosignaling. VGLL4 is required for an anti-proliferative response to these select compounds, and genetic deletion of VGLL4 causes resistance to these moleculesin vitroandin vivo. Our data reveal a category of molecules that facilitate the repressive VGLL4–TEAD interaction and open up new understandings for curbing the oncogenic activity of Hippo pathway deregulation.
Standard-flow targeted proteomics for quantification of enzymes in glucosinolate biosynthetic pathways
Authors: Vik Daniel
Published: November 2024

Insights gained from quantitative proteomics studies show that the relationship between transcript and protein abundance is not generally linear. Quantitative measurement of both proteins and transcripts is required to reveal their actual relationship. Whereas quantitative analysis of transcripts is widely established, there is a need for easily accessible protein level technologies. Mass spectrometry-based proteomics is a promising solution, provided that it can be made accessible to a broader user group than it currently is. Developments in proteomics methodology show that relatively simple instrumentation allows for targeted proteomics which provides a reliable and accessible technology platform for protein quantification. I here describe the successful implementation of standard-flow targeted proteomics and its use to quantify 12 enzymes in the glucosinolate biosynthetic pathways in Arabidopsis thaliana. Enabled by targeted proteomics, I analyzed a series of transcription factor mutants and found that transcript and protein generally correlated well under these unchallenged conditions. When I treated wild-type plants with the phytohormone methyl-jasmonate, I observed uncoupling of metabolite, transcript and protein levels, suggesting post-transcriptional and/or -translational in addition to transcriptional regulation.
The genome assembly of the westslope cutthroat trout,Oncorhynchus lewisi, reveals interspecific chromosomal rearrangements with the rainbow trout
Authors: Flores Anne-Marie , Christensen Kris A. , Godin Theresa , Palti Yniv , Campbell Matthew R. , Waldbieser Geoffrey C. , Simpson Sheron A. , Scheffler Brian E. , Smith Seth R. , Whiteley Andrew R. , Kovach Ryan P. , Luikart Gordon , Boyer Matthew C. , Kardos Marty , Relyea Scott , Wells Craig , Koop Ben F.
Published: November 2024

Cutthroat trout (Oncorhynchus clarkii) are popular among anglers throughout their native range along the West Coast and interior of North America. As they colonized the interior of North America, cutthroat trout diverged into several genetically distinct groups. Many of these groups are now threatened by habitat destruction, hybridization with rainbow trout (O. mykiss), and competition from introduced species. These groups were previously classified as subspecies, but recent research suggests they may represent distinct species. In this study, we produced a chromosomal-level genome assembly and a genetic map for one of the species in the cutthroat trout species complex, the westslope cutthroat trout (O. lewisi—formerlyO. clarki lewisi). We also constructed haplotype-resolved assemblies from a westslope cutthroat-rainbow trout F1 hybrid. We used the new genome assemblies to identify major interspecific chromosomal rearrangements between the two sister species, including fusions, fissions, and inversions. These genome assemblies and chromosome data provide valuable insights regarding genetic variation within cutthroat trout and in hybrids between rainbow and cutthroat trout.

Article Summary

Westslope cutthroat trout inhabit bodies of water in several states and provinces near the Rocky Mountains and are well-known among anglers. In this study, we produced the first publicly available genome assemblies and a high-density genetic map for this species. These are research tools that allow detailed genetic analyses, including identifying differences among the genomes of related species. These comparisons allow researchers to understand the evolution of these species better and may provide insight into why successful interbreeding is possible among cutthroat and rainbow trout.
Identification of the MRTFA/SRF pathway as a critical regulator of quiescence in cancer
Authors: Panesso-Gómez Santiago , Cole Alexander J. , Wield Alyssa , Anyaeche Vivian I. , Shah Jaynish , Jiang Qi , Ebai Tonge , Sharrow Allison C. , Tseng George , Yoon Euisik , Brown Daniel D. , Clark Amanda M. , Larsen Scott D , Eder Ian , Gau David , Roy Partha , Dahl Kris N. , Tran Lam , Jiang Hui , McAuliffe Priscilla F , Lee Adrian V , Buckanovich Ronald J.
Published: November 2024

Chemoresistance is a major driver of cancer deaths. One understudied mechanism of chemoresistance is quiescence. We used single cell culture to identify, retrieve, and RNA-Seq profile primary quiescent ovarian cancer cells (qOvCa). We found that many qOvCa differentially expressed genes are transcriptional targets of the Myocardin Related Transcription Factor/Serum Response Factor (MRTF/SRF) pathway. We also found that genetic disruption of MRTF-SRF interaction, or an MRTF/SRF inhibitor (CCG257081) impact qOvCa gene expression and induce a quiescent state in cancer cells. Suggesting a broad role for this pathway in quiescence, CCG257081 treatment induced quiescence in breast, lung, colon, pancreatic and ovarian cancer cells. Furthermore, CCG081 (i) maintained a quiescent state in patient derived breast cancer organoids and, (ii) induced tumor growth arrest in ovarian cancer xenografts. Together, these data suggest that MRTF/SRF pathway is a critical regulator of quiescence in cancer and a possible therapeutic target.

