Unexpected relationships between four large deletions in the human β-globin gene cluster.

Two independent gamma delta beta-thalassemias are each associated with large deletions. We show, by comparing DNA sequences, that the deletions are due to non-homologous DNA exchanges. The 5' breakpoints are located approximately the same distance apart and in the same order along the DNA as their 3' breakpoints. Two independent cases of hereditary persistence of fetal hemoglobin, also involving large deletions, show the same unexpected relationship between their 5' and 3' breakpoints. This relationship is most simply explained if, within each pair, the deletions are of approximately the same length. The results suggest that the four deletions were generated by a common mechanism. Perhaps their 5' and 3' breakpoints are physically close in the nucleus, although far apart on the linear DNA

Large salp bloom export from the upper ocean and benthic community response in the abyssal northeast Pacific: Day to week resolution

A large bloom of Salpa spp. in the northeastern Pacific during the spring of 2012 resulted in a major deposition of tunics and fecal pellets on the seafloor at ∼ 4000 m depth (Sta. M) over a period of 6 months. Continuous monitoring of this food pulse was recorded using autonomous instruments: sequencing sediment traps, a time‐lapse camera on the seafloor, and a bottom‐transiting vehicle measuring sediment community oxygen consumption (SCOC). These deep‐sea measurements were complemented by sampling of salps in the epipelagic zone by California Cooperative Ocean Fisheries Investigations. The particulate organic carbon (POC) flux increased sharply beginning in early March, reaching a peak of 38 mg C m−2 d−1 in mid‐April at 3400 m depth. Salp detritus started appearing in images of the seafloor taken in March and covered a daily maximum of 98% of the seafloor from late June to early July. Concurrently, the SCOC rose with increased salp deposition, reaching a high of 31 mg C m−2 d−1 in late June. A dominant megafauna species, Peniagone sp. A, increased 7‐fold in density beginning 7 weeks after the peak in salp deposition. Estimated food supply from salp detritus was 97–327% of the SCOC demand integrated over the 6‐month period starting in March 2012. Such large episodic pulses of food sustain abyssal communities over extended periods of time

Large salp bloom export from the upper ocean and benthic community response in the abyssal northeast Pacific: Day to week resolution

Abstract A large bloom of Salpa spp. in the northeastern Pacific during the spring of 2012 resulted in a major deposition of tunics and fecal pellets on the seafloor at , 4000 m depth (Sta. M) over a period of 6 months. Continuous monitoring of this food pulse was recorded using autonomous instruments: sequencing sediment traps, a timelapse camera on the seafloor, and a bottom-transiting vehicle measuring sediment community oxygen consumption (SCOC). These deep-sea measurements were complemented by sampling of salps in the epipelagic zone by California Cooperative Ocean Fisheries Investigations. The particulate organic carbon (POC) flux increased sharply beginning in early March, reaching a peak of 38 mg C m 22 d 21 in mid-April at 3400 m depth. Salp detritus started appearing in images of the seafloor taken in March and covered a daily maximum of 98% of the seafloor from late June to early July. Concurrently, the SCOC rose with increased salp deposition, reaching a high of 31 mg C m 22 d 21 in late June. A dominant megafauna species, Peniagone sp. A, increased 7-fold in density beginning 7 weeks after the peak in salp deposition. Estimated food supply from salp detritus was 97-327% of the SCOC demand integrated over the 6-month period starting in March 2012. Such large episodic pulses of food sustain abyssal communities over extended periods of time

Characterization of sequences in human TWIST required for nuclear localization

<p>Abstract</p> <p>Background</p> <p>Twist is a transcription factor that plays an important role in proliferation and tumorigenesis. Twist is a nuclear protein that regulates a variety of cellular functions controlled by protein-protein interactions and gene transcription events. The focus of this study was to characterize putative nuclear localization signals (NLSs) ³⁷RKRR⁴⁰and ⁷³KRGKK⁷⁷in the human TWIST (H-TWIST) protein.</p> <p>Results</p> <p>Using site-specific mutagenesis and immunofluorescences, we observed that altered TWIST^NLS1K38R, TWIST^NLS2K73R and K77R constructs inhibit nuclear accumulation of H-TWIST in mammalian cells, while TWIST^NLS2K76R expression was un-affected and retained to the nucleus. Subsequently, co-transfection of TWIST mutants K38R, K73R and K77R with E12 formed heterodimers and restored nuclear localization despite the NLSs mutations. Using a yeast-two-hybrid assay, we identified a novel TWIST-interacting candidate TCF-4, a basic helix-loop-helix transcription factor. The interaction of TWIST with TCF-4 confirmed using NLS rescue assays, where nuclear expression of mutant TWIST^NLS1with co-transfixed TCF-4 was observed. The interaction of TWIST with TCF-4 was also seen using standard immunoprecipitation assays.</p> <p>Conclusion</p> <p>Our study demonstrates the presence of two putative NLS motifs in H-TWIST and suggests that these NLS sequences are functional. Furthermore, we identified and confirmed the interaction of TWIST with a novel protein candidate TCF-4.</p

