bluuebunny/crossref_metadata_2025 huggingface dataset:
Subtemporal, Transapical, and Transcavernous Approach to Clip Low-Lying Basilar Tip Aneurysm: 2-Dimensional Operative Video
Authors: Abecassis Isaac Josh , Zeeshan Qazi , Feroze Abdullah H , Ene Chibawanye , Vellimana Ananth K , Sekhar Laligam N
Published: February 2021

Basilar tip aneurysm clipping is technically challenging because of the depth of operative corridor, rarity in presentation, and important perforators supplying deep, critical structures. Two major approaches to basilar tip aneurysms include (1) a frontotemporal (transorbital) trans-sylvian approach for most aneurysms and (2) a modified subtemporal approach for aneurysms with low-lying necks.

A 53-yr-old woman presented to our institution with a large unruptured basilar tip aneurysm notable for a low, broad neck (6.4 mm). After discussion of risks and benefits of endovascular vs surgical options, the patient consented to operative intervention. She underwent a right frontotemporal craniotomy with zygomatic osteotomy, intradural petrous apicectomy, elective sectioning of the fourth cranial nerve (CN IV), and intracavernous removal of the dorsum sellae and posterior clinoid process to provide more space for aneurysm dissection. After temporary clipping of the basilar artery, the perforating arteries were dissected free from the aneurysm and the aneurysm occluded with 2 fenestrated clips.

Important technical nuances of the approach include (1) achieving ample working room for temporary occlusion aneurysm dissection, (2) careful dissection of the perforators and contralateral P1, and (3) utilization of 2 fenestrated clips to accommodate and preserve the ipsilateral P1 segment.

Postoperative angiogram showed complete aneur-ysmal occlusion. Postoperatively, the patient demonstrated mild cognitive impairment and a right CN IV palsy. At 6-wk follow-up, cognition recovered to normalcy. More recently, at 12-mo follow-up, the patient noted intermittent diplopia. Formal neuro-ophthalmologic assessment confirmed persistence of a CN IV palsy treated with prism lenses but no other neurological deficits.
Risky Routes, Safe Suspicions: Gender, Class, and Cabs in Hyderabad, India
Authors: Annavarapu Sneha
Published: February 2021

A robust body of literature documents how women manage their self-presentation and perceptions of sexual risk when navigating city spaces. Yet we know less about how these strategies and tactics interact with existing class relations in society. This study investigates how, in the metropolitan city of Hyderabad in India, upwardly mobile women who commute via ride-share apps and lower-class men employed as drivers navigate the temporarily shared space of the car ride within the broader context of growing public anxiety around women’s safety in the city. Drawing on interview data and participant observation, I show two empirical patterns: 1) women commuters and men cabdrivers each view the other through the lens of suspicion as relatively more powerful than themselves; and 2) while women construct men drivers as sexually rapacious and dangerous, men understand the upwardly mobile woman commuter as entitled and abusive of her class power. I argue that competing understandings of risk exacerbate social distance and reproduce class and gender hierarchies between men drivers and women commuters. I suggest that the desire for safety vocalized by women passengers, while understandable, seems to rest on a set of processes that further pathologize and “otherize” the lower-class male subject.
Glucose-6-Phosphate Isomerase FgGPI, a β2 Tubulin-Interacting Protein, Is Indispensable for Fungal Development and Deoxynivalenol Biosynthesis in Fusarium graminearum
Authors: Zhou Zehua , Zhang Jie , Lu Fei , Duan Yabing , Zhou Mingguo
Published: February 2021

Glucose-6-phosphate isomerase (GPI) is ubiquitous in most organisms, catalyzing the reversible isomerization of glucose-6-phosphate and fructose-6-phosphate. In this study, we investigated biological and genetic functions of FgGPI in the phytopathogen Fusarium graminearum. We found that hyphal growth, conidial germination, and septa formation were significantly inhibited in FgGPI deletion mutant ∆FgGPI. FgGPI was also positively associated with glucose metabolism, ATP biosynthesis, and carbon source utilization. In addition, pyruvate production, deoxynivalenol (DON) biosynthesis, and virulence were reduced in ∆FgGPI. A coimmunoprecipitation assay demonstrated that FgGPI interacts with Fgβ2. More importantly, the coimmunoprecipitation assay showed that carbendazim-resistant substitutions in β2 tubulin could reduce the interaction intensity between FgGPI and Fgβ2, thereby increasing FgGPI expression and accelerating DON biosynthesis in carbendazim-resistant strains. Taken together, our work revealed the indispensable role of FgGPI in fungal developmental processes, DON biosynthesis, and pathogenicity in F. graminearum.
A prospective study of the relationships between change in body composition and cardiovascular risk factors across the menopause
Authors: Dehghan Aaron , Vasan Senthil K. , Fielding Barbara A. , Karpe Fredrik
Published: February 2021

Objective:

Menopause increases the risk of cardiovascular disease (CVD) which in part has been attributed to the rise in cholesterol and blood pressure (BP). This study examined the hypothesis that menopausal changes in body composition and regional fat depots relate to the change in CVD risk factors.

Methods:

A prospective recall study was designed to capture premenopausal women to be re-examined soon after menopause. A total of 97 women from the Oxford Biobank underwent dual x-ray absorptiometry, blood biochemistry, and BP readings pre- and postmenopause.

