High fat diet reveals sex-specific fecal and liver metabolic alterations in C57BL/6J obese mice.

Obesity is a major health concern that poses significant risks for many other diseases, including diabetes, cardiovascular disease, and cancer. Prevalence of these diseases varies by biological sex. This study utilizes a mouse (C57BL/6J) model of obesity to analyze liver and fecal metabolic profiles at various time points of dietary exposure: 5, 9, and 12 months in control or high fat diet (HFD)-exposed mice. Our study discovered that the female HFD group has a more discernable perturbation and set of significant changes in metabolic profiles than the male HFD group. In the female mice, HFD fecal metabolites including pyruvate, aspartate, and glutamate were lower than control diet-exposed mice after both 9th and 12th month exposure time points, while lactate and alanine were significantly downregulated only at the 12th month. Perturbations of liver metabolic profiles were observed in both male and female HFD groups, compared to controls at the 12th month. Overall, the female HFD group showed higher lactate and glutathione levels compared to controls, while the male HFD group showed higher levels of glutamine and taurine compared to controls. These metabolite-based findings in both fecal and liver samples for a diet-induced effect of obesity may help guide future pioneering discoveries relating to the analysis and prevention of obesity in people, especially for females.

Diepoxybutane induces the p53-dependent transactivation of the CCL4 gene that mediates apoptosis in exposed human lymphoblasts.

Diepoxybutane (DEB) is the most toxic metabolite of the environmental chemical 1,3-butadiene. We previously demonstrated the occurrence of DEB-induced p53-mediated apoptosis in human lymphoblasts. The p53 protein functions as a master transcriptional regulator in orchestrating the genomic response to a variety of stress signals. Transcriptomic analysis indicated that C-C chemokine ligand 4 (CCL4) gene expression was elevated in a p53-dependent manner in DEB-exposed p53-proficient TK6 cells, but not in DEB-exposed p53-deficient NH32 cells. Thus, the objective of this study was to determine whether the CCL4 gene is a transcriptional target of p53 and deduce its role in DEB-induced apoptosis in human lymphoblasts. Endogenous and exogenous wild-type p53 transactivated the activity of the CCL4 promoter in DEB-exposed lymphoblasts, but mutant p53 activity on this promoter was reduced by ∼80% under the same experimental conditions. Knockdown of the upregulated CCL4 mRNA levels in p53-proficient TK6 cells inhibited DEB-induced apoptosis by ∼45%-50%. Collectively, these observations demonstrate for the first time that the CCL4 gene is upregulated by wild-type p53 at the transcriptional level, and this upregulation mediates apoptosis in DEB-exposed human lymphoblasts.

Diepoxybutane induces the expression of a novel p53-target gene XCL1 that mediates apoptosis in exposed human lymphoblasts.

Diepoxybutane (DEB) is the most potent active metabolite of the environmental chemical 1,3-butadiene (BD). BD is a human carcinogen that exhibits multiorgan systems toxicity. Our previous studies demonstrated that the X-C motif chemokine ligand 1 (XCL1) gene expression was upregulated 3.3-fold in a p53-dependent manner in TK6 lymphoblasts undergoing DEB-induced apoptosis. The tumor-suppressor p53 protein is a transcription factor that regulates a wide variety of cellular processes, including apoptosis, through its various target genes. Thus, the objective of this study was to determine whether XCL1 is a novel direct p53 transcriptional target gene and deduce its role in DEB-induced toxicity in human lymphoblasts. We utilized the bioinformatics tool p53scan to search for known p53 consensus sequences within the XCL1 promoter region. The XCL1 gene promoter region was found to contain the p53 consensus sequences 5'-AGACATGCCTAGACATGCCT-3' at three positions relative to the transcription start site (TSS). Furthermore, the XCL1 promoter region was found, through reporter gene assays, to be transactivated at least threefold by wild-type p53 promoter in DEB-exposed human lymphoblasts. Inactivation of the XCL1 promoter p53-binding motif located at -2.579 kb relative to TSS reduced the transactivation function of p53 on this promoter in DEB-exposed cells by 97%. Finally, knockdown of XCL1 messenger RNA with specific small interfering RNA inhibited DEB-induced apoptosis in human lymphoblasts by 50%. These observations demonstrate, for the first time, that XCL1 is a novel DEB-induced direct p53 transcriptional target gene that mediates apoptosis in DEB-exposed human lymphoblasts.

