Microstructure and crystallographic texture data in modern giant clam shells (Tridacna squamosa and Hippopus hippopus).

This article provides novel data on the microstructure and crystallographic texture of modern giant clam shells (Tridacna squamosa and Hippopus hippopus) from the Coral Triangle region of northeast Borneo. Giant clams have two aragonitic shell layers-the inner and outer shell layer. This dataset focuses on the inner shell layer as this is well preserved and not affected by diagenetic alteration. To prepare samples for analysis, shells were cut longitudinally at the axis of maximum growth and mounted onto thin sections. Data collection involved scanning electron microscopy (SEM) to determine microstructure and SEM based electron backscatter diffraction (EBSD) for quantitative measurement of crystallographic orientation and texture. Post-acquisition reanalysis of saved EBSD patterns to optimize data quality included changing the number of reflectors and band detection mode. We provide EBSD data as band contrast images and colour-coded orientation maps (inverse pole figure maps). Crystallographic co-orientation strength obtained with multiple of uniform density (MUD) values are derived from density distributed pole figures of indexed EBSD points. Raw EBSD data files are also given to ensure repeatability of the steps provided in this article and to allow extraction of further crystallographic properties for future researchers. Overall, this dataset provides 1. a better understanding of shell growth and biomineralization in giant clams and 2. important steps for optimizing data collection with EBSD analyses in biogenic carbonates.

Marine litter pollution on coral reefs of Darvel Bay (East Sabah, Malaysia).

Marine litter is recognized as an increasing component of marine ecosystem pollution. In this baseline study, we document the magnitude, types, sources, and potential impacts of litter on six coral reefs in East Sabah. We applied a simplified classification of litter to extract abundance data from video transects. The average density was 10.7 items per 100 m2. Plastics represent 91% and the remaining 9% were metal, glass, and wood. Most (~70%) plastics are single-use items derived from dumping. Discarded fishing gear accounts for ~25%. Litter pollution increases closer to urban developments, with Sakar reef having higher densities (51 items per 100 m2), and higher Clean Coast Index (CCI = 10.2, dirty) and higher Plastic Abundance Index (PAI = 4.68) scores. This method could and should be readily integrated into ongoing monitoring programs to support assessments of the extent and magnitude of marine litter pollution on reefs worldwide.

Differences in extinction rates drove modern biogeographic patterns of tropical marine biodiversity.

Marine biodiversity in the Coral Triangle is several times higher than anywhere else, but why this is true is unknown because of poor historical data. To address this, we compared the first available record of fossil cheilostome bryozoans from Indonesia with the previously sampled excellent record from the Caribbean. These two regions differ several-fold in species richness today, but cheilostome diversity was strikingly similar until the end of the Miocene 5.3 million years ago so that the modern disparity must have developed more recently. However, the Miocene faunas were ecologically very different, with a greater proportion of erect and free-living species in the Caribbean compared to the less well-known Coral Triangle. Our results support the hypothesis that modern differences in diversity arose primarily from differential extinction of Caribbean erect and free-living species concomitant with oceanographic changes due to the uplift of the Isthmus of Panama, rather than exceptional rates of diversification in the Indo-Pacific.

Empty Niches after Extinctions Increase Population Sizes of Modern Corals.

Large environmental fluctuations often cause mass extinctions, extirpating species and transforming communities [1, 2]. While the effects on community structure are evident in the fossil record, demographic consequences for populations of individual species are harder to evaluate because fossils reveal relative, but not absolute, abundances. However, genomic analyses of living species that have survived a mass extinction event offer the potential for understanding the demographic effects of such environmental fluctuations on extant species. Here, we show how environmental variation since the Pliocene has shaped demographic changes in extant corals of the genus Orbicella, major extant reef builders in the Caribbean that today are endangered. We use genomic approaches to estimate previously unknown current and past population sizes over the last 3 million years. Populations of all three Orbicella declined around 2-1 million years ago, coincident with the extinction of at least 50% of Caribbean coral species. The estimated changes in population size are consistent across the three species despite their ecological differences. Subsequently, two shallow-water specialists expanded their population sizes at least 2-fold, over a time that overlaps with the disappearance of their sister competitor species O. nancyi (the organ-pipe Orbicella). Our study suggests that populations of Orbicella species are capable of rebounding from reductions in population size under suitable conditions and that the effective population size of modern corals provides rich standing genetic variation for corals to adapt to climate change. For conservation genetics, our study suggests the need to evaluate genetic variation under appropriate demographic models.

Formation of the Isthmus of Panama.

