Miracle-dz/UniFAR-FTUs huggingface dataset:
Intestinal vitamin D receptor protects mice from dysbiosis via modulating JAK/STAT pathway in tumorigenesis

Low vitamin D receptor (VDR) expression and diminished vitamin D/VDR signaling are observed in patients with colon cancer. We reported that intestinal epithelial VDR deletion (VDRΔIEC ) leads to dysbiosis and increases susceptibility to colitis. The JAK/STAT pathway plays a critical role in intestinal and microbial homeostasis. We hypothesized intestinal VDR protects mice from dysbiosis via modulating the JAK/STAT pathway in tumorigenesis. We used an azoxymethane/Dextran sulfate sodium ‐induced cancer model in VDRΔIEC mice. VDRΔIEC mice have higher tumor numbers with tumor location shifted from distal to proximal colon. Fecal microbiota analysis showed that lacking VDR leads to bacterial profile shift from normal to susceptible carcinogenesis. We found enhanced bacterial staining in mouse tumors. These data are consisted with our findings in human tumor sample. VDR deletion decreased Jak2 at protein and mRNA levels. By CHIP assay, we identified that VDR protein bound to the Jak2 promoter, suggesting that VDR transcriptionally regulated Jak2. JAK/STAT was the upstream of the proinflammatory NF‐kappa B pathway. Furthermore, IκBα expression was significantly decreased in VDRΔIEC tumors. Our observations suggest that absence of intestinal epithelial VDR leads to dysbiosis and susceptibility to colon cancer via reducing JAK/STAT signaling and dampening inflammatory responses. Our study provides new insight into the molecular mechanism of VDR regulating the JAK/STAT pathway in bacterial‐host interaction and tumorigenesis. Our studies also indicate a new target—microbiome and VDR signaling for prevention of colon cancer.
Metagenomic Analyses of Glacier Ice

The largest part of the Earth s microbial biomass is stored in cold environments, which represent almost untapped reservoirs of novel species, processes, and genes. In this study, the first metagenomic survey of the metabolic and phylogenetic diversity of a glacial microbial community was conducted. In addition, the so far unexplored habitat glacier ice was exploited with respect to novel genes encoding DNA-modifying enzymes. DNA was isolated from glacial ice of the Northern Schneeferner, Germany. The phylogenetic composition of the microbial community was assessed by evaluation of a pyrosequencing-derived dataset, sequencing of 16S rRNA genes, and cultivation. The Proteobacteria (mainly, Betaproteobacteria), Bacteroidetes, and Actinobacteria were the dominant phylogenetic groups. As expected for microorganisms living in a low-nutrient environment, a high metabolic versatility with respect to degradation of organic substrates was detected. The presence of autotrophic microorganisms was indicated by identification of genes typical for different ways of carbon fixation. In accordance with the results of the phylogenetic studies, in which mainly aerobic and facultative aerobic bacteria were detected, genes typical for central metabolism of aerobes were found. Nevertheless, the capability of growth under anaerobic conditions was indicated by genes involved in dissimilatory nitrate/nitrite reduction. Numerous characteristics for metabolic adaptations associated with a psychrophilic lifestyle, such as formation of cryoprotectants and maintenance of membrane fluidity by incorporation of unsaturated fatty acids, were detected. Metagenomic libraries were constructed from the isolated glacial DNA in plasmids and fosmids that harbor approximately 1.07 Gbp of DNA. The libraries were screened for DNA polymerase-encoding genes by complementation of an Escherichia coli polA mutant. Nine novel genes encoding complete DNA polymerases I or typical domains of these proteins were recovered by employing this rapid screening approach. Although polA genes are highly conserved, the identified putative DNA polymerases displayed low sequence identities to known polymerases. This indicated that libraries derived from a permanently frozen habitat are a rich resource for the discovery of genes that originate from uncharacterized organisms. Furthermore, the phylogenetic and metabolic analysis of the glacial metagenome provided insight into microbial live in frozen habitats on Earth, thereby possibly shedding light onto microbial life in analogous extraterrestrial environments.
Aquaporins in Magnaporthe oryzae

