bluuebunny/crossref_metadata_2025 huggingface dataset:
Improving Preventive Care for Children With Sickle Cell Anemia: A Quality Improvement Initiative
Authors: Cabana Michael D. , Marsh Anne , Treadwell Marsha J. , Stemmler Peggy , Rowland Michael , Bender M. A. , Bhasin Neha , Chung Jong H. , Hassell Kathryn , Abdul Rashid N. F. Nik , Wong Trisha E. , Bardach Naomi S.
Published: December 2020

Introduction:

Sickle cell disease is a complex chronic disorder associated with increased morbidity and early mortality. The Pediatric Quality Measures Program has developed new sickle cell-specific quality measures focused on hydroxyurea (HU) counseling and annual transcranial Doppler (TCD) screening; however, these measures have not been used in a clinical setting to inform quality improvement (QI) efforts.

Methods:

From 2017 to 2018, 9 sickle cell subspecialty clinics from the Pacific Sickle Cell Regional Collaborative conducted a year-long QI collaborative focused on improving the percentage of patients with HU counseling and TCD screening based on the new quality measures. After an initial kick-off meeting, the 9 sites participated in monthly conference calls. We used run charts annotated with plan-do-study-act cycle activities to track each site’s monthly progress and the overall mean percentage for the entire collaborative.

Results:

There was an overall improvement in the aggregate HU counseling from 85% to 98% (P < 0.01). For TCD screening, referral frequency changed from 85% to 90% (P = 0.76). For both measures, the variation in frequencies decreased over the year.

Conclusion:

Over 1 year, we found that a regional QI collaborative increased HU counseling. Although referral for TCD screening increased, there was no overall change in TCD completion. Overall, this QI report’s findings can help clinicians adopt and implement these quality measures to improve outcomes in children.
Brief Report: HIV Testing, Diagnosis of HIV Infection, Linkage to Medical Care, and Interview for Partner Services Among Transgender Persons—United States, 2012–2017
Authors: Mulatu Mesfin S. , Wang Guoshen , Song Wei , Keatley JoAnne , Kudon Hui Zhang , Wan Choi , Rao Shubha
Published: December 2020

Background:

Transgender persons are at high risk for HIV infection. Testing is a key component of the national effort to end the HIV epidemic in the United States.

Setting:

Sixty-one local and state health departments and 150 community-based organizations funded by the Centers for Disease Control and Prevention to conduct HIV testing programs.

Methods:

We analyzed HIV testing data submitted to the Centers for Disease Control and Prevention by funded health departments and community-based organizations during 2012–2017. Descriptive analysis examined patterns of HIV testing and key outcomes (diagnosis of HIV infection, linkage to HIV medical care, and interview for partner services) among transgender persons. Multivariate robust Poisson regression was used to assess associations between HIV testing outcomes and demographic characteristics, census region, and test setting.

Results:

A total of 82,818 HIV tests were provided to transgender persons. Of these, 2280 (2.8%) transgender persons were diagnosed with HIV infection; 1556 (1.9%) received a new and 724 (0.9%) a previous diagnosis with HIV infection. The highest percentage of new HIV diagnosis was found among persons tested in correctional settings (4.6%), non-Hispanic Blacks (3.5%) and transgender women (2.4%). Among newly diagnosed persons, 85.0% were linked to HIV medical care ≤90 days after diagnosis and 63.5% were interviewed for partner services.

Conclusions:

HIV positivity was high, and the delivery of partner services was low, among transgender persons. HIV testing outcomes among transgender persons varied significantly by demographic characteristics and test setting. HIV prevention programs that are responsive to the needs of transgender persons may address gender-related disparities in HIV testing outcomes.
International Delphi Expert Consensus on Safe Return to Surgical and Endoscopic Practice
Authors: Asbun Horacio J. , Abu Hilal Mohammad , Kunzler Filipe , Asbun Domenech , Bonjer Jaap , Conlon Kevin , Demartines Nicolas , Feldman Liane S. , Morales-Conde Salvador , Pietrabissa Andrea , Pryor Aurora D. , Schlachta Christopher M. , Sylla Patricia , Targarona Eduardo M. , Agra Yolanda , Besselink Marc G. , Callery Mark , Cleary Sean P. , De La Cruz Luis , Eckert Philippe , Evans Chad , Han Ho-Seong , Jones Daniel B. , Gan Tong Joo , Koch Daniel , Lillemoe Keith D. , Lomanto Davide , Marks Jeffrey , Matthews Brent , Mellinger John , Melvin William Scott , Moreno-Paquentin Eduardo , Navarrete Claudio , Pawlik Timothy M. , Pessaux Patrick , Ricciardi Walter , Schwaitzberg Steven , Shah Paresh , Szokol Joseph , Talamini Mark , Torres Ricardo , Triboldi Alessandro , Udomsawaengsup Suthep , Valsecchi Federica , Vauthey Jean-Nicolas , Wallace Michael , Wexner Steven D. , Zinner Michael , Francis Nader
Published: December 2020

Objective:

The aim of this work is to formulate recommendations based on global expert consensus to guide the surgical community on the safe resumption of surgical and endoscopic activities.

Background:

The COVID-19 pandemic has caused marked disruptions in the delivery of surgical care worldwide. A thoughtful, structured approach to resuming surgical services is necessary as the impact of COVID-19 becomes better controlled. The Coronavirus Global Surgical Collaborative sought to formulate, through rigorous scientific methodology, consensus-based recommendations in collaboration with a multidisciplinary group of international experts and policymakers.

