Simulation of Lake Victoria Circulation Patterns Using the Regional Ocean Modeling System (ROMS)

Lake Victoria provides important ecosystem services including transport, water for domestic and industrial uses and fisheries to about 33 million inhabitants in three East African countries. The lake plays an important role in modulating regional climate. Its thermodynamics and hydrodynamics are also influenced by prevailing climatic and weather conditions on diel, seasonal and annual scales. However, information on water temperature and circulation in the lake is limited in space and time. We use a Regional Oceanographic Model System (ROMS) to simulate these processes from 1^st January 2000 to 31^st December 2014. The model is based on real bathymetry, river runoff and atmospheric forcing data using the bulk flux algorithm. Simulations show that the water column exhibits annual cycles of thermo-stratification (September–May) and mixing (June–August). Surface water currents take different patterns ranging from a lake-wide northward flow to gyres that vary in size and number. An under flow exists that leads to the formation of upwelling and downwelling regions. Current velocities are highest at the center of the lake and on the western inshore waters indicating enhanced water circulation in those areas. However, there is little exchange of water between the major gulfs (especially Nyanza) and the open lake, a factor that could be responsible for the different water quality reported in those regions. Findings of the present study enhance understanding of the physical processes (temperature and currents) that have an effect on diel, seasonal, and annual variations in stratification, vertical mixing, inshore—offshore exchanges and fluxes of nutrients that ultimately influence the biotic distribution and trophic structure. For instance information on areas/timing of upwelling and vertical mixing obtained from this study will help predict locations/seasons of high primary production and ultimately fisheries productivity in Lake Victoria.     

Variation in carbohydrate source–sink relations of forest and treeline white spruce in southern, interior and northern Alaska

Two opposing hypotheses have been presented to explain reduced tree growth at the treeline, compared with growth in lower elevation or lower latitude forests: the carbon source and sink limitation hypotheses. The former states that treeline trees have an unfavorable carbon balance and cannot support growth of the magnitude observed at lower elevations or latitudes, while the latter argues that treeline trees have an adequate carbon supply, but that cold temperatures directly limit growth. In this study, we examined the relative importance of source and sink limitation in forest and treeline white spruce (Picea glauca) in three mountain ranges from southern to northern Alaska. We related seasonal changes in needle nonstructural carbohydrate (NSC) content with branch extension growth, an approach we argue is more powerful than using needle NSC concentration. Branch extension growth in the southernmost Chugach Mountains was much greater than in the White Mountains and the Brooks Range. Trees in the Chugach Mountains showed a greater seasonal decline in needle NSC content than trees in the other mountain ranges, and the seasonal change in NSC was correlated with site-level branch growth across mountain ranges. There was no evidence of a consistent difference in branch growth between the forest and treeline sites, which differ in elevation by approximately 100 m. Our results point to a continuum between source and sink limitation of growth, with high-elevation trees in northern and interior Alaska showing greater evidence of sink limitation, and those in southern Alaska showing greater potential for source limitation.     

Tuberculosis and nonsteroidal anti-inflammatory drugs.

In 1980 and 1982 two case reports documented reactivation of pulmonary tuberculosis in patients who had used nonsteroidal anti-inflammatory drugs (NSAIDs). A case-control study was designed to test the hypothesis that such an association does exist. Data for 38 patients were obtained from the patients'' family physicians, and each patient was matched with a control from the same practice for age, sex, race and length of time in that practice. A statistically significant relation was found between the reactivation of tuberculosis and the use of NSAIDs. However, further research is imperative to determine whether the association is direct, indirect or secondary to an unknown factor. Physicians should keep in mind that NSAIDs are potent anti-inflammatory agents and may thus activate, spread and mask infections.     

Cancer stem cells: A guide for skeptics

Cancer stem cells (CSC) were postulated to exist many years ago as cells within a tumor that regenerate the tumor following treatment. A stochastic clonal evolution model was used to explain observed tumor heterogeneity. Recently, xenotransplantation studies have demonstrated that prospectively identifiable subpopulations from human cancers can initiate tumors in immune deficient mice, and these results along with recent advances in stem cell biology have generated much excitement in the cancer field. The modern CSC theory posits a hierarchy of cells analogous to normal stem cell development. Some controversy remains, however, as to whether these tumor initiating cells truly represent CSC, and whether the modern CSC field can live up to the promise of providing improved cancer treatments based on a novel model of cancer biology. Recent data from CSC investigators are discussed critically. J. Cell. Biochem. 106: 745–749, 2009. © 2009 Wiley‐Liss, Inc.     