The Ascomycete fungus Magnaporthe oryzae is the causative agent of Rice Blast, and has become the predominant model organism for study of fungal phytopathogens and other appressorium-forming fungi. I identified and attempted to elucidate the function of the six aquaporin genes in the M. oryzae genome. These small membrane channels have been implicated in the transport of water, glycerol, and a variety of other small molecules. We speculated that these functions might be important in the formation of the appressorium – a specialised infection structure that relies on the generation of turgor. The role of these proteins in general fungal biology is poorly understood, and this project endeavoured to correct this gap. A phylogenetic analysis of aquaporins in extant fungi revealed the significant expansion of this gene family in Pezizomycete and Basidiomycete fungi, with up to 17 genes in some species. I characterised the expression pattern of the six identified aquaporins in the M. oryzae genome during pathogenic development and found there to be substantial up-regulation co-incident with appressorial turgor generation. Single knock-outs of each aquaporin gene were fully pathogenic, with normal infection-related development and axenic growth. I speculated that the absence of a strong phenotype may have been caused by functional redundancy, and used qRT-PCR investigate the incidence of transcriptional up-regulation of remaining family members in the knock-out backgrounds. This uncovered a putative reciprocal relationship between two genes MoAQP1 and MoAQP2 , suggesting that deletion of one results in up-regulation of the other. I subsequently tested the substrate permeability of this gene pair and found them to be permeable to hydrogen peroxide. However, deletion of one of these genes did not appear to affect the rate of flux of hydrogen peroxide across the plasma membrane. My attempt to characterise the cellular localisation of these proteins using GFP fusions was largely unsuccessful with the exception of a single gene, MoAGP2 , which appears to be located on the endoplasmic reticulum.
Effect of seed scarification, rhizobium inoculation and phosphorus fertilization on root development of barseem and soil composition.

Barseem (Trifolium alexandrinum L.) is a common rabi grown legume fodder crop that fits well in the farming system at the irrigated lands in Pakistan. Variation in per acre productivity could be attributed to varietals differences and variation in agronomic practices. The current experiment was designed to assess the effect of seed scarification, phosphorus fertilization and rhizobium inoculation on post-harvest soil nitrogen and root development of barseem. The five treatments viz; (A) control, (B) scarified seeds, (C) P-fertilization, (D) Rhizobium inoculation and (E) Rhizobium inoculation + P-fertilization were applied in a Complete Randomized Block Design using three replicates per treatment. Plant height remained the same during the first three and fifth cuts, however, significant (P < 0.05) differences were observed during the fourth cut of barseem. Treatment C and E yielded the maximum height followed by treatment D, A and B. Mean plant height during the successive cuts were 30.1, 47.1, 52.1, 56.7, and 54.3 cm, respectively. Pre-trial soil nitrogen content was 0.12%, which apparently did not change in response to any treatment. Mean soil-N after the last cutting of barseem was 0.068% across the five treatments. Post-harvest phosphorus content in the soil increased in plots, which were fertilized with phosphorus. The low mean phosphorus content in the fodder (0.21 %) may be attributed to the low pre-trial soil phosphorus concentration (71 mg kg). Phosphorus application and rhizobium inoculation in isolation or in combination tended to enhance root development i.e., root length, number of nodules and root hairs per plant in the present study but due to large variation between the replicates with in the treatment the effect on root development was statistically insignificant. The average number of nodules per plant (138) in the present study was markedly higher than the maximum number (71) reported in literature. Phosphorus fertilization in isolation or in combination with rhizobium inoculation enhanced phosphorus reserves of the soil and strengthened the root vigour to support more yielding cuts.
InsP3 and ryanodine receptors and capacitative Ca2+ entry in canine pulmonary arterial myocytes

