Demographic Clusters Identified within the Northern Gulf of Mexico Common Bottlenose Dolphin (Tursiops truncates) Unusual Mortality Event: January 2010 - June 2013

A multi-year unusual mortality event (UME) involving primarily common bottlenose dolphins (Tursiops truncates) was declared in the northern Gulf of Mexico (GoM) with an initial start date of February 2010 and remains ongoing as of August 2014. To examine potential changing characteristics of the UME over time, we compared the number and demographics of dolphin strandings from January 2010 through June 2013 across the entire GoM as well as against baseline (1990-2009) GoM stranding patterns. Years 2010 and 2011 had the highest annual number of stranded dolphins since Louisiana’s record began, and 2011 was one of the years with the highest strandings for both Mississippi and Alabama. Statewide, annual numbers of stranded dolphins were not elevated for GoM coasts of Florida or Texas during the UME period. Demographic, spatial, and temporal clusters identified within this UME included increased strandings in northern coastal Louisiana and Mississippi (March-May 2010); Barataria Bay, Louisiana (August 2010-December 2011); Mississippi and Alabama (2011, including a high prevalence and number of stranded perinates); and multiple GoM states during early 2013. While the causes of the GoM UME have not been determined, the location and magnitude of dolphin strandings during and the year following the 2010 Deepwater Horizon oil spill, including the Barataria Bay cluster from August 2010 to December 2011, overlap in time and space with locations that received heavy and prolonged oiling. There are, however, multiple known causes of previous GoM dolphin UMEs, including brevetoxicosis and dolphin morbillivirus. Additionally, increased dolphin strandings occurred in northern Louisiana and Mississippi before the Deepwater Horizon oil spill. Identification of spatial, temporal, and demographic clusters within the UME suggest that this mortality event may involve different contributing factors varying by location, time, and bottlenose dolphin populations that will be better discerned by incorporating diagnostic information, including histopathology.     

Characterization of surface motility in <Emphasis Type="Italic">Sinorhizobium meliloti</Emphasis>: regulation and role in symbiosis

Sinorhizobium meliloti can exhibit diverse modes of surface translocation whose manifestation depends on the strain. The mechanisms involved and the role played by the different modes of surface motility in the establishment of symbiosis are largely unknown. In this work, we have characterized the surface motility shown by two S. meliloti reference strains (Rm1021 and GR4) under more permissive conditions for surface spreading and analyzed the symbiotic properties of two flagella-less S. meliloti mutants with different behavior on surfaces. The use of Noble agar in semisolid minimal medium induces surface motility in GR4, a strain described so far as non-motile on surfaces. The motility exhibited by GR4 is swarming as revealed by the non-motile phenotype of the flagella-less flaAB mutant. Intriguingly, a flgK mutation which also abolishes flagella production, triggers surface translocation in GR4 through an as yet unknown mechanism. In contrast to GR4, Rm1021 moves over surfaces using mostly a flagella-independent motility which is highly reliant on siderophore rhizobactin 1021 production. Surprisingly, this motility is absent in a flagella-less flgE mutant. In addition, we found that fadD loss-of-function, known to promote surface motility in S. meliloti, exerts different effects on the two reference strains: while fadD inactivation promotes a flagella-independent type of motility in GR4, the same mutation interferes with the surface translocation exhibited by the Rm1021 flaAB mutant. The symbiotic phenotypes shown by GR4flaAB and GR4flgK, non-flagellated mutants with opposite surface motility behavior, demonstrate that flagella-dependent motility positively influences competitiveness for nodule occupation, but is not crucial for optimal infectivity.     

A comparative study of the non-acidic chemically mediated antifoulant properties of three sympatric species of ascidians associated with seagrass habitats

The present study investigated aspects of the antifoulant properties of three sympatric species of ascidians found in seagrass habitats of the Gulf of Mexico, Southern Atlantic Ocean, and Caribbean. Field observations in Saint Joseph Bay, Florida indicate that all three species are common and that the tunic of the solitary ascidian Molgula occidentalis is often heavily fouled, while the outer surfaces of both the colonial ascidians Amaroucium stellatum and Botryllus planus are free of fouling organisms. Antifoulant activities of a suite of increasing hydrophilic organic extracts prepared from the tunic of M. occidentalis and whole colonies of A. stellatum and B. planus were measured using both sympatric microbial (bacteria) and macroinvertebrate (cyprid larvae of Balanus amphitrite) fouling organisms in laboratory bioassays. In addition, field antifoulant assays were conducted by combining organic extracts with controlled-release resin and subsequently coating this material on to acrylic rods deployed in the field for a 72 h period. Extracts of the tunic of M. occidentalis generally did not inhibit bacterial growth. The exception was the methanol extract, which inhibited growth in one of the six marine bacteria tested. Moreover, only the highest concentrations of hexane and methanol tunic extracts tested prevented attachment of cyprid larvae. Field assays revealed no antifoulant activity on rods coated with resin containing extracts of M. occidentalis. Inhibition of both microbial growth and cyprid settlement were much more pronounced in whole-organism extracts of the two colonial ascidians. Most potent were the aqueous methanol extracts of colonies of B. planus and A. stellatum which inhibited growth in five of the six marine bacteria tested. In addition, hydrophilic and lipophilic extracts of the colonial ascidians significantly inhibited attachment of cyprid larvae, in many instances across a wide range of extract concentrations. Field antifoulant assays indicated that extracts of both colonial ascidians inhibited settlement of bryozoans and barnacles. The findings indicate that the colonial ascidians B. planus and A. stellatum possess chemical antifoulant properties. In contrast, the solitary ascidian M. occidentalis appears to either tolerate fouling or possess other non-chemical mechanisms to cope with the risks associated with epibiont overgrowth.     

