Transcription factors (TFs) are major players in gene regulatory networks and interactions between TFs and their target genes furnish spatiotemporal patterns of gene expression. Establishing the ...architecture of regulatory networks requires gathering information on TFs, their targets in the genome, and the corresponding binding sites. We have developed GRASSIUS (Grass Regulatory Information Services) as a knowledge-based Web resource that integrates information on TFs and gene promoters across the grasses. In its initial implementation, GRASSIUS consists of two separate, yet linked, databases. GrassTFDB holds information on TFs from maize (Zea mays), sorghum (Sorghum bicolor), sugarcane (Saccharum spp.), and rice (Oryza sativa). TFs are classified into families and phylogenetic relationships begin to uncover orthologous relationships among the participating species. This database also provides a centralized clearinghouse for TF synonyms in the grasses. GrassTFDB is linked to the grass TFome collection, which provides clones in recombination-based vectors corresponding to full-length open reading frames for a growing number of grass TFs. GrassPROMDB contains promoter and cis-regulatory element information for those grass species and genes for which enough data are available. The integration of GrassTFDB and GrassPROMDB will be accomplished through GrassRegNet as a first step in representing the architecture of grass regulatory networks. GRASSIUS can be accessed from www.grassius.org.
Phoneutria nigriventer is one of the largest existing true spiders and one of the few considered medically relevant. Its venom contains several neurotoxic peptides that act on different ion channels ...and chemical receptors of vertebrates and invertebrates. Some of these venom toxins have been shown as promising models for pharmaceutical or biotechnological use. However, the large diversity and the predominance of low molecular weight toxins in this venom have hampered the identification and deep investigation of the less abundant toxins and the proteins with high molecular weight. Here, we combined conventional and next-generation cDNA sequencing with Multidimensional Protein Identification Technology (MudPIT), to obtain an in-depth panorama of the composition of P. nigriventer spider venom. The results from these three approaches showed that cysteine-rich peptide toxins are the most abundant components in this venom and most of them contain the Inhibitor Cysteine Knot (ICK) structural motif. Ninety-eight sequences corresponding to cysteine-rich peptide toxins were identified by the three methodologies and many of them were considered as putative novel toxins, due to the low similarity to previously described toxins. Furthermore, using next-generation sequencing we identified families of several other classes of toxins, including CAPs (Cysteine Rich Secretory Protein-CRiSP, antigen 5 and Pathogenesis-Related 1-PR-1), serine proteinases, TCTPs (translationally controlled tumor proteins), proteinase inhibitors, metalloproteinases and hyaluronidases, which have been poorly described for this venom. This study provides an overview of the molecular diversity of P. nigriventer venom, revealing several novel components and providing a better basis to understand its toxicity and pharmacological activities.
Using approaches of transcriptomics and proteomics we have shown that the phenotype of Bothrops jararaca venom undergoes a significant rearrangement upon neonate to adult transition. Most regulatory ...processes in biology are intrinsically related to modifications of protein structure, function, and abundance. However, it is unclear to which extent intrinsic proteolysis affects toxins and snake venom phenotypes upon ontogenesis. Here we assessed the natural N-terminome of Bothrops jararaca newborn and adult venoms and explored the degree of N-terminal protein truncation in ontogenetic-based proteome variation. To this end we applied the Terminal Amine Isotopic Labeling of Substrates (TAILS) technology to characterize venom collected in the presence of proteinase inhibitors. We identified natural N-terminal sequences in the newborn (71) and adult (84) venoms, from which only 37 were common to both. However, truncated toxins were found in higher number in the newborn (212) than in the adult (140) venom. Moreover, sequences N-terminally blocked by pyroglutamic acid were identified in the newborn (55) and adult (49) venoms. Most toxin classes identified by their natural N-terminal sequences showed a similar number of unique peptides in the newborn and adult venoms, however, those of serine proteinases and C-type lectins were more abundant in the adult venom. Truncated sequences from at least ten toxin classes were detected, however the catalytic and cysteine-rich domains of metalloproteinases were the most prone to proteolysis, mainly in the newborn venom. Our results underscore the pervasiveness of truncations in most toxin classes and highlight variable post-translational events in newborn and adult venoms.
•TAILS N-terminomic analysis of newborn and adult Bothrops jararaca venoms.•Numerous natural N-terminal sequences are distinct between the venoms.•Truncated sequences were found in higher number in the newborn venom.•In both venoms truncation mostly occurs in metalloproteinases.•Variable post-translational events in newborn and adult venoms.
