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Low nephron (the functional unit in the kidney) numbers are linked to the development of hypertension and chronic kidney disease (CKD), which are both significant health problems. Our lab has established a novel inbred genetic animal model (HSRA rat) to study the genetic and physiological impact of low nephron number. In the HSRA model, ~75% of offspring are born with a single kidney (HSRA-S) compared to normal two-kidney littermates (HSRA-C). HSRA-S rats also exhibit altered development in the solitary kidney leading to ~20% less nephrons vs. individual kidney from the HSRA-C. Although the underlying genetic causes in the HSRA remains unknown, we hypothesize that there are genetic variants in the HSRA-S that promote altered expression of specific genes during kidney development leading to failure of one kidney to develop and reduced nephrons (compared to HSRA-C). To better understand the genes/pathways that may be involved in the altered kidney development, single nuclei (sn)RNA-seq was performed on kidneys of 4-week-old male HSRA rats (n=4 -S and -C kidneys). Nuclei were isolated from frozen kidney samples using 10X Chromium Nuclei Isolation Kit and processed through the 10X Genomics Chromium Single Cell 3’ protocol v3.1 per manufactures’ instruction. Libraries were sequenced on the Illumina NextSeq 2000 per 10X generating on average 40,000 reads per cell, >30,000 cells. FASTQ were processed using Cellranger mkfastq(v6.1.1)(10x Genomics) and for differential expression between the samples, the output files from each count were combined using Cellranger aggr(v6.1.1) to generate a combined cloupe file and visualized in Loupe browser 6. The cell specific clusters were grouped based on canonical cell-specific markers. The preliminary analysis of snRNA-seq of HSRA-S vs. HSRA-C kidneys identified distinct clusters of kidney-specific cell types, including podocytes, proximal tubule (PTCs1-3), Loop of Henle, and endothelial cells, among others. Differentially expressed genes (DEGs) were identified between -S and -C for most cell types, with proximal tubule cells accounting for largest number (n=41). Interestingly, a top downregulated DEG in the –S was leukemia inhibitory factor receptor (LIFR), which has recently been associated with renal malformations. In addition, studies are underway involving timed breeding of HSRA rats and subsequent isolation of fetal kidney at different days of gestation (GD14.5-17.5) for multi-omics analysis, including snRNA-seq, smallRNA-seq, and reduced-representation bisulfite sequencing. To date, we’ve collected n=23 fetal kidneys from E17.5 [2K= 8 (5m/3f); SK=15 (8m/7f)] and n=19 at E16.5 [2K= 10 (8m/2f); SK=9 (4m/5f)]. The analysis of snRNA-seq data in young HSRA and at early developmental points will provide insight into genes/pathways involved in kidney development that can increase predisposition to hypertension and CKD later in life. Graduate School of Health Sciences at UMMC; NIH R01HL137673; P20GM103476; P20GM104357 This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

For better infectious disease surveillance, there is growing interest in the detection of subtle changes in cardiovascular physiology in response to viral infection. This is not only important for earlier diagnosis and better prognosis of symptomatic carriers, but also useful to diagnose asymptomatic carriers of the virus. In our previous study, we found changes in cardiovascular physiology induced in A/Puerto Rico/8/34 (PR8) influenza infections in female and male C57BL/6J mice. Reduction in activity, blood pressure (BP) and heart rate (HR) for females was observed approximately 3-13 days post infection (dpi) and males approximately 5-12 dpi. Additionally, we found sex differences in inflammatory maker expression in lungs at 7dpi with bulk RNA sequencing (RNA-seq) data of lungs and Bio-plex cytokine assay for blood. In this study, we aim to associate changes in cardiovascular measurements with biomarkers throughout infection. Blood, brain, heart, lung, kidney, and nasal septum were collected at 1, 3, 5, and 9 dpi from influenza infected and naïve C57BL/6J female and male mice (n=6 for each time point and experimental group). Using body weight loss as a marker for disease in mice, we found both females and males had significant decrease in body weight at 9 dpi, yet infected females had a significant increase in brain, lung, and kidney weight at 9 dpi compared to naïve females. We are currently in process of analyzing pathological impacts of each tissue with histology and differing patterns of inflammatory maker expression in lungs throughout infection by analyzing bulk RNA sequencing (RNA-seq) data of lungs and Bio-plex cytokine assay for blood. Both cardiovascular measurements and molecular markers throughout influenza infection help to distinguish sex differences caused by influenza virus infection for better, earlier disease diagnosis. Hypertension and Cardiorenal Diseases Research Training Program T32HL105324 (NIH) This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Staphylococcus epidermidis infections can be challenging to diagnose due to the species frequent contamination of clinical specimens and indolent course of infection. Nevertheless, S. epidermidis is the major cause of late-onset sepsis among premature infants and of intravascular infection in all age groups.

