bluuebunny/crossref_metadata_2025 huggingface dataset:
Rhinoplasty Technique for Improving Nasal Base Aesthetics
Authors: Cabbarzade Cavid
Published: March 2023

Background

One of the most important factors in nasal base aesthetics is symmetry. In the age of social media, the expectations of rhinoplasty patients and the rate of requests for a more symmetrical nose have increased. In this article, a lateral columellar grafting technique that can be applied to augment the more defective side of the columella and obtain a more symmetrical nasal base is presented.

Methods

A total of 86 patients (women, 79; men, 7) were included in this study. The surfaces of the right and left lateral margins of the columella were evaluated from the basal view at the final stage of surgery, and a lateral columellar graft was placed on the more defective side. All patients who were included in the study were assessed with the Rhinoplasty Outcome Evaluation questionnaire before and 1 year after surgery.

Results

The median age of the patients was 28.3 years (range, 18–56 years). Eighty-two patients were primary rhinoplasty patients, and 4 patients were secondary rhinoplasty patients. The median Rhinoplasty Outcome Evaluation score was 68.3 points before surgery and 92.3 points 1 year after surgery, showing a significant increase (P = 0.003). Patient satisfaction was found to be excellent in 93% of the included patients.

Conclusions

Using the lateral columellar grafting technique, greater symmetry of the columella and nostrils can be obtained by augmenting the more defective side of the lateral columellar surface.
Insertion sequences related to ISAjo2 target pdif and dif sites and belong to a new IS family, the IS1202 family
Authors: Harmer Christopher J. , Pong Carol H. , Hall Ruth M.
Published: March 2023

Several insertion sequences (IS) found in various

Acinetobacter

species exhibit target specificity. They are found, in the same orientation, 5 bp from the XerC binding site of the pdif sites associated with dif modules in

Acinetobacter

plasmids, and searches revealed they are also found near chromosomal dif sites of

Acinetobacter

species. These IS are 1.5 kb long, bounded by 24–26 bp imperfect terminal inverted repeats (TIRs) and encode a large transposase of 441–457 aa. They generate 5 bp target site duplications (TSDs). Structural predictions of the ISAjo2 transposase, TnpAjo2, modelled on TnsB of Tn7 revealed two N-terminal HTH domains followed by an RNaseH fold (DDE domain), a β barrel and a C-terminal domain. Similar to Tn7, the outer IS ends are 5′-TGT and ACA-3′, and an additional Tnp binding site, corresponding to the internal portion of the IR, is found near each end. However, the

Acinetobacter

IS do not encode further proteins related to those required by Tn7 for targeted transposition, and the transposase may interact directly with XerC bound to a dif-like site. We propose that these IS, currently in the IS1202 group in the not characterized yet (NCY) category in ISFinder, are part of a distinct IS1202 family. Other IS listed as in the IS1202 group encode transposases related to TnpAjo2 (25–56 % amino acid identity) and have similar TIRs but fall into three groups based on the TSD length (3–5, >15, 0 bp). Those with 3–5 bp TSDs may also target dif-like sites but targets were not found for the other groups.
Large library docking for cannabinoid-1 receptor agonists with reduced side effects
Authors: Tummino Tia A. , Iliopoulos-Tsoutsouvas Christos , Braz Joao M. , O’Brien Evan S. , Stein Reed M. , Craik Veronica , Tran Ngan K. , Ganapathy Suthakar , Liu Fangyu , Shiimura Yuki , Tong Fei , Ho Thanh C. , Radchenko Dmytro S. , Moroz Yurii S. , Rosado Sian Rodriguez , Bhardwaj Karnika , Benitez Jorge , Liu Yongfeng , Kandasamy Herthana , Normand Claire , Semache Meriem , Sabbagh Laurent , Glenn Isabella , Irwin John J. , Kumar Kaavya Krishna , Makriyannis Alexandros , Basbaum Allan I. , Shoichet Brian K.
Published: March 2023

Large library docking can reveal unexpected chemotypes that complement the structures of biological targets. Seeking new agonists for the cannabinoid-1 receptor (CB1R), we docked 74 million tangible molecules, prioritizing 46 high ranking ones forde novosynthesis and testing. Nine were active by radioligand competition, a 20% hit-rate. Structure-based optimization of one of the most potent of these (Ki= 0.7 µM) led to‘4042, a 1.9 nM ligand and a full CB1R agonist. A cryo-EM structure of the purified enantiomer of‘4042(‘1350) in complex with CB1R-Gi1confirmed its docked pose. The new agonist was strongly analgesic, with generally a 5-10-fold therapeutic window over sedation and catalepsy and no observable conditioned place preference. These findings suggest that new cannabinoid chemotypes may disentangle characteristic cannabinoid side-effects from their analgesia, supporting the further development of cannabinoids as pain therapeutics.
Influence of Body Position on the Motor Development of Preterm Infants: A Randomized Clinical Trial
Authors: de Morais Cardoso Rodrigues Vitória Regina , Cordovil Rita , de Andrade Brunherotti Marisa Afonso , Andrade Brunherotti Marisa Afonso
Published: March 2023

Background

To analyze the influence of body position on the motor development of preterm infants in the first year of life corrected for prematurity.

Methods

This controlled, randomized, open trial included 30 preterm infants randomly assigned to one of the following three groups: prone group (n = 9), supine group (n = 10), and control group (n = 11). Intervention: Motor development was assessed at four time points using the Alberta Infant Motor Scale: first outpatient visit and at 4, 8 and 12 months corrected age.

