Oxidation-induced destabilization of the fibrinogen αC-domain dimer investigated by molecular dynamics simulations.

Upon activation, fibrinogen is converted to insoluble fibrin, which assembles into long strings called protofibrils. These aggregate laterally to form a fibrin matrix that stabilizes a blood clot. Lateral aggregation of protofibrils is mediated by the αC domain, a partially structured fragment located in a disordered region of fibrinogen. Polymerization of αC domains links multiple fibrin molecules with each other enabling the formation of thick fibrin fibers and a fibrin matrix that is stable but can also be digested by enzymes. However, oxidizing agents produced during the inflammatory response have been shown to cause thinner fibrin fibers resulting in denser clots, which are harder to proteolyze and pose the risk of deep vein thrombosis and lung embolism. Oxidation of Met476 located within the αC domain is thought to hinder its ability to polymerize disrupting the lateral aggregation of protofibrils and leading to the observed thinner fibers. How αC domains assemble into polymers is still unclear and yet this knowledge would shed light on the mechanism through which oxidation weakens the lateral aggregation of protofibrils. This study used temperature replica exchange molecular dynamics simulations to investigate the αC-domain dimer and how this is affected by oxidation of Met476 . Analysis of the trajectories revealed that multiple stable binding modes were sampled between two αC domains while oxidation decreased the likelihood of dimer formation. Furthermore, the side chain of Met476 was observed to act as a docking spot for the binding and this function was impaired by its conversion to methionine sulfoxide.

Genomic Changes Associated with the Evolutionary Transitions of Nostoc to a Plant Symbiont.

Cyanobacteria belonging to the genus Nostoc comprise free-living strains and also facultative plant symbionts. Symbiotic strains can enter into symbiosis with taxonomically diverse range of host plants. Little is known about genomic changes associated with evolutionary transition of Nostoc from free-living to plant symbiont. Here, we compared the genomes derived from 11 symbiotic Nostoc strains isolated from different host plants and infer phylogenetic relationships between strains. Phylogenetic reconstructions of 89 Nostocales showed that symbiotic Nostoc strains with a broad host range, entering epiphytic and intracellular or extracellular endophytic interactions, form a monophyletic clade indicating a common evolutionary history. A polyphyletic origin was found for Nostoc strains which enter only extracellular symbioses, and inference of transfer events implied that this trait was likely acquired several times in the evolution of the Nostocales. Symbiotic Nostoc strains showed enriched functions in transport and metabolism of organic sulfur, chemotaxis and motility, as well as the uptake of phosphate, branched-chain amino acids, and ammonium. The genomes of the intracellular clade differ from that of other Nostoc strains, with a gain/enrichment of genes encoding proteins to generate l-methionine from sulfite and pathways for the degradation of the plant metabolites vanillin and vanillate, and of the macromolecule xylan present in plant cell walls. These compounds could function as C-sources for members of the intracellular clade. Molecular clock analysis indicated that the intracellular clade emerged ca. 600 Ma, suggesting that intracellular Nostoc symbioses predate the origin of land plants and the emergence of their extant hosts.

Early evolution of the land plant circadian clock.

While angiosperm clocks can be described as an intricate network of interlocked transcriptional feedback loops, clocks of green algae have been modelled as a loop of only two genes. To investigate the transition from a simple clock in algae to a complex one in angiosperms, we performed an inventory of circadian clock genes in bryophytes and charophytes. Additionally, we performed functional characterization of putative core clock genes in the liverwort Marchantia polymorpha and the hornwort Anthoceros agrestis. Phylogenetic construction was combined with studies of spatiotemporal expression patterns and analysis of M. polymorpha clock gene mutants. Homologues to core clock genes identified in Arabidopsis were found not only in bryophytes but also in charophytes, albeit in fewer copies. Circadian rhythms were detected for most identified genes in M. polymorpha and A. agrestis, and mutant analysis supports a role for putative clock genes in M. polymorpha. Our data are in line with a recent hypothesis that adaptation to terrestrial life occurred earlier than previously expected in the evolutionary history of charophyte algae. Both gene duplication and acquisition of new genes was important in the evolution of the plant circadian clock, but gene loss has also contributed to shaping the clock of bryophytes.

The MOSS Physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain.

