Subclass Of Class Research Articles

Molecular Characterization, Expression Pattern and Function Analysis of Glycine-Rich Protein Genes Under Stresses in Chinese Cabbage (Brassica rapa L. ssp. pekinensis).

Plant Glycine-rich proteins (GRP), a superfamily with a glycine-rich domain, play an important role in various stresses such as high or low temperature stress and drought stress. GRP genes have been studied in many plants, but seldom in Chinese cabbage (Brassica rapa L. ssp. pekinensis). In this study, a total of 64 GRP genes were identified in Chinese cabbage by homology comparative analysis. The physical and chemical characteristics predicted by ProtParam tool revealed that 62.5% of BrGRPs were alkaline, 53.1% were stable, and 79.7% were hydrophilic. Conserved domain analysis by MEME and TBtools showed that 64 BrGRPs contained 20 of the same conserved motifs, based on which BrGRPs were classified into five main classes and four subclasses in class IV to clarify their evolutionary relationship. Our results demonstrated that The BrGRP genes were located on ten chromosomes and in three different subgenomes of Chinese cabbage, and 43 pairs of orthologous GRP genes were found between Chinese cabbage and Arabidopsis. According to the transcriptome data, 64 BrGRP genes showed abnormal expression under high temperature stress, 52 under low temperature stress, 39 under drought stress, and 23 responses to soft rot. A large number of stress-related cis-acting elements, such as DRE, MYC, MYB, and ABRE were found in their promoter regions by PlantCare, which corresponded with differential expressions. Two BrGRP genes-w546 (Bra030284) and w1409 (Bra014000), both belonging to the subfamily Subclass IVa RBP-GRP (RNA binding protein-glycine rich protein), were up-regulated under 150 mmol⋅L–1 NaCl stress in Chinese cabbage. However, the overexpressed w546 gene could significantly inhibit seed germination, while w1409 significantly accelerated seed germination under 100 mmol⋅L–1 NaCl or 300 mmol⋅L−1 mannitol stresses. In short, most BrGRP genes showed abnormal expression under adversity stress, and some were involved in multiple stress responses, suggesting a potential capacity to resist multiple biotic and abiotic stresses, which is worthy of further study. Our study provides a systematic investigation of the molecular characteristics and expression patterns of BrGRP genes and promotes for further work on improving stress resistance of Chinese cabbage.

An Upper Bound of the Third Hankel Determinant for a Subclass of q-Starlike Functions Associated with k-Fibonacci Numbers

In this paper, we use q-derivative operator to define a new class of q-starlike functions associated with k-Fibonacci numbers. This newly defined class is a subclass of class A of normalized analytic functions, where class A is invariant (or symmetric) under rotations. For this function class we obtain an upper bound of the third Hankel determinant.

Molecular docking of ligands promising for IgG sorption from biological fluids

Hyperproduction of immunoglobulin G (IgG) is a major pathogenic factor in autoimmune diseases. Specific sorbents are used to eliminate the high level of IgG. Molecular docking can be used as a tool for theoretical search for sorbent ligands for the IgG removal from biological fluids. Using docking, modeling of amino acid interactions with IgG ligands was performed. Based on the docking results, active amino acids were identified and possible combinations of them were proposed for the creation of diand tripeptide sequences. As a result, aromatic amino acids (Tyr, Trp, Phe), di-and tripeptides based on them (Trp-DTyr, Phe-DTyr, Trp-Phe-DTyr, Phe-Trp-DTyr) were found to have high activity for IgG proteins, and three peptides (Trp-Phe-DTyr, Phe-Trp-DTyr) not only show high activity to total IgG, but can also be divided in their activity relative to subclasses of class G immunoglobulins.

Incremental Subclass Support Vector Machine

Support Vector Machine (SVM) is a very competitive linear classifier based on convex optimization problem, were support vectors fully describe decision boundary. Hence, SVM is sensitive to data spread and does not take into account the existence of class subclasses, nor minimizes data dispersion for classification performance improvement. Thus, Kernel subclass SVM (KSSVM) was proposed to handle multimodal data and to minimize data dispersion. Nevertheless, KSSVM has difficulties in classifying sequentially obtained data and handling large scale datasets, since it is based on batch learning. For this reason, we propose a novel incremental KSSVM (iKSSVM) which handles dynamic and large data in a proper manner. The iKSSVM is still based on convex optimization problem and minimizes data dispersion within and between data subclasses incrementally, in order to improve discriminative power and classification performance. An extensive comparative evaluation of the iKSSVM to batch KSSVM, as well as, other contemporary incremental classifiers, on real world datasets, has shown clearly its superiority in terms of classification accuracy.