The formation of the Isthmus of Panama stands as one of the greatest natural events of the Cenozoic, driving profound biotic transformations on land and in the oceans. Some recent studies suggest that the Isthmus formed many millions of years earlier than the widely recognized age of approximately 3 million years ago (Ma), a result that if true would revolutionize our understanding of environmental, ecological, and evolutionary change across the Americas. To bring clarity to the question of when the Isthmus of Panama formed, we provide an exhaustive review and reanalysis of geological, paleontological, and molecular records. These independent lines of evidence converge upon a cohesive narrative of gradually emerging land and constricting seaways, with formation of the Isthmus of Panama sensu stricto around 2.8 Ma. The evidence used to support an older isthmus is inconclusive, and we caution against the uncritical acceptance of an isthmus before the Pliocene.

Are coral reefs victims of their own past success?

As one of the most prolific and widespread reef builders, the staghorn coral Acropora holds a disproportionately large role in how coral reefs will respond to accelerating anthropogenic change. We show that although Acropora has a diverse history extended over the past 50 million years, it was not a dominant reef builder until the onset of high-amplitude glacioeustatic sea-level fluctuations 1.8 million years ago. High growth rates and propagation by fragmentation have favored staghorn corals since this time. In contrast, staghorn corals are among the most vulnerable corals to anthropogenic stressors, with marked global loss of abundance worldwide. The continued decline in staghorn coral abundance and the mounting challenges from both local stress and climate change will limit the coral reefs' ability to provide ecosystem services.

The future of the past in the present: biodiversity informatics and geological time.

The biological and palaeontological communities have approached the problem of informatics separately, creating a divide between communities that is both technological and sociological in nature. In this paper we describe one new advance towards solving this problem - expanding the Scratchpads platform to deal with geological time. In creating this system we have attempted to make our work open to existing communities by providing a webservice of geological time data via the GBIF Vocabularies site. We have also ensured that our system can adapt to changes in the definition of geological time intervals and is capable of querying datasets independently of the format of geological age data used.

The CRAL/TRIO and GOLD domain protein TAP-1 regulates RAF-1 activation.

The activation of the protein kinase Raf at the cell membrane is a critical step in cell signaling during development, but the mechanisms that regulate Raf activity remain incompletely defined. We previously demonstrated that the C. elegans cgr-1 gene encodes a CRAL/TRIO domain-containing protein that is a critical modulator of Ras-dependent cell fate specification during C. elegans development. Here we identify the mammalian alpha-tocopherol associated protein-1 (TAP-1) as a functional ortholog of cgr-1. TAP-1 mRNA was expressed in many tissues, and TAP-1 protein colocalized with Ras and Raf at the cell membrane. Reducing TAP-1 expression by RNA interference increased Ras/ERK signaling in multiple cell types. These functional studies demonstrate that CRAL/TRIO domain proteins play a conserved role in regulating Ras signaling. Biochemical analyses indicated that TAP-1 operates at the level of Raf, since TAP-1 function negatively regulated the amount of Raf-1 recruited to GTP-bound Ras at the cell membrane. TAP-1 plays a significant physiological role in controlling cell division, since reducing TAP-1 expression increased the oncogenic capacity of Ras transformed human cancer cell lines. These studies identify TAP-1 as a critical modulator of Ras-mediated cellular signaling.

Caribbean reef development was independent of coral diversity over 28 million years.

The relationship between natural variations in coral species diversity, reef development, and ecosystem function on coral reefs is poorly understood. Recent coral diversity varies 10-fold among geographic regions, but rates of reef growth are broadly similar, suggesting that diversity is unimportant for reef development. Differences in diversity may reflect regional differences in long-term biotic history in addition to environmental conditions. Using a combination of new and published fossil and stratigraphic data, we compared changes in coral diversity and reef development within the tropical western Atlantic over the past 28 million years. Reef development was unrelated to coral diversity, and the largest reef tracts formed after extinction had reduced diversity by 50%. High diversity is thus not essential for the growth and persistence of coral reefs.

Environmental change preceded Caribbean extinction by 2 million years.

