Warming and acidification threaten glass sponge Aphrocallistes vastus pumping and reef formation.

The glass sponge Aphrocallistes vastus contributes to the formation of large reefs unique to the Northeast Pacific Ocean. These habitats have tremendous filtration capacity that facilitates flow of carbon between trophic levels. Their sensitivity and resilience to climate change, and thus persistence in the Anthropocene, is unknown. Here we show that ocean acidification and warming, alone and in combination have significant adverse effects on pumping capacity, contribute to irreversible tissue withdrawal, and weaken skeletal strength and stiffness of A. vastus. Within one month sponges exposed to warming (including combined treatment) ceased pumping (50-60%) and exhibited tissue withdrawal (10-25%). Thermal and acidification stress significantly reduced skeletal stiffness, and warming weakened it, potentially curtailing reef formation. Environmental data suggests conditions causing irreversible damage are possible in the field at +0.5 °C above current conditions, indicating that ongoing climate change is a serious and immediate threat to A. vastus, reef dependent communities, and potentially other glass sponges.

Assessing condition and ecological role of deep-water biogenic habitats: Glass sponge reefs in the Salish Sea.

Biogenic habitats play important roles in shallow-water ecosystems, but their roles in deeper waters are less well-studied. We quantitatively assessed 19 glass sponge reefs in the Salish Sea for live reef-building sponge cover and biodiversity, explored potential drivers behind variation observed among reefs, and quantified individual and collective roles the reefs play in filtration and carbon removal. The reefs support diverse and abundant communities of invertebrates and fish, with 115 unique taxonomic groups observed. Sponge cover varied widely between reefs: percent live reef-building sponge cover ranged from 0.2 to 17.5% and proportion of live reef habitat category ranged from 0.2 to 92%. These differences were predominantly driven by the seabed terrain characteristics such as seafloor rugosity, curvature, and depth; human pressure measures explored in this study - density of anthropogenic objects and fishing footprint over the past 17 years - did not mask the natural influence of seabed terrain. The difference in sponge cover between the reefs led to wide variation in ecosystem function with individual reefs processing between 465 and 47,300 L/m2 per day. Collectively, each day the 19 reefs filter 1.04 × 1011 L of water which corresponds to 1% of the total water volume in Strait of Georgia and Howe Sound combined. The reefs remove up to 1 g of carbon per m2 per day, comparable to carbon sequestration rates reported for terrestrial old growth forests and to "blue carbon" sequestration rates by marine vegetation. Implications for sponge reef conservation and monitoring are discussed.

The relationship between physical ill-health and mental ill-health in adults with intellectual disabilities.

BACKGROUND: People with intellectual disabilities face a much greater burden and earlier onset of physical and mental ill-health than the general adult population. Physical-mental comorbidity has been shown to result in poorer outcomes in the general population, but little is known about this relationship in adults with intellectual disabilities. AIMS: To identify whether physical ill-health is associated with mental ill-health in adults with intellectual disabilities and whether the extent of physical multi-morbidity can predict the likelihood of mental ill-health. To identify any associations between types of physical ill-health and mental ill-health. METHOD: A total of 1023 adults with intellectual disabilities underwent comprehensive health assessments. Binary logistic regressions were undertaken to establish any association between the independent variables: total number of physical health conditions, physical conditions by International Classification of Disease-10 chapter and specific physical health conditions; and the dependent variables: problem behaviours, mental disorders of any type. All regressions were adjusted for age, gender, level of intellectual disabilities, living arrangements, neighbourhood deprivation and Down syndrome. RESULTS: The extent of physical multi-morbidity was not associated with mental ill-health in adults with intellectual disabilities as only 0.8% of the sample had no physical conditions. Endocrine disease increased the risk of problem behaviours [odds ratio (OR): 1.22, 95% confidence interval (CI): 1.02-1.47], respiratory disease reduced the risk of problem behaviours (OR: 0.73, 95% CI: 0.54-0.99) and mental ill-health of any type (OR: 0.73, 95% CI: 0.58-0.92), and musculoskeletal disease reduced the risk of mental ill-health of any type (OR: 0.84, 95% CI: 0.73-0.98). Ischaemic heart disease increased the risk of problem behaviours approximately threefold (OR: 3.29, 95% CI: 1.02-10.60). CONCLUSIONS: The extent of physical multi-morbidity in the population with intellectual disabilities is overwhelming, such that associations are not found with mental ill-health. Mental health interventions and preventative measures are essential for the entire population with intellectual disabilities and should not be focussed on subgroups based on overall health burden.

