Contrast sensitivity of pattern transient VEP components: contribution from M and P pathways

The purpose of this study was to compare contrast sensitivity estimated from transient visual evoked potentials (VEPs) elicited by achromatic pattern-reversal and pattern-onset/offset modes. The stimuli were 2-cpd, achromatic horizontal gratings presented either as a 1 Hz pattern reversal or a 300 ms onset/700 ms offset stimulus. Contrast thresholds were estimated by linear regression to amplitudes of VEP components vs. the logarithm of the stimulus contrasts, and these regressions were extrapolated to the zero amplitude level. Contrast sensitivity was defined as the inverse of contrast threshold. For pattern reversal, the relation between the P100 amplitude and log of the stimulus contrast was best described by two separate linear regressions. For the N135 component, a single straight line was sufficient. In the case of pattern onset/offset for both the C1 and C2 components, single straight lines described their amplitude vs. log contrast relations in the medium-to-low contrast range. Some saturation was observed for C2 components. The contrast sensitivity estimated from the low-contrast limb of the P100, from the N135, and from the C2 were all similar but higher than those obtained from the high-contrast limb of the P100 and C1 data, which were also similar to each other. With 2 cpd stimuli, a mechanism possibly driven by the M pathway appeared to contribute to the P100 component at medium-to-low contrasts and to the N135 and C2 components at all contrast levels, whereas another mechanism, possibly driven by the P and M pathways, appeared to contribute to the P100 component at high contrast and C1 component at all contrast levels.

Probing the anomalous extinction of four young star clusters: the use of colour-excess, main-sequence fitting and fractal analysis

Aims. We studied four young star clusters to characterise their anomalous extinction or variable reddening and asses whether they could be due to contamination by either dense clouds or circumstellar effects. Methods. We evaluated the extinction law (R-V) by adopting two methods: (i) the use of theoretical expressions based on the colour-excess of stars with known spectral type; and (ii) the analysis of two-colour diagrams, where the slope of the observed colour distribution was compared to the normal distribution. An algorithm to reproduce the zero-age main-sequence (ZAMS) reddened colours was developed to derive the average visual extinction (A(V)) that provides the closest fit to the observational data. The structure of the clouds was evaluated by means of a statistical fractal analysis, designed to compare their geometric structure with the spatial distribution of the cluster members. Results. The cluster NGC 6530 is the only object of our sample affected by anomalous extinction. On average, the other clusters suffer normal extinction, but several of their members, mainly in NGC 2264, seem to have high R-V, probably because of circumstellar effects. The ZAMS fitting provides A(V) values that are in good agreement with those found in the literature. The fractal analysis shows that NGC 6530 has a centrally concentrated distribution of stars that differs from the substructures found in the density distribution of the cloud projected in the A(V) map, suggesting that the original cloud was changed by the cluster formation. However, the fractal dimension and statistical parameters of Berkeley 86, NGC 2244, and NGC 2264 indicate that there is a good cloud-cluster correlation, when compared to other works based on an artificial distribution of points.

Lithium in M 67: From the main sequence to the red giant branch

Context. Lithium abundances in open clusters are a very effective probe of mixing processes, and their study can help us to understand the large depletion of lithium that occurs in the Sun. Owing to its age and metallicity, the open cluster M 67 is especially interesting on this respect. Many studies of lithium abundances in M 67 have been performed, but a homogeneous global analysis of lithium in stars from subsolar masses and extending to the most massive members, has yet to be accomplished for a large sample based on high-quality spectra. Aims. We test our non-standard models, which were calibrated using the Sun with observational data. Methods. We collect literature data to analyze, for the first time in a homogeneous way, the non-local thermal equilibrium lithium abundances of all observed single stars in M 67 more massive than similar to 0.9 M-circle dot. Our grid of evolutionary models is computed assuming a non-standard mixing at metallicity [Fe/H] = 0.01, using the Toulouse-Geneva evolution code. Our analysis starts from the entrance into the zero-age main-sequence. Results. Lithium in M 67 is a tight function of mass for stars more massive than the Sun, apart from a few outliers. A plateau in lithium abundances is observed for turn-off stars. Both less massive (M >= 1.10 M-circle dot) and more massive (M >= 1.28 M-circle dot) stars are more depleted than those in the plateau. There is a significant scatter in lithium abundances for any given mass M <= 1.1 M-circle dot. Conclusions. Our models qualitatively reproduce most of the features described above, although the predicted depletion of lithium is 0.45 dex smaller than observed for masses in the plateau region, i.e. between 1.1 and 1.28 solar masses. More work is clearly needed to accurately reproduce the observations. Despite hints that chromospheric activity and rotation play a role in lithium depletion, no firm conclusion can be drawn with the presently available data.