Results:

Despite minimal changes in body weight over the 5.1 ± 0.9 year follow-up period, there was an increase in total fat mass and a decline in lean mass, where the proportional change of regional fat mass was the greatest for the visceral fat depot (+22%, P < 0.01). Plasma ApoB (+12%, P < 0.01) and C-reactive protein (+45%, P < 0.01) increased as did systolic (+7%, P < 0.001) and diastolic BP (+5%, P < 0.001). Plasma nonesterified fatty acids decreased (−20%, P < 0.05) which may reflect on a change in adipose tissue function across the menopause. PCSK-9 decreased (−26%, P < 0.01) which suggests a compensation for the postmenopausal reduction in low-density lipoprotein receptor activity. Using multilinear regression analyses the changes in ApoB and diastolic BP were associated with visceral fat mass change, but this association was lost when adjusted for total fat mass change.

Conclusion:

The increase in CVD risk factor burden across menopause may not be driven by changes in body composition, rather by functional changes in end organs such as adipose tissue and liver.
The genitourinary syndrome of menopause
Authors: Phillips Nancy A. , Bachmann Gloria A.
Published: February 2021

Genitourinary syndrome of menopause (GSM) refers to a collection of symptoms resulting from diminished hormonal, primarily estrogenic stimulation to the vulvovaginal or lower urinary tract and may affect up to 50% of postmenopausal women. Symptoms, which are typically progressive and unlikely to resolve spontaneously, may include, but are not limited to, vulvovaginal dryness, burning or irritation, dyspareunia, or urinary symptoms of urgency, dysuria or recurrent urinary tract infection. These symptoms are typically progressive and unlikely to resolve spontaneously. Diagnosis is clinical. Telemedicine may play a role in diagnosis, initiation of treatment, and follow-up of women with GSM. Effective treatments include moisturizers and lubricants, local hormonal therapy with estrogen or dehydroepiandrosterone, and oral selective estrogen receptor agonists. Laser or radiofrequency procedures, although currently utilized, are being studied to comprehensively understand their overall effectiveness and safety. Additionally, the influence and effect of the vaginal microbiome, as well as potential of treatment via its manipulation, is being studied. We performed a literature search of PubMed, Google Scholar, and Ovid with search terms of vulvovaginal atrophy and GSM and reviewed major US Society Guidelines to create this narrative review of this topic. The literature suggests that healthcare providers can make a significant impact of the health and quality of life of women by being proactive about discussing and providing interventions for GSM. A systematic approach with consideration of current guidelines and attention to developing protocols for interventions should be employed.

Video Summary:

http://links.lww.com/MENO/A702.
Sphingomonas panacisoli sp. nov., bacterium isolated from soil in South Korea
Authors: Maeng Soohyun , Liu Qingzhen , Park Yuna , Bai Jaewoo , Im Wan-Taek
Published: February 2021

A newly isolated bacterial strain designated as HKS19 was isolated from a ginseng cultivation soil sample collected in South Korea. Cells of the strain HKS19 were Gram-stain-negative, rod, oval-shaped and they formed yellow colonies when grown on R2A agar at 30 °C. HKS19 showed the highest 16S rRNA gene sequence similarity (98.6%) with

Sphingomonas asaccharolytica

NBRC 15499T. Its growth was observed at 10–37 °C (optimum 30 °C), pH 6–9 (optimum pH 7), and in the presence of 0–1% NaCl (optimum 0%). The genome size of HKS19 was 3.4 Mb and the G+C content was 65.1 mol%. The main polar lipid of strain HKS19 was diphosphatidylglycerol (DPG), the predominant respiratory quinone was Q-10 and the major fatty acids were a summed feature 8 (C18 : 1
ω6c / C18 : 1
ω7c) and C16 : 0. Based on the phylogenetic, genotypic, phenotypic and chemotaxonomic analysis, strain HKS19 represents a newly isolated species of the genus

Sphingomonas

, for which the name Sphingomonas panacisoli is proposed. The type strain is HKS19T (=KACC 18881T=LMG 29564 T).
GUNC: Detection of Chimerism and Contamination in Prokaryotic Genomes
Authors: Orakov Askarbek , Fullam Anthony , Coelho Luis Pedro , Khedkar Supriya , Szklarczyk Damian , Mende Daniel R , Schmidt Thomas SB , Bork Peer
Published: February 2021

Genomes are critical units in microbiology, yet ascertaining quality in prokaryotic genomes remains a formidable challenge. We present GUNC (the Genome UNClutterer), a tool that accurately detects and quantifies genome chimerism based on the lineage homogeneity of individual contigs using a genome’s full complement of genes. GUNC complements existing approaches by targeting previously underdetected types of contamination: we conservatively estimate that 5.7% of genomes in GenBank, 5.2% in RefSeq, and 15-30% of pre-filtered ‘high quality’ metagenome-assembled genomes in recent studies are undetected chimeras. GUNC provides a fast and robust tool to substantially improve prokaryotic genome quality. Source code (GPLv3+):https://github.com/grp-bork/gunc
RISK FACTORS FOR INFECTION AND HEALTH IMPACTS OF THE COVID-19 PANDEMIC IN PEOPLE WITH AUTOIMMUNE DISEASES
Authors: Fitzgerald Kathryn C. , Mecoli Christopher A. , Douglas Morgan , Harris Samantha , Aravidis Berna , Albayda Jemima , Sotirchos Elias S. , Hoke Ahmet , Orbai Ana-Maria , Petri Michelle , Christopher-Stine Lisa , Baer Alan N. , Paik Julie J. , Adler Brittany L. , Tiniakou Eleni , Timlin Homa , Bhargava Pavan , Newsome Scott D. , Venkatesan Arun , Chaudhry Vinay , Lloyd Thomas E. , Pardo Carlos A. , Stern Barney J. , Lazarev Mark , Truta Brindusa , Saidha Shiv , Chen Edward S. , Sharp Michelle , Gilotra Nisha , Kasper Edward K. , Gelber Allan C. , Bingham Clifton O. , Shah Ami A. , Mowry Ellen M.
Published: February 2021

Background

People with autoimmune or inflammatory conditions who take immunomodulatory/suppressive medications may have a higher risk of novel coronavirus disease 2019 (COVID-19). Chronic disease care has also changed for many patients, with uncertain downstream consequences.