Attaining and maintaining strong vocal synapses in female Xenopus laevis

Synaptic efficacy at the laryngeal neuromuscular synapse differs markedly in adult male and female Xenopus laevis. Here, we examined the relation between circulating estrogen and synapse strength in developing and adult female frogs. Circulating estrogen levels in males and females during juvenile and adult stages were measured using radioimmunoassays. Synaptic strength was determined by quantal analysis in isolated female larynges. In males, estrogen levels are low (<40 pg/mL) throughout development. In females, estrogen levels are similar to those in males until 9 months after metamorphosis is complete and then increase throughout development. Female laryngeal synapses have low quantal contents until 24 months; quantal content increases significantly between 24 and 26 months, and high quantal contents are maintained thereafter. Measures of reproductive maturation, ovary, and oviduct weights, are strongly and positively correlated with estrogen level in 16- to 26-month females, while oocyte maturation is age dependent. Estrogen level and quantal content are not well correlated in these females. Ovariectomy at 24 months prevents the expected increase in quantal content and ovariectomy at 28 months results in a decrease in quantal content. Thus, the sex difference in efficacy of the laryngeal synapse develops under the influence of the ovary and requires the ovary for maintenance of strong synapses in adulthood. While the influence of the ovary is most likely due to estrogen secretion, the pattern of estrogen secretion required for maturation of the synapse in females is not known. © 1998 John Wiley & Sons, Inc. J Neurobiol 37: 441–448, 1998     

Neoplasia driven by mutant c-KIT is mediated by intracellular, not plasma membrane, receptor signaling

Activating mutations in c-KIT are associated with gastrointestinal stromal tumors, mastocytosis, and acute myeloid leukemia. In attempting to establish a murine model of human KIT(D816V) (hKIT(D816V))-mediated leukemia, we uncovered an unexpected relationship between cellular transformation and intracellular trafficking. We found that transport of hKIT(D816V) protein was blocked at the endoplasmic reticulum in a species-specific fashion. We exploited these species-specific trafficking differences and a set of localization domain-tagged KIT mutants to explore the relationship between subcellular localization of mutant KIT and cellular transformation. The protein products of fully transforming KIT mutants localized to the Golgi apparatus and to a lesser extent the plasma membrane. Domain-tagged KIT(D816V) targeted to the Golgi apparatus remained constitutively active and transforming. Chemical inhibition of intracellular transport demonstrated that Golgi localization is sufficient, but plasma membrane localization is dispensable, for downstream signaling mediated by KIT mutation. When expressed in murine bone marrow, endoplasmic reticulum-localized hKIT(D816V) failed to induce disease in mice, while expression of either Golgi-localized HyKIT(D816V) or cytosol-localized, ectodomain-deleted KIT(D816V) uniformly caused fatal myeloproliferative diseases. Taken together, these data demonstrate that intracellular, non-plasma membrane receptor signaling is sufficient to drive neoplasia caused by mutant c-KIT and provide the first animal model of myelomonocytic neoplasia initiated by human KIT(D816V).     

Circulating angiopoietin-2 as a biomarker in ANCA-associated vasculitis

The endothelial-specific Angiopoietin-Tie2 ligand-receptor system is an important regulator of endothelial activation. Binding of angiopoietin-2 (Ang-2) to Tie2 receptor renders the endothelial barrier responsive to pro-inflammatory cytokines. We previously showed that circulating Ang-2 correlated with disease severity in a small cohort of critically ill patients with anti-neutrophil cytoplasmic antibody (ANCA)-associated glomerulonephritis. The current study reassessed Ang-2 as a biomarker of disease activity and relapse in AAV. Circulating Ang-2 was measured in 162 patients with severe AAV (BVAS/WG≥3, with or without glomerulonephritis) in a clinical trial. Ang-2 levels during active AAV were compared to levels in the same patients during remission (BVAS/WG = 0). Levels in clinical subsets of AAV were compared, and association with future disease course was assessed. Ang-2 levels were elevated in severe disease (median 3.0 ng/ml, interquartile range 1.9–4.4) compared to healthy controls (1.2, 0.9–1.5). However, they did not reliably decline with successful treatment (median 2.6 ng/ml, interquartile range 1.9–3.8, median change −0.1). Ang-2 correlated weakly with BVAS/WG score (r = 0.17), moderately with markers of systemic inflammation (r = 0.25–0.41), and inversely with renal function (r = −0.36). Levels were higher in patients with glomerulonephritis, but levels adjusted for renal dysfunction were no different in patients with or without glomerulonephritis. Levels were higher in patients with newly diagnosed AAV and lower in patients in whom treatment had recently been started. Ang-2 levels during active disease did not predict response to treatment, and Ang-2 levels in remission did not predict time to flare. Thus, Ang-2 appears to have limited practical value in AAV as a biomarker of disease activity at time of measurement or for predicting future activity.     

