bluuebunny/crossref_metadata_2025 huggingface dataset:
The metabolomic signature of weight loss in the Diabetes Remission Clinical Trial (DiRECT)
Authors: Corbin Laura J. , Hughes David A. , Bull Caroline J. , Vincent Emma E. , Smith Madeleine L. , McConnachie Alex , Messow Claudia-Martina , Welsh Paul , Taylor Roy , Lean Michael E. J. , Sattar Naveed , Timpson Nicholas J.
Published: July 2022

Use of high-throughput metabolomics technologies in a variety of study designs has demonstrated a strong and consistent metabolomic signature of overweight and type 2 diabetes. However, the extent to which these metabolomic patterns can be recovered with weight loss and diabetes remission has not been investigated. We aimed to characterise the metabolomic consequences of a weight loss intervention in diabetes, within an existing randomised controlled trial – the Diabetes Remission Clinical Trial (DiRECT) – to provide insight into how weight loss-induced metabolic changes could lead to improved health. Decreases in branched chain amino acids, sugars and LDL triglycerides, and increases in sphingolipids, plasmalogens and metabolites related to fatty acid metabolism were associated with the intervention. The change in metabolomic pattern with mean 8.8kg weight loss thus reverses many features associated with the development of type 2 diabetes. Furthermore, metabolomic profiling also appears to capture variation in response to treatment seen across patients.
COVID-19 Prevention at Institutions of Higher Education, United States, 2020 – 2021: Implementation of Nonpharmaceutical Interventions
Authors: Moreland Sarah , Zviedrite Nicole , Ahmed Faruque , Uzicanin Amra
Published: July 2022

Background

In early 2020, following the start of the coronavirus disease 2019 (COVID-19) pandemic, institutions of higher education (IHEs) across the United States rapidly pivoted to distance learning to reduce risk of on-campus virus transmission.

Objective

To explore IHE use of nonpharmaceutical interventions (NPIs) during the subsequent pandemic-affected academic year 2020–2021.

Design

Cross-sectional study of data collected January – June 2021. Setting: US four-year, undergraduate IHEs.

Patients (or Participants)

All public (n=547) and a stratified random sample of private (n=300) IHEs.

Measurements

From IHE websites, we documented NPIs, including changes to the calendar, learning environment, housing, common areas, and dining; COVID-19 testing; and facemask protocols, and performed weighted analysis to assess congruence with the US Centers for Disease Control and Prevention (CDC) guidance for IHEs. We used weighted multivariable linear regression to explore the association between IHE characteristics and the summated number of implemented NPIs.

Results

Overall, 20% of IHEs implemented all surveyed CDC-recommended NPIs. The most frequently utilized were learning environment changes (91%), practiced as one or more of the following: distance or hybrid learning opportunities (98%), 6-feet spacing (60%), and reduced class sizes (51%). Additionally, 88% of IHEs specified facemask protocols, 78% physically modified common areas, and 67% offered COVID-19 testing. Among the 33% of IHEs offering ≥50% of courses in person, having <1,000 students was associated with having implemented fewer NPIs than IHEs with ≥1,000 students.

Limitations

Data collected from publicly available sources may introduce observation biases but allow for large sample size.

Conclusion

Only 1 in 5 IHEs implemented all surveyed CDC recommendations, while a majority implemented a subset. IHE size and location were associated with degree of NPI implementation. Additional research is needed to assess adherence to NPI implementation in IHE settings.

Funding Source

United States Centers for Disease Control and Prevention
Carotid atherosclerosis in people of European, South Asian and African Caribbean ethnicity in the Southall and Brent Revisited study (SABRE)
Authors: Anbar Rayan , Chaturvedi Nish , Eastwood Sophie V. , Tillin Therese , Hughes Alun D.
Published: July 2022

Background

Atherosclerotic cardiovascular disease (CVD) risk differs by ethnicity. In comparison with Europeans (EA) South Asian (SA) people in UK experience higher risk of coronary heart disease and stroke, while African Caribbean people have a lower risk of coronary heart disease but a higher risk of stroke.

Aim

To compare carotid atherosclerosis in EA, SA and AC participants in the Southall and Brent Revisited (SABRE) study and establish if any differences were explained by established or novel CVD risk factors.

Methods

Cardiovascular risk factors were measured, and carotid ultrasound was performed in 985 individuals (438 EA, 325 SA, 228 AC). Carotid plaques, and intima-media thickness (cIMT) were measured. Associations of carotid atherosclerosis with ethnicity were investigated using regression analyses, with and without adjustment for potential confounders (age, sex) and mediators (education, diabetes, hypertension, total cholesterol, HDL-C, alcohol consumption, current smoking).

Results

Prevalence of any plaque was similar in EA and SA, and lower in AC (17%, 17%, and 6% respectively; p < 0.001 by ANOVA). Total plaque area was also similar in EA and SA but reduced in AC, but there were no major differences in the maximum height or length of plaques in people with plaques by ethnic group. These ethnic differences were unaffected by adjustment for potential confounders or mediators. After adjustment for age and sex cIMT was higher in AC but this difference was attenuated by adjustment for CVD risk factors.