Objective

Assess whether COVID-19 risk is higher among those on immunomodulating or suppressive agents and characterize pandemic-associated changes to care.

Design

Longitudinal registry study

Participants

4666 individuals with autoimmune or inflammatory conditions followed by specialists in neurology, rheumatology, cardiology, pulmonology or gastroenterology at Johns Hopkins

Measurements

Periodic surveys querying comorbidities, disease-modifying medications, exposures, COVID-19 testing and outcomes, social behaviors, and disruptions to healthcare

Results

A total of 265 (5.6%) developed COVID-19 over 9 months of follow-up (April-December 2020). Patient characteristics (age, race, comorbidity, medication exposure) were associated with differences in social distancing behaviors during the pandemic. Glucocorticoid exposure was associated with higher odds of COVID-19 in multivariable models incorporating behavior and other potential confounders (OR: 1.43; 95%CI: 1.08, 1.89). Other medication classes were not associated with COVID-19 risk. Diabetes (OR: 1.72; 95%CI: 1.08, 2.73), cardiovascular disease (OR: 1.68; 95%CI: 1.24, 2.28), and chronic kidney disease (OR: 1.76; 95%CI: 1.04, 2.97) were each associated with higher odds of COVID-19. Pandemic-related disruption to care was common. Of the 2156 reporting pre-pandemic utilization of infusion, mental health or rehabilitative services, 975 (45.2%) reported disruptions. Individuals experiencing changes to employment or income were at highest odds of care disruption.

Limitations

Results may not be generalizable to all patients with autoimmune or inflammatory conditions. Information was self-reported.

Conclusions

Exposure to glucocorticoids may increase risk of COVID-19 in people with autoimmune or inflammatory conditions. Disruption to healthcare and related services was common. Those with pandemic-related reduced income may be most vulnerable to care disruptions.
Capacity of countries to reduce biological invasions
Authors: Latombe Guillaume , Seebens Hanno , Lenzner Bernd , Courchamp Franck , Dullinger Stefan , Golivets Marina , Kühn Ingolf , Leung Brian , Roura-Pascual Núria , Cebrian Emma , Dawson Wayne , Diagne Christophe , Jeschke Jonathan M. , Perez-Granados Cristian , Liu Chunlong , Moser Dietmar , Turbelin Anna , Visconti Piero , Essl Franz
Published: February 2021

The extent and impacts of biological invasions on biodiversity are largely shaped by an array of socio-ecological predictors, which exhibit high variation among countries. Yet a global synthetic perspective of how these factors vary across countries is currently lacking. Here, we investigate how a set of five socio-ecological predictors (Governance, Trade, Environmental Performance, Lifestyle and Education, Innovation) explain i) country-level established alien species (EAS) richness of eight taxonomic groups, and ii) country capacity to prevent and manage biological invasions and their impacts. Trade and Governance together best predicted the average EAS richness, increasing variance explained by up to 54% compared to models based on climatic and spatial variables only. Country-level EAS richness increased strongly with Trade, whereas high level of Governance resulted in lower EAS richness. Historical (1996) levels of Governance and Trade better explained response variables than current (2015) levels. Thus, our results reveal a historical legacy of these two predictors with profound implications for the future of biological invasions. We therefore used Governance and Trade to define a two-dimensional socio-economic space in which the position of a country captures its capacity to address issues of biological invasions. Our results provide novel insights into the complex relationship between socio-ecological predictors and biological invasions. Further, we highlight the need for designing better policies and management measures for alien species, and for integrating biological invasions in global environmental scenarios.
The Case for Retaining Natural Language Descriptions of Phenotypes in Plant Databases and a Web Application as Proof of Concept
Authors: Braun Ian R. , Yanarella Colleen F. , Durairaj Rajeswari Jyothi Prasanth , Bassham Diane C. , Lawrence-Dill Carolyn J.
Published: February 2021

Similarities in phenotypic descriptions can be indicative of shared genetics, metabolism, and stress responses, to name a few. Finding and measuring similarity across descriptions of phenotype is not straightforward, with previous successes in computation requiring a great deal of expert data curation. Natural language processing of free text descriptions of phenotype is often less resource intensive than applying expert curation. It is therefore critical to understand the performance of natural language processing techniques for organizing and analyzing biological datasets and for enabling biological discovery. For predicting similar phenotypes, a wide variety of approaches from the natural language processing domain perform as well as curation-based methods. These computational approaches also show promise both for helping curators organize and work with large datasets and for enabling researchers to explore relationships among available phenotype descriptions. Here we generate networks of phenotype similarity and share a web application for querying a dataset of associated plant genes using these text mining approaches. Example situations and species for which application of these techniques is most useful are discussed.

