Fish, Coral, and Sponge Assemblages Associated With Altiphotic and Mesophotic Reefs Along the Guánica Biosphere Reserve Continental Shelf Edge, Southwest Puerto Rico

The benthic and fish communities of the central portion of the Guánica, Puerto Rico shelf edge were studied to determine species abundance, distributions and species overlap between two depth stratifications, 20 and 45 m, at eight sites. A total of 67 fish species belonging to 21 families were identified. Similar species richness estimates were observed between depths, though fish assemblage composition differed significantly, with observable changes in feeding guild contributions of herbivore and omnivore (20 m) to a deeper assemblage composed of piscivores and planktivores (45 m). Coral assemblages consisted of 31 species at 20 m and 11 species at 45 m, accounting for 17.0% (±1.76 SE) and 2.6% (±0.89 SE) benthic cover for the altiphotic and mesophotic surveys, respectively. The altiphotic and mesophotic coral reef communities support different scleractinian coral assemblages with minimal species overlap. Altiphotic surveys of sponges yielded a higher species richness than mesophotic, with 60 and 54 species respectively, and an overall total of 71 species identified from both depths, with 45 species overlapping (63.0%). The percent cover of sponges surveyed at altiphotic reefs accounted for 9.0% (±1.04 SE), while the percent cover of sponges surveyed at mesophotic reefs was 14.0% (±1.96 SE). Our data show fish, coral, and sponge assemblages are differentiated between 20 and 45 m along the Guánica shelf edge offshore of the Guánica Biosphere Reserve. This study represents the first observations for species distributions of adjacent altiphotic and mesophotic coral reef habitats along the Guánica shelf edge, as well as provides an annotated species list of the local sponge fauna. Combined, these results highlight the need for continued environmental stewardship and conservation in the area

LKB1 loss links serine metabolism to DNA methylation and tumorigenesis

Intermediary metabolism generates substrates for chromatin modification, enabling the potential coupling of metabolic and epigenetic states. Here we identify a network linking metabolic and epigenetic alterations that is central to oncogenic transformation downstream of the liver kinase B1 (LKB1, also known as STK11) tumour suppressor, an integrator of nutrient availability, metabolism and growth. By developing genetically engineered mouse models and primary pancreatic epithelial cells, and employing transcriptional, proteomics, and metabolic analyses, we find that oncogenic cooperation between LKB1 loss and KRAS activation is fuelled by pronounced mTOR-dependent induction of the serine-glycine-one-carbon pathway coupled to S-adenosylmethionine generation. At the same time, DNA methyltransferases are upregulated, leading to elevation in DNA methylation with particular enrichment at retrotransposon elements associated with their transcriptional silencing. Correspondingly, LKB1 deficiency sensitizes cells and tumours to inhibition of serine biosynthesis and DNA methylation. Thus, we define a hypermetabolic state that incites changes in the epigenetic landscape to support tumorigenic growth of LKB1-mutant cells, while resulting in potential therapeutic vulnerabilities

Crystal Structure of the PIM2 Kinase in Complex with an Organoruthenium Inhibitor

BACKGROUND: The serine/threonine kinase PIM2 is highly expressed in human leukemia and lymphomas and has been shown to positively regulate survival and proliferation of tumor cells. Its diverse ATP site makes PIM2 a promising target for the development of anticancer agents. To date our knowledge of catalytic domain structures of the PIM kinase family is limited to PIM1 which has been extensively studied and which shares about 50% sequence identity with PIM2. PRINCIPAL FINDINGS: Here we determined the crystal structure of PIM2 in complex with an organoruthenium complex (inhibition in sub-nanomolar level). Due to its extraordinary shape complementarity this stable organometallic compound is a highly potent inhibitor of PIM kinases. SIGNIFICANCE: The structure of PIM2 revealed several differences to PIM1 which may be explored further to generate isoform selective inhibitors. It has also demonstrated how an organometallic inhibitor can be adapted to the binding site of protein kinases to generate highly potent inhibitors. ENHANCED VERSION: This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1

Growth dynamics in Acropora cervicornis and A. prolifera in southwest Puerto Rico

