bluuebunny/crossref_metadata_2025 huggingface dataset:
Non-ST-elevation acute coronary syndromes with previous coronary artery bypass grafting: a meta-analysis of invasive vs. conservative management
Authors: Kelham Matthew , Vyas Rohan , Ramaseshan Rohini , Rathod Krishnaraj , de Winter Robbert J , de Winter Ruben W , Bendz Bjorn , Thiele Holger , Hirlekar Geir , Morici Nuccia , Myat Aung , Michalis Lampros K , Sanchis Juan , Kunadian Vijay , Berry Colin , Mathur Anthony , Jones Daniel A
Published: May 2024

Background and Aims

A routine invasive strategy is recommended in the management of higher risk patients with non-ST-elevation acute coronary syndromes (NSTE-ACSs). However, patients with previous coronary artery bypass graft (CABG) surgery were excluded from key trials that informed these guidelines. Thus, the benefit of a routine invasive strategy is less certain in this specific subgroup.

Methods

A systematic review and meta-analysis of randomized controlled trials (RCTs) was conducted. A comprehensive search was performed of PubMed, EMBASE, Cochrane, and ClinicalTrials.gov. Eligible studies were RCTs of routine invasive vs. a conservative or selective invasive strategy in patients presenting with NSTE-ACS that included patients with previous CABG. Summary data were collected from the authors of each trial if not previously published. Outcomes assessed were all-cause mortality, cardiac mortality, myocardial infarction, and cardiac-related hospitalization. Using a random-effects model, risk ratios (RRs) with 95% confidence intervals (CIs) were calculated.

Results

Summary data were obtained from 11 RCTs, including previously unpublished subgroup outcomes of nine trials, comprising 897 patients with previous CABG (477 routine invasive, 420 conservative/selective invasive) followed up for a weighted mean of 2.0 (range 0.5–10) years. A routine invasive strategy did not reduce all-cause mortality (RR 1.12, 95% CI 0.97–1.29), cardiac mortality (RR 1.05, 95% CI 0.70–1.58), myocardial infarction (RR 0.90, 95% CI 0.65–1.23), or cardiac-related hospitalization (RR 1.05, 95% CI 0.78–1.40).

Conclusions

This is the first meta-analysis assessing the effect of a routine invasive strategy in patients with prior CABG who present with NSTE-ACS. The results confirm the under-representation of this patient group in RCTs of invasive management in NSTE-ACS and suggest that there is no benefit to a routine invasive strategy compared to a conservative approach with regard to major adverse cardiac events. These findings should be validated in an adequately powered RCT.
A cyanobacterial chemotaxis-like system controls phototactic orientation via phosphorylation of two antagonistic response regulators
Authors: Han Yu , Hammerl Jonas , Flemming Felicitas E , Schuergers Nils , Wilde Annegret
Published: May 2024

Photosynthetic cyanobacteria exhibit phototaxis, utilizing type IV pili (T4P) to navigate either toward or away from a light source. The Tax1 system is a chemotaxis-like signal transduction pathway that controls the switch in cell polarity, which is crucial for positive phototaxis in Synechocystis sp. PCC 6803. The system consists of the blue/green light sensor PixJ, which controls the histidine kinase PixL and two CheY-like response regulators, PixG and PixH. However, the molecular mechanism by which Tax1 regulates T4P activity and polarity is poorly understood. Here, we investigated the phosphotransfer between PixL and its cognate response regulators in vitro and analyzed the localization and function of wild-type and phosphorylation-deficient PixG and PixH during phototaxis. We found that both PixG and PixH are phosphorylated by PixL but have different roles in phototaxis regulation. Only phosphorylated PixG interacts with the T4P motor protein PilB1 and localizes to the leading cell pole under directional light, thereby promoting positive phototaxis. In contrast, PixH is a negative regulator of PixG phosphorylation and inhibits positive phototaxis. We also demonstrated that the C-terminal receiver domain of PixL is essential for positive phototaxis, and modulates the kinase activity of PixL. Our findings reveal the molecular basis of positive phototaxis regulation by the Tax1 system and provide insights into the division of labor between PatA-type and CheY-like response regulators in cyanobacterial chemotaxis-like systems. Furthermore, these findings highlight similarities in the regulation of movement direction during twitching motility in phototactic and chemotactic bacteria.
Chloroplast protein StFC-II was manipulated by a Phytophthora effector to enhance host susceptibility
Authors: Xu Meng , Sun Xinyuan , Wu Xinya , Qi Yetong , Li Hongjun , Nie Jiahui , Yang Zhu , Tian Zhendong
Published: May 2024