Our recent studies show that canine pulmonary arterial smooth muscle cells (cPASMCs) have independent InsP3 and ryanodine (RY) sensitive Ca2+ stores, that capacitative Ca2+ entry (CCE) is activated only with depletion of both Ca2+ stores, that CCE is important to hypoxia induced Ca2+ release and contractility and that cPASMCs express mRNA encoding transient receptor potential channels TRPC4, 6 and 7. TRPC4 is a likely candidate for CCE, with channel opening coupled to InsP3 receptor (InsP3R) activation. Thus, we tested the hypothesis that CCE in cPASMCs is dependent on InsP3R opening by imaging Fura‐2 loaded cells. InsP3 and RY Ca2+ store depletion raised [Ca2+]i 59±11 nM n=28 above basal levels (i.e. CCE) in the presence of 10 μM cyclopiazonic acid and 10 μM RY. The InsP3R blockers XeC at 20 μM and 2APB at 50–75 μM inhibited 10 μM 5‐HT induced [Ca2+]i transients as well as CCE, where [Ca2+]i was 4±10 nM n=15 and 19±15 nM n=23 below baseline respectively. 300 μM RY, which alters RYR gating, did not reduce CCE, Ca2+ rose 51±20 nM n=8 above baseline. Mn2+ quench of fura‐2 confirmed this finding. SR Ca2+ store depletion increased the quench‐rate by 38% in the absence and 50% in the presence of 300 μM RY. In comparison, sustained 10 mM caffeine exposure, which inhibits InsP3Rs, inhibited 5‐HT induced [Ca2+]i transients (IC50 = 687 μM) as well as CCE where [Ca2+]i was 4±10 nM n=10 below basal values. These data illustrate that CCE in cPASMCs is contingent on InsP3R activation, which is linked to InsP3‐ as well as RY‐sensitive Ca2+ store depletion, but not RYR conformational changes. NIH HL49254, P20RR15518 from NCRR, HL10476, AI55462.
Informatics tools for the analysis and assignment of phosphorylation status in proteomics

Presently, progress in the field of phosphoproteomics has been accelerated by mass spectrometry. This is not a surprise owing to not only the accuracy, precision and high-throughput capabilities of MS but also due to the support it receives from informaticians whom allow the automated analysis; making the task of going from a complex sample to a statistically satisfactory set of phosphopeptides and corresponding site positions with relative ease. However, the process of identifying and subsequently pinpointing the phosphorylation moiety is not straightforward and remains a challenging task. Furthermore, it has been suggested that not all phosphorylation sites are of equal functional importance, to the extent that some may even lack function altogether. Clearly, such sites will confound the efforts towards functional characterisation. The work in this thesis is aimed at these two issues; accurate site localisation and functional annotation. To address the first issue, I adopt a multi-tool approach for identification and site localisation; utilising the different underlying algorithms of each tool and thereby allowing an orthogonal perspective on the same tandem mass spectra. Doing so enhanced accuracy over any single tool by itself. The power of this multi-tool approach stemmed from its ability to not predict more true positives but rather by removal of false positives. For the second issue, I first investigated the hypothesis that those of functional consequence exhibit stronger phosphorylation-characteristic features such as the degree of conservation and disorder. Indeed, it was found that some features were enriched for the functional group. More surprisingly, there were also some that were enriched for the less-functional; suggesting their incorporation into a prediction algorithm would hinder functional prediction. With this in mind, I train and optimise several machine-learning algorithms, using different combinations of features in an attempt to (separately) improve general phosphorylation and functional prediction.
Undergraduate Students’ Perceptions of Culturally Responsive Teaching And Their Sense of Belonging And Academic Self-Efficacy In Higher Education

To address the U.S. labor shortage in the fields of agriculture and STEM, higher education needs to recruit, retain, and prepare more underrepresented minority students into agricultural and STEM disciplines. Teachers play important roles in student learning, which can lead to student academic and professional success. With university classrooms becoming more diverse, faculty need to adopt inclusive teaching methods in order to accommodate the needs and expectations of diverse students. Culturally responsive teaching embraces and integrates students’ culture into the teaching and learning process. As a result, culturally responsive teaching can offer a more engaging learning experience for all students; however, in the context of higher education, there is a lack of understanding and application of culturally responsive teaching by faculty. This study examined students’ perceptions of culturally responsive teaching practices in their first college mathematics course through a developed and modified instrument for higher education. Further, this study used a structural equation model to predict the relationships among students’ perceptions of culturally responsive teaching, sense of belonging and academic self-efficacy. Data were collected through the anonymous questionnaire administrated through Qualtrics. Participants of this study were undergraduate students enrolled in the college of agriculture, college of science and college of liberal arts at a predominately white institution (PWI) and an Historically Black College and University (HBCU). Five conclusions were generated from the study. First, the scale developed to measure students’ perceptions of culturally responsive teaching in higher education was a valid instrument. Second, college students observed and sensed different types of culturally responsive teaching differently. Third, students’ perceptions of culturally responsive teaching predicted students’ academic self-efficacy and sense of belonging. Fourth, students who had a higher sense of belonging were more confident as college students. Finally, African American students at an HBCU had higher perceptions of culturally responsive teaching. Implications for practice were provided to help promote the application of culturally responsive teaching in higher education. Recommendations for future research were also discussed to inform future studies regarding culturally responsive teaching in university settings.
F-actin and integrin like proteins in Phytophthora cinnamomi