Conclusions

Prevalence of carotid artery atherosclerotic plaques varies by ethnicity, independent of risk factors. The similarity of plaque burden in SA and EA despite established differences in CVD risk in these ethnic groups casts some doubt on the utility of carotid ultrasound as a means of assessing risk across ethnic groups.
Influence of vitamin D supplementation on SARS-CoV-2 vaccine efficacy and immunogenicity
Authors: Jolliffe David A , Vivaldi Giulia , Chambers Emma S , Cai Weigang , Li Wenhao , Faustini Sian E , Gibbons Joseph M , Pade Corinna , Richter Alex G , McKnight Áine , Martineau Adrian R
Published: July 2022

Background & Aims

Vitamin D deficiency has been reported to associate with impaired development of antigen-specific responses following vaccination. We aimed to determine whether vitamin D supplements might boost immunogenicity and efficacy of SARS-CoV-2 vaccination.

Methods

We conducted three sub-studies nested within the CORONAVIT randomised controlled trial, which investigated effects of offering vitamin D supplements at a dose of 800 IU/day or 3200 IU/day vs. no offer on risk of acute respiratory infections, including COVID-19, in UK adults with circulating 25-hydroxyvitamin D concentrations <75 nmol/L. Sub-study 1 (n=2808) investigated effects of vitamin D supplementation on risk of breakthrough SARS-CoV-2 infection following two doses of SARS-CoV-2 vaccine. Sub-study 2 (n=1853) investigated effects of vitamin D supplementation on titres of combined IgG, IgA and IgM (IgGAM) anti-Spike antibodies in eluates of dried blood spots collected after SARS-CoV-2 vaccination. Sub-study 3 (n=100) investigated effects of vitamin D supplementation on neutralising antibody and cellular responses in venous blood samples collected after SARS-CoV-2 vaccination.

Results

1945/2808 (69.3%) sub-study 1 participants received two doses of ChAdOx1 nCoV-19 (Oxford–AstraZeneca); the remainder received two doses of BNT162b2 (Pfizer). Vitamin D supplementation did not influence risk of breakthrough SARS-CoV-2 infection (800 IU/day vs. no offer: adjusted hazard ratio 1.28, 95% CI 0.89 to 1.84; 3200 IU/day vs. no offer: 1.17, 0.81 to 1.70). Neither did it influence IgGAM anti-Spike titres, neutralising antibody titres or IFN-γ concentrations in supernatants of S peptide-stimulated whole blood.

Conclusions

Among adults with sub-optimal baseline vitamin D status, vitamin D replacement at a dose of 800 or 3200 IU/day did not influence protective efficacy or immunogenicity of SARS-CoV-2 vaccination.

Clinical Trial Registration

ClinicalTrials.govNCT04579640.
Internet-based Cognitive Behaviour Therapy for the Prevention, Treatment and Relapse Prevention of Eating Disorders: A Systematic Review
Authors: Hamid Nilima
Published: July 2022

Background and Objectives

Eating disorders (EDs) are undertreated worldwide. In the UK the lag between recognition of symptoms and treatment ranges from about 15 months to in excess of two years. Internet-based Cognitive Behaviour Therapy (ICBT) could be a viable alternative to face-to-face Cognitive Behaviour Therapy (CBT) that avoids the negative impacts of delayed interventions. Based on evidence from randomised controlled trials (RCTs) this systematic review investigated the effectiveness of minimally guided self-help ICBT, without face-to-face therapy, for the prevention, treatment and relapse prevention of all types of EDs in adults.

Methods

The electronic databases MEDLINE, PsychINFO, CENTRAL, Scopus, and Web of Science were searched between 1991 to 2021. Inclusion criteria specified RCTs with ICBT versus inactive comparison groups. The Cochrane Risk of Bias Tool was used for quality assessments. Qualitative synthesis and meta-analyses were conducted.

Results

Findings showed medium and large significant beneficial effect sizes for the prevention and treatment studies, respectively, whereas relapse prevention yielded mainly small non-significant beneficial effect sizes. Only the treatment studies reached clinical significance and cognitive symptoms improved more than behavioural symptoms.

Conclusions

This systematic review reinforces the vital need to provide evidence-based Internet interventions at times when face-to-face treatment is not an option as has been the case during the COVID-19 pandemic. Although ICBT is a promising intervention for eating disorders in adults and may be more effective than face-to-face CBT for treating cognitive symptoms further high-quality ED RCTs are required to increase the evidence-base and enable more precise meta-analyses to reach definitive conclusions.

Highlights

Findings showed medium and large significant beneficial effect sizes for the prevention and treatment studies, respectively, whereas relapse prevention yielded mainly small non-significant beneficial effect sizes.

For the treatment studies, 35% of effect estimates were clinically important. None of the effect estimates for either the prevention or the relapse prevention studies reached clinical significance.

There were statistically significant improvements on comorbid depression and anxiety for the treatment programmes.

Cognitive symptoms improved more than behavioural symptoms and it is suggested that ICBT may be more effective than face-to-face CBT for treating cognitive symptoms.
Analysis of SARS-CoV-2 amino acid mutations in New York City Metropolitan wastewater (2020-2022) reveals multiple traits with human health implications across the genome and environment-specific distinctions
Authors: Archana Anand , Long Chenghua , Chandran Kartik
Published: July 2022

