Proximity in chromatin : opportunities for innovations

Mammalian chromosomes extensively communicate with each other via long-range chromatin interactions. These interactions are mostly mediated by proteins, which work as teams to control genes in the cells. These interactions could also help to unravel the mechanisms of diseases such as cancer, from new perspectives. The packaging of the chromatin fiber and how it relates to epigenetic marks that regulate its accessibility to govern lineage-specific gene expression repertoires is currently the focus of immense efforts worldwide. Moreover, how chromosomes are hierarchically folded and how they relate to each other as well as to structural hallmarks of the nucleus is a largely unchartered territory in large cell populations not to mention in individual cells. This thesis has an emphasis on the analysis of pivotal chromatin features of single cells. Thus, interactions between a genome organizer termed CTCF and a factor involved in DNA repair, PARP1, could be demonstrated using the ISPLA technique. Such interactions likely underlie the formation of chromatin networks. Next, novel strategies/techniques were developed to visualize chromosomal structures and 3D networks by scoring for chromatin proximities within individual cells. One strategy included a novel method termed Chromatin In Situ Proximity (ChrISP) to visualize and identify proximities between chromatin fibers and other structural hallmarks in single cells at a resolution < 170 Å beyond that of the light microscope. Thus, large-scale changes in conformations of a single human chromosome upon the administration of reprogramming cues could be visualized. Finally, this innovation was further developed to explore differences in proximities of chromatin fibers that organize chromosome territories. The novel design, termed “rainbow ChrISP” translates physical distances in 3D, between chromatin fibres into different colors visualized with conventional microscope. This technique produced new insights into chromosome conformations and their regulation to enhance our understanding of their governing principles in single cells during development and disease

The expression and signalling patterns of CD180 toll like receptor in Chronic Lymphocytic Leukaemia (CLL)

Chronic lymphocytic leukaemia (CLL) is characterised by a progressive accumulation of mature CD5+CD20+CD23+ lymphocytes. Despite the remarkable progress in our understanding of the immunobiology of CLL, the aetiology of the disease remains unknown. The consensus is that CLL cells are driven by (auto)antigen(s) through the B cell receptor (BCR) and are regulated by a variety of signals received from the microenvironment, including toll-like receptors (TLR).Our group has previously shown that engagement of the CD180 orphan TLR expressed by approximately 60% of CLL cells, can re-wire the sIgM-mediated signalling from a pro-survival pathway, involving phosphatidylinositol-4,5-bisphosphate3-kinase (PI3K) and protein kinase B (AKT) to the potentially pro-apoptotic pathway through mitogen-activated protein kinase (p38MAPK). However, little is known about the function of the other BCR - sIgD in CLL and its possible interaction with CD180. Here we studied intracellular signalling and apoptosis of CLL cells following sole or sequential ligation of CD180 and sIgD. Our data indicated that following sequential ligation of CD180 and sIgD, CLL samples demonstrated enhanced p38MAPK phosphorylation leading to increased apoptosis of CLL cells indicating synergistic relationship between CD180 and sIgD. To better understand the prognostic importance of CD180 expression we sought to determine whether CD180 and other prognostic markers such as CD38 and ZAP70 displayed any correlation with the known cytogenetic aberrations:TP53 and DLEU1. Our results suggested that CLL cells with DLEU1 deletion are characterised by the negative expression of both, CD180 and CD38, and this might have a significance for CLL prognosis. To explain this correlation, we hypothesised that interaction of CLL cells with their microenvironment through TLRs leads to the expansion of leukaemic clones, in vivo, in lymph nodes. Our results indicated that CD180 is heterogeneously expressed in the paraffin tissue sections of the lymph nodes of CLL patients and its expression positively correlates with the expression of Ki-67. Our data demonstrated, that although CD180 expression and signaling might have negative prognostic importance in CLL due to the enhanced proliferation of leukaemic cells, its interaction with sIgD would re-direct leukaemic cells towards apoptosis thus opening new opportunities for the disease immunotherapy

Anopheline salivary protein genes and gene families: an evolutionary overview after the whole genome sequence of sixteen Anopheles species