Microbial community dynamics during anaerobic co-digestion of corn stover and swine manure at different solid content, carbon to nitrogen ratio and effluent volumetric percentages.

The methane production and the microbial community dynamics of thermophilic anaerobic co-digestion (AD) of corn stover, swine manure and effluent were conducted at total solid (TS) content of 5%, 10% and 15%, the carbon to nitrogen ratio (C/N) of 20, 30 and 40 and the effluent volumetric percentage (EVP) of 20%, 40% and 60%. For batches with 5% TS, the highest methane yield of 238.5-283.1 mL g-1 volatile solid (VS) and the specific methane productivity of 138.5-152.2 mL g-1 initial VS were obtained at the C/N ratios of 20 and 30. For the mixtures with 10% and 15% TS, the highest methane yield was 341.9 mL g-1 VS and 351.2 mL g-1 VS, respectively, when the C/N ratio of 20% and 60% EVP conditions were maintained. Co-digestion of swine manure with corn stover caused an obvious shift in microbial population, in which the archaeal population changed from 0.3% to 2.8% and the bacterial community changed from 97.2% to 99.7%. The experimental batches with the highest relative abundance of the archaeal population (2.00% of total microbial population for 5% TS, 1.74% for 10% TS and 2.76% for 15% TS) had the highest rate of methanogenesis subsequently enhancing methane production (283.08 mL g-1 VS for 5% TS, 341.91 mL g-1 VS for 10% TS and 351.23 mL g-1 VS for 15% TS). The results of microbiome analysis enabled understanding the key populations in biomethane generation.

The identification of risk factors associated with patient and healthcare system delays in the treatment of tuberculosis in Tabriz, Iran.

BACKGROUND: Tuberculosis (TB) is a serious health concern, particularly in developing countries. Various delays, such as patient delay (PD) and healthcare system delay (HSD) in the TB process, are exacerbating the disease burden and increasing the rates of transmission and mortality in various global communities. Therefore, the aim of this study is to identify risk factors associated with PD and HSD in TB patients in Tabriz, Iran. METHODS: A cross-sectional study was conducted on 173 TB patients in Tabriz, Iran from 2012 to 2014. Patients were interviewed with a semi-structured questionnaire. Frequencies and percentages were reported for patient categories of sex, age, and education. The median and interquartile range (IQR) were reported for the time intervals of delays. Univariate and multivariate logistic regressions of delay in respect to socio-demographic and clinical variables were performed. Statistical significance was set at p < 0.05. RESULTS: The median values for delays were 53 days for HSD (IQR = 73) and 13 days for PD (IQR = 57). Odds ratios (OR) associated with PD were: employed vs. unemployed (OR = 5.86, 95% CI: 1.59 to 21.64); public hospitals vs. private hospitals (OR = 2.64, 95% CI: 1.01 to 6.85); ≥ 3 vs. < 3 visits to health facilities before correct diagnosis (OR = 2.35, 95% CI: 1.08 to 5.11); and male vs. female (OR = 2.28, 95% CI: 1.29 to 4.39). The OR associated with HSD were: ≥ 3 vs. < 3 visits to health facilities before correct diagnosis (OR = 9.44, 95% CI: 4.50 to 19.82), without vs. with access to TB diagnostic services (OR = 3.56, 95% CI: 1.85 to 6.83), and misdiagnosis as cold or viral infection vs. not (OR = 2.62, 95% CI: 1.40 to 4.91). CONCLUSIONS: The results provide for an important understanding of the risk factors associated with PD and HSD. One of the major recommendations is to provide more TB diagnostic knowledge and tools to primary health providers and correct diagnoses for patients during their initial visit to the health care facilities. The knowledge generated from this study will be helpful for prioritizing and developing strategies for minimizing delays, initiating early treatment to TB patients, and improving TB-related training programs and healthcare systems in Tabriz, Iran.

