A compilation of tri-allelic SNPs from 1000 Genomes and use of the most polymorphic loci for a large-scale human identification panel.

In a directed search of 1000 Genomes Phase III variation data, 271,934 tri-allelic single nucleotide polymorphisms (SNPs) were identified amongst the genotypes of 2,504 individuals from 26 populations. The majority of tri-allelic SNPs have three nucleotide substitution-based alleles at the same position, while a much smaller proportion, which we did not compile, have a nucleotide insertion/deletion plus substitution alleles. SNPs with three alleles have higher discrimination power than binary loci but keep the same characteristic of optimum amplification of the fragmented DNA found in highly degraded forensic samples. Although most of the tri-allelic SNPs identified had one or two alleles at low frequencies, often single observations, we present a full compilation of the genome positions, rs-numbers and genotypes of all tri-allelic SNPs detected by the 1000 Genomes project from the more detailed analyses it applied to Phase III sequence data. A total of 8,705 tri-allelic SNPs had overall heterozygosities (averaged across all 1000 Genomes populations) higher than the binary SNP maximum value of 0.5. Of these, 1,637 displayed the highest average heterozygosity values of 0.6-0.666. The most informative tri-allelic SNPs we identified were used to construct a large-scale human identification panel for massively parallel sequencing, designed for the identification of missing persons. The large-scale MPS identification panel comprised: 1,241 autosomal tri-allelic SNPs and 29 X tri-allelic SNPs (plus 46 microhaplotypes adapted for genotyping from reduced length sequences). Allele frequency estimates are detailed for African, European, South Asian and East Asian population groups plus the Peruvian population sampled by 1000 Genomes for the 1,270 tri-allelic SNPs of the final MPS panel. We describe the selection criteria, kinship simulation experiments and genomic analyses used to select the tri-allelic SNP components of the panel. Approximately 5 % of the tri-allelic SNPs selected for the large-scale MPS identification panel gave three-genotype patterns in single individual samples or discordant genotypes for genomic control DNAs. A likely explanation for some of these unreliably genotyped loci is that they map to multiple sites in the genome - highlighting the need for caution and detailed scrutiny of multiple-allele variant data when designing future forensic SNP panels, as such patterns can arise from common structural variation in the genome, such as segmental duplications.

Electron-density distributions in selected ferrocenyl-pyrazolyl late transition-metal complexes.

57Fe Mössbauer spectroscopy has been used to study electronic dispersions in complexes of Fe, Co, Ni and Pd anchored onto 3-ferrocenyl-5-methylpyrazolylmethylenepyridine and 3-ferrocenylpyrazolylmethylenepyridine ligands. Mössbauer spectroscopy shows that pyrazolyl-derivatizing of ferrocene increases the electron-density at the Fe-centre as well as facilitating the Fe to cyclopentadienyl ring back-donation of electron-density. The coordination of the ferrocenyl-pyrazolyl ligand to transition metals such as Fe, Co, Ni and Pd reduces the electron-density at the Fe-centre of the ferrocenyl moiety while increasing the electron-density at the coordinated metal centre, especially in the Fe complexes. The electron-density change at the coordination metal centre is inversely proportional to the electronegativity of the halide substituent. Furthermore, the type of substituent (Me or H) at position 5 on the pyrazolyl moiety has an influence on the electron density at the ferrocenyl-Fe and the coordinated metal centre. The methyl group as a substituent reduces the π-acceptor ability of the pyrazolyl and therefore increases the electron-density at the ferrocenyl-Fe centre. However, when the substituent is hydrogen, the electron-density at the coordination metal centre increases. Similarly, for other metals (i.e., Co, Ni and Pd) the electron density at the ferrocenyl-Fe is also significantly reduced upon coordination of the ligand to the metal. Additionally, Mössbauer experiments reveal a trivalent Fe species in the synthesized complexes which is not discerned by X-ray and elemental analysis. The species has been identified as the oxidative product [Fe(iii)X4]- where X = Cl or Br. The study also highlights and cautions on the possibility of photo-oxidation processes involving both ferrocene and the coordinating Fe-halides under standard lighting conditions with possible contributions from aerated solvents.

Measuring respiration rates in marine fish larvae: challenges and advances.