Database URLs

The database and analytical tool called QuOATS are available athttps://quoats.dill-picl.org/. Code for the web application is available athttps://git.io/Jtv9J. Datasets are available for direct access viahttps://zenodo.org/record/7947342#.ZGwAKOzMK3I. The code for the analyses performed for the publication is available athttps://github.com/Dill-PICL/Plant-dataandhttps://github.com/Dill-PICL/NLP-Plant-Phenotypes.
Heterogeneous nuclear ribonucleoprotein K is overexpressed in acute myeloid leukemia and causes myeloproliferative disease in mice via altered Runx1 splicing
Authors: Aitken Marisa J. L. , Malaney Prerna , Zhang Xiaorui , Herbrich Shelley M. , Chan Lauren , Ma Huaxian , Jacamo Rodrigo , Duan Ruizhi , Link Todd M. , Kornblau Steven M. , Kanagal-Shamanna Rashmi , Bueso-Ramos Carlos E. , Post Sean M.
Published: February 2021

Acute myeloid leukemia (AML) is driven by numerous molecular events that contribute to disease progression. Herein, we identified hnRNP K overexpression as a recurrent abnormality in AML that is associated with inferior patient outcomes. In murine hematopoietic stem and progenitor cells, hnRNP K overexpression altered self-renewal and differentiation potential. Furthermore, murine transplantation models revealed that hnRNP K overexpression resulted in fatal myeloproliferative phenotypes. Using unbiased approaches, we discovered a direct relationship between hnRNP K and RUNX1—a master transcriptional regulator of hematopoiesis often dysregulated in leukemia. Molecular analyses revealed hnRNP K-dependent alternative splicing of RUNX1, resulting in the generation of a functionally distinct isoform. Taken together, we have established hnRNP K as an oncogene in myeloid leukemia that binds RUNX1 RNA, altering its splicing and subsequent transcriptional activity. These findings shed new light on a mechanism of myeloid leukemogenesis, paving the way for new drug discovery efforts.

Highlights

hnRNP K, an RNA binding protein, is overexpressed in AML and correlates with poor clinical outcomes

hnRNP K overexpression in murine HSPCs drives fatal myeloproliferative phenotypes in mice

hnRNP K’s oncogenicity can be attributed, at least in part, to its ability to bind and influence the splicing of the RUNX1 transcript
Characterization of a novel Fgf10CreERT2 knock-in mouse line targeting postnatal lung Fgf10 lineages
Authors: Chu Xuran , Taghizadeh Sara , Vasquez-Armendariz Ana Ivonne , Herold Susanne , Chong Lei , Chen Chengshui , Zhang Jin-San , Agha Elie El , Bellusci Saverio
Published: February 2021

Fgf10 is a key gene during development, homeostasis and repair after injury. We previously reported a Fgf10CreERT2 line (with the CreERT2 cassette inserted in frame with the start codon of exon 1), called thereafter Fgf10Ki-v1, to target Fgf10Pos cells. While this line allowed fairly efficient and specific labeling of Fgf10Pos cells during the embryonic stage, it failed to target these cells after birth, particularly in the postnatal lung, which has been the focus on our research. We report here the generation and validation of a new Fgf10CreERT2 (called thereafter Fgf10Ki-v2) with the insertion of the expression cassette in frame with the stop codon of exon 3. This new Fgf10Ki-v2 line exhibited comparable Fgf10 expression level to their wild type counterpart. However, a disconnection between the Fgf10 and the Cre expression was observed in Fgf10Ki-v2/+ lungs. In addition, lung and limb agenesis were observed in homozygous embryos suggesting a loss of Fgf10 functional allele in Fgf10Ki-v2 mice. Bio-informatics analysis shows that the 3’UTR, where the CreERT2 cassette is inserted, contains numerous putative transcription factor binding sites. By crossing this line with tdTomato reporter line, we demonstrated that tdTomato expression faithfully recapitulated Fgf10 expression during development. Significantly, Fgf10Ki-v2 mouse is capable of significantly targeting Fgf10Pos cells in the adult lung. Therefore, despite the aforementioned limitations, this new Fgf10Ki-v2 line opens the way for future mechanistic experiments involving the postnatal lung.
In vivo magnetic resonance spectroscopy of hyperpolarized [1-13C] pyruvate in a male guinea pig model of life-long Western diet consumption and non-alcoholic fatty liver disease development
Authors: Smith Lauren M. , Pitts Conrad B. , Friesen-Waldner Lanette J. , Prabhu Neetin H. , Mathers Katherine E. , Sinclair Kevin J. , Wade Trevor P. , Regnault Timothy R.H. , McKenzie Charles A.
Published: February 2021

BACKGROUND

Alterations in glycolysis and oxidative pathways are central to the increasing incidence of non-alcoholic fatty liver disease (NAFLD), highlighting a need forin vivo, non-invasive technologies to understand the development of hepatic metabolic aberrations in lean NAFLD.

PURPOSE/HYPOTHESIS

To use hyperpolarized magnetic resonance spectroscopy (MRS) and proton density fat fraction (PDFF) MRI techniques to investigate effects of a chronic, life-long exposure to the Western Diet (WD) in a model of NAFLD and identify cellular metabolite changes and correlations related to enzyme activity. It is hypothesized that exposure to the WD will result in NAFLD in association with altered pyruvate metabolism.

STUDY TYPE

Prospective POPULATION/SUBJECTS/PHANTOM/SPECIMEN/ANIMAL MODEL: 28 male guinea pigs were weaned onto a control diet or WD.

FIELD STRENGTH/SEQUENCE

3T; T1, T2, IDEAL, broadband PRESS MRS.

ASSESSMENT

Median PDFF was calculated in the liver and hind limbs. [1-13C]pyruvate dynamic MRS in the liver was quantified by the time to peak (TTP), calculated as the time from pyruvate peak to metabolite peak. After a recovery period, animals were euthanized, and tissue was analyzed for lipid and cholesterol concentration and enzyme level and activity.

