Building Research Data Services at Mount Holyoke College

Objective: Mount Holyoke College ranks high among liberal arts colleges in faculty research activities and has just initiated a new program in Data Science. In this context, and given the recent growth in the use of very large datasets in research, more coherent and comprehensive campus support for the management and storage of faculty research data at Mount Holyoke has become essential. This poster will describe how Library, Information, and Technology Services (LITS) at Mount Holyoke (a merged library and IT organization), strove to analyze faculty research data management and storage needs, develop policies and procedures for meeting these needs, set out support models for research data lifecycle management, and determined responsibilities for consultation and support. Methods: In 2015-2016, a working group of MHC librarians and technologists from the Research and Instructional Support (RIS) Department began exploring the need for data services at MHC. The RIS team focussed on studying data services models at other institutions, administered a survey to learn about faculty research data practices, and finally developed a proposal for expanded data services at MHC. Also in the spring of 2016, a cross-functional team was formed to meet faculty data storage and backup needs. Ten members were drawn from multiple library and IT departments. This team developed use cases and personas to begin guiding the development of policies and procedures and planning infrastructure provisioning. Additionally, metadata librarians, research and instruction librarians, and digital assets managers planned support models for metadata creation and research data management planning. Results: Gathering information from the faculty survey and interviews, along with background study of data services models elsewhere, gave LITS a better understanding of our users’ needs. These insights guided LITS in developing matrices of needs, services, and support responsibilities that allow us to better meet support requirements and future infrastructure provisioning for data storage and processing. LITS has also developed resources to support faculty in crafting research data management plans (DMPs) and creating metadata for archiving newly created data sets. LITS has recently arranged access for Mount Holyoke researchers to the Massachusetts Green High Performance Computing Center (MGHPCC) and created an MHC Data Center to provide data storage and backup on LITS maintained servers. Conclusion: The work of the Research and Instructional Support team and the LITS cross-functional team for research data support has given us a much clearer picture of how Mount Holyoke researchers are using and managing their data and has allowed us to begin plotting a path to a more coherent and robust set of services to support them in their work

A comparison of direct versus self-report measures for assessing physical activity in adults: a systematic review

<p>Abstract</p> <p>Background</p> <p>Accurate assessment is required to assess current and changing physical activity levels, and to evaluate the effectiveness of interventions designed to increase activity levels. This study systematically reviewed the literature to determine the extent of agreement between subjectively (self-report e.g. questionnaire, diary) and objectively (directly measured; e.g. accelerometry, doubly labeled water) assessed physical activity in adults.</p> <p>Methods</p> <p>Eight electronic databases were searched to identify observational and experimental studies of adult populations. Searching identified 4,463 potential articles. Initial screening found that 293 examined the relationship between self-reported and directly measured physical activity and met the eligibility criteria. Data abstraction was completed for 187 articles, which described comparable data and/or comparisons, while 76 articles lacked comparable data or comparisons, and a further 30 did not meet the review's eligibility requirements. A risk of bias assessment was conducted for all articles from which data was abstracted.</p> <p>Results</p> <p>Correlations between self-report and direct measures were generally low-to-moderate and ranged from -0.71 to 0.96. No clear pattern emerged for the mean differences between self-report and direct measures of physical activity. Trends differed by measure of physical activity employed, level of physical activity measured, and the gender of participants. Results of the risk of bias assessment indicated that 38% of the studies had lower quality scores.</p> <p>Conclusion</p> <p>The findings suggest that the measurement method may have a significant impact on the observed levels of physical activity. Self-report measures of physical activity were both higher and lower than directly measured levels of physical activity, which poses a problem for both reliance on self-report measures and for attempts to correct for self-report – direct measure differences. This review reveals the need for valid, accurate and reliable measures of physical activity in evaluating current and changing physical activity levels, physical activity interventions, and the relationships between physical activity and health outcomes.</p

Necrotic cardiac myocytes skew macrophage polarization towards a classically activated phenotype