Genetic markers in Andean Puya species (Bromeliaceae) with implications on plastome evolution and phylogeny

The Andean plant endemic Puya is a striking example of recent and rapid diversification from central Chile to the northern Andes, tracking mountain uplift. This study generated 12 complete plastomes representing nine Puya species and compared them to five published plastomes for their features, genomic evolution, and phylogeny. The total size of the Puya plastomes ranged from 159,542 to 159,839 bp with 37.3%–37.4% GC content. The Puya plastomes were highly conserved in organization and structure with a typical quadripartite genome structure. Each of the 17 consensus plastomes harbored 133 genes, including 87 protein‐coding genes, 38 tRNA (transfer RNA) genes, and eight rRNA (ribosomal RNA) genes; we found 69–78 tandem repeats, 45–60 SSRs (simple sequence repeats), and 8–22 repeat structures among 13 species. Four protein‐coding genes were identified under positive site‐specific selection in Puya. The complete plastomes and hypervariable regions collectively provided pronounced species discrimination in Puya and a practical tool for future phylogenetic studies. The reconstructed phylogeny and estimated divergence time for the lineage suggest that the diversification of Puya is related to Andean orogeny and Pleistocene climatic oscillations. This study provides plastome resources for species delimitation and novel phylogenetic and biogeographic studies.     

Transformation of hematopoietic cell lines to growth-factor independence and induction of a fatal myelo- and lymphoproliferative disease in mice by retrovirally transduced TEL/JAK2 fusion genes.

Recent reports have demonstrated fusion of the TEL gene on 12p13 to the JAK2 gene on 9p24 in human leukemias. Three variants have been identified that fuse the TEL pointed (PNT) domain to (i) the JAK2 JH1-kinase domain, (ii) part of and (iii) all of the JH2 pseudokinase domain. We report that all of the human TEL/JAK2 variants, and a human/mouse chimeric hTEL/mJAK2(JH1) fusion gene, transform the interleukin-3 (IL-3)-dependent murine hematopoietic cell line Ba/F3 to IL-3-independent growth. Transformation requires both the TEL PNT domain and JAK2 kinase activity. Furthermore, all TEL/JAK2 variants strongly activated STAT 5 by phosphotyrosine Western blots and by electrophoretic mobility shift assays (EMSA). Mice (n = 40) transplanted with bone marrow infected with the MSCV retrovirus containing either the hTEL/mJAK2(JH1) fusion or its human counterpart developed a fatal mixed myeloproliferative and T-cell lymphoproliferative disorder with a latency of 2-10 weeks. In contrast, mice transplanted with a TEL/JAK2 mutant lacking the TEL PNT domain (n = 10) or a kinase-inactive TEL/JAK2(JH1) mutant (n = 10) did not develop the disease. We conclude that all human TEL/JAK2 fusion variants are oncoproteins in vitro that strongly activate STAT 5, and cause lethal myelo- and lymphoproliferative syndromes in murine bone marrow transplant models of leukemia.     

SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution

The sensitivity of massively-parallel sequencing has confirmed that most cancers are oligoclonal, with subpopulations of neoplastic cells harboring distinct mutations. A fine resolution view of this clonal architecture provides insight into tumor heterogeneity, evolution, and treatment response, all of which may have clinical implications. Single tumor analysis already contributes to understanding these phenomena. However, cryptic subclones are frequently revealed by additional patient samples (e.g., collected at relapse or following treatment), indicating that accurately characterizing a tumor requires analyzing multiple samples from the same patient. To address this need, we present SciClone, a computational method that identifies the number and genetic composition of subclones by analyzing the variant allele frequencies of somatic mutations. We use it to detect subclones in acute myeloid leukemia and breast cancer samples that, though present at disease onset, are not evident from a single primary tumor sample. By doing so, we can track tumor evolution and identify the spatial origins of cells resisting therapy.