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Hernandez, K.

Publications and source records attributed to Hernandez, K..

9 recordsLinked to original sources

A strong start for sustained success: inclusivity through a national group mentorship program for first-year graduate students

In the United States, STEM graduate programs and workforce do not represent the demographics of the population. Obstacles, including a lack of transparency, community, and accessible information in navigating academia, disproportionately affect students from underserved backgrounds. Peer mentoring networks can address these disparities. Here, we describe Cientifico Latino, Inc.s Graduate Student Engagement and Community (CL-GSEC) program, a nationwide, group-based peer mentorship program that has served first-year graduate students across the U.S., especially those from underserved backgrounds. Surveys indicate CL-GSEC positively impacts the first-year graduate experience. We highlight key program features, challenges, and insights, such as financial strains faced by first-year graduate students. We offer suggestions for how faculty and departments can better support students during this critical early stage of graduate training. We hope that reporting on CL-GSECs program structure, evaluations, and findings will guide educational leaders in expanding programming for junior graduate students.

scientific communication and education↗

Uncovering a new player in ischemic stroke: a study of intra-arterial interferon-gamma-producing monocytes in hyperacute stroke

Stroke triggers a rapid and complex immune response that is not yet fully understood, especially within hours after an ischemic infarct. Our previous study in stroke patients revealed a significant increase in interferon- gamma (IFN-{gamma}) immediately (hyperacute) and downstream of the ischemic ictus, within the arterial compartment. The present study investigated the source, inciting factors, and role of IFN-{gamma} in a preclinical murine model. Stroke was produced using transient middle cerebral artery occlusion, and immune cells within the arterial vasculature distal to the occlusion (pre- and post-occlusion) were characterized using flow cytometry. Compared with the control samples, the post-occlusion samples presented an increase in IFN-{gamma}+ and CD69+ cells, whereas no significant increase was detected in IL17+, IL4+, and CD25+ cells. Further analysis of the IFN-{gamma}+ population revealed two novel attributes. First, interrogation of the identity of these IFN-{gamma}+ cells revealed that the increase in IFN-{gamma} production was largely driven by CD14+ cells in the post- occlusion sample, with negligible contributions from other canonical IFN-{gamma}-producing cells (CD4, CD8). Second, the IFN-{gamma}+ cells exhibited two distinct clusters, an IFN-{gamma}low and an IFN-{gamma}hi population. Further analysis revealed that the IFN-{gamma} low population was largely composed of CD14+ cells, whereas the IFN-{gamma}hi population was dominated by CD4+ T-cells. To explore the conditions driving IFN-{gamma} production, an in vitro ischemia model involving oxygen-glucose deprivation (OGD) was employed. Co-culturing of naive splenocytes with OGD-treated CNS cells and OGD-derived supernatant resulted in a significant increase in IFN-{gamma}+CD14+ cells, as compared to normoxic controls, an effect that coincided with marked loss of DAPI+ and NeuN+DAPI+ cells in mixed cortical (neuronal and glial) cultures. In summary, this study identified intra-arterial CD14+ monocytes as novel early sources of IFN-{gamma} in the hyperacute phase of stroke, a role traditionally attributed to adaptive immune cells. Using in vivo and in vitro ischemia models, the findings reveal that injury-associated signals from CNS cells are sufficient to directly induce IFN-{gamma} production in CD14+ cells, redefining early stroke immunopathology and uncovering a potential target for timely immunomodulation.

immunology↗

Microbial communities from weathered outcrops of a sulfide-rich ultramafic intrusion, and implications for mine waste management

The Duluth Complex, Northeastern Minnesota, contains sulfide-rich magmatic intrusions that, collectively, represent one of the worlds largest known economic deposits of copper, nickel, and platinum group elements (Cu-Ni-PGEs). Previous work showed that microbial communities associated with experimentally-weathered Duluth Complex waste rock and tailings were dominated by uncultivated taxa and other populations not typically associated with mine waste. However, those experiments were designed for kinetic testing and do not necessarily represent the conditions expected for reclaimed mine waste or long-term weathering in the environment. We therefore used 16S rRNA gene methods to characterize the microbial communities present on the surfaces of naturally-weathered and historically disturbed outcrops of Duluth Complex material, as well as a circumneutral seep draining a reclaimed blast pit. Rock surfaces were dominated by diverse uncultured Ktedonobacteria, Acetobacteria, and Actinobacteria while seeps were dominated by Proteobacteria, including Leptothrix spp. and Methylovulum spp. All samples had abundant algae and other phototrophs. These communities were distinct from previously-described microbial assemblages from experimentally-weathered Duluth Complex rocks, suggested different energy and nutrient resources in the reclaimed rocks, outcrops, and seeps. Sulfide mineral incubations performed with and without algae showed that photosynthetic microorganisms could have an inhibitory effect on some of the autotrophic populations from the site, resulting in slightly lower sulfate release and differences in the dominant microorganisms. The microbial assemblages from these weathered outcrops show how communities are expected to develop during natural weathering of sulfide-rich Duluth Complex rocks, and represent baseline data that could be used to evaluate the effectiveness of future reclamation of tailings and waste rock produced by large scale mining operations.