Results

In the third assessment at 8 months corrected age, the supine group exhibited better motor development than the other groups (p = 0.02). In the control group, the number of infants with normal development decreased from 11 (100%) in the first assessment to 5 (45.45%) in the last assessment. Most infants of mothers who received guidance on body positioning achieved normal motor development in the first year of life (63.1%). Greater dispersion from normal Alberta Infant Motor Scale scores was observed in infants at 8 and 12 months of age.

Conclusions

Guidance on body positioning of preterm infants at home appears to have a positive influence in the first year of life. Child care strategies after hospitalization should be supported to permit full development of the child.

What’s New

This study reinforces home care programs with specialized orientation for motor development of preterm newborns. By the end of the first year of life most infants in the experimental groups (supine and prone positions) achieved a normal motor development, which did not happen in the control group.
AI chatbots not yet ready for clinical use
Authors: Yeung Joshua Au , Kraljevic Zeljko , Luintel Akish , Balston Alfred , Idowu Esther , Dobson Richard J , Teo James T
Published: March 2023

As large language models (LLMs) expand and become more advanced, so does the natural language processing capabilities of conversational AI, or ‘chatbots’. OpenAI’s recent release, ChatGPT, uses a transformer-based model to enable human-like text generation and question-answering on general domain knowledge, while a healthcare-specific Large Language Model (LLM) such as GatorTron has focused on the real-world healthcare domain knowledge. As LLMs advance to achieve near human-level performances on medical question and answering benchmarks, it is probable that Conversational AI will soon be developed for use in healthcare. In this article we discuss the potential and compare the performance of two different approaches to generative pretrained transformers – ChatGPT, the most widely used general conversational LLM, and Foresight, a GPT (generative pretrained transformer) based model focused on modelling patients and disorders. The comparison is conducted on the task of forecasting relevant diagnoses based on clinical vignettes. We also discuss important considerations and limitations of transformer-based chatbots for clinical use.
Hippocampal Glutamate, Resting Perfusion and the Effects of Cannabidiol in Psychosis Risk
Authors: Davies Cathy , Bossong Matthijs G. , Martins Daniel , Wilson Robin , Appiah-Kusi Elizabeth , Blest-Hopley Grace , Allen Paul , Zelaya Fernando , Lythgoe David J. , Brammer Michael , Perez Jesus , McGuire Philip , Bhattacharyya Sagnik
Published: March 2023

Background

Preclinical and human data suggest that the onset of psychosis involves hippocampal glutamatergic dysfunction, driving hyperactivity/hyperperfusion in a hippocampal-midbrain-striatal circuit. Whether glutamatergic dysfunction is related to cerebral perfusion in patients at Clinical High Risk (CHR) for psychosis, and whether cannabidiol (CBD) has ameliorative effects on glutamate or its relationship with blood flow remains unknown.

Methods

Using a double-blind, parallel-group design, 33 CHR patients were randomised to 600mg CBD or placebo; 19 healthy controls did not receive any drug. Proton magnetic resonance spectroscopy was used to measure glutamate concentrations in left hippocampus. We examined differences relating to CHR status (controls vs placebo), effects of CBD (placebo vs CBD) and linear between-group effects, such that placebo>CBD>controls or controls>CBD>placebo. We also examined group x glutamate x cerebral perfusion (measured using arterial spin labelling) interactions.

Results

Compared to controls, CHR-placebo patients had significantly lower hippocampal glutamate (p=.015) and a significant linear relationship was observed across groups, such that glutamate was highest in controls, lowest in CHR-placebo and intermediate in patients under CBD (p=.031). There was also a significant interaction between group (controls vs CHR-placebo), hippocampal glutamate and perfusion in the putamen and insula (pFWE=.012), driven by a strong positive correlation in the CHR-placebo group vs a negative correlation in controls.

Conclusions

Our findings suggest that hippocampal glutamate is lower in CHR patients and may be partially normalised by CBD treatment. Furthermore, we provide the firstin vivoevidence of an abnormal relationship between hippocampal glutamate and resting perfusion in the striatum and insula in these patients.
Daily biofeedback to modulate heart rate oscillations affects structural volume in hippocampal subregions targeted by the locus coeruleus in older adults but not younger adults
Authors: Yoo Hyun Joo , Nashiro Kaoru , Dutt Shubir , Min Jungwon , Cho Christine , Thayer Julian F. , Lehrer Paul , Chang Catie , Mather Mara
Published: March 2023

Using data from a clinical trial, we tested the hypothesis that daily sessions modulating heart rate oscillations affect older adults’ volume of a region-of-interest (ROI) comprised of adjacent hippocampal subregions with relatively strong locus coeruleus (LC) noradrenergic input. Younger and older adults were randomly assigned to one of two daily biofeedback practices for 5 weeks: 1) engage in slow-paced breathing to increase the amplitude of oscillations in heart rate at their breathing frequency (Osc+); 2) engage in self-selected strategies to decrease heart rate oscillations (Osc-). The interventions did not significantly affect younger adults’ hippocampal volume. Among older adults, the two conditions affected volume in the LC-targeted hippocampal ROI differentially as reflected in a significant condition x time-point interaction on ROI volume. These condition differences were driven by opposing changes in the two conditions (increased volume in Osc+ and decreased volume in Osc-) and were mediated by the degree of heart rate oscillation during training sessions.
Low-attenuation Coronary Plaque Volume and Cardiovascular Events in Patients with Distinct Metabolic Phenotypes
Authors: Otsuka Kenichiro , Ishikawa Hirotoshi , Shimada Kenei , Hojo Kana , Yamaura Hiroki , Kono Yasushi , Kasayuki Noriaki , Fukuda Daiju
Published: March 2023

Background

This study aimed to investigate the association between diabetes mellitus (DM), high-risk coronary plaque burden, and risk of cardiovascular outcomes across metabolic phenotypes in patients with suspected coronary artery disease (CAD) who underwent coronary computed tomography angiography (CCTA).