Premise of research. Numerous biotic and abiotic factors can contribute to local selection and lead to geographic structure and genetic divergence between populations. The southwestern United State...

Premise of research. Population connectivity, the exchange of genes among geographically separated subpopulations, is thought to be a key process for the maintenance of genetic diversity and the su...

In many populous cities across the world, parking tends to be at the forefront of traffic concerns. Many cities have seen rises in urban population as people move to the cities for job opportunities. The increase in population also means more cars in the city making parking spaces valuable commodities. In many of these cities, parking spaces near venues and other services are reserved for disabled parking. In the United States, federal law sets the requirements for the number of spaces that must be made available along with the size of each area. Requirements for authorization to park in these spaces are also set by federal offices and the authorized person is given a placard designating their legal right to park in these designated parking spaces for the disabled. Our proposed method, which adds RFID and database authentication to the use of ultrasonic sensors, LED, and cloud technology methods, will assist with ensuring that the limited disabled-parking spaces are used by those authorized to do so, and will alert the parking authority when a space is occupied by an unauthenticated person. Our goal is to explain how some of the currently researched smart parking methods can be used for disabled parking management and improved with the addition of authenticating disabled parking authorization.

Studies of major depressive disorder (MDD) in postmortem brain tissue report enhanced binding to inhibitory serotonin-1A autoreceptors in midbrain dorsal raphe and reductions in length of axons expressing the serotonin transporter (SERT) in dorsolateral prefrontal cortex. The length density of axons expressing SERT in the orbitofrontal cortex (OFC) was determined in 18 subjects with MDD and 17 age-matched control subjects. A monoclonal antibody was used to immunohistochemically label the SERT in fixed sections of OFC. The 3-dimensional length density of SERT-immunoreactive (ir) axons in layer VI of OFC was estimated. The age of subjects with MDD was negatively correlated with SERT axon length (r=−0.77, p

Significance Epidemics of AMR pathogens are often only identified years or decades after they first evolved and distant from their place of origin. Consequently, evidence-based strategies for early containment of AMR epidemics are limited. This study employs whole-genome sequence data to reconstruct the “pre-detection” evolutionary and epidemiological history of an extensively drug-resistant Mycobacterium tuberculosis strain in KwaZulu-Natal, South Africa. We localize the geographic origin of this strain to an area hundreds of kilometers away from where the first clinical cases were reported and identify key host- and pathogen-specific factors that contributed to the rise of this important threat to global tuberculosis control. We propose that similar strategies can support the early identification and containment of AMR pathogens in the future., Antimicrobial-resistant (AMR) infections pose a major threat to global public health. Similar to other AMR pathogens, both historical and ongoing drug-resistant tuberculosis (TB) epidemics are characterized by transmission of a limited number of predominant Mycobacterium tuberculosis (Mtb) strains. Understanding how these predominant strains achieve sustained transmission, particularly during the critical period before they are detected via clinical or public health surveillance, can inform strategies for prevention and containment. In this study, we employ whole-genome sequence (WGS) data from TB clinical isolates collected in KwaZulu-Natal, South Africa to examine the pre-detection history of a successful strain of extensively drug-resistant (XDR) TB known as LAM4/KZN, first identified in a widely reported cluster of cases in 2005. We identify marked expansion of this strain concurrent with the onset of the generalized HIV epidemic 12 y prior to 2005, localize its geographic origin to a location in northeastern KwaZulu-Natal ∼400 km away from the site of the 2005 outbreak, and use protein structural modeling to propose a mechanism for how strain-specific rpoB mutations offset fitness costs associated with rifampin resistance in LAM4/KZN. Our findings highlight the importance of HIV coinfection, high preexisting rates of drug-resistant TB, human migration, and pathoadaptive evolution in the emergence and dispersal of this critical public health threat. We propose that integrating whole-genome sequencing into routine public health surveillance can enable the early detection and local containment of AMR pathogens before they achieve widespread dispersal.