Oomycete secretes a range of RxLR effectors into host cells to manipulate plant immunity by targeting proteins from several organelles. In this study, we report that chloroplast protein StFC-II is hijacked by a pathogen effector to enhance susceptibility. Phytophthora infestans RxLR effector Pi22922 is activated during the early stages of P. infestans colonization. Stable overexpression of Pi22922 in plants suppresses flg22-triggered reactive oxygen species (ROS) burst and enhances leaf colonization by P. infestans. A potato ferrochelatase 2 (FC-II, a nuclear-encoded chloroplast-targeted protein), a key enzyme for heme biosynthesis in chloroplast, was identified as a target of Pi22922 in the cytoplasm. The pathogenicity of Pi22922 in plants is partially dependent on FC-II. Overexpression of StFC-II decreases resistance of potato and Nicotiana benthamiana against P. infestans, and silencing of NbFC-II in N. benthamiana reduces P. infestans colonization. Overexpression of StFC-II increases heme content and reduces chlorophyll content and photosynthetic efficiency in potato leaves. Moreover, ROS accumulation both in chloroplast and cytoplasm is attenuated and defense-related genes are down-regulated in StFC-II overexpression transgenic potato and N. benthamiana leaves. Pi22922 inhibits E3 ubiquitin ligase StCHIP-mediated StFC-II degradation in the cytoplasm and promotes its accumulation in chloroplasts. In summary, this study characterizes a new mechanism that an oomycete RxLR effector suppresses host defenses by promoting StFC-II accumulation in chloroplasts, thereby compromising the host immunity and promoting susceptibility.
Simulation testing performance of ensemble models when catch data are underreported
Authors: Brooks Elizabeth N , Brodziak Jon K T
Published: May 2024

Ensemble model use in stock assessment is increasing, yet guidance on construction and an evaluation of performance relative to single models is lacking. Ensemble models can characterize structural uncertainty and avoid the conundrum of selecting a “best” assessment model when alternative models explain observed data equally well. Through simulation, we explore the importance of identifying candidate models for both assessment and short-term forecasts and the consequences of different ensemble weighting methods on estimated quantities. Ensemble performance exceeded a single best model only when the set of candidate models spanned the true model configuration. Accuracy and precision depended on the model weighting scheme, and varied between two case studies investigating the impact of catch accuracy. Information theoretic weighting methods performed well in the case study with accurate catch, while equal weighting performed best when catch was underreported. In both cases, equal weighting produced multimodality. Ensuring that an ensemble spans the true state of nature will be challenging, but we observed that a change in sign of Mohn’s rho across candidate models coincided with the true OM being bounded. Further development of protocols to select an objective and balanced set of candidate models, and diagnostics to assess adequacy of candidates are recommended.
Spliced-Leader RNA as a Dynamic Marker for Monitoring Viable Leishmania Parasites During and After Treatment
Authors: Hendrickx Rik , Melkamu Roma , Tadesse Dagimawie , Teferi Tedla , Feijens Pim-Bart , Vleminckx Margot , van Henten Saskia , Alves Fabiana , Shibru Tamiru , van Griensven Johan , Caljon Guy , Pareyn Myrthe
Published: May 2024

Accurate detection of viable Leishmania parasites is critical for evaluating visceral leishmaniasis (VL) treatment response at an early timepoint. We compared the decay of kinetoplast DNA (kDNA) and spliced-leader RNA (SL-RNA) in vitro, in vivo, and in a VL patient cohort. An optimized combination of blood preservation and nucleic acid extraction improved efficiency for both targets. SL-RNA degraded more rapidly during treatment than kDNA, and correlated better with microscopic examination. SL-RNA quantitative polymerase chain reaction emerges as a superior method for dynamic monitoring of viable Leishmania parasites. It enables individualized treatment monitoring for improved prognoses and has potential as an early surrogate endpoint in clinical trials.
RIL-seq reveals extensive involvement of small RNAs in virulence and capsule regulation in hypervirulent Klebsiella pneumoniae
Authors: Goh Kwok Jian , Altuvia Yael , Argaman Liron , Raz Yair , Bar Amir , Lithgow Trevor , Margalit Hanah , Gan Yunn-Hwen
Published: May 2024

Hypervirulent Klebsiella pneumoniae (hvKp) can infect healthy individuals, in contrast to classical strains that commonly cause nosocomial infections. The recent convergence of hypervirulence with carbapenem-resistance in K. pneumoniae can potentially create ‘superbugs’ that are challenging to treat. Understanding virulence regulation of hvKp is thus critical. Accumulating evidence suggest that posttranscriptional regulation by small RNAs (sRNAs) plays a role in bacterial virulence, but it has hardly been studied in K. pneumoniae. We applied RIL-seq to a prototypical clinical isolate of hvKp to unravel the Hfq-dependent RNA-RNA interaction (RRI) network. The RRI network is dominated by sRNAs, including predicted novel sRNAs, three of which we validated experimentally. We constructed a stringent subnetwork composed of RRIs that involve at least one hvKp virulence-associated gene and identified the capsule gene loci as a hub target where multiple sRNAs interact. We found that the sRNA OmrB suppressed both capsule production and hypermucoviscosity when overexpressed. Furthermore, OmrB base-pairs within kvrA coding region and partially suppresses translation of the capsule regulator KvrA. This agrees with current understanding of capsule as a major virulence and fitness factor. It emphasizes the intricate regulatory control of bacterial phenotypes by sRNAs, particularly of genes critical to bacterial physiology and virulence.
Interpretable prediction of mRNA abundance from promoter sequence using contextual regression models
Authors: Wang Song , Wang Wei
Published: May 2024