Identification of novel components of NAD-utilizing metabolic pathways and prediction of their biochemical functions

Nicotinamide adenine dinucleotide (NAD) is a ubiquitous cofactor participating in numerous redox reactions. It is also a substrate for regulatory modifications of proteins and nucleic acids via the addition of ADP-ribose moieties or removal of acyl groups by transfer to ADP-ribose. In this study, we use in-depth sequence, structure and genomic context analysis to uncover new enzymes and substrate-binding proteins in NAD-utilizing metabolic and macromolecular modification systems. We predict that Escherichia coli YbiA and related families of domains from diverse bacteria, eukaryotes, large DNA viruses and single strand RNA viruses are previously unrecognized components of NAD-utilizing pathways that probably operate on ADP-ribose derivatives. Using contextual analysis we show that some of these proteins potentially act in RNA repair, where NAD is used to remove 2'-3' cyclic phosphodiester linkages. Likewise, we predict that another family of YbiA-related enzymes is likely to comprise a novel NAD-dependent ADP-ribosylation system for proteins, in conjunction with a previously unrecognized ADP-ribosyltransferase. A similar ADP-ribosyltransferase is also coupled with MACRO or ADP-ribosylglycohydrolase domain proteins in other related systems, suggesting that all these novel systems are likely to comprise pairs of ADP-ribosylation and ribosylglycohydrolase enzymes analogous to the DraG-DraT system, and a novel group of bacterial polymorphic toxins. We present evidence that some of these coupled ADP-ribosyltransferases/ribosylglycohydrolases are likely to regulate certain restriction modification enzymes in bacteria. The ADP-ribosyltransferases found in these, the bacterial polymorphic toxin and host-directed toxin systems of bacteria such as Waddlia also throw light on the evolution of this fold and the origin of eukaryotic polyADP-ribosyltransferases and NEURL4-like ARTs, which might be involved in centrosomal assembly. We also infer a novel biosynthetic pathway that might be involved in the synthesis of a nicotinate-derived compound in conjunction with an asparagine synthetase and AMPylating peptide ligase. We use the data derived from this analysis to understand the origin and early evolutionary trajectories of key NAD-utilizing enzymes and present targets for future biochemical investigations.

Decreasing the number of false positives in sequence classification

Abstract Background A large number of probabilistic models used in sequence analysis assign non-zero probability values to most input sequences. To decide when a given probability is sufficient the most common way is bayesian binary classification, where the probability of the model characterizing the sequence family of interest is compared to that of an alternative probability model. We can use as alternative model a null model. This is the scoring technique used by sequence analysis tools such as HMMER, SAM and INFERNAL. The most prevalent null models are position-independent residue distributions that include: the uniform distribution, genomic distribution, family-specific distribution and the target sequence distribution. This paper presents a study to evaluate the impact of the choice of a null model in the final result of classifications. In particular, we are interested in minimizing the number of false predictions in a classification. This is a crucial issue to reduce costs of biological validation. Results For all the tests, the target null model presented the lowest number of false positives, when using random sequences as a test. The study was performed in DNA sequences using GC content as the measure of content bias, but the results should be valid also for protein sequences. To broaden the application of the results, the study was performed using randomly generated sequences. Previous studies were performed on aminoacid sequences, using only one probabilistic model (HMM) and on a specific benchmark, and lack more general conclusions about the performance of null models. Finally, a benchmark test with P. falciparum confirmed these results. Conclusions Of the evaluated models the best suited for classification are the uniform model and the target model. However, the use of the uniform model presents a GC bias that can cause more false positives for candidate sequences with extreme compositional bias, a characteristic not described in previous studies. In these cases the target model is more dependable for biological validation due to its higher specificity.