We characterize variant diversity, amino acid mutation frequency, functionality and associations with COVID-19 infections in one of the largest datasets of SARS-CoV-2 genome sequences collected from wastewater in the New York metropolitan area. Variant diversity differed within parts of the New York City sewershed and between wastewater sludge and influent samples. P314L, D614G and T3255I occurred in >95% of wastewater samples. Enhanced infectivity, transmissibility and escape from antibody neutralization were dominant traits in the wastewater. Strikingly, over 60% of the most frequently occurring mutations were found in regions other than the spike (S) protein, and nearly 50% remain uncharacterized for functional impacts warranting further investigation. We demonstrate strong correlations between P314L, D614G, T95I, G50E, G50R, G204R, R203K, G662S, P10S, P13L and mortality rates, percent positive test results, hospitalization rates and % of population fully vaccinated. The results from our study suggest that there are relatively understudied mutations in the spike protein (H655Y, T95I) and understudied mutations occurring in non-spike proteins (N, ORF1b, ORF9b and ORF9c), that are enhancing transmissibility and infectivity among human populations, warranting further investigation.
Delineating organizational principles of the endogenous L-A virus by cryo-EM and computational analysis of native cell extracts
Authors: Schmidt Lisa , Tüting Christian , Kyrilis Fotis L. , Hamdi Farzad , Semchonok Dmitry A. , Hause Gerd , Meister Annette , Ihling Christian , Shah Pranav N. M. , Stubbs Milton T. , Sinz Andrea , Stuart David I. , Kastritis Panagiotis L.
Published: July 2022

The high abundance of most viruses in infected host cells benefits their structural characterization; endogenous viruses are present in low copy numbers, however, and are therefore challenging to investigate. Here, we retrieve cell extracts enriched with an endogenous virus, the yeast L-A virus. The determined cryo-EM structure discloses capsid-stabilizing cation-π stacking and an interplay of non-covalent interactions from ten distinct capsomere interfaces. The capsid-embedded mRNA decapping active site trench is supported by a constricting movement of two opposite-facing loops. tRNA-loaded polysomes and other biomacromolecules, presumably mRNA, are found in virus proximity while stacked dsRNA bundles and the sub-stoichiometric polymerase localize underneath the capsid surface. Mature viruses participate in larger viral communities resembling their rare in-cell equivalents in terms of size, composition, and inter-virus distances. Our results collectively describe a 3D-architecture of a viral milieu, opening the door to cellextract-based high-resolution structural virology.
A Multi-Tissue Comparison and Molecular Characterization of Canine Organoids
Authors: Zdyrski Christopher , Gabriel Vojtech , Ospina Oscar , Wickham Hannah , Sahoo Dipak K. , Dao Kimberly , Aguilar Meza Leeann S. , Ralston Abigail , Bedos Leila , Bastian William , Honold Sydney , Piñeyro Pablo , Douglass Eugene F. , Mochel Jonathan P. , Allenspach Karin
Published: July 2022

Organoids are 3-dimensional (3D) stem cell-derived cell culture lines that offer a variety of technical advantages compared to traditional 2-dimensional (2D) cell cultures. Although murine models have proved useful in biomedical research, rodent models often fail to adequately mimic human physiology and disease progression, resulting in poor preclinical prediction of therapeutic drug efficacy and toxicity. With the advent of organoid technology, many of these challenges can be overcome. Previously, the use of canine organoids in drug testing and disease modeling was limited to organoids originating from the intestine, liver, kidney, lung, and urinary bladder. Here, we report the cultivation, maintenance, and molecular characterization of two novel adult-stem cell-derived canine organoid cell lines, including the endometrium and pancreas, in addition to previously reported bladder, lung, and liver organoids from two genetically related canines. Five tissues and organoid lines from each donor were characterized using bulk RNA-seq, allowing for a unique, multi-organ comparison between these two individuals and identification of specific cell types such as glandular epithelial cells in endometrial organoids.
Programming the lifestyles of engineered bacteria for cancer therapy
Authors: Fu Shengwei , Zhang Rongrong , Gao Yanmei , Xiong Jiarui , Li Ye , Pu Lu , Xia Aiguo , Jin Fan
Published: July 2022

Bacteria can be genetically engineered to act as therapeutic delivery vehicles in the treatment of tumors, killing cancer cells or activating the immune system. This is known as Bacteria-Mediated Cancer Therapy (BMCT). Tumor invasion, colonization and tumor regression are major biological events, which are directly associated with antitumor effects and are uncontrollable due to the influence of tumor microenvironments during the BMCT process. Here, we developed a genetic circuit for dynamically programming bacterial lifestyles (planktonic, biofilm or lysis), to precisely manipulate the process of bacterial adhesion, colonization and drug release in BMCT process, via hierarchical modulation of the lighting power density (LPD) of near-infrared (NIR) light. The deep tissue penetration of NIR offers us a modality for spatiotemporal and noninvasive control of bacterial genetic circuits in vivo. By combining computational modeling with high throughput characterization device, we optimized the genetic circuits in engineered bacteria to program the process of bacterial lifestyle transitions by altering the illumination scheme of NIR. Our results showed that programming intratumoral bacterial lifestyle transitions allows precise control of multiple key steps throughout the BMCT process, and therapeutic efficacy can be greatly improved by controlling the localization and dosage of therapeutic agents via optimizing the illumination scheme.
Resting State Neural Networks at Complex Visual Hallucinations in Charles Bonnet Syndrome
Authors: Hanoglu Taha , Velioglu Halil Aziz , Salar Behram Ali , Yıldız Sultan , Bayraktaroglu Zübeyir , Yulug Burak , Hanoglu Lutfu
Published: July 2022

Background

Charles Bonnet syndrome (CBS) is a prototype phenomenon for investigating complex visual hallucination. Our research focuses on resting state neural networks features of CBS patients with a comparison of patients with equally matched visual loss and healthy subjects in order to investigate the mechanism behind complex visual hallucinations.