While machine learning models have been successfully applied to predicting gene expression from promoter sequences, it remains a great challenge to derive intuitive interpretation of the model and reveal DNA motif grammar such as motif cooperation and distance constraint between motif sites. Previous interpretation approaches are often time-consuming or have difficulty to learn the combinatory rules. In this work, we designed interpretable neural network models to predict the mRNA expression levels from DNA sequences. By applying the Contextual Regression framework we developed, we extracted weighted features to cluster samples into different groups, which have different gene expression levels. We performed motif analysis in each cluster and found motifs with active or repressive regulation on gene expression. By comparing the co-occurrence locations of discovered motifs, we also uncovered multiple grammars of motif combination including communities of cooperative motifs and distance constraints between motif pairs. These results revealed new insights of the regulatory architecture of promoter sequences.
Impact of Multidisciplinary Prehabilitation Interventions on Postoperative Hospital Length of Stay and Functional Capacity in Patients Undergoing Resection of Colorectal Cancer: A Systematic Review and Meta-analysis
Authors: Marmol-Perez Andres , Corres Pablo , Fernández-Escabias Manuel , Carrilho-Candeias Sofia , Ruiz Jonatan R. , Amaro-Gahete Francisco J. , Carneiro-Barrera Almudena
Published: May 2024

BACKGROUND:

Although surgery is commonly regarded as the primary curative treatment for colorectal cancer, it could potentially be associated with postoperative morbidity and mortality.

OBJECTIVE:

To determine the pooled effect of exercise and multidisciplinary prehabilitation interventions on postoperative hospital length of stay and functional capacity in patients undergoing resection of colorectal cancer.

DATA SOURCES:

A systematic search was conducted in MEDLINE (via PubMed) and Web of Science databases from inception to November 2022.

STUDY SELECTION:

The original systematic search retrieved 2005 studies. After the removal of duplicates and screening by title and abstract, 77 eligible full-text documents were evaluated for final inclusion in the meta-analysis. A total of 12 randomized controlled trials, 5 nonrandomized controlled trials, and 3 uncontrolled before-and-after studies were selected.

MAIN OUTCOME MEASURES:

Postoperative hospital length of stay (in days) and functional capacity (assessed with the peak of oxygen consumption [VO2 peak] and 6-minute walking test) were the outcome measures.

RESULTS:

The meta-analysis was conducted on 20 studies (3805 participants). Randomized controlled trials and nonrandomized controlled trials showed significant reductions in postoperative hospital length of stay (d = –0.10, nearly 2 days) and significant incremental improvements in VO2 peak (d = 0.27) and 6-minute walking test (d = 0.31). Regarding the before-and-after studies, the pooled effect of multidisciplinary prehabilitation interventions was positively significant for VO2 peak (d = 0.29) and 6-minute walking test (d = 0.29). There was no risk of publication bias (Egger test: p > 0.05), with a score of 0.71 (0–1) on average.

LIMITATIONS:

There was a high between-studies heterogeneity, and several outcomes did not have the required number of studies for a desirable statistical power.

CONCLUSIONS:

These findings suggest that multidisciplinary prehabilitation interventions might be effective at decreasing postoperative hospital length of stay (nearly 2 days) and improving functional capacity.

REGISTRATION:

PROSPERO registration number CRD42022373982.
Crystalline Hepatopathy Associated With Bietti Crystalline Dystrophy: A Striking Manifestation of Disordered Fatty Acid Metabolism
Authors: Dulken Ben W. , Bahceci Dorukhan , Leung Loh-Shan , Mahajan Vinit B. , Choi Won-Tak , Tan Serena Y.
Published: May 2024

Bietti crystalline dystrophy (BCD) is a rare heritable retinal disease characterized by crystal deposition primarily in the retina. It is associated with atrophy of the retinal pigment epithelium (RPE) and is caused by variants in CYP4V2, which encodes a cytochrome P450 hemethiolate protein superfamily member. CYP4V2 is involved in the selective hydrolysis of saturated medium chain fatty acids, and patients with BCD demonstrate abnormalities in fatty acid metabolism, including abnormal lipid profiles and the accumulation of the pathogenic crystals within the RPE, which leads to the visual pathologies characteristic of BCD. However, the precise identity of the crystals is currently unknown, and BCD has no established extraocular manifestations. Here, we report granulomatous hepatitis associated with abundant diffuse crystalline clefts in the hepatic parenchyma in 3 patients with retinal dystrophy and dyslipidemia: 2 with pathogenic CYP4V2 variants and 1 patient with clinical ophthalmologic findings suggestive of BCD but without available genetic testing. The unique and striking histologic features unifying the liver biopsies in all 3 patients strongly support a process related to abnormal fatty acid metabolism underlying the genetic disease of BCD, expanding the spectrum of BCD and shedding light on the importance of CYP4V2 in systemic fatty acid metabolism.
Complement receptor 3-dependent engagement by
Candida glabrata
β-glucan modulates dendritic cells to induce regulatory T-cell expansion
Authors: Kunanopparat Areerat , Dinh Truc Thi Huong , Ponpakdee Pranpariya , Padungros Panuwat , Kaewduangduen Warerat , Ariya-anandech Kasirapat , Tummamunkong Phawida , Samaeng Amanee , Sae-ear Pannagorn , Leelahavanichkul Asada , Hirankarn Nattiya , Ritprajak Patcharee
Published: May 2024

