Modeling of the potential coiled-coil structure of snapin protein and its interaction with SNARE complex

Autism is a developmental disability causing learning and memory disorder. The heart of the search for a cure for this syndrome is the need to understand dendrite branch patterning, a process crucial for proper synaptic transmission. Due to the association of snapin with the SNARE complex and its role in synaptic transmission it is reported as a potential drug target for autism therapies. We wish to impart the noesis of the 3D structure of the snapin protein, and in this chase we predict the native structure from its sequence of amino acid residues using the classical Comparative protein structure modeling methods. The predicted protein model can be of great assistance in understanding the structural insights, which is necessary to understand the protein function. Understanding the interactions between snapin and SNARE complex is crucial in studying its role in the neurotransmitter release process. We also presented a computational model that shows the interaction between the snapin and SNAP-25 protein, a part of the larger SNARE complex.     

Modeling senescence changes of the pubic symphysis in historic Italian populations: A comparison of the Rostock and forensic approaches to aging using transition analysis

Age‐related anatomical changes to the surface of the pubic symphysis are well‐documented in the literature. However, aligning these morphological changes with chronological age has proven problematic, often resulting in biased age estimates. Statistical modeling provides an avenue for forensic anthropologists and bioarchaeologists to increase the accuracy of traditional aging methods. Locating appropriate samples to use as a basis for modeling age estimations can be challenging due to differing sample age distributions and potentially varying patterns of senescence. We compared two approaches, Rostock and Forensic, coupled with a Bayesian methodology, to address these issues. Transition analysis was run specific to each method (which differ by sample selection). A Gompertz model was derived from an informative prior that yielded the mortality and senescence parameters for constructing highest posterior density ranges, i.e., coverages, which are analogous to age ranges. These age ranges were generated from both approaches and are presented as reference tables useful for historic male and female Italian samples. The age ranges produced from each approach were tested on an historic Italian sample, using cumulative binomial tests. These two approaches performed similarly, with the Forensic approach showing a slight advantage. However, the Forensic approach is unable to identify varying senescence patterns between populations, thus preference for one approach over the other will depend on research design. Finally, we demonstrate that while populations exhibit similar morphological changes with advancing age, there are no significant sex differences in these samples, and the timing of these changes varies from population to population. Am J Phys Anthropol 156:466–473, 2015. © 2014 Wiley Periodicals, Inc.     

The amino-terminal tails of the core histones and the translational position of the TATA box determine TBP/TFIIA association with nucleosomal DNA.

We establish that the TATA binding protein (TBP) in the presence of TFIIA recognizes the TATA box in nucleosomal DNA dependent on the dissociation of the amino-terminal tails of the core histones from the nucleosome and the position of the TATA box within the nucleosome. We examine TBP/TFIIA access to the TATA box with this sequence placed in four distinct rotational frames with reference to the histone surface and at three distinct translational positions at the edge, side and dyad axis of the nucleosome. Under our experimental conditions, we find that the preferential translational position at which TBP/TFIIA can bind the TATA box is within linker DNA at the edge of the nucleosome and that binding is facilitated if contacts made by the amino-terminal tails of the histones with nucleosomal DNA are eliminated. TBP/TFIIA binding to DNA at the edge of the nucleosome occurs with the TATA box in all four rotational positions. This is indicative of TBP/TFIIA association directing the dissociation of the TATA box from the surface of the histone octamer.     

Incomplete Protection against Dengue Virus Type 2 Re-infection in Peru

Background

Nearly half of the world’s population is at risk for dengue, yet no licensed vaccine or anti-viral drug is currently available. Dengue is caused by any of four dengue virus serotypes (DENV-1 through DENV-4), and infection by a DENV serotype is assumed to provide life-long protection against re-infection by that serotype. We investigated the validity of this fundamental assumption during a large dengue epidemic caused by DENV-2 in Iquitos, Peru, in 2010–2011, 15 years after the first outbreak of DENV-2 in the region.