Electrophysiological mechanisms of vandetanib-induced cardiotoxicity: Comparison of action potentials in rabbit Purkinje fibers and pluripotent stem cell-derived cardiomyocytes

Vandetanib, a multi-kinase inhibitor used for the treatment of various cancers, has been reported to induce several adverse cardiac effects. However, the underlying mechanisms of vandetanib-induced cardiotoxicity are unclear. This study aimed to investigate the mechanism of vandetanib-induced cardiotoxicity using intracellular electrophysiological recordings on human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), rabbit Purkinje fibers, and HEK293 cells transiently expressing human ether-a-go-go-related gene (hERG; the rapidly activating delayed rectifier K+ channel, IKr), KCNQ1/KCNE1 (the slowly activating delayed rectifier K+ current, IKs), KCNJ2 (the inwardly rectifying K+ current, IK1) or SCN5A (the inward Na+ current, INa). Purkinje fiber assays and ion channel studies showed that vandetanib at concentrations of 1 and 3 μM inhibited the hERG currents and prolonged the action potential duration. Alanine scanning and in silico hERG docking studies demonstrated that Y652 and F656 in the hERG S6 domain play critical roles in vandetanib binding. In hiPSC-CMs, vandetanib markedly reduced the maximum rate of depolarization during the AP upstroke. Ion channel studies revealed that hiPSC-CMs were more sensitive to inhibition of the INa by vandetanib than in a heterogeneously expressed HEK293 cell model, consistent with the changes in the AP parameters of hiPSC-CMs. The subclasses of Class I antiarrhythmic drugs inhibited INa currents in a dose-dependent manner in hiPSC-CMs and SCN5A-encoded HEK293 cells. The inhibitory potency of vandetanib for INa was much higher in hiPSC-CMs (IC50: 2.72 μM) than in HEK293 cells (IC50: 36.63 μM). These data suggest that AP and INa assays using hiPSC-CMs are useful electrophysiological models for prediction of drug-induced cardiotoxicity.

A novel protein quality control mechanism contributes to heat shock resistance of worldwide-distributed Pseudomonas aeruginosa clone C strains.

Pseudomonas aeruginosa is a highly successful nosocomial pathogen capable of causing a wide variety of infections with clone C strains most prevalent worldwide. In this study, we initially characterize a molecular mechanism of survival unique to clone C strains. We identified a P. aeruginosa clone C-specific genomic island (PACGI-1) that contains the highly expressed small heat shock protein sHsp20c, the founding member of a novel subclass of class B bacterial small heat shock proteins. sHsp20c and adjacent gene products are involved in resistance against heat shock. Heat stable sHsp20c is unconventionally expressed in stationary phase in a wide temperature range from 20 to 42°C. Purified sHsp20c has characteristic features of small heat shock protein class B as it is monodisperse, forms sphere-like 24-meric oligomers and exhibits significant chaperone activity. As the P. aeruginosa clone C population is significantly more heat shock resistant than genetically unrelated P. aeruginosa strains without sHsp20c, the horizontally acquired shsp20c operon might contribute to the survival of worldwide-distributed clone C strains.

The structure of PccH from Geobacter sulfurreducens – a novel low reduction potential monoheme cytochrome essential for accepting electrons from an electrode

The structure of cytochrome c (GSU3274) designated as PccH from Geobacter sulfurreducens was determined at a resolution of 2.0 Å. PccH is a small (15 kDa) cytochrome containing one c-type heme, found to be essential for the growth of G. sulfurreducens with respect to accepting electrons from graphite electrodes poised at -300 mV versus standard hydrogen electrode. with fumarate as the terminal electron acceptor. The structure of PccH is unique among the monoheme cytochromes described to date. The structural fold of PccH can be described as forming two lobes with the heme sandwiched in a cleft between the two lobes. In addition, PccH has a low reduction potential of -24 mV at pH 7, which is unusual for monoheme cytochromes. Based on difference in structure, together with sequence phylogenetic analysis, we propose that PccH can be regarded as a first characterized example of a new subclass of class I monoheme cytochromes. The low reduction potential of PccH may enable the protein to be redox active at the typically negative potential ranges encountered by G. sulfurreducens. Because PccH is predicted to be located in the periplasm of this bacterium, it could not be involved in the first step of accepting electrons from the electrode but is very likely involved in the downstream electron transport events in the periplasm.