Candida glabrata
is an important pathogen causing invasive infection associated with a high mortality rate. One mechanism that causes the failure of
Candida
eradication is an increase in regulatory T cells (Treg), which play a major role in immune suppression and promoting
Candida
pathogenicity. To date, how
C. glabrata
induces a Treg response remains unclear. Dendritic cells (DCs) recognition of fungi provides the fundamental signal determining the fate of the T-cell response. This study investigated the interplay between
C. glabrata
and DCs and its effect on Treg induction. We found that
C. glabrata
β-glucan was a major component that interacted with DCs and consequently mediated the Treg response. Blocking the binding of
C. glabrata
β-glucan to dectin-1 and complement receptor 3 (CR3) showed that CR3 activation in DCs was crucial for the induction of Treg. Furthermore, a ligand–receptor binding assay showed the preferential binding of
C. glabrata
β-glucan to CR3. Our data suggest that
C. glabrata
β-glucan potentially mediates the Treg response, probably through CR3-dependent activation in DCs. This study contributes new insights into immune modulation by
C. glabrata
that may lead to a better design of novel immunotherapeutic strategies for invasive
C. glabrata
infection.
Staphylococcus aureus  associated with post-operative wound infections in Western Kenya reveals genomic hotspots for pathogen evolution

Authors: MOGOI NICHOLAS NYABERA , Sifuna Anthony Wawire , Okoth Patrick Kirsteen , Reva Oleg , Malaba Rose , Negesa Ruth , Nyongesa Peter Kuloba , Osoro Ezra Kombo , Welch Martin
Published: May 2024

Objectives.  Staphylococcus aureus is one of the most common pathogens attributed to hospital infections. Although S. aureus infections have been well studied in developed countries, far less is known about the biology of the pathogen in sub-Saharan Africa. 
Methods. Here, we report on the isolation, antibiotic resistance profiling, whole genome sequencing, and genome comparison of six multi-drug resistant isolates of S. aureus obtained from a referral hospital in Kakamega, Western Kenya.
Results. Five of the six isolates contained a 20.7-kb circular plasmid carrying blaZ (associated with resistance to b-lactam antibiotics). These five strains all belonged to the same sequence type, ST152. Despite the similarity of the plasmid these isolates, whole genome sequencing revealed that the strains differed, depending on whether they were associated with hospital-acquired or community-acquired infections.
Conclusion. The intriguing finding is that the hospital acquired and the community acquired isolates of S. aureusbelonging to the same genotype ST152 formed two separate sub-clusters in the phylogenetic tree and differed by the repertoire of accessory virulence genes suggesting an ongoing adaptive evolution and significant genomic plasticity.
Optimisation of a DNA extraction protocol for improving the bacterial and fungal classification based on Nanopore sequencing
Authors: Thu May Soe , Sawaswong Vorthon , Chanchaem Prangwalai , Klomkliew Pavit , Campbell Barry J. , Hirankarn Nattiya , Fothergill Joanne L , Payungporn Sunchai
Published: May 2024

Ribosomal RNA gene amplicon sequencing is commonly used to evaluate microbiome profiles in health and disease and document the impact of interventional treatments. Nanopore sequencing is attractive since it can provide greater classification at the species level. However, optimised protocols to target marker genes for bacterial and fungal profiling are needed. To achieve an increased taxonomic resolution, we developed extraction and full-length amplicon PCR-based approaches using Nanopore sequencing. Three lysis conditions were applied to a mock microbial community, including known bacterial and fungal species; the ZymoBIOMICSTM lysis buffer (ML) alone, incorporating bead-beating (MLB), or bead-beating plus MetaPolyzyme enzymatic treatment (MLBE). Profiling of bacterial comparison to reference data, MLB had more statistically different bacterial phyla and genera than the others. Fungal profiling, MLB had a significant increase of Ascomycota and a decline of Basidiomycota, subsequently failing to detect Malassezia and Cryptococcus. Also, the principal coordinates analysis (PCoA) plot by the Bray-Curtis metric showed a significant difference among groups for bacterial (p = 0.033) and fungal (p = 0.012) profiles, highlighting the importance of understanding the biases present in pretreatment. Overall, the microbial profiling and diversity analysis revealed that ML and MLBE have more similarity than MLB for both bacteria and fungi; therefore, using this specific pipeline, bead-beating is not recommended for whole gene amplicon sequencing. However, ML alone was suggested as an optimal approach considering DNA yield, taxonomic classification, reagent cost and hands-on time. This could be an initial proof-of-concept study for simultaneous human bacterial and fungal microbiome studies.
Exceptional association of two species of bacteria causing acute appendicitis: Haemophilus influenzae and Enterobacter cloacae
Authors: Adil Fatima Zahra , Benaissa Elmostafa , Ben Lahlou Yassine , Laamara Leila , Bssaibis Fatna , Maleb Adil , Chadli Mariama , Elouennass Mostafa
Published: May 2024

Appendicitis, typically caused by appendiceal lumen obstruction, is a prevalent abdominal surgical emergency worldwide. While most cases involve Enterobacterales, Haemophilus influenzae, primarily known for upper respiratory infections, is infrequently associated with gastrointestinal infections. This article presents an exceptional case of acute appendicitis caused by both Haemophilus influenza and Enterobacter cloacae in a 15-year-old child, highlighting the significance of recognizing uncommon pathogens in appendicitis and emphasizing the necessity for thorough microbiological investigations to refine diagnostic approaches.
Gordonia prachuapensis sp. nov. and Gordonia sesuvii sp. nov., two novel actinobacteria isolated from mangrove sediments and leaves of halophyte Sesuvium portulacastrum in Thailand
Authors: Suphannarot Aekasit , Butdee Waranya , Suriyachadkun Chanwit , Duangmal Kannika , Mingma Ratchanee
Published: May 2024