Methods:

Recommendations were developed following a Delphi process. Domain topics were formulated and subsequently subdivided into questions pertinent to different aspects of surgical care in the COVID-19 crisis. Forty-four experts from 15 countries across 4 continents drafted statements based on the specific questions. Anonymous Delphi voting on the statements was performed in 2 rounds, as well as in a telepresence meeting.

Results:

One hundred statements were formulated across 10 domains. The statements addressed terminology, impact on procedural services, patient/staff safety, managing a backlog of surgeries, methods to restart and sustain surgical services, education, and research. Eighty-three of the statements were approved during the first round of Delphi voting, and 11 during the second round. A final telepresence meeting and discussion yielded acceptance of 5 other statements.

Conclusions:

The Delphi process resulted in 99 recommendations. These consensus statements provide expert guidance, based on scientific methodology, for the safe resumption of surgical activities during the COVID-19 pandemic.
Intraoperative Red Blood Cell Transfusion Decision-making
Authors: Baker Laura , Park Lily , Gilbert Richard , Ahn Hilalion , Martel Andre , Lenet Tori , Davis Alexandra , McIsaac Daniel I. , Tinmouth Alan , Fergusson Dean A. , Martel Guillaume
Published: December 2020

Objectives:

The objective of this work was to carry out a systematic review of clinical practice guidelines (CPGs) pertaining to intraoperative red blood cell (RBC) transfusions, in terms of indications, decision-making, and supporting evidence base.

Summary of Background Data:

RBC transfusions are common during surgery and there is evidence of wide variability in practice.

Methods:

Major electronic databases (MEDLINE, EMBASE, and CINAHL), guideline clearinghouses and Google Scholar were systematically searched from inception to January 2019 for CPGs pertaining to indications for intraoperative RBC transfusion. Eligible guidelines were retrieved and their quality assessed using AGREE II. Relevant recommendations were abstracted and synthesized to allow for a comparison between guidelines.

Results:

Ten guidelines published between 1992 and 2018 provided indications for intraoperative transfusions. No guideline addressed intraoperative transfusion decision-making as its primary focus. Six guidelines provided criteria for transfusion based on hemoglobin (range 6.0–10.0 g/dL) or hematocrit (<30%) triggers. In the absence of objective transfusion rules, CPGs recommended considering other parameters such as blood loss (n = 7), signs of end organ ischemia (n = 5), and hemodynamics (n = 4). Evidence supporting intraoperative recommendations was extrapolated primarily from the nonoperative setting. There was wide variability in the quality of included guidelines based on AGREE II scores.

Conclusion:

This review has identified several clinical practice guidelines providing recommendations for intraoperative transfusion. The existing guidelines were noted to be highly variable in their recommendations and to lack a sufficient evidence base from the intraoperative setting. This represents a major knowledge gap in the literature.
Racial Differences in Isolated Aortic, Concomitant Aortoiliac, and Isolated Iliac Aneurysms
Authors: de Guerre Livia E.V.M. , Rice Jayne , Cheng Jane , Li Chun , Dansey Kirsten D. , Marcaccio Christina , Wang Grace J. , Hughes Kakra , van Herwaarden Joost A. , Schermerhorn Marc L.
Published: December 2020

Objective:

Our aim was to describe the racial and ethnic differences in presentation, baseline and operative characteristics, and outcomes after aortoiliac aneurysm repair.

Summary of Background Data:

Previous studies have demonstrated racial and ethnic differences in prevalence of abdominal aortic aneurysms and showed more complex iliac anatomy in Asian patients.

Methods:

We identified all White, Black, Asian, and Hispanic patients undergoing aortoiliac aneurysm repair in the VQI from 2003 to 2019. We compared baseline comorbidities, operative characteristics, and perioperative outcomes by race and ethnicity.

Results:

In our 60,435 patient cohort, Black patients, followed by Asian patients, were most likely to undergo repair for aortoiliac (W:23%, B:38%, A:31%, H:22%, P < 0.001) and isolated iliac aneurysms (W:1.0%, B:3.1%, A:1.5%, H:1.6%, P < 0.001), and White and Hispanic patients were most likely to undergo isolated aortic aneurysm repair (W:76%, B:59%, A:68%, H:76%, P < 0.001). Black patients were more likely to undergo symptomatic repair and underwent rupture repair at a smaller aortic diameter. The iliac aneurysm diameter was largest in Black and Asian patients. Asian patients were most likely to have aortic neck angulation above 60 degree, graft oversizing above 20%, and completion endoleaks. Also, Asian patients were more likely to have a hypogastric artery aneurysm and to undergo hypogastric coiling.

