The whole-organism heavy chain B cell repertoire from Zebrafish self-organizes into distinct network features

Background  

The adaptive immune system is based on selected populations of molecularly distinct individual B and T cell clones. However, it has not been possible to characterize these clones in a comprehensive and informatics manner to date; attempts have been limited by the number of cells in the adaptive immune system and an inability to quantify them. Recently, using the Zebrafish (ZF) Danio rerio as a model organism and parallel sequencing as the quantifying technology, Weinstein et al. overcame this major hurdle and quantified the entire heavy chain B-cell repertoire in ZF. Here, we present a novel network analysis of the data from the Weinstein group, providing new insights into the network structure of the B-cell repertoire.     

A Note on Correction of Information Time in a Survival Trial Using an Alpha Spending Function

Spending functions allow flexible monitoring of a clinical trial in that neither the number nor timing of the interim analyses need be pre-specified. Instead, we specify a function dictating the amount of alpha to be spent by different fractions of information. With a survival outcome, information is proportional to the number of patients who will have an event by the end of the trial. If the initial estimate of the number of events is incorrect, then we will spend an undesirable amount of alpha at interim looks. This note shows that for the most popular spending functions, which spend very little alpha early, we can fix an underestimate of the final information with very little effect on the boundaries.     

Transactivation of the epidermal growth factor receptor mediates parathyroid hormone and prostaglandin F2 alpha-stimulated mitogen-activated protein kinase activation in cultured transgenic murine osteoblasts

Recent data suggest that G protein-coupled receptors (GPCRs), including those for PTH and prostaglandins (PGs), contribute to the proliferation and differentiation of osteoblasts in vivo. To understand how these signals are transduced, we studied activation of the ERK1/2 MAPK cascade in cultures of differentiating TMOb murine osteoblasts. In TMOb cells, stimulation of endogenous Gs/Gq-coupled PTH receptors, Gq-coupled PGF2 alpha receptors, and Gi/Gq-coupled lysophosphatidic acid receptors, but not Gs-coupled PGE2 receptors, caused a rapid 5- to 10-fold increase in ERK1/2 phosphorylation. GPCR-stimulated ERK1/2 activation coincided with increased tyrosine phosphorylation of epidermal growth factor (EGF) receptors and was blocked by the EGF receptor inhibitor, tyrphostin AG1478, and the metalloprotease inhibitor, batimastat, suggesting that the response involved transactivation of EGF receptors through the proteolytic release of an EGF receptor ligand. To further examine the mechanism of PTH-stimulated EGF receptor transactivation, we employed COS-7 cells expressing the rat PTH receptor. Here, stimulation with PTH(1-34) caused proteolysis of hemagglutinin epitope-tagged heparin binding-EGF, increased tyrosine autophosphorylation of EGF receptors, and AG1478-sensitive ERK1/2 activation. When PTH receptor-expressing COS-7 cells were placed in a mixed culture with cells lacking the PTH receptor but expressing a green fluorescent protein-tagged ERK2, stimulation with PTH(1-34) induced phosphorylation of green fluorescent protein-ERK2 that was abolished by either batimastat or tyrphostin AG1478. These data suggest that autocrine/paracrine cross-talk between EGF receptors and Gi- or Gq/11-coupled GPCRs represents the predominant mechanism of GPCR-mediated activation of ERK1/2 in cultured TMOb osteoblasts.     

3D nuclear organization of telomeres in the Hodgkin cell lines U-HO1 and U-HO1-PTPN1: PTPN1 expression prevents the formation of very short telomeres including "t-stumps"

Background  

In cancer cells the three-dimensional (3D) telomere organization of interphase nuclei into a telomeric disk is heavily distorted and aggregates are found. In Hodgkin's lymphoma quantitative FISH (3D Q-FISH) reveals a major impact of nuclear telomere dynamics during the transition form mononuclear Hodgkin (H) to diagnostic multinuclear Reed-Sternberg (RS) cells. In vitro and in vivo formation of RS-cells is associated with the increase of very short telomeres including "t-stumps", telomere loss, telomeric aggregate formation and the generation of "ghost nuclei".     