A polyphasic approach was used to characterize two novel actinobacterial strains, designated PKS22-38T and LSe1-13T, which were isolated from mangrove soils and leaves of halophyte Sesuvium portulacastrum (L.), respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that they belonged to the genus Gordonia and were most closely related to three validly published species with similarities ranging from 98.6 to 98.1 %. The genomic DNA G+C contents of strains PKS22-38T and LSe1-13T were 67.3 and 67.2 mol%, respectively. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the two strains were 93.3 and 54.9 %, respectively, revealing that they are independent species. Meanwhile, the ANI and dDDH values between the two novel strains and closely related type strains were below 80.5 and 24.0 %, respectively. Strains PKS22-38T and LSe1-13T contained C16 : 0, C18 : 1
 ω9c and C18 : 0 10-methyl (TBSA) as the major fatty acids and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as the main phospholipids. The predominant menaquinone was MK-9(H2). Based on phenotypic, chemotaxonomic, phylogenetic and genomic data, strains PKS22-38T and LSe1-13T are considered to represent two novel species within the genus Gordonia, for which the names Gordonia prachuapensis sp. nov. and Gordonia sesuvii sp. nov. are proposed, with strain PKS22-38T (=TBRC 17540T=NBRC 116256T) and strain LSe1-13T (=TBRC 17706T=NBRC 116396T) as the type strains, respectively.
Natural killer cells associate with epithelial cells in the pancreatic ductal adenocarcinoma tumor microenvironment
Authors: Malchiodi Zoe X. , Suter Robert K. , Deshpande Atul , Peran Ivana , Harris Brent T. , Duttargi Anju , Chien Min-Ju , Hariharan Samika , Wetherill Lucia , Jablonski Sandra A. , Ho Won Jin , Fertig Elana J. , Weiner Louis M.
Published: May 2024

Background

Pancreatic ductal adenocarcinoma (PDAC) is the most common form of pancreatic cancer. PDAC’s poor prognosis and resistance to immunotherapy are attributed in part to its dense, fibrotic tumor microenvironment (TME), which is known to inhibit immune cell infiltration. We recently demonstrated that PDAC patients with higher natural killer (NK) cell content and activation have better survival rates. However, NK cell interactions in the PDAC TME have yet to be deeply studied. We show here that NK cells are present and active in the human PDAC TME.

Methods

We used imaging mass cytometry (IMC) to assess NK cell content, function, and spatial localization in human PDAC samples. Then, we used CellChat, a tool to infer ligand-receptor interactions, on a human PDAC scRNAseq dataset to further define NK cell interactions in PDAC.

Results

Spatial analyses showed for the first time that active NK cells are present in the PDAC TME, and both associate and interact with malignant epithelial cell ducts. We also found that fibroblast-rich, desmoplastic regions limit NK cell infiltration in the PDAC TME. CellChat analysis identified that the CD44 receptor on NK cells interacts with PDAC extracellular matrix (ECM) components such as collagen, fibronectin and laminin expressed by fibroblasts and malignant epithelial cells. This led us to hypothesize that these interactions play roles in regulating NK cell motility in desmoplastic PDAC TMEs. Using 2D and 3Din vitroassays, we found that CD44 neutralization significantly increased NK cell invasion through matrix.

Conclusions

Targeting ECM-immune cell interactions may increase NK cell invasion into the PDAC TME.

Graphical Abstract
Supersize me: torpor assists pre-hibernation fattening in a boreal bat
Authors: Fjelldal Mari A. , Fritzén Niclas R. , Suominen Kati M. , Lilley Thomas M.
Published: May 2024

Hibernators face an energetic dilemma in the autumn at northern latitudes; while temperatures and food availability decrease, hibernating species need to build fat deposits to survive the winter. During this critical fattening phase, insectivorous boreal bats use torpor to build and conserve their reserves. However, we still know little about temporal variability in torpor use employed by bats in autumn and how decreasing temperatures and food availability in combination with increasing individual body mass impact this. Here we present two general hypotheses for explaining temporal torpor patterns observed in a boreal bat (Eptesicus nilssonii), in which torpor use I) facilitates rapid mass gain or II) conserves stored body mass. Although temporally separated in our dataset, temperature, insect abundance and body mass throughout autumn in the study system indicate thatE. nilssoniireaches a majority of its overwintering mass before the onset of increasing daily and nightly torpor use. In combination with generally low food availability by this point in time, these observations suggest that torpor expression might be intended to conserve gained reserves. Our study is intended as a first proof-of-concept for disentangling temporal drivers of torpor in bats during the pre-hibernation fattening phase.
Gene regulatory activity associated with PCOS revealedDENND1A-dependent testosterone production
Authors: Sankaranarayanan Laavanya , Brewer Kelly J , Johnson Graham D , Barrera Alejandro , Venukuttan Revathy , Sisk Ryan , Dunaif Andrea , Reddy Timothy E
Published: May 2024

Polycystic ovary syndrome (PCOS) is among the most common disorders affecting up to 15% of the menstruating population globally. It is the leading cause of anovulatory infertility and a major risk factor for type 2 diabetes. Elevated testosterone levels are a core endophenotype. Despite that prevalence, the underlying causes remain unknown. PCOS genome-wide association studies (GWAS) have reproducibly mapped a number of susceptibility loci, including one encompassing a gene regulating androgen biosynthesis, DENND1A. Identifying the causal variants within these loci will provide fundamental insight into the precise biological pathways that are disrupted in PCOS. We report the discovery of gene regulatory mechanisms that help explain genetic association with PCOS in the GATA4, FSHB and DENND1A loci using a combination of high throughput reporter assays, CRISPR-based epigenome editing, and genetic association analysis from PCOS case and control populations. In addition, we found that increased endogenous DENND1A expression causes elevated testosterone levels in an adrenal cell model, specifically by perturbing candidate regulatory elements. These results further highlight the potential for combining genetic variant analyses with experimental approaches to fine map genetic associations with disease risk.
Modeling the Impact of Seasonality on Mosquito Population Dynamics: Insights for Vector Control Strategies
Authors: Baafi Joseph , Hurford Amy
Published: May 2024

