A Single Disulfide Bond Disruption in the β3 Integrin Subunit Promotes Thiol/Disulfide Exchange,a Molecular Dynamics Study

The integrins are a family of membrane receptors that attach a cell to its surrounding and play a crucial function in cell signaling. The combination of internal and external stimuli alters a folded non-active state of these proteins to an extended active configuration. The β3 subunit of the platelet αIIbβ3 integrin is made of well-structured domains rich in disulfide bonds. During the activation process some of the disulfides are re-shuffled by a mechanism requiring partial reduction of some of these bonds; any disruption in this mechanism can lead to inherent blood clotting diseases. In the present study we employed Molecular Dynamics simulations for tracing the sequence of structural fluctuations initiated by a single cysteine mutation in the β3 subunit of the receptor. These simulations showed that in-silico protein mutants exhibit major conformational deformations leading to possible disulfide exchange reactions. We suggest that any mutation that prevents Cys560 from reacting with one of the Cys⁵⁶⁷–Cys⁵⁸¹ bonded pair, thus disrupting its ability to participate in a disulfide exchange reaction, will damage the activation mechanism of the integrin. This suggestion is in full agreement with previously published experiments. Furthermore, we suggest that rearrangement of disulfide bonds could be a part of a natural cascade of thiol/disulfide exchange reactions in the αIIbβ3 integrin, which are essential for the native activation process.     

Comparative Characterization of Laminarinases from the Filamentous Marine Fungi Chaetomium Indicum Corda and Trichoderma Aureviride Rifai

Marine filamentous fungi (103 strains) isolated from various marine habitats were studied for their ability to produce extracellular O-glycosylhydrolases. Cultural filtrates of these strains were shown to contain a series of glycanases (laminarinases, amylases, cellulases, pustulanases) and glycosidases (β-glucosidases, N-acetyl-β-glucosaminidases, β-galactosidases, α-mannosidases).Two species of marine fungi from different habitats were chosen for isolation of laminarinases and detailed study on enzyme properties. The fungus Chaetomium indicum associated with the alga Fucus evanescens C. Agardh was collected near the Kuril Islands, and T. aureviride was sampled from bottom deposits of South China Sea. Properties of extracellular laminarinases were similar: temperature optimums (40–45 ^∘C), molecular masses (54–56 kDa), K _m (0.1–0.3 mg ml⁻¹). Temperature stability of laminarinase of C. indicum was significantly higher than those from T. aureveride. It is shown that these enzymes are specific to β-1,3-bonds in glucans, release predominantly glucose from laminaran and do not catalyze reaction of transglycosylation. Accoding to these data enzymes are exo-1,3-β-D-glucan-glucanohydrolases (EC 3.2.1.58). Inhibitor analysis demonstrated the significant role of tryptophan and tyrosine residues in the catalytic activity of enzymes. Molecules of T. aureviride laminarinase contained the functionally important thiol group.     

Scaling Up ITO‐Free Solar Cells

Indium‐tin‐oxide‐free (ITO‐free) polymer solar cells with composite electrodes containing current‐collecting grids and a semitransparent poly(3,4‐ethylenedioxythiophene):polystyrenesulfonate) (PEDOT:PSS) conductor are demonstrated. The up‐scaling of the length of the solar cell from 1 to 6 cm and the effect of the grid line resistance are explored for a series of devices. Laser‐beam‐induced current (LBIC) mapping is used for quality control of the devices. A theoretical modeling study is presented that enables the identification of the most rational cell dimension for the grids with different resistances. The performance of ITO‐free organic solar cells with different dimensions and different electrode resistances are evaluated for different light intensities. The current generation and electric potential distribution are found to not be uniformly distributed in large‐area devices at simulated 1 Sun illumination. The generated current uniformity increases with decreasing light intensities.     

Automation of clip localization in Digital Tomosynthesis for setup of breast cancer patients

The objective of this study is to develop an automatic clip localization procedure for breast cancer patient setup based on Digital Tomosynthesis (DTS) and to characterize its performance with respect to the overall registration accuracy and robustness. The study was performed under an IRB-approved protocol for 12 breast cancer patients with surgical clips implanted around the tumor cavity. The registration of DTS images to planning CTs was performed using an automatic algorithm developed to overcome specific challenges of localization and registration of clips in the breast setup images. The automatic method consisted of auto-segmentation (intensity-based thresholding with a priori knowledge about clip size and location to distinguish clips from bony features) and auto-registration of the segmented clip clusters. To determine the inherent accuracy and robustness of the registration algorithm, additional simulated DTS data was analyzed. The developed algorithm is efficient in removing false positives and negatives and provides an accuracy of better than 2.3 mm for 60° and 3.3 mm for 40° DTS. When incorporated in clinical software, this algorithm helps to facilitate fast and accurate setup evaluation with minimal dose delivered to patients.     

Proteinivorax tanatarense gen. nov., sp. nov., an anaerobic, haloalkaliphilic, proteolytic bacterium isolated from a decaying algal bloom, and proposal of Proteinivoraceae fam. nov.