Material and Methods

Four CBS patients CBS(+), three patients with visual loss but no visual hallucinations CBS(-) and 15 healthy individuals (HS) undergo resting state fMRI recordings and their resting state data is analyzed for Default Mode Network (DMN) changes through dual regression analysis. Cognitive functions of the participants were also evaluated through Mini Mental State Examination and University of Miami - Parkinson’s Disease Hallucination Questionnaire (um-PDHQ)

Results

Although we found no difference in Default Mode Networks between CBS(-) and CBS(+), and between the CBS(-) and HC groups, we detected decreased connectivity in CBS(+) compared to the HC group especially in visual heteromodal association centers (bilateral lateral occipital gyrus, bilateral lingual gyrus, occipital pole, right medial temporal cortex, right temporo-occipital cortex) when left angular gyrus was selected as ROI.

Similarly, we detected decreased connectivity in CBS(+) compared to HC in right medial frontal gyrus, right posterior cingulate gyrus, left inferior temporal gyrus, right supramarginal gyrus, and right angular gyrus when selected right superior frontal gyrus as ROI. In contrast, increased connectivity was detected in CBS +compared to HC, in bilateral occipital poles, bilateral occipital fusiform gyrus, bilateral intracalcarine cortex, right lingual gyrus and precuneus regions when left medial temporal gyrus was selected as ROI.

Conclusion

Our findings suggest a combined mechanism in CBS related to increased internal created images caused by decreased visual external input causing visual hallucinations as well as impaired frontotemporal resource tracking system that together impair cognitive processing.
The role ofGmXTH1, a new xyloglucan endotransglycosylase/hydrolase from soybean, in regulating soybean root growth at seedling stage
Authors: Song Yang , Zhang Ye , Du Ye-yao , Fan Sujie , Qin Di , Zhang Zhuo , Wang Pi-wu
Published: July 2022

Soybean is an important crop for both food and oil, providing high quality protein and oil for humans and animals. Drought stress has an significant effect on the yield and quality of soybean. In the early vegetative stage of soybean, the developed root system can effectively improve the tolerance of soybean plant to drought. Xyloglucan endoglycosylase/hydrolase (XTH) is a cell wall remodeling enzyme involved in cell wall expansion and degradation. However, there are few studies on XTH’s regulation of root growth and response to drought stress in soybean seedlings.The objectives of this study were to clone GmXTH1 gene and determine the effects of over and interference-expression of GmXTH1 on soybean root development at seedling stage. A 1,015 bp full-length of the GmXTH1 gene was cloned from soybean (Glycine max L. Merril) cv. RM18 with a 840 bp open reading frame (ORF) of a putative protein. The over and interference expression vectors of GmXTH1 were transformed into soybean using Agrobacterium method. Transformed strains OEA1, OEA3, IEA4, IEA5 were identified by molecular detection methods. The roots of transformed strains OEA1and OEA3 with GmXTH1 gene overexpression are clearly developed and the root phenotypic attributes, including main root length, primary root number, lateral root length, root surface area, root volume, root dry weight, root fresh weight are higher than the control. In contrast, root attributes of IEA4 and IEA5 with GmXTH1 gene interference expression were significantly lower than those of the control, suggesting that the expression of GmXTH1 gene has an important effect on the soybean root growth and development at seedling stage. Under drought stress conditions, the activities of Superoxide dismutase (SOD), Peroxidase(POD)and Catalase(CAT)in the transgenic strains with an overexpression of the GmXTH1 gene were significantly increased, and the root activity, leaf relative water content and total chlorophyll content were ranked in order of OEAs, CK, and IEAs. In conclusion, GmXHT1 plays an important role in the growth of soybean root at seedling stage. Overexpression of GmXTH1 gene can promote root development of soybean seedling. The results of activities of protective enzymes (SOD, POD, CAT), root activity, leaf relative water content and total chlorophyll content under drought stress indicated that transgenic strains OEA1 and OEA3 with overexpressing GmXTH1 gene were resistant to drought stress, suggesting that GmXTH1 may play a positive role in responding to drought stress at soybean seedling stage.
Switches to slow rhythmic neuronal activity lead to a plasticity-induced reset in synaptic weights
Authors: Jacquerie Kathleen , Minne Caroline , Ponnet Juliette , Benghalem Nora , Sacré Pierre , Drion Guillaume
Published: July 2022

Memory formation relies on changes in synaptic connections via synaptic plasticity, which is driven by neuronal activity. Simultaneously, behavior is controlled by switches in brain states: quiet waking is characterized by large low-frequency fluctuations in cortical activity that are strongly suppressed during active waking. We use computational modeling to study how switches in brain states interact with memory formation. We show that the low-frequency rhythmic bursting activity reminiscent of quiet waking induces a reset in synaptic weights. This reset occurs regardless of the implemented synaptic plasticity rule, whether phenomenological or biophysical, and is robust to biological variability and network heterogeneity. Mathematical analysis shows that the reset is rooted in the endogenous nature of the low-frequency quiet waking rhythmic activity. This brain state-dependent reset in synaptic weights restores the ability to learn through synaptic plasticity rules between periods of active waking, which could be a key component of memory homeostasis.
Bottlenecks can constrain and channel evolutionary paths
Authors: Gamblin Jasmine , Gandon Sylvain , Blanquart François , Lambert Amaury
Published: July 2022