Significance

Quiescence is a critical driver of chemoresistance. The MRFT-SRF pathway regulates cancer cell quiescence and inhibiting the MRTF-SRF pathway can prevent the outgrowth of quiescent cancer cells and improve cancer outcomes.
Intravenous gene therapy improves lifespan and clinical outcomes in feline Sandhoff Disease
Authors: Maguire Anne S. , Ta Linh , Gross Amanda L. , Osterhoudt Devin E. , Cannon Jessica S. , Hall Paige I. , Sandey Maninder , Seyfried Thomas N. , Gray-Edwards Heather L. , Sena-Esteves Miguel , Martin Douglas R.
Published: November 2024

Sandhoff Disease (SD), a fatal neurodegenerative disorder, is caused by the absence of ß-hexosaminidase (Hex) and subsequent accumulation of GM2 ganglioside in lysosomes. Previous studies have led to adeno-associated virus (AAV) gene therapy for children with GM2 gangliosidosis in both expanded access and Phase I/II clinical trials via intracranial and/or cerebrospinal fluid-based delivery. The current study investigated intravenous (IV) gene therapy of SD cats, treated at one month of age with a bicistronic AAV vector. While untreated SD cats lived to 4.3±0.2 months, cats treated with low and high doses lived to 8.3±1.2 and 12.4±2.7 months, respectively. In-life assessments revealed clear clinical benefit of AAV treatment, with the most dramatic improvement seen in the reduction of overt full-body tremors. Cerebrospinal fluid levels of aspartate aminotransferase (AST) and lactate dehydrogenase (LDH) were decreased, indicating a reduction of cell damage within the central nervous system. Magnetic resonance imaging (MRI) and spectroscopy (MRS) acquired on a 7 Tesla scanner indicated that structural pathology and metabolite abnormalities are partially normalized by AAV treatment. Dose-dependent reduction of GM2 ganglioside storage and increases in Hex activity were most substantial in the caudal regions of the brain and in the spinal cord. Immunohistochemistry revealed reduction in neuroinflammatory cell populations and partial correction of myelin deficits. These results support the dose-dependent efficacy of AAV delivered IV for significant restoration of clinical metrics and Hex function in a feline model of SD.

One Sentence Summary

Intravenous administration of AAV gene therapy is safe and efficacious in a feline model of Sandhoff disease.
Heat-Triggered Transcriptional Reprogramming in Microspores Disrupts Progression of Pollen Development inBrassica napusL
Authors: Lohani Neeta , Singh Mohan B. , Bhalla Prem L.
Published: November 2024

Rising temperatures due to climate change pose significant threats to global food security, particularly by impacting crop fertility and yield. Despite the known susceptibility of male reproductive development to heat stress, the specific adaptive mechanisms and critical regulatory genes involved in the stage-specific heat stress response in crops are still not well understood. This study examines the impact of acute heat stress on pollen development in Brassica napus (Canola), an essential oilseed crop, with a focus on the uninucleate microspore stage. We demonstrate that a brief exposure to 40°C during the uninucleate microspore stage results in loss of cellular polarity, failed asymmetric cell division, loss of cytoplasm, and pollen abortion, leading to a significant decline in pollen viability. Transcriptome analysis reveals the complexity of heat-induced transcriptional reprogramming in microspores, identifying 8.1% (6,245) of the expressed genes as responsive to high temperature, with a higher degree of downregulation. Fourteen differentially expressed transcription factors (TFs) belonging to diverse TF families were identified in heat-stressed microspores, with overrepresented target genes. The differential regulation of cell cycle control genes in heat-stressed microspores supports our microscopic observations and details the transcriptional reprogramming underlying the failure of heat-stressed microspores to undergo the first and second pollen mitotic divisions (PMI and PMII), resulting in aberrant pollen development inB. napus. Heat stress disrupts key biological pathways such as transcription, mRNA processing, translational control, protein homeostasis, autophagy, phytohormone signaling, and reactive oxygen species (ROS) homeostasis. Heat stress alters the intricate network of multiple signaling pathways, potentially disrupting the regulatory pathways underlying pollen development, with evident crosstalk underscoring the complexity of the heat stress response in pollen development. These findings underscore the critical vulnerability of the microspore stage to heat stress in Canola. Understanding the identified heat-responsive genes and regulatory networks provides valuable insights for breeding climate-resilient Canola varieties, thereby contributing to global food security amidst changing climatic conditions.