Metabolic costs can be extremely high in marine fish larvae and gaining reliable estimates of the effects of intrinsic and extrinsic factors on those costs is important to understand environmental constraints on early growth and survival. This review provides an historical perspective of measurements of larval marine fish respiration (O2 consumption) including the methods (Winkler, manometric, polarographic, paramagnetic and optodes) and systems (closed system to intermittent-flow) used. This study compares and systematically reviews the results (metabolic rates, ontogenetic changes and taxonomic differences) obtained from 59 studies examining 53 species from 30 families. Standard (anaesthetized or darkness), routine and active respiration rates were reported in 14, 94 and 8% of the studies and much more work has been performed on larvae of temperate (88%) compared with tropical (9%) and polar (3%) species. More than 35% of the studies have been published since 2000 owing to both advances in oxygen sensors and the growing emphasis on understanding physiological effects of environmental change. Common protocols are needed to facilitate cross-taxa comparisons such as the effect of temperature (Q10 : 1·47-3·47), body mass (slope of allometric changes in O2 consumption rate from 0·5 to 1·3) and activity level on metabolic costs as measured via respiration rate. A set of recommendations is provided that will make it easier for researchers to design measurement systems, to judge the reliability of measurements and to make inter-comparisons among studies and species.

Born small, die young: Intrinsic, size-selective mortality in marine larval fish.

Mortality during the early stages is a major cause of the natural variations in the size and recruitment strength of marine fish populations. In this study, the relation between the size-at-hatch and early survival was assessed using laboratory experiments and on field-caught larvae of the European sardine (Sardina pilchardus). Larval size-at-hatch was not related to the egg size but was significantly, positively related to the diameter of the otolith-at-hatch. Otolith diameter-at-hatch was also significantly correlated with survival-at-age in fed and unfed larvae in the laboratory. For sardine larvae collected in the Bay of Biscay during the spring of 2008, otolith radius-at-hatch was also significantly related to viability. Larval mortality has frequently been related to adverse environmental conditions and intrinsic factors affecting feeding ability and vulnerability to predators. Our study offers evidence indicating that a significant portion of fish mortality occurs during the endogenous (yolk) and mixed (yolk /prey) feeding period in the absence of predators, revealing that marine fish with high fecundity, such as small pelagics, can spawn a relatively large amount of eggs resulting in small larvae with no chances to survive. Our findings help to better understand the mass mortalities occurring at early stages of marine fish.

Standard metabolism and growth dynamics of laboratory-reared larvae of Sardina pilchardus.

This study provides the first measurements of the standard respiration rate (R(S)) and growth dynamics of European sardine Sardina pilchardus larvae reared in the laboratory. At 15° C, the relationship between RS (µl O(2) individual(-1) h(-1)) and larval dry mass (M(D), µg) was equal to: R(S) = 0·0057(±0·0007, ± s.e.)·M(D) (0·8835(±0·0268)), (8-11% M(D) day(-1)). Interindividual differences in RS were not related to interindividual differences in growth rate or somatic (Fulton's condition factor) or biochemical-based condition (RNA:DNA).

Climate change effects on fishes and fisheries: towards a cause-and-effect understanding.

Ongoing climate change is predicted to affect individual organisms during all life stages, thereby affecting populations of a species, communities and the functioning of ecosystems. These effects of climate change can be direct, through changing water temperatures and associated phenologies, the lengths and frequency of hypoxia events, through ongoing ocean acidification trends or through shifts in hydrodynamics and in sea level. In some cases, climate interactions with a species will also, or mostly, be indirect and mediated through direct effects on key prey species which change the composition and dynamic coupling of food webs. Thus, the implications of climate change for marine fish populations can be seen to result from phenomena at four interlinked levels of biological organization: (1) organismal-level physiological changes will occur in response to changing environmental variables such as temperature, dissolved oxygen and ocean carbon dioxide levels. An integrated view of relevant effects, adaptation processes and tolerance limits is provided by the concept of oxygen and capacity-limited thermal tolerance (OCLT). (2) Individual-level behavioural changes may occur such as the avoidance of unfavourable conditions and, if possible, movement into suitable areas. (3) Population-level changes may be observed via changes in the balance between rates of mortality, growth and reproduction. This includes changes in the retention or dispersion of early life stages by ocean currents, which lead to the establishment of new populations in new areas or abandonment of traditional habitats. (4) Ecosystem-level changes in productivity and food web interactions will result from differing physiological responses by organisms at different levels of the food web. The shifts in biogeography and warming-induced biodiversity will affect species productivity and may, thus, explain changes in fisheries economies. This paper tries to establish links between various levels of biological organization by means of addressing the effective physiological principles at the cellular, tissue and whole organism levels.

