bluuebunny/crossref_metadata_2025 huggingface dataset:
Endometrial Carcinosarcomas are Almost Exclusively of p53abn Molecular Subtype After Exclusion of Mimics
Authors: Huvila Jutta , Jamieson Amy , Pors Jennifer , Hoang Lynn , Mirkovic Jelena , Cochrane Dawn , McAlpine Jessica N. , Gilks C. Blake
Published: February 2024

Our aim was to assess the molecular subtype(s) and perform a detailed morphologic review of tumors diagnosed as carcinosarcoma in a population-based cohort. Forty-one carcinosarcomas were identified from a cohort of 973 endometrial carcinomas diagnosed in 2016. We assessed immunostaining and sequencing data and undertook expert pathology reviews of these cases as well as all subsequently diagnosed (post-2016) carcinosarcomas of no specific molecular profile (NSMP) molecular subtype (n=3) from our institutions. In the 2016 cohort, 37 of the 41 carcinosarcomas (91.2%) were p53abn, 2 (4.9%) were NSMP, and 1 each (2.4%) were POLEmut and mismatch repair deficiency molecular subtypes, respectively. Of the 4 non-p53abn tumors on review, both NSMP tumors were corded and hyalinized (CHEC) pattern endometrioid carcinoma, the mismatch repair deficiency tumor was a grade 1 endometrioid carcinoma with reactive stromal proliferation, and the POLEmut tumor was grade 3 endometrioid carcinoma with spindle cell growth, that is, none were confirmed to be carcinosarcoma on review. We found 11 additional cases among the 37 p53abn tumors that were not confirmed to be carcinosarcoma on the review (3 undifferentiated or dedifferentiated carcinomas, 5 carcinomas with CHEC features, 2 carcinomas showing prominent reactive spindle cell stroma, and 1 adenosarcoma). In the review of institutional cases reported as NSMP carcinosarcoma after 2016, 3 were identified (1 adenosarcoma and 2 mesonephric-like adenocarcinoma on review). In this series, all confirmed endometrial carcinosarcomas were p53abn. The finding of any other molecular subtype in a carcinosarcoma warrants pathology review to exclude mimics.
The national profile of the prosthetic and orthotic workforce in the UK: Sociodemographics and employment characteristics
Authors: Leone Enza , Eddison Nicola , Healy Aoife , Jackson Caroline , Pluckrose Bracken , Chockalingam Nachiappan
Published: February 2024

Background:

Prosthetists and orthotists (POs) are essential members of the health care workforce and one of the United Kingdom’s (UK’s) allied health professions. There is a paucity of information on their demographics, which is essential for the development of the profession. To fill this void, this study has attempted to comprehensively explore the sociodemographics and work-related characteristics of the entire workforce.

Methods:

Data were collected in 2022 through multiple sources, including surveys of POs, private companies employing POs, and freedom of information requests to National Health Service Trusts/Health Boards and higher education institutes offering programs leading to registration as a prosthetist/orthotist.

Results:

The workforce survey had 641 respondents (74% response rate). The estimated national ratio of POs per million population was 13, with all bar of the 12 regions below the World Health Organization minimum recommendation of 15 POs per million population. Most of the survey respondents were female (47.6%) and younger than male respondents, were British (75.8%), and in the White ethnic group (74.3%). Most of them were employed by private companies (59.9% vs. 31.4% employed by the National Health Service) and had clinical duties (94%), permanent contracts (90%), worked full-time (75%), and treated a wide range of clinical conditions.

Conclusions:

The national UK prosthetist and orthotist ratio falls below the recommended international standards. The versatility and broad skill set of POs highlight their crucial role in multidisciplinary teams. Establishing a centralized prosthetist and orthotist workforce database system is recommended for data-driven strategic planning.
COVID-19 Severity in People With HIV Compared With Those Without HIV
Authors: Nguyen Vu-Thuy , Nagavedu Kshema , Morrison Monica , Chen Tom , Randall Liisa M. , Landazabal Claudia , John Betsey , Klompas Michael , Cocoros Noelle M.
Published: February 2024

Background:

People with HIV (PWH) may be at risk for more severe COVID-19 outcomes. We compared risk for severe COVID-19 in PWH with matched individuals without HIV.

Methods:

We identified adults in Massachusetts with a positive SARS-CoV-2 test, March 2020–July 2022, using electronic medical record data from 3 large clinical practice groups. We then used regression models to compare outcomes among PWH versus propensity score–matched people without HIV (matched 20:1) for severe COVID-19 (pneumonia or acute respiratory distress syndrome), hospitalization, and hospital length of stay.

Results:

We identified 171,058 individuals with COVID-19; among them, 768 PWH were matched to 15,360 individuals without HIV. Overall, severe COVID-19 and hospitalization were similar in PWH and those without HIV (severe COVID-19: 3.8% vs 3.0%, adjusted odds ratio [OR] 1.27, 95% confidence interval [CI]: 0.86–1.87; hospitalization: 12.1% vs 11.3%, adjusted OR: 1.08, 95% CI: 0.87 to 1.35). Compared with people without HIV, PWH with low CD4 T-cell counts (<200 cells/mm3) had more severe COVID-19 (adjusted OR: 3.99, 95% CI: 2.06 to 7.74) and hospitalization (adjusted OR: 2.26, 95% CI: 1.35 to 3.80), but PWH with high CD4 counts had lower odds of hospitalization (adjusted OR: 0.73, 95% CI: 0.52 to 1.03).