Paleontologists typically treat major episodes of extinction as single and distinct events in which a major environmental perturbation results in a synchronous evolutionary response. Alternatively, the causes of biotic change may be multifaceted and extinction may lag behind the changes ultimately responsible because of nonlinear ecological dynamics. We examined these alternatives for the major episode of Caribbean extinction 2 million years ago (Ma). Isolation of the Caribbean from the Eastern Pacific by uplift of the Panamanian Isthmus was associated with synchronous changes in Caribbean near shore environments and community composition between 4.25 and 3.45 Ma. Seasonal fluctuations in Caribbean seawater temperature decreased 3-fold, carbonate deposition increased, and there was a striking, albeit patchy, shift in dominance of benthic ecosystems from heterotrophic mollusks to mixotrophic reef corals and calcareous algae. All of these changes correspond well with a simple model of decreased upwelling and collapse in planktonic productivity associated with the final stages of the closure of the isthmian barrier. However, extinction rates of mollusks and corals did not increase until 3-2 Ma and sharply peaked between 2 and 1 Ma, even though extinction overwhelmingly affected taxa commonly associated with high productivity. This time lag suggests that something other than environmental change per se was involved in extinction that does not occur as a single event. Understanding cause and effect will require more taxonomically refined analysis of the changing abundance and distribution patterns of different ecological guilds in the 2 million years leading up to the relatively sudden peak in extinction.

CD22 is a functional ligand for SH2 domain-containing protein-tyrosine phosphatase-1 in primary T cells.

The intracellular Src homology 2 (SH2) domain-containing protein-tyrosine phosphatase (SHP-1) has been characterized as a negative regulator of T cell function, contributing to the definition of T cell receptor signaling thresholds in developing and peripheral mouse T lymphocytes. The activation of SHP-1 is achieved through the engagement of its tandem SH2 domains by tyrosine-phosphorylated proteins; however, the identity of the activating ligand(s) for SHP-1, within mouse primary T cells, is presently unresolved. The identification of SHP-1 ligand(s) in primary T cells would provide crucial insight into the molecular mechanisms by which SHP-1 contributes to in vivo thresholds for T cell activation. Here we present a combination of biochemical and yeast genetic analyses indicating CD22 to be a T cell ligand for the SHP-1 SH2 domains. Based on these observations we have confirmed that CD22 is indeed expressed on mouse primary T cells and capable of associating with SHP-1. Significantly, CD22-deficient T cells demonstrate enhanced proliferation in response to anti-CD3 or allogeneic stimulation. Furthermore, the co-engagement of CD3 and CD22 results in a raising of TCR signaling thresholds hence demonstrating a previously unsuspected functional role for CD22 in primary T cells.

Targeting of CD45 protein tyrosine phosphatase activity to lipid microdomains on the T cell surface inhibits TCR signaling.

CD45, a transmembrane protein tyrosine phosphatase (PTP), can either positively or negatively regulate Src-family protein tyrosine kinase (PTK) activity in vivo. It is proposed that TCR-initiated signaling requires the segregation of PTP activities from the engaged TCR, based upon the differential membrane compartmentalization on the T cell surface. To test the importance of CD45 exclusion from lipid microdomains for proper TCR signaling, a chimeric molecule was generated by fusing the CD45 cytoplasmic region, which contains the PTP domains, to the amino-terminal 12 amino acids of Lck, which target Lck to lipid microdomains. Using 3A9 T lymphocyte hybridoma (3A9H) cells whose TCR recognizes hen egg-white lysozyme (HEL), Lck-CD45 expression resulted in its targeting to lipid microdomains. The 3A9H cells expressing Lck-CD45 were reduced in their responses to HEL or co-cross-linking of CD3 and CD4, as assessed by IL-2 production and Ca(2+) mobilization. Src-family PTK activity associated with lipid microdomains was also decreased. These results suggest that the segregation of CD45 from proximal TCR signaling components is necessary for TCR signaling and that the targeting of CD45 PTP activity to lipid microdomains on the T cell surface results in decreased sensitivity of TCR-mediated signaling.

Polar redistribution of the sialoglycoprotein CD43: implications for T cell function.

Contact between T cells and APCs results in the orchestrated segregation of molecules at the cell-cell interface and formation of a specialized structure termed the immunological synapse. This model predicts the topological seclusion of large molecules such as CD43 from the site of closest contact between the T cell and APC, allowing for the close apposition of cell membranes and effective TCR engagement. Similarly, during T cell migration segregation of CD43 to the uropod is thought to aid integrin adhesion at the leading edge of the cell by removing steric hindrance. We show in this work that CD43 distribution on T cells is regulated by a membrane proximal ezrin binding site and that failure to displace CD43 from the immunological synapse has no inhibitory effects on primary T cell activation. We also report that CD43 expression at the contact zone between T cells and matrix does not negatively regulate motility but may regulate LFA-1 de-adhesion. These results suggest that the steric barrier model of CD43 is inadequate and that alternative mechanisms account for the negative regulatory properties of CD43.