Mosquitoes are important vectors for the transmission of some major infectious diseases of humans, i.e., malaria, dengue, West Nile Virus and Zika virus. The burden of these diseases is different for different regions, being highest in tropical and subtropical areas, which have high annual rainfall, warm temperatures, and less pronounced seasonality. The life cycle of mosquitoes consists of four distinct stages: eggs, larvae, pupae, and adults. These life stages have different mortality rates and only adults can reproduce. Seasonal weather may affect the population dynamics of mosquitoes, and the relative abundance of different mosquito stages. We developed a stage-structured model that considers laboratory experiments describing how temperature and rainfall affects the reproduction, maturation and survival of different Anopheles mosquito stages, the species that transmits the parasite that causes malaria. We consider seasonal temperature and rainfall patterns and describe the stage-structured population dynamics of the Anopheles mosquito in Ain Mahbel, Algeria, Cape Town, South Africa, Nairobi, Kenya and Kumasi, Ghana. We find that neglecting seasonality leads to significant overestimation or underestimation of mosquito abundance. We find that depending on the region, mosquito abundance: peaks one, two or four times a year, periods of low abundance are predicted to occur for durations ranging from six months (Ain Mahbel) to not at all (Nairobi); and seasonal patterns of relative abundance of stages are sub-stantially different. The region with warmer temperatures and higher rainfall across the year, Kumasi, Ghana, is predicted to have higher mosquito abundance, which is broadly consistent with reported malaria deaths relative to the other countries considered by our study. Our analysis reveals distinct patterns in mosquito abundance across different months and regions. Control strategies often target one specific life stage, for example, applying larvicides to kill mosquito larvae, or spraying insecticides to kill adult mosquitoes. Our findings suggest that differences in seasonal weather affect mosquito stage structure, and that the best approaches to vector control may differ between regions in timing, duration, and efficacy.
LotOfCells: data visualization and statistics of single cell metadata
Authors: González-Velasco Óscar
Published: May 2024

Single-cell sequencing unveils a treasure trove into the biological and molecular characteristics of samples. Yet, within this flood of data, the challenge to draw meaningful conclusions sometimes can be time consuming and a tortuous process.

Here we introduce LotOfCells: a simple R package designed to explore the intricate landscape of phenotypic data within single-cell studies. Normally, we are interested in visualizing and measuring if the differences in the proportion of number of cells across various covariates is significant or biologically relevant. As an example, one of the most common questions is the proportion of different cell types across conditions in our experiment, or the cluster composition before and after treatment (e.g.: difference in cell type proportions between wild type and mutant). LotOfCells helps with the interpretation and visualization of meta-data of these recurrent scenarios, including the test of proportion changes across multiple ordered stages. Additionally, it computes a symmetric divergence score to measure global deregulation of cell proportions due to a condition.

Code repository

R package, manual and relevant examples can be accessed on the GitHub repository:https://github.com/OscarGVelasco/LotOfCells
Bispecific GD2 x B7-H3 Antibody Improves Tumor Targeting and Reduces Toxicity while Maintaining Efficacy for Neuroblastoma
Authors: Erbe Amy K. , Feils Arika S. , Hampton Alina , Rosenkrans Zachary T , Felder Mildred , Wiwczar Jessica , Gerhardt Daniel J. , Bercher Mark , Wenke Belinda , Haertle Callie , Heck Mackenzie , VandenHeuvel Sabrina N. , Frankel Lizzie , Nielsen Megan , Spiegelman Dan , Tsarovsky Noah , Zaborek Jen , Rakhmilevich Alexander L. , Hank Jacquelyn A. , Aluicio-Sarduy Eduardo , Engle Jonathan W. , Davis Jonathan H. , Glaser Bryan , Subbotin Vladimir , Green Roland , Hernandez Reinier , Hammer Bonnie , Sondel Paul M.
Published: May 2024

The current treatment for neuroblastoma involves an immunotherapy regimen that includes a monoclonal antibody that recognizes disialoganglioside (GD2), expressed at high levels on neuroblastoma. GD2 is not present on most normal tissues but is expressed on nerves. Thus, anti-GD2 treatment causes substantial, dose-limiting, neuropathic pain. B7-H3 is overexpressed on multiple tumor types, including neuroblastoma, with minimal normal cell expression and is absent on nerves. We designed a bispecific antibody (bsAb) that requires simultaneous binding of these two tumor antigens to achieve tight-binding of tumor cells. Our preclinical research shows that when compared to an anti-GD2 monospecific antibody, the GD2xB7-H3 bsAb has improved tumor specificity with similar efficacy and reduced toxicity. Since this bsAb does not bind to nerves, it may be possible to administer increased or additional doses beyond the tolerable dose of monospecific anti-GD2 antibodies, which could improve therapeutic efficacy and quality of life for patients with neuroblastoma.
Structure-activity relationships and crucial mechanisms of the coumarin family as germination inhibitors
Authors: Fukuda Kazuma , Hyakutake Sota , Oishi Taiga , Yoshida Michinari , Koga Mizuho , Egami Chisato , Matsura Hyuga , Ito Ryusei , Tsukahara Kosei , Noda Mitsuki , Yoshida Takako , Ryuda Noriko , Nagano Yukio , Matsutaka Kazuhide
Published: May 2024

