Analysis of messenger RNAs detectable in medium conditioned by tumour cells in serum from breast cancer patients

Biomarkers have great potential for cancer detection and monitoring, with much of this type of analysis being carried out using tumour biopsies. This approach requires invasive procedures to obtain suitable specimens and only allows analysis of gene expression at one particular time point in the history of a cancer and from one location in the body. Biomarkers detectable in readily accessible body fluids, such as scrum, saliva or urine would allow on-going/ sequential monitoring of the course of disease (progression, response to therapy, etc.). A small number of studies have indicated the possibility of amplifying extracellular mRNA from the serum and/or plasma of cancer patients supporting the potential of this route of analysis. Limitations of these studies include the small numbers of serum/plasma specimens analysed; limited numbers of gene transcripts analysed; and discrepancies in protocols used, leading to a possibility that cells circulating in the bloodstream may be included in the RNA isolations; and the fact that a standard technique in general, was not employed. This thesis aims to address these issues by firstly establishing the possibility of routinely extracting and amplifying extracellular mRNA from the conditioned media (CM) of cultured cells. Having established, in principle, that amplifiable RNA could be isolated, comparison and optimisation of methods of extracting RNA was carried out to identify a reliable and reproducible method. Once this was established, CM samples from different cancer cell lines were investigated for expression of known tumour- related mRNAs by RTPCR and microarray technology was employed to investigate the global expression of mRNAs with both known and unknown functions. A slightly modified version of this method was also applied to mRNA extracted from serum of breast cancer patients and normal volunteers, enabling approx. 55,000 transcripts/ variants represented on the whole human genome chips to be analysed to identify mRNAs suitable for further analysis as potential future biomarkers

Avaliação do impacto da poluição ambiental no processo da corrosão atmosférica de metais através de redes neurais artificiais

Orientador: Prof. Dr. Ramon S.C. ParedesCo-orientador: Prof. Dr. Luiz Alkimin de LacerdaTese (doutorado) - Universidade Federal do Paraná, Setor de Tecnologia, Programa de Pós-Graduaçao em Engenharia - PIPE. Defesa: Curitiba, 08/06/2009Inclui bibliografiaÁrea de concentraçao: Engenharia e ciencia de materiai

Avian Resistance to Campylobacter jejuni Colonization Is Associated with an Intestinal Immunogene Expression Signature Identified by mRNA Sequencing

peer-reviewedThis research was funded by the The Irish Department of Agriculture and Food’s Food Institutional Research Measure (http://www.agriculture.gov.ie/ research/foodinstitutionalresearchmeasurefirm) – Grant No: 06_RDD_486.Campylobacter jejuni is the most common cause of human bacterial gastroenteritis and is associated with several post-infectious manifestations, including onset of the autoimmune neuropathy Guillain-Barré syndrome, causing significant morbidity and mortality. Poorly-cooked chicken meat is the most frequent source of infection as C. jejuni colonizes the avian intestine in a commensal relationship. However, not all chickens are equally colonized and resistance seems to be genetically determined. We hypothesize that differences in immune response may contribute to variation in colonization levels between susceptible and resistant birds. Using high-throughput sequencing in an avian infection model, we investigate gene expression associated with resistance or susceptibility to colonization of the gastrointestinal tract with C. jejuni and find that gut related immune mechanisms are critical for regulating colonization. Amongst a single population of 300 4-week old chickens, there was clear segregation in levels of C. jejuni colonization 48 hours post-exposure. RNAseq analysis of caecal tissue from 14 C. jejuni-susceptible and 14 C. jejuni-resistant birds generated over 363 million short mRNA sequences which were investigated to identify 219 differentially expressed genes. Significantly higher expression of genes involved in the innate immune response, cytokine signaling, B cell and T cell activation and immunoglobulin production, as well as the renin-angiotensin system was observed in resistant birds, suggesting an early active immune response to C. jejuni. Lower expression of these genes in colonized birds suggests suppression or inhibition of a clearing immune response thus facilitating commensal colonization and generating vectors for zoonotic transmission. This study describes biological processes regulating C. jejuni colonization of the avian intestine and gives insight into the differential immune mechanisms incited in response to commensal bacteria in general within vertebrate populations. The results reported here illustrate how an exaggerated immune response may be elicited in a subset of the population, which alters host-microbe interactions and inhibits the commensal state, therefore having wider relevance with regard to inflammatory and autoimmune disease