Effects of Aedes aegypti salivary components on dendritic cell and lymphocyte biology

Abstract Background Saliva is a key element of interaction between hematophagous mosquitoes and their vertebrate hosts. In addition to allowing a successful blood meal by neutralizing or delaying hemostatic responses, the salivary cocktail is also able to modulate the effector mechanisms of host immune responses facilitating, in turn, the transmission of several types of microorganisms. Understanding how the mosquito uses its salivary components to circumvent host immunity might help to clarify the mechanisms of transmission of such pathogens and disease establishment. Methods Flow cytometry was used to evaluate if increasing concentrations of A. aegypti salivary gland extract (SGE) affects bone marrow-derived DC differentiation and maturation. Lymphocyte proliferation in the presence of SGE was estimated by a colorimetric assay. Western blot and Annexin V staining assays were used to assess apoptosis in these cells. Naïve and memory cells from mosquito-bite exposed mice or OVA-immunized mice and their respective controls were analyzed by flow cytometry. Results Concentration-response curves were employed to evaluate A. aegypti SGE effects on DC and lymphocyte biology. DCs differentiation from bone marrow precursors, their maturation and function were not directly affected by A. aegypti SGE (concentrations ranging from 2.5 to 40 μg/mL). On the other hand, lymphocytes were very sensitive to the salivary components and died in the presence of A. aegypti SGE, even at concentrations as low as 0.1 μg/mL. In addition, A. aegypti SGE was shown to induce apoptosis in all lymphocyte populations evaluated (CD4+ and CD8+ T cells, and B cells) through a mechanism involving caspase-3 and caspase-8, but not Bim. By using different approaches to generate memory cells, we were able to verify that these cells are resistant to SGE effects. Conclusion Our results show that lymphocytes, and not DCs, are the primary target of A. aegypti salivary components. In the presence of A. aegypti SGE, naïve lymphocyte populations die by apoptosis in a caspase-3- and caspase-8-dependent pathway, while memory cells are selectively more resistant to its effects. The present work contributes to elucidate the activities of A. aegypti salivary molecules on the antigen presenting cell-lymphocyte axis and in the biology of these cells.

The venom composition of the parasitic wasp Chelonus inanitus resolved by combined expressed sequence tags analysis and proteomic approach

Background Parasitic wasps constitute one of the largest group of venomous animals. Although some physiological effects of their venoms are well documented, relatively little is known at the molecular level on the protein composition of these secretions. To identify the majority of the venom proteins of the endoparasitoid wasp Chelonus inanitus (Hymenoptera: Braconidae), we have randomly sequenced 2111 expressed sequence tags (ESTs) from a cDNA library of venom gland. In parallel, proteins from pure venom were separated by gel electrophoresis and individually submitted to a nano-LC-MS/MS analysis allowing comparison of peptides and ESTs sequences. Results About 60% of sequenced ESTs encoded proteins whose presence in venom was attested by mass spectrometry. Most of the remaining ESTs corresponded to gene products likely involved in the transcriptional and translational machinery of venom gland cells. In addition, a small number of transcripts were found to encode proteins that share sequence similarity with well-known venom constituents of social hymenopteran species, such as hyaluronidase-like proteins and an Allergen-5 protein. An overall number of 29 venom proteins could be identified through the combination of ESTs sequencing and proteomic analyses. The most highly redundant set of ESTs encoded a protein that shared sequence similarity with a venom protein of unknown function potentially specific of the Chelonus lineage. Venom components specific to C. inanitus included a C-type lectin domain containing protein, a chemosensory protein-like protein, a protein related to yellow-e3 and ten new proteins which shared no significant sequence similarity with known sequences. In addition, several venom proteins potentially able to interact with chitin were also identified including a chitinase, an imaginal disc growth factor-like protein and two putative mucin-like peritrophins. Conclusions The use of the combined approaches has allowed to discriminate between cellular and truly venom proteins. The venom of C. inanitus appears as a mixture of conserved venom components and of potentially lineage-specific proteins. These new molecular data enrich our knowledge on parasitoid venoms and more generally, might contribute to a better understanding of the evolution and functional diversity of venom proteins within Hymenoptera.

Complete Genome Sequence of Treponema paraluiscuniculi, Strain Cuniculi A: The Loss of Infectivity to Humans Is Associated with Genome Decay.