Annotating nucleic acid-binding function based on protein structure

Many of the targets of structural genomics will be proteins with little or no structural similarity to those currently in the database. Therefore, novel function prediction methods that do not rely on sequence or fold similarity to other known proteins are needed. We present an automated approach to predict nucleic-acid-binding (NA-binding) proteins, specifically DNA-binding proteins. The method is based on characterizing the structural and sequence properties of large, positively charged electrostatic patches on DNA-binding protein surfaces, which typically coincide with the DNA-binding-sites. Using an ensemble of features extracted from these electrostatic patches, we predict DNA-binding proteins with high accuracy. We show that our method does not rely on sequence or structure homology and is capable of predicting proteins of novel-binding motifs and protein structures solved in an unbound state. Our method can also distinguish NA-binding proteins from other proteins that have similar, large positive electrostatic patches on their surfaces, but that do not bind nucleic acids.     

Crop husbandry activities and wild plant gathering,use and consumption at the EPPNB Tell Qarassa North (south Syria)

The Early Pre-Pottery Neolithic B (EPPNB) in southwest Asia is a fundamental period in research on the origins of domesticated plants. However, there are few archaeobotanical data with which to characterise the plant-based subsistence and crop husbandry activities during this time, which hinders the understanding of the factors that triggered the appearance of plant domestication. In this paper, analyses of non-woody plant macro-remains provide new insights into subsistence activities such as crop cultivation (husbandry activities and storage) and plant use (wild plant gathering and food preparation) during the EPPNB at Tell Qarassa North (south Syria). We make comparisons between Tell Qarassa North and the evidence at earlier and later periods as to how plants were used, and highlight similarities and differences in the practices attested, as well as describing some of the consequences that these plant-related activities may have had in terms of labour and social organization during EPPNB.     

Four genes in two diverged subfamilies encode the ribulose-1,5-bisphosphate carboxylase small subunit polypeptides of Arabidopsis thaliana

The multigene family encoding the small subunit polypeptides of ribulose-1,5-bisphosphate carboxylase/oxygenase in the crucifer Arabidopsis thaliana has been isolated and the organization and structure of the individual members determined. The family consists of four genes which have been divided into two subfamilies on the basis of linkage and DNA and amino acid sequence similarities. Three of the genes, designated ats1B, ats2B, and ats3B, reside in tandem on an 8 kb stretch of the chromosome. These genes share greater than 95% similarity in DNA sequence and encode polypeptides identical in length and 96.7% similar in amino acid sequence. The fourth gene, ats1A, is at least 10 kb removed from, or completely unlinked to the B subfamily. The B subfamily genes are more similar to each other than to ats1A in nucleotide and amino acid sequence. All four genes are interupted by two introns whose placement within the coding region of the genes is conserved. The introns of the B subfamily genes are similar in length and nucleotide sequence, but show no similarity to the introns of ats1A. Comparison of the DNA sequences within the immediate 5 and 3 flanking sequences among the genes revealed only limited regions of homology. S1 analysis shows that all four genes are expressed.     

MptpB, a virulence factor from Mycobacterium tuberculosis, exhibits triple-specificity phosphatase activity

Bacterial pathogens have developed sophisticated mechanisms of evading the immune system to survive in infected host cells. Central to the pathogenesis of Mycobacterium tuberculosis is the arrest of phagosome maturation, partly through interference with PtdIns signalling. The protein phosphatase MptpB is an essential secreted virulence factor in M. tuberculosis. A combination of bioinformatics analysis, enzyme kinetics and substrate-specificity characterization revealed that MptpB exhibits both dual-specificity protein phosphatase activity and, importantly, phosphoinositide phosphatase activity. Mutagenesis of conserved residues in the active site signature indicates a cysteine-based mechanism of dephosphorylation and identifies two new catalytic residues, Asp165, essential in catalysis, and Lys164, apparently involved in substrate specificity. Sequence similarities with mammalian lipid phosphatases and a preference for phosphoinositide substrates suggests a potential novel role of MptpB in PtdIns metabolism in the host and reveals new perspectives for the role of this phosphatase in mycobacteria pathogenicity.     

Der Feldbegriff in seiner Anwendung auf das Problem der Zellteilung

Summary The authors show that in certain isolated tissues (cornea of frog, mouse cancer) the mitotic processes continue during at least one hour. They are very strongly stimulated by heat and also by mitogenetic radiation. In the case of the cancer cells new mitoses are promoted in considerable number. A detailed analysis of both energy factors leads to the conclusion that they effect a disturbance of the unstable constellations (structures) of the elementary particles in the cell-body. Thus a certain degree of disorganisation of its plasma seems to stimulate cell-division. This statement is, in the opinion of the authors a proof that cell-division is controlled by a field, the trajectories of the elementary particles of the cell-body being a function of their coordinates relative to the cell-axes.

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Résumé Les auteurs démontrent que dans certains tissus survivants (la cornée des yeux de grenouille et le cancer de souris) les mitoses continuent leur processus d'évolution durant au moins une heure. Par l'application de chaleur aussi bien que par l'irradiation mitogénétique on peut accélérer beaucoup le rhythme des mitoses en cours d'évolution et provoquer (dans les cas de cancer seulement) l'apparition d'un nombre considérable de nouvelles mitoses. L'analyse de l'action de ces deux facteurs d'énergie aboutit à la conclusion qu'il ne peut s'agir que d'un dérangement des constellations instables des éléments du corps cellulaire. On peut en déduire qu'un certain degré de désorganisation du plasme est favorable aux divisions cellulaires. En poursuivant et en développant cette conception, les auteurs arrivent à la conception du champ cellulaire de division, définissant les trajectoires des particules élémentaires comme fonction de ses coordonnés relativement aux axes des cellules.