HLA-D types and serum IgG responses to Capnocytophaga in diabetes and periodontitis.

Serum IgG responses to the cell envelope proteins (CEPs) from Capnocytophaga sputigena, Capnocytophaga ochracea, and Capnocytophaga gingivalis were examined in periodontally healthy and periodontitis subjects, both with and without type 1 diabetes (n = 60). Serum IgG responses to CEPs were determined by immunoblotting with biotin-goat anti-human IgG and an alkaline phosphatase-streptavidin system. Reactivity was analyzed by transmission densitometry, digitization, and computer manipulation. The patients with diabetes showed significantly (p < 0.01) fewer responses to 14 CEPs (from 81 to 10 kDa) from C. sputigena, 5 CEPs (from 90 to 17 kDa) from C. gingivalis, and the 27-kDa CEP from C. ochracea than in the non-diabetic group. The periodontitis patients showed significantly (p < 0.01) fewer responses to the 25- and 11-kDa CEPs from C. sputigena, the 125- and 17-kDa CEPs from C. gingivalis, and the 42-kDa CEP from C. ochracea than in the periodontally healthy group. HLA-DR4, HLA-DR53, and HLA-DQw3 were associated with periodontitis, while only HLA-DR4 was associated with diabetes (p < 0.02). Significant (p < 0.01) correlations were found between HLA-DR2 and IgG reactivity patterns associated with non-diabetics, and between HLA-DR4 and IgG reactivity patterns associated with diabetic and periodontitis subjects. These results indicate that both type 1 diabetics and periodontitis subjects have a depressed IgG antibody profile to Capnocytophaga, which may account for an increased susceptibility to periodontitis infection. Periodontitis in type 1 diabetes may be related more to the HLA-D type and altered immune function than to the diabetes itself.

Purification and characterization of Porphyromonas gingivalis outer membrane antigens.

Porphyromonas gingivalis is strongly associated with periodontal disease. Significant titres of specific IgG antibodies to P. gingivalis can be found in healthy individuals and those with periodontitis. In this study, 22 outer membrane antigens ranging from 15.5 to 107.6 kDa were recognized by sera from persons with periodontitis and controls. Serum from individuals with periodontitis showed a significantly higher IgG response to a 31.4-kDa antigen (p < 0.05); serum from those with gingivitis demonstrated a significantly higher response to a 15.5-kDa antigen (p < 0.05). The response to the 15.5-kDa antigen might represent a protective immune response while that to the 31.4-kDa could serve as a marker for disease susceptibility. These two antigens were purified to homogeneity and their N-terminal amino acid sequences determined. The sequences did not correspond to any previously described P. gingivalis antigens. The role of these two antigens in the pathogenesis of periodontal disease remains to be determined.

An analysis of the outcome of 301 malignant colorectal tumors.

The results of surgical treatment of 301 patients with malignant tumors of the colon and rectum presenting to two small district general hospitals in the years 1972 to 1977 were analyzed. Two hundred seventy-four patients (91 per cent) underwent surgery with an operative mortality of 8.7 per cent. Curative resections were performed in 58 per cent of the patients. The overall crude five-year survival rate was 32 per cent. The crude five-year survival rates for curative resection, palliative procedures, and inoperable patients were 47 per cent, 11 per cent, and 0 per cent, respectively. Survival rates were considerably improved in patients in the 40-to-50-year age group with 9 to 12 months' duration of symptoms, and in those with early unfixed, resected tumors. It was diminished in patients with bowel perforation presenting as an emergency, and in patients with two weeks or less duration of symptoms. Survival was not related to the site or grade of the tumor.

Does fixity affect prognosis in colorectal tumours?

In a retrospective series of 301 colorectal tumours, tumour fixity was assessed, and was found to be of prognostic significance in relation to 5-year survival. Fixity of the tumour was associated with low curative resection rate and advanced tumour state. Fixation did not correlate significantly with the site or differentiation of the tumour nor with operative mortality.