Methods

We included 530 patients who underwent CCTA. Metabolic syndrome (MetS) was defined as the presence of a visceral adipose tissue area ≥ 100 cm2in patients with DM (n = 58), or two or more MetS components excluding DM (n = 114). Remaining patients were categorized into non-MetS patients with DM (n = 52) and non-MetS patients without DM (n = 306). CCTA-based high-risk plaque was defined as low-attenuation plaque (LAP) volume > 4 %. Primary endpoint was presence of a major cardiovascular event (MACE), which was defined as a composite of cardiovascular death, acute coronary syndrome, and coronary revascularization.

Results

Incidence of MACE was highest in the non-MetS with DM group, followed hierarchically by the MetS with DM, MetS without DM, and non-MetS without DM groups. In the multivariable Cox hazard model analysis, DM as a predictor was associated with MACE independent of LAP volume > 4 % (hazard ratio, 2.68; 95% confidence interval, 1.16–6.18; p = 0.02), although MetS did not remain an independent predictor. LAP volume > 4 % remained a predictor of MACE independent of each metabolic phenotype or DM.

Conclusions

This study demonstrated that DM, rather than MetS, is a predictor of coronary events independent of high-risk plaque volume in patients who underwent CCTA.

Clinical Perspective

What Is New?

This study investigated the association between diabetes mellitus (DM), high-risk coronary plaque burden, and major adverse cardiovascular events (MACE) across metabolic phenotypes stratified by the presence or absence of metabolic syndrome (MetS) and DM in patients with suspected coronary artery disease (CAD) who underwent coronary computed tomography angiography (CCTA).

Among the four metabolic phenotypes, incidence of MACE was highest in the non-MetS with DM group, followed hierarchically by the MetS with DM, MetS without DM, and non-MetS without DM groups. Low-attenuation coronary plaque (LAP) volume > 4% was a robust predictor of MACE among the metabolic phenotypes. Furthermore, DM, independent of LAP volume > 4%, was a predictor of MACE, while MetS did not show a significant predictive value.

What Are the Clinical Implications?

Our results demonstrate that individuals with DM alone have a significantly higher risk of developing cardiovascular events than those with MetS, indicating that DM is an independent predictor of cardiovascular events irrespective of the presence of obstructive CAD or LAP volume greater than 4%.
Mid-Life Plasmalogens and Other Metabolites with Anti-Inflammatory Properties are Inversely Associated with Long term Cardiovascular Disease Events: Heart SCORE Study
Authors: Saeed Anum , McKennan Chris , Duan Jiaxuan , Kip Kevin E. , Finegold David , Vu Michael , Swanson Justin , Lopez Oscar , Cohen Ann , Mapstone Mark , Reis Steven E.
Published: March 2023

Background

Preclinical data have shown that low levels of plasmalogens and other metabolites with anti-inflammatory properties may impact metabolic disease processes. However, the association between mid-life levels of such metabolites and late-life atherosclerotic cardiovascular disease (ASCVD) is not known.

Methods

We characterized the midlife plasma metabolomic profile (1,228 metabolites) of 1,852 participants (age 58.1±7.5 years, 69.6% female, 43.6% self-identified as Black) enrolled in the Heart Strategies Concentrating on Risk Evaluation (Heart SCORE) study. Participants were followed for ∼16 years for incident ASCVD events (nonfatal MI, acute ischemic syndrome, coronary revascularization and ASCVD mortality). We used regression model to assess associations of metabolites with ASCVD events. We assessed the impact of genetic variants using whole-exome sequencing with single-variant analysis for common variants and gene-based burden tests for rare variants. We used unbiased and candidate gene approaches to explore genetic associations with metabolites found to be associated with ASCVD events.

Results

A total of twelve metabolites were independently associated with incident ASCVD in fully adjusted models over a median of 12.1 years. A subset of plasmalogens showed an independent inverse association with incident ASCVD events [1-(1-enyl-palmitoyl)-2-arachidonoyl-GPC (OR, 0.54; 95% CI, 0.40-0.74); 1-(1-enyl-palmitoyl)-2-arachidonoyl-GPE (OR, 0.57; 95% CI, 0.42-0.78), 1-methylnicotinamide1-(1-enyl-stearoyl)-2-arachidonoyl-GPE (OR, 0.76; 95% CI, 0.65-0.89)]. Metabolome-wide genetic analysis revealed that two of these plasmalogen metabolites were strongly influenced by polymorphisms of the rs174535, an eQTL for FADS1 and FADS2 genotype. Two amino acid metabolites (2-oxoarginine [OR, 0.42; 95% CI, 0.25-0.69], alpha-ketobutyrate [OR, 0.62; 95% CI, 0.49-0.80]) and a bilirubin degradation product (C16H18N2O5[OR, 0.50; 95% CI, 0.38-0.66) were inversely associated with ASCVD events.