Population bottlenecks are commonplace in experimental evolution, specifically in serial passaging experiments where microbial populations alternate between growth and dilution. Natural populations also experience such fluctuations caused by seasonality, resource limitation, or host-to-host transmission for pathogens. Yet, how unlimited growth with periodic bottlenecks influence the adaptation of populations is not fully understood. Here we study theoretically the effects of bottlenecks on the accessibility of evolutionary paths and on the rate of evolution. We model an asexual population evolving on a minimal fitness landscape consisting of two types of beneficial mutations with the empirically supported trade-off between mutation rate and fitness advantage, in the regime where multiple beneficial mutations may segregate simultaneously. In the limit of large population sizes and small mutation rates, we show the existence of a unique most likely evolutionary scenario, determined by the size of the wild-type population at the beginning and at the end of each cycle. These two key demographic parameters determine which adaptive paths may be taken by the evolving population by controlling the supply of mutants during growth and the loss of mutants at the bottleneck. We do not only show that bottlenecks act as a deterministic control of evolutionary paths but also that each possible evolutionary scenario can be forced to occur by tuning demographic parameters. This work unveils the effects of demography on adaptation of periodically bottlenecked populations and can guide the design of evolution experiments.
Liver sinusoidal endothelial cells orchestrate NK cell recruitment and activation in acute inflammatory liver injury
Authors: Papaioannou Sophia , See Jia-Xiang , Jeong Mingeum , De La Torre Carolina , Reiners-Koch Philipp-Sebastian , Sati Ankita , Mogler Carolin , Platten Michael , Cerwenka Adelheid , Stojanovic Ana
Published: July 2022

In both steady-state and during endotoxicosis, liver sinusoidal endothelial cells (LSECs) can rapidly clear lipopolysaccharide (LPS) from the bloodstream. They are located along blood sinusoids of the liver, and establish intimate contact with circulating and tissue-resident immune cells. However, their role in regulating immune responses during LPS-induced endotoxicosis remains poorly understood. Here, we show that LSECs play a dual role in regulating inflammatory responses, acting as modulators of NK cell pro-inflammatory output and as major producers of immune cell-attracting chemokines. We demonstrate that LSECs switch their chemokine expression pattern driven by LPS and IFN-γ, resulting in the production of the myeloid-attracting chemokine CCL2 and the lymphoid-attracting chemokine CXCL10, which accumulate in the serum of LPS-challenged animals. In livers of LPS-injected mice, monocytes and Kupffer cells expressed highest amounts of the pro-inflammatory cytokineIl12aandIl18transcripts, while NK cells expressed the highest amounts ofIfng. NK cell exposure to LSECsin vitroled to global transcriptomic changes, and primed NK cells to produce higher amounts of IFN-γ in response to IL-12 and IL-18. LSECs required exposure to IFN-γ forCxcl10expression, andCxcl10gene-deletion in endothelial cells abrogated NK cell accumulation in the liver after LPS treatment. Thus, our data indicate that LSECs occupy a unique temporal and spatial position acting as central regulators that respond to both LPS and immune-derived inflammatory signals, and fuel a positive feedback loop of immune cell attraction and activation in the inflamed liver tissue.

Abstract Figure
Computationally profiling peptide:MHC recognition by T-cell receptors and T-cell receptor-mimetic antibodies
Authors: Raybould Matthew I. J. , Nissley Daniel A. , Kumar Sandeep , Deane Charlotte M.
Published: July 2022

T-cell receptor-mimetic antibodies (TCRms) targeting disease-associated peptides presented by Major Histocompatibility Complexes (pMHCs) are set to become a major new drug modality. However, we lack a general understanding of how TCRms engage pMHC targets, which is crucial for predicting their specificity and safety. Several new structures of TCRm:pMHC complexes have become available in the past year, providing sufficient initial data for a holistic analysis of TCRms as a class of pMHC binding agents. Here, we profile the complete set of TCRm:pMHC complexes against representative TCR:pMHC complexes to quantify the TCR-likeness of their pMHC engagement. We find that intrinsic molecular differences between antibodies and TCRs lead to fundamentally different roles for their heavy/light chains and Complementarity-Determining Region loops during antigen recognition. The idiotypic properties of antibodies may increase the likelihood of TCRms engaging pMHCs with less peptide selectivity than TCRs. However, the pMHC recognition features of some TCRms, including the two TCRms currently in clinical trials, can be remarkably TCR-like. The insights gained from this study will aid in the rational design and optimisation of next-generation TCRms.
Actomyosin contractility in olfactory placode neurons opens the skin epithelium to form the nostril
Authors: Baraban Marion , Pi Clara Gordillo , Bonnet Isabelle , Gilles Jean-François , Lejeune Camille , Cabrera Mélody , Tep Florian , Breau Marie Anne
Published: July 2022

Despite their barrier function, epithelial layers can locally lose their integrity to create physiological openings during morphogenesis. The cellular and molecular mechanisms driving the formation of these epithelial breaks are only starting to be investigated. Here, we studied the formation of the zebrafish nostril (the olfactory orifice), which opens in the skin epithelium to expose the olfactory neurons to external odorant cues. Combining live imaging, drug treatments, laser ablation and tissue-specific functional perturbations, we demonstrate that the formation of the orifice is driven by a mechanical interplay between the olfactory placode neurons and the skin: the neurons pull on the overlying skin cells in an actomyosin-dependent manner, thus triggering the opening of the orifice. This work unravels an original mechanism to break an epithelial sheet, in which an adjacent group of cells instructs and mechanically assists the epithelium to induce its local rupture.
Mouse and cellular models of KPTN-related disorder implicate mTOR signalling in cognitive and progressive overgrowth phenotypes
Authors: Levitin Maria O. , Rawlins Lettie E , Sanchez-Andrade Gabriela , Arshad Osama A. , Collins Stephan C. , Sawiak Stephen J. , Iffland Phillip H. , Andersson Malin H.L. , Bupp Caleb , Cambridge Emma L. , Coomber Eve L. , Ellis Ian , Herkert Johanna C. , Ironfield Holly , Jory Logan , Kretz Perrine F. , Kant Sarina G. , Neaverson Alexandra , Nibbeling Esther , Rowley Christine , Relton Emily , Sanderson Mark , Scott Ethan M. , Stewart Helen , Shuen Andrew Y. , Schreiber John , Tuck Liz , Tonks James , Terkelsen Thorkild , van Ravenswaaij-Arts Conny , Vasudevan Pradeep , Wenger Olivia , Wright Michael , Day Andrew , Hunter Adam , Patel Minal , Lelliott Christopher J. , Crino Peter B. , Yalcin Binnaz , Crosby Andrew , Baple Emma L. , Logan Darren W. , Hurles Matthew E. , Gerety Sebastian S.
Published: July 2022

