Simulation of the effects of Acanthaster planci on the population structure of massive corals in the genus Porites: evidence of population resilience?

Scleractinian corals in the genus Porites are slow growing, can live for centuries, and can attain great size. In these respects they differ from the majority of coral species, which grow faster and live for years to decades. The predatory starfish Acanthaster planci L. feeds on a wide range of coral species including Porites spp., and during outbreaks in its populations, causes high coral mortality and injury over much of the affected reefs. Because they are slow growing and because recent outbreaks of the starfish occurred only 15 years apart, it may be argued that the Porites populations on affected reefs will be sent into a period of prolonged decline. The present study uses a size stage model of the transition matrix type to predict effects of starfish outbreaks of various frequencies on Porites populations. A transition matrix characterizing the mortality and injury caused in different Porites size classes at John Brewer Reef during an outbreak year was determined from field data. Transition matrices for non-outbreak years were constructed on the basis of realistic growth rates and postulated survivorship and recruitment schedules. The medium term (100 years) effects of outbreaks were simulated by alternation of a single iteration of the outbreak matrix with many iterations of each non-outbreak matrix. By varying the interval between simulated outbreaks it was possible to define combinations of growth rate, survivorship and recruitment which were viable for various outbreak intervals. Simulations based on estimates of the initial size frequency distribution, recruitment rates and colony growth rates for the John Brewer Reef population predicted that the population would remain viable in the face of outbreaks every 15 years only if juvenile and adult survivorship were high. However, within the range of colony growth rates known to occur throughout the Great Barrier Reef and at recruitment rates of the same order as those estimated in the field population, it appears that a much wider range of survivorship schedules could lead to parity or even sustained growth in the face of outbreaks recurring at intervals of from 1 to 3 decades. It is suggested that because the key measurable parameters (initial size structure, damage characteristics, recruitment rate and growth rate) are likely to be very patchy at the scale of whole reefs, no general statement concerning the prognosis for Porites would be meaningful. However the model provides a tool by which a standardized evaluation of this type of field data may be made on a reef by reef basis.     

Quantitative video sampling of coral reef benthos: large-scale application

The feasibility of reliably estimating percent cover of coral reef benthos by video techniques is examined. Video belt transects were recorded within study areas on Davies and John Brewer Reefs in the central Great Barrier Reef during September 1988. Two years later in September 1990, the study area at Davies Reef was resampled concurrently by video and line intercept transects. Percent cover data of major coral growth forms and non-biotic physionomic attributes were extracted from video footage by scoring the identity of items located at even or random spaced points along the transect. A cost-benefit analysis which compared increases in precision with increases in sampling effort suggested that the optimum regime for analyzing 200 m long video transects was five subsamples of 110 random points or one sample of 550. This regime resolved both spatial variability at large and smaller spatial scales (between study areas and among transects) and temporal change (within a single study area over a two year period) for total live coral and individual growth forms. The strengths of the technique lie in its cost-savings in filed expenses, and in the production of a permanent visual record. The limitations of the technique lie in reduced taxonomic resolution when compared with hands on field techniques. The results suggest that for broad taxonomic categories of coral reef benthos reliable estimates of relative abundance can be obtained by video techniques.     

Regional and local variability in recovery of shallow coral communities: Moorea,French Polynesia and central Great Barrier Reef

Coral communities at Moorea, French Polynesia, and on the Great Barrier Reef (GBR), Australia, were severely depleted by disturbances early in the 1980s. Corals were killed by the predatory starfish Acanthaster planci, by cyclones, and/or by depressed sea level. This study compares benthic community structure and coral population structures on three disturbed reefs (Vaipahu-Moorea; Rib and John Brewer Reefs-GBR) and one undisturbed reef (Davies Reef-GBR) in 1987–89. Moorea barrier reefs had been invaded by tall macrophytes Turbinaria ornata and Sargassum sp., whereas the damaged GBR reefs were colonised by a diverse mixture of short macrophytes, turfs and coralline algae. The disturbed areas had broadly similar patterns of living and dead standing coral, and similar progress in recolonisation, which suggests their structure may converge towards that of undisturbed Davies Reef. Corals occupying denuded areas at Vaipahu, Rib and John Brewer were small (median diameter 5 cm in each case) and sparse (means 4–8 m^-2) compared to longer established corals at Davies Reef (median diameter 9 cm; mean 18 m^-2). At Moorea, damselfish and sea urchins interacted with corals in ways not observed in the GBR reefs. Territories of the damselfish Stegastes nigricans covered much of Moorea's shallow reef top. They had significantly higher diversity and density of post-disturbance corals than areas outside of territories, suggesting that the damselfish exerts some influences on coral community dynamics. Sea urchins on Moorea (Diadema setosum Echinometra mathaei, Echinotrix calamaris) were causing widespread destruction of dead standing coral skeletons. Overall, it appears that the future direction and speed of change in the communities will be explicable more in terms of local than regional processes.     