microbiology↗

DNA Origami Presenting the Receptor Binding Domain of SARS-CoV-2 Elicit Robust Protective Immune Response

Effective and safe vaccines are invaluable tools in the arsenal to fight infectious diseases. The rapid spreading of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible of the coronavirus disease 2019 pandemic has highlighted the need to develop methods for rapid and efficient vaccine development. DNA origami nanoparticles (DNA-NPs) presenting multiple antigens in prescribed nanoscale patterns have recently emerged as a safe, efficient, and easily scalable alternative for rational design of vaccines. Here, we are leveraging the unique properties of these DNA-NPs and demonstrate that precisely patterning ten copies of a reconstituted trimer of the receptor binding domain (RBD) of SARS-CoV-2 along with CpG adjuvants on the DNA-NPs is able to elicit a robust protective immunity against SARS-CoV-2 in a mouse model. Our results demonstrate the potential of our DNA-NP-based approach for developing safe and effective nanovaccines against infectious diseases.

bioengineering↗

Generation and characterization of Ccdc28b mutant mice links the Bardet-Biedl associated gene with social behavioral phenotypes

CCDC28B (coiled-coil domain-containing protein 28B) was identified as a modifier in the ciliopathy Bardet-Biedl syndrome (BBS). Our previous work in cells and zebrafish showed that CCDC28B plays a role regulating cilia length in a mechanism that is not completely understood. Here we report the generation of a Ccdc28b mutant mouse using CRISPR/Cas9 (Ccdc28b mut). After confirming the depletion of Ccdc28b we performed a phenotypic characterization showing that Ccdc28b mut animals present a mild phenotype: i) do not present clear structural cilia affectation, although we did observe mild defects in cilia density and cilia length in some tissues, ii) reproduce normally, and iii) do not develop retinal degeneration or obesity, two hallmark features of reported BBS murine models. In contrast, Ccdc28b mut mice did show clear social interaction defects as well as stereotypical behaviors suggestive of autism spectrum disorder (ASD). This finding is indeed relevant regarding CCDC28B as a modifier of BBS since behavioral phenotypes have been documented in BBS. Importantly however, our data suggests a possible causal link between CCDC28B and ASD-like phenotypes that exceeds the context of BBS: filtering for rare deleterious variants, we found CCDC28B mutations in eight probands from the Simmons Simplex Collection cohort. Furthermore, a phenotypic analysis showed that CCDC28B mutation carriers present lower BMI and mild communication defects compared to a randomly selected sample of SSC probands. Thus, our results suggest that mutations in CCDC28B lead to mild autism-like features in mice and humans. Overall, this work reports a novel mouse model that will be key to continue evaluating genetic interactions in BBS, deciphering the contribution of CCDC28B to modulate the presentation of BBS phenotypes. In addition, our data underscores a novel link between CCDC28B and ASD-like phenotypes, providing a novel opportunity to further our understanding of the genetic, cellular, and molecular basis of ASD. AUTHOR SUMMARYBardet-Biedl syndrome (BBS) is caused by mutations in any of 21 genes known to date. In some families, BBS can be inherited as an oligogenic trait whereby mutations in more than one BBS gene collaborate in the presentation of the syndrome. In addition, CCDC28B was identified as a modifier of BBS, associated with a more severe presentation of the syndrome. Different mechanisms, all relying on functional redundancy, have been proposed to explain this genetic interaction and the characterization of different BBS proteins supported this possibility as they were shown to play roles in the same cellular organelle, the primary cilium. Similarly, CCDC28B also participates in cilia biology regulating the length of the organelle: knockdown of CCDC28B in cells results in cilia shortening and depletion in zebrafish also results in early embryonic phenotypes characteristic of other cilia mutants. Here, we sought to generate a mouse Ccdc28b mutant to determine whether it would be sufficient to cause a ciliopathy phenotype, and to generate a reagent critical to further dissect its modifying role in the context of BBS. Overall, Ccdc28b mutant mice presented a mild phenotype, a finding fully compatible with a modifier rather than a causal BBS gene. In addition, we found that Ccdc28b mutants showed a clear autism-like behavior, and autism is indeed a feature of several BBS patients. Importantly, we identified multiple individuals with autism from the Simmos Simplex Collection to carry disruptive mutations in CCDC28B suggesting that this gene is causally associated with autism independently of BBS.

genetics↗

Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission

The COVID-19 pandemic has sparked an urgent need to uncover the underlying biology of this devastating disease. Though RNA viruses mutate more rapidly than DNA viruses, there are a relatively small number of single nucleotide polymorphisms (SNPs) that differentiate the main SARS-CoV-2 clades that have spread throughout the world. In this study, we investigated over 7,000 SARS-CoV-2 datasets to unveil both intrahost and interhost diversity. Our intrahost and interhost diversity analyses yielded three major observations. First, the mutational profile of SARS-CoV-2 highlights iSNV and SNP similarity, albeit with high variability in C>T changes. Second, iSNV and SNP patterns in SARS-CoV-2 are more similar to MERS-CoV than SARS-CoV-1. Third, a significant fraction of small indels fuel the genetic diversity of SARS-CoV-2. Altogether, our findings provide insight into SARS-CoV-2 genomic diversity, inform the design of detection tests, and highlight the potential of iSNVs for tracking the transmission of SARS-CoV-2.