KPTN-related disorder (KRD) is an autosomal recessive disorder associated with germline variants in KPTN (kaptin), a component of the mTOR regulatory complex KICSTOR. To gain further insights into the pathogenesis of KRD, we analysed mouse knockout and human stem cell KPTN loss-of-function models. Kptn−/− mice display many of the key KRD phenotypes, including brain overgrowth, behavioural abnormalities, and cognitive deficits. Assessment of affected individuals has identified concordant selectivity of cognitive deficits, postnatal onset of brain overgrowth, and a previously unrecognised KPTN dosage-sensitivity, resulting in increased head circumference in their heterozygous parents. Molecular and structural analysis of Kptn−/− mice revealed pathological changes, including differences in brain size, shape, and cell numbers primarily due to abnormal postnatal brain development. Both the mouse and differentiated iPSC models of the disorder display transcriptional and biochemical evidence for altered mTOR pathway signalling, supporting the role of KPTN in regulating mTORC1. Increased mTOR signalling downstream of KPTN is rapamycin sensitive, highlighting possible therapeutic avenues with currently available mTOR inhibitors. These findings place KRD in the broader group of mTORC1 related disorders affecting brain structure, cognitive function, and network integrity.
Variation in microbial feature perception in the Rutaceae family with immune receptor conservation in citrus
Authors: Trinh Jessica , Li Tianrun , Franco Jessica Y. , Toruño Tania Y. , Stevens Danielle M. , Thapa Shree P. , Wong Justin , Pineda Rebeca , Ávila de Dios Emmanuel , Kahn Tracy L. , Seymour Danelle K. , Ramadugu Chandrika , Coaker Gitta L.
Published: July 2022

Although much is known about the responses of model plants to microbial features, we still lack an understanding of the extent of variation in immune perception across members of a plant family. In this work, we analyzed immune responses inCitrusand wild relatives, surveying 86 Rutaceae genotypes with differing leaf morphologies and disease resistances. We found that responses to microbial features vary both within and between members. Species in two subtribes, the Balsamocitrinae and Clauseninae, can recognize all tested microbial features (flg22, csp22, chitin), including one fromCandidatusLiberibacter species (csp22CLas), the bacterium associated with citrus greening disease aka Huanglongbing. We investigated differences at the receptor level for flagellin perception (FLS2 receptor) and chitin perception (LYK5 receptor) in citrus genotypes. We were able to characterize two genetically linkedFLS2homologs from ‘Frost Lisbon’ lemon (responsive) and ‘Washington navel’ orange (non-responsive). Surprisingly,FLS2homologs from responding and non-responding genotypes were expressed in citrus and functional when transferred to a heterologous system. ‘Washington navel’ orange weakly responds to chitin, but ‘Tango’ mandarin exhibits a robust response. LYK5 alleles were identical or nearly-identical between the two genotypes and able to complement theArabidopsis lyk4/lyk5-2mutant with respect to chitin perception. Collectively, our data indicates that differences in chitin and flg22 perception in these citrus genotypes are not the result of sequence polymorphisms at the receptor level. These findings shed light onto the diversity of perception of microbial features and highlight genotypes capable of recognizing polymorphic pathogen features.
A comprehensive update to theMycobacterium tuberculosisH37Rv reference genome
Authors: Chitale Poonam , Lemenze Alexander D. , Fogarty Emily C. , Shah Avi , Grady Courtney , Odom-Mabey Aubrey R. , Johnson W. Evan , Yang Jason H. , Eren A. Murat , Brosch Roland , Kumar Pradeep , Alland David
Published: July 2022

H37Rv is the most widely usedM. tuberculosisstrain. Its genome is globally used as theM. tuberculosisreference sequence. We developed Bact-Builder, a pipeline that leverages consensus building to generate complete and highly accurate gap-closed bacterial genomes and applied it to three independently sequenced cultures of a parental H37Rv laboratory stock. Two of the 4,417,942 base-pair long H37Rv assemblies were 100% identical, with the third differing by a single nucleotide. Compared to the existing H37Rv reference, the new sequence contained approximately 6.4 kb additional base pairs encoding ten new regions. These regions included insertions in PE/PPE genes and new paralogs ofesxNandesxJ, which were differentially expressed compared to the reference genes. Additional sequencing and assembly with Bact-Builder confirmed that all 10 regions were also present in widely accepted strains of H37Rv: NR123 and TMC102. Bact-builder shows promise as an improved method to perform extremely accurate and reproduciblede novoassemblies of bacterial genomes. Furthermore, our findings provide important updates to the primary tuberculosis reference genome.
An oblique plane microscope for mesoscopic imaging of freely moving organisms with cellular resolution
Authors: Singh Rajwinder , Subramanian Kaushikaram , Power Rory M. , Paix Alexandre , Ikmi Aissam , Prevedel Robert
Published: July 2022