Conclusions:

PWH with low CD4 T-cell counts had worse COVID-19 outcomes compared with people without HIV, but outcomes for those with high CD4 counts were similar to, or better than, those without HIV. It is unclear whether these findings are generalizable to settings where PWH have less access to and engagement with health care.
Characterization and Determinants of Long-Term Immune Recovery Under Suppressive Antiretroviral Therapy
Authors: Turk Teja , Labarile Marco , Braun Dominique L. , Rauch Andri , Stöckle Marcel , Cavassini Matthias , Hoffmann Matthias , Calmy Alexandra , Bernasconi Enos , Notter Julia , Pasin Chloé , Günthard Huldrych F. , Kouyos Roger D. ,   the Swiss HIV Cohort Study
Published: February 2024

Objective:

We developed a robust characterization of immune recovery trajectories in people living with HIV on antiretroviral treatment (ART) and relate our findings to epidemiological risk factors and bacterial pneumonia.

Methods:

Using data from the Swiss HIV Cohort Study and the Zurich Primary HIV Infection Cohort Study (n = 5907), we analyzed the long-term trajectories of CD4 cell and CD8 cell counts and their ratio in people living with HIV on ART for at least 8 years by fitting nonlinear mixed-effects models. The determinants of long-term immune recovery were investigated using generalized additive models. In addition, prediction accuracy of the modeled trajectories and their impact on the fit of a model for bacterial pneumonia was assessed.

Results:

Overall, our population showed good immune recovery (median plateau [interquartile range]-CD4: 718 [555–900] cells/μL, CD8: 709 [547–893] cells/μL, CD4/CD8: 1.01 [0.76–1.37]). The following factors were predictive of recovery: age, sex, nadir/zenith value, pre-ART HIV-1 viral load, hepatitis C, ethnicity, acquisition risk, and timing of ART initiation. The fitted models proved to be an accurate and efficient way of predicting future CD4 and CD8 cell recovery dynamics: Compared with carrying forward the last observation, mean squared errors of the fitted values were lower by 1.3%–18.3% across outcomes. When modeling future episodes of bacterial pneumonia, using predictors derived from the recovery dynamics improved most model fits.

Conclusion:

We described and validated a method to characterize individual immune recovery trajectories of people living with HIV on suppressive ART. These trajectories accurately predict long-term immune recovery and the occurrence of bacterial pneumonia.
Epigenetic regulatory differentiation of hematopoietic stem cells to the red lineage Running head: Epigenetics of erythropoiesis
Authors: Li Hong-Xing , Chai Yi-Hong , Sun Xiao-Hong , He Xiao-Xia , Xi Ya-Ming
Published: February 2024

The differentiation process from hematopoietic (HSCs) to mature red blood cells (RBCs) is characterized by remarkable precision and is tightly controlled from the initial lineage commitment to eventual terminal differentiation. Erythropoiesis is the dynamic journey of HSCs through various functional and phenotypic stages. The physiological course of erythrogenesis is intricately linked to significant changes in chromatin accessibility, necessitating precise coordination of transcription factors and epigenetic elements. This review presents a comprehensive overview of recent investigations into the molecular-level epigenetic regulatory factors that influence differentiation of the erythroid lineage. This encompasses the exploration of transcriptional, post-transcriptional, and post-translational regulatory processes. The intricate interplay of epigenetic and transcriptional regulatory networks in erythroid differentiation not only enhances our understanding of this fundamental biological process, but also provides valuable insights into the underlying mechanisms contributing to the pathogenesis of disorders associated with abnormal erythroid development. These findings hold significant promise for the development of novel therapeutic strategies to address these diseases and improve patient outcomes.
Rare Occurrence of Scapulothoracic and Ischiogluteal Bursitis Signifying Poorly Controlled Rheumatoid Arthritis
Authors: Chow Tsz-Kit
Published: February 2024

A 74-year-old man with poorly controlled seropositive rheumatoid arthritis was referred for 18F-FDG PET/CT for follow-up of lung cancer, which demonstrated intense FDG activity in atlantoaxial, sternoclavicular, glenohumeral, and hip joints consistent with active rheumatoid arthritis. There was also unexpected intense uptake at scapulothoracic, ischiogluteal, and trochanteric bursae signifying active bursitis.
Can Weight of The Resected Stomach Predict Weight Loss Results After Laparoscopic Sleeve Gastrectomy?
Authors: Sobutay Erman , Bilgiç Çağri , Kabaoğlu Burçak , Yavuz Yunus
Published: February 2024

Background:

Laparoscopic sleeve gastrectomy (LSG) is the most commonly performed bariatric procedure worldwide. Many factors have been investigated in the literature to predict weight loss outcomes after LSG. However, insufficient data regarding the resected stomach weight (RGW) exists. This retrospective study aimed to investigate the association between RGW and weight loss outcomes 1 year after LSG.

Materials and Methods:

Fifty-four patients who underwent LSG in a tertiary care center were evaluated retrospectively. The statistical analyses were performed to investigate the correlation between preoperative demographics, RGW, and the excess weight loss percentage (%EWL) and percent total weight loss (%TWL).

Results:

The mean RGW was 169.7±40.1, ranging from 101 to 295 grams. The RGW was significantly correlated with preoperative weight (r=0.486;P<0.001), body mass index (r=0.420;P=0.002), and age (r=0.327;P=0.01). However, RGW did not predict postoperative weight loss, as measured by percent total weight loss (%TWL) and percent excess weight loss (%EWL), respectively (r=0.044;P=0.75 andr=−0.216;P=0.11). Multiple linear regression analysis identified age as a negative predictor for both %TWL (β=−0.351,P=0.005) and %EWL (β=−0.265,P=0.03), while preoperative body mass index was a negative predictor for %EWL (β=−0.469,P<0.001).