STATISTICAL TESTS

Unpaired Student’s t-tests were used to determine differences in measurements between the two diet groups. The Pearson correlation coefficient was calculated to determine correlations between measurements.

RESULTS

Life-long WD consumption resulted in significantly higher liver PDFF correlated with elevated triglyceride content in the liver. The WD group exhibited a decreased TTP for lactate production, andex vivoanalysis highlighted increased liver lactate dehydrogenase (LDH) activity. DATA CONCLUSION: PDFF MRI results suggest differential fat deposition patterns occurring in animals fed a life-long WD, corresponding with increased liver triglyceride levels characteristic of lean NAFLD. The decreased liver lactate TTP and increasedex vivoLDH activity suggest lipid accumulation occurs in association with a shift from oxidative metabolism to anaerobic glycolytic metabolism in WD livers.
IL-1-driven stromal-neutrophil interaction in deep ulcers defines a pathotype of therapy non-responsive inflammatory bowel disease
Authors: Friedrich Matthias , Pohin Mathilde , Jackson Matthew A. , Korsunsky Ilya , Bullers Samuel , Rue-Albrecht Kevin , Christoforidou Zoe , Sathananthan Dharshan , Ravindran Rahul , Peres Raphael Sanches , Sharpe Hannah , Wei Kevin , Watts Gerald F. M. , Mann Elizabeth H. , Geremia Alessandra , Thomas Tom , Attar Moustafa ,   Oxford IBD Cohort Investigators,   Roche Fibroblast Network Consortium, McCuaig Sarah , Thomas Lloyd , Collantes Elena , Uhlig Holm H. , Sansom Stephen , Easton Alistair , Raychaudhuri Soumya , Travis Simon P. , Powrie Fiona M.
Published: February 2021

Current inflammatory bowel disease (IBD) therapies are ineffective in a high proportion of patients. Combining bulk and single-cell transcriptomics, quantitative histopathology, and in situ localisation, we describe heterogeneity of the tissular inflammatory response in IBD treatment failure. Among inflammatory pathotypes, we found high neutrophil infiltration, activation of fibroblasts, and vascular remodelling at sites of deep ulceration was a feature of non-response to several anti-inflammatory therapies. Activated fibroblasts in the ulcer bed display neutrophil chemoattractant properties that are IL-1R- but not TNF-dependent. The identification of distinct, localised, tissular pathotypes associated with treatment non-response will aid precision targeting of current therapeutics and provide a biological rationale for IL-1 signalling blockade in ulcerating disease.
Osteomacs support osteoclast-mediated resorption and contribute to bone pathology in a postmenopausal osteoporosis mouse model
Authors: Batoon Lena , Millard Susan M. , Raggatt Liza J. , Wu Andy C. , Kaur Simranpreet , Sun Lucas W.H. , Williams Kyle , Sandrock Cheyenne , Ng Pei Ying , Bartnikowski Michal , Glatt Vaida , Pavlos Nathan J. , Pettit Allison R.
Published: February 2021

Osteal macrophages (osteomacs) support osteoblast function and promote bone anabolism, but their contribution to osteoporosis has not been explored. While mouse ovariectomy models have been repeatedly used, variation in strain, experimental design and assessment modalities, have contributed to no single model being confirmed as comprehensively replicating the full gamut of osteoporosis pathological manifestations. We validated an ovariectomy model in adult C3H/HeJ mice and demonstrated that it presents with human post-menopausal osteoporosis features, including reduced bone volume in axial and appendicular bone and bone loss in both trabecular and cortical bone including increased cortical porosity. Bone loss was associated with increased osteoclasts on trabecular and endocortical bone and decreased osteoblasts on trabecular bone. Importantly, this OVX model was characterised by delayed fracture healing. Using this validated model, we demonstrated that osteomacs are increased post-ovariectomy on both trabecular and endocortical bone. Dual F4/80 (pan-macrophage marker) and TRAP staining revealed osteomacs frequently located near TRAP+osteoclasts and containing TRAP+intracellular vesicles. Using anin vivoinducible macrophage depletion model that does not simultaneously deplete osteoclasts, we observed that osteomac loss was associated with elevated extracellular TRAP in bone marrow interstitium and increased serum TRAP. Usingin vitrohigh-resolution confocal imaging of mixed osteoclast-macrophage cultures on bone substrate, we observed macrophages juxtaposed to osteoclast basolateral functional secretory domains scavenging degraded bone by-products. These data demonstrate a role for osteomacs in supporting osteoclastic bone resorption through phagocytosis and sequestration of resorption by-products. Finally, usingSiglec1knockout mice, we demonstrated that loss of the macrophage-restricted molecule Siglec-1/CD169 is sufficient to cause age-associated low bone mass, emphasizing the macrophages, independent of osteoclasts, contribute to optimal skeletal health. Overall, our data expose a novel role for osteomacs in supporting osteoclast function and provide the first evidence of their involvement in osteoporosis pathogenesis.
Long-term antitumor CD8+T cell immunity induced by endogenously engineered extracellular vesicles
Authors: Ferrantelli Flavia , Manfredi Francesco , Chiozzini Chiara , Olivetta Eleonora , Giovannelli Andrea , Leone Patrizia , Federico Maurizio
Published: February 2021