Detection of urinary bladder mass in CT urography with SPAN

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134872/1/mp2503.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134872/2/mp2503_am.pd

Urinary bladder segmentation in CT urography using deepâ learning convolutional neural network and level sets

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134923/1/mp4498.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134923/2/mp4498_am.pd

Human IgG antibody profiles differentiate between symptomatic patients with and without colorectal cancer

Abstract OBJECTIVE: Patients with cancer have antibodies against tumour antigens. Characterising the antibody repertoire may provide insights into aberrant cellular mechanisms in cancer development, ultimately leading to novel diagnostic or therapeutic targets. The aim of this study was to characterise the antibody profiles in patients whose symptoms warranted colonoscopy, to see if there was a difference in patients with and without colorectal cancer. METHODS: Patients were recruited from a colonoscopy clinic. Individual serum samples from 43 patients with colorectal cancer and 40 patients with no cancer on colonoscopy were profiled on a 37 830 clone recombinant human protein array. Antigen expression was evaluated by quantitative reverse transcription-PCR and by immunohistochemistry on tissue microarrays. RESULTS: Using a sex- and age-matched training set, 18 antigens associated with cancer and 4 associated with the absence of cancer (p\u3c0.05) were identified and confirmed. To investigate the mechanisms triggering antibody responses to these antigens, antigen expression was examined in normal colorectal mucosa and colorectal carcinoma of the same patients. The identified antigens showed cellular accumulation (p53), aberrant cellular expression (high mobility group B1 (HMGB1)) and overexpression (tripartite motif-containing 28 (TRIM28), p53, HMGB1, transcription factor 3 (TCF3), longevity assurance gene homologue 5 (LASS5) and zinc finger protein 346 (ZNF346)) in colorectal cancer tissue compared with normal colorectal mucosa. CONCLUSIONS: It is demonstrated for the first time that screening high-density protein arrays identifies unique antibody profiles that discriminate between symptomatic patients with and without colorectal cancer. The differential expression of identified antigens suggests their involvement in aberrant cellular mechanisms in cance

Long-lasting behavioural consequences of neonatal iron deficiency in high-risk children

AbstractLittle consideration has been given to the long-term consequences of iron deficiency in new-born infants. Fetal iron accretion is compromised by multiple pregnancy complications including preterm birth, gestational diabetes mellitus and fetal growth restriction, while our work has identified increased risks from maternal lifestyle factors such as smoking and obesity for low iron stores at birth. Early-life events, including C-section delivery, also add to this cumulative risk of neonatal iron deficiency, predisposing infants to iron deficiency later in infancy and early childhood. This study aimed to investigate the effect of neonatal iron deficiency on neurological development up to 5 years of age in term-born participants of a maternal-infant birth cohort in Ireland. In the Cork BASELINE Birth Cohort, 697 maternal-infant dyads with prospectively collected lifestyle and clinical data from 15 weeks’ gestation had umbilical cord serum ferritin concentrations measured. Neurological assessments were performed at 2 (Bayley Scales of Infant Development and Child Behaviour Checklist [CBCL]) and 5 (Kaufman Brief Intelligence Test and CBCL) years of age. In the cohort, median [IQR] cord ferritin concentrations were 200.9 [139.0,265.8] μg/L; 7.5% had neonatal iron deficiency (&lt; 76μg/L). Using the risk factors for neonatal iron deficiency that we previously identified (smoking, obesity, C-section delivery, SGA) in this cohort, as selection criteria, we conducted an a priori sensitivity analysis in 306 children. Of the 306 children identified as high-risk, 12.4% had neonatal iron deficiency. Those with neonatal iron deficiency had higher median [IQR] CBCL internal (9.0 [5.3,12.0] vs. 5.0 [3.0,10.0]), external (7.5 [4.0,14.8] vs. 5.0 [2.0,10.0]) and total problem (24.5 [15.3,40.8] vs. 16.0 [10.0,30.0], all P &lt; 0.05) scores at 5 years compared to those without neonatal deficiency. This adverse effect was especially apparent in children of obese mothers (n = 85) who were iron deficient at birth, with a total problem score at 5 years of 42.0 [24.5,54.5] compared to 16.0 [8.8,29.3] in those not deficient (P = 0.008). Associations were robust to adjustment for confounding factors. No effect on cognition or intelligence at 2 or 5 years was observed in this cohort. This study has identified behavioural consequences of neonatal iron deficiency. Interventions targeting the fetal/neonatal period could, therefore, represent a key opportunity for prevention of iron deficiency and its associated long-term neurological consequences. A dual approach is required, comprising public health strategies targeting prevention, through improving nutrition and health in women, and the development of screening strategies for early detection of iron deficiency in new-borns.</jats:p