Evaluation of the Potency, Neutralizing Antibody Response, and Stability of a Recombinant Fusion Protein Vaccine for Streptococcus pyogenes.

Streptococcus pyogenes or group A streptococcus (GAS) is a Gram-positive bacterium that can cause a wide range of diseases, including pharyngitis, impetigo, scarlet fever, necrotizing fasciitis, rheumatic fever, and streptococcal toxic shock syndrome. Despite the increasing burden on global health caused by GAS, there is currently no licensed vaccine available. In this study, we evaluated immunogenicity, induction of neutralizing antibodies, and stability of a new recombinant fusion protein vaccine that targets infections from GAS. The recombinant fusion protein (SpeAB) combines inactive mutant forms of streptococcal pyrogenic exotoxin A (SpeA) and streptococcal pyrogenic exotoxin B (SpeB). The SpeAB vaccine evaluated in this study was adsorbed to an aluminum adjuvant and demonstrated robust immunogenicity, eliciting production of specific neutralizing antibodies against SpeA and SpeB, two major virulence factors of S. pyogenes. Stability studies suggest that the vaccine will retain immunogenicity for at least 2 years when stored at refrigerated temperatures. This novel vaccine shows great potential to provide protection against GAS infections and to reduce the burden of GAS disease globally.

Vertebrate seed dispersers maintain the composition of tropical forest seedbanks.

The accumulation of seeds in the soil (the seedbank) can set the template for the early regeneration of habitats following disturbance. Seed dispersal is an important factor determining the pattern of seed rain, which affects the interactions those seeds experience. For this reason, seed dispersal should play an important role in structuring forest seedbanks, yet we know little about how that happens. Using the functional extirpation of frugivorous vertebrates from the island of Guam, together with two nearby islands (Saipan and Rota) that each support relatively intact disperser assemblages, we aimed to identify the role of vertebrate dispersers in structuring forest seedbanks. We sampled the seedbank on Guam where dispersers are absent, and compared this with the seedbank on Saipan and Rota where they are present. Almost twice as many species found in the seedbank on Guam, when compared with Saipan and Rota, had a conspecific adult within 2 m. This indicates a strong role of vertebrate dispersal in determining the identity of seeds in the seedbank. In addition, on Guam, a greater proportion of samples contained no seeds and overall species richness was lower than on Saipan. Differences in seed abundance and richness between Guam and Rota were less clear, as seedbanks on Rota also contained fewer species than Saipan, possibly due to increased post-dispersal seed predation. Our findings suggest that vertebrate seed dispersers can have a strong influence on the species composition of seedbanks. Regardless of post-dispersal processes, without dispersal, seedbanks no longer serve to increase the species pool of recruits during regeneration.

Effects of submarine power transmission cables on a glass sponge reef and associated megafaunal community.

We examined the effects of submarine power transmission cable installation and operation on glass sponge reef condition and associated megafauna. Video and still imagery were collected using a Remotely Operated Vehicle twice a year for 4 years following cable installation. The effects of cables on glass sponges were assessed by comparing sponge cover along fixed transects and at marked index sites. Megafauna counts along transects were used to explore the effects on associated community. We found no evidence of cable movement across the sponge reef surface. Live sponge cover was found to be consistently lower along cable transects and at cable index sites compared to controls. Live sponge cover was the lowest (55 ± 1.1% decrease) at cable index sites 1.5 years after installation and recovered to 85 ± 30.6% of the original size over the following 2 years. Our data suggest 100% glass sponge mortality along the direct cable footprint and 15% mortality in the surrounding 1.5 m corridor 3.5 years after cable installation. Growth rate of a new glass sponge was 1 and 3 cm/year in first and second year, respectively, and appeared to be seasonal. We observed a diverse megafaunal community with representatives from 7 phyla and 14 classes. Total megafauna, spot prawn, and other Arthropoda abundances were slightly lower along cable transects although the effect of cable presence was not statistically significant. The following measures could be taken to reduce the amount of damage to glass sponge reefs and associated fauna: routing the cable around reefs, whenever possible, minimizing cable movement across the surface of the reef at installation and routine operation, and assessing potential damage to glass sponges prior to decommissioning.