Treponema paraluiscuniculi is the causative agent of rabbit venereal spirochetosis. It is not infectious to humans, although its genome structure is very closely related to other pathogenic Treponema species including Treponema pallidum subspecies pallidum, the etiological agent of syphilis. In this study, the genome sequence of Treponema paraluiscuniculi, strain Cuniculi A, was determined by a combination of several high-throughput sequencing strategies. Whereas the overall size (1,133,390 bp), arrangement, and gene content of the Cuniculi A genome closely resembled those of the T. pallidum genome, the T. paraluiscuniculi genome contained a markedly higher number of pseudogenes and gene fragments (51). In addition to pseudogenes, 33 divergent genes were also found in the T. paraluiscuniculi genome. A set of 32 (out of 84) affected genes encoded proteins of known or predicted function in the Nichols genome. These proteins included virulence factors, gene regulators and components of DNA repair and recombination. The majority (52 or 61.9%) of the Cuniculi A pseudogenes and divergent genes were of unknown function. Our results indicate that T. paraluiscuniculi has evolved from a T. pallidum-like ancestor and adapted to a specialized host-associated niche (rabbits) during loss of infectivity to humans. The genes that are inactivated or altered in T. paraluiscuniculi are candidates for virulence factors important in the infectivity and pathogenesis of T. pallidum subspecies.

Fibrillins: Sequence, phylogeny and carboxy terminal domain proteolytic processing

Fibrillin-1 and -2 are large secreted glycoproteins that are known to be components of extracellular matrix microfibrils located in the vasculature, basement membrane and various connective tissues. These microfibrils are often associated with a superstructure known as the elastic fiber. During the development of elastic tissues, fibrillin microfibrils precede the appearance of elastin and may provide a scaffolding for the deposition and crosslinking of elastin. Using RT/PCR, we cloned and sequenced 3.85Kbp of the FBN2 gene. Five differences were found between our contig sequence and that published by Zhang et al. (1995). Like many extracellular matrix proteins, the fibrillins are modular proteins. We compared analogous domains of the two fibrillins and also members of the latent TGF-$\beta$ binding protein (LTBP) family to determine their phylogenetic relationship. We found that the two families are homologous. LTBP-2 is the most similar to the fibrillin family while FBN-1 is the most similar to the LTBP family. The fibrillin-1 carboxy terminal domain is proteolytically processed. Two eukaryotic protein expression systems, baculoviral and CHO-K1, were developed to examine the proteolytic processing of the carboxy terminal domain of the fibrillin-1 protein. Both expression systems successfully processed the domain and both processed a mutant less efficiently. In the CHO-K1 cells, processing occurred intracellularly. ^

From stellar nebula to planets: The refractory components

Context. To date, calculations of planet formation have mainly focused on dynamics, and only a few have considered the chemical composition of refractory elements and compounds in the planetary bodies. While many studies have been concentrating on the chemical composition of volatile compounds (such as H2O, CO, CO2) incorporated in planets, only a few have considered the refractory materials as well, although they are of great importance for the formation of rocky planets. Aims. We computed the abundance of refractory elements in planetary bodies formed in stellar systems with a solar chemical composition by combining models of chemical composition and planet formation. We also considered the formation of refractory organic compounds, which have been ignored in previous studies on this topic. Methods. We used the commercial software package HSC Chemistry to compute the condensation sequence and chemical composition of refractory minerals incorporated into planets. The problem of refractory organic material is approached with two distinct model calculations: the first considers that the fraction of atoms used in the formation of organic compounds is removed from the system (i.e., organic compounds are formed in the gas phase and are non-reactive); and the second assumes that organic compounds are formed by the reaction between different compounds that had previously condensed from the gas phase. Results. Results show that refractory material represents more than 50 wt % of the mass of solids accreted by the simulated planets with up to 30 wt % of the total mass composed of refractory organic compounds. Carbide and silicate abundances are consistent with C/O and Mg/Si elemental ratios of 0.5 and 1.02 for the Sun. Less than 1 wt % of carbides are present in the planets, and pyroxene and olivine are formed in similar quantities. The model predicts planets that are similar in composition to those of the solar system. Starting from a common initial nebula composition, it also shows that a wide variety of chemically different planets can form, which means that the differences in planetary compositions are due to differences in the planetary formation process. Conclusions. We show that a model in which refractory organic material is absent from the system is more compatible with observations. The use of a planet formation model is essential to form a wide diversity of planets in a consistent way.