Tip growth is the primary form of growth in hyphal organisms and some plant cells. Tip growth in hyphae is highly dependent on F-actin, which acts to regulate and support. growth. One of the models suggested for tip growth, the amebae model of tip growth, suggests that F-actin may also be the primary source of protrusive force for tip growth in some conditions, and that proteins with a similar function to animal integrins would be present an involved in tip growth (Heath and Steinberg 1999). In this thesis we examine the role of F-actin in the growth of the oomycete Phytophthora cinnamomi and the effects on growth of the F-actin disrupting compound Latrunculin B. We demonstrate that F-actin plays a critical role in the tip growth of Phytophthora cinnamomi with it's disruption causing rapid cessation in directional growth, followed by significant subapical swelling. Further more we examine Phytophthora cinnamomi for the presence of an B4 integrin like protein that has been previously reported in the oomycete Achlya bisexualis (Chitcholtan & Garrill 2005) and show that the B4 integrin like protein is not present in Phytophthora cinnamomi. These experiments help further our understanding of tip growth in Phytophthora cinnamomi an economically important plant pathogen.
Microbiology : A Photographic Atlas for the Laboratory

1. Microscopes and Their Use in the Study of Cells and Viruses. 2. Microscopic Observation of Bacteria, Fungi, and Protozoa. 3. Staining Bacteria. 4. Cultivation of Bacteria and Fungi. 5. Biochemical Tests for the Identification of Bacteria. 6. Bacterial Identification Methods. 7. Evaluating Antibacterial Chemical Agents. 8. Soil and Water Microbiology. 9. Survey of Microbial Pathogens. 10. Arthropod Vectors of Human Diseases. 11. Multicellular Parasites. 12. Clinical Applications of Host Responses to Infection. Index.
Effects of Altered Superoxide Dismutase Expression on Age-related Functional Declines and Survival in Drosophila

s Martin, I. , Duttaroy, A. and Grotewiel, M.S., Graded reduction of manganese- superoxide dismutase causes a proportional acceleration of function aging. Drosophila Research Conference, Philadelphia, PA, March 2007. 209 Martin, I. and Grotewiel, M.S. The effects of superoxide dismutase overexpression on age-related functional declines in Drosophila melanogaster. Graduate Research Symposium, VCU, April 2006. Martin, I. , Warner-Gargano, J., Bhandari, P. and Grotewiel, M.S. Effect of genetic background and life span-extending mutations on locomotor activity senescence. Drosophila Research Conference, San Diego, CA, April 2005. Martin, I. , LaPrairie, J.L. and Lonstein, J.S. Effects of dopamine D1 and D2 receptor antagonists in the preoptic area on maternal behavior in lactating rats. Society for Neuroscience, San Diego, CA, October 2004. Grotewiel, M.S., Warner-Gargano, J., Bhandari, P. and Martin, I. Rapid iterative geotaxis (RIG), a new method for assessing locomotor behavior. Drosophila Research Conference, Washington DC, March 2004. Borisenko, G. , Martin, I. , Zhao, Q. , Jiang, J.F. and Kagan, V. Specific detection of GS• generated by peroxidase metabolism of phenolic compounds in live cells using acridine- tempo. Oxygen Society, San Antonio, TX, November 2002. Epperly, M.W. , Osipov, A.N. , Martin, I. , Kawai, K.K. , Borisenko, G.G. , Tyurina Y.Y. , Jefferson, M. , Bernarding, M. , Greenberger J.S. and Kagan, V.E. Ascorbate as a“redox- sensor” and protector against γ-irradiation-induced oxidative stress: EPR evidence in 32 D cl 3 and MnSOD-transfected 32D 2C6 cells. Radiation Research Society, Reno, NV, April 2002. Jiang, J., Borisenko, G.G. , Osipov, A. , Martin, I. , Chen, R. , Graham, S.H. and Kagan, V.E. Arachidonic acid-induced carbon-centered radicals and phospholipid peroxidation in cyclo-oxygenase-2-transfected PC12 cells. Society of Toxicology, Nashville, TN, March 2002. Teaching 2001 Teaching Assistant: Biological Effects of Radiation-Generated Free Radicals lecture, EOH2130 Survey of Radiation Health course, University of Pittsburgh.
The temporal and spatial variation of soil respiration in pepper ( Capsicum annuum L.), eggplant (Solanum melongena L.) and maize (Zea mays L.) agro-ecosystems in Northwest of China

Soil respiration is a crucial factor in estimating the carbon budget accurately. In order to explore the temporal and the spatial variation of soil respiration in different agro-ecosystems, soil respiration and environmental factors were measured in pepper (Capsicum annuum L.), eggplant ( Solanum melongena L.) and maize ( Zea mays L.) ecosystems during the growing season from June to September in 2009. The pronounced seasonal and diurnal variations of soil respiration behaved similarly in the three ecosystems. The soil respiration reached a seasonal peak in July and a seasonal trough in September. The diurnal maximum values appeared between 1300h and 1500h, and the minimum values were between 0300h and 0500h. The seasonal and diurnal variations were significantly affected by soil temperature (Q 10 value from 1.32 to 2.71) and air temperature (Q 10 value from 1.25 to 2.03), but not significantly to soil moisture and air relative humidity in the three ecosystems. Soil respiration was measured near the plant, between plants in the rows (inter-plants) and between rows (inter-rows). The results showed a significant tendency of soil respiration near the plant > inter plants > inter rows in the maize ecosystem, but not in pepper and eggplant ecosystems, indicating spatial variation and vegetation type are needed to be considered when estimating carbon emissions from soil respiration.
Pyrimidine dimer excision in Escherichia coli strains deficient in exonucleases V and VII and in the 5'. -->. 3' exonuclease of DNA polymerase I. [uv radiation]

An isogenic series of Escherichia coli strains deficient in various combinations of three 5' . -->. 3' exonucleases (exonuclease V, exonuclease VII, and the 5' .-->. 3' exonuclease of DNA polymerase I) was constructed and examined for the ability to excise pyrimidine dimers after uv irradiation. Although the recB and recC mutations (deficient in exonuclease V) proved to be incompatible with the polA(Ex) mutation (deficient in the 5' .-->. 3' exonuclease of DNA polymerase I), it was possible to reduce the level of the recB,C exonuclease by the use of temperature-sensitivite recB270 recC271 mutants. It was found that, by employing strains deficient in exonuclease V, postirradiation DNA degradation could be reduced and dimer excision measurements could be facilitated. Mutants deficient in exonuclease V were found to excise dimers at a rate comparable to that of the wild type. Mutants deficient in exonuclease V and the 5' . -->. 3' exonuclease of DNA polymerase I are slightly slower than the wild type at removing dimers accumulated after doses in excess of 40 J/m/sup 2/. However, although strains with reduced levels of exonuclease VII excised dimers at the same rate as the wild type, the addition of an exonuclease VII deficiency to a strainmore » with reduced levels of exonuclease V and the 5' . -->. 3' exonuclease of DNA polymerase I caused a marked decrease in the rate and extent of dimer excision. These observations support previous indications that the 5' . -->. 3' exonuclease of DNA polymerase I is important in dimer removal and also suggest a role for exonuclease VII in the excision repair process. « less
Longevity and milk production economics in Romanian Black and White cows reared in the south-western Romania.

The aim of the paper was to quantify the longevity and milk production economics of a Romanian Black and White cow population from Timis (TM) and Caras-Severin (CS) counties. A number of 625 cows from TM and 62 cows from CS that finished their productive life by 01.01. 2007 were studied. Life length, from birth to cull, was 6 years 11 months and 10 days in TM, being by 2 years and 26 days shorter than in CS (9 years and 6 days, p 0.05), cows from TM produced a higher milk yield than cows in CS (16461.1 kg vs. 14173.29 kg, p 0.05). In conclusion, the milk production economics was higher in cows from TM than for cows from CS.