Body size and sexual size dimorphism in primates: influence of climate and net primary productivity.

Understanding the evolution of body size and sexual size dimorphism has been a longstanding goal in evolutionary biology. Previous work has shown that environmental stress can constrain male-biased sexual size dimorphism at the population level, but we know little about how this might translate to geographical patterns of body size and sexual size dimorphism at the species level. Environmental constraints due to a highly seasonal, resource-poor and/or variable environment have often been cited to explain the unusual lack of sexual size dimorphism among Madagascar's diverse and numerous primate taxa; however, empirical tests of this hypothesis are lacking. Using a phylogenetic approach and a geographical information system platform, we explored the role of seasonality, interannual variability and annual measures of temperature and rainfall, and net primary productivity on patterns of body size and sexual size dimorphism across 130 species of primates. Phylogenetically controlled comparisons showed no support for a role of environmental constraints in moderating sexual size dimorphism at the interspecific level, despite significant associations of environmental variables with body mass. Results suggest that the focus of discussions that have dominated in the last two decades regarding the role of environmental constraints in driving patterns of monomorphism of Madagascar's lemurs should be reconsidered; however, the conundrum remains.

Evolution of sexual size monomorphism: the influence of passive mate guarding.

Some species have potential for intense mate competition yet exhibit little or no sexual size dimorphism, despite predictions from sexual selection theory. Using a conceptual model, we show the conditions for which passive mate guarding with copulatory plugs can be an alternative and more successful strategy to active (direct) guarding, reducing selection pressure on large male size. The model predicts that copulatory plugs in mammals should be favoured in species for which females have short sexual receptivity periods. Using data on 62 primate species and a phylogenetic regression approach, we show that, as predicted, copulatory plugs are negatively associated with degree of sexual dimorphism and females' sexual receptivity length. Penile spines are also significantly associated with plug use and short receptivity periods suggesting a possible offensive role in sperm competition. Results highlight that life-history characteristics, such as sexual receptivity lengths, may alter the costs and benefits of alternative male strategies and thus alter the strength of sexual selection.

Detection of two porcine circovirus type 2 genotypic groups in United States swine herds.

In late 2005, sporadic cases of an acute onset disease of high mortality were observed in 10- to 16-week-old growing pigs among several swine herds of the United States. Tissues from the affected pigs in Kansas, Iowa, and North Carolina were examined, and porcine circovirus type 2 (PCV2) was detected consistently among these tissues. Phylogenetically, PCV2 can be divided into two major genotypic groups, PCV2-group 1 and PCV2-group 2. Whereas PCV2-group 1 isolates were detected in all the diseased animals, only two of the diseased animals harbored PCV2-group 2 isolates. This observation is important because PCV2-group 1 isolates had never been reported in the United States before (GenBank as of May 16, 2006), and they are closely related to the PCV2-group 1 isolates that have been described in Europe and Asia, previously. Our analysis revealed that each genotypic group contains a distinct stretch of nucleotide or amino acid sequence that may serve as a signature motif for PCV2-group 1 or PCV2-group 2 isolates.

The DNA sequence and biological annotation of human chromosome 1.

The reference sequence for each human chromosome provides the framework for understanding genome function, variation and evolution. Here we report the finished sequence and biological annotation of human chromosome 1. Chromosome 1 is gene-dense, with 3,141 genes and 991 pseudogenes, and many coding sequences overlap. Rearrangements and mutations of chromosome 1 are prevalent in cancer and many other diseases. Patterns of sequence variation reveal signals of recent selection in specific genes that may contribute to human fitness, and also in regions where no function is evident. Fine-scale recombination occurs in hotspots of varying intensity along the sequence, and is enriched near genes. These and other studies of human biology and disease encoded within chromosome 1 are made possible with the highly accurate annotated sequence, as part of the completed set of chromosome sequences that comprise the reference human genome.