Conclusion:

Asian and Black patients were more likely to undergo repair for aortoiliac and isolated iliac aneurysms compared to White and Hispanic patients who were more likely to undergo repair for isolated aortic aneurysms. Moreover, there were significant racial differences in the demographics and anatomic characteristics that could be used to inform operative approach and device development.
Smoking and SARS-CoV-2 Impair Dendritic Cells and Regulate DC-SIGN Expression in Tissues
Authors: Cai Guoshuai , Bossé Yohan , Du Mulong , Albrecht Helmut , Qin Fei , Yu Xuanxuan , Luo Xizhi , Androulakis Michelle , Zhu Xia , Zhou Jun , Cui Xiang , Yi Changhua , Cheng Chao , Nagarkatti Mitzi , Nagarkatti Prakash , Christiani David , Whitfield Michael , Amos Christopher , Xiao Feifei
Published: December 2020

The current spreading novel coronavirus SARS-CoV-2 is highly infectious and pathogenic. In this study, we screened the gene expression of three SARS-CoV-2 host receptors (ACE2, DC-SIGN and L-SIGN) and DC status in bulk and single cell transcriptomic datasets of upper airway, lung or blood of smokers, non-smokers and COVID-19 patients. We found smoking increased DC-SIGN gene expression and inhibited DC maturation and its ability of T cell stimulation. In COVID-19, DC-SIGN gene expression was interestingly decreased in lung DCs but increased in blood DCs. Strikingly, DCs shifted from cDCs to pDCs in COVID-19, but the shift was trapped in an immature stage (CD22+ or ANXA1+ DC) with MHCII downregulation in severe cases. This observation indicates that DCs in severe cases stimulate innate immune responses but fail to specifically recognize SARS-CoV-2. Our study provides insights into smoking effect on COVID-19 risk and the profound modulation of DC function in severe COVID-19.

Graphical Abstract

Highlights

Smoking upregulates the expression of ACE2 and CD209 and inhibits DC maturation in lungs. SARS-CoV-2 modulates the DCs proportion and CD209 expression differently in lung and blood.

Severe infection is characterized by DCs less capable of maturation, antigen presentation and MHCII expression.

DCs shift from cDCs to pDCs with SARS-CoV-2 infection but are trapped in an immature stage in severe cases.
Plasmodium falciparum genomic surveillance reveals spatial and temporal trends, association of genetic and physical distance, and household clustering
Authors: Sy Mouhamad , Deme Awa , Warren Joshua L. , Daniels Rachel F. , Dieye Baba , Ndiaye Pape Ibrahima , Diedhiou Younous , Mbaye Amadou Moctar , Volkman Sarah K. , Hartl Daniel L. , Wirth Dyann F. , Ndiaye Daouda , Bei Amy K.
Published: December 2020

Molecular epidemiology using genomic data can help identify relationships between malaria parasite population structure, malaria transmission intensity, and ultimately help generate actionable data to assess the effectiveness of malaria control strategies. Genomic data, coupled with geographic information systems data, can further identify clusters or hotspots of malaria transmission, parasite genetic and spatial connectivity, and parasite movement by human or mosquito mobility over time and space. In this study, we performed longitudinal genomic surveillance in a cohort of 70 participants over four years from different neighborhoods and households in Thiès, Senegal—a region of exceptionally low malaria transmission (entomological inoculation rate (EIR) less than 1). Genetic identity (identity by state) was established using a 24 single nucleotide polymorphism molecular barcode and a multivariable linear regression model was used to establish genetic and spatial relationships. Our results show clustering of genetically similar parasites within households and a decline in genetic similarity of parasites with increasing distance. One household showed extremely high diversity and warrants further investigation as to the source of these diverse genetic types. This study illustrates the utility of genomic data with traditional epidemiological approaches for surveillance and detection of trends and patterns in malaria transmission not only by neighborhood but also by household. This approach can be implemented regionally and countrywide to strengthen and support malaria control and elimination efforts.
“GrimAge,” an epigenetic predictor of mortality, is accelerated in Major Depressive Disorder
Authors: Protsenko Ekaterina , Yang Ruoting , Nier Brent , Reus Victor , Hammamieh Rasha , Rampersaud Ryan , Wu Gwyneth W. Y. , Hough Christina M. , Epel Elissa , Prather Aric , Jett Marti , Gautam Aarti , Mellon Synthia H. , Wolkowitz Owen M.
Published: December 2020

Major Depressive Disorder (MDD) is associated with premature mortality and is an independent risk factor for a broad range of diseases, especially those associated with aging, such as cardiovascular disease, diabetes, and Alzheimer’s Disease. However, the pathophysiology underlying increased rates of somatic disease in MDD remains unknown. It has been proposed that MDD represents a state of accelerated cellular aging, and several measures of cellular aging have been developed in recent years. Among such metrics, estimators of biological age based on predictable age-related patterns of DNA methylation (DNAm), so called ‘epigenetic clocks’, have shown particular promise for their ability to capture accelerated aging in psychiatric disease. The recently developed DNAm metric known as ‘GrimAge’ is unique in that it was trained on time-to-death data and has outperformed its predecessors in predicting both morbidity and mortality. Yet, GrimAge has not been investigated in MDD. Here we measured GrimAge in 49 somatically healthy unmedicated individuals with MDD and 60 age-matched healthy controls. We found that individuals with MDD exhibited significantly greater GrimAge relative to their chronological age (‘AgeAccelGrim’) compared to healthy controls (p=0.001), with a median of two years of excess cellular aging. This difference remained significant after controlling for sex, current smoking status and body-mass index (p=0.015). These findings are consistent with prior suggestions of accelerated cellular aging in MDD, but are the first to demonstrate this with an epigenetic metric predictive of premature mortality.
Staff to staff transmission as a driver of healthcare worker infections with COVID-19
Authors: Gordon Claire L , Trubiano Jason A , Holmes Natasha E , Chua Kyra YL , Feldman Jeff , Young Greg , Sherry Norelle L , Grayson M Lindsay , Kwong Jason C
Published: December 2020

Objectives

To investigate the COVID-19 infections among staff at our institution and determine the interventions required to prevent subsequent staff infections.

Design

Retrospective cohort study

Participants and setting

Staff working at a single tertiary referral hospital who returned a positive test result for SARS-CoV-2 between 25 January 2020 and 25 November 2020.

Main outcome measures

Source of COVID-19 infection.

Results

Of 45 staff who returned a positive test result for SARS-CoV-2, 19 were determined to be acquired at Austin Health. Fifteen (15/19; 79% [95% CI: 54–94%]) of these were identified through contact tracing and testing following exposures to other infected staff and were presumed to be staff-staff transmission, including 10 healthcare workers (HCWs) linked to a single ward that cared for COVID-19 patients. Investigation of the outbreak identified the staff tearoom as the likely location for transmission, with subsequent reduction in HCW infections and resolution of the outbreak following implementation of enhanced control measures in tearoom facilities. No HCW contacts (0/204; 0% [95% CI: 0–2%]) developed COVID-19 infection following exposure to unrecognised patients with COVID-19.

Conclusions

Unrecognised infections among staff may be a significant driver of HCW infections in healthcare settings. Control measures should be implemented to prevent acquisition from other staff as well as patient-staff transmission.
Public adherence to precautionary measures and preventive guidelines against COVID-19 in Sudan: An application of the Health Belief Model
Authors: Mehanna Azza , Mohammed Elhadi Yasir Ahmed , Lucero-Prisno Don Eliseo
Published: December 2020

Background

Corona virus disease (COVID-19) is highly infectious disease caused by the novel corona virus (SARS-CoV-2). Several public health and social protective measures that may prevent or slow down the transmission of COVID-19 were introduced. However, these measures are unfortunately neglected or deliberately ignored by some individuals.

Methods

We did a cross sectional online based survey to identify possible factors influencing intention to adhere to precautionary measures and preventive guidelines against COVID-19 during lockdown periods in Sudan. The questionnaire was used to collect socio-demographic data of study participants, their health beliefs and intention regarding adherence to precautionary measures against COVID-19 based on the constructs of the Health Belief Model.

Results

Total of 680 respondents completed and returned the online questionnaire. Significant predictors of intention to adhere to the precautionary measures against COVID-19 were gender (β =3.34, P <0.001), self-efficacy (β= 0.476, P<0.001), perceived benefits (β= 0.349, P<0.001) and perceived severity (β= 0.113, P=0.005). These factors explained 43% of the variance in respondents’ intention to adhere to COVID-19 precautionary measures. Participants who were female, confident in their ability to adhere to the protective measures when available, believing in the benefits of the protective measures against COVID-19 and perceiving that the disease could have serious consequences were more likely to be willing to adhere to the protective measures.

Conclusion

Female respondents and respondents having higher self-efficacy, higher perceived benefits and higher perceived severity were more likely to be willing to adhere to the protective measures against COVID-19 in Sudan.
Digging behavior discrimination test to probe burrowing and exploratory digging in male and female mice
Authors: Pond Heather L. , Heller Abigail T. , Gural Brian M. , McKissick Olivia P. , Wilkinson Molly K. , Manzini M. Chiara
Published: December 2020

Digging behavior is often used to test motor function and repetitive behaviors in mice. Different digging paradigms have been developed for behaviors related to anxiety and compulsion in mouse lines generated to recapitulate genetic mutations leading to psychiatric and neurological disorders. However, the interpretation of these tests has been confounded by the difficulty of determining the motivation behind digging in mice. Digging is a naturalistic mouse behavior, that can be focused toward different goals, i.e. foraging for food, burrowing for shelter, burying objects, or even for recreation as has been shown for dogs, ferrets, and human children. However, the interpretation of results from current testing protocols assumes the motivation behind the behavior often concluding that increased digging is a repetitive or compulsive behavior. We asked whether providing a choice between different types of digging activities would increase sensitivity to assess digging motivation. Here, we present a test to distinguish between burrowing and exploratory digging in mice. We found that mice prefer burrowing when the option is available. When food restriction was used to promote a switch from burrowing to exploration, males readily switched from burrowing to digging outside, while females did not. In addition, when we tested a model of intellectual disability and autism spectrum disorder that had shown inconsistent results in the marble burying test, theCc2d1aconditional knock-out mouse, we found greatly reduced burrowing only in males. Our findings indicate that digging is a nuanced motivated behavior and suggest that male and female rodents may perform it differently.

Significance Statement

Digging behavior is commonly assessed in mice to study features of neurodevelopmental, psychiatric and neurological disorder. However, existing digging assays fail to discriminate between types of digging complicating data interpretation. Here we present a modified digging behavior discrimination task that can produce sensitive results in 30 minutes with easy to gather measures, making it accessible to wide variety of labs and experimental paradigms.
Using Genetic Information to Improve the Prediction of Individual Food Choice: A Case Study of Alcoholic Beverages
Authors: Zhu Chen , Beatty Timothy , Zhao Qiran , Si Wei , Chen Qihui
Published: December 2020