Necrotic and dying cells release damage-associated molecular patterns (DAMPs) that can initiate sterile inflammatory responses in the heart. Although macrophages are essential for myocardial repair and regeneration, the effect of DAMPs on macrophage activation remains unclear. To address this gap in knowledge we studied the effect of necrotic cardiac myocyte extracts on primary peritoneal macrophage (PPM) cultures in vitro. We first performed unbiased transcriptomic profiling with RNA-sequencing of PPMs cultured for up to 72 hours in the presence and absence of: 1) necrotic cell extracts (NCEs) from necrotic cardiac myocytes in order to mimic the release of DAMPs; 2) lipopolysaccharide (LPS), which is known to polarize macrophages towards a classically activated phenotype and 3) Interleukin-4 (IL-4), which is known to promote polarization of macrophages towards an alternatively activated phenotype. NCEs provoke changes in differential gene expression (DEGs) that had considerable overlap with LPS-induced changes, suggesting that NCEs promote macrophage polarization towards a classically activated phenotype. Treating NCEs with proteinase-K abolished the effects of NCEs on macrophage activation, whereas NCE treatment with DNase and RNase did not affect macrophage activation. Stimulation of macrophage cultures with NCEs and LPS resulted in a significant increase in macrophage phagocytosis and interleukin-1β secretion, whereas treatment with IL-4 had no significant effect on phagocytosis and interleukin-1β. Taken together, our findings suggest that proteins released from necrotic cardiac myocytes are sufficient to skew the polarization of macrophages towards a classically activated phenotype

Signature of long-lived memory CD8+ T cells in acute SARS-CoV-2 infection

Immunological memory is a hallmark of adaptive immunity and facilitates an accelerated and enhanced immune response upon re-infection with the same pathogen$^{1,2}$. Since the outbreak of the ongoing COVID-19 pandemic, a key question has focused on which SARS-CoV-2-specific T cells stimulated during acute infection give rise to long-lived memory T cells$^{3}$. Here, using spectral flow cytometry combined with cellular indexing of transcriptomes and T cell receptor sequencing, we longitudinally characterized individual SARS-CoV-2-specific CD8$^{+}$ T cells of patients with COVID-19 from acute infection to 1 year into recovery and found a distinct signature identifying long-lived memory CD8$^{+}$ T cells. SARS-CoV-2-specific memory CD8$^{+}$ T cells persisting 1 year after acute infection express CD45RA, IL-7 receptor-α and T cell factor 1, but they maintain low expression of CCR7, thus resembling CD45RA$^{+}$ effector memory T cells. Tracking individual clones of SARS-CoV-2-specific CD8$^{+}$ T cells, we reveal that an interferon signature marks clones that give rise to long-lived cells, whereas prolonged proliferation and mechanistic target of rapamycin signalling are associated with clonal disappearance from the blood. Collectively, we describe a transcriptional signature that marks long-lived, circulating human memory CD8$^{+}$ T cells following an acute viral infection

Biophysical Characteristics of Lipid-Induced Aβ Oligomers Correlate to Distinctive Phenotypes In Transgenic Mice