In order to establish a reference for analysis of the function of auxin and the auxin biosynthesis regulators SHORT INTERNODE/STYLISH (SHI/STY) during Physcomitrella patens reproductive development, we have described male (antheridial) and female(archegonial) development in detail, including temporal and positional information of organ initiation. This has allowed us to define discrete stages of organ morphogenesis and to show that reproductive organ development in P. patens is highly organized and that organ phyllotaxis differs between vegetative and reproductive development. Using the PpSHI1 and PpSHI2 reporter and knockout lines, the auxin reporters GmGH3(pro):GUS and PpPINA(pro):GFP-GUS, and the auxin-conjugating transgene PpSHI2(pro):IAAL, we could show that the PpSHI genes, and by inference also auxin, play important roles for reproductive organ development in moss. The PpSHI genes are required for the apical opening of the reproductive organs, the final differentiation of the egg cell, and the progression of canal cells into a cell death program. The apical cells of the archegonium, the canal cells, and the egg cell are also sites of auxin responsiveness and are affected by reduced levels of active auxin, suggesting that auxin mediates PpSHI function in the reproductive organs.

Homologues of the Arabidopsis thaliana SHI/STY/LRP1 genes control auxin biosynthesis and affect growth and development in the moss Physcomitrella patens.

The plant hormone auxin plays fundamental roles in vascular plants. Although exogenous auxin also stimulates developmental transitions and growth in non-vascular plants, the effects of manipulating endogenous auxin levels have thus far not been reported. Here, we have altered the levels and sites of auxin production and accumulation in the moss Physcomitrella patens by changing the expression level of homologues of the Arabidopsis SHI/STY family proteins, which are positive regulators of auxin biosynthesis genes. Constitutive expression of PpSHI1 resulted in elevated auxin levels, increased and ectopic expression of the auxin response reporter GmGH3pro:GUS, and in an increased caulonema/chloronema ratio, an effect also induced by exogenous auxin application. In addition, we observed premature ageing and necrosis in cells ectopically expressing PpSHI1. Knockout of either of the two PpSHI genes resulted in reduced auxin levels and auxin biosynthesis rates in leafy shoots, reduced internode elongation, delayed ageing, a decreased caulonema/chloronema ratio and an increased number of axillary hairs, which constitute potential auxin biosynthesis sites. Some of the identified auxin functions appear to be analogous in vascular and non-vascular plants. Furthermore, the spatiotemporal expression of the PpSHI genes and GmGH3pro:GUS strongly overlap, suggesting that local auxin biosynthesis is important for the regulation of auxin peak formation in non-vascular plants.

Rapamycin-Induced Feedback Activation of eIF4E-EIF4A Dependent mRNA Translation in Pancreatic Cancer.

Pancreatic cancer cells adapt molecular mechanisms to activate the protein synthesis to support tumor growth. This study reports the mTOR inhibitor rapamycin's specific and genome-wide effect on mRNA translation. Using ribosome footprinting in pancreatic cancer cells that lack the expression of 4EBP1, we establish the effect of mTOR-S6-dependent mRNAs translation. Rapamycin inhibits the translation of a subset of mRNAs including p70-S6K and proteins involved in the cell cycle and cancer cell growth. In addition, we identify translation programs that are activated following mTOR inhibition. Interestingly, rapamycin treatment results in the translational activation of kinases that are involved in mTOR signaling such as p90-RSK1. We further show that phospho-AKT1 and phospho-eIF4E are upregulated following mTOR inhibition suggesting a feedback activation of translation by rapamycin. Next, targeting eIF4E and eIF4A-dependent translation by using specific eIF4A inhibitors in combination with rapamycin shows significant growth inhibition in pancreatic cancer cells. In short, we establish the specific effect of mTOR-S6 on translation in cells lacking 4EBP1 and show that mTOR inhibition leads to feedback activation of translation via AKT-RSK1-eIF4E signals. Therefore, targeting translation downstream of mTOR presents a more efficient therapeutic strategy in pancreatic cancer.

Bayesian model and selection signature analyses reveal risk factors for canine atopic dermatitis.