The DNA sequence and analysis of human chromosome 13.

Chromosome 13 is the largest acrocentric human chromosome. It carries genes involved in cancer including the breast cancer type 2 (BRCA2) and retinoblastoma (RB1) genes, is frequently rearranged in B-cell chronic lymphocytic leukaemia, and contains the DAOA locus associated with bipolar disorder and schizophrenia. We describe completion and analysis of 95.5 megabases (Mb) of sequence from chromosome 13, which contains 633 genes and 296 pseudogenes. We estimate that more than 95.4% of the protein-coding genes of this chromosome have been identified, on the basis of comparison with other vertebrate genome sequences. Additionally, 105 putative non-coding RNA genes were found. Chromosome 13 has one of the lowest gene densities (6.5 genes per Mb) among human chromosomes, and contains a central region of 38 Mb where the gene density drops to only 3.1 genes per Mb.

Prevalence, risk factors, and genetic diversity of Bartonella henselae infections in pet cats in four regions of the United States.

Blood was collected from a convenience sample of 271 pet cats aged 3 months to 2 years (mean age, 8 months, median and mode, 6 months) between May 1997 and September 1998 in four areas of the United States (southern California, Florida, metropolitan Chicago, and metropolitan Washington, D.C.). Sixty-five (24%) cats had Bartonella henselae bacteremia, and 138 (51%) cats were seropositive for B. henselae. Regional prevalences for bacteremia and seropositivity were highest in Florida (33% and 67%, respectively) and California (28% and 62%, respectively) and lowest in the Washington, D.C. (12% and 28%, respectively) and Chicago (6% and 12%, respectively) areas. No cats bacteremic with B. clarridgeiae were found. The 16S rRNA type was determined for 49 B. henselae isolates. Fourteen of 49 cats (28.6%) were infected with 16S rRNA type I, 32 (65.3%) with 16S rRNA type II, and three (6.1%) were coinfected with 16S rRNA types I and II. Flea infestation was a significant risk factor for B. henselae bacteremia (odds ratio = 2.82, 95% confidence interval, 1.1 to 7.3). Cats >or=13 months old were significantly less likely to be bacteremic than cats

Localisation of a novel region of recurrent amplification in follicular lymphoma to an approximately 6.8 Mb region of 13q32-33.

Follicular lymphoma (FL) is characterised by the presence of the t(14;18)(q32;q21) and represents approximately 25% of new cases of non-Hodgkin's lymphoma. While the t(14;18) is a well-documented rearrangement, the role of secondary cytogenetic abnormalities in the development and progression of these tumours remains unclear. Comparative genomic hybridisation was used to characterise changes in DNA copy number in tumour DNA from patients with this malignancy. The mean numbers of deletion and amplification events found in each of the 45 samples studied were 1.8 and 2.3, respectively. Regions of recurrent (>10% tumour samples) gain involved chromosomes 2p13-16 (16%), 7 (20%), 12 (16%), 13q21-33 (18%), 18 (27%), and X (36%) and frequent losses localised to 6q (29%) and 17p (20%). Amplification of chromosome 13 represents a novel finding in FL. The minimal amplified region was refined to a 6.8-Mb interval of 13q32-33 between the BAC clones 88K16 and 44H20 by fluorescence in situ hybridisation studies using metaphase chromosomes derived from tumour material. There are a number of reports in the literature suggesting that amplification of chromosome 13 also occurs in other human cancers. The location of the putative oncogene on 13q described here in follicular and transformed lymphoma may also be important in the evolution of many other malignancies.

Frequency of nonspecific clinical signs in dogs with separation anxiety, thunderstorm phobia, and noise phobia, alone or in combination.