Alzheimer\u27s disease (AD) is a progressive neurodegenerative disorder that affects cognition and memory. Recent advances have helped identify many clinical sub-types in AD. Mounting evidence point toward structural polymorphism among fibrillar aggregates of amyloid-β (Aβ) to being responsible for the phenotypes and clinical manifestations. In the emerging paradigm of polymorphism and prion-like propagation of aggregates in AD, the role of low molecular weight soluble oligomers, which are long known to be the primary toxic agents, in effecting phenotypes remains inconspicuous. In this study, we present the characterization of three soluble oligomers of Aβ42, namely 14LPOs, 16LPOs, and GM1Os with discreet biophysical and biochemical properties generated using lysophosphatidyl glycerols and GM1 gangliosides. The results indicate that the oligomers share some biophysical similarities but display distinctive differences with GM1Os. Unlike the other two, GM1Os were observed to be complexed with the lipid upon isolation. It also differs mainly in detection by conformation-sensitive dyes and conformation-specific antibodies, temperature and enzymatic stability, and in the ability to propagate morphologically-distinct fibrils. GM1Os also show distinguishable biochemical behavior with pronounced neuronal toxicity. Furthermore, all the oligomers induce cerebral amyloid angiopathy (CAA) and plaque burden in transgenic AD mice, which seems to be a consistent feature among all lipid-derived oligomers, but 16LPOs and GM1Os displayed significantly higher effect than the others. These results establish a correlation between molecular features of Aβ42 oligomers and their distinguishable effects in transgenic AD mice attuned by lipid characteristics, and therefore help bridge the knowledge gap in understanding how oligomer conformers could elicit AD phenotypes

Human memory B cells show plasticity and adopt multiple fates upon recall response to SARS-CoV-2

The B cell response to different pathogens uses tailored effector mechanisms and results in functionally specialized memory B (B$_{m}$) cell subsets, including CD21$^{+}$ resting, CD21$^{–}$CD27$^{+}$ activated and CD21$^{–}$CD27$^{–}$ B$_{m}$ cells. The interrelatedness between these B$_{m}$ cell subsets remains unknown. Here we showed that single severe acute respiratory syndrome coronavirus 2-specific B$_{m}$ cell clones showed plasticity upon antigen rechallenge in previously exposed individuals. CD21$^{–}$ B$_{m}$ cells were the predominant subsets during acute infection and early after severe acute respiratory syndrome coronavirus 2-specific immunization. At months 6 and 12 post-infection, CD21$^{+}$ resting B$_{m}$ cells were the major B$_{m}$ cell subset in the circulation and were also detected in peripheral lymphoid organs, where they carried tissue residency markers. Tracking of individual B cell clones by B cell receptor sequencing revealed that previously fated B$_{m}$ cell clones could redifferentiate upon antigen rechallenge into other B$_{m}$ cell subsets, including CD21$^{–}$CD27$^{–}$ B$_{m}$ cells, demonstrating that single B$_{m}$ cell clones can adopt functionally different trajectories

Things come in threes: A new complex allele and a novel deletion within the CFTR gene complicate an accurate diagnosis of cystic fibrosis

Background: Despite consolidated guidelines, the clinical diagnosis and prognosis of cystic fibrosis (CF) is still challenging mainly because of the extensive phenotypic heterogeneity and the high number of CFTR variants, including their combinations as complex alleles. Results: We report a family with a complicated syndromic phenotype, which led to the suspicion not only of CF, but of a dominantly inherited skeletal dysplasia (SD). Whereas the molecular basis of the SD was not clarified, segregation analysis was central to make a correct molecular diagnosis of CF, as it allowed to identify three CFTR variants encompassing two known maternal mutations and a novel paternal microdeletion. Conclusion: This case well illustrates possible pitfalls in the clinical and molecular diagnosis of CF; presence of complex phenotypes deflecting clinicians from appropriate CF recognition, and/or identification of two mutations assumed to be in trans but with an unconfirmed status, which underline the importance of an in-depth molecular CFTR analysis

CRISPR-Cas ribonucleoprotein mediated homology-directed repair for efficient targeted genome editing in microalgae Nannochloropsis oceanica IMET1