Canine atopic dermatitis is an inflammatory skin disease with clinical similarities to human atopic dermatitis. Several dog breeds are at increased risk for developing this disease but previous genetic associations are poorly defined. To identify additional genetic risk factors for canine atopic dermatitis, we here apply a Bayesian mixture model adapted for mapping complex traits and a cross-population extended haplotype test to search for disease-associated loci and selective sweeps in four dog breeds at risk for atopic dermatitis. We define 15 associated loci and eight candidate regions under selection by comparing cases with controls. One associated locus is syntenic to the major genetic risk locus (Filaggrin locus) in human atopic dermatitis. One selection signal in common type Labrador retriever cases positions across the TBC1D1 gene (body weight) and one signal of selection in working type German shepherd controls overlaps the LRP1B gene (brain), near the KYNU gene (psoriasis). In conclusion, we identify candidate genes, including genes belonging to the same biological pathways across multiple loci, with potential relevance to the pathogenesis of canine atopic dermatitis. The results show genetic similarities between dog and human atopic dermatitis, and future across-species genetic comparisons are hereby further motivated.

Orienting attention during phonetic training facilitates learning.

The role of consciously directed attention toward speech input in learning has not yet been determined. Previous phonetic learning studies have manipulated acoustic signals and response feedback, but not conscious control over attentional orienting. This study tests whether directed attention facilitates learning of phonetic information. Two monolingual English-speaking groups were trained with feedback on the same auditory stimuli: Hindi words. One group was instructed to attend to the consonants and the other to the vowels. The consonant-oriented group, but not the vowel-oriented group, demonstrated post-training improvement in consonant perception, confirming a role for consciously directed attentional mechanisms during phonetic learning.

Bidirectional C and N transfer and a potential role for sulfur in an epiphytic diazotrophic mutualism.

In nitrogen-limited boreal forests, associations between feathermoss and diazotrophic cyanobacteria control nitrogen inputs and thus carbon cycling, but little is known about the molecular regulators required for initiation and maintenance of these associations. Specifically, a benefit to the cyanobacteria is not known, challenging whether the association is a nutritional mutualism. Targeted mutagenesis of the cyanobacterial alkane sulfonate monooxygenase results in an inability to colonize feathermosses by the cyanobacterium Nostoc punctiforme, suggesting a role for organic sulfur in communication or nutrition. Isotope probing paired with high-resolution imaging mass spectrometry (NanoSIMS) demonstrated bidirectional elemental transfer between partners, with carbon and sulfur both being transferred to the cyanobacteria, and nitrogen transferred to the moss. These results support the hypothesis that moss and cyanobacteria enter a mutualistic exosymbiosis with substantial bidirectional material exchange of carbon and nitrogen and potential signaling through sulfur compounds.

Is Substance Use a Team Sport? Attraction to Team, Perceived Norms, and Alcohol and Marijuana Use Among Male and Female Intercollegiate Athletes.

This research examined the role of attraction to one's team in predicting alcohol and marijuana use among intercollegiate athletes. Attraction to team and alcohol-related information were collected via an online survey and marijuana use-related information was gathered in a live setting. We investigated the influence of attraction to one's team above and beyond the influence of gender and perceived norms, and attraction to team as a moderator of these relationships. Attraction to one's team accounted for significant variance in marijuana use, and alcohol-related consequences after controlling for alcohol consumption. Regression analyses revealed significant interactions between gender, attraction to team, and norms in predicting alcohol and marijuana use. Stronger attraction to one's team may increase alcohol use but decrease marijuana use among male athletes, suggesting the importance of attraction to team when developing interventions for athletes.

Genome Sequencing of Pleurozium schreberi: The Assembled and Annotated Draft Genome of a Pleurocarpous Feather Moss.

The pleurocarpous feather moss Pleurozium schreberi is a ubiquitous moss species which plays a fundamental role in many terrestrial ecosystems, for instance within the boreal forest, the Earth's largest terrestrial biome, this species plays a significant role in driving ecosystem nitrogen and carbon inputs and fluxes. By hosting dinitrogen (N2)-fixing cyanobacteria, the moss-cyanobacteria symbiosis constitutes the main nitrogen input into the ecosystem and by the high productivity and the low decomposability of the moss litter, Pschreberi contributes significantly to build-up soil organic matter, and therefore long-term C sequestration. Knowledge on P. schreberi genome will facilitate the development of 'omics' and system's biology approaches to gain a more complete understanding of the physiology and ecological adaptation of the moss and the mechanisms underpinning the establishment of the symbiosis. Here we present the de novo assembly and annotation of P. schreberi genome that will help investigating these questions. The sequencing was performed using the HiSeq X platform with Illumina paired-end and mate-pair libraries prepared with CTAB extracted DNA. In total, the assembled genome was approximately 318 Mb, while repetitive elements account for 28.42% of the genome and 15,992 protein-coding genes were predicted from the genome, of which 84.23% have been functionally annotated. We anticipate that the genomic data generated will constitute a significant resource to study ecological and evolutionary genomics of P. schreberi, and will be valuable for evo-devo investigations as well as our understanding of the evolution of land plants by providing the genome of a pleurocarpous moss.

Measuring alcohol-related protective behavioral strategies among college students: further examination of the Protective Behavioral Strategies Scale.

Heavy drinking among college students has been recognized as a public health problem on American college campuses (e.g., R. Hingson, T. Heeren, M. Winter, & H. Wechsler, 2005). Recently, protective behavioral strategies, or cognitive-behavioral strategies that can be implemented when using alcohol to reduce consumption and resulting negative consequences, have been shown to be associated with less alcohol use and fewer alcohol-related problems (e.g., S. L. Benton et al., 2004; M. P. Martens et al., 2005). The purpose of the present study was to conduct additional psychometric work on a measure designed to assess the use of such strategies: the Protective Behavioral Strategies Scale (PBSS; M. P. Martens et al., 2005). Data were collected on 505 undergraduate students from 2 universities who reported having consumed alcohol at least once in the past 30 days. Results of a confirmatory factor analysis supported the hypothesized 3-factor version of the PBSS, and scores on each subscale were correlated in the expected direction with both alcohol use and alcohol-related problems. Thus, the PBSS appears to be reliable and valid for use among college student drinkers.

Attenuation of scopolamine-induced learning deficits by LVV-hemorphin-7 in rats in the passive avoidance and water maze paradigms.

Central administration of angiotensin IV (Ang IV) analogues attenuates scopolamine-induced amnesia. Ang IV mediates its effects by binding to a high affinity, binding site, AT(4) receptor, that has recently been identified as insulin regulated aminopeptidase (IRAP). The purpose of this study was to examine the effect of the distinct AT(4) ligand, LVV-hemorphin-7 (LVV-H7), on scopolamine-induced learning deficits, one which involves fear-conditioning and the other spatial learning. Rats were pretreated with an intracerebroventricular (ICV) dose of scopolamine hydrobromide followed by treatment with 1 nmol LVV-H7 or artificial cerebrospinal fluid (aCSF). During the acquisition phase of the water maze task, daily ICV infusions of 1 nmol of LVV-H7 25 min after scopolamine treatment produced marked improvement in both the latency and distance swum in order to locate the submerged platform using visual cues compared to animals treated with scopolamine only. In addition, the same dose of LVV-H7 attenuated the learning deficit observed for scopolamine-treated animals in the passive avoidance task. These studies clearly demonstrate that LVV-H7, like Ang IV, is a pharmacologically active AT(4) ligand that attenuates the deleterious effects of scopolamine on learning performance in two different behavioral paradigms.

Directional auxin transport mechanisms in early diverging land plants.

The emergence and radiation of multicellular land plants was driven by crucial innovations to their body plans. The directional transport of the phytohormone auxin represents a key, plant-specific mechanism for polarization and patterning in complex seed plants. Here, we show that already in the early diverging land plant lineage, as exemplified by the moss Physcomitrella patens, auxin transport by PIN transporters is operational and diversified into ER-localized and plasma membrane-localized PIN proteins. Gain-of-function and loss-of-function analyses revealed that PIN-dependent intercellular auxin transport in Physcomitrella mediates crucial developmental transitions in tip-growing filaments and waves of polarization and differentiation in leaf-like structures. Plasma membrane PIN proteins localize in a polar manner to the tips of moss filaments, revealing an unexpected relation between polarization mechanisms in moss tip-growing cells and multicellular tissues of seed plants. Our results trace the origins of polarization and auxin-mediated patterning mechanisms and highlight the crucial role of polarized auxin transport during the evolution of multicellular land plants.