Global endometrial transcriptomic profiling: transient immune activation precedes tissue proliferation and repair in healthy beef cows

peer-reviewedBackground: All cows experience bacterial contamination and tissue injury in the uterus postpartum, instigating a local inflammatory immune response. However mechanisms that control inflammation and achieve a physiologically functioning endometrium, while avoiding disease in the postpartum cow are not succinctly defined. This study aimed to identify novel candidate genes indicative of inflammation resolution during involution in healthy beef cows. Previous histological analysis of the endometrium revealed elevated inflammation 15 days postpartum (DPP) which was significantly decreased by 30 DPP. The current study generated a genome-wide transcriptomic profile of endometrial biopsies from these cows at both time points using mRNA-Seq. The pathway analysis tool GoSeq identified KEGG pathways enriched by significantly differentially expressed genes at both time points. Novel candidate genes associated with inflammatory resolution were subsequently validated in additional postpartum animals using quantitative real-time PCR (qRT-PCR). Results: mRNA-Seq revealed 1,107 significantly differentially expressed genes, 73 of which were increased 15 DPP and 1,034 were increased 30 DPP. Early postpartum, enriched immune pathways (adjusted P < 0.1) included the T cell receptor signalling pathway, graft-versus-host disease and cytokine-cytokine receptor interaction pathways. However 30 DPP, where the majority of genes were differentially expressed, the enrichment (adjusted P < 0.1) of tissue repair and proliferative activity pathways was observed. Nineteen candidate genes selected from mRNA-Seq results, were independently assessed by qRT-PCR in additional postpartum cows (5 animals) at both time points. SAA1/2, GATA2, IGF1, SHC2, and SERPINA14 genes were significantly elevated 30 DPP and are functionally associated with tissue repair and the restoration of uterine homeostasis postpartum. Conclusions: The results of this study reveal an early activation of the immune response which undergoes a temporal functional change toward tissue proliferation and regeneration during endometrial involution in healthy postpartum cows. These molecular changes mirror the activation and resolution of endometrial inflammation during involution previously classified by the degree of neutrophil infiltration. SAA1/2, GATA2, IGF1, SHC2, and SERPINA14 genes may become potential markers for resolution of endometrial inflammation in the postpartum cow

The Pine Needle, April 1947

Libraries and archives collect materials from different cultures and time periods to preserve and make available the historical record. As a result, materials such as those presented here may reflect sexist, misogynistic, abusive, racist, or discriminatory attitudes or actions that some may find disturbing, harmful, or difficult to view. Both a humor and literary magazine, The Pine Needle was a University of Maine student-produced periodical that began publication in the fall of 1946, the first post-World War II semester that saw GIs returni to campus. The Needle reflected an edginess and rebellion not found in previous UMaine student publications. While past student publications relied on euphemisms for alcohol and dating on campus, The Needle overtly sexualized co-eds and discussed the use of drugs, tobacco, and alcohol by students who experienced war. Cover art for this issue is an unsigned ink illustration of three students seated in a lecture hall taking an exam

Urinary bladder cancer staging in CT urography using machine learning

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/139956/1/mp12510.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/139956/2/mp12510_am.pd