Background: Mosquito saliva is a complex cocktail whose pharmacological properties play an essential role in blood feeding by counteracting host physiological response to tissue injury. Moreover, vector borne pathogens are transmitted to vertebrates and exposed to their immune system in the context of mosquito saliva which, in virtue of its immunomodulatory properties, can modify the local environment at the feeding site and eventually affect pathogen transmission. In addition, the host antibody response to salivary proteins may be used to assess human exposure to mosquito vectors. Even though the role of quite a few mosquito salivary proteins has been clarified in the last decade, we still completely ignore the physiological role of many of them as well as the extent of their involvement in the complex interactions taking place between the mosquito vectors, the pathogens they transmit and the vertebrate host. The recent release of the genomes of 16 Anopheles species offered the opportunity to get insights into function and evolution of salivary protein families in anopheline mosquitoes. Results: Orthologues of fifty three Anopheles gambiae salivary proteins were retrieved and annotated from 18 additional anopheline species belonging to the three subgenera Cellia, Anopheles, and Nyssorhynchus. Our analysis included 824 full-length salivary proteins from 24 different families and allowed the identification of 79 novel salivary genes and re-annotation of 379 wrong predictions. The comparative, structural and phylogenetic analyses yielded an unprecedented view of the anopheline salivary repertoires and of their evolution over 100 million years of anopheline radiation shedding light on mechanisms and evolutionary forces that contributed shaping the anopheline sialomes. Conclusions: We provide here a comprehensive description, classification and evolutionary overview of the main anopheline salivary protein families and identify two novel candidate markers of human exposure to malaria vectors worldwide. This anopheline sialome catalogue, which is easily accessible as hyperlinked spreadsheet, is expected to be useful to the vector biology community and to improve the capacity to gain a deeper understanding of mosquito salivary proteins facilitating their possible exploitation for epidemiological and/or pathogen-vector-host interaction studies

Utah Science Vol. 46 No. 3, Fall 1985

72 BIOTECHNOLOGY FOR UTAH AGRICULTURE: HARNESSING THE NEW TECHNOLOGY An overview of the biotechnology\u27s potential contributions and a synopsis of some of the related research supported by the Experiment Station. 80 UNDERSTANDING THE CAPRICIOUS GREAT SALT LAKE G. E. Bingham, E. A. Richardson, and G. L. Ashcroft Researchers have used several analytical techniques and a variety of data in their attempts to discover why water levels change in the Great Salt Lake. They have discovered important precipitation patterns and apparently identified the additional information needed to help them predict changes in lake level. 86 DETERMINING AGRICULTURE\u27S CONTRIBUTION TO UTAH\u27S ECONOMY D. L. Snyder, J. E. Keith, J. C. Andersen, and C. Diamond Economists use an input-output model to determine the economic impact of agriculture. Results indicate that agricultural development has a substantial impact on income and employment. 90 HYBRID CROPS THAT ‘CLONE\u27 THEMSELVES J. G. Carman, C. F. Crane, and J. E. Hughes Researchers are attempting to transfer apomixis, a form of asexual reproduction in which seeds are identical to the parent plant, to wheat. The resulting hybrids would dramatically increase yields and cut farmers\u27 seed bills. 95 AGRICULTURAL DEVELOPMENT OR EXPANSION IN UTAH D. L. Snyder and T. F. Glover There appear to be substantial opportunities to increase revenue from specialty crops if producers hone their marketing skills. 100 VACANT FEDERAL GRAZING ALLOTMENTS IN THE WEST E. B. Godfrey, D. B. Nielsen, and D. D. Lytle Some grazing lands administered by the Forest Service and Bureau of Land Management are in high demand while others aren\u27t. Although relatively few grazing allotments appear to be vacant, there are indications that more may become vacant in the future, particularly if costs of using these lands increase. 103 APPLICATION OF HYBRIDOMA TECHNOLOGY TO AVIAN COCCIDIOSIS M. A. Laxer, M. C. Healey, and N. N. Youssef Biotechnology may lead to the development of new vaccines against avian coccidiosis. Results might eventually let researchers genetically engineer bacteria to produce antibodies in the body 106 HOUSEHOLD APPLIANCES AND HOUSEWORK: MORE EQUIPMENT MAY NOT MEAN LESS WORK Jane McCullough Those who buy household appliances to reduce work loads may be disappointed. Results of a recent survey indicate that appliances often don\u27t significantly reduce the amount of time spent on household chores, and that, except for maintaining the home and yard, most husbands spend little time on household tasks