Jag1 functions as a tumor suppressor in delaying pancreatic cancer precursor, while at the same time, promotes a phenotypic switch from benign cystic lesions to invasive carcinoma of the pancreas., Notch signaling exerts both oncogenic and tumor-suppressive functions in the pancreas. In this study, deletion of Jag1 in conjunction with oncogenic KrasG12D expression in the mouse pancreas induced rapid development of acinar-to-ductal metaplasia and early stage pancreatic intraepithelial neoplasm; however, culminating in cystic neoplasms rather than ductal adenocarcinoma. Most cystic lesions in these mice were reminiscent of serous cystic neoplasm, and the rest resembled intraductal papillary mucinous neoplasm. Jag1 expression was lost or decreased in cystic lesions but retained in adenocarcinoma in these mice, so was the expression of Sox9. In pancreatic cancer patients, JAG1 expression is higher in cancerous tissue, and high JAG1 is associated with poor overall survival. Expression of SOX9 is correlated with JAG1, and high SOX9 is also associated with poor survival. Mechanistically, Jag1 regulates expression of Lkb1, a tumor suppressor involved in the development of pancreatic cystic neoplasm. Collectively, Jag1 can act as a tumor suppressor in the pancreas by delaying precursor lesions, whereas loss of Jag1 promoted a phenotypic switch from malignant carcinoma to benign cystic lesions.

Notch signaling exerts both oncogenic and tumor-suppressive functions in the pancreas. In this study, deletion of Jag1 in conjunction with oncogenic KrasG12D expression in the mouse pancreas induced rapid development of acinar-to-ductal metaplasia and early stage pancreatic intraepithelial neoplasm; however, culminating in cystic neoplasms rather than ductal adenocarcinoma. Most cystic lesions in these mice were reminiscent of serous cystic neoplasm, and the rest resembled intraductal papillary mucinous neoplasm. Jag1 expression was lost or decreased in cystic lesions but retained in adenocarcinoma in these mice, so was the expression of Sox9. In pancreatic cancer patients, JAG1 expression is higher in cancerous tissue, and high JAG1 is associated with poor overall survival. Expression of SOX9 is correlated with JAG1, and high SOX9 is also associated with poor survival. Mechanistically, Jag1 regulates expression of Lkb1, a tumor suppressor involved in the development of pancreatic cystic neoplasm. Collectively, Jag1 can act as a tumor suppressor in the pancreas by delaying precursor lesions, whereas loss of Jag1 promoted a phenotypic switch from malignant carcinoma to benign cystic lesions.

Clonal complex 5 methicillin-resistant Staphylococcus aureus (CC5-MRSA) includes multiple prevalent clones that cause hospital-associated infections in the Western Hemisphere. Here, we present a phylogenomic study of these MRSA to reveal their phylogeny, spatial and temporal population structure, and the evolution of selected traits. We studied 598 genome sequences, including 409 newly generated sequences, from 11 countries in Central, North, and South America, and references from Asia and Europe. An early-branching CC5-Basal clade is well-dispersed geographically, is methicillin-susceptible and MRSA predominantly of ST5-IV such as the USA800 clone, and includes separate subclades for avian and porcine strains. In the early 1970s and early 1960s, respectively, two clades appeared that subsequently underwent major expansions in the Western Hemisphere: a CC5-I clade in South America and a CC5-II clade largely in Central and North America. The CC5-I clade includes the ST5-I Chilean/Cordobes clone, and the ST228-I South German clone as an early offshoot, but is distinct from other ST5-I clones from Europe that nest within CC5-Basal. The CC5-II clade includes divergent strains of the ST5-II USA100 clone, various other clones, and most known vancomycin-resistant strains of S. aureus, but is distinct from ST5-II strain N315 from Japan that nests within CC5-Basal. The recombination rate of CC5 was much lower than has been reported for other S. aureus genetic backgrounds, which indicates that recurrence of vancomycin resistance in CC5 is not likely due to an enhanced promiscuity. An increased number of antibiotic resistances and decreased number of toxins with distance from the CC5 tree root were observed. Of note, the expansions of the CC5-I and CC5-II clades in the Western Hemisphere were preceded by convergent gains of resistance to fluoroquinolone, macrolide, and lincosamide antibiotics, and convergent losses of the staphylococcal enterotoxin p (sep) gene from the immune evasion gene cluster of phage ΦSa3. Unique losses of surface proteins were also noted for these two clades. In summary, our study has determined the relationships of different clades and clones of CC5 and has revealed genomic changes for increased antibiotic resistance and decreased virulence associated with the expansions of these MRSA in the Western Hemisphere. Fil: Challagundla, Lavanya. University of Mississippi; Estados Unidos Fil: Reyes, Jinnethe. Universidad El Bosque; Colombia Fil: Rafiqullah, Iftekhar. University of Mississippi; Estados Unidos Fil: Sordelli, Daniel Oscar. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; Argentina Fil: Echaniz-Aviles, Gabriela. Instituto Nacional de Salud Pùblica; México Fil: Velazquez-Meza, Maria E.. Instituto Nacional de Salud Pública; México Fil: Castillo-Ramírez, Santiago. Universidad Nacional Autónoma de México; México Fil: Fittipaldi, Nahuel. University of Toronto; Canadá. Public Health Ontario Laboratory; Canadá Fil: Feldgarden, Michael. National Institutes of Health; Estados Unidos Fil: Chapman, Sinéad B.. Broad Institute of MIT and Harvard; Estados Unidos Fil: Calderwood, Michael S.. Dartmouth–Hitchcock Medical Center; Estados Unidos Fil: Carvajal, Lina P.. Universidad El Bosque; Colombia Fil: Rincon, Sandra. Universidad El Bosque; Colombia Fil: Blake, Hanson. University of Texas; Estados Unidos Fil: Planet, Paul J.. University of Pennsylvania; Estados Unidos Fil: Arias, Cesar A.. Universidad El Bosque; Colombia. University of Texas; Estados Unidos Fil: Diaz, Lorena. Universidad El Bosque; Colombia Fil: Robinson, D. Ashley. University of Mississippi; Estados Unidos

The USA300 North American epidemic (USA300-NAE) clone of methicillin-resistant Staphylococcus aureus has caused a wave of severe skin and soft tissue infections in the United States since it emerged in the early 2000s, but its geographic origin is obscure. Here we use the population genomic signatures expected from the serial founder effects of a geographic range expansion to infer the origin of USA300-NAE and identify polymorphisms associated with its spread. Genome sequences from 357 isolates from 22 U.S. states and territories and seven other countries are compared. We observe two significant signatures of range expansion, including decreases in genetic diversity and increases in derived allele frequency with geographic distance from the Pennsylvania region. These signatures account for approximately half of the core nucleotide variation of this clone, occur genome wide, and are robust to heterogeneity in temporal sampling of isolates, human population density, and recombination detection methods. The potential for positive selection of a gyrA fluoroquinolone resistance allele and several intergenic regions, along with a 2.4 times higher recombination rate in a resistant subclade, is noted. These results are the first to show a pattern of genetic variation that is consistent with a range expansion of an epidemic bacterial clone, and they highlight a rarely considered but potentially common mechanism by which genetic drift may profoundly influence bacterial genetic variation., IMPORTANCE The process of geographic spread of an origin population by a series of smaller populations can result in distinctive patterns of genetic variation. We detect these patterns for the first time with an epidemic bacterial clone and use them to uncover the clone’s geographic origin and variants associated with its spread. We study the USA300 clone of methicillin-resistant Staphylococcus aureus, which was first noticed in the early 2000s and subsequently became the leading cause of skin and soft tissue infections in the United States. The eastern United States is the most likely origin of epidemic USA300. Relatively few variants, which include an antibiotic resistance mutation, have persisted during this clone’s spread. Our study suggests that an early chapter in the genetic history of this epidemic bacterial clone was greatly influenced by random subsampling of isolates during the clone’s geographic spread.

Major Depressive Disorder (MDD) is a common psychiatric disorder for which available medications are often not effective. The high prevalence of MDD and modest response to existing therapies compels efforts to better understand and treat the disorder. Decreased hippocampal volume with increasing duration of depression suggests altered gene expression or even a decrease in neurogenesis. Tissue punches from the dentate gyrus were collected postmortem from 23 subjects with MDD and 23 psychiatrically-normal control subjects. Total RNA was isolated and whole transcriptome paired-end RNA-sequencing was performed using an Illumina NextSeq 500. For each sample, raw RNA-seq reads were aligned to the Ensembl GRCh38 human reference genome. Analysis revealed 30 genes differentially expressed in MDD compared to controls (FDR

Claudin-low breast cancer (CLBC) is a poor prognosis molecular subtype showing stemness and mesenchymal features. We previously discovered that deletion of a Notch signaling modulator, Lunatic Fringe (Lfng), in the mouse mammary gland induced a subset of tumors resembling CLBC. Here we report that deletion of one copy of p53 on this background not only accelerated mammary tumor development but also led to a complete penetrance of the mesenchymal stem-like phenotype. All mammary tumors examined in the Lfng/p53 compound mutant mice displayed a mesenchymal/spindloid pathology. These tumors showed high level expressions of epithelial-to-mesenchymal transition (EMT) markers including Vimentin, Twist, and PDGFRα, a gene known to be enriched in CLBC. Prior to tumor onset, Lfng/p53 mutant mammary glands exhibited increased levels of Vimentin and E-cadherin, but decreased expressions of cytokeratin 14 and cytokeratin 8, accompanied by elevated basal cell proliferation and an expanded mammary stem cell-enriched population. Lfng/p53 mutant glands displayed increased accumulation of Notch3 intracellular fragment, up-regulation of Hes5 and down-regulation of Hes1. Analysis in human breast cancer datasets found the lowest HES1 and second lowest LFNG expressions in CLBC among molecular subtypes, and low level of LFNG is associated with poor survival. Immunostaining of human breast cancer tissue array found correlation between survival and LFNG immunoreactivity. Finally, patients carrying TP53 mutations express lower LFNG than patients with wild type TP53. Taken together, these data revealed genetic interaction between Lfng and p53 in mammary tumorigenesis, established a new mouse model resembling CLBC, and may suggest targeting strategy for this disease.

Background Major Depressive Disorder (MDD) is a common psychiatric disease for which available medications are often not effective. Full remission from depression is achieved by less than 50 percent of patients using medications that mainly target serotonin or norepinephrine systems (Berton and Nestler, 2006; Rush et al., 2006). The economic burden of depression in the U.S., along with comorbid conditions, is estimated at over $170B and depressive disorders are the leading contributors to global burden of disease (Greenberg et al., 2015; Whiteford et al., 2013). The high prevalence of MDD and modest response to existing therapies compels efforts to better understand and treat the disorder. One promising avenue of research suggests that decreases in hippocampal volume with increasing duration of depression results from a decrease in neurogenesis or altered gene expression (Sheline et al., 1996, Cobb et al., 2013). Methods Tissue punches from the dentate gyrus were collected from 23 subjects (MDD, medication-free) and 23 demographically-matched normal controls. Of the 23 subjects with MDD, 17 died by suicide and 17 had multiple depressive episodes. High quality total RNA, RNA Quality Index > 6, was isolated and whole transcriptome paired-end shotgun sequencing was performed using an Illumina NextSeq. 500. For each sample, raw RNA-seq reads (adapter-trimmed fastq files) were aligned to the Ensembl GRCh38 human reference genome using GSNAP (Genomic Short-read-Nucleotide Alignment Program). Differential gene expression was determined using cuffdiff, and core biological processes, molecular networks, and pathways pathologically disrupted in MDD were identified using Ingenuity Pathway Analysis. Results For each sample, 37 to 112 million reads were obtained and 64 to 96% were mapped successfully to the human genome, with most samples mapping above 85%. ‘Cuffdiff’ analysis in the Tuxedo suite revealed 30 significant genes differentially expressed in all MDD compared to controls (Lumenogix™, FDR Discussion The key finding in the primary MDD dataset as well as in the subsets is the overrepresentation of neuroinflammation related genes. Inflammatory and neurogenesis-related (ERK/MAPK) signaling pathways were significantly altered in the hippocampal dentate gyrus in MDD, with cytokine signaling and inflammatory pathways preferentially altered in MDD-suicide vs. MDD-non-suicide. Together this suggests that neuroinflammation, mediated by microglia and astrocytes may play a crucial role in major depressive disorder. These findings suggest a novel approach by seeking targets for new treatment of MDD that includes anti-inflammatory and neuroprotective properties.

Microsatellites occur in all plant genomes and provide useful markers for studies of genetic diversity and structure. Chloroplast microsatellites (cpSSRs) are frequently targeted because they are more easily isolated than nuclear microsatellites. Here, we quantified the frequency and uses of cpSSRs based on a literature review of over 400 studies published 1995–2013. These markers are an important and economical tool for plant biologists and continue to be used alongside modern genomics approaches to study genetic diversity and structure, evolutionary history, and hybridization in native and agricultural species. Studies using species-specific primers reported a greater number of polymorphic loci than those employing universal primers. A major disadvantage to cpSSRs is fragment size homoplasy; therefore, we documented its occurrence at several cpSSR loci within and between species of Acmispon (Fabaceae). Based on our empirical data set, we recommend targeted sequencing of a subset of samples combined with fragment genotyping as a cost-efficient, data-rich approach to the use of cpSSRs and as a test of homoplasy. The availability of genomic resources for plants aids in the development of primers for new study systems, thereby enhancing the utility of cpSSRs across plant biology.