Conclusions

Higher mid-life levels of three plasmalogens, two amino acid metabolites, and a bilirubin degradation product, all of which have anti-inflammatory properties, are associated with lower risk of late-life ASCVD events. Further research is needed to determine whether these metabolites play a causal role in ASCVD and may be a target for future therapies.
Integrating extracellular vesicle and circulating cell-free DNA analysis on a single plasma aliquot from breast cancer patients improves the detection of HER2 positivity
Authors: Mugoni Vera , Ciani Yari , Quaini Orsetta , Tomasini Simone , Notarangelo Michela , Vannuccini Federico , Marinelli Alessia , Leonardi Elena , Pontalti Stefano , Martinelli Angela , Rossetto Daniele , Pesce Isabella , Mansy Sheref S. , Barbareschi Mattia , Ferro Antonella , Caffo Orazio , Attard Gerhardt , Di Vizio Dolores , D’Agostino Vito Giuseppe , Nardella Caterina , Demichelis Francesca
Published: March 2023

Background

Multi-analyte liquid biopsies represents an emerging opportunity for non-invasive cancer assessment. We developed ONCE (ONe Aliquot for Circulating Elements), a novel multi-analytes liquid biopsy approach for the isolation of extracellular vesicles (EVs) and cell-free DNA (cfDNA) from a single aliquot of blood.

Methods

We assessed ONCE performance to classify HER2-positive early-stage breast cancer (BrCa) patients by combining RNA and DNA signals on n=64 healthy donors (HD) and non–metastatic BrCa patients. Specifically, we investigated EVs-derived RNA (EV-RNA) and cfDNA by next-generation sequencing (NGS) and by digital droplet PCR (ddPCR). Additionally, we utilized imaging flow cytometry to evaluate EVs as potential carriers of the HER2 protein.

Results

Western blot analysis and immunocapture assay revealed that EVs-enriched proteins were detected at similar levels among the HER2+ and HER2- subtypes. Sequencing of cfDNA and EV-RNA from HER2- and HER2+ patients demonstrated concordance within situmolecular analyses of matched tissues. Combined analysis of the two circulating analytes by ddPCR showed increased sensitivity inERBB2/HER2 detection compared to single nucleic acid components. Multi-analyte liquid biopsy prediction performance was comparable to tissue-based sequencing results from TCGA. Also, we observed HER2 protein on the surface of EVs isolated from the HER2+ BrCa plasma, thus corroborating the potential relevance of studying EVs as companion analyte to cfDNA.

Conclusions

This data confirms the relevance of combining cfDNA and EV-RNA analytes for cancer assessment and supports the ONCE approach as a valuable tool for multi-analytes liquid biopsies’ clinical implementation.
Persistent DNA methylation changes associated with prenatal NO2exposure in a Canadian prospective birth study
Authors: Lee Samantha , Sbihi Hind , MacIsaac Julia L. , Subbarao Padmaja , Mandhane Piushkumar J. , Moraes Theo J. , Turvey Stuart E. , Duan Qingling , Ambalavanan Amirthagowri , Brauer Michael , Brook Jeffrey , Kobor Michael S. , Jones Meaghan J.
Published: March 2023

Background

Accumulating evidence suggests prenatal air pollution exposure alters DNA methylation (DNAm), which could go on to affect long-term health. However, it remains unclear whether prenatal DNAm alterations persist through early life. Identifying DNAm changes that persist from birth into childhood would provide greater insight into the molecular mechanisms that most likely contribute to the association of prenatal air pollution exposure with health outcomes such as atopic disease.

Objectives

This study investigated the persistence of DNAm changes associated with prenatal NO2exposure (a surrogate measure of traffic-related air pollution) at age one to begin characterizing which DNAm changes most likely to contribute to atopic disease.

Methods

We used an atopy-enriched subset of CHILD study participants (N=145) to identify individual and regional cord blood DNAm differences associated with prenatal NO2, followed by an investigation of persistence in age one peripheral blood. As we had repeated DNAm measures, we also isolated postnatal-specific DNAm changes and examined their association with NO2exposure in the first year of life. MANOVA tests were used to examine the association between DNAm changes associated with NO2and child wheeze and atopy.

Results

We identified 24 regions of altered cord blood DNAm, with several annotated toHOXgenes. Two regions annotated toMPDU1andC5orf63were significantly associated with age one wheeze. Further, we found the effect of prenatal NO2exposure across CpGs within all altered regions remained similar at age one. A single region of postnatal-specific DNAm annotated toHOXB6was associated with year one NO2and age one atopy.

Discussion

Regional cord blood DNAm changes associated with prenatal NO2exposure persist through at least the first year of life, and some of these changes are associated with age one wheeze. The early-postnatal period remains a sensitive window to DNAm perturbations that may also influence child health.
Delineating memory reactivation in sleep with verbal and non-verbal retrieval cues
Authors: Guttesen Anna á V. , Gaskell M. Gareth , Cairney Scott A.
Published: March 2023

Sleep supports memory consolidation via the reactivation of newly formed memory traces. One way to investigate memory reactivation in sleep is by exposing the sleeping brain to auditory retrieval cues; a paradigm known as targeted memory reactivation (TMR). To what extent to acoustic properties of memory cues influence the effectiveness of TMR, however, has received limited attention. We addressed this question by exploring how verbal and non-verbal memory cues affect oscillatory activity linked to memory reactivation in slow-wave sleep. Fifty-one healthy adult males learned to associate visual stimuli with spoken words (verbal cues) and environmental sounds (non-verbal cues). Subsets of the verbal and non-verbal cues were then replayed during sleep, alongside previously unheard control cues. For a subset of the participants, the voice of the verbal cues was mismatched between sleep and learning. Memory cues (relative to control cues) prompted an increase in theta/alpha and spindle power, which have been heavily implicated in sleep-associated memory processing. Moreover, verbal memory cues were associated with a stronger increase in spindle power than non-verbal memory cues. There were no significant differences between the matched and mismatched conditions when analysing verbal memory cues in isolation. Our findings suggest that verbal memory cues may be more effective than non-verbal memory cues for triggering memory reactivation in sleep, as indicated by an amplified spindle response.
SifA SUMOylation governsSalmonellaTyphimurium intracellular survival via modulation of lysosomal function
Authors: Chandrasekhar Hridya , Mohapatra Gayatree , Singh Mukesh , Rana Sarika , Kaur Navneet , Sharma Sheetal , Tuli Amit , Das Prasenjit , Srikanth C. V.
Published: March 2023