Siliceous components of Pliocene-Holocene sediments of the South Atlantic

The Pliocene-Holocene sediments recovered on ODP Leg 114 from Holes 699A, 701C, and 704B are the subject of a detailed investigation to interpret changes in the Oceanographic environment of the South Atlantic in the vicinity of the Polar Front Zone (PFZ). The cores sample sediments at shallow (Hole 704B, 2532 m), intermediate (Hole 699A, 3716 m), and basinal (Hole 701C, 4647 m) depths. Sites 699 and 704 come under the influence of the Antarctic Circumpolar Current (ACC) and Circumpolar Deep Water. It is possible that the upper reaches of Antarctic Bottom Water (AABW) may also affect Hole 699A. Site 701 is influenced by AABW. Closely spaced samples were analyzed for grain-size distribution, sand fraction components, biosiliceous microfossils, organic carbon, and water content. PFZ migrations are traced using changes in bulk sedimentaccumulation rates and the abundance of the diatoms Actiniscus ssp. and Genus et species indet. 1 Fenner (1991), as well as changes in sediment grain size and composition. Diatomaceous sediments of Gilbert age in Hole 699A indicate that the PFZ was positioned over this site, but during the Gauss it migrated north, bringing in less productive Antarctic Surface Water. All cores document a very gradual southerly movement of the PFZ throughout the Matuyama (with some sharp fluctuations of the northen PFZ border over Site 704 between 1.45 and 1.83 m.y.). This regressive shift culminated in the late Matuyama. The latest Matuyama to earliest Brunhes record in Hole 699A has been removed by a hiatus lasting from 1.0 to 0.6 m.y., which was probably caused by intensification of the deep-reaching ACC. The corresponding interval in Hole 704B, the shallowest core, contains evidence of winnowing. Sharp fluctuations of large amplitude and high frequency in the lithology of the sediments from Hole 704B in the eastern South Atlantic, starting at about 0.75 m.y. and characterizing the whole Brunhes Epoch, record the rapid movement of the northern border of the PFZ over the site. These reflect strong glacial/interglacial alternations in climate. To a lesser extent, lithologic fluctuations in Hole 701C reflect the same phenomenon, whereas in Hole 699A the lithology does not vary as dramatically.

Grains size and components distribution in turbidite layesr of ODP Leg 101

Textural and compositional differences were found between gravity-flow sheets in an open-ocean environment on the northern slope of Little Bahama Bank (Site 628, Pliocene turbidite sequence) and in a closed-basin depositional setting (Site 632, Quaternary turbidite sequence). Mud-supported debris-flow sheets were cored at Site 628. Average mean grain size of the turbidite samples was lower, mud content was higher, and sorting was poorer than in comparable samples from Site 632. This reflects the deposition of proximal, low-energy turbidity currents and debris flows on a base-ofslope carbonate apron. No mud-supported debris-flow sheets were deposited in the investigated sediment sequence of Hole 632A. Many larger turbidity currents from around the margins of Exuma Sound may have reached this central basin setting, depositing sediments that had been transported over longer distances. Planktonic components dominate in the grain-sized fraction (500-1000 µm) of turbidite samples from Hole 628A, while platform detritus is rare. We interpreted this as resulting from the erosion and reworking of a large area of open-ocean slope sediments by gravity flows. In contrast, large amounts of benthic and platform components were found in the turbidite samples of Hole 632A. This may be explained by the fact that the slopes of the enclosed Exuma Sound are steep, and turbidity currents bypassed much of these slopes through pronounced channels, delivering more shallow-water detritus to the deep basin. Erosion of slope sediments, a possible source area of planktonic detritus, is assumed to be low. The small slope area in relation to the larger surrounding platform areas and lower production of planktonic components in the enclosed waters of Exuma Sound may also explain the observed low number of planktonic components at Hole 632A. Turbidite material from both open-ocean and enclosed-basin environments was deposited at Site 635.

Texture description and distribution of components in ODP Hole 103-639D (Figure 2)

A detailed analysis of the texture, matrix, and elements of the microfacies from the carbonate sequence recovered in ODP Hole 639D resulted in a typological classification of 10 major microfacies types and their variants. The variations in distribution and succession of type microfacies allowed us to divide the carbonate sequence into 12 facies-defined subunits. Based on the analyzed characteristics and their relations, we also propose a paleoenvironmental interpretation involving a mixed carbonate/terrigenous ramp model instead of the previous, classical zoned carbonate platform.