Natural population recovery of Acropora palmata, A. cervicornis and their hybrid, Acropora prolifera, have fluctuated significantly after their Caribbean-wide, disease-induced mass mortality in the early 1980s. Even though significant recovery has been observed in a few localities, recurrent disease outbreaks, bleaching, storm damage, local environmental deterioration, algae smothering, predation, low sexual recruitment and low survivorship have affected the expected, quick recovery of these weedy species. In this study, the status of three recovering populations of A. cervicornis and two of A. prolifera were assessed over one year using coral growth and mortality metrics, and changes in their associated algae and fish/invertebrate communities in three localities in the La Parguera Natural Reserve (LPNR), southwest coast of Puerto Rico. Five branches were tagged in each of 29, medium size (1-2 m in diameter) A. cervicornis and 18 A. prolifera colonies in the Media Luna, Mario and San Cristobal reefs off LPNR. Branches were measured monthly, together with observations to evaluate associated disease(s), algae accumulation and predation. A. cervicornis grew faster [3.1 +/- 0.44 cm/month (= 37.2 cm/y)] compared to A. prolifera [2.6 +/- 0.41 cm/month (= 31.2 cm/y)], and growth was significantly higher during Winter-Spring compared to Summer-Fall for both taxa (3.5 +/- 0.58 vs. 0.53 +/- 0.15 cm/month in A. cervicornis, and 2.43 +/- 0.71 vs. 0.27 +/- 0.20 cm/month in A. prolifera, respectively). Algal accumulation was only observed in A. cervicornis, and was higher during Spring-Summer compared to Fall-Winter (6.1 +/- 0.91 cm/month and 3.8 +/- 0.29 cm/month, respectively, (PERMANOVA, df = 2, MS = 10.2, p = 0.37)). Mortality associated with white band disease, algae smothering and fish/invertebrate predation was also higher in A. cervicornis and varied among colonies within sites, across sites and across season. The balance between tissue grow and mortality determines if colonies survive. This balance seems to be pushed to the high mortality side often by increasing frequency of high thermal anomalies, inducing bleaching and disease outbreaks and other factors, which have historically impacted the natural recovery of these taxa in the La Parguera Natural Reserve in Puerto Rico and possibly other areas in the region. Overall, results indicate variability in both growth and mortality rates in both taxa across localities and seasons, with A. cervicornis showing overall higher mortalities compared to A. prolifera

Cetacean sightings in Puerto Rican waters: including the first underwater photographic documentation of a minke whale (Balaenoptera acutorostrata)

Opportunistic encounters by experts and the public (i.e. fishermen, tourists) can be great assets to understanding cetacean distribution, especially in areas where surveys are limited. Sightings of Puerto Rican pelagic cetaceans have been reported in the past, with known seasonality in some species. Within this report, we document sightings for eight species, report new monthly distributions for three of these species, as well as the presence of rough-toothed dolphins close to the coast, and the first underwater sighting of a minke whale (Balaenoptera acutorostrata) off San Juan, Puerto Rico. Unfortunately, the lack of long-term studies due to limited funding and resources has been an obstacle in determining species diversity and overall health of cetacean populations. However, this note provides evidence that collaboration between marine biologists and citizen-based science is possible and desired, and serves as a valuable resource to protect and conserve native, pelagic, and transient cetacean species around Puerto Rican waters

De novo transcriptome assembly of the coral Agaricia lamarcki (Lamarck's sheet coral) from mesophotic depth in southwest Puerto Rico

The plating coral, Agaricia lamarcki is a widely distributed species inhabiting reefs across the Caribbean basin and Florida. This species is of interest since it is considered a depth-generalist, found from 10 to 70 m. Given the scope of contemporary studies on this coral's population dynamics and physiology, as well as, the potential of mesophotic reefs to be refuge habitats for deteriorated shallow water reefs, we present the first de novo transcriptome assembly of an important mesophotic coral. Using next-generation paired-end sequencing (Illumina Hiseq4000; 2 × 150 bp), we obtained a total of 82,506,058 raw reads. The novel transcriptome assembly strategy included the recently developed National Center for Genome Analysis Support de novo transcriptome assembly pipeline. Assembly produced a total of 101,322 biologically true, non-redundant transcripts with an average contig length of 959 and N50 of 1830. EvidentialGene and TransDecoder were used to identify open reading frames (ORFs) with homology insight provided by the UniProtKb and PFAM databases. ORF prediction resulted in 38,517 putative ORFs of which 12,107 ORFs were annotated as genes dealing with molecular function, 1266 with biological processes and 416 with cellular components