Identification and characterization of a novel phosphodiesterase from the metagenome of an Indian coalbed.

Phosphoesterases are involved in the degradation of organophosphorus compounds. Although phosphomonoesterases and phosphotriesterases have been studied in detail, studies on phosphodiesterases are rather limited. In our search to find novel phosphodiesterases using metagenomic approach, we cloned a gene encoding a putative phosphodiesterase (PdeM) from the metagenome of the formation water collected from an Indian coal bed. Bioinformatic analysis showed that PdeM sequence possessed the characteristic signature motifs of the class III phosphodiesterases and phylogenetic study of PdeM enabled us to identify three distinct subclasses (A, B, and C) within class III phosphodiesterases, PdeM clustering in new subclass IIIB. Bioinformatic, biochemical and biophysical characterization of PdeM further revealed some of the characteristic features of the phosphodiesterases belonging to newly described subclass IIIB. PdeM is a monomer of 29.3 kDa, which exhibits optimum activity at 25°C and pH 8.5, but low affinity for bis(pNPP) as well as pNPPP. The recombinant PdeM possessed phosphodiesterase, phosphonate-ester hydrolase and nuclease activity. It lacked phosphomonoesterase, phosphotriesterase, and RNAse activities. Overexpression of PdeM in E.coli neither affected catabolite respression nor did the recombinant protein hydrolyzed cAMP in vitro, indicating its inability to hydrolyze cAMP. Although Mn2+ was required for the activity of PdeM, but addition of metals (Mn2+ or Fe3+) did not induce oligomerization. Further increase in concentration of Mn2+ upto 3 mM, increased α-helical content as well as the phosphodiesterase activity. Structural comparison of PdeM with its homologs showed that it lacked critical residues required for dimerization, cAMP hydrolysis, and for the high affinity binding of bis(pNPP). PdeM, thus, is a novel representative of new subclass of class III phosphodiesterases.

Exploiting disjointness axioms to improve semantic similarity measures

Representing domain knowledge in biology has traditionally been accomplished by creating simple hierarchies of classes with textual annotations. Recently, expressive ontology languages, such as Web Ontology Language, have become more widely adopted, supporting axioms that express logical relationships other than class-subclass, e.g. disjointness. This is improving the coverage and validity of the knowledge contained in biological ontologies. However, current semantic tools still need to adapt to this more expressive information. In this article, we propose a method to integrate disjointness axioms, which are being incorporated in real-world ontologies, such as the Gene Ontology and the chemical entities of biological interest ontology, into semantic similarity, the measure that estimates the closeness in meaning between classes. We present a modification of the measure of shared information content, which extends the base measure to allow the incorporation of disjointness information. To evaluate our approach, we applied it to several randomly selected datasets extracted from the chemical entities of biological interest ontology. In 93.8% of these datasets, our measure performed better than the base measure of shared information content. This supports the idea that semantic similarity is more accurate if it extends beyond the hierarchy of classes of the ontology. joao.ferreira@lasige.di.fc.ul.pt. Supplementary data are available at Bioinformatics online.

Expanding the biocatalytic toolbox of flavoprotein monooxygenases from Rhodococcus jostii RHA1