Conclusion:

The RGW, although correlated with patient characteristics, does not serve as a reliable predictor of postoperative weight loss in the first year after LSG. Further research is needed to improve predictive models and patient care in bariatric surgery.
Intraoperative Monitoring of Scoliosis Surgery in Young Patients
Authors: Manning Erin , Emerson Ronald
Published: February 2024

Intraoperative neurophysiologic monitoring has added substantially to the safety of spinal deformity surgery correction since its introduction over four decades ago. Monitoring routinely includes both somatosensory evoked potentials and motor evoked potentials. Either modality alone will detect almost all instances of spinal cord injury during deformity correction. The combined use of the two modalities provides complementary information, can permit more rapidly identification of problems, and enhances safety though parallel redundancy should one modality fail. Both techniques are well established and continue to be refined. Although there is room for provider preference, proper monitoring requires attention to technical detail, understanding of the underlying physiology, and familiarity with effects of commonly used anesthetic agents.
Auditory influence on stickiness perception: an fMRI study of multisensory integration
Authors: Lee In-Seon , Kang Jae-Hwan , Kim Junsuk
Published: February 2024

This study explored how the human brain perceives stickiness through tactile and auditory channels, especially when presented with congruent or incongruent intensity cues. In our behavioral and functional MRI (fMRI) experiments, we presented participants with adhesive tape stimuli at two different intensities. The congruent condition involved providing stickiness stimuli with matching intensity cues in both auditory and tactile channels, whereas the incongruent condition involved cues of different intensities. Behavioral results showed that participants were able to distinguish between the congruent and incongruent conditions with high accuracy. Through fMRI searchlight analysis, we tested which brain regions could distinguish between congruent and incongruent conditions, and as a result, we identified the superior temporal gyrus, known primarily for auditory processing. Interestingly, we did not observe any significant activation in regions associated with somatosensory or motor functions. This indicates that the brain dedicates more attention to auditory cues than to tactile cues, possibly due to the unfamiliarity of conveying the sensation of stickiness through sound. Our results could provide new perspectives on the complexities of multisensory integration, highlighting the subtle yet significant role of auditory processing in understanding tactile properties such as stickiness.
A hydrocele revealing epididymal tuberculosis
Authors: Ben Lahlou Yassine , Laanibi Zakaria , Malihy Zakaria , Benaissa Elmostapha , Maleb Adil , Chadli Mariam , Elouennass Mostapha
Published: February 2024

Abstract:

Urogenital tuberculosis is a severe form of extrapulmonary tuberculosis. The organs most commonly affected are the epididymis and the testis. Clinical manifestations may include epididymitis, orchi-epididymitis, hydrocele, associated with leukocyturia, and significant hematuria.
We report a case of a patient with a hydrocele that revealed epididymal tuberculosis.
Three novel species of the genus Flavobacterium, Flavobacterium odoriferum sp. nov., Flavobacterium fragile sp. nov. and Flavobacterium luminosum sp. nov., isolated from activated sludge
Authors: Ran Qi , Du Xinran , Han Lin , Wang Jingjing , Li Yue-zhong
Published: February 2024

Three Gram-stain-negative, rod-shaped, non-spore-forming bacteria were isolated from activated sludge samples. The results of phylogenetic analysis based on the 16S rRNA gene sequences indicated that the three strains, designated HXWNR29T, HXWNR69T and HXWNR70T, had the highest sequence similarity to the type strains Flavobacterium cheniae NJ-26T, Flavobacterium channae KSM-R2A30T and Flavobacterium amniphilum KYPY10T with similarities of 97.66 %, 98.66 and 98.14 %, respectively. The draft genomes of these three strains were 2.93 Mbp (HXWNR29T), 2.69 Mbp (HXWNR69T) and 2.65 Mbp (HXWNR70T) long with DNA G+C contents of 31.84 %, 32.83 % and 34.66 %, respectively. These genomes contained many genes responsible for carbohydrate degradation and antibiotic resistance. The major fatty acids (>5 %) included iso-C15 : 0, iso-C15 : 0 3-OH and iso-C17 : 0 3-OH. The major menaquinone was MK-6 for all the three strains. The average nucleotide identity (ANI; 72.7–88.5 %) and digital DNA–DNA hybridization (dDDH; 19.6–35.3 %) results further indicated that these three strains represented three novel species within the genus Flavobacterium, for which the names Flavobacterium odoriferum sp. nov. (type strain HXWNR29T = KCTC 92446T = CGMCC 1.61821T), Flavobacterium fragile sp. nov. (type strain HXWNR69T = KCTC 92468T = CGMCC 1.61442T) and Flavobacterium luminosum sp. nov. (type strain HXWNR70T = KCTC 92447T = CGMCC 1.61443T) are proposed.
Pharmacogenomics of Coronary Artery Response to Intravenous Gamma Globulin in Kawasaki Disease
Authors: Shrestha Sadeep , Wiener Howard W , Chowdhury Sabrina , Kajimoto Hidemi , Srinivasasainagendra Vinodh , Mamaeva Olga A , Brahmbhatt Ujval N , Ledee Dolena , Lau Yung , Padilla Luz A , Chen Jake , Dahdah Nagib , Tiwari Hemant K , Portman Michael A
Published: February 2024

Background

Kawasaki disease (KD) is a multisystem inflammatory illness of infants and young children that can result in acute vasculitis. The pathological walls of afflicted coronary arteries show propensity for forming thrombosis and aneurysms. The mechanism of coronary artery aneurysms (CAA) despite intravenous gamma globulin (IVIG) treatment is not known.

