Diverse microbial communities and numerous energy-yielding activities occur in deeply buried sediments of the eastern Pacific Ocean. Distributions of metabolic activities often deviate from the standard model. Rates of activities, cell concentrations, and populations of cultured bacteria vary consistently from one subseafloor environment to another. Net rates of major activities principally rely on electron acceptors and electron donors from the photosynthetic surface world. At open-ocean sites, nitrate and oxygen are supplied to the deepest sedimentary communities through the underlying basaltic aquifer. In turn, these sedimentary communities may supply dissolved electron donors and nutrients to the underlying crustal biosphere.

Coastal hypoxia is an increasingly recognized environmental issue of global concern to both the scientific community and the general public. We assessed the relative contributions from marine and terrestrially sourced organic matter that were responsible for oxygen consumption in a well-studied seasonal coastal hypoxic zone, the East China Sea off the Changjiang Estuary. Our fieldwork was conducted in August 2011 during reinstatement of a subsurface hypoxia, when we observed a continuous decline of dissolved oxygen along with production of dissolved inorganic carbon resulting from organic carbon remineralization. On the basis of a three end-member mixing model and determinations of the stable isotopic compositions of dissolved inorganic carbon (δ13CDIC), the end product of particulate organic carbon (POC) degradation, we quantified the δ13C value of the remineralized organic carbon (δ13COCx), which was −18.5 ± 1.0‰. This isotopic composition was very similar to the δ13C of marine sourced POC produced in situ (−18.5 ± 0.3‰) rather than that of the terrestrially sourced POC (−24.4 ± 0.2‰). We concluded that marine-sourced organic matter, formed by eutrophication-induced marine primary production, was the dominant oxygen consumer in the subsurface hypoxic zone in the East China Sea off the Changjiang Estuary.

Versican is a large chondroitin sulfate proteoglycan belonging to the lectican family. Alternative splicing of versican generates at least four isoforms named V0, V1, V2, and V3. We have shown that the versican V1 isoform not only enhanced cell proliferation, but also modulated cell cycle progression and protected the cells from apoptosis. Futhermore, the V1 isoform was able to not only activate proto-oncogene EGFR expression and modulate its downstream signaling pathway, but also induce p27 degradation and enhance CDK2 kinase activity. As well, the V1 isoform down-regulated the expression of the proapoptotic protein Bad. By contrast, the V2 isoform exhibited opposite biological activities by inhibiting cell proliferation and down-regulated the expression of EGFR and cyclin A. Furthermore, V2 did not contribute apoptotic resistance to the cells. In light of these results, we are reporting opposite functions for the two versican isoforms whose expression is differentially regulated. Our studies suggest that the roles of these two isoforms are associated with the subdomains CS␤ and CS␣, respectively. These results were confirmed by silencing the expression of versican V1 with small interfering RNA (siRNA), which abolished V1-enhanced cell proliferation and V1-induced reduction of apoptosis.

We identified a barely noticed contributor, submarine groundwater discharge (SGD), to acidification of a coastal fringing reef system in Sanya Bay in the South China Sea based on time-series observations of Ra isotopes and carbonate system parameters. This coastal system was characterized by strong diel changes throughout the spring to neap tidal cycle of dissolved inorganic carbon (DIC), total alkalinity, partial pressure of CO2 (pCO2) and pH, in the ranges of 1851-2131 μmol kg(-1), 2182-2271 μmol kg(-1), 290-888 μatm and 7.72-8.15, respectively. Interestingly, the diurnal amplitudes of these parameters decreased from spring to neap tides, governed by both tidal pumping and biological activities. In ebb stages during the spring tide, we observed the lowest salinities along with the highest DIC, pCO2 and Ra isotopes, and the lowest pH and aragonite saturation state. These observations were consistent with a concurrent SGD rate up to 25 and 44 cm d(-1), quantified using Darcy's law and (226)Ra, during the spring tide ebb, but negligible at flood tides. Such tidal-driven SGD of low pH waters is another significant contributor to coastal acidification, posing additional stress on coastal coral systems, which would be even more susceptible in future scenarios under higher atmospheric CO2.