Several important questions in biology require non-invasive and three-dimensional imaging techniques with appropriate spatiotemporal resolution that permit live organisms to move in an unconstrained fashion over an extended field-of-view. While selective-plane illumination microscopy (SPIM) has emerged as a powerful method to observe live biological specimens at high spatio-temporal resolution, typical implementations often necessitate constraining sample mounting or lack the required volumetric speed. Here, we report on an open-top, dual-objective oblique plane microscope (OPM) capable of observing millimeter sized, freely moving animals at cellular resolution. We demonstrate the capabilities of our mesoscopic OPM (MesOPM) by imaging the behavioural dynamics of the sea anemone Nematostella vectensis over 1.56 × 1.56 × 0.25 mm at 1.5 × 2.8 × 5.3µm resolution and 0.5Hz volume rate.
Probing the KRas Switch II Groove by Fluorine NMR Spectroscopy
Authors: Peacock D. Matthew , Kelly Mark J. S. , Shokat Kevan M.
Published: July 2022

While there has been recent success in the development of KRasG12C inhibitors, unmet needs for selective inhibitors and tool compounds targeting the remaining oncogenic KRas proteins remain. Here, we applied trifluoromethyl-containing ligands of KRas proteins as competitive probe ligands to assay the occupancy of the switch II pocket by 19F NMR spectroscopy. Structure-activity-relationship studies of probe ligands increased the sensitivity of the assay and identified structures that differentially detected each nucleotide state of KRasG12D. These differences in selectivity, combined with the high resolution of 19F NMR spectroscopy, enabled this method to be expanded to assay both nucleotide states of the protein simultaneously.

Abstract Figure
Directional invariance in the Drosophila giant fiber escape circuit
Authors: Jang HyoJong , Goodman David P , von Reyn Catherine R
Published: July 2022

An animal’s nervous system recognizes visual features regardless of where the visual feature is located. However, the underlying mechanisms that enable location invariant feature detection are not fully understood, particularly when visual feature information contributed by each eye needs to be resolved. Here we investigate directional invariance of looming responses in descending neurons (DN) of Drosophila melanogaster. We find multiple looming responsive DN integrate looming information across both eyes, even though their dendrites are unilateral. One DN in particular, the giant fibers (GF), generates invariant looming responses across approach directions. We confirm visual information propagates to the GF from the contralateral eye through an as of yet unidentified pathway and demonstrate the absence of this pathway alters GF responses to looming stimuli from the ipsilateral eye. Our data highlight a role for bilateral visual integration in generating consistent escape responses that are robust across a wide range of stimulus locations and parameters.
Efficient knock-in method enabling lineage tracing in zebrafish
Authors: Mi Jiarui , Andersson Olov
Published: July 2022

The CRISPR-Cas9 system aids generation of knock-in zebrafish lines, but it has been hard to integrate large constructs and avoid disrupting the targeted genes. Here we devised a 3’ knock-in strategy of PCR-amplified dsDNA, which coded for fluorescence proteins and Cre recombinase in frame with the endogenous gene but separated from each other by self-cleavable peptides. Primers with 5’ AmC6 end-protections generated improved PCR amplicons harboring either short or long homologous arms, which were co-injected with pre-assembled Cas9/gRNA ribonucleoprotein complexes for early integration. We targeted four genetic loci (krt92,nkx6.1, krt4,andid2a) and generated ten knock-in lines, which function as reporters for the endogenous gene expression. The knocked-in iCre or CreERT2 were used for lineage tracing, which suggestednkx6.1+cells are multipotent pancreatic progenitors that gradually restrict to bipotent duct; whileid2a+cells are multipotent in both liver and pancreas and gradually restrict to ductal cells. Additionally, hepaticid2a+duct show progenitor properties upon extreme hepatocyte loss. Thus, we present an efficient knock-in technique with widespread use for both cellular labelling and lineage tracing.
Correlates of protection for booster doses of the BNT162b2 vaccine
Authors: Hertz Tomer , Levy Shlomia , Ostrovsky Daniel , Oppenheimer Hannah , Zismanov Shosh , Kuzmina Alona , Friedman Lilach M , Trifkovic Sanja , Brice David , Chun-Yang Lin , Shemer-Avni Yonat , Cohen-Lahav Merav , Amichay Doron , Keren-Naus Ayelet , Voloshin Olga , Weber Gabriel , Najjar-Debbiny Ronza , Chazan Bibiana , McGargill Maureen A. , Webby Richard , Chowers Michal , Novack Lena , Novack Victor , Taube Ran , Nesher Lior , Weinstein Orly
Published: July 2022