We developed a novel approach to induce antigen-specific CD8+T cytotoxic lymphocyte (CTL) immunity based onin vivoengineering of extracellular vesicles (EVs). This is an innovative vaccination approach employing a DNA vector expressing a mutated HIV-1 Nef protein (Nefmut) that has lost the anti-cellular effects typical of the wild-type isoform, meanwhile showing an unusual efficiency of incorporation into EVs. This function persists even when foreign antigens are fused to its C-terminus. In this way, Nefmuttraffics large amounts of antigens fused to it into EVs spontaneously released by cells expressing the Nefmut_based DNA vector. We previously provided evidence that the inoculation in mice of a DNA vector expressing the Nefmut/HPV16-E7 fusion protein induced an E7-specific CTL immune response as detected 2 weeks after the second immunization. In an effort to optimize the anti-HPV16 CD8+T cell immune response, we found that the co-injection of DNA vectors expressing Nefmutfused with E6 and E7 generated a stronger anti-HPV16 immune response compared to that we observed in mice injected with the single vectors. When TC-1 cells, i.e., a tumor cell line co-expressing E6 and E7, were implanted before immunization, all mice survived until day 44, whereas no mice injected with either void or Nefmut_expressing vectors survived until day 32 after tumor implantation. A substantial part of mice (7 out of 12) cleared the tumor. When cured mice were re-challenged with a second sub cute implantation of TC-1 cells, and followed for additional 135 days, whereas none of them developed tumors. Both E6- and E7-specific CD8+T immunity was still detectable at the end of the observation time.

Hence, the immunity elicited by engineered EVs, besides curing already developed tumors, is strong enough to guarantee the resistance to additional tumor attack. This results is of relevance for therapy against both metastatic and relapsing tumors.
Alternative splice variants and germline polymorphisms in human immunoglobulin light chain genes
Authors: Mikocziova Ivana , Peres Ayelet , Gidoni Moriah , Greiff Victor , Yaari Gur , Sollid Ludvig M.
Published: February 2021

Immunoglobulin loci are rich in germline polymorphisms and identification of novel polymorphic variants can be facilitated by germline inference of B cell receptor repertoires. Germline gene inference is complicated by somatic hypermutations, errors arising from PCR amplification, and DNA sequencing as well as from the varying length of reference alleles. Inference of light chain genes is even more challenging than inference of heavy chain genes due to large gene duplication events on the kappa locus as well as absence of D genes in the rearranged light chain transcripts. Here, we analyzed the light chain cDNA sequences from naïve BCR repertoires of a Norwegian cohort of 100 individuals. We optimized light chain allele inference by tweaking parameters within TIgGER functions, extending the germline reference sequences, and establishing mismatch frequency patterns at polymorphic positions to filter out false positive candidates. As a result, we identified 48 previously unreported variants of light chain variable genes. Altogether, we selected 14 candidates for novel light chain polymorphisms for validation and successfully validated 11 by Sanger sequencing. Additional clustering of light chain 5’UTR, L-PART1 and L-PART2 revealed partial intron retention in alternative splice variants in 11 kappa and 9 lambda V alleles. The alternatively spliced transcripts were only observed in genes with low expression levels, suggesting a possible role in expression regulation. Our results provide novel insight into germline variation in human light chain immunoglobulin loci.
Enhanced genetic analysis of type 1 diabetes by selecting variants on both effect size and significance, and by integration with autoimmune thyroid disease
Authors: Crouch Daniel J. M. , Inshaw Jamie R.J. , Robertson Catherine C. , Zhang Jia-Yuan , Chen Wei-Min , Onengut-Gumuscu Suna , Cutler Antony J. , Sidore Carlo , Cucca Francesco , Pociot Flemming , Concannon Patrick , Rich Stephen S. , Todd John A.
Published: February 2021

For polygenic traits, associations with genetic variants can be detected over many chromosome regions, owing to the availability oflarge sample sizes. Most variants, however, have small effects on disease risk and, therefore, unravelling the causal variants, target genes, and biology of these variants is challenging. Here, we define the Bigger or False Discovery Rate (BFDR) as the probability that either a variant is a false-positive or a randomly drawn, true-positive association exceeds it in effect size. Using the BFDR, we identified 302 previously unreported signals with larger effect associations with type 1 diabetes and autoimmune thyroid disease. Out of 239 genome-wide significant signals in both diseases, only 66 (28%) show evidence for having a large effect using the BFDR, further demonstrating how using a combination of effect size and significance, rather than significance alone, is important in identifying SNPs and candidate genes for further investigation.
Larval nutrition impacts survival to adulthood, body size, and the allometric scaling of metabolic rate in adult honeybees
Authors: Nicholls Elizabeth , Rossi Marta , Niven Jeremy E.
Published: February 2021

Resting metabolic rate (RMR) is a fundamental physiological measure linked to numerous aspects of organismal function, including lifespan. Although dietary restriction in insects during larval growth/development affects adult RMR, the impact of larval dietqualityon adult RMR has not been studied. Usingin vitrorearing to control larval diet quality, we determined the effect of dietary protein and carbohydrate on honeybee survival-to-adulthood, time-to-eclosion, body mass/size and adult RMR. High carbohydrate larval diets increased survival-to-adulthood and time-to-eclosion compared to both low carbohydrate and high protein diets. Upon emergence, bees reared on the high protein diet were smaller and lighter than those reared on other diets, whilst those raised on the high carbohydrate diet varied more in body mass. Newly emerged adult bees’ reared on the high carbohydrate diet showed a significantly steeper increase in allometric scaling of RMR compared to those reared on other diets. This suggests that diet quality influences survival-to-adulthood, time-to-eclosion, and the allometric scaling of RMR. Given that agricultural intensification and increasing urbanisation have led to a decrease in both forage availability and dietary diversity for bees, our results are critical to improving understanding of the impacts of poor developmental nutrition on bee growth/development and physiology.