Methods

We performed a Whole Genome Sequencing (WGS) association analysis in a racially diverse cohort of KD patients treated with IVIG, both using AHA guidelines. We defined coronary aneurysm (CAA) (N = 234) as coronary z>2.5 and large coronary aneurysm (CAA/L) (N = 92) as z>5.0. We conducted logistic regression models to examine the association of genetic variants with CAA/L during acute KD and with persistence >6 weeks using an additive model between cases and 238 controls with no CAA. We adjusted for age, gender and three principal components of genetic ancestry. We performed functional mapping and annotation (FUMA) analysis and further assessed the predictive risk score of genomic risk loci using the area under the receiver operating characteristic curve (AUC).

Results

The top significant variants associated with CAA/L were in the intergenic regions (rs62154092 p<6.32E-08 most significant). Variants inSMAT4, LOC100127,PTPRD, TCAF2andKLRC2were the most significant non-intergenic SNPs. FUMA identified 12 genomic risk loci with eQTL or chromatin interactions mapped to 48 genes. Of theseNDUFA5has been implicated in KD CAA andMICUandZMAT4has potential functional implications. Genetic risk score using these 12 genomic risk loci yielded an AUC of 0.86.

Conclusions

This pharmacogenomics study provides insights into the pathogenesis of CAA/L in IVIG-treated KD patients. We have identified multiple novel SNPs associated with CAA/L and related genes with potential functional implications. The study shows that genomics can help define the cause of CAA/L to guide management and improve risk stratification of KD patients.
Thyroid hormone receptor beta (THRB) dependent regulation of diurnal hepatic lipid metabolism in adult male mice
Authors: de Assis Leonardo Vinicius Monteiro , Harder Lisbeth , Inderhees Julica , Jöhren Olaf , Mittag Jens , Oster Henrik
Published: February 2024

Thyroid hormones (THs) are critical regulators of systemic energy metabolism and homeostasis. In the liver, high TH action protects against steatosis by enhancing cholesterol and triglyceride turnover, with thyroid hormone receptor beta (THRB) signaling playing a pivotal role. This study probed the potential interaction between THRB action and another critical regulator of liver energy metabolism, the circadian clock. Liver transcriptome analysis of THRB deficient (THRBKO) mice under normal chow conditions revealed a markedly modest impact of THRB deletion. Temporal transcriptome and lipidome profiling uncovered significant alterations in diurnal metabolic rhythms attributable to THRB deficiency pointing to a pro-steatotic state with elevated levels of cholesterol, tri- and diacylglycerides, and fatty acids. These findings were confirmed by THRB agonization in hepatocytes under steatosis-promoting conditionsin vitro. Integration of transcriptome profiles from THRBKOmice and mice with induced high or low TH action identified a subset of TH responsive but THRB insensitive genes implicated in immune processes. In summary, our study reveals a complex time-of-day dependent interaction of different TH-related signals in the regulation of liver physiology indicating an opportunity for chronopharmacological approaches to TH/THR(B) manipulation in fatty liver diseases.
Moth resonant mechanics are tuned to wingbeat frequency and energetic demands
Authors: Wold Ethan S. , Aiello Brett , Harris Manon , Sikandar Usama Bin , Lynch James , Gravish Nick , Sponberg Simon
Published: February 2024

An insect’s wingbeat frequency is a critical determinant of its flight performance and varies by multiple orders of magnitude across Insecta. Despite potential energetic and kine-matic benefits for an insect that matches its wingbeat frequency to its resonant frequency, recent work has shown that moths may operate off of their resonant peak. We hypothesized that across species, wingbeat frequency scales with resonance frequency to maintain favorable energetics, but with an offset in species that use frequency modulation as a means of flight control. The moth superfamily Bombycoidea is ideal for testing this hypothesis because their wingbeat frequencies vary across species by an order of magnitude, despite similar morphology and actuation. We used materials testing, high-speed videography, and a “spring-wing” model of resonant aerodynamics to determine how components of an insect’s flight apparatus (thoracic properties, wing inertia, muscle strain, and aerodynamics) vary with wingbeat frequency. We find that the resonant frequency of a moth correlates with wingbeat frequency, but resonance curve shape (described by the Weis-Fogh number) and peak location vary within the clade in a way that corresponds to frequency-dependent biomechanical demands. Our results demonstrate that a suite of adaptations in muscle, exoskeleton and wing drive variation in resonant mechanics, reflecting potential constraints on matching wingbeat and resonant frequencies.
Simulated Microgravity Enhances Adipocyte Maturation and Glucose Uptake via Increased Cortical Actin Remodeling
Authors: Anvari Golnaz , Struss Michael , Bellas Evangelia
Published: February 2024