Gene expression profiling of alveolar soft-part sarcoma (ASPS)

<p>Abstract</p> <p>Background</p> <p>Alveolar soft-part sarcoma (ASPS) is an extremely rare, highly vascular soft tissue sarcoma affecting predominantly adolescents and young adults. In an attempt to gain insight into the pathobiology of this enigmatic tumor, we performed the first genome-wide gene expression profiling study.</p> <p>Methods</p> <p>For seven patients with confirmed primary or metastatic ASPS, RNA samples were isolated immediately following surgery, reverse transcribed to cDNA and each sample hybridized to duplicate high-density human U133 plus 2.0 microarrays. Array data was then analyzed relative to arrays hybridized to universal RNA to generate an unbiased transcriptome. Subsequent gene ontology analysis was used to identify transcripts with therapeutic or diagnostic potential. A subset of the most interesting genes was then validated using quantitative RT-PCR and immunohistochemistry.</p> <p>Results</p> <p>Analysis of patient array data versus universal RNA identified elevated expression of transcripts related to angiogenesis (ANGPTL2, HIF-1 alpha, MDK, c-MET, VEGF, TIMP-2), cell proliferation (PRL, IGFBP1, NTSR2, PCSK1), metastasis (ADAM9, ECM1, POSTN) and steroid biosynthesis (CYP17A1 and STS). A number of muscle-restricted transcripts (ITGB1BP3/MIBP, MYF5, MYF6 and TRIM63) were also identified, strengthening the case for a muscle cell progenitor as the origin of disease. Transcript differentials were validated using real-time PCR and subsequent immunohistochemical analysis confirmed protein expression for several of the most interesting changes (MDK, c-MET, VEGF, POSTN, CYP17A1, ITGB1BP3/MIBP and TRIM63).</p> <p>Conclusion</p> <p>Results from this first comprehensive study of ASPS gene expression identifies several targets involved in angiogenesis, metastasis and myogenic differentiation. These efforts represent the first step towards defining the cellular origin, pathogenesis and effective treatment strategies for this atypical malignancy.</p

Functional Diversity of Human Basic Helix-Loop-Helix Transcription Factor TCF4 Isoforms Generated by Alternative 5′ Exon Usage and Splicing

BACKGROUND: Transcription factor 4 (TCF4 alias ITF2, E2-2, ME2 or SEF2) is a ubiquitous class A basic helix-loop-helix protein that binds to E-box DNA sequences (CANNTG). While involved in the development and functioning of many different cell types, recent studies point to important roles for TCF4 in the nervous system. Specifically, human TCF4 gene is implicated in susceptibility to schizophrenia and TCF4 haploinsufficiency is the cause of the Pitt-Hopkins mental retardation syndrome. However, the structure, expression and coding potential of the human TCF4 gene have not been described in detail. PRINCIPAL FINDINGS: In the present study we used human tissue samples to characterize human TCF4 gene structure and TCF4 expression at mRNA and protein level. We report that although widely expressed, human TCF4 mRNA expression is particularly high in the brain. We demonstrate that usage of numerous 5' exons of the human TCF4 gene potentially yields in TCF4 protein isoforms with 18 different N-termini. In addition, the diversity of isoforms is increased by alternative splicing of several internal exons. For functional characterization of TCF4 isoforms, we overexpressed individual isoforms in cultured human cells. Our analysis revealed that subcellular distribution of TCF4 isoforms is differentially regulated: Some isoforms contain a bipartite nuclear localization signal and are exclusively nuclear, whereas distribution of other isoforms relies on heterodimerization partners. Furthermore, the ability of different TCF4 isoforms to regulate E-box controlled reporter gene transcription is varied depending on whether one or both of the two TCF4 transcription activation domains are present in the protein. Both TCF4 activation domains are able to activate transcription independently, but act synergistically in combination. CONCLUSIONS: Altogether, in this study we have described the inter-tissue variability of TCF4 expression in human and provided evidence about the functional diversity of the alternative TCF4 protein isoforms

The timing and duration of the Karoo igneous event, southern Gondwana

A volcanic event of immense scale occurred within a relatively short period in early Jurassic time over large regions of the contiguous Gondwana supercontinent. In southern Africa, associated remnants of thick volcanic successions of lava flows and extensive dike and sill complexes of similar composition have been grouped together as the Karoo Igneous Province. Correlative volcanic and plutonic rocks occur in Antarctica and Australia as the Ferrar Province