Two strains of a novel anaerobic, protein- and nucleoside-utilizing bacterium, Z-910^T and Z-810, were isolated. The strains were spore-forming, mainly nonmotile rods, exhibiting positive Gram reaction with Gram-positive cell wall structure. The strains were mesophilic and haloalkaliphilic. Cultures used proteins and proteinaceous substrates as carbon, nitrogen, and energy sources. Both strains used also ribonucleosides, cellobiose, pyruvate, and glycerol. Ribose and nucleobases did not support growth. The fermentation products from all utilized substrates were identical but varied in content and included straight and branched acids, as well as hydrogen and ammonia. When grown on tryptone, strain Z-910^T was able to reduce fumarate, dimethyl sulfoxide, thiosulfate, and elemental sulfur. Neither nitrate nor sulfate was reduced. The DNA G + C content of strain Z-910^T was 32.2 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence similarity revealed that strains Z-910^T and Z-810 represented a new branch within the order Clostridiales, with 90.2 % similarity to the nearest genus with a validly published name Anaerobranca gottschalkii DSM 13577^T. According to their physiological, chemotaxonomic, and phylogenetic properties, strains Z-910^T and Z-810 represented a new genus and novel species, for which the name Proteinivorax tanatarense gen. nov., sp. nov. was proposed. Phylogenetic analysis showed that the genera Proteinivorax gen. nov. and Anaerobranca formed a separate cluster within the order Clostridiales. The family Proteinivoraceae fam. nov. comprising the genera Proteinivorax gen. nov. and Anaerobranca was therefore proposed within the order Clostridiales of the phylum Firmicutes with Proteinivorax as a type genus of the new family.     

One Beringian genus less: A re‐assesment of Pacifimyxas Kruglov & Starobogatov, 1985 (Mollusca: Gastropoda: Lymnaeidae) questions the current estimates of Beringian biodiversity

The taxonomic position of three nominal species of lymnaeid snails placed by Kruglov & Starobogatov (1993) into the subgenus Lymnaea (Pacifimyxas) Kruglov & Starobogatov, 1985, has been re‐assessed based on a molecular genetic study of topotypic specimens and an examination of the type series and other materials available. It has been shown that the two species, Lymnaea (Pacifimyxas) magadanensis Kruglov & Starobogatov, 1985 and Lymnaea (Pacifimyxas) streletzkajae Kruglov & Starobogatov, 1985, are identical with the species Kamtschaticana kamtschatica (Middendorff, 1850) and must be treated as its junior synonyms. Hence, Pacifimyxas becomes a junior synonym of Kamtschaticana Kruglov & Starobogatov, 1984. The taxonomic identity of the third species of Pacifimyxas, Lymnaea (Pacifimyxas) perpolita, remains obscure, and this species is considered here as taxon inquirendum. Two other nominal species, Lymnaea aberrans (Westerlund, 1897) and Lymnaea middendorffi (W. Dybowski, 1904), have been synonymized with K. kamtschatica based on morphological and geographical evidence. The lectotype of Limnaea peregra var. middendorffi is designated. The actual level of species richness in the Beringian freshwater malacofauna may be 20–25% lower than it was determined on the basis of the traditional system. Some implications of this outcome for the biogeography of the Beringian freshwater fauna are discussed.     

State 1 and State 2 in Photosynthetic Apparatus of Red Microalgae and Cyanobacteria

Biochemistry (Moscow) - Imbalanced light absorption by photosystem I (PSI) and photosystem II (PSII) in oxygenic phototrophs leads to changes in interaction of photosystems altering the linear...     

Comparative genomics of the social amoebae <Emphasis Type="Italic">Dictyostelium discoideum</Emphasis> and <Emphasis Type="Italic">Dictyostelium purpureum</Emphasis>

Background

The social amoebae (Dictyostelia) are a diverse group of Amoebozoa that achieve multicellularity by aggregation and undergo morphogenesis into fruiting bodies with terminally differentiated spores and stalk cells. There are four groups of dictyostelids, with the most derived being a group that contains the model species Dictyostelium discoideum.

Results

We have produced a draft genome sequence of another group dictyostelid, Dictyostelium purpureum, and compare it to the D. discoideum genome. The assembly (8.41 × coverage) comprises 799 scaffolds totaling 33.0 Mb, comparable to the D. discoideum genome size. Sequence comparisons suggest that these two dictyostelids shared a common ancestor approximately 400 million years ago. In spite of this divergence, most orthologs reside in small clusters of conserved synteny. Comparative analyses revealed a core set of orthologous genes that illuminate dictyostelid physiology, as well as differences in gene family content. Interesting patterns of gene conservation and divergence are also evident, suggesting function differences; some protein families, such as the histidine kinases, have undergone little functional change, whereas others, such as the polyketide synthases, have undergone extensive diversification. The abundant amino acid homopolymers encoded in both genomes are generally not found in homologous positions within proteins, so they are unlikely to derive from ancestral DNA triplet repeats. Genes involved in the social stage evolved more rapidly than others, consistent with either relaxed selection or accelerated evolution due to social conflict.

Conclusions

The findings from this new genome sequence and comparative analysis shed light on the biology and evolution of the Dictyostelia.