EVALUATION OF HUSBANDRY AND MORTALITY IN LESSER HEDGEHOG TENRECS (ECHINOPS TELFAIRI).

Causes of morbidity and mortality for various species of tenrecs have not been widely published, aside from several reports of neoplasia, and these data are crucial for advancing objectives for preventive medicine, diagnosis, and treatment. A survey on husbandry, morbidity, and mortality of lesser hedgehog tenrecs ( Echinops telfairi ) in Association of Zoos and Aquariums (AZA) institutions was conducted. Out of 32 institutions, 20 responded with data for 98 living and 93 dead animals. The most common causes of mortality among the dead animals were neoplasia (24%), hepatic lipidosis (11%), septicemia (8.6%), pneumonia (8.6%), cardiomyopathy (7.5%), renal disease (6.5%), osteomyelitis (3.2%), and trauma (3.2%). There was no statistically significant correlation between sex and neoplasia. Data about educational usage were specifically provided by survey respondents for 50 of the tenrecs, with only 42% being excluded from educational programming. Tenrecs are common to many AZA institutions as both educational and exhibit animals, and this study provides a helpful reference for expected health problems and highlights the need for future investments into medical diagnosis and treatment for these animals.

Humoral response to calicivirus in captive tigers given a dual-strain vaccine.

The current feline vaccine with a single strain of calicivirus has been used for captive tigers, yet it may not protect against virulent systemic calicivirus infections. A cross-institutional study investigated the humoral response to a new dual-strain, killed-virus calicivirus vaccine for nine captive tigers. The subspecies of these tigers were Amur (Panthera tigris altaica), Bengal (Panthera tigris tigris), and Malayan (Panthera tigris jacksoni). Serum neutralization titers for virulent feline calicivirus strain FCV-DD1 were higher following dual-strain vaccine administration. There were no reports of adverse vaccine reactions. Dual-strain vaccination may afford broadened cross-protection against different calicivirus strains and is desirable to reduce the risk of virulent systemic calicivirus disease in tigers.

Retrospective Study of the Prevalence, Histopathology, Therapy, and Survival Time of Neoplastic Disease in Fish.

This study evaluated neoplasia in fish using medical records from zoos, aquariums, and exotic animal veterinarians. The parameters evaluated included geographic location, habitat type, signalment, anatomic location of neoplasia, type of neoplasia as confirmed with histologic examination, survival time, and treatments provided for each patient. These data were entered into the Exotic Species Cancer Research Alliance (ESCRA) database. Out of 455 cases from across the United States and England, most animals submitted were from zoologic parks or aquariums (62.9%), followed by private ownership (1.5%). The percent of female (19.3%) and male (17.8%) patients were similar, and the mean age at the time of diagnosis was 99.45 months, with a range of 12 to 300 months. The species with the highest neoplasia prevalence was koi (18.5%), followed by goldfish (10.8%). The eye was the most commonly reported site for a primary neoplasm (8.4%), and the most prevalent diagnosis across all organ systems was soft tissue sarcoma (26.2%). Only 13 patients in this study (2.9%) received any form of treatment, with a mean survival time of 8.85 months post-treatment. These data demonstrate that while information related to clinical therapy of cancer in fish species is lacking, surgical excision of tumors in fish, when feasible for the patient and client, may improve patient outcomes.

Evaluation of Neoplasia, Treatments, and Survival in Lizard Species.