Adipose tissue (AT) regulates whole-body metabolism and is subject to various forces during movement, exercise, and during rest. Adipocytes are mechanically responsive cells, yet little is known about how the lack of mechanical loading may affect adipocytes and their function. To model the lack of mechanical loading, we exposed engineered AT constructs to simulated microgravity (sµg) conditions for 28 days. We found sµg enhanced lipid accumulation (lipogenesis) and lipid mobilization (lipolysis). Adipocyte maturation involves a phenotypic switch from actin stress fiber disruption and cortical actin formation. Sµg exposure increased cortical actin formation through mechanoresponsive signaling pathways involving Ras homolog family member A (RhoA) and Rho Associated Coiled-Coil Containing Protein Kinase 1 (ROCK1) downstream targets, cofilin and actin-related protein 2/3 (ARP2/3). Adipocytes cultured in sµg have increased glucose transporter type 4 (GLUT4) translocation to the cell membrane and insulin-stimulated glucose uptake, independent of the canonical Akt pathway. GLUT4 translocation to the cell membrane and insulin-stimulated glucose uptake was limited when we inhibited new formation of branched cortical actin using an ARP2/3 inhibitor, CK-666. This study demonstrated that sµg enhances adipocyte maturation via increased lipogenesis and lipolysis and cortical actin remodeling which further enhanced glucose uptake. Therefore, targeting these mechanosensitive pathways pharmacologically or simulating microgravity on earth as a non-pharmacological modality are novel approaches to improving adipocyte function and AT metabolism and possibly for treating related comorbidities such as type 2 diabetes and obesity.
Microphysiological Modeling of Vascular Adipose Tissue for Multi-Throughput Applications
Authors: Struss Michael , Bellas Evangelia
Published: February 2024

Adipose tissue (AT) is a highly vascularized endocrine organ which regulates whole-body metabolic homeostasis. Key AT functions which rely on vascularization include insulin-stimulated glucose uptake and lipolysis (lipid mobilization to supply energy). Most in vitro AT models do not include the vasculature, and while microphysiological systems (MPS) incorporate spatial organization of cells, 3D environments, and perfusion by external pumps, they are too large to fit traditional cultureware. Thus, we developed a novel miniaturized vascularized adipose tissue (µAT) platform compatible with traditional 24 well plates. Using this µAT platform, we quantified vascular permeability and adipocyte function by insulin-stimulated glucose uptake and lipolysis assays. Shear flow decreased vascular permeability and increased insulin-stimulated glucose uptake. Treatment with forskolin, an adenyl cyclase agonist, increased lipolysis, and decreased vascular permeability. This µAT platform allows for the facile screening of compounds in a physiologically relevant system where both adipocyte and vascular function can be evaluated.
Caspase prime-side active-site characterization with non-hydrolyzable peptides assists in the design of a caspase-7-selective irreversible probe
Authors: Solania Angelo , Xu Janice H. , Wolan Dennis W.
Published: February 2024

Limited structural information and biochemical studies are available that demonstrate how the prime side of cysteine protease active sites, such as for human caspases, are used for substrate recognition and how these binding regions can be exploited in the design of inhibitors and probes. Reported small molecules that interact with, and are optimized for, the prime side of caspase active sites are limited to methylketone leaving groups and other nonpeptidic inhibitor moieties, such as aza-Michael acceptors. We present the design, synthesis, and co-complex x-ray structures of the first prime-side elongated non-hydrolyzable peptidomimetic ketomethylene inhibitors designed to interrogate the S4-S4’ active-site binding pockets of the executioner caspases-3 and -7. In addition to our structures depicting the first examples of an active-site cysteine in complex with a P1 residue trapped in a non-covalent tetrahedral intermediate, we elucidated prime-side binding interactions for pockets S1’ through S4’ with our biologically relevant peptide Ac-DEVD-Propionate-AAA. Despite the substantial homology among the caspase active sites, we identified a key difference in the prime-side architecture within binding distance to the P2’ inhibitor alanine whereby caspase-3 F128 is substituted for caspase-7 Y151. We exploited this prime-side difference in side chains and their reactivities in the design of non-hydrolyzable ketomethylene-based probes bearing a C-terminal tyrosine-reactive 4-phenyl-1,2,4-triazole-3,5-dione moiety. Our probe selectively labels caspase-7 over caspase-3 and we posit that further characterization of protease active-site prime sides with similar non-hydrolyzable molecules will yield additional tool-like compounds that will assist in establishing the non-redundant roles of caspase family members and other cysteine proteases.
Microbiota-Short Chain Fatty Acid Relationships Underlie Clinical Heterogeneity and Identify Key Microbial Targets in Irritable Bowel Syndrome (IBS)
Authors: Shin Andrea , Xing Yue , Waseem Mohammed Rayyan , Siwiec Robert , James-Stevenson Toyia , Rogers Nicholas , Bohm Matthew , Wo John , Lockett Carolyn , Gupta Anita , Kadariya Jhalka , Toh Evelyn , Anderson Rachel , Xu Huiping , Gao Xiang
Published: February 2024

Background

Identifying microbial targets in irritable bowel syndrome (IBS) and other disorders of gut-brain interaction (DGBI) is challenging due to the dynamic nature of microbiota-metabolite-host interactions. SCFA are key microbial metabolites that modulate intestinal homeostasis and may influence IBS pathophysiology. We aimed to assess microbial features associated with short chain fatty acids (SCFA) and determine if features varied across IBS subtypes and endophenotypes. Among 96 participants who were screened, 71 completed the study. We conducted in-depth investigations of stool microbial metagenomes, stool SCFA, and measurable IBS traits (stool bile acids, colonic transit, stool form) in 41 patients with IBS (IBS with constipation [IBS-C] IBS with diarrhea [IBS-D]) and 17 healthy controls. We used partial canonical correspondence analyses (pCCA), conditioned on transit, to quantify microbe-SCFA associations across clinical groups. To explore relationships between microbially-derived SCFA and IBS traits, we compared gut microbiome-encoded potential for substrate utilization across groups and within a subset of participants selected by their stool characteristics as well as stool microbiomes of patients with and without clinical bile acid malabsorption.