With the aim to enlarge the set of available flavoprotein monooxygenases, we have cloned 8 unexplored genes from Rhodococcus jostii RHA1 that were predicted to encode class B flavoprotein monooxygenases. Each monooxygenase can be expressed as soluble protein and has been tested for conversion of sulfides and ketones. Not only enantioselective sulfoxidations, but also enantioselective Baeyer–Villiger oxidations could be performed with this set of monooxygenases. Interestingly, in contrast to known class B flavoprotein monooxygenases, all studied biocatalysts showed no nicotinamide coenzyme preference. This feature coincides with the fact that the respective sequences appear to form a discrete group of sequence related proteins, distinct from the known class B flavoprotein monooxygenases subclasses: the so-called flavin-containing monooxygenases (FMOs), N-hydroxylating monooxygenases (NMOs) and Type I Baeyer–Villiger monooxygenases (BVMOs). Taken together, these data reveal the existence of a new subclass of class B flavoprotein monooxygenases, which we coined as Type II FMOs, that can perform Baeyer–Villiger oxidations and accept both NADPH and NADH as coenzyme. The uncovered biocatalytic properties of the studied Type II FMOs make this newly recognized subclass of monooxygenases of potential interest for biocatalytic applications.

Molecular and Functional Evolution of Class I Chitinases for Plant Carnivory in the Caryophyllales

Proteins produced by the large and diverse chitinase gene family are involved in the hydrolyzation of glycosidic bonds in chitin, a polymer of N-acetylglucosamines. In flowering plants, class I chitinases are important pathogenesis-related proteins, functioning in the determent of herbivory and pathogen attack by acting on insect exoskeletons and fungal cell walls. Within the carnivorous plants, two subclasses of class I chitinases have been identified to play a role in the digestion of prey. Members of these two subclasses, depending on the presence or absence of a C-terminal extension, can be secreted from specialized digestive glands found within the morphologically diverse traps that develop from carnivorous plant leaves. The degree of homology among carnivorous plant class I chitinases and the method by which these enzymes have been adapted for the carnivorous habit has yet to be elucidated. This study focuses on understanding the evolution of carnivory and chitinase genes in one of the major groups of plants that has evolved the carnivorous habit: the Caryophyllales. We recover novel class I chitinase homologs from species of genera Ancistrocladus, Dionaea, Drosera, Nepenthes, and Triphyophyllum, while also confirming the presence of two subclasses of class I chitinases based upon sequence homology and phylogenetic affinity to class I chitinases available from sequenced angiosperm genomes. We further detect residues under positive selection and reveal substitutions specific to carnivorous plant class I chitinases. These substitutions may confer functional differences as indicated by protein structure homology modeling.

Characteristics and influence factors of pathologic transformation in the subclasses of class IV lupus nephritis

The study explored the characteristics and correlation factors of transformation in subclasses of class IV lupus nephritis. Patients with class IV lupus nephritis were subjected to repeat biopsies after 6months of induction treatment. Transformation rate between two subclasses, class IV-S and class IV-G, was compared. Influence Factors of transformation were evaluated. Class IV-G had more severe hypertension and higher score of immunofluorescence index, glomerular active lesions, tubular and vascular lesions. Class IV-S had a higher percentage of glomerular fibrinoid necrosis. Class IV-S appeared a higher rate of transformation to class II than class IV-G (57% vs. 27%). In each subclass, active lesion also showed a higher rate of transformation to class II than active/chronic lesion (IV-G: 41.2% vs. 12.5%; IV-S: 71.4% vs. 42.8%). Patients who maintained class IV had higher blood pressure, obvious proteinuria, declined kidney function, and lower C3 level. Immunosuppressive therapy, urine protein, and vascular lesions were independent risk factors for the pathologic transformation. The rate of transformation in class IV-S was higher than that in class IV-G. The transformation is most likely to benefit from immunosuppressive therapy. Urine protein and vascular lesions are correlated with the transformation in class IV lupus nephritis.

Automaton recognition of doubly connected labyrinths with finite cyclic diameter

The problem of existence of a recognizing automaton for a subclass of an infinite class of chess labyrinths (denoted as C 0) is studied. It is proved in [1] that, for C 0, there does not exist a recognizing automaton. In [2], it is proved that there exists a recognizing collective of type (1, 1) (collective consisting of an automaton and stone). In this paper, it is proved that there exists a recognizing automaton for some subclass of the class of chess labyrinths with finite cyclic diameter.