Individual food choices and consumption are closely relating to one’s diet, nutrition, and health. Using the case of alcoholic beverages, this study extends the random-utility framework by incorporating genetic information into consumer demand models, and demonstrates the significant impact of genetic factors on individual food choice decisions in a novel way. Integrating individual-level responses of discrete choice experiments (DCE), genotyping data, and socioeconomic/demographic characteristics of 484 participants collected from face-to-face interviews in mainland China, we employ a machine learning-based classification (MLC) approach to identify and predict individual choices. We show that genetic factors are critical to explaining variations in both general drinking behavior and choices of particular products. We systematically compared the performance of traditional discrete choice models and MLC models without and with genetic factors. The MLC predictive model with both socio-demographic and genetic features yields the highest accuracy of 74.7% and AUC-ROC of 0.85. Our findings warrant further economic studies of human behaviors with the integration of genetic data.
The size of helical pitch is important for microtubule plus end dynamic instability
Authors: Liu Chenshu , Prahl Louis , He Yu , Wang Yan , Zhu Ruijun , Mao Yinghui
Published: December 2020

Microtubule (MT) dynamic instability is a conserved phenomenon underlying essential cellular functions such as cell division, cell migration and intracellular transport, and is a key target of many chemotherapeutic agents. However, it remains unclear how the organization of tubulin dimers at the nanometer scale translates into dynamic instability as an emergent property at the micrometer scale. Tubulin dimers are organized into left-handed helical MT lattice, and most present-day MTs converge at a 1.5 dimer helical pitch that causes a seam in an otherwise symmetric helix. Because presently there are no experimental methods that can precisely manipulate tubulin subunit with sub-dimer resolution, the impact of helical pitch on dynamic instability remains unknown. Here by using stochastic simulations of microtubule assembly dynamics we demonstrate that helical pitch plays essential roles in MT plus end dynamic instability. By systematically altering helical pitch size, one half-dimer at a time, we found that a helical pitch as small as one half-dimer is sufficient to inhibit short-term MT length plateaus associated with diminishing GTP-tubulin cap. Notably, MT plus end dynamics quantitatively scale with the size of helical pitch, rather than being clustered by the presence or absence of helical symmetry. Microtubules with a 1.5 dimer helical pitch exhibit growth and shrinkage phases and undergo catastrophe and rescue similar to experimentally observed microtubules. Reducing helical pitch to 0 promotes rapid disassembly, while increasing it causes microtubules to undergo persistent growth, and it is the 1.5 dimer helical pitch that yields the highest percentage of MTs that undergo alternating growth and shrinkage without being totally disassembled. Finally, although the 1.5 dimer helical pitch is conserved among most present-day MTs, we find that other parameters, such as GTP hydrolysis rate, can partially compensate for changes in helical pitch. Together our results indicate that helical pitch is a determinant of MT plus end dynamic instability and that the evolutionarily conserved 1.5 dimer helical pitch promotes dynamic instability required for microtubule-dependent cellular functions.
Activity-Dependent Modulation of Synapse-Regulating Genes in Astrocytes
Authors: Farhy-Tselnicker I , Boisvert MM , Liu H , Dowling C , Erikson GA , Blanco-Suarez E , Farhy C , Shokhirev M , Ecker JR , Allen NJ
Published: December 2020

Astrocytes regulate the formation and function of neuronal synapses via multiple signals, however, what controls regional and temporal expression of these signals during development is unknown. We determined the expression profile of astrocyte synapse-regulating genes in the developing mouse visual cortex, identifying astrocyte signals that show differential temporal and layer-enriched expression. These patterns are not intrinsic to astrocytes, but regulated by visually-evoked neuronal activity, as they are absent in mice lacking glutamate release from thalamocortical terminals. Consequently, synapses remain immature. Expression of synapse-regulating genes and synaptic development are also altered when astrocyte signaling is blunted by diminishing calcium release from astrocyte stores. Single nucleus RNA sequencing identified groups of astrocytic genes regulated by neuronal and astrocyte activity, and a cassette of genes that show layer-specific enrichment. Thus, the development of cortical circuits requires coordinated signaling between astrocytes and neurons, identifying astrocytes as a target to manipulate in neurodevelopmental disorders.
NMDA receptor–BK channel coupling regulates synaptic plasticity in the barrel cortex
Authors: Gómez Ricardo , Maglio Laura E. , Gonzalez-Hernandez Alberto J. , Rivero-Pérez Belinda , Bartolomé-Martín David , Giraldez Teresa
Published: December 2020

Postsynaptic N-methyl-D-aspartate receptors (NMDARs) are crucial mediators of synaptic plasticity due to their ability to act as coincidence detectors of presynaptic and postsynaptic neuronal activity. However, NMDARs exist within the molecular context of a variety of postsynaptic signaling proteins, which can fine-tune their function. Here we describe a novel form of NMDAR suppression by large-conductance Ca2+- and voltage-gated K+(BK) channels in the basal dendrites of a subset of barrel cortex layer 5 pyramidal neurons. We show that NMDAR activation increases intracellular Ca2+in the vicinity of BK channels, thus activating K+efflux and strong negative feedback inhibition. We further show that neurons exhibiting such NMDAR–BK coupling serve as high-pass filters for incoming synaptic inputs, precluding the induction of spike-timing-dependent plasticity. Together, these data suggest that NMDAR-localized BK channels regulate synaptic integration and provide input-specific synaptic diversity to a thalamocortical circuit.
A genome-scale yeast library with inducible expression of individual genes
Authors: Arita Yuko , Kim Griffin , Li Zhijian , Friesen Helena , Turco Gina , Wang Rebecca Y. , Climie Dale , Usaj Matej , Hotz Manuel , Stoops Emily , Baryshnikova Anastasia , Boone Charles , Botstein David , Andrews Brenda J. , McIsaac R. Scott
Published: December 2020