Results

Overall stool microbiome composition and individual taxa abundances differed between clinical groups. Microbes-SCFA associations differed across groups and revealed key taxa includingDoreasp. CAG:317 andBifidobacterium pseudocatenulatumin IBS-D andAkkermansia muciniphilaandPrevotella copriin IBS-C that that may drive subtype-specific microbially-mediated mechanisms. Strongest microbe-SCFA associations were observed in IBS-D and several SCFA-producing species surprisingly demonstrated inverse correlations with SCFA. Fewer bacterial taxa were associated with acetate to butyrate ratios in IBS compared to health. In participants selected by stool form, we demonstrated differential abundances of microbial genes/pathways for SCFA metabolism and degradation of carbohydrates and mucin across groups. SCFA-producing taxa were reduced in IBS-D patients with BAM.

Conclusion

Keystone taxa responsible for SCFA production differ according to IBS subtype and traits and the IBS microbiome is characterized by reduced functional redundancy. Differences in microbial substrate preferences are also linked to bowel functions. Focusing on taxa that drive SCFA profiles and stool form may be a rational strategy for identifying relevant microbial targets in IBS and other DGBI.
Leveraging Machine Learning-Guided Molecular Simulations Coupled with Experimental Data to Decipher Membrane Binding Mechanisms of Aminosterols
Authors: Muscat Stefano , Errico Silvia , Danani Andrea , Chiti Fabrizio , Grasso Gianvito
Published: February 2024

Understanding the molecular mechanisms of the interactions between specific compounds and cellular membranes is essential for numerous biotechnological applications, including targeted drug delivery, elucidation of drug mechanism of action, pathogen identification, and novel antibiotic development. However, the estimation of the free energy landscape associated with solute binding to realistic biological systems is still a challenging task. In this work, we leverage the Time-lagged Independent Component Analysis (TICA) in combination with neural networks (NN) through the Deep-TICA approach for determining the free energy associated with the membrane insertion processes of two natural aminosterol compounds, trodusquemine (TRO) and squalamine (SQ). These compounds are particularly noteworthy because they interact with the outer layer of neuron membranes protecting them from the toxic action of misfolded proteins involved in neurodegenerative disorders, both in their monomeric and oligomeric forms. We demonstrate how this strategy could be used to generate an effective collective variable for describing solute absorption in the membrane and for estimating free energy landscape of translocation via On-the-fly probability enhanced sampling (OPES) method. In this context, the computational protocol allowed an exhaustive characterization of the aminosterols entry pathway into a neuron-like lipid bilayer. Furthermore, it provided accurate prediction of membrane binding affinities, in close agreement with the experimental binding data obtained by using fluorescently-labelled aminosterols and large unilamellar vesicles (LUVs). The findings contribute significantly to our comprehension of aminosterol entry pathways and aminosterol-lipid membrane interactions. Finally, the deployed computational methods in this study further demonstrate considerable potential for investigating membrane binding processes.
A range expanding ecosystem engineer influences historical and expanded habitats via the same causal pathways
Authors: Roy Michael S. , Johnson David Samuel , Byrnes Jarrett E. K.
Published: February 2024

Species are shifting their ranges in response to climate change. There remain many unknowns about relative impacts of range-expanding ecosystem engineers between historical and expanded habitats, however. The mud fiddler crabMinuca pugnax(=Uca pugnax) is shifting its range northward likely due to increased warming in the Gulf of Maine. A burrowing crab,M. pugnaxaffects ecosystem functioning in salt marshes south of Cape Cod, Massachusetts with unknown effects in expanded marsh habitats over 150km to the north. We therefore studied theM. pugnaxrange expansion to determine the extent that range expanding ecosystem engineers are influencing ecosystem functioning expanded rangesrelative tohistorical habitats. We installed in 2017 and 2018 a series of crab-inclusion cages at both the UMass Boston Nantucket Field Station (historical range) and the Plum Island Estuary Long Term Ecological Research site (PIE-LTER, expanded range). For each site, year, and block, we measured in the beginning and end of the three-month experiment metrics of sediment strength, primary production, and decomposition. We developed and tested causal models using structural equation modeling (SEM) to determine direct and indirect effects of fiddler crabs on ecosystem functions. Despite site, year, and block variability, local environment influenced burrow density, which directly affected sediment strength and indirectly affected primary production in both ranges. Overall, understanding range-expanding ecosystem engineers in historical ranges was predictive for how they influence expanded habitats, despite inter-site heterogeneity. Therefore, it is critical to study relative impacts of range-expanding ecosystem engineers to understand total impacts of global range shifts.
Seedless: On-the-fly pulse calculation for NMR experiments
Authors: Buchanan Charles , Bhole Gaurav , Karunanithy Gogulan , Casablancas-Antràs Virginia , Poh Adeline , Davis Benjamin G. , Jones Jonathan A. , Baldwin Andrew J.
Published: February 2024