Gastroenteritis causing pathogenSalmonellaTyphimurium (S.Tm) during its infection in host cells thrives in a vacuolated compartment,SalmonellaContaining Vacuole (SCV), which sequentially acquires host endosomal and lysosomal markers. Long tubular structures, called asSalmonellainduced filaments (SIFs), are known to be required for SCV’s nutrient acquisition, membrane maintenance and stability. A tightly coordinated interactions involving prominent effector SifA and various host adapters PLEKHM1, PLEKHM2 and Rab GTPases govern SCV integrity and SIF formation. Here, we report for the first time, the functional regulation of SifA is modulated by its SUMOylation at lysine 11.S.Tm expressing lysine 11 mutant SifA (SifAK11R) is defective in intracellular proliferation due to compromised SIF formation and enhanced lysosomal acidification. Furthermore, murine competitive index experiments reveal defective in vivo proliferation and weakened virulence of SifAK11Rmutant. Concisely, our results demonstrate that SUMO deficient SifA mutant nearly behaves like a SifA knockout strain which impacts PLEKHM2-M6PR mediated lysosomal acidification pathway. Thus, our results bring forth a novelS.Tm-host crosstalk mechanism involving host mediated effector SUMOylation critical for pathogenicity.
Vascular adaptation model from force balance:Physarum polycephalumas a case study
Authors: Marbach Sophie , Ziethen Noah , Alim Karen
Published: March 2023

Understanding vascular adaptation, namely what drives veins to shrink or grow, is key for the self-organization of flow networks and their optimization. From the top-down principle of minimizing flow dissipation at a fixed metabolic cost within flow networks, flow shear rate resulting from the flows pervading veins is hypothesized to drive vein adaptation. Yet, there is no bottom-up derivation of how flow forces impact vein dynamics. From the physical principle of force balance, shear rate acts parallel to vein walls, and hence, naively shear rate could only stretch veins and not dilate or shrink them. We, here, resolve this paradox by theoretically investigating force balance on a vein wall in the context of the vascular network of the model organismP. polycephalum. We propose, based on previous mechanical studies of cross-linked gels, that shear induces a nonlinear, anisotropic response of the actomyosin gel, making up vein walls that can indeed drive vein dilatation. Furthermore, our force balance approach allows us to identify that shear feedback occurs with a typical timescale and with a typical target shear rate that are not universal properties of the material but instead depend smoothly on the location of the vein within the network. In particular, the target shear rate is related to the vein’s hydrostatic pressure, which highlights the role of pressure in vascular adaptation. Finally, since our derivation is based on force balance and fluid mechanics, we believe our approach can be extended to vascular adaptation in other organisms.
Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following marine heatwaves
Authors: George Matthew N. , Cattau Olivia , Middleton Mollie , Lawson Delaney , Vadopalas Brent , Gavery Mackenzie , Roberts Steven
Published: March 2023

Polyploidy has been shown to negatively impact environmental stress tolerance, resulting in increased susceptibility to extreme climate events such as marine heatwaves (MHWs). In this study, we used the response of the Pacific oysterCrassostrea gigasto MHWs as a model system to identify key ploidy-specific differences in the physiological and transcriptomic response of oysters to environmental stress. In this study, adult diploid (2n) and triploid (3n) oysters were exposed to elevated seawater temperature (single stressor; 30°C), elevated temperature followed by acute desiccation stress (multiple stressor; 30°C + emersion at an aerial temperature of 44°C for 4h), or a control (17°C) within a hatchery setting. Oyster mortality rate was elevated within stress treatments with respect to the control and was significantly higher in triploids than diploids following multiple stress exposure (36.4% vs. 14.8%). Triploids within the multiple stressor treatment exhibited signs of energetic limitation, including metabolic depression, a significant reduction in ctenidium Na+/K+ATPase activity, and the dysregulated expression of key genes associated with heat tolerance, the inhibition of apoptosis, and mitochondrial function. Functional enrichment analysis of ploidy-specific gene sets identified that biological processes associated with metabolism, stress tolerance, and immune function were overrepresented within triploids across stress treatments. Our results demonstrate that triploidy impacts the transcriptional regulation of key metabolic processes that underly the environmental stress response of Pacific oysters, resulting in downstream shifts in physiological tolerance limits that may be detrimental to survival. The impact of chromosome set manipulation on the climate resilience of marine populations has important implications for the adaptability of marine populations and domestic food security within future climate scenarios, especially as triploidy induction becomes an increasingly popular tool to elicit reproductive control across a wide range of marine organisms used within marine aquaculture.
Human Vascularized Bile Duct-on-a Chip: A multi-cellular micro-physiological system for studying Primary Sclerosing Cholangitis
Authors: Du Yu , Gupta Kapish , Waisbourd-Zinman Orith , Har-Zahav Adi , Soroka Carol J. , Boyer James L. , Llewellyn Jessica , Liu Chengyang , Naji Ali , Polacheck William J. , Wells Rebecca G.
Published: March 2023

Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease in which the bile ducts of the liver become inflamed and scarred. Scarred bile ducts eventually narrow and obstruct and can cause additional liver pathology including liver failure, repeated infections, and tumors. The pathogenesis of PSC remains largely unknown, partly due to difficulty in obtaining cholangiocytes and partly due to a paucity ofin vitromodels that capture the various factors contributing to disease progression. Here we report the development of a human vascularized bile duct-on-a-chip that models blood vessels and bile ducts structurally and functionally in three dimensions and includes cholangiocytes derived from control and PSC patient tissue and bile. The flow of blood and bile was modeled by perfusion of cell-lined channels, and cholangiocytes and endothelial cells displayed differential responses to perfusion. Normal and PSC cholangiocytes polarized normally, formed mature tight junctions and displayed similar permeability, comparable toex vivomeasurements. The model with PSC cholangiocytes, however, became more inflammatory than the normal under the stimulation of IL-17A, which induced PBMC and differentiated Th17 cells in the vascular channel to transmigrate more through the endothelial layer of the vascular compartment. In sum, this human vascularized bile duct-on-a-chip recapitulated the vascular-biliary interface structurally and functionally and represents a novel multicellular platform to study inflammatory and fibrotic cholangiopathies such as PSC.
Oligodendrocyte Development and Myelin Sheath Formation are Regulated by the Antagonistic Interaction between the Rag-Ragulator Complex and TFEB
Authors: Bouchard Ellen L. , Meireles Ana M. , Talbot William S.
Published: March 2023

Myelination by oligodendrocytes is critical for fast axonal conduction and for the support and survival of neurons in the central nervous system. Recent studies have emphasized that myelination is plastic and that new myelin is formed throughout life. Nonetheless, the mechanisms that regulate the number, length, and location of myelin sheaths formed by individual oligodendrocytes are incompletely understood. Previous work showed that lysosomal transcription factor TFEB represses myelination by oligodendrocytes and that the RagA GTPase inhibits TFEB, but the step or steps of myelination in which TFEB plays a role have remained unclear. Here, we show that TFEB regulates oligodendrocyte differentiation and also controls the number and length of myelin sheaths formed by individual oligodendrocytes. In the dorsal spinal cord oftfebmutants, individual oligodendrocytes produce fewer myelin sheaths, and these sheaths are longer than those produced by wildtype cells. Transmission electron microscopy shows that there are more myelinated axons in the dorsal spinal cord oftfebmutants than in wildtype animals, but no significant change in axon diameter. In contrast totfebmutants, oligodendrocytes inrragamutants produce shorter myelin sheaths. The sheath length inrraga; tfebdouble mutants is not significantly different from wildtype, consistent with the antagonistic interaction between RagA and TFEB. Finally, we find that the GTPase activating protein Flcn and the RagCa and RagCb GTPases are also necessary for myelination by oligodendrocytes. These findings demonstrate that TFEB coordinates myelin sheath length and number during myelin formation in the central nervous system.

Graphical Abstract
CD4+T cells display a spectrum of recall dynamics during re-infection with malaria parasites
Authors: Lee Hyun Jae , Moreira Marcela L. , Li Shihan , Williams Cameron G. , Skinner Oliver P. , Asad Saba , Asatsuma Takahiro , Bramhall Michael , Jiang Zhe , Engel Jessica A. , Soon Megan S. F. , Straube Jasmin , Barrera Irving , Murray Evan , Chen Fei , Nideffer Jason , Jagannathan Prasanna , Haque Ashraful
Published: March 2023

Children in malaria-endemic regions can experience multiplePlasmodiuminfections over a short period of time, within vitroCD4+T cell recall responses becoming more regulatory with increasing age and exposure. This suggests that repeated infection qualitatively changes CD4+T cells, although the heterogeneity and dynamics of these responses await systematic analysisin vivo. Here, we examined TCR transgenic PbTII and polyclonal CD4+T cells duringPlasmodiumre-infection in mice, in conjunction with scRNA-seq/TCR-seq and spatial transcriptomics at near single-cell resolution. PbTII cells gave rise to multiple antigen-experienced states in different areas of the spleen after primary infection and antimalarial treatment, including ongoing GC responses and T-cell zone memory. Upon re-infection, Th1-memory PbTII cells initiated a rapid effector response prior to proliferating, while GC Tfh cells of the same antigen specificity were entirely refractory within the same organ. Transcriptome dynamic modelling and network analysis of Th1 recall revealed a biphasic wave of RNA processing that firstly preceded immune effector transcription, and later accompanied cellular proliferation. Importantly, Th1 recall constituted a partial facsimile of primary Th1 responses, with no unique genes amongst the small subset of those upregulated upon re-infection. Finally, we noted a similar spectrum of antigen-experienced states and recall dynamics by polyclonal CD4+T cells with diverse TCRs. Therefore, during re-infection withPlasmodium, persisting GC Tfh cells remained unaltered transcriptionally, Tcm/Tfh-like cells exhibited minimal proliferation, and Th1-memory cells displayed a rapid, proliferating IL-10-producing Tr1 response consistent with a shift towards immune-regulation. These data highlight a broad spectrum of simultaneous CD4+T cell responses that occur in the spleen during re-infection with malaria parasites.

Highlights

Splenic TCR transgenic CD4+T cells are highly heterogeneous prior to re-infection.

Persisting GC Tfh cells are refractory to re-activation during re-infection.