Highlights

Acute heat stress during microspore stage inBrassica napusdisrupts pollen development.

Heat stress induces complex transcriptional reprogramming in microspores, with higher degree of downregulation.

Transcriptional control, RNA processing, coordination of protein homeostasis and translational control is altered in heat-stressed microspores

Misregulation of cell cycle control genes supports the loss of cellular polarity and failure to undergo asymmetric cell division in heat stressed microspores.
Interferon Epsilon Protects Epithelial Barriers from Viral Infection through Autocrine Intracellular Signaling
Authors: Casazza Rebecca L. , Skavicus Samantha , Hare David , Cooley Kaila A. , Heaton Nicholas S. , Coyne Carolyn B.
Published: November 2024

Antiviral defenses at mucosal barriers are essential for preventing viral entry and systemic infection. Interferon epsilon (IFNε), a unique type I interferon not induced by infection, is constitutively expressed in the female reproductive tract (FRT), where it provides broad antiviral protection and fluctuates with hormone status. The role of IFNε outside the FRT remains unclear, although it is expressed in the intestinal epithelium. We generated an IFNε knockout mouse (Ifnε-/-) and confirmed its antiviral activity in the FRT. Using single-cell RNA sequencing of the cycling mouse FRT, we show thatIfnεexpression is restricted to specific epithelial cells, is not hormonally regulated, and induces basal interferon-stimulated genes in an autocrine manner. scRNASeq of WT andIfnε-/-uteruses showed that loss ofIfnεreduced basal ISG levels inIfnε-expressing epithelial cells without impacting other cell types. Consistent with this, IFNε was retained intracellularly in primary human FRT cells. scRNASeq of human stem cell-derived enteroids and tissue revealed that multiple GI epithelial cells express high basal IFNε levels, andIfnε-/-mice are more susceptible to enteric viral infection. Our findings reveal that IFNε is an intracellular IFN that provides mucosal immunity across various epithelial tissues, extending its protective functions beyond the FRT.
Rapid wing size evolution in African fig flies (Zaprionus indianus) following temperate colonization
Authors: Gray Weston J. , Rakes Logan M. , Cole Christine , Gunter Ansleigh , He Jerry , Morgan Samantha , Walsh-Antzak Camille R. , Yates Jillian A. , Erickson Priscilla A
Published: November 2024

Invasive species often encounter novel selective pressures in their invaded range, and understanding their potential for rapid evolution is critical for developing effective management strategies. Zaprionus indianus is an invasive drosophilid native to Africa that reached Florida in 2005 and likely re-establishes temperate North American populations each year. We addressed two evolutionary questions in this system: first, do populations evolve phenotypic changes in the generations immediately following colonization of temperate environments? Second, does Z. indianus evolve directional phenotypic changes along a latitudinal cline? We established isofemale lines from wild collections across space and time and measured twelve ecologically relevant phenotypes, using a reference population as a control. Z. indianus evolved smaller wings following colonization, suggesting early colonizers have larger wings, but smaller wings are favorable after colonization. No other phenotypes changed significantly following colonization or across latitudes, but we did see significant post-colonization changes in principal components of all phenotypes. We documented substantial laboratory evolution and effects of the laboratory environment across multiple phenotypes, emphasizing the importance of controlling for both possibilities when conducting common garden studies. Our results demonstrate the potential for rapid adaptation in Z. indianus, which could contribute to its success and expansion throughout invaded ecosystems.
GWAC: A machine learning method to identify functional variants in data-constrained species
Authors: Sharo Andrew G.
Published: November 2024