Methodology/Principal Findings

We estimated the age-dependent prevalence of serotype-specific DENV antibodies from longitudinal cohort studies conducted between 1993 and 2010. During the 2010–2011 epidemic, active dengue cases were identified through active community- and clinic-based febrile surveillance studies, and acute inapparent DENV infections were identified through contact tracing studies. Based on the age-specific prevalence of DENV-2 neutralizing antibodies, the age distribution of DENV-2 cases was markedly older than expected. Homologous protection was estimated at 35.1% (95% confidence interval: 0%–65.2%). At the individual level, pre-existing DENV-2 antibodies were associated with an incomplete reduction in the frequency of symptoms. Among dengue cases, 43% (26/66) exhibited elevated DENV-2 neutralizing antibody titers for years prior to infection, compared with 76% (13/17) of inapparent infections (age-adjusted odds ratio: 4.2; 95% confidence interval: 1.1–17.7).

Conclusions/Significance

Our data indicate that protection from homologous DENV re-infection may be incomplete in some circumstances, which provides context for the limited vaccine efficacy against DENV-2 in recent trials. Further studies are warranted to confirm this phenomenon and to evaluate the potential role of incomplete homologous protection in DENV transmission dynamics.     

NADH as electron donor for the photosynthetic membrane of Chlamydomonas reinhardii

A chloroplast fraction from Chlamydomonas reinhardii cells can oxidize NADH in the light, unlike chloroplasts of higher plants. The Chlamydomonas preparation catalyzes electron flow from NADH to methylviologen or ferredoxin to evolve hydrogen (in the presence of a hydrogenase) or take up oxygen. The NADH photooxidation is sensitive to rotenone, dibromothymoquinone and dicyclohexylcarbodiimide. This suggests that a rotenone sensitive NADH dehydrogenase is coupled on the plastoquinone reduction site of the potosynthetic electron flow system. On sonication of the particles NADH photooxidation is lost but may be restored by a protein fraction from an acetone extract plus plastocyanin.Abbreviations DAD diaminodurene - DCCD dicyclohexylcarbodiimide - DCMU (3,3-dichlorphenyl)-N·N dimethyl urea - DBMIB dibromothymoquinone - DNP-INT dinitro-phenylether of 2-iodo-4-nitrothymol - MV methylviologen - chl chlorophyll Dedicated to Professor Dr. O. Kandler on the occasion of his 60th birthday     

A sperm-activating peptide controls a cGMP-signaling pathway in starfish sperm

Peptides released from eggs of marine invertebrates play a central role in fertilization. About 80 different peptides from various phyla have been isolated, however, with one exception, their respective receptors on the sperm surface have not been unequivocally identified and the pertinent signaling pathways remain ill defined. Using rapid mixing techniques and novel membrane-permeable caged compounds of cyclic nucleotides, we show that the sperm-activating peptide asterosap evokes a fast and transient increase of the cGMP concentration in sperm of the starfish Asterias amurensis, followed by a transient cGMP-stimulated increase in the Ca(2+) concentration. In contrast, cAMP levels did not change significantly and the Ca(2+) response evoked by photolysis of caged cAMP was significantly smaller than that using caged cGMP. By cloning of cDNA and chemical crosslinking, we identified a receptor-type guanylyl cyclase in the sperm flagellum as the asterosap-binding protein. Sperm respond exquisitely sensitive to picomolar concentrations of asterosap, suggesting that the peptide serves a chemosensory function like resact, a peptide involved in chemotaxis of sperm of the sea urchin Arbacia punctulata. A unifying principle emerges that chemosensory transduction in sperm of marine invertebrates uses cGMP as the primary messenger, although there may be variations in the detail.     

Effect of long term fumigation with ozone on the turnover of the D-1 reaction center polypetide of photosystem II in spruce (Picea abies)

Long term fumigation of 4-year-old spruce trees with ozone concentrations up to 200 nl l⁻¹ has only minor effects on the photosynthetic activities measured as chlorophyll a fluorescence. Nevertheless, it drastically changes the turnover of the D-1 reaction center polypeptide of photosystem II. During summer, fumigation with ozone for 2 weeks resulted in an almost 4-fold stimulation of the light dependent incorporation of [¹⁴C] leucine into the D-1 protein in the exposed trees. The amount of immunodetectable D-1 protein remained constant when based on chlorophyll. This indicates that exposure to ozone stimulates both the synthesis and the degradation of the D-1 protein. When spruce trees were exposed during winter for 4 weeks to 100 and 200 nl l⁻¹ ozone, respectively, an almost 3-fold increase of the amount of immunodetectable D-1 protein per chlorophyll in the exposed trees was observed. This can be explained by a varying stimulation of D-1 protein synthesis and degradation depending on the different physiological conditions. Since so far the D-1 protein has been found only as a component of photosystem II reaction centers, one has to assume that the relative content of photosystem II reaction centers also increases under certain stress conditions. The increased turnover of the D-1 protein in trees exposed to ozone explains the synergistic effects of stress conditions and high light intensities often observed in the field.     

