Molecular mechanism of anaerobic ammonium oxidation

Two distinct microbial processes, denitrification and anaerobic ammonium oxidation (anammox), are responsible for the release of fixed nitrogen as dinitrogen gas (N(2)) to the atmosphere. Denitrification has been studied for over 100 years and its intermediates and enzymes are well known. Even though anammox is a key biogeochemical process of equal importance, its molecular mechanism is unknown, but it was proposed to proceed through hydrazine (N(2)H(4)). Here we show that N(2)H(4) is produced from the anammox substrates ammonium and nitrite and that nitric oxide (NO) is the direct precursor of N(2)H(4). We resolved the genes and proteins central to anammox metabolism and purified the key enzymes that catalyse N(2)H(4) synthesis and its oxidation to N(2). These results present a new biochemical reaction forging an N-N bond and fill a lacuna in our understanding of the biochemical synthesis of the N(2) in the atmosphere. Furthermore, they reinforce the role of nitric oxide in the evolution of the nitrogen cycle.     

Role of sulphuric acid, ammonia and galactic cosmic rays in atmospheric aerosol nucleation

Atmospheric aerosols exert an important influence on climate through their effects on stratiform cloud albedo and lifetime and the invigoration of convective storms. Model calculations suggest that almost half of the global cloud condensation nuclei in the atmospheric boundary layer may originate from the nucleation of aerosols from trace condensable vapours, although the sensitivity of the number of cloud condensation nuclei to changes of nucleation rate may be small. Despite extensive research, fundamental questions remain about the nucleation rate of sulphuric acid particles and the mechanisms responsible, including the roles of galactic cosmic rays and other chemical species such as ammonia. Here we present the first results from the CLOUD experiment at CERN. We find that atmospherically relevant ammonia mixing ratios of 100 parts per trillion by volume, or less, increase the nucleation rate of sulphuric acid particles more than 100-1,000-fold. Time-resolved molecular measurements reveal that nucleation proceeds by a base-stabilization mechanism involving the stepwise accretion of ammonia molecules. Ions increase the nucleation rate by an additional factor of between two and more than ten at ground-level galactic-cosmic-ray intensities, provided that the nucleation rate lies below the limiting ion-pair production rate. We find that ion-induced binary nucleation of H(2)SO(4)-H(2)O can occur in the mid-troposphere but is negligible in the boundary layer. However, even with the large enhancements in rate due to ammonia and ions, atmospheric concentrations of ammonia and sulphuric acid are insufficient to account for observed boundary-layer nucleation.     

Genetic determinants of neuronal vulnerability to apoptosis

Apoptosis is a common mode of cell death that contributes to neuronal loss associated with neurodegeneration. Single-nucleotide polymorphisms (SNPs) in chromosomal DNA are contributing factors dictating natural susceptibility of humans to disease. Here, the most common SNPs affecting neuronal vulnerability to apoptosis are reviewed in the context of neurological disorders. Polymorphic variants in genes encoding apoptotic proteins, either from the extrinsic (FAS, TNF-α, CASP8) or the intrinsic (BAX, BCL2, CASP3, CASP9) pathways could be highly valuable in the diagnosis of neurodegenerative diseases and stroke. Interestingly, the Arg72Pro SNP in TP53, the gene encoding tumor suppressor p53, was recently revealed a biomarker of poor prognosis in stroke due to its ability to modulate neuronal apoptotic death. Search for new SNPs responsible for genetic variability to apoptosis will ensure the implementation of novel diagnostic and prognostic tools, as well as therapeutic strategies against neurological diseases.     

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.     

Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease

Using variants from the 1000 Genomes Project pilot European CEU dataset and data from additional resequencing studies, we densely genotyped 183 non-HLA risk loci previously associated with immune-mediated diseases in 12,041 individuals with celiac disease (cases) and 12,228 controls. We identified 13 new celiac disease risk loci reaching genome-wide significance, bringing the number of known loci (including the HLA locus) to 40. We found multiple independent association signals at over one-third of these loci, a finding that is attributable to a combination of common, low-frequency and rare genetic variants. Compared to previously available data such as those from HapMap3, our dense genotyping in a large sample collection provided a higher resolution of the pattern of linkage disequilibrium and suggested localization of many signals to finer scale regions. In particular, 29 of the 54 fine-mapped signals seemed to be localized to single genes and, in some instances, to gene regulatory elements. Altogether, we define the complex genetic architecture of the risk regions of and refine the risk signals for celiac disease, providing the next step toward uncovering the causal mechanisms of the disease.     

Responses of pink shrimp Farfantepenaeus brasiliensis (Latreille, 1817) (Penaeoidea) to physico-chemical parameters in a marine protected area: changes in abundance and distribution after 20 years

ABSTRACT

This study analysed the influence of temperature, salinity and sediment texture on the distribution of pink shrimp juveniles (Farfantepenaeus brasiliensis) over a 20-year period. The shrimps were sampled monthly in Fortaleza Bay, north coast of São Paulo, Brazil, in November 1988–October 1989 (period 1) and then 20 years later in November 2008–October 2009 (period 2). In period 1 we captured 80 juveniles whereas in period 2 we captured 226. The abundance and distribution of F. brasiliensis seemed to be modulated by temperature and sediment texture, along with the fishing activity. The management strategies established between the samplings might have been responsible for the higher abundance of juveniles seen during period 2. The strategies included the limitation of fishing effort, regulation of fishing equipment and the establishment of environmental protection areas and temporary fishing ban.     

Thermal ecology,activity pattern,habitat, and microhabitats used by the skink Mabuya arajara (Squamata: Scincidae) in the Araripe Plateau,northeastern Brazil

ABSTRACT

We evaluated the activity period, thermal ecology, habitats, and preference for microhabitats of the skink Mabuya arajara in a humid forest environment on the slope of the Araripe Plateau, Brazil. A total of 283 lizards were observed. The lizards were found to be diurnally active (unimodal type pattern), with peak activity during the hottest hours of the day (1100 to 1200). About habitat use, the majority of individuals (73.8% N = 209) were recorded in the narrow transitional area, in the edges of the forest; while 26.4% of individuals were observed in open areas and no observations were made in dense forest. Seven different types of microhabitats were used, with fallen palm leaves (Arecaceae) being the preferred (47.7% N = 135). Considering all lizards, microhabitat niche breadth was 3.27. Males and females presented a high overlap (0.95) in microhabitat use. The average T_c recorded for M. arajara was 32.06 ± 2.72°C. Body size (SVL) did not influence body temperature (F = 0.51, P = > 0.05). Most of the animals were observed with their bodies completely exposed (67.84%, N = 192), 18.37% (N = 52) were semi-exposed and 13.79% (N = 39) were in shelters. Among animals with some degree of sunlight exposure, 57.59% (N = 163) were in shadows, 25.10% (N = 71) were under sunlight filtered by vegetation, and 17.31% (N = 49) were under direct sunlight.A review of the ecology of Mabuya spp. shows that several features appear to be conserved among members of the genus.     

The DNA sequence of human chromosome 22

Knowledge of the complete genomic DNA sequence of an organism allows a systematic approach to defining its genetic components. The genomic sequence provides access to the complete structures of all genes, including those without known function, their control elements, and, by inference, the proteins they encode, as well as all other biologically important sequences. Furthermore, the sequence is a rich and permanent source of information for the design of further biological studies of the organism and for the study of evolution through cross-species sequence comparison. The power of this approach has been amply demonstrated by the determination of the sequences of a number of microbial and model organisms. The next step is to obtain the complete sequence of the entire human genome. Here we report the sequence of the euchromatic part of human chromosome 22. The sequence obtained consists of 12 contiguous segments spanning 33.4 megabases, contains at least 545 genes and 134 pseudogenes, and provides the first view of the complex chromosomal landscapes that will be found in the rest of the genome.