Summary statement

We show, for the first time, that the nutritional quality of insect larval diets affects the scaling of metabolic rate with body mass in newly emerged adult honeybees.
Suppression of miR-199a-5p alleviates ulcerative colitis by upregulating endoplasmic reticulum stress component XBP1
Authors: Wang Shanshan , Shen Lei , Peng Shuai , Tian Minxiu , Li Xiangjie , Luo Hesheng
Published: February 2021

Aims: This study aimed to explore the biological activities of miR-199a-5p in dextran sulphate sodium (DSS)-induced ulcerative colitis and apoptosis and identify the direct target of miR-199a-5p in this process. Main methods: HT-29 cells and C57BL/6 mice were used to examine the function of miR-199a-5p in vitro and in vivo, respectively. Expression of miRNA and mRNA was measured using quantitative real-time PCR and western blotting was used to measure the change in protein expression. Flow cytometry was subsequently employed to determine cell apoptosis, and a luciferase assay was used to confirm the direct target of miR-199a-5p. Results: Expression of miR-199a-5p was increased by DSS treatment in mice. In parallel, miR-199a-5p is found to be involved in endoplasmic reticulum stress (ERS) and cell apoptosis in HT-29 cells, and its upregulation induced ERS, apoptosis, weight loss, and ulcerative colitis in mice in vivo, which could be prevented by the suppression of miR-199a-5p. Luciferase assay confirmed that the 3′ untranslated region (3′-UTR) of XBP1 is the target binding site of miR-199a-5p. Conclusion: miR-199a-5p promotes ulcerative colitis and cell apoptosis by targeting the 3′-UTR of XBP1. Our findings reveal a new regulatory mechanism for ERS signaling and suggest that miR-199a-5p might be a potential target for UC therapy.
G9a/GLP methyltransferases inhibit autophagy by methylation-mediated ATG12 protein degradation
Authors: Kim Chang-Hoon , Park Kyung-Tae , Ju Shin-Yeong , Lee Cheol-Ju , Lee Sang-Hun
Published: February 2021

Previous studies have shown that G9a, a lysine methyltransferase, inhibits autophagy by repressing the transcription of autophagy genes. Here, we demonstrate a novel mechanism whereby G9a/GLP inhibit autophagy through post-translational modification of ATG12, a protein critical for the initiation of autophagosome formation. Under non-stress conditions, G9a/GLP directly methylate ATG12. The methylated ATG12 undergoes ubiquitin-mediated protein degradation, thereby inhibiting autophagy induction. By contrast, under stress conditions that elevate intracellular Ca2+levels, the activated calpain system cleaves the G9a/GLP proteins, leading to G9a/GLP protein degradation. The reduced G9a/GLP levels allow ATG12 to accumulate and form the ATG12-ATG5 conjugate, thus expediting autophagy initiation. Collectively, our findings reveal a distinct signaling pathway that links cellular stress responses involving Ca2+/calpain to G9a/GLP-mediated autophagy regulation. Moreover, our model proposes that the methylation status of ATG12 is a molecular rheostat that controls autophagy induction.
The lysosomal chloride-proton exchanger CLC7 functions in melanosomes as a negative regulator of human pigmentation
Authors: Koroma Donald C. , Scales Jessica L. , Trotman Joshaya C. , Wakamatsu Kazumasa , Ito Shosuke , Oancea Elena
Published: February 2021

Mutations in the Cl−/H+exchanger CLC7 and its subunit OSTM1 result in osteopetrosis, lysosomal disorders, and pigmentation defects in mice and humans. How CLC7/OSTM1 regulates pigmentation in skin and hair melanocytes remains unexplored. In human epidermal melanocytes, we found CLC7/OSTM1 localized to melanosomes, the organelles in which melanin is synthesized, where it negatively regulates melanin production. Using a novel ratiometric melanosomal pH indicator, we showed that CLC7 acidifies melanosomes, opposing the function of the oculocutaneous albinism II (OCA2) Cl−ion channel. Thede novoCLC7 variant (CLC7-Y715C) that causes albinism in humans and mice, decreased melanocytes pigmentation, which was restored by coexpression of OCA2. Remarkably, the enlarged hyperacidic vacuoles caused by CLC7-Y715C were also rescued by OCA2 coexpression in both melanocytes and non-melanocytic cells. Our data uncover a novel mechanism by which CLC7 regulates melanocyte pigmentation and identifies OCA2 as a tool to counteract the effects of CLC7 activating mutations.
Cotranslational folding of a periplasmic protein domain inEscherichia coli
Authors: Sandhu Hena , Hedman Rickard , Cymer Florian , Kudva Renuka , Ismail Nurzian , von Heijne Gunnar
Published: February 2021

In Gram-negative bacteria, periplasmic domains in inner membrane proteins are cotranslationally translocated across the inner membrane through the SecYEG translocon. To what degree such domains also start to fold cotranslationally is generally difficult to determine using currently available methods. Here, we apply Force Profile Analysis (FPA) – a method where a translational arrest peptide is used to detect folding-induced forces acting on the nascent polypeptide – to follow the cotranslational translocation and folding of the large periplasmic domain of theE. coliinner membrane protease LepBin vivo. Membrane insertion of LepB’s two N-terminal transmembrane helices is initiated when their respective N-terminal ends reach 45-50 residues away from the peptidyl transferase center (PTC) in the ribosome. The main folding transition in the periplasmic domain involves all but the ~15 most C-terminal residues of the protein and happens when the C-terminal end of the folded part is ~70 residues away from the PTC; a smaller putative folding intermediate is also detected. This implies that wildtype LepB folds post-translationallyin vivo, and shows that FPA can be used to study both co- and post-translational protein folding in the periplasm.
Delayed auditory encoding and variable representation of stimulus regularity in cerebellar lesion patients
Authors: Schwartze Michael , Kotz Sonja A.
Published: February 2021