Stress-induced chlorosis and increase in D1-protein turnover precede photoinhibition in spinach suffering under magnesium/sulphur deficiency

To test wether chlorosis is induced by photoinhibitory damage to photosystem II (PSII), onset of chlorosis and loss of PSII function were compared in young spinach (Spinaciae oleracea L.) plants suffering under a combined magnesium and sulphur deficiency. Loss of chlorophyll already occurred after the first week of deficiency and preceded any permanent functional inhibition of the photosynthetic apparatus. Permanent disturbancies of photosynthetic electron transport measured in isolated thylakoids and of PSII function, determined via the ratio of variable fluorescence to maximal fluorescence, F_v/F_m, could be detected only after the second week of deficiency. After the third week, the plants had lost about 60% of their chlorophyll; even so, fluorescence data indicated that 85% of the existing PSII was still capable of initiating photosynthetic electron transport. However, quenching analysis of steady-state fluorescence showed an early increase in non-photochemical quenching and in down-regulated PSII centres with low steady-state quantum efficiency. Together with the down-regulation of PSII centres, a 1.4-fold increase in D1-protein synthesis, measured as incorporation of [¹⁴C]leucine, could be observed at the end of the first week before any loss of D1 protein, chlorophyll or photosynthetic activity could be detected. Immunological determiation by Western-blotting did not show a change in D1-protein content; thus, at this time, D1 protein was not only faster synthesised but was also faster degraded than before the imposition of mineral deficiency. The increased turnover was high enough to prevent any loss or functional inhibition of PSII. After 3 weeks, D1-protein synthesis on a chlorophyll basis was further stimulated by a factor of 2. However, this was not enough to prevent a net loss of D1 protein of about 70%, showing that the D1-protein was now degraded faster than it was synthesised. Immunological determination and electron-transport measurements showed that together with the loss of D1 protein the other polypetides of PSII were also degraded, resulting in a specific loss of PSII centres. The degradation of PSII centres prevented a large accumulation of damaged PSII centres. We assume that the decrease in PSII centres initiates the breakdown of the other thylakoid proteins.Abbreviations Fo yield of intrinsic fluorescence when all PSII centres are open in the dark - F_m yield of maximal fluorescence when all reaction centres are closed - F_m fluorescence yield when all reaction centres are closed under steady-state conditions - F_v yield of variable fluorescence, (difference between F_o and F_m) - F yield of variable fluorescence under steady-state conditions, difference between F_m and F_t, the fluorescence yield under steady-state conditions - PFD photon flux density - Q_A primary quinone acceptor of PSII - Q_B secondary quinone acceptor of PSII - q_p photochemical quenching - q_n non-photochemical quenching This work was supported by grants from the Bundesminister für Forschung und Technologie and the German Israeli Foundation. The authors thank Prof. I. Ohad (Department of Biological Chemistry, Hebrew University, Jerusalem, Israel) for fruitful discussions.     

Influence of air pollutants and nutrient deficiency on D-1 protein content and photosynthesis in young spruce trees

Long-term fumigation with different mixtures of air pollutants, such as O₃, NO₂ and SO₂, in combination with potassium deficiency in 4-year-old spruce trees shows clearly that the photosynthetic apparatus reacts very sensitively to environmental stress. Even when no change in photosynthetic oxygen evolution of the leaves was measurable, the content of D-1 protein in the reaction center of photosystem II already increased significantly at low stress conditions. With increasing concentrations of pollutants, the content of D-1 protein decreased considerably. This pattern was observed with all combinations of gases, although they differed in effectiveness. The most potent effect on the content of D-1 protein was found with a combined fumigation of SO₂ plus NO₂. Obviously, the ratio between synthesis and degradation of the D-1 protein is influenced by stress factors. However, the content of D-1 protein was not strongly correlated with photosynthetic oxygen evolution in whole needles nor with electron transport rate in isolated thylakoids. Under controlled potassium deficiency, effects similar to those observed upon ozone fumigation developed. The results suggest unspecific stress answers for the D-1 content and the photosynthetic reactions rather than specific responses.