Members of the coumarin family, including coumarin and its derivatives, are molecules produced by various higher plants, such as cherry trees, and are noted for their diverse physiological activities. Notably, these compounds serve as germination inhibitors, which is considered their primary role. However, the structural basis underpinning the germination-inhibitory effects of the coumarin family is not well understood. Our research investigated the structure-activity relationships using coumarin analogs and revealed that the benzene ring and ester bond within the coumarin skeleton play a crucial role in germination inhibition. We also identified a correlation between the topological polar surface area (TPSA) and the inhibitory effects on germination. Furthermore, while the physiological effects of coumarin on seeds prior to germination have been reported variably, the mechanisms of germination inhibition remain largely unknown. Using RNA-Seq analysis, we have discovered a novel mechanism that is pivotal for germination inhibition, where coumarin suppresses the expression of genes associated with cellulose fiber reassembly. This study holds significant importance in understanding how the coumarin family contributes to plant competition in nature and promises future contributions to the agricultural field through the development of novel growth regulation methods.
Community Collaboration in Public Health Genetic Literacy: Co-Designing Educational Resources for Equitable Genomics Research and Practice
Authors: Salunke Juhi , Byfield Grace , Powell Sabrina N. , Torres Daniel , Leon-Lozano Grace , Jackson Jahnelle , Orphanides Andreas K. , Shaw Jonathan , Owens Thomas , Berg Jonathan S. , Branch Elizabeth , Caro Lennin , Giric Stefanija , O’Daniel Julianne M. , Powell Bradford C. , Ray Ken , Roberts Megan C. , Robinson Carla , Schilling Samantha , Shaw Nicole , Song Erin , Waltz Margaret , Foreman Ann Katherine M. , Foss Kimberly , Milko Laura V.
Published: May 2024

Introduction

Unequal representation in genetic and genomic research is due to various factors including historically inequitable and unjust institutional research practices, potential mistrust of biomedical research among underrepresented populations, and lack of access to or awareness of research opportunities. Facilitating sustainable dialogue between diverse communities and genetic researchers can cultivate trusting, bidirectional relationships, potentially encouraging greater participation in research. Herein, we describe the co-creation of public health educational materials and dissemination plans.

Methods

We describe co-creation by genetics clinicians, researchers, and community members of Genetics and Genomics Educational modules. These modules are aimed at enhancing genetic literacy with a goal to facilitate informed decision-making regarding genetic research and health services. We used Designing for Dissemination and Sustainability, which is grounded in Dissemination and Implementation science, and the Fit to Context process framework to guide the process. This approach ensures the public health context and diverse audience for the modules are considered throughout their development. Additionally, it ensures that broader goals such as dissemination, equity, and sustainability are integrated from the outset, fostering long-term impact and effectiveness.

Conclusion

This article offers an evidence-based template for adoption or adaptation by other community-engaged groups, aimed at bolstering equity and sustainability in the development of health care interventions, with an emphasis on accessible public health literacy. The co-creation of both materials and dissemination plans between researchers and community members may improve the cultural appropriateness and relevance of public health genetics campaigns. Ongoing research is needed to assess the impact on receptiveness and participation.
Repetitive mild closed-head injury induced synapse loss and increased local BOLD-fMRI signal homogeneity
Authors: Markicevic Marija , Mandino Francesca , Toyonaga Takuya , Cai Zhengxin , Fesharaki-Zadeh Arman , Shen Xilin , Strittmatter Stephen M. , Lake Evelyn
Published: May 2024

Repeated mild head injuries due to sports, or domestic violence and military service are increasingly linked to debilitating symptoms in the long term. Although symptoms may take decades to manifest, potentially treatable neurobiological alterations must begin shortly after injury. Better means to diagnose and treat traumatic brain injuries, requires an improved understanding of the mechanisms underlying progression and means through which they can be measured. Here, we employ a repetitive mild closed-head injury (rmTBI) and chronic variable stress (CVS) mouse model to investigate emergent structural and functional brain abnormalities. Brain imaging is achieved with [18F]SynVesT-1 positron emission tomography, with the synaptic vesicle glycoprotein 2A ligand marking synapse density and BOLD (blood-oxygen-level-dependent) functional magnetic resonance imaging (fMRI). Animals were scanned six weeks after concluding rmTBI/Stress procedures. Injured mice showed widespreaddecreasesin synaptic density coupled with an increasein local BOLD-fMRI synchrony detected as regional homogeneity. Injury-affected regions withhighersynapse density showed agreater increasein fMRI regional homogeneity. Taken together, these observations may reflect compensatory mechanisms following injury. Multimodal studies are needed to provide deeper insights into these observations.
Cdbgtricks: Strategies to update a compacted de Bruijn graph
Authors: Hannoush Khodor , Marchet Camille , Peterlongo Pierre
Published: May 2024