Fish, coral, and sponge assemblages associated with altiphotic and mesophotic reefs along the Guánica biosphere reserve continental shelf edge, Southwest Puerto Rico

The benthic and fish communities of the central portion of the Guánica, Puerto Rico shelf edge were studied to determine species abundance, distributions and species overlap between two depth stratifications, 20 and 45 m, at eight sites. A total of 67 fish species belonging to 21 families were identified. Similar species richness estimates were observed between depths, though fish assemblage composition differed significantly, with observable changes in feeding guild contributions of herbivore and omnivore (20 m) to a deeper assemblage composed of piscivores and planktivores (45 m). Coral assemblages consisted of 31 species at 20 m and 11 species at 45 m, accounting for 17.0% (±1.76 SE) and 2.6% (±0.89 SE) benthic cover for the altiphotic and mesophotic surveys, respectively. The altiphotic and mesophotic coral reef communities support different scleractinian coral assemblages with minimal species overlap. Altiphotic surveys of sponges yielded a higher species richness than mesophotic, with 60 and 54 species respectively, and an overall total of 71 species identified from both depths, with 45 species overlapping (63.0%). The percent cover of sponges surveyed at altiphotic reefs accounted for 9.0% (±1.04 SE), while the percent cover of sponges surveyed at mesophotic reefs was 14.0% (±1.96 SE). Our data show fish, coral, and sponge assemblages are differentiated between 20 and 45 m along thes provides an annotated species list of the local sponge fauna. Combined, these results highlight the need for con Guánica shelf edge offshore of the Guánica Biosphere Reserve. This study represents the first observations for species distributions of adjacent altiphotic and mesophotic coral reef habitats along the Guánica shelf edge, as well atinued environmental stewardship and conservation in the area

Associated organisms inhabiting the calcareous sponge Clathrina lutea in La Parguera, Puerto Rico

Sponges provide an array of ecological services and benefits for Caribbean coral reefs. They function as habitats for a bewildering variety of species, however limited attention has been paid in the systematics and distribution of sponge-associated fauna in the class Calcarea or for that matter of sponges in the Caribbean. The goal of this study was to characterize infaunal assemblages from a calcareous sponge, Clathrina lutea, across multiple reefs from the La Parguera Natural Reserve, Puerto Rico. The associated fauna from 43 C. lutea specimens yielded a total of 2,249 associated infauna distributed in seven invertebrate phyla. Arthropoda was the most abundant phylum accounting for 62.5% of total abundance, followed by Annelida (21.0%) and Nematoda (5.5%). Limited patterns of temporal or spatial variability were surmised due to the opportunistic sampling effort afforded to this investigation from the cryptic nature of this species. A concordance between our data set and those for the class Demospongiae were observed, with the most abundant associated fauna being copepods and polychaetes. However, when compared to other Calcarea, the present study found considerably more associated fauna

Reconstructing past disturbance in coral communities using U-Th dating of dead coral skeletons

In the absence of detailed broad-scale studies, both spatially and temporally, the overall status (disturbed, recovering, or in decline) of many of the reefs that make up the Great Barrier Reef remains uncertain. Moreover, of the numerous and varied threats, their relative role in impacting individual reefs is generally unclear. Here, we adopt a novel approach to reliably reconstruct historical disturbance events at Rib and Davies Reefs, two mid-shelf reefs, using uranium-thorium (U-Th) dating of dead corals. Corrected 230Th ages obtained from dead Acropora spp. bracket time periods of lowest coral cover observed during independent ecological surveys in the late 1980s and 2000s at 1988.2 ± 1.3 and 2003.9 ± 6.2 CE, shortly after the arrival of crown-of-thorns starfish (CoTS) at Rib Reef in 1983–1985 and 2000–2002, respectively. At Davies Reef, 230Th ages dated to 1999.2 ± 1.2 CE when coral cover was halved as a result of Cyclone Tessi and an “unknown” disturbance in 2000–2001. Prior to modern surveys, there is remarkable overlap in 230Th ages between reefs, with repeated peaks in the age distribution having a return period of ∼10–15 years, akin to the periodicity of modern CoTS outbreaks. Our findings suggest that U-Th dating of dead corals can provide a robust foundation for understanding disturbance history and show promise in contributing to the effective monitoring of coral communities by providing a reliable benchmark with which to assess recovery