Background: Microalgae are considered as a sustainable feedstock for the production of biofuels and other value-added compounds. In particular, Nannochloropsis spp. stand out from other microalgal species due to their capabilities to accumulate both triacylglycerol (TAG) and polyunsaturated fatty acids (PUFAs). However, the commercialization of microalgae-derived products is primarily hindered by the high production costs compared to less sustainable alternatives. Efficient genome editing techniques leading to effective metabolic engineering could result in strains with enhanced productivities of interesting metabolites and thereby reduce the production costs. Competent CRISPR-based genome editing techniques have been reported in several microalgal species, and only very recently in Nannochloropsis spp. (2017). All the reported CRISPR-Cas-based systems in Nannochloropsis spp. rely on plasmid-borne constitutive expression of Cas9 and a specific guide, combined with repair of double-stranded breaks (DSB) by non-homologous end joining (NHEJ) for the target gene knockout. Results: In this study, we report for the first time an alternative approach for CRISPR-Cas-mediated genome editing in Nannochloropsis sp.; the Cas ribonucleoproteins (RNP) and an editing template were directly delivered into microalgal cells via electroporation, making Cas expression dispensable and homology-directed repair (HDR) possible with high efficiency. Apart from widely used SpCas9, Cas12a variants from three different bacterium were used for this approach. We observed that FnCas12a from Francisella novicida generated HDR-based targeted mutants with highest efficiency (up to 93% mutants among transformants) while AsCas12a from Acidaminococcus sp. resulted in the lowest efficiency. We initially show that the native homologous recombination (HR) system in N. oceanica IMET1 is not efficient for easy isolation of targeted mutants by HR. Cas9/sgRNA RNP delivery greatly enhanced HR at the target site, generating around 70% of positive mutant lines. Conclusion: We show that the delivery of Cas RNP by electroporation can be an alternative approach to the presently reported plasmid-based Cas9 method for generating mutants of N. oceanica. The co-delivery of Cas-RNPs along with a dsDNA repair template efficiently enhanced HR at the target site, resulting in a remarkable higher percentage of positive mutant lines. Therefore, this approach can be used for efficient generation of targeted mutants in Nannochloropsis sp. In addition, we here report the activity of several Cas12a homologs in N. oceanica IMET1, identifying FnCas12a as the best performer for high efficiency targeted genome editing.</p

Biophysical and Functional Characterization of Rhesus Macaque IgG Subclasses

Antibodies raised in Indian rhesus macaques [Macaca mulatta (MM)] in many preclinical vaccine studies are often evaluated in vitro for titer, antigen-recognition breadth, neu- tralization potency, and/or effector function, and in vivo for potential associations with protection. However, despite reliance on this key animal model in translation of promising candidate vaccines for evaluation in first in man studies, little is known about the proper- ties of MM immunoglobulin G (IgG) subclasses and how they may compare to human IgG subclasses. Here, we evaluate the binding of MM IgG1, IgG2, IgG3, and IgG4 to human Fc gamma receptors (FcγR) and their ability to elicit the effector functions of human FcγR-bearing cells, and unlike in humans, find a notable absence of subclasses with dramatically silent Fc regions. Biophysical, in vitro, and in vivo characterization revealed MM IgG1 exhibited the greatest effector function activity followed by IgG2 and then IgG3/4. These findings in rhesus are in contrast with the canonical understanding that IgG1 and IgG3 dominate effector function in humans, indicating that subclass-switching profiles observed in rhesus studies may not strictly recapitulate those observed in human vaccine studies

Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.

The QT interval, an electrocardiographic measure reflecting myocardial repolarization, is a heritable trait. QT prolongation is a risk factor for ventricular arrhythmias and sudden cardiac death (SCD) and could indicate the presence of the potentially lethal mendelian long-QT syndrome (LQTS). Using a genome-wide association and replication study in up to 100,000 individuals, we identified 35 common variant loci associated with QT interval that collectively explain ∼8-10% of QT-interval variation and highlight the importance of calcium regulation in myocardial repolarization. Rare variant analysis of 6 new QT interval-associated loci in 298 unrelated probands with LQTS identified coding variants not found in controls but of uncertain causality and therefore requiring validation. Several newly identified loci encode proteins that physically interact with other recognized repolarization proteins. Our integration of common variant association, expression and orthogonal protein-protein interaction screens provides new insights into cardiac electrophysiology and identifies new candidate genes for ventricular arrhythmias, LQTS and SCD