The dynamic and fleeting nature of sound necessitates the rapid encoding and use of information distributed over time. Here we investigated cerebellar contributions to these abilities. We measured EEG from cerebellar patients and healthy controls while they listened to “oddball” sound sequences consisting of infrequent pitch-deviant and frequent standard tones. Inter-stimulus-intervals were temporally regular (600 ms) or irregular (200-1000 ms). This allowed probing early event-related potentials (ERP; P50, N100) that reflect repetitive and changing stimulus characteristics in temporally regular or less (irregular) predictable sequences. Further, time-frequency data provided an index of temporal processing variability at the stimulation frequencies. We expected that cerebellar lesions lead to aberrant encoding and use of auditory information, reflected in the ERP morphology of peak amplitudes, latencies and typical suppression effects linked to stimulus predictability. Results confirm longer P50 peak latencies in patients and variable processing at stimulation frequencies covarying with the location of cerebellar damage. These findings further support the idea that the cerebellum might play a generalizable role in the encoding of auditory stimulation over time.
Temporo-cerebellar connectivity underlies timing constraints in audition
Authors: Stockert Anika , Schwartze Michael , Poeppel David , Anwander Alfred , Kotz Sonja A.
Published: February 2021

The flexible and efficient adaptation to dynamic, rapid changes in the auditory environment likely involves generating and updating of internal models. Such models arguably exploit connections between the neocortex and the cerebellum, supporting proactive adaptation. Here we test the functional mechanisms associated with temporo-cerebellar connectivity, verifying these mechanisms for speech sounds. First, we identify lesion-specific deficits for the encoding of short timescale spectro-temporal non-speech and speech properties in patients with left posterior temporal cortex stroke. Second, using lesion-guided probabilistic tractography in healthy participants, we reveal bidirectional temporo-cerebellar connectivity with cerebellar dentate nuclei and crura I/II. These findings imply that the encoding and modeling of rapidly modulated auditory spectro-temporal properties engage a temporo-cerebellar interface. The data further support the conjecture that proactive adaptation to a dynamic environment via internal models is a generalizable principle.

Significance Statement

Asymmetric sampling in time, the principle of duration-sensitive hemispheric specialization of the cerebral cortex in the sensory decomposition of sound, is a widely tested hypothesis in auditory neuroscience. This functional organization is mirrored in the cerebellar cortex, implicated in the internal forward-modeling of sensory feedback that arises from motor actions. The potential structural and functional integration of these systems is not well understood. Using a unique combination of causal lesion-symptom mapping in persons with temporal lobe damage and diffusion-weighted magnetic resonance neuroimaging in healthy persons, we identify one key missing link and provide evidence for cross-lateral temporo-cerebellar connectivity using probabilistic white matter fiber tractography. These cerebellar-pontine-temporal cortex connections not only support asymmetric sampling in time but also establish the basis for a generalizable role of cerebellar forward-modeling in sensation beyond the monitoring of sensory feedback in the motor domain.
Cortico-subcortical β burst dynamics underlying movement cancellation in humans
Authors: Diesburg Darcy A. , Greenlee Jeremy D. W. , Wessel Jan R.
Published: February 2021

Dominant neuroanatomical models hold that humans regulate their movements via loop-like cortico-subcortical networks, including the subthalamic nucleus (STN), thalamus, and sensorimotor cortices (SMC). Inhibitory commands across these networks are purportedly sent via transient, burst-like signals in the β frequency (15-29Hz). However, since human depth-recording studies are typically limited to one recording site, direct evidence for this proposition is hitherto lacking. Here, we present simultaneous multi-site depth-recordings from SMC and either STN or thalamus in humans performing the stop-signal task. In line with their purported function as inhibitory signals, subcortical β-bursts were increased on successful stop-trials and were followed within 50ms by increased β-bursting over SMC. Moreover, between-site comparisons (including in a patient with simultaneous recordings from all three sites) confirmed that β-bursts in STN precede thalamic β-bursts. This provides first empirical evidence for the role of β-bursts in conveying inhibitory commands along long-proposed cortico-subcortical networks underlying movement regulation in humans.
Molecular and structural mechanisms of ZZ domain-mediated cargo recognition by autophagy receptor Nbr1
Authors: Wang Ying-Ying , Zhang Jianxiu , Liu Xiao-Man , Dong Meng-Qiu , Ye Keqiong , Du Li-Lin
Published: February 2021

In selective autophagy, cargo selectivity is determined by autophagy receptors. However, it remains scarcely understood how autophagy receptors recognize specific protein cargos. In the fission yeastSchizosaccharomyces pombe, a selective autophagy pathway termed Nbr1-mediated vacuolar targeting (NVT) employs Nbr1, an autophagy receptor conserved across eukaryotes including humans, to target cytosolic hydrolases into the vacuole. Here, we identify two new NVT cargos, the mannosidase Ams1 and the aminopeptidase Ape4, that bind competitively to the first ZZ domain of Nbr1 (Nbr1-ZZ1). High-resolution cryo-EM analyses reveal how a single ZZ domain recognizes two distinct protein cargos. Nbr1-ZZ1 not only recognizes the N-termini of cargos via a conserved acidic pocket, similar to other characterized ZZ domains, but also engages additional parts of cargos in a cargo-specific manner. Our findings unveil a single-domain bispecific mechanism of autophagy cargo recognition, elucidate its underlying structural basis, and expand the understanding of ZZ domain-mediated protein-protein interactions.