To investigate phylogenetic relationships among plasmons in Triticum and Aegilops, PCR-single-strand conformational polymorphism (PCR-SSCP) analyses were made of 14.0-kb chloroplast (ct) and 13.7-kb mitochondrial (mt)DNA regions that were isolated from 46 alloplasmic wheat lines and one euplasmic line. These plasmons represent 31 species of the two genera. The ct and mtDNA regions included 10 and 9 structural genes, respectively. A total of 177 bands were detected, of which 40.6% were variable. The proportion of variable bands in ctDNA (51.1%) was higher than that of mtDNA (28.9%). The phylogenetic trees of plasmons, derived by two different models, indicate a common picture of plasmon divergence in the two genera and suggest three major groups of plasmons (Einkorn, Triticum, and Aegilops). Because of uniparental plasmon transmission, the maternal parents of all but one polyploid species were identified. Only one Aegilops species, Ae. speltoides, was included in the Triticum group, suggesting that this species is the plasmon and B and G genome donor of all polyploid wheats. ctDNA variations were more intimately correlated with vegetative characters, whereas mtDNA variations were more closely correlated with reproductive characters. Plasmon divergence among the diploids of the two genera largely paralleled genome divergence. The relative times of origin of the polyploid species were inferred from genetic distances from their putative maternal parents.Genetic diversity among plasmons within two genera, Triticum and Aegilops, was first reported by Kihara (1). On producing alloplasmic lines of common wheat (2n ϭ 6x ϭ 42, nuclear genome AABBDD), and then tracking plasmon-specific phenotypic variations, we were able to classify the plasmons of Triticum and Aegilops species into 16 types (2). The next logical step was to identify molecular variation of their organellar DNAs. First, the discovery of RFLP (restriction fragment length polymorphism) variation among ct and mtDNAs was reported (3). Second, physical maps of common wheat ctDNA were constructed by using three restriction enzymes (4). The ctDNA maps were refined by using 13 restriction enzymes, after which we discovered that the chloroplast genomes of 33 Triticum and Aegilops species fell into 16 types (5). Eventually, RFLP analyses of mtDNAs from 17 species allowed us to distinguish their mitochondrial genomes from each other (6). Even though sequencing analyses are not as thorough as the RFLP analyses, the sequence of one chloroplast gene (rbcL, for the Rubisco large subunit) from seven Triticum and Aegilops species indicated that Ae. speltoides is the donor of both the plasmon and B genome of common wheat (7).Although RFLP and sequencing analyses have been employed, sequencing lags behind. RFLP analyses are relatively easy but are insensitive to fine-structure variation. Sequencing is the ultimate way to detect variation, but it is cumbersome when applied to large numbers of species and DNA regions. This paper reports a new technique, PCR-single-stran...

Although vertebrate hematopoiesis is the focus of intense study, immunocyte development is well-characterized in only a few invertebrate groups. The sea urchin embryo provides a morphologically simple model for immune cell development in an organism that is phylogenetically allied to vertebrates. Larval immunocytes, including pigment cells and several blastocoelar cell subtypes, emerge from a population of non-skeletal mesodermal (NSM) precursors that is specified at the blastula stage. This ring of cells is first partitioned into oral and aboral fields with distinct blastocoelar and pigment cell gene regulatory programs. The oral field is subsequently specified into several distinct immune and non-immune cell types during gastrulation. Here we characterize the oral NSM expression and downstream function of two homologs of key vertebrate hematopoietic transcription factors: SpGatac, an ortholog of vertebrate Gata-1/2/3 and SpScl, an ortholog of Scl/Tal-2/Lyl-1. Perturbation of SpGatac affects blastocoelar cell migration at gastrulation and later expression of immune effector genes, whereas interference with SpScl function disrupts segregation of pigment and blastocoelar cell precursors. Homologs of several transcription regulators that interact with Gata-1/2/3 and Scl factors in vertebrate hematopoiesis are also co-expressed in the oral NSM, including SpE-protein, the sea urchin homolog of vertebrate E2A/HEB/E2-2 and SpLmo2, an ortholog of a dedicated cofactor of the Scl-GATA transcription complex. Regulatory analysis of SpGatac indicates that oral NSM identity is directly suppressed in presumptive pigment cells by the transcription factor SpGcm. These findings provide part of a comparative basis to understand the evolutionary origins and regulatory biology of deuterostome immune cell differentiation in the context of a tractable gene regulatory network model.

The purple sea urchin (Strongylocentrotus purpuratus) genome sequence contains a complex repertoire of genes encoding innate immune recognition proteins and homologs of important vertebrate immune regulatory factors. To characterize how this immune system is deployed within an experimentally tractable, intact animal, we investigate the immune capability of the larval stage. Sea urchin embryos and larvae are morphologically simple and transparent, providing an organism-wide model to view immune response at cellular resolution. Here we present evidence for immune function in five mesenchymal cell types based on morphology, behavior and gene expression. Two cell types are phagocytic; the others interact at sites of microbial detection or injury. We characterize immune-associated gene markers for three cell types, including a perforin-like molecule, a scavenger receptor, a complement-like thioester-containing protein and the echinoderm-specific immune response factor 185/333. We elicit larval immune responses by (1) bacterial injection into the blastocoel and (2) seawater exposure to the marine bacterium Vibrio diazotrophicus to perturb immune state in the gut. Exposure at the epithelium induces a strong response in which pigment cells (one type of immune cell) migrate from the ectoderm to interact with the gut epithelium. Bacteria that accumulate in the gut later invade the blastocoel, where they are cleared by phagocytic and granular immune cells. The complexity of this coordinated, dynamic inflammatory program within the simple larval morphology provides a system in which to characterize processes that direct both aspects of the echinoderm-specific immune response as well as those that are shared with other deuterostomes, including vertebrates.

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