Zika virus (ZIKV) infection during pregnancy can cause a set of severe abnormalities in the fetus known as congenital Zika syndrome (CZS). Experiments with animal models and in vitro systems have ...substantially contributed to our understanding of the pathophysiology of ZIKV infection. Here, to investigate the molecular basis of CZS in humans, we used a systems biology approach to integrate transcriptomic, proteomic, and genomic data from the postmortem brains of neonates with CZS. We observed that collagens were greatly reduced in expression in CZS brains at both the RNA and protein levels and that neonates with CZS had several single-nucleotide polymorphisms in collagen-encoding genes that are associated with osteogenesis imperfecta and arthrogryposis. These findings were validated by immunohistochemistry and comparative analysis of collagen abundance in ZIKV-infected and uninfected samples. In addition, we showed a ZIKV-dependent increase in the expression of cell adhesion factors that are essential for neurite outgrowth and axon guidance, findings that are consistent with the neuronal migration defects observed in CZS. Together, these findings provide insights into the underlying molecular alterations in the ZIKV-infected brain and reveal host genes associated with CZS susceptibility.
The effects of thermal aging of stainless steel weld-overlay claddings of nuclear reactor pressure vessels on the microstructure and hardness of the claddings were investigated using atom probe ...tomography and nanoindentation testing. The claddings were aged at 400°C for periods of 100–10,000h. The fluctuation in Cr concentration in the δ-ferrite phase, which was caused by spinodal decomposition, progressed rapidly after aging for 100h, and gradually for aging durations greater than 1000h. On the other hand, NiSiMn clusters, initially formed after aging for less than 1000h, had the highest number density after aging for 2000h, and coarsened after aging for 10,000h. The hardness of the δ-ferrite phase also increased rapidly for short period of aging, and saturated after aging for longer than 1000h. This trend was similar to the observed Cr fluctuation concentration, but different from the trend seen in the formation of the NiSiMn clusters. These results strongly suggest that the primary factor responsible for the hardening of the δ-ferrite phase owing to thermal aging is Cr spinodal decomposition.
Venom variability is commonly reported for venomous snakes including Bothrops atrox. Here, we compared the composition of venoms from B. atrox snakes collected at Amazonian conserved habitats ...(terra-firme upland forest and várzea) and human modified areas (pasture and degraded areas). Venom samples were submitted to shotgun proteomic analysis as a whole or compared after fractionation by reversed-phase chromatography. Whole venom proteomes revealed a similar composition among the venoms with predominance of SVMPs, CTLs, and SVSPs and intermediate amounts of PLA2s and LAAOs. However, when distribution of particular isoforms was analyzed by either method, the venom from várzea snakes showed a decrease in hemorrhagic SVMPs and an increase in SVSPs, and procoagulant SVMPs and PLA2s. These differences were validated by experimental approaches including both enzymatic and in vivo assays, and indicated restrictions in respect to antivenom efficacy to variable components. Thus, proteomic analysis at the isoform level combined to in silico prediction of functional properties may indicate venom biological activity. These results also suggest that the prevalence of functionally distinct isoforms contributes to the variability of the venoms and could reflect the adaptation of B. atrox to distinct prey communities in different Amazon habitats.
In this report, we compared isoforms present in venoms from snakes collected at different Amazonian habitats. By means of a species venom gland transcriptome and the in silico functional prediction of each isoform, we were able to predict the principal venom activities in vitro and in animal models. We also showed remarkable differences in the venom pools from snakes collected at the floodplain (várzea habitat) compared to other habitats. Not only was this venom less hemorrhagic and more procoagulant, when compared to the venom pools from the other three habitats studied, but also this enhanced procoagulant activity was not efficiently neutralized by Bothrops antivenom. Thus, using a functional proteomic approach, we highlighted intraspecific differences in B. atrox venom that could impact both in the ecology of snakes but also in the treatment of snake bite patients in the region.
•Variability in venom composition was detected in snakes collected at close but distinct habitats.•Venom variability was noticeable at isoforms expressed rather than toxin groups.•Variability in venom composition correlated to functional variability.•Particular isoforms in floodplain venom compromised neutralization of coagulopathy.