Variants of concern (VOC) of SARS-CoV2 and waning immunity pose a serious global problem. Overall, vaccination and prior infection appear to provide significant protection to the majority of individuals, but some remain susceptible to infection and severe disease. Rigorously identifying a broad spectrum of correlates of protection (COP) is necessary to identify these susceptible populations. The extent to which additional booster doses provide protection is also poorly understood. To address this need, we conducted a multicenter prospective study assessing the association between serological profiles and the risk for SARS-CoV-2 infection, comparing those vaccinated with three to four doses of Pfizer BNT162b2 vaccine. Of 608 healthy adults, 365 received three doses and 243 received four doses. During the first 90 days of followup, 239 (39%) were infected, of whom 165/365 (45%) received 3 doses and 74/243 (30%) four doses. We found that the fourth dose elicited a significant rise in antibody binding and neutralizing titers against multiple variants, and reduced the risk of symptomatic infection by 37% [95% I, 15% - 54%]. We identified several parameters based on IgG and IgA binding that were COPs. The strongest association with infection risk was reduced IgG levels to RBD mutants and IgA levels to VOCs, which was a COP in the three-dose group (HR=6.34, p=0.008) and in the four-dose group (HR=8.14, p=0.018). A combination of two commercially available ELISA assays were also associated with protection in both groups (HR = 1.84, p = 0.002; HR = 2.01, p = 0.025, respectively). Most importantly, we identified a subset of individuals with low antibody levels after three doses of vaccine that responded with a significant boost in neutralizing antibody titers after a fourth dose, but were still at significantly increased susceptibility to infection when compared to those who had pre-existing high levels of neutralizing antibodies. Thus, we identify a highly susceptible population that remains susceptible despite apparent responsiveness to vaccines. Further, we develop several specific and sensitive COPs that show dramatic effect sizes and may be utilized to identify individuals most at risk from future exposures.
Attitudes toward COVID-19 pandemic among fully vaccinated individuals: evidence from Greece two years after the pandemic
Authors: Galanis Petros , Vraka Irene , Katsiroumpa Aglaia , Siskou Olga , Konstantakopoulou Olympia , Katsoulas Theodoros , Mariolis-Sapsakos Theodoros , Kaitelidou Daphne
Published: July 2022

Background

Considering the major effects of COVID-19 pandemic on health, social, economic, and political dimensions of all countries, positive attitudes toward COVID-19 pandemic are essential to control the pandemic. In our study, we investigated attitudes toward COVID-19 pandemic among fully COVID-19 vaccinated individuals two years after the pandemic and we identified predictors of attitudes.

Materials and Methods

We conducted an on-line cross-sectional study with 815 fully COVID-19 vaccinated individuals in Greece during May 2022. A self-administered and valid questionnaire was disseminated through social media platforms. We measured socio-demographic variables and COVID-19-related variables as potential predictors of attitudes toward COVID-19 pandemic. The outcome variable was attitudes toward COVID-19 pandemic (compliance with hygiene measures, trust in COVID-19 vaccination, fear of COVID-19, and information regarding the COVID-19 pandemic and vaccination).

Results

We found a very high level of compliance with hygiene measures, a high level of trust and information about the COVID-19 pandemic and vaccination, and a moderate level of fear of COVID-19. Also, we identified that females, participants with a higher educational level, those with a chronic disease, those with a better self-perceived physical health, and those without a previous COVID-19 diagnosis adhered more in hygiene measures. Trust in COVID-19 vaccination was higher among females, older participants, those with a higher educational level, those with a better self-perceived physical health, and those without a previous COVID-19 diagnosis. Moreover, females, older participants, those with a higher educational level, those with a chronic disease, those with a better self-perceived physical health, those that received a flu vaccine in previous season, and those without a previous COVID-19 diagnosis experienced more fear of the COVID-19. Finally, level of information regarding COVID-19 pandemic and vaccination was higher for participants with a higher educational level, those without a chronic disease, those with a better self-perceived physical health, and those that received a flu vaccine in previous season.

Conclusions

Understanding predictors of attitudes toward COVID-19 pandemic among fully vaccinated individuals is crucial for developing appropriate public health campaigns in the future. Vaccination should be accompanied by positive attitudes in order to decrease the frequency of negative outcomes of COVID-19, such as hospitalization, complications and mortality.
An Analysis of Oxycodone and Hydrocodone Distribution Trends in Delaware, Maryland, & Virginia Between 2006-2014
Authors: Eufemio Conor M. , Hagedorn Joseph D. , McCall Kenneth L. , Piper Brian J.
Published: July 2022

Objective

Understanding opioid use and distribution trends by geographic area is critical in addressing the ongoing opioid epidemic in the United States. This study is a county level analysis of oxycodone and hydrocodone use in Delaware, Maryland, and Virginia between 2006-2014.

Materials and Methods

A retrospective analysis of oxycodone and hydrocodone distributed as collected by the Drug Enforcement Administration’s (DEA) Washington Post Automation of Reports and Consolidated Orders System (ARCOS) in Delaware, Maryland, and Virginia. Raw drug weights in each county were adjusted to “daily average dose” (grams/county population/365). Purchasing data collected from ARCOS was used to compare distribution trends during this period.

Results

There was a 57.59% in the weight of oxycodone and hydrocodone between 2006-2014. Oxycodone prescriptions increased by 75.50% and hydrocodone by 11.05%. Oxycodone increased across all three states between 2006-2010 and declined until 2014. Hydrocodone also increased but to a lesser extent than oxycodone. There was substantial variability in daily average dose of both opioids at the county level in all states. Pharmacies accounted for largest portion of oxycodone (69.17%) and hydrocodone (75.27%) purchased in the region. Hospitals accounted for 26.67% of oxycodone and 22.76% hydrocodone purchased. Practitioners and mid-level providers did not significantly contribute to this increase.

Conclusion

In the states of Maryland, Delaware, and Virginia, the distribution of the prescription opioids oxycodone and hydrocodone increased by 57.59%. Daily average dose increased between 2006-2010 in all three states followed by a decline until 2014. Variability in daily average dose by county highlights the relationship between geography and likelihood of receiving high dose opioids. It may further allude to effects of targeted distribution by pharmaceutical manufacturers and prescribing habits of geographically distinct healthcare entities. Relationships between location and opioid usage should continue to be investigated to promote rational use of controlled substances.