All NMR experiments require sequences of RF ‘pulses’ to manipulate nuclear spins. Signal is lost due to non-uniform excitation of nuclear spins resonating at different energies (chemical shifts) and inhomogeneity in the RF actually generated by hardware over the sample volume. Here, we present Seedless, a tool to calculate NMR pulses that compensate for these effects to enhance control of magnetisation and boost signal. The calculations take only a few seconds using an optimised GRadient Ascent Pulse Engineering (GRAPE) implementation, allowing pulses to be generated ‘on-the-fly’, optimised for individual samples and spectrometers. Each calculated pulse requires bands of chemical shift to be identified, over which one of 4 transforms will be performed, selected from a set that covers all commonly used applications: a universal rotation (e.g. 90° about the x axis), including as a special case an identity operation (return spins in the same state as they started), state-to-state (e.g. Z->Y), an XYcite (Z->XY plane), or a novel type, a suppression, that leaves spins minimally perturbed at all times during the pulse. Using imaging experiments we demonstrate our pulses effectively increase the size of the coil volume and effectively increase signal-to-noise in all experiments. We illustrate the approach by devising ultra-broadband pulses (300 ppm excitation pulse for19F 1D spectra), a15N HSQC with 58% increased S/N (950 MHz spectrometer + cryoprobe), triple resonance biomolecular NMR experiments such as HNCACO with 55% increased S/N (600 MHz spectrometer + RT probe), and a highly efficient pulse sequence for water suppression. The 8 optimised pulse sequences presented required 54 bespoke pulses all calculated on-the-fly. Seedless provides a means to enhance sensitivity in all pulse sequences in a manner that can be tailored to all samples/hardware being used.
Investigating low frequency somatic mutations inArabidopsiswith Duplex Sequencing
Authors: Waneka Gus , Pate Braden , Monroe J. Grey , Sloan Daniel B.
Published: February 2024

Mutations are the source of novel genetic diversity but can also lead to disease and maladaptation. The conventional view is that mutations occur randomly with respect to their environment-specific fitness consequences. However, intragenomic mutation rates can vary dramatically due to transcription coupled repair and based on local epigenomic modifications, which are non-uniformly distributed across genomes. One sequence feature associated with decreased mutation is higher expression level, which can vary depending on environmental cues. To understand whether the association between expression level and mutation rate creates a systematic relationship with environment-specific fitness effects, we perturbed expression through a heat treatment inArabidopsis thaliana. We quantified gene expression to identify differentially expressed genes, which we then targeted for mutation detection using Duplex Sequencing. This approach provided a highly accurate measurement of the frequency of rare somatic mutations in vegetative plant tissues, which has been a recent source of uncertainty in plant mutation research. We included mutant lines lacking mismatch repair (MMR) and base excision repair (BER) capabilities to understand how repair mechanisms may drive biased mutation accumulation. We found wild type (WT) and BER mutant mutation frequencies to be very low (mean variant frequency 1.8×10-8and 2.6×10-8, respectively), while MMR mutant frequencies were significantly elevated (1.13×10-6). These results show that somatic variant frequencies are extremely low in WT plants, indicating that larger datasets will be needed to address the fundamental evolutionary question as to whether environmental change leads to gene-specific changes in mutation rate.

SIGNIFICANCE

Accurately measuring mutations in plants grown under different environments is important for understanding the determinants of mutation rate variation across a genome. Given the low rate ofde novomutation in plant germlines, such measurements can take years to obtain, hindering tests of mutation accumulation under varying environmental conditions. We implemented highly accurate Duplex Sequencing to study somatic mutations in plants grown in two different temperatures. In contrast to plants with deficiencies in DNA mismatch repair machinery, we found extremely low mutation frequencies in wild type plants. These findings help resolve recent uncertainties about the somatic mutation rate in plant tissues and indicate that larger datasets will be necessary to understand the interaction between mutation and environment in plant genomes.
Opposing roles of resident and infiltrating immune cells in the defence againstLegionella longbeachaevia IL-18R/IFN-γ/ROS axis
Authors: Oberkircher Lara M. , Scheiding Victoria M. , Rafeld H. Linda , Hanssen Eric , Hansen Jan N. , Fleischmann Markus J. , Kessler Nina , Pitsch David , Wachten Dagmar , Kastenmüller Wolfgang , Brown Andrew S. , Hartland Elizabeth L. , van Driel Ian R. , Ng Garrett Z. , Garbi Natalio
Published: February 2024

The immune response againstLegionella longbeachae, a causative agent of the often-fatal Legionnaires’ pneumonia, is poorly understood. Here we investigated the specific roles of tissue-resident alveolar macrophages (AM) and infiltrating phagocytes during infection with this pathogen. AM were the predominant cell type that phagocytosed bacteria o day after infection. Three and five days after infection, AM numbers were greatly reduced while there was an influx of neutrophils and later monocyte-derived cells (MC) into lung tissue. AM carried greater numbers of viableL. longbeachaethan neutrophils and MC, which correlated with a higher capacity ofL. longbeachaeto translocate bacterial effector proteins required for bacterial replication into the AM cytosol. Cell ablation experiments demonstrated that AM promoted infection whereas neutrophils and MC were required for efficient bacterial clearance. IL-18 was important for IFN-γ production by IL-18R+NK cells and T cells which, in turn, stimulated ROS-mediated bactericidal activity in neutrophils resulting in restriction ofL. longbeachaeinfection. Ciliated epithelial cells also expressed IL-18R but did not play a role in IL-18-mediatedL. longbeachaeclearance. Our results have identified opposing innate functions of tissue-resident and infiltrating immune cells duringL. longbeachaeinfection that may be manipulated to improve protective responses.

Highlights

AM serve as a replicative niche and promoteL. longbeachaeinfection.

Infiltrating neutrophils and MC killL. longbeachae.