The Structure of the Dizinc Subclass B2 Metallo-β-Lactamase CphA Reveals that the Second Inhibitory Zinc Ion Binds in the Histidine Site

Bacteria can defend themselves against beta-lactam antibiotics through the expression of class B beta-lactamases, which cleave the beta-lactam amide bond and render the molecule harmless. There are three subclasses of class B beta-lactamases (B1, B2, and B3), all of which require Zn2+ for activity and can bind either one or two zinc ions. Whereas the B1 and B3 metallo-beta-lactamases are most active as dizinc enzymes, subclass B2 enzymes, such as Aeromonas hydrophila CphA, are inhibited by the binding of a second zinc ion. We crystallized A. hydrophila CphA in order to determine the binding site of the inhibitory zinc ion. X-ray data from zinc-saturated crystals allowed us to solve the crystal structures of the dizinc forms of the wild-type enzyme and N220G mutant. The first zinc ion binds in the cysteine site, as previously determined for the monozinc form of the enzyme. The second zinc ion occupies a slightly modified histidine site, where the conserved His118 and His196 residues act as metal ligands. This atypical coordination sphere probably explains the rather high dissociation constant for the second zinc ion compared to those observed with enzymes of subclasses B1 and B3. Inhibition by the second zinc ion results from immobilization of the catalytically important His118 and His196 residues, as well as the folding of the Gly232-Asn233 loop into a position that covers the active site.

The future role of bio-ontologies for developing a general data standard in biology: chance and challenge for zoo-morphology

Due to lack of common data standards, the communicability and comparability of biological data across various levels of organization and taxonomic groups is continuously decreasing. However, the interdependence between molecular and higher levels of organization is of growing interest and calls for co-operations between biologists from different methodological and theoretical backgrounds. A general data standard in biology would greatly facilitate such co-operations. This article examines the role that defined and formalized vocabularies (i.e., ontologies) could have in developing such a data standard. I suggest basic criteria for developing data standards on grounds of distinguishing content, concept, nomenclatural, and format standards and discuss the role of data bases and their use of bio-ontologies in current activities for data standardization in biology. General principles of ontology development are introduced, including foundational ontology properties (e.g. class–subclass, parthood), and how concepts are defined. After addressing problems that are specific to morphological data, the notion of a general structure concept for morphology is introduced and why it is required for developing a morphological ontology. The necessity for a general morphological ontology to be taxon-independent and free of homology assumptions is discussed and how it can solve the problems of morphology. The article concludes with an outlook on how the use of ontologies will likely establish some sort of general data standard in biology and why the development of a set of commonly used foundational ontology properties and the use of globally unique identifiers for all classes defined in ontologies is crucial for its success.

Crystal Structure of KPC-2: Insights into Carbapenemase Activity in Class A β-Lactamases,

Beta-lactamases inactivate beta-lactam antibiotics and are a major cause of antibiotic resistance. The recent outbreaks of Klebsiella pneumoniae carbapenem resistant (KPC) infections mediated by KPC type beta-lactamases are creating a serious threat to our "last resort" antibiotics, the carbapenems. KPC beta-lactamases are serine carbapenemases and are a subclass of class A beta-lactamases that have evolved to efficiently hydrolyze carbapenems and cephamycins which contain substitutions at the alpha-position proximal to the carbonyl group that normally render these beta-lactams resistant to hydrolysis. To investigate the molecular basis of this carbapenemase activity, we have determined the structure of KPC-2 at 1.85 A resolution. The active site of KPC-2 reveals the presence of a bicine buffer molecule which interacts via its carboxyl group with conserved active site residues S130, K234, T235, and T237; these likely resemble the interactions the beta-lactam carboxyl moiety makes in the Michaelis-Menten complex. Comparison of the KPC-2 structure with non-carbapenemases and previously determined NMC-A and SME-1 carbapenemase structures shows several active site alterations that are unique among carbapenemases. An outward shift of the catalytic S70 residue renders the active sites of the carbapenemases more shallow, likely allowing easier access of the bulkier substrates. Further space for the alpha-substituents is potentially provided by shifts in N132 and N170 in addition to concerted movements in the postulated carboxyl binding pocket that might allow the substrates to bind at a slightly different angle to accommodate these alpha-substituents. The structure of KPC-2 provides key insights into the carbapenemase activity of emerging class A beta-lactamases.

MOSFET implementation of class I* neurons coupled by gap junctions

We propose a two-dimensional class I* neuron circuit coupled by gap junctions (GJs) consisting of enhancement-type metal-oxide-semiconductor field-effect-trangistors (MOSFETