An Integrated Approach Utilizing Liquid Separations, Protein Microarrays and Tandem Mass Spectrometry Towards Understanding Phosphorylation, Glycosylation and Humoral Response Changes in Cancer.

The development and application of an integrated approach that utilizes liquid separations, protein microarrays and mass spectrometry with the goal of understanding breast, pancreatic and colon cancer progression is described. In order to understand breast cancer progression, two liquid separation techniques for the generation of protein microarrays from pre-malignant and malignant breast cancer cell lines which were subsequently probed for phosphoproteins was pursued. Out of 140 positively phosphorylated array spots, 85 were differentially phosphorylated. This corresponded to 75 unique proteins. 51 phosphorylation sites were identified by tandem MS/MS in 27 of these proteins. Phosphorylation changes were dominant in proteins involved in transcriptional and translational control as well as apoptosis and cytoskeletal regulation. A strategy for global glycoprotein profiling in serum and plasma was also developed. Glycoprotein microarrays of enriched and separated N-linked glycoproteins from serum and plasma from normal controls and patients with pancreatic cancer and colorectal cancer were generated. The specific sugar moieties on glycans were assessed using biotinylated lectins coupled with Alexa-flor conjugated streptavidin. In both cancers sialylation and fucosylation changes were dominant. Principal component analysis and hierarchical clustering analysis showed that this strategy successfully classified serum/plasma groups based on overall glycan expression profiles. The utility of protein microarrays for identifying potential markers of pancreatic cancer was also explored. Proteins from MIAPACA, a pancreatic cancer cell line, were fractionated in 2 dimensions and arrayed on nitrocellulose slides. The slides were hybridized with multiple serum samples from normal controls and patients diagnosed with pancreatic cancer in order to find specific cancer proteins that elicited an antigen-antibody response to the serum samples. Wilcoxon rank sum tests followed by the PAM classification algorithm highlighted 9 fractions that together classified serum samples with 87% accuracy and sensitivity and specificity of 93% and 80% respectively. Further validation experiments with recombinant proteins showed good correlation for two of the identified proteins, phosphoglycerate kinase and histone H4. A modified arraying technique utilizing CNBr digestion was also successful, suggesting that exposure of binding sites to serum during hybridization is critical in maximizing the sensitivity of the microarray.Ph.D.ChemistryUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/60880/1/tpatwa_1.pd

The assessment in the awareness regarding nutrition in pregnancy in population attending Dhiraj hospital and effect of taboos, customs and food availability on such population

Background: Food taboos have great effect on pregnant women through prohibited essential food and/or drinks. It is transferred from generation to generation and has negative effect on pregnant mothers' health. The objective was to assess magnitude of food taboo and associated factors among pregnant women attending antenatal care at Dhiraj hospital, Waghodiya, Vadodara.Methods: Institutional based cross-sectional study was conducted. 180 pregnant women were selected for the study. Multiple logistic regression analysis was conducted to identify independent predictors of food taboo.Results: Twenty-seven percent of pregnant mother encountered food taboos. Avoided food items by pregnant mothers were linseed, coffee, tea, cabbage, meat, wheat bread, banana, groundnut, salty diet, sugarcane, pumpkin, and coca drinks. Reasons mentioned for avoidance of this food items were plastered on the fetal head, making fatty baby which is difficult for delivery, fear of abortion, and fetal abnormality. Age of the mother AOR=2.97 (1.71-5.16), income AOR=0.28 (0.11-0.72), and previous antenatal care AOR=2.33 (1.89-5.47) were significantly associated with food taboo.Conclusions: Our study revealed that considerable proportion of food taboo exists during pregnancy in the study area. This can be improved by strengthening the nutrition counselling components of antenatal care follow-up

Understanding, acknowledging and accepting the knowledge regarding the complication of post-placental intrauterine contraceptive device insertion

Background: Intrauterine devices are an effective and increasingly popular from of reversible contraception and are most effective method of long-term contraception. Post placental intrauterine contraceptive devices insertion is done within 48 hours of birth which is ideal period ass women are strongly motivated to do so at this time. Aim was to understand knowledge, acceptance and complication of post placental intrauterine contractive device insertion.Methods: This was a prospective observational study conducted in obstetrics and gynecology department of a tertiary care centre from 1st September 2021 to 28th February 2022.Results: Total 84 patient were counselled out which 50 were willing for PPIUCD out of which 48 (58%) patients PPIUCD was inserted and 2 patients were deferred.Conclusions: PPIUCD was accepted in 50 (60%) of counselled total patients out which most of the patient were 20-29 years having graduate degrees and were mutipara most common cause of acceptance was that it is long term method of contraception most of the patient were counselled intrapartum and had vaginal method of delivery patient were minimum complications with most common complication of missing threads and expulsion

Comprehensive analysis of proteins of pH fractionated samples using monolithic LC/MS/MS, intact MW measurement and MALDI-QIT-TOF MS

A comprehensive platform that integrates information from the protein and peptide levels by combining various MS techniques has been employed for the analysis of proteins in fully malignant human breast cancer cells. The cell lysates were subjected to chromatofocusing fractionation, followed by tryptic digestion of pH fractions for on-line monolithic RP-HPLC interfaced with linear ion trap MS analysis for rapid protein identification. This unique approach of direct analysis of pH fractions resulted in the identification of large numbers of proteins from several selected pH fractions, in which approximately 1.5 µg of each of the pH fraction digests was consumed for an analysis time of ca 50 min. In order to combine valuable information retained at the protein level with the protein identifications obtained from the peptide level information, the same pH fraction was analyzed using nonporous (NPS)-RP-HPLC/ESI-TOF MS to obtain intact protein MW measurements. In order to further validate the protein identification procedures from the fraction digest analysis, NPS-RP-HPLC separation was performed for off-line protein collection to closely examine each protein using MALDI-TOF MS and MALDI-quadrupole ion trap (QIT)-TOF MS, and excellent agreement of protein identifications was consistently observed. It was also observed that the comparison to intact MW and other MS information was particularly useful for analyzing proteins whose identifications were suggested by one sequenced peptide from fraction digest analysis. Copyright © 2007 John Wiley & Sons, Ltd.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/55964/1/1163_ftp.pd

The Phenotype-Fitness Map in Experimental Evolution of Phages

Evolutionary biologists commonly interpret adaptations of organisms by reference to a phenotype-fitness map, a model of how different states of a phenotype affect fitness. Notwithstanding the popularity of this approach, it remains difficult to directly test these mappings, both because the map often describes only a small subset of phenotypes contributing to total fitness and because direct measures of fitness are difficult to obtain and compare to the map. Both limitations can be overcome for bacterial viruses (phages) grown in the experimental condition of unlimited hosts. A complete accounting of fitness requires 3 easily measured phenotypes, and total fitness is also directly measurable for arbitrary genotypes. Yet despite the presumed transparency of this system, directly estimated fitnesses often differ from fitnesses calculated from the phenotype-fitness map. This study attempts to resolve these discrepancies, both by developing a more exact analytical phenotype-fitness map and by exploring the empirical foundations of direct fitness estimates. We derive an equation (the phenotype-fitness map) for exponential phage growth that allows an arbitrary distribution of lysis times and burst sizes. We also show that direct estimates of fitness are, in many cases, plausibly in error because the population has not attained stable age distribution and thus violates the model underlying the phenotype-fitness map. In conjunction with data provided here, the new understanding appears to resolve a discrepancy between the reported fitness of phage T7 and the substantially lower value calculated from its phenotype-fitness map

Probing BFKL Dynamics in the Dijet Cross Section at Large Rapidity Intervals in ppbar Collisions at sqrt{s}=1800 and 630 GeV

Inclusive dijet production at large pseudorapidity intervals (delta_eta) between the two jets has been suggested as a regime for observing BFKL dynamics. We have measured the dijet cross section for large delta_eta in ppbar collisions at sqrt{s}=1800 and 630 GeV using the DO detector. The partonic cross section increases strongly with the size of delta_eta. The observed growth is even stronger than expected on the basis of BFKL resummation in the leading logarithmic approximation. The growth of the partonic cross section can be accommodated with an effective BFKL intercept of a_{BFKL}(20GeV)=1.65+/-0.07.Comment: Published in Physical Review Letter

Search for R-parity Violating Supersymmetry in Dimuon and Four-Jets Channel

We present results of a search for R-parity-violating decay of the neutralino chi_1^0, taken to be the Lightest Supersymmetric Particle. It is assumed that this decay proceeds through one of the lepton-number violating couplings lambda-prime_2jk (j=1,2; k=1,2,3). This search is based on 77.5 pb-1 of data, collected by the D0 experiment at the Fermilab Tevatron in ppbar collisions at a center of mass energy of 1.8 TeV in 1992-1995.Comment: 10 pages, 3 figure

Spin Correlation in tt-bar Production from pp-bar Collisions at sqrt(s)=1.8 TeV

The D0 collaboration has performed a study of spin correlation in tt-bar production for the process tt-bar to bb-bar W^+W^-, where the W bosons decay to e-nu or mu-nu. A sample of six events was collected during an exposure of the D0 detector to an integrated luminosity of approximately 125 pb^-1 of sqrt{s}=1.8 TeV pp-bar collisions. The standard model (SM) predicts that the short lifetime of the top quark ensures the transmission of any spin information at production to the tt-bar decay products. The degree of spin correlation is characterized by a correlation coefficient k. We find that k>-0.25 at the 68% confidence level, in agreement with the SM prediction of k=0.88.Comment: Submitted to PRL, Added references, minor changes to tex

Search for Electroweak Production of Single Top Quarks in ppbar Collisions

We present a search for electroweak production of single top quarks in the electron+jets and muon+jets decay channels. The measurements use ~90 pb^-1 of data from Run 1 of the Fermilab Tevatron collider, collected at 1.8 TeV with the DZero detector between 1992 and 1995. We use events that include a tagging muon, implying the presence of a b jet, to set an upper limit at the 95% confidence level on the cross section for the s-channel process ppbar->tb+X of 39 pb. The upper limit for the t-channel process ppbar->tqb+X is 58 pb.Comment: 11 pages, 2 figures. This is the published versio

A Quasi-Model-Independent Search for New Physics at Large Transverse Momentum

We apply a quasi-model-independent strategy ("Sleuth") to search for new high p_T physics in approximately 100 pb^-1 of ppbar collisions at sqrt(s) = 1.8 TeV collected by the DZero experiment during 1992-1996 at the Fermilab Tevatron. Over thirty-two e mu X, W+jets-like, Z+jets-like, and 3(lepton/photon)X exclusive final states are systematically analyzed for hints of physics beyond the standard model. Simultaneous sensitivity to a variety of models predicting new phenomena at the electroweak scale is demonstrated by testing the method on a particular signature in each set of final states. No evidence of new high p_T physics is observed in the course of this search, and we find that 89% of an ensemble of hypothetical similar experimental runs would have produced a final state with a candidate signal more interesting than the most interesting observed in these data.Comment: 28 pages, 17 figures. Submitted to Physical Review