Induction of Apoptotic Cell Death on Human Cervix Cancer HeLa cells by Extract from <Emphasis Type="Italic">Loranthus yadoriki</Emphasis>

Loranthus yadoriki, one of the Korean mistletoe species, has been already known for anti-viral effects, but the molecular basis that it caused apoptosis in cancer cells was not definitely revealed yet. The aim of this study was to estimate the mechanisms of apoptotic cell death of the extract from Loranthus yadoriki (named as ELY) in human cervix HeLa cells. We identified that ELY prevented the proliferation of HeLa cells between 50 and 300 μg/mL which did not affect non-cancerous HaCaT cells. In addition, ELY induced a morphological change and nucleus disruption as well as an accumulation of sub-G1 phase in HeLa cells. The mechanism study, by using western blot analysis, showed that the phosphorylation of Fas-associated death domain (FADD), Bim and Bak was up-regulated by ELY treatment. Furthermore, the expression of cytochrome c and Apaf-1 was increased by ELY treatment. In immunofluorescence staining, the increased intensity of cleaved caspase-3 and cleaved PARP was also observed under ELY treatment. Sequentially, the caspase cascade was activated by ELY from caspase-8 to caspase-3 and from caspase-9 to caspase-3, in both extrinsic and intrinsic pathways. The results of this study demonstrate that ELY has anti-cancer effects on human cervix cancer HeLa cells via caspase cascade in apoptotic signaling pathways.     

Structural aspects of nucleic acid-sensing Toll-like receptors

Invading pathogens elicit potent immune responses in cells through interactions between structurally conserved molecules derived from the pathogens and specialized innate immune receptors such as the Toll-like receptors (TLRs). Nucleic acid is one of the principal TLR ligands. Nucleic acid-sensing TLRs recognize an array of nucleic acids, including double-stranded RNA, single-stranded RNA, and DNAs with specific sequence motifs. Although ligand-induced dimerization is commonly observed followed by TLR activation, both the specific recognition mechanisms and the ligand–receptor interactions vary among different TLRs. In this review, we highlight our current understanding of how these receptors recognize their cognate ligands based on the recent advances in structural biology.     

Distribution Survey and Threat Assessment of the Yellow-tailed Woolly Monkey (<Emphasis Type="BoldItalic">Oreonax flavicauda;</Emphasis> Humboldt 1812), Northeastern Peru

Peruvian yellow-tailed woolly monkeys (Oreonax flavicauda) are considered Critically Endangered (IUCN Categories A4c). The International Primatological Society also considers them one of the world’s 25 most endangered primate species and therefore a conservation priority. However, there is little concerted conservation action, and the existing protected area network may be inadequate to protect this species from extinction. Until recently this species has been the focus of few studies and its distributional limits remain unknown. I present results of a range-wide survey of Oreonax flavicauda in northeastern Peru. I conducted 53 presence/absence field surveys at 43 sites between March 2007 and March 2010, with data collected for an additional 7 sites from other researchers. I chose sites where the species was previously reported or following suggestions from predictive GIS modeling. Oreonax flavicauda was present at 35 sites, all presence records were in Ficus spp.–dominated cloud forests between 1500 and 2650 m above sea level. I give the geographical limits of this species distribution throughout the north, east, and west of its range; the exact extent of its range to the south requires further investigation. Oreonax flavicauda continues to be threatened throughout its range. The major threats I identified at the survey locations were the continued conversion of forests to cattle pasture, opening of new access routes into virgin areas, and both commercial and subsistence hunting. My results suggest that existing conservation measures may be inadequate at protecting this species but that substantial opportunities do exist. Further surveys need to be made in the southern distribution of this species to determine more accurately extant habitat.     

<Emphasis Type="Italic">Sphedamnocarpus andersonii</Emphasis> (Malpighiaceae), a new species from Madagascar

Sphedamnocarpus andersonii, a new species from the Ihorombe Region of Madagascar, is described and illustrated. The twiggy, white-flowered shrubs are characterized by linear leaves, unique in the genus.