Characterisation of two ornithine-containing lipids from Erwina aroideae

An apparently pure ornithine-containing lipid (OCL) was isolated from Erwina aroideae by solvent extraction and thin-layer chromatography (TLC). However, selective hydrolysis of the lipid under acidic and basic conditions and analysis of hydrolysates by gas chromatography-mass spectrometry (GCMS) showed that two structurally similar OCL were in fact present. These lipids both contained a 3-hydroxyhexadecanoic acid moiety which was linked to ornithine by an amide group formed between the 2-amino group of ornithine and the carboxyl group of the acid. The two lipids, however, differ in the nature of the fatty acid bound through an ester linkage to the hydroxyl group of the 3-hydroxyhexadecanoic acid moiety. One lipid is the ester of hexadecanoic acid whereas the other lipid is the ester of octadecenoic acid. These lipids are present in approximately equal amounts.     

Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals

Background

In recent years large bibliographic databases have made much of the published literature of biology available for searches. However, the capabilities of the search engines integrated into these databases for text-based bibliographic searches are limited. To enable searches that deliver the results expected by comparative anatomists, an underlying logical structure known as an ontology is required.

Development and Testing of the Ontology

Here we present the Mammalian Feeding Muscle Ontology (MFMO), a multi-species ontology focused on anatomical structures that participate in feeding and other oral/pharyngeal behaviors. A unique feature of the MFMO is that a simple, computable, definition of each muscle, which includes its attachments and innervation, is true across mammals. This construction mirrors the logical foundation of comparative anatomy and permits searches using language familiar to biologists. Further, it provides a template for muscles that will be useful in extending any anatomy ontology. The MFMO is developed to support the Feeding Experiments End-User Database Project (FEED, https://feedexp.org/), a publicly-available, online repository for physiological data collected from in vivo studies of feeding (e.g., mastication, biting, swallowing) in mammals. Currently the MFMO is integrated into FEED and also into two literature-specific implementations of Textpresso, a text-mining system that facilitates powerful searches of a corpus of scientific publications. We evaluate the MFMO by asking questions that test the ability of the ontology to return appropriate answers (competency questions). We compare the results of queries of the MFMO to results from similar searches in PubMed and Google Scholar.

Results and Significance

Our tests demonstrate that the MFMO is competent to answer queries formed in the common language of comparative anatomy, but PubMed and Google Scholar are not. Overall, our results show that by incorporating anatomical ontologies into searches, an expanded and anatomically comprehensive set of results can be obtained. The broader scientific and publishing communities should consider taking up the challenge of semantically enabled search capabilities.     

Mutations in CSPP1 Cause Primary Cilia Abnormalities and Joubert Syndrome with or without Jeune Asphyxiating Thoracic Dystrophy

Joubert syndrome (JBTS) is a recessive ciliopathy in which a subset of affected individuals also have the skeletal dysplasia Jeune asphyxiating thoracic dystrophy (JATD). Here, we have identified biallelic truncating CSPP1 (centrosome and spindle pole associated protein 1) mutations in 19 JBTS-affected individuals, four of whom also have features of JATD. CSPP1 mutations explain ∼5% of JBTS in our cohort, and despite truncating mutations in all affected individuals, the range of phenotypic severity is broad. Morpholino knockdown of cspp1 in zebrafish caused phenotypes reported in other zebrafish models of JBTS (curved body shape, pronephric cysts, and cerebellar abnormalities) and reduced ciliary localization of Arl13b, further supporting loss of CSPP1 function as a cause of JBTS. Fibroblasts from affected individuals with CSPP1 mutations showed reduced numbers of primary cilia and/or short primary cilia, as well as reduced axonemal localization of ciliary proteins ARL13B and adenylyl cyclase III. In summary, CSPP1 mutations are a major cause of the Joubert-Jeune phenotype in humans; however, the mechanism by which these mutations lead to both JBTS and JATD remains unknown.     

Predicting Novel Human Gene Ontology Annotations Using Semantic Analysis

The correct interpretation of many molecular biology experiments depends in an essential way on the accuracy and consistency of the existing annotation databases. Such databases are meant to act as repositories for our biological knowledge as we acquire and refine it. Hence, by definition, they are incomplete at any given time. In this paper, we describe a technique that improves our previous method for predicting novel GO annotations by extracting implicit semantic relationships between genes and functions. In this work, we use a vector space model and a number of weighting schemes in addition to our previous latent semantic indexing approach. The technique described here is able to take into consideration the hierarchical structure of the Gene Ontology (GO) and can weight differently GO terms situated at different depths. The prediction abilities of 15 different weighting schemes are compared and evaluated. Nine such schemes were previously used in other problem domains, while six of them are introduced in this paper. The best weighting scheme was a novel scheme, n2tn. Out of the top 50 functional annotations predicted using this weighting scheme, we found support in the literature for 84 percent of them, while 6 percent of the predictions were contradicted by the existing literature. For the remaining 10 percent, we did not find any relevant publications to confirm or contradict the predictions. The n2tn weighting scheme also outperformed the simple binary scheme used in our previous approach.     

Effects of post-breeding moult and energetic condition on timing of songbird migration into the tropics

Each autumn billions of songbirds migrate between the temperate zone and tropics, but little is known about how events on the breeding grounds affect migration to the tropics. Here, we use light level geolocators to track the autumn migration of wood thrushes Hylocichla mustelina and test for the first time if late moult and poor physiological condition prior to migration delays arrival on the winter territory. Late nesting thrushes postponed feather moult, and birds with less advanced moult in August were significantly farther north on 10 October while en route to the tropics. Individuals in relatively poor energetic condition in August (high β-Hydroxybutyrate, low triglyceride, narrow feather growth bars) passed into the tropics significantly later in October. However, late moult and poor pre-migratory condition did not result in late arrival on the winter territory because stopover duration was highly variable late in migration. Although carry-over effects from the winter territory to spring migration may be strong in migratory songbirds, our study suggests that high reproductive effort late in the season does not impose time constraints that delay winter territory acquisition.     

The use of whole genome amplification in the study of human disease

The availability of large amounts of genomic DNA is of critical importance for many of the molecular biology assays used in the analysis of human disease. However, since the amount of patient tissue available is often limited and as particular foci of interest may consist of only a few hundred cells, the yield of DNA is often insufficient for extensive analysis. To address this problem, several whole genome amplification (WGA) methodologies have been developed. Initial WGA approaches were based on the polymerase chain reaction (PCR). However, recent reports have described the use of non-PCR-based linear amplification protocols for WGA. Using these methods, it is possible to generate microgram quantities of DNA starting with as little as 1mg of genomic DNA. This review will provide an overview of WGA approaches and summarize some of the uses for amplified DNA in various high-throughput genetic applications.     

Coral growth on three reefs: development of recovery benchmarks using a space for time approach

This 14-year study (1989–2003) develops recovery benchmarks based on a period of very strong coral recovery in Acropora-dominated assemblages on the Great Barrier Reef (GBR) following major setbacks from the predatory sea-star Acanthaster planci in the early 1980s. A space for time approach was used in developing the benchmarks, made possible by the choice of three study reefs (Green Island, Feather Reef and Rib Reef), spread along 3 degrees of latitude (300 km) of the GBR. The sea-star outbreaks progressed north to south, causing death of corals that reached maximum levels in the years 1980 (Green), 1982 (Feather) and 1984 (Rib). The reefs were initially surveyed in 1989, 1990, 1993 and 1994, which represent recovery years 5–14 in the space for time protocol. Benchmark trajectories for coral abundance, colony sizes, coral cover and diversity were plotted against nominal recovery time (years 5–14) and defined as non-linear functions. A single survey of the same three reefs was conducted in 2003, when the reefs were nominally 1, 3 and 5 years into a second recovery period, following further Acanthaster impacts and coincident coral bleaching events around the turn of the century. The 2003 coral cover was marginally above the benchmark trajectory, but colony density (colonies.m⁻²) was an order of magnitude lower than the benchmark, and size structure was biased toward larger colonies that survived the turn of the century disturbances. The under-representation of small size classes in 2003 suggests that mass recruitment of corals had been suppressed, reflecting low regional coral abundance and depression of coral fecundity by recent bleaching events. The marginally higher cover and large colonies of 2003 were thus indicative of a depleted and aging assemblage not yet rejuvenated by a strong cohort of recruits.