Th1-memory cells rapidly upregulate RNA processing prior to effector function and proliferation.

Th1-recall is an imperfect but faithful facsimile of primary Th1 responses.

A spectrum of recall states is observed in polyclonal CD4+T cells with diverse TCRs.
Mechanisms underpinning morphogenesis of symbiotic organ specialized for hosting indispensable microbial symbiont in stinkbug
Authors: Oishi Sayumi , Harumoto Toshiyuki , Okamoto-Furuta Keiko , Moriyama Minoru , Fukatsu Takema
Published: March 2023

Microbial mutualists are pivotal for insect adaptation, which often entails the evolution of elaborate organs for symbiosis. Addressing what mechanisms underpin the development of such organs is of evolutionary interest. Here we investigated the stinkbugPlautia staliwhose posterior midgut is transformed into a specialized symbiotic organ. Despite being a simple tube in newborns, it developed numerous crypts in four rows, whose inner cavity hosts a specific bacterial symbiont, during 1stto 2ndnymphal instar. Visualization of dividing cells revealed that active cell proliferation was coincident with the crypt formation, although spatial patterns of the proliferating cells did not reflect the crypt arrangement. Visualization of visceral muscles in the midgut, consisting of circular muscles and longitudinal muscles, uncovered that, strikingly, circular muscles exhibited a characteristic arrangement running between the crypts specifically in the symbiotic organ. Even in early 1stinstar when no crypts were seen, two rows of epithelial areas delineated by bifurcated circular muscles were identified. In 2ndinstar, crossing muscle fibers newly appeared and connected the adjacent circular muscles, whereby the midgut epithelium was divided into four rows of crypt-to-be areas. The crypt formation proceeded even in aposymbiotic nymphs, uncovering autonomous nature of the crypt development. We propose a mechanistic model of crypt formation wherein the spatial arrangement of muscle fibers and the proliferation of epithelial cells underpin the formation of crypts as midgut evaginations.

IMPORTANCE

Diverse organisms are associated with microbial mutualists, in which specialized host organs often develop for retaining the microbial partners. In the light of the origin of evolutionary novelties, it is important to understand what mechanisms underpin the elaborate morphogenesis of such symbiotic organs, which must have been shaped through interactions with the microbial symbionts. Using the stinkbugPlautia stalias a model, we demonstrated that visceral muscular patterning and proliferation of intestinal epithelial cells during early nymphal stages are involved in the formation of numerous symbiont-harboring crypts arranged in four rows in the posterior midgut to constitute the symbiotic organ. Strikingly, the crypt formation occurred normally even in symbiont-free nymphs, uncovering that the crypt development proceeds autonomously. These findings suggest that the crypt formation is deeply implemented into the normal development ofP. stali, which must reflect the considerably ancient evolutionary origin of the midgut symbiotic organ in stinkbugs.
Polygenic score informed by genome-wide association studies of multiple ancestries and related traits improves risk prediction for coronary artery disease
Authors: Patel Aniruddh P. , Wang Minxian , Ruan Yunfeng , Koyama Satoshi , Clarke Shoa L. , Yang Xiong , Tcheandjieu Catherine , Agrawal Saaket , Fahed Akl C. , Ellinor Patrick T. ,   Genes & Health Research Team,   the Million Veteran Program, Tsao Phillip S. , Sun Yan V. , Cho Kelly , Wilson Peter W. F. , Assimes Themistocles L. , van Heel David A. , Butterworth Adam S. , Aragam Krishna G. , Natarajan Pradeep , Khera Amit V.
Published: March 2023

Accurate stratification of coronary artery disease (CAD) risk remains a critical need. A new polygenic score (GPSMult) incorporates CAD genome-wide association data across five ancestries (>269,000 cases, >1,178,000 controls) with genetic association data for ten CAD risk factors. GPSMultassociates with an OR/SD 2.14, (95%CI:2.10-2.19,P<0.001) for prevalent CAD and HR/SD 1.73 (95%CI 1.70-1.76,P<0.001) for incident CAD. When compared with the previously published GPS2018in external datasets, GPSMultdemonstrated 73%, 46%, and 113% increase in effect size for individuals of African, European, and South Asian ancestry, respectively, and significantly outperformed recently published CAD polygenic scores. GPSMultidentifies individuals with CAD risk extremes, including the top 3% of the population at equivalent risk for a new CAD event as those with prior CAD having a second event. Integrating GPSMultwith the Pooled Cohort Equations results in 7.0% [95%CI:5.9%-8.2%,P<0.001] net reclassification improvement at the 7.5% threshold. Large-scale integration genetic association data for CAD and related traits from diverse populations meaningfully improves polygenic risk prediction.
RNA Polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation
Authors: Martell Danya J. , Merens Hope E. , Fiorini Claudia , Caulier Alexis , Ulirsch Jacob C. , Ietswaart Robert , Choquet Karine , Graziadei Giovanna , Brancaleoni Valentina , Domenica Cappellini Maria , Scott Caroline , Roberts Nigel , Proven Melanie , Roy Noémi BA , Babbs Christian , Higgs Douglas R. , Sankaran Vijay G. , Churchman L. Stirling
Published: March 2023