Cell migration and chimerism after whole‐organ transplantation: The basis of graft acceptance

Improvements in the prevention or control of rejection of the kidney and liver have been largely interchangeable (1, 2) and then applicable, with very little modification, to thoracic and other organs. However, the mechanism by which anti rejection treatment permits any of these grafts to be “accepted” has been an immunological enigma (3, 4). We have proposed recently that the exchange of migratory leukocytes between the transplant and the recipient with consequent long-term cellular chimerism in both is the basis for acceptance of all whole-organ allografts and xenografts (5). Although such chimerism was demonstrated only a few months ago, the observations have increased our insight into transplantation immunology and have encouraged the development of alternative therapeutic strategies (6)

Multiple Roles of Brd4 in the Human Papillomavirus Life Cycle

ABSTRACT MULTIPLE ROLES OF BRD4 IN THE HUMAN PAPILLOMAVIRUS LIFE CYCLE Christine M. Helfer Jianxin You While human papillomavirus (HPV) vaccines protect against acquiring new infections, there is currently no antiviral treatment for eradicating persistent HPV infections. In this study, I demonstrated that the cellular chromatin binding protein, Brd4, in association with HPV E2 protein, is important for multiple HPV functions including replication, maintenance of viral genomes, and regulation of viral gene transcription. These studies suggest that the E2–Brd4 complex could be an effective target to disrupt the HPV life cycle. Using bimolecular fluorescence complementation, we demonstrate that E2 from high–risk HPV16 interacts with Brd4 on cellular chromosomes throughout mitosis while the BET bromodomain inhibitor, JQ1(&plus;), dissociates Brd4–E2 complexes from mitotic chromosomes. These results suggest that Brd4 is important for tethering HPV16 E2 to mitotic chromosomes for stable viral genome maintenance and that abrogating Brd4\u27s chromatin association might disrupt stable HPV genome maintenance. I also found that JQ1(&plus;) treatment of cells stably maintaining papillomavirus genomes reduces viral mRNA levels, demonstrating that HPV association with cellular chromatin through Brd4 is essential for HPV transcription and further supporting the importance of Brd4 for the HPV life cycle. My work also identified a novel role of Brd4 in HPV16 DNA replication. Immunofluorescence analyses show Brd4 is recruited to nuclear foci actively replicating HPV16 genomes. Replication assays further confirm that Brd4 is essential for HPV16 genome replication. Interestingly, JQ1(&plus;) treatment stimulates viral genome replication. Since HPV genome amplification is normally limited to upper epithelial layers, we predict premature stimulation of viral DNA amplification induced by JQ1(&plus;) in basal epithelial cells might activate host immune responses to clear HPV infection. Finally, this work identified a specific function of Brd4 in papillomavirus transcription activation. Using ChIP analysis and an E2–responsive luciferase assay, we show Brd4 actively recruits P–TEFb to papillomavirus genomes to support E2 transactivation function. Together, this study uncovers two novel functions of Brd4 in the HPV life cycle, improving our understanding of this complex virus–host relationship. Furthermore, we identify the E2–Brd4 complex as a promising antiviral target for eliminating HPV persistent infection

Genetic Relationships and Therapeutic Options for Relapsed Acute Lymphoblastic Leukemia

Acute lymphoblastic leukemia (ALL) is the most common form of cancer among children and can be lethal to the adult population. Though 80% of patients with ALL reach complete remission after treatment, about 20% of those diagnosed fail to remain cancer-free. Genetic rearrangements are the hallmark of relapsed ALL, but the mechanism by which these rearrangements occur is still unclear. Recent research suggests these mutations may be detectable during initial diagnosis. If researchers are able to accurately assess the probability of relapse during diagnosis by analyzing the genome of the leukemic cells, the likelihood of administering effective therapy would increase. Providing patients with a more appropriate therapy early on may prevent relapse altogether or increase survival rates after treatment for relapsed ALL patients

Characterising Chinese Hamster Ovary Cell Line Stability in Bioproduction of Therapeutic Proteins

No abstract