As environments change, the ability of species to adapt depends on the functional variation they harbor. Identifying these functional variants is an important challenge in conservation genetics. Due to the limited data available for most species of conservation interest, genome-wide selection scans that link specific genetic variants with a phenotype are not feasible. However, functional variants may still be identified by considering predicted consequence, evolutionary conservation, and other sequence-based features. We developed Genome-Wide vAriant Classification (GWAC), a supervised machine learning framework to prioritize genome-wide variants by functional impact. GWAC requires only features that can be generated from an annotated genome. We evaluate GWAC by first using a set of human data constrained to match what may be available for threatened species. We find that GWAC weights features more heavily that are known to be predictive of functional variation and prioritizes both single nucleotide variants and indels, consistent with mutational constraint found in population genetics studies. GWAC performs nearly as well as CADD, a leading genome-wide predictor in humans that uses substantially more features and data that are typically available only for model organisms. While it is not possible to empirically evaluate GWAC on a species for which no functional variants are known, we find that a version of GWAC generated for the greater prairie chicken (Tympanuchus cupido pinnatus) weights features similarly to our human version. We compare the results of using a species-specific variant impact predictor against lifting-over variants from a closely related model organism and find that the species-specific approach retains functional variants that are lost during lift-over. We anticipate GWAC could be used to estimate conservation metrics such as genetic load and adaptive capacity, while also enabling researchers to identify individual variants responsible for adaptive phenotypes.
Improved detection of differentially abundant proteins through FDR-control of peptide-identity-propagation
Authors: Solivais Alexander J. , Boekweg Hannah , Smith Lloyd M. , Noble William S. , Shortreed Michael R. , Payne Samuel H. , Keich Uri
Published: November 2024

The goal of proteomics is to identify and quantify peptides and proteins within a biological sample. Almost all algorithms for the identification of peptides in LC-MS/MS data employ two steps: peptide/spectrum matching and peptide-identity-propagation (PIP), also known as match-between-runs. PIP was originally envisioned as a backup method to overcome measurement stochasticity. However, current PIP implementations can routinely account for up to 40% of all results, with that proportion rising as high as 75% in single-cell proteomics. Unlike peptide identities derived through peptide/spectrum matches, for which error estimation has been strictly enforced for decades, peptide identities derived through PIP have not historically been subject to statistical evaluation. As an indispensable component of label free quantification, PIP needs a simple and statistically rigorous method for estimating its error rates. Although several tools claim to control the false discovery rate (FDR) of PIP, these claims cannot be validated as there is currently no accepted method to assess the accuracy of the stated FDR. We present a method for FDR control of PIP, called PIP-ECHO, and devise a rigorous protocol for evaluating FDR control of any PIP method. Using three different benchmark datasets, we evaluate PIP-ECHO alongside the PIP procedures implemented by FlashLFQ, IonQuant, and MaxQuant. These analyses show that only PIP-ECHO can accurately control the FDR of PIP at 1% across all datasets, including single cell. When analyzing spike-in datasets where different known amounts of yeast or E. coli peptides are added to a constant background of human peptides, PIP-ECHO increases both the accuracy and sensitivity of differential expression analysis, yielding 53% more differentially abundant proteins than MaxQuant and 146% more than IonQuant.
Characterization of the Subclinical Perilesional Zone in the Macula of Early-Stage ABCA4 Disease
Authors: Zee Aiden , Lee Winston , Su Pei-Yin , Zernant Jana , Tsang Stephen H. , Allikmets Rando
Published: November 2024

Abstract

Purpose

To characterize photoreceptor layer thinning in clinically unremarkable regions adjacent to the atrophic lesion in early-stage ABCA4 disease eyes.

Methods

27 patients with confined atrophic lesions (≤3.5mm in diameter) were included. Two pathogenic alleles were confirmed by sequencing of theABCA4locus. Multimodal imaging included color fundus photography, short wavelength-autofluorescence (SW-AF) and near infrared-autofluorescence (NIR-AF) imaging. Total receptor+ (TREC+) thickness was segmented in spectral domain-optical coherence tomography (SD-OCT) scans in patient eyes (n=27) along with age-matched healthy control eyes (n=20).

Results

µageof the study cohort was 24.1 years and 15/27 (55.6%) patients harbored genotypes consisting of the p.(Gly1961Glu) variant inABCA4. Atrophic lesions in the central macula ranged from 0.61 to 3.13 mm in diameter (µ= 1.73,σ= 0.70). Six patients had mild RPE mottling adjacent to the lesion on NIR-AF. The atrophic lesion corresponded to a disruption of photoreceptor-attributable bands on SD-OCT while all layers were visibly intact outside the lesion. TREC+ thickness in patient eyes were <0.15 mm or below 4σof normal control eyes immediately adjacent to the lesion edge and gradually normalized to within±2σat≈1.2 mm eccentricity from the fovea.