Neoplasia has been reported in lizards, but more research is needed to accurately document the prevalence and prognosis of the various known neoplasms that affect lizards. This study reviewed medical records from an online database, the Exotic Species Cancer Research Alliance (ESCRA), and reviewed published literature to determine the prevalence of neoplasia, malignancy, metastasis, treatment strategies, and outcomes by species and sex. Records from 55 individual lizards, 20 different species, and 37 different tumors were identified. In the literature, 219 lizards, 59 species, and 86 unique tumors were identified from 72 published case reports. Potential signalment factors such as age, sex, and species were evaluated to see if they affected case outcome. Additional factors including neoplasia type, presence of metastasis, and types of pursued treatments were also evaluated. Statistical analysis was performed to determine whether a factor was significantly associated with animal death due to the identified neoplasia or with animal survival or death due to other causes (non-neoplastic outcomes). Komodo dragons and savannah monitors were more likely to die from neoplasia compared to other lizard species. Cases where the status of metastasis was unknown were significantly associated with death due to neoplasia. Having an unknown status of male versus female was significantly associated with non-neoplastic outcomes of death. Leukemia and islet cell carcinoma were significantly associated with death due to neoplastic causes. Chondrosarcoma, myxosarcoma, osteosarcoma, and squamous cell carcinoma were significantly associated with non-neoplastic outcomes of death. Surgery alone and radiation therapy alone each were significantly associated with non-neoplastic outcomes of death, while lizards not receiving treatment were significantly associated with death due to neoplasia. Benign neoplasia was significantly associated with non-neoplastic outcomes of death. These results will aid in the improved diagnosis and management of neoplasia in lizard species, as well as expanding our understanding of prognostic indicators of neoplasia in lizards.

Connecting gut microbiomes and short chain fatty acids with the serotonergic system and behavior in Gallus gallus and other avian species.

The chicken gastrointestinal tract has a diverse microbial community. There is increasing evidence for how this gut microbiome affects specific molecular pathways and the overall physiology, nervous system and behavior of the chicken host organism due to a growing number of studies investigating conditions such as host diet, antibiotics, probiotics, and germ-free and germ-reduced models. Systems-level investigations have revealed a network of microbiome-related interactions between the gut and state of health and behavior in chickens and other animals. While some microbial symbionts are crucial for maintaining stability and normal host physiology, there can also be dysbiosis, disruptions to nutrient flow, and other outcomes of dysregulation and disease. Likewise, alteration of the gut microbiome is found for chickens exhibiting differences in feather pecking (FP) behavior and this alteration is suspected to be responsible for behavioral change. In chickens and other organisms, serotonin is a chief neuromodulator that links gut microbes to the host brain as microbes modulate the serotonin secreted by the host's own intestinal enterochromaffin cells which can stimulate the central nervous system via the vagus nerve. A substantial part of the serotonergic network is conserved across birds and mammals. Broader investigations of multiple species and subsequent cross-comparisons may help to explore general functionality of this ancient system and its increasingly apparent central role in the gut-brain axis of vertebrates. Dysfunctional behavioral phenotypes from the serotonergic system moreover occur in both birds and mammals with, for example, FP in chickens and depression in humans. Recent studies of the intestine as a major site of serotonin synthesis have been identifying routes by which gut microbial metabolites regulate the chicken serotonergic system. This review in particular highlights the influence of gut microbial metabolite short chain fatty acids (SCFAs) on the serotonergic system. The role of SCFAs in physiological and brain disorders may be considerable because of their ability to cross intestinal as well as the blood-brain barriers, leading to influences on the serotonergic system via binding to receptors and epigenetic modulations. Examinations of these mechanisms may translate into a more general understanding of serotonergic system development within chickens and other avians.

The Association of Toxoplasma gondii IgG and Liver Injury in US Adults.

BACKGROUND: Toxoplasma gondii (T. gondii) is a ubiquitous obligatory intracellular parasite which infects over 40 million Americans and causes toxoplasmosis. Inside the human body, T. gondii can damage tissues and invade vital organs. METHODS: This study evaluated the association of T. gondii infection and liver disease using data from the National Health and Nutrition Examination Survey (NHANES) 2009-2010, with a sample size of 3371 participants (age 20-80 years). Toxoplasma infection was determined by the level of T. gondii IgG antibody in serum samples. Liver disease was assessed by liver injury biomarkers and the Fatty Liver Index (US-FLI). The evaluation of the association between T. gondii infection and liver disease included the calculation of the Mantel-Haenszel risk ratio (RRMH), Rho-Scott chi-square bivariate analyses, design-based t-tests, and linear and logistic regression models which were adjusted for demographic and anthropometric covariates. RESULTS: Mean levels of aspartate aminotransferase (AST) and alkaline phosphatase (ALP) were significantly more elevated in the T. gondii IgG-positive (IgG+) participants as compared to T. gondii-negative (IgG-) participants, p = 0.0435 and 0.0310, respectively. In linear regression analysis, exposure to T. gondii IgG+ had statistically significant positive associations with AST (p = 0.0211), alanine aminotransferase (ALT) (p = 0.0221), and gamma-glutamyl transferase (GGT) (p = 0.0258) after adjusting for BMI, age, gender, and race. T. gondii exposure was associated with an elevated relative risk of chronic liver disease (CLD) (RRMH = 1.26, 95% CI: 1.05-1.51). This association was more pronounced in certain occupations, such as construction, agriculture, forestry, and fishing, where Toxoplasma infection is more common (p = 0.0477). Moreover, Toxoplasma infection increased the odds of nonalcoholic fatty liver disease (NAFLD) (OR = 6.99, 95% CI = 1.85-26.32, p = 0.0237). CONCLUSION: T. gondii IgG+ antibody was significantly associated with liver injury biomarkers (ALT, AST, GGT, and ALP) and an increased risk of CLD and NAFLD. Moreover, the association of Toxoplasma with CLD was more evident in specific occupations where the prevalence of Toxoplasma was high. The findings of this study provide insight into utilizing liver biomarkers and US-FLI to assess the health complications of Toxoplasma when imaging tests are not accessible.

Experimental Evolution of Copper Resistance in Escherichia coli Produces Evolutionary Trade-Offs in the Antibiotics Chloramphenicol, Bacitracin, and Sulfonamide.

The rise in antimicrobial resistant bacteria have prompted the need for antibiotic alternatives. To address this problem, significant attention has been given to the antimicrobial use and novel applications of copper. As novel applications of antimicrobial copper increase, it is important to investigate how bacteria may adapt to copper over time. Here, we used experimental evolution with re-sequencing (EER-seq) and RNA-sequencing to study the evolution of copper resistance in Escherichia coli. Subsequently, we tested whether copper resistance led to rifampicin, chloramphenicol, bacitracin, and/or sulfonamide resistance. Our results demonstrate that E. coli is capable of rapidly evolving resistance to CuSO4 after 37 days of selection. We also identified multiple de novo mutations and differential gene expression patterns associated with copper, most notably those mutations identified in the cpx gene. Furthermore, we found that the copper resistant bacteria had decreased sensitivity when compared to the ancestors in the presence of chloramphenicol, bacitracin, and sulfonamide. Our data suggest that the selection of copper resistance may inhibit growth in the antimicrobials tested, resulting in evolutionary trade-offs. The results of our study may have important implications as we consider the antimicrobial use of copper and how bacteria may respond to increased use over time.

A Multi-Institutional Collaboration to Understand Neoplasia, Treatment and Survival of Snakes.

This multi-institutional collaborative study of neoplasia in snakes reviewed medical records of snakes at each facility to determine species prevalence, survival, and methods of treatment. Complete species numbers of snakes were also collected at each facility. In total, 65 species, 133 snakes, and 149 unique neoplasias were included in this study. Affected species, age, sex, and their tumor prevalence, tumor type and location, metastasis, treatment, and survival data are reported. The highest species-specific tumor prevalence was in Common or Northern Watersnakes (Nerodia sipedon) (30.8%, n = 4 of 13), Eastern Diamond-Backed Rattlesnakes (Crotalus adamanteus) (26.3%, n = 5 of 19), and Timber rattlesnakes (Crotalus horridus) (22.7%, n = 5 of 22). Malignant tumors predominated (86.6%, n = 129 of 149) with soft tissue sarcomas being the most common (30.2%, n = 45 of 149). Snakes with malignant neoplasia, metastases, or indeterminate presence of metastases were statistically more likely to die from their neoplasms than snakes having either benign neoplasia or no diagnosed metastases (p < 0.05). Gender, taxonomic family, and species of those evaluated did not significantly affect the outcome of snakes with neoplasia. Only 27.1% (n = 36 of 133) of snakes received a reported form of treatment and, for those treated, surgical excision was the most common treatment modality. There was not a significant difference in outcome based on treatment; however, surgery and chemotherapy were associated with death from a cause other than their tumor.

Model-based reasoning: using visual tools to reveal student learning.

Using visual models is common in science and should become more common in classrooms. Our research group has developed and completed studies on the use of a visual modeling tool, the Concept Connector. This modeling tool consists of an online concept mapping Java applet that has automatic scoring functions we refer to as Robograder. The Concept Connector enables students in large introductory science courses to visualize their thinking through online model building. The Concept Connector's flexible scoring system, based on tested grading schemes as well as instructor input, has enabled >1,000 physiology students to build maps of their ideas about plant and animal physiology with the guidance of automatic and immediate online scoring of homework. Criterion concept maps developed by instructors in this project contain numerous expert-generated or "correct" propositions connecting two concept words together with a linking phrase. In this study, holistic algorithms were used to test automated methods of scoring concept maps that might work as well as a human grader.

Too much of a good thing: Adaption to iron (II) intoxication in Escherichia coli.

BACKGROUND: There has been an increased usage of metallic antimicrobial materials to control pathogenic and multi-drug resistant bacteria. Yet, there is a corresponding need to know if this usage leads to genetic adaptations that could produce more harmful strains. METHODOLOGY: Experimental evolution was used to adapt Escherichia coli K-12 MG1655 to excess iron (II) with subsequent genomic analysis. Phenotypic assays and gene expression studies were conducted to demonstrate pleiotropic effects associated with this adaptation and to elucidate potential cellular responses. RESULTS: After 200 days of adaptation, populations cultured in excess iron (II), showed a significant increase in 24-h optical densities compared to controls. Furthermore, these populations showed increased resistance toward other metals [iron (III) and gallium (III)] and to traditional antibiotics (bacitracin, rifampin, chloramphenicol and sulfanilamide). Genomic analysis identified selective sweeps in three genes; fecA, ptsP and ilvG unique to the iron (II) resistant populations, and gene expression studies demonstrated that their cellular response may be to downregulate genes involved in iron transport (cirA and fecA) while increasing the oxidative stress response (oxyR, soxS and soxR) prior to FeSO4 exposure. CONCLUSIONS AND IMPLICATIONS: Together, this indicates that the selected populations can quickly adapt to stressful levels of iron (II). This study is unique in that it demonstrates that E. coli can adapt to environments that contain excess levels of an essential micronutrient while also demonstrating the genomic foundations of the response and the pleiotropic consequences. The fact that adaptation to excess iron also causes increases in general antibiotic resistance is a serious concern. Lay summary: The evolution of iron resistance in E. coli leads to multi-drug and general metal resistance through the acquisition of mutations in three genes (fecA, ptsP and ilvG) while also initiating cellular defenses as part of their normal growth process.

Dissecting the human plasma proteome and inflammatory response biomarkers.

A central focus of clinical proteomics is to search for biomarkers in plasma for diagnostic and therapeutic use. We studied a set of plasma proteins accessed from the Healthy Human Individual's Integrated Plasma Proteome (HIP(2)) database, a larger set of curated human proteins, and a subset of inflammatory proteins, for overlap with sets of known protein biomarkers, drug targets, and secreted proteins. Most inflammatory proteins were found to occur in plasma, and over three times the level of biomarkers were found in inflammatory plasma proteins and their interacting protein neighbors compared to the sets of plasma and curated human proteins. Percentage overlaps with Gene Ontology terms were similar between the curated human set and plasma protein set, yet the set of inflammatory plasma proteins had a distinct ontology-based profile. Most of the major hub proteins within protein-protein interaction networks of tissue-specific sets of inflammatory proteins were found to occur in disease pathways. The present study presents a systematic approach for profiling a plasma subproteome's relationship to both its potential range of clinical application and its overlap with complex disease.

Inflammation and Kidney Injury in Diabetic African American Men.

African Americans are disproportionately burdened by diabetic kidney disease (DKD). However, little is known about the cellular and molecular mechanisms underlying the onset and progression of DKD in this population. The goal of the current study was to determine the association between specific inflammation markers and kidney injury in diabetic African American men. To this end, we recruited diabetic patients either with (n = 20) or without (n = 87) diagnosed kidney disease along with age-matched nondiabetic controls (n = 81). Urinary albumin-to-creatinine ratios (UACRs) and estimated glomerular filtration rates (eGFR) were used for biochemical assessment of kidney function. We then measured plasma and urinary levels of seven inflammatory markers, including adiponectin, C-reactive protein (CRP), tumor necrosis factor-α (TNF-α), TNF receptor 1 (TNFR1), TNF receptor 2 (TNFR2), interleukin-6 (IL-6), and intercellular cell adhesion molecule-1 (ICAM-1). Plasma levels of TNF-α, TNFR1, and TNFR2 were significantly higher in diabetics with macroalbuminuria compared to nondiabetic controls and diabetics with normoalbuminuria or microalbuminuria. Likewise, urinary levels of ICAM-1 were higher in diabetics with macroalbuminuria compared to the other groups. Indeed, urinary ICAM-1, plasma TNF-α, and adiponectin had moderate positive correlations with UACR while plasma TNFR1 and TNFR2 levels were strongly correlated with kidney injury, indicated by multiple biomarkers of kidney injury. In contrast, though plasma CRP was elevated in diabetic subjects relative to nondiabetic controls, its levels did not correlate with kidney injury. Together, these data suggest that inflammation, particularly that mediated by the TNF-α/NF-κB signaling axis, may play a role in the pathogenesis of DKD in African American men.

Experimental evolution of gallium resistance in Escherichia coli.

BACKGROUND AND OBJECTIVES: Metallic antimicrobial materials are of growing interest due to their potential to control pathogenic and multidrug-resistant bacteria. Yet we do not know if utilizing these materials can lead to genetic adaptations that produce even more dangerous bacterial varieties. METHODOLOGY: Here we utilize experimental evolution to produce strains of Escherichia coli K-12 MG1655 resistant to, the iron analog, gallium nitrate (Ga(NO3)3). Whole genome sequencing was utilized to determine genomic changes associated with gallium resistance. Computational modeling was utilized to propose potential molecular mechanisms of resistance. RESULTS: By day 10 of evolution, increased gallium resistance was evident in populations cultured in medium containing a sublethal concentration of gallium. Furthermore, these populations showed increased resistance to ionic silver and iron (III), but not iron (II) and no increase in traditional antibiotic resistance compared with controls and the ancestral strain. In contrast, the control populations showed increased resistance to rifampicin relative to the gallium-resistant and ancestral population. Genomic analysis identified hard selective sweeps of mutations in several genes in the gallium (III)-resistant lines including: fecA (iron citrate outer membrane transporter), insl1 (IS30 tranposase) one intergenic mutations arsC →/→ yhiS; (arsenate reductase/pseudogene) and in one pseudogene yedN ←; (iapH/yopM family). Two additional significant intergenic polymorphisms were found at frequencies > 0.500 in fepD ←/→ entS (iron-enterobactin transporter subunit/enterobactin exporter, iron-regulated) and yfgF ←/→ yfgG (cyclic-di-GMP phosphodiesterase, anaerobic/uncharacterized protein). The control populations displayed mutations in the rpoB gene, a gene associated with rifampicin resistance. CONCLUSIONS: This study corroborates recent results observed in experiments utilizing pathogenic Pseudomonas strains that also showed that Gram-negative bacteria can rapidly evolve resistance to an atom that mimics an essential micronutrient and shows the pleiotropic consequences associated with this adaptation. LAY SUMMARY: We utilize experimental evolution to produce strains of Escherichia coli K-12 MG1655 resistant to, the iron analog, gallium nitrate (Ga(NO3)3). Whole genome sequencing was utilized to determine genomic changes associated with gallium resistance. Computational modeling was utilized to propose potential molecular mechanisms of resistance.