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The next step beyond conventional scaffold-based tissue engineering is cell-based direct biofabrication techniques. In industrial processes, various three-dimensional (3D) prototype models have been ...fabricated using several different rapid prototyping methods, such as stereo-lithography, 3D printing and laser sintering, as well as others, in which a variety of chemical materials are utilized. However, with direct cell-based biofabrication, only biocompatible materials can be used, and the manufacturing process must be performed under biocompatible and physiological conditions. We have developed a direct 3D cell printing system using inkjet and gelation techniques with inkjet droplets, and found that it had good potential to construct 3D structures with multiple types of cells. With this system, we have used alginate and fibrin hydrogel materials, each of which has advantages and disadvantages. Herein, we discuss the roles of hydrogel for biofabrication and show that further developments in biofabrication technology with biomatrices will play a major part, as will developments in manufacturing technology. It is important to explore suitable biomatrices as the next key step in biofabrication techniques.
Efforts to describe toxins from the two major families of venomous snakes (Viperidae and Elapidae) usually reveal proteins belonging to few structural types, particular of each family. Here we ...carried on an effort to determine uncommon cDNAs that represent possible new toxins from Lachesis muta (Viperidae). In addition to nine classes of typical toxins, atypical molecules never observed in the hundreds of Viperidae snakes studied so far are highly expressed: a diverging C-type lectin that is related to Viperidae toxins but appears to be independently originated; an ohanin-like toxin, which would be the third member of the most recently described class of Elapidae toxins, related to human butyrophilin and B30.2 proteins; and a 3FTx-like toxin, a new member of the widely studied three-finger family of proteins, which includes major Elapidae neurotoxins and CD59 antigen. The presence of these common and uncommon molecules suggests that the repertoire of toxins could be more conserved between families than has been considered, and their features indicate a dynamic process of venom evolution through molecular mechanisms, such as multiple recruitments of important scaffolds and domain exchange between paralogs, always keeping a minimalist nature in most toxin structures in opposition to their nontoxin counterparts.
This retrospective cohort study examined the effects of the crossed raised arm (CRA) position in contrast-enhanced computed tomography (CECT) on contrast medium influx and image quality relative to ...the conventional position.
Contrast medium influx into the collateral veins on CECT images was evaluated in 92 participants. The CT values of the pulmonary artery, descending aorta, and spleen were obtained in both positions and compared. Anatomical changes in the diameters and area of the subclavian vein and costoclavicular distance were also analyzed.
Contras 27 and 6 patients in the conventional and CRA positions, respectively. The influx risk ratio in the CRA position versus that in the conventional position was 0.22 (95% confidence interval, 0.10–0.51). Elevations in the median CT value of the pulmonary artery, descending aorta, and spleen in the CRA position were 7.0% (p < .001), 7.4% (p < .001), and 9.8% (p < .001), respectively. Enlargements in the major and minor diameters of the subclavian vein, subclavian vein area, and costoclavicular distance in the CRA position versus those in the conventional position were 19.3% (p < .001), 28.1% (p < .001), 53.6%, and 30.0% (p < .001), respectively.
The CRA position effectively prevented contrast medium influx into the collateral veins due to SVS and increased CT values in the target organs in CECT. The diameters and area of the subclavian vein and costoclavicular distance were enlarged at the thoracic outlet, which improved the flow of the contrast medium into the targeted organs.
The CRA position can contribute to obtaining better CECT images during common clinical assessments at no additional cost.
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Absorption of excess light energy by the photosynthetic machinery results in the generation of reactive oxygen species (ROS), such as H2O2. We investigated the effects in vivo of ROS to clarify the ...nature of the damage caused by such excess light energy to the photosynthetic machinery in the cyanobacterium Synechocystis sp. PCC 6803. Treatments of cyanobacterial cells that supposedly increased intracellular concentrations of ROS apparently stimulated the photodamage to photosystem II by inhibiting the repair of the damage to photosystem II and not by accelerating the photodamage directly. This conclusion was confirmed by the effects of the mutation of genes for H2O2‐scavenging enzymes on the recovery of photosystem II. Pulse labeling experiments revealed that ROS inhibited the synthesis of proteins de novo. In particular, ROS inhibited synthesis of the D1 protein, a component of the reaction center of photosystem II. Northern and western blot analyses suggested that ROS might influence the outcome of photodamage primarily via inhibition of translation of the psbA gene, which encodes the precursor to D1 protein.
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