Abstract

We proposeCdbgtricks, a new method for updating a compacted de Bruijn graph when adding novel sequences, such as full genomes. Our method indexes the graph, enabling to identify in constant time the location (unitig and offset) of anyk-mer. The update operation that we propose also updates the index. Our results show thatCdbgtricksis faster thanBifrostandGGCAT. We benefit from the index of the graph to provide new functionalities, such as reporting the subgraph that shares a desired percentage ofk-mers with a query sequence with the ability to query a set of reads. The open-sourceCdbgtrickssoftware is available athttps://github.com/khodor14/Cdbgtricks.
Comprehensive multi-site profiling of the malignant pleural mesothelioma micro-environment identifies candidate molecular determinants of histopathologic type
Authors: Severson David T , Freyaldenhoven Samuel , Wadowski Benjamin , Hughes Travis , Hung Yin P , Chirieac Lucien , Jensen Roderick V , Richards William G , Sadek Ahmed A , Gustafson Corinne E , Vermilya Kimberly , Inoccenti Simona , Korle Stephani , Barlow Julianne S , Couger Matthew B , Anderson Jamie , Meyerovitz Jason , Wang Vivian , Dao Mary N. , Shalek Alex K. , De Rienzo Assunta , Bueno Raphael
Published: May 2024

Pleural mesothelioma (PM) comprises sarcomatoid, epithelioid and biphasic histologic subtypes. Bulk PM RNA-sequencing identifies a histology-associated molecular gradient with features of epithelial-mesenchymal (EM) transition but cannot parse malignant, stromal, and immune tumor components. The mechanisms driving PM malignant cell phenotype and associated histology is not well-characterized. Here, we use single-cell RNA-sequencing (scRNA-seq) paired with exome, bulk RNA-sequencing, and histologic analysis of adjacent samples to characterize malignant cell EM state, parse the tumor microenvironment (TME), and identify candidate drivers of PM cell fate. We observe EM variation in malignant cells analogous to bulk samples. We characterize epithelioid and sarcomatoid malignant cell programs and identify a new uncommitted malignant cell EM phenotype enriched in biphasic histology samples. Using inferred CNVs we observe that single individual PM clones consist of cells exhibiting all three EM cell states. We find that distinct non-malignant microenvironments associated with tumors consisting of mostly cells in each state, and identifyWNTinhibition,GAS6-AXL, andHBEGF-EGFRsignaling as pathways associated with distinct EM cell states. These findings provide deeper insight into the molecular drivers of PM malignant cells and identify non-malignant cell signals as potential EMT and growth drivers in PM.
GRanges: A Rust Library for Genomic Range Data
Authors: Buffalo Vince
Published: May 2024

Motivation

The Rust programming language is a fast, memory-safe language that is increasingly used in computational genomics and bioinformatics software development. However, it can have a steep learning curve, which can make writing specialized, high performance bioinformatics software difficult.

Results

GRanges is a Rust library that provides an easy-to-use and expressive way to load genomic range data into memory, compute and process overlapping ranges, and summarize data in a tidy way. The GRanges library outperforms established tools like plyranges and bedtools.

Availability

The GRanges library is available athttps://github.com/vsbuffalo/grangesandhttps://crates.io/crates/granges.
Novel enzyme-based reduced representation method for DNA methylation profiling with low inputs
Authors: Liu Qianli , Helmin Kathryn A. , Dortzbach Zachary D. , Reyes Flores Carla P. , Torres Acosta Manuel A. , Gurkan Jonathan K. , Joudi Anthony M. , Mambetsariev Nurbek , Morales-Nebreda Luisa , Kang Mengjia , Rasmussen Luke , Pérez-Leonor Xóchitl G. , Abdala-Valencia Hiam , Singer Benjamin D.
Published: May 2024

DNA methylation at cytosine-phospho-guanine (CpG) residues is a vital biological process that regulates cell identity and function. Although widely used, bisulfite-based cytosine conversion procedures for DNA methylation sequencing require high temperature and extreme pH, which lead to DNA degradation, especially among unmethylated cytosines. Enzymatic methylation sequencing (EM-seq), an enzyme-based cytosine conversion method, has been proposed as a less biased alternative for methylation profiling. Compared to bisulfite-based methods, EM-seq boasts greater genome coverage with less GC bias and has the potential to cover more CpGs with the same number of reads (i.e., higher signal-to-noise ratio). Reduced representation approaches enrich samples for CpG-rich genomic regions, thereby enhancing throughput and cost effectiveness. We hypothesized that enzyme-based technology could be adapted for reduced representation methylation sequencing to enable high-resolution DNA methylation profiling on low-input samples, including those obtained from clinical specimens. We leveraged the well-established differences in methylation profile between mouse CD4+ T cell populations to compare the performance of a novel reduced representation EM-seq (RREM-seq) procedure against an established reduced representation bisulfite sequencing (RRBS) protocol. While the RRBS method failed to generate reliable DNA libraries when using <2 ng of DNA (equivalent to DNA from around 350 cells), the RREM-seq method successfully generated reliable DNA libraries from 1–25 ng of mouse and human DNA. Ultra-low-input (<2-ng) RREM-seq libraries’ final concentration, regulatory genomic element coverage, and methylation status within lineage-defining Treg cell-specific super-enhancers were comparable to RRBS libraries with more than 10-fold higher DNA input. RREM-seq also successfully detected lineage-defining methylation differences between alveolar Tconv and Treg cells obtained from mechanically ventilated patients with severe SARS-CoV-2 pneumonia. Our RREM-seq method enables single-nucleotide resolution methylation profiling using low-input samples, including from clinical sources.