Integrating CRISPR-Cas9 Technology into Undergraduate Courses: Perspectives from a National Science Foundation (NSF) Workshop for Undergraduate Faculty, June 2018.

As CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 technology becomes more mainstream in life science research, it becomes critical for undergraduate instructors to devise engaging ways to bring the technology into their classrooms. To help meet this challenge, the National Science Foundation sponsored a workshop for undergraduate instructors in June 2018 at The Ohio State University in conjunction with the annual Association of Biology Laboratory Educators meeting based on a workflow developed by the workshop's facilitators. Over the course of two and a half days, participants worked through a modular workflow for the use of CRISPR-Cas9 in a course-based (undergraduate) research experience (CURE) setting while discussing the barriers each of their institutions had to implementing such work, and how such barriers could be overcome. The result of the workshop was a team with newfound energy and confidence to implement CRISPR-Cas9 technology in their courses and the development of a community of undergraduate educators dedicated to supporting each other in the implementation of the workflow either in a CURE or modular format. In this article, we review the activities and discussions from the workshop that helped each participant devise their own tailored approaches of how best to bring this exciting new technology into their classes.

ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining.

BACKGROUND: New systems biology studies require researchers to understand how interplay among myriads of biomolecular entities is orchestrated in order to achieve high-level cellular and physiological functions. Many software tools have been developed in the past decade to help researchers visually navigate large networks of biomolecular interactions with built-in template-based query capabilities. To further advance researchers' ability to interrogate global physiological states of cells through multi-scale visual network explorations, new visualization software tools still need to be developed to empower the analysis. A robust visual data analysis platform driven by database management systems to perform bi-directional data processing-to-visualizations with declarative querying capabilities is needed. RESULTS: We developed ProteoLens as a JAVA-based visual analytic software tool for creating, annotating and exploring multi-scale biological networks. It supports direct database connectivity to either Oracle or PostgreSQL database tables/views, on which SQL statements using both Data Definition Languages (DDL) and Data Manipulation languages (DML) may be specified. The robust query languages embedded directly within the visualization software help users to bring their network data into a visualization context for annotation and exploration. ProteoLens supports graph/network represented data in standard Graph Modeling Language (GML) formats, and this enables interoperation with a wide range of other visual layout tools. The architectural design of ProteoLens enables the de-coupling of complex network data visualization tasks into two distinct phases: 1) creating network data association rules, which are mapping rules between network node IDs or edge IDs and data attributes such as functional annotations, expression levels, scores, synonyms, descriptions etc; 2) applying network data association rules to build the network and perform the visual annotation of graph nodes and edges according to associated data values. We demonstrated the advantages of these new capabilities through three biological network visualization case studies: human disease association network, drug-target interaction network and protein-peptide mapping network. CONCLUSION: The architectural design of ProteoLens makes it suitable for bioinformatics expert data analysts who are experienced with relational database management to perform large-scale integrated network visual explorations. ProteoLens is a promising visual analytic platform that will facilitate knowledge discoveries in future network and systems biology studies.