IFN-γ from IL-18R+NK and T cells stimulates ROS and bacterial clearance.
Programmable RNA writing with trans-splicing
Authors: Schmitt-Ulms Cian , Kayabolen Alisan , Manero-Carranza Marcos , Zhou Nathan , Donnelly Keira , Nuccio Sabrina Pia , Kato Kazuki , Nishimasu Hiroshi , Gootenberg Jonathan S. , Abudayyeh Omar O.
Published: February 2024

RNA editing offers the opportunity to introduce either stable or transient modifications to nucleic acid sequence without permanent off-target effects, but installation of arbitrary edits into the transcriptome is currently infeasible. Here, we describe Programmable RNA Editing & Cleavage for Insertion, Substitution, and Erasure (PRECISE), a versatile RNA editing method for writing RNA of arbitrary length and sequence into existing pre-mRNAs via 5′ or 3′ trans-splicing. In trans-splicing, an exogenous template is introduced to compete with the endogenous pre-mRNA, allowing for replacement of upstream or downstream exon sequence. Using Cas7-11 cleavage of pre-mRNAs to bias towards editing outcomes, we boost the efficiency of RNA trans-splicing by 10–100 fold, achieving editing rates between 5–50% and 85% on endogenous and reporter transcripts, respectively, while maintaining high-fidelity. We demonstrate PRECISE editing across 11 distinct endogenous transcripts of widely varying expression levels, showcasing more than 50 types of edits, including all 12 possible transversions and transitions, insertions ranging from 1 to 1,863 nucleotides, and deletions. We show high efficiency replacement of exon 4 of MECP2, addressing most mutations that drive the Rett Syndrome; editing of SHANK3 transcripts, a gene involved in Autism; and replacement of exon 1 of HTT, removing the hallmark repeat expansions of Huntington′s disease. Whole transcriptome sequencing reveals the high precision of PRECISE editing and lack of off-target trans-splicing activity. Furthermore, we combine payload engineering and ribozymes for protein-free, high-efficiency trans-splicing, with demonstrated efficiency in editing HTT exon 1 via AAV delivery. We show that the high activity of PRECISE editing enables editing in non-dividing neurons and patient-derived Huntington’s disease fibroblasts. PRECISE editing markedly broadens the scope of genetic editing, is straightforward to deliver over existing gene editing tools like prime editing, lacks permanent off-targets, and can enable any type of genetic edit large or small, including edits not otherwise possible with existing RNA base editors, widening the spectrum of addressable diseases.
Microtubules ensure transport of vegetative nuclei and sperm cells by fine-tuning their home positions
Authors: Motomura Kazuki , Tsuchi Haruna , Komojiri Marin , Matsumoto Ayumi , Sugi Naoya , Susaki Daichi , Takeda Atsushi , Kinoshita Tetsu , Maruyama Daisuke
Published: February 2024

The pollen tube plays a pivotal role in double fertilization by delivering sperm cells (SCs) to the ovule. InArabidopsis thaliana, a pair of SCs tightly connects with the vegetative nucleus (VN) to form the male germ unit (MGU), which is located in the apical region during pollen-tube growth, keeping the VN ahead of the SCs. MGU transport relies on independent motility of VN and SC pairs. However, the complexity of this dual motive force has hindered our understanding of MGU behavior, including its positioning and nuclear order. We usedArabidopsismutants or transgenic plants that produced semi-motile MGUs with aberrant VNs or SCs to analyze the positioning of VN or SCs after stochastically disconnecting the MGU. In pollen tubes with an immotile SC pair, the VN was ∼70 μm away from the tip, whereas in pollen tubes with an immotile VN, the SC pair was ∼100 μm away from the tip, implying that the VN and SCs have independent home positions. The position of MGU moved forward owing to the loss of the microtubule-destabilizing kinesinKINESIN-13A. Conversely, microtubule depolymerization by oryzalin treatment or introducing mutations inTUBULIN BETA 4(TUB4) deregulated the position of the MGU and shifted its position backward. In addition,tub4plants exhibited reduced fertility. These data indicate a significant role of microtubules in stable MGU positioning to ensure reproductive success.
Trait prediction through computational intelligence and machine learning applied to soybean (Glycine max) breeding in shaded environments
Authors: da Silva Júnior Antônio Carlos , Costa Weverton Gomes da , Guimarães Amanda Gonçalves , de Melo Moura Waldênia , Bhering Leonardo Lopes , Cruz Cosme Damião , Batista Renata Oliveira , dos Santos Jose Barbosa , Campos Wellington Ferreira , Evaristo Anderson Barbosa
Published: February 2024

This study aims to identify more relevant predictors traits, considering different prediction approaches in soybean under different shading levels in the field, using methodologies based on artificial intelligence and machine learning. The experiments were carried out under different shading levels in a greenhouse and in the field, using sixteen cultivars. We have evaluated grain yield, which was used as a response trait, and 22 other attributes as explanatory traits. Three levels of shading were used to restrict photosynthetically active radiation (RPAR): 0%, 25%, and 48%. At full sun level (0% RPAR), the traits that presented better predictive performances using a multilayer perceptron were specific leaf area, plant height and number of pods. In the three levels of shading, the plant height trait exhibited the best performance for the radial base function network. Plant height showed the best predictive efficiency for grain yield at 25% and 48% RPAR, for all machine learning methodologies. Computational intelligence and machine learning methodologies have proven to be efficient in predicting soybean grain yield, regardless of shading level.