The ability to switch a gene from off to on and monitor dynamic changes provides a powerful approach for probing gene function and elucidating causal regulatory relationships, including instances of feedback control. Here, we developed and characterized YETI (Yeast Estradiol strains with Titratable Induction), a collection in which 5,687 yeast genes are engineered for transcriptional inducibility with single-gene precision at their native loci and without plasmids. Each strain contains Synthetic Genetic Array (SGA) screening markers and a unique molecular barcode, enabling high-throughput yeast genetics. We characterized YETI using quantitative growth phenotyping and pooled BAR-seq screens, and we used a YETI allele to characterize the regulon ofROF1,showing that it is a transcriptional repressor. We observed that strains with inducible essential genes that have low native expression can often grow without inducer. Analysis of data from other eukaryotic and prokaryotic systems shows that low native expression is a critical variable that can bias promoter-perturbing screens, including CRISPRi. We engineered a second expression system, Z3EB42, that gives lower expression than Z3EV, a feature enabling both conditional activation and repression of lowly expressed essential genes that grow without inducer in the YETI library.
Detectability of biotin tags by LC-MS/MS
Authors: Nierves Lorenz , Lange Philipp F.
Published: December 2020

The high affinity of biotin to streptavidin has made it one of the most widely used affinity tags in proteomics. Early methods used biotin for enrichment alone and mostly ignored the biotin labeled peptide. Recent advances in labeling led to an increase in biotinylation efficiency and shifted the interest to detection of the site of biotinylation. This increased confidence in identification and provides additional structural information yet it requires efficient release of the biotinylated protein/peptide and sensitive separation and detection of biotinylated peptides by LC-MS/MS. Despite its long use in affinity proteomics the effect of biotinylation on the chromatographic, ionization, and fragmentation behaviour and ultimate detection of peptides is not well understood. To address this we compare two commercially-available biotin labels EZ-Link Sulfo-NHS-Biotin and Sulfo-NHS-SS-Biotin, the latter one containing a labile linker to efficiently release biotin to determine the effects of peptide modification on peptide detection. We describe an increase of hydrophobicity and charge reduction with increasing number of biotin labels attached. Based on our data we recommend gradient optimization to account for more hydrophobic biotinylated peptides and include singly charged precursors to account for charge reduction by biotin.
A novel and effective Cre/lox-based genetic tool for repeated, targeted and markerless gene integration
Authors: Zhou Qinghua , Jiao Liangcheng , Li Wenjuan , Hu Zhiming , Li Yunchong , Zhang Houjin , Xu Li , Yan Yunjun
Published: December 2020

The unconventional yeastYarrowia lipolyticais extensively applied in bioproduction fields owing to its excellent metabolite and protein production ability. Nonetheless, utilization of this promising host is still restricted by limited availability of precise and effective gene integration tools. In this study, a novel and efficient genetic tool was developed for targeted, repeated, and markerless gene integration based on Cre/loxsite-specific recombination system. The developed tool required only a single selection marker and could completely excise all of the unnecessary sequences. A total of three plasmids were created and seven rounds of marker-free gene integration were examined inY. lipolytica. All the integration efficiencies remained above 90%, and analysis of protein production and growth characteristics of the engineered strains confirmed that genome modification via the novel genetic tool was feasible. Further work also confirmed the genetic tool was effective for integration of other genes, loci, and strains. Thus, this study significantly promotes the application of Cre/loxsystem and presents a powerful tool for genome engineering inY. lipolytica.

Graphical abstract

The novel genetic tool comprised three plasmids, namely, Cre-Y1, Cre-Y2, and Cre-Y3. Cre-Y1 was introduced into the Upleu locus of Po1f, and then recombination between twolox71 sites could remove unnecessary plasmid elements and produce an initial strain harboring alox71 site. Subsequently, Cre-Y2 was integrated onto theleu2locus, forming a transitional strain with threeloxsites (lox71,lox66, and rclox66). Recombination reactions among these threeloxsites could excise unnecessary DNA fragments and retain alox72 site, an rclox66 site, and a target gene expression cassette in the genome. Similarly, integration of Cre-Y3 produced strains harboring two target gene expression cassettes. Consequently, repeated, targeted, and markerless gene integration could be efficiently realized following iterative integration of Cre-Y2 and Cre-Y3.

Highlights

A powerful genetic tool was developed for targeted and markerless gene integration

The genetic tool was effective for various genes, loci, and strains

Only a single selection marker was adequate for repeated gene integration

All of the useless and redundant sequences would be excised

All integration efficiencies could remain above 90%
Rif2 protects Rap1-depleted telomeres from MRX-mediated degradation inSaccharomyces cerevisiae
Authors: Rosas Bringas Fernando R. , Stinus Sonia , de Zoeten Pien , Cohn Marita , Chang Michael
Published: December 2020

Rap1 is the main protein that binds double-stranded telomeric DNA inSaccharomyces cerevisiae. Examination of the telomere functions of Rap1 is complicated by the fact that it also acts as a transcriptional regulator of hundreds of genes and is encoded by an essential gene. In this study, we disrupt Rap1 telomere association by expressing a mutant telomerase RNA subunit (tlc1-tm) that introduces mutant telomeric repeats.tlc1-tmcells grow similar to wild-type cells, although depletion of Rap1 at telomeres causes defects in telomere length regulation and telomere capping. Rif2 is a protein normally recruited to telomeres by Rap1, but we show that Rif2 can still associate with Rap1-depletedtlc1-tmtelomeres, and that this association is required to inhibit telomere degradation by the MRX complex. We find that Rap1, Rif2, and the Ku complex work in parallel to prevent telomere degradation, and absence of all three at telomeres causes lethality. The partially redundant mechanisms may explain the rapid evolution of telomere components in budding yeast species.
Evidence for nutrient-dependent regulation of the COPII coat by O-GlcNAcylation
Authors: Bisnett Brittany J. , Condon Brett M. , Linhart Noah A. , Lamb Caitlin H. , Huynh Duc T. , Bai Jingyi , Smith Timothy J. , Hu Jimin , Georgiou George R. , Boyce Michael
Published: December 2020

O-linked β-N-acetylglucosamine (O-GlcNAc) is a dynamic form of intracellular glycosylation common in animals, plants and other organisms. O-GlcNAcylation is essential in mammalian cells and is dysregulated in myriad human diseases, such as cancer, neurodegeneration and metabolic syndrome. Despite this pathophysiological significance, key aspects of O-GlcNAc signaling remain incompletely understood, including its impact on fundamental cell biological processes. Here, we investigate the role of O-GlcNAcylation in the coat protein II complex (COPII), a system universally conserved in eukaryotes that mediates anterograde vesicle trafficking from the endoplasmic reticulum. We identify new O-GlcNAcylation sites on Sec24C, Sec24D and Sec31A, core components of the COPII system, and provide evidence for potential nutrient-sensitive pathway regulation through site-specific glycosylation. Our work suggests a new connection between metabolism and trafficking through the conduit of COPII protein O-GlcNAcylation.
De novosynthesis of phosphatidylcholine is essential for the promastigote but not amastigote stage inLeishmania major
Authors: Moitra Samrat , Basu Somrita , Pawlowic Mattie , Hsu Fong-fu , Zhang Kai
Published: December 2020

Phosphatidylcholine (PC) is the most abundant type of phospholipids in eukaryotes constituting ~30% of total lipids inLeishmania. PC synthesis mainly occurs via the choline branch of the Kennedy pathway (choline ⇒ choline-phosphate ⇒ CDP-choline ⇒ PC) and the N-methylation of phosphatidylethanolamine (PE). In addition,Leishmaniaparasites can acquire PC and other lipids from the host or culture medium. In this study, we assessed the function and essentiality of choline ethanolamine phosphotransferase (CEPT) inLeishmania majorwhich is responsible for the final step of thede novosynthesis of PC and PE. Our data indicate that CEPT is localized in the endoplasmic reticulum and possesses the activity to generate PC from CDP-choline and diacylglycerol. Targeted deletion ofCEPTis only possible in the presence of an episomalCEPTgene in the promastigote stage ofL. major. These chromosomal null parasites require the episomal expression ofCEPTto survive in culture, confirming its essentiality during the promastigote stage. In contrast, duringin vivoinfection of BALB/c mice, these chromosomal null parasites appeared to lose the episomal copy ofCEPTwhile maintaining normal levels of virulence, replication and cellular PC. Therefore, while thede novosynthesis of PC/PE is indispensable for the proliferation of promastigotes, intracellular amastigotes appear to acquire most of their lipids through salvage and remodeling.
Cheese or cheese infusions – ecological traps for mosquitoes and spotted wing Drosophila
Authors: Peach Daniel , Almond Max , Ko Elton , Meraj Sanam , Gries Regine , Gries Gerhard
Published: December 2020

We tested the hypothesis that the “ecological trap” phenomenon (a mismatch between a habitat’s perceived attractiveness and its actual quality, resulting in a population sink) is exploitable for pest control. We selected mosquitoes as modal organisms, because selection of an oviposition site by adult female mosquitoes in response to its perceived attractiveness is of paramount importance for the development and survival of their larval offspring. In laboratory and/or field experiments, we show that (i) each of five cheese varieties tested (Raclette, Pecorino, Brie, Gruyere, Limburger) strongly attracts females of both the yellow fever mosquito,Aedes aegypti, and the common house mosquito,Cx. pipiens;(ii) cheese infusions, or headspace odorant extracts (HOEs) of cheese infusions, significantly affect oviposition choices byCx. pipiensandAe. aegypti, (iii) HOEs contain at least 13 odorants; (iv) in field settings, cheese infusions more effectively stimulate oviposition byCx. pipiensandCuliseta incidensthan bluegrass (Poasp.) infusions, and also capture (by drowning) the spotted wingDrosophila(SWD); (v) the microbe composition of home-made cheese infusions modulates oviposition choices by mosquitoes; and (vi) the type of cheese infusion coupled with its nutritional content strongly affects the survivorship of mosquito larvae. In combination, our data show that microbial metabolites associated with cheese and cheese infusions are both attractive to adult mosquitoes seeking hosts and oviposition sites, respectively, and are toxic to mosquito larvae. These microbes and their metabolites could thus be coopted for both the attract and the kill function of “attract & kill” mosquito control tactics. Implementation of customizable and non-conventional nutritional media, such as home-made cheese infusions, as microbe-based ecological traps presents a promising concept which exploits insect ecology for insect control.
Evolution oflbxspinal cord expression and function
Authors: Juárez-Morales José Luis , Weierud Frida , England Samantha J. , Demby Celia , Santos Nicole , Grieb Ginny , Mazan Sylvie , Lewis Katharine E.
Published: December 2020

Ladybird homeobox (Lbx) transcription factors have crucial functions in muscle and nervous system development in many animals. Amniotes have twoLbxgenes, but onlyLbx1is expressed in spinal cord. In contrast, teleosts have threelbxgenes and we show here that zebrafishlbx1a,lbx1bandlbx2are expressed by distinct spinal cell types, and thatlbx1ais expressed in dI4, dI5 and dI6 interneurons, as in amniotes. Our data examininglbxexpression inScyliorhinus caniculaandXenopus tropicalissuggest that the spinal interneuron expression of zebrafishlbx1ais ancestral, whereaslbx1bhas acquired a new expression pattern in spinal cord progenitor cells.lbx2spinal expression was probably acquired in the ray-finned lineage, as this gene is not expressed in the spinal cords of either amniotes orS. canicula. We also show that the spinal function of zebrafishlbx1ais conserved with mouse Lbx1. In zebrafishlbx1amutants, there is a reduction in the number of inhibitory spinal interneurons and an increase in the number of excitatory spinal interneurons, similar to mouseLbx1mutants. Interestingly, the number of inhibitory spinal interneurons is also reduced inlbx1bmutants, although in this case the number of excitatory interneurons is not increased.lbx1a;lbx1bdouble mutants have a similar spinal interneuron phenotype tolbx1asingle mutants. Taken together these data suggest thatlbx1bandlbx1amay be required in succession for correct specification of dI4 and dI6 spinal interneurons, although onlylbx1ais required for suppression of excitatory fates in these cells.

Research Highlights

lbx1spinal expression and function is conserved in vertebrates. In contrast, zebrafishlbx1bandlbx2have novel spinal expression patterns that probably evolved in the ray-finned vertebrate lineage (lbx2) or teleosts (lbx1b).
Sequencing of clinical samples reveals that adaptation keeps establishing during H7N9 virus infection in humans
Authors: Li Liqiang , Ma Jinmin , Li Jiandong , Yuan Jianying , Su Wei , jin Tao , Wang Xinfa , Zhang Renli , Zou Rongrong , Li Lei , Li Jianming , Fang Shisong , Yuan Jing , Yang Chentao , Qi Yanwei , Gao Qi , Ji Jingkai , Ma Kailong , Fan Guangyi , pei Na , Deng Yong , Zhou Yang , Lin Dechun , Li Fei , Ouyang Wenjie , Jia Huijue , Liu Xin , Jiang Hui , Yang Huanming , Xu Xun , Wang Hui , Liu Yingxia
Published: December 2020

The H7 subtype avian influenza viruses (AIV) have a much longer history and their adaptation through evolution pose continuous threat to humans1. Since 2013 March, the novel reasserted H7N9 subtype have transmitted to humans through their repeated assertion in the poultry market. Through repeated transmission, H7N9 gradually became the second AIV subtype posing greater public health risk after H5N12,3. After infection, how the virus tunes its genome to adapt and evolve in humans remains unknown. Through direct amplification of H7N9 and high throughput (HT) sequencing of full genomes from the swabs and lower respiratory tract samples collected from infected patients in Shenzhen, China, we have analyzed thein vivoH7N9 mutations at the level of whole genomes and have compared with the genomes derived byin vitrocultures. These comparisons and frequency analysis against the H7N9 genomes in the public database, 40 amino acids were identified that play potential roles in virus adaptation during H7N9 infection in humans. Various synonymous mutations were also identified that might be crucial to H7N9 adaptation in humans. The mechanism of these mutations occurred in a single infection are discussed in this study.
Boosting detection of low abundance proteins in thermal proteome profiling experiments by addition of an isobaric trigger channel to TMT multiplexes
Authors: Justice Sarah A. Peck , McCracken Neil A. , Victorino José F. , Wijeratne Aruna B. , Mosley Amber L.
Published: December 2020

The study of low abundance proteins is a challenge to discovery-based proteomics. Mass-spectrometry (MS) applications, such as thermal proteome profiling (TPP) face specific challenges in detection of the whole proteome as a consequence of the use of nondenaturing extraction buffers. TPP is a powerful method for the study of protein thermal stability, but quantitative accuracy is highly dependent on consistent detection. Therefore, TPP can be limited in its amenability to study low abundance proteins that tend to have stochastic or poor detection by MS. To address this challenge, we incorporated an affinity purified protein complex sample at submolar concentrations as an isobaric trigger channel into a mutant TPP (mTPP) workflow to provide reproducible detection and quantitation of the low abundance subunits of the Cleavage and Polyadenylation Factor (CPF) complex. The inclusion of an isobaric protein complex trigger channel increased detection an average of 40x for previously detected subunits and facilitated detection of CPF subunits that were previously below the limit of detection. Importantly, these gains in CPF detection did not cause large changes in melt temperature (Tm) calculations for other unrelated proteins in the samples, with a high positive correlation between Tmestimates in samples with and without isobaric trigger channel addition. Overall, the incorporation of affinity purified protein complex as an isobaric trigger channel within a TMT multiplex for mTPP experiments is an effective and reproducible way to gather thermal profiling data on proteins that are not readily detected using the original TPP or mTPP protocols.