The controlled release of promoter-proximal paused RNA polymerase II (Pol II) into productive elongation is a major step in gene regulation. However, functional analysis of Pol II pausing is difficult because factors that regulate pause release are almost all essential. In this study, we identified heterozygous loss-of-function mutations inSUPT5H, which encodes SPT5, in individuals with β-thalassemia unlinked toHBBmutations. During erythropoiesis in healthy human cells, cell cycle genes were highly paused at the transition from progenitors to precursors. When the pathogenic mutations were recapitulated bySUPT5Hediting, Pol II pause release was globally disrupted, and the transition from progenitors to precursors was delayed, marked by a transient lag in erythroid-specific gene expression and cell cycle kinetics. Despite this delay, cells terminally differentiate, and cell cycle phase distributions normalize. Therefore, hindering pause release perturbs proliferation and differentiation dynamics at a key transition during erythropoiesis, revealing a role for Pol II pausing in the temporal coordination between the cell cycle and differentiation.
Electron microscopic analysis of the influence of iPSC-derived motor neurons on bioengineered human skeletal muscle tissues
Authors: Nguyen Christine T. , Chávez-Madero Carolina , Jacques Erik , Musgrave Brennen , Yin Ting , Saraci Kejzi , Gilbert Penney M. , Stewart Bryan A.
Published: March 2023

3D bioengineered skeletal muscle macrotissues are increasingly important for studies of cell biology and development of therapeutics. Tissues derived from immortalized cells obtained from patient samples or from stem cells can be co-cultured with motor-neurons to create models of human neuromuscular junctions in culture. In this study, we present foundational work on 3D cultured muscle ultrastructure, with and without motor neurons, which is enabled by the development of a new co-culture platform. Our results show that tissues from Duchenne muscular dystrophy patients are poorly organized compared to tissues grown from healthy donor and that the presence of motor neurons invariably improves sarcomere organization. Electron micrographs show that in the presence of motor neurons, filament directionality, banding patterns, z-disc continuity and appearance of presumptive SSR and T-tubule profiles all improve in healthy, DMD and iPSC derived muscle tissue. Further work to identify the underlying defects of DMD tissue disorganization and the trophic mechanisms by which motor neurons support muscle are likely to yield potential new therapeutic approaches for treating patients suffering from Duchenne muscular dystrophy.
The geometry of appetitive-aversive value representations in medial prefrontal networks
Authors: Winke Nanci , Herry Cyril , Jercog Daniel
Published: March 2023

The value of rewards and punishments – namely, how good or bad they are perceived – guides approach or avoidance behaviors. Valence refers to the negative or positive “sign” of the state elicited by an event, whereas salience refers to the amount of attention an event attracts, disregarding its valence. While identifying these signals conveys critical information for understanding circuits involved in emotional processing, they are often confounded due to their underlying correlation. Moreover, whereas the study of the neural basis of value coding has been intensively investigated in the appetitive domain, the neural substrates for how aversive values are established for different threat intensities and guide defensive behavior have yet to be discovered. The dorsomedial prefrontal cortex (dmPFC) is a key region in the control of defensive actions, although how different aversive values are encoded at the neuronal level within this region and drive defensive behaviors remains unknown.

Here, we developed an instrumental approach/avoidance task in mice that, by matching motivational salience levels elicited by cues predicting rewards or punishments, allows univocally disentangling the presence of either salience, valence, or value coding from brain signals. We performed freely moving large neuronal population calcium imaging in the dmPFC of mice performing our task, conducting appetitive/aversive outcome devaluation/revaluation behavioral tests. We found that, while a similar fraction of single neurons decoded valence and value information, and only a minor fraction decoded salience, value coding was observed at the neuronal population level. Moreover, different value representations of the same valence lay within similar subspaces of the neural state space while values of opposed valence were encoded in orthogonal subspaces, unveiling how the brain stores associative appetitive and aversive information in medial prefrontal networks.
The ups and downs of biological oscillators: A comparison of time-delayed negative feedback mechanisms
Authors: Rombouts Jan , Verplaetse Sarah , Gelens Lendert
Published: March 2023

Many biochemical oscillators are driven by the periodic rise and fall of protein concentrations or activities. A negative feedback loop underlies such oscillations. The feedback can act on different parts of the biochemical network. Here, we mathematically compare time-delay models where the feedback affects production and degradation. We show a mathematical connection between the linear stability of the two models, and derive how both mechanisms impose different constraints on the production and degradation rates that allow oscillations. We show how oscillations are affected by the inclusion of a distributed delay, of double regulation (acting on production and degradation), and of enzymatic degradation.
Efficiency Estimates for Electromicrobial Production of Branched-chain Hydrocarbons
Authors: Sheppard Timothy J. , Specht David A. , Barstow Buz
Published: March 2023

Electromicrobial production is a process where microorganisms use electricity as a charge and energy source for the production of complex molecules, often from starting compounds as simple as CO2. The aviation industry is in need for sustainable fuel alternatives that can meet their requirements of high-altitude performance while also meeting 21stcentury carbon emissions standards. The electromicrobial production of jet fuel components with CO2-derived carbon provides a unique opportunity to generate jet fuel blends that are compatible with modern engines with net-neutral carbon emissions. In this study, we analyze the pathways necessary to generate single- and multi-branched-chain hydrocarbonsin vivoutilizing both extracellular electron uptake (EEU) and H2-oxidation as methods for electron delivery, the Calvin cycle for CO2-fixation and the ADO decarboxylation pathway. We find the maximum electrical-to-fuel energy conversion efficiencies for single- and multi-branched chain hydrocarbons areand. Utilizing this information, as well as previously collected predictions on straight-chain alkane and terpenoid biosynthesis, we calculate the efficiency of electromicrobial production of jet fuel blends containing straight-chain, branched-chain, and terpenoid components. Increasing the fraction of branched-chain alkanes in the blend from zero to 47% only lowers the electrical energy conversion efficiency fromto.