Conclusion

A uniform subclinical perilesional zone (SPZ) of photoreceptor thinning extends around the perimeter of early-stage atrophic lesions in ABCA4 disease. This region spatially maps to known regions of vision loss and more accurately approximates the extent of photoreceptor abnormality compared to the disease changes visible on standard fundus imaging.

Translational relevance

Semi-automated segmentation of SD-OCT scans identifies a consistent subclinical biomarker relevant to early photoreceptor degeneration in ABCA4 disease.
The relationships between cochlear nerve health and AzBio sentence scores in quiet and noise in postlingually deafened adult cochlear implant users
Authors: Gao Zi , Yuan Yi , Oleson Jacob J. , Mueller Christopher R. , Bruce Ian C. , Gifford René H. , He Shuman
Published: November 2024

Objectives

This study investigated the relationships between the cochlear nerve (CN) health and sentence-level speech perception outcomes measured in quiet and noise in postlingually deafened adult cochlear implant (CI) users.

Design

Study participants included 24 postlingually deafened adult CI users with a Cochlear® Nucleus™ device. For each participant, only one ear was tested. Neural health of the CN was assessed at three or four electrode locations across the electrode array using two parameters derived from results of the electrically evoked compound action potential (eCAP). One parameter was the phase locking value (PLV) which estimated neural synchrony in the CN. The other parameter was the sensitivity of the eCAP amplitude growth function (AGF) slope to changes in the interphase gap (IPG) of biphasic electrical pulses (i.e., the IPGEslope). Speech perception was tested using AzBio sentences in both quiet and a ten-talker babble background noise with +5 dB and +10 dB signal-to-noise ratios (SNR). IPGEslopeand PLV values were averaged across electrodes for each subject, both with and without weighting by the frequency importance function (FIF) of the AzBio sentences. Pearson and Spearman correlations were used to assess the pairwise relationships between the IPGEslope, the PLV, and age. Multiple linear regression models with AzBio score as the outcome and the PLV and the IPGEslopeas predictors were used to evaluate the associations between the three variables while controlling for age.

Results

The correlation between the IPGEslopeand the PLV was negligible and not statistically significant. The PLV, but not the IPGEslope, differed significantly across electrodes, where the apical electrodes had larger PLVs (better neural synchrony) than the basal electrodes. The IPGEslope, but not the PLV, was significantly correlated with participant’s age, where smaller IPGEslopevalues (poorer CN health) were associated with more advanced age. The PLV, but not the IPGEslope, was significantly associated with AzBio scores in noise, where larger PLVs predicted better speech perception in noise. Neither the PLV nor the IPGEslopewas significantly associated with AzBio score in quiet. The result patterns remained the same regardless of whether the mean values of the IPGEslopeand the PLV were weighted by the AzBio FIF.

Conclusions

The IPGEslopeand the PLV quantify different aspects of CN health. The positive association between the PLV and AzBio scores suggests that neural synchrony is important for speech perception in noise in adult CI users. The lack of association between age and the PLV indicates that reduced neural synchrony in the CN is unlikely the primary factor accounting for the greater deficits in understanding speech in noise observed in elderly, as compared to younger, CI users.
PDE5 inhibition and Alzheimer’s disease risk: a mendelian randomisation study
Authors: Alcalde-Herraiz Marta , Woolf Benjamin , Xie Junqing , Anderson Emma , Gill Dipender , Tzoulaki Ioanna , Winchester Laura M , Yarmolinsky James , Prieto-Alhambra Daniel , Newby Danielle
Published: November 2024

INTRODUCTION

While preclinical studies suggest that Phosphodiesterase 5 (PDE5) inhibition may reduce cognitive impairment, findings from observational studies on whether PDE5 inhibitors reduce Alzheimer’s disease (AD) risk have been inconsistent.

METHODS

A two-samplecis-Mendelian Randomisation (MR) analysis was conducted to estimate the causal effect of PDE5 inhibition on AD risk. The analysis was performed across four different genome-wide association studies (GWAS) of AD to enhance evidence reliability through triangulation. Additionally, a sex-stratified MR analysis using data from UK Biobank was performed to assess potential sex-specific effects.

RESULTS

No evidence of a causal association between PDE5 inhibition and AD risk was found in the main analyses or sex-stratified analysis.

DISCUSSION

MR findings suggest that PDE5 inhibitors are unlikely to decrease the risk of AD. Further research is needed to thoroughly understand the impact of PDE5 inhibitors on the risk of Alzheimer’s disease.