genomics↗

Uniform Genomic Data Analysis in the NCI Genomic Data Commons

The goal of the National Cancer Institute (NCI) Genomic Data Commons (GDC) is to provide the cancer research community with a data repository of uniformly processed genomic and associated clinical data that enables data sharing and collaborative analysis in the support of precision medicine. The initial GDC dataset include genomic, epigenomic, proteomic, clinical and other data from the NCI TCGA and TARGET programs. Data production for the GDC started in June, 2015 using an OpenStack-based private cloud. By June of 2016, the GDC had analyzed more than 50,000 raw sequencing data inputs, as well as multiple other data types. Using the latest human genome reference build GRCh38, the GDC generated a variety of data types from aligned reads to somatic mutations, gene expression, miRNA expression, DNA methylation status, and copy number variation. In this paper, we describe the pipelines and workflows used to process and harmonize the data in the GDC. The generated data, as well as the original input files from TCGA and TARGET, are available for download and exploratory analysis at the GDC Data Portal and Legacy Archive (https://gdc.cancer.gov/).

bioinformatics↗

Coordinate Enhancer Reprogramming by GATA3 and AP1 Promotes Phenotypic Plasticity to Achieve Breast Cancer Endocrine Resistance

Acquired therapy resistance is a major problem for anticancer treatment, yet the underlying molecular mechanisms remain unclear. Using an established breast cancer cellular model for endocrine resistance, we show that hormone resistance is associated with enhanced phenotypic plasticity, indicated by a general downregulation of luminal/epithelial differentiation markers and upregulation of basal/mesenchymal invasive markers. Our extensive omics studies, including GRO-seq on enhancer landscapes, demonstrate that the global enhancer gain/loss reprogramming driven by the differential interactions between ER and other oncogenic transcription factors (TFs), predominantly GATA3 and AP1, profoundly alters breast cancer transcriptional programs. Our functional studies in multiple biological systems including culture and xenograft models of MCF7 and T47D lines support a coordinate role of GATA3 and AP1 in enhancer reprogramming that promotes phenotypic plasticity and endocrine resistance. Collectively, our study implicates that changes in TF-TF and TF-enhancer interactions can lead to genome-wide enhancer reprogramming, resulting in transcriptional dysregulations that promote plasticity and cancer therapy-resistance progression.

cancer biology↗

Caprine humoral response to Burkholderia pseudomallei antigens during acute melioidosis from aerosol exposure

Burkholderia pseudomallei causes melioidosis, a common source of pneumonia and sepsis in Southeast Asia and Northern Australia, that results in high mortality rates. A caprine melioidosis model of aerosol infection that leads to a systemic infection has the potential to characterize the humoral immune response. This could help identify immunogenic proteins for new diagnostics and vaccine candidates. Outbred goats may more accurately mimic human infection, in contrast to the inbred mouse models used to date. B. pseudomallei infection was delivered as an intratracheal aerosol. Antigenic protein profiling was generated from the infecting strain MSHR511. Humoral immune responses were analyzed by ELISA and western blot, and the antigenic proteins were identified by mass spectrometry. Throughout the course of the infection the assay results demonstrated a much greater humoral response with IgG antibodies, in both breadth and quantity, compared to IgM antibodies. Pre-infection sera showed multiple immunogenic proteins already reactive for IgG (7-20) and IgM (0-12) in most of the goats despite no previous exposure to B. pseudomallei. After infection, the number of IgG reactive proteins showed a marked increase as the disease progressed. Early stage infection (day 7) showed immune reaction to chaperone proteins (GroEL, EF-Tu, and DnaK). These three proteins were detected in all serum samples after infection, with GroEL immunogenically dominant. Seven common reactive antigens were selected for further analysis using ELISA. The heat shock protein GroEL1 elicited the strongest goat antibody immune response compared to the other six antigens. Most of the six antigens showed the peak IgM reactivity at day 14, whereas the IgG reactivity increased further as the disease progressed. An overall MSHR511 proteomic comparison between the goat model and human sera showed that many immune reactive proteins are common between humans and goats with melioidosis.\n\nAuthor SummaryB. pseudomallei infection, the causative agent of melioidosis, results in severe disseminated or localized infections. A systemic study of the humoral immune response to B. pseudomallei infection using the B. pseudomallei aerosol caprine model would help understand the detectable antigenic proteins as the infection progresses. To study the immune response, IgG and IgM antibody responses to whole cell lysate proteins were identified and analyzed. Antigenic carbohydrates were also studied. From the results, this study suggests that the caprine humoral immune response to aerosolized B. pseudomallei has similarities to human melioidosis and may facilitate the analysis of the temporal antibody responses. In addition, commonly detected immunogenic proteins may be used as biomarkers for the future point of care (POC) diagnostics.

immunology↗