OBJECTIVE: To determine the frequency of nonspecific clinical signs in dogs with separation anxiety, thunderstorm phobia, noise phobia, or any combination of these conditions and determine whether these conditions are associated in dogs. DESIGN: Case series. ANIMALS: 141 dogs. PROCEDURE: Diagnoses were established using specific criteria. Owners of dogs completed a questionnaire on how frequently their dogs exhibited destructive behavior, urination, defecation, vocalization, and salivation when the owners were absent and the types and frequency of reactions to thunderstorms, fireworks, and other noises. RESULTS: Associations of the 3 conditions and of various nonspecific clinical signs within and between diagnoses were nonrandom. The probability that a dog would have separation anxiety given that it had noise phobia was high (0.88) and approximately the same as the probability it would have separation anxiety given that it had thunderstorm phobia (0.86). However, the probability that a dog would have noise phobia given that it had separation anxiety (0.63) was higher than the probability that it would have thunderstorm phobia given that it had separation anxiety (0.52). The probability that a dog would have noise phobia given that it had thunderstorm phobia (0.90) was not equivalent to the converse (0.76). CONCLUSIONS AND CLINICAL RELEVANCE: Results suggested that dogs with any of these conditions should be screened for the others. Interactions among these conditions are important in the assessment and treatment of dogs with > 1 of these conditions. Responses to noise were different from those to thunderstorms, possibly because of the unpredictability and uncertainty of thunderstorms.

Resource allocation-based life histories: a conceptual basis for studies of ecological toxicology.

Whereas ecological assessments of contaminants are concerned with populations and higher levels of organization, most mechanistic work in toxicology is directed at effects on individuals and their parts. We propose that studies based on individuals can be useful in ecological analysis of polluted systems when based on the concepts of resource allocation-based life history analysis. At the heart of the resource allocation approach is the concept of operative environments of individuals (i.e., environmental factors influencing birth, death, or migration). Contaminants can have strong influences on operative environments, modifying resource allocation strategies that reflect changes in energy assimilation and demands. By examining contaminant-induced responses of individuals from the perspective of changing operative environments, individual-based changes and population dynamics can be addressed in an ecologically rigorous manner.

Initial sequencing and analysis of the human genome.

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

A physical map of the human genome.

The human genome is by far the largest genome to be sequenced, and its size and complexity present many challenges for sequence assembly. The International Human Genome Sequencing Consortium constructed a map of the whole genome to enable the selection of clones for sequencing and for the accurate assembly of the genome sequence. Here we report the construction of the whole-genome bacterial artificial chromosome (BAC) map and its integration with previous landmark maps and information from mapping efforts focused on specific chromosomal regions. We also describe the integration of sequence data with the map.

The physical maps for sequencing human chromosomes 1, 6, 9, 10, 13, 20 and X.

We constructed maps for eight chromosomes (1, 6, 9, 10, 13, 20, X and (previously) 22), representing one-third of the genome, by building landmark maps, isolating bacterial clones and assembling contigs. By this approach, we could establish the long-range organization of the maps early in the project, and all contig extension, gap closure and problem-solving was simplified by containment within local regions. The maps currently represent more than 94% of the euchromatic (gene-containing) regions of these chromosomes in 176 contigs, and contain 96% of the chromosome-specific markers in the human gene map. By measuring the remaining gaps, we can assess chromosome length and coverage in sequenced clones.

Contigs built with fingerprints, markers, and FPC V4.7.

Contigs have been assembled, and over 2800 clones selected for sequencing for human chromosomes 9, 10 and 13. Using the FPC (FingerPrinted Contig) software, the contigs are assembled with markers and complete digest fingerprints, and the contigs are ordered and localised by a global framework. Publicly available resources have been used, such as, the 1998 International Gene Map for the framework and the GSC Human BAC fingerprint database for the majority of the fingerprints. Additional markers and fingerprints are generated in-house to supplement this data. To support the scale up of building maps, FPC V4.7 has been extended to use markers with the fingerprints for assembly of contigs, new clones and markers can be automatically added to existing contigs, and poorly assembled contigs are marked accordingly. To test the automatic assembly, a simulated complete digest of 110 Mb of concatenated human sequence was used to create datasets with varying coverage, length of clones, and types of error. When no error was introduced and a tolerance of 7 was used in assembly, the largest contig with no false positive overlaps has 9534 clones with 37 out-of-order clones, that is, the starting coordinates of adjacent clones are in the wrong order. This paper describes the new features in FPC, the scenario for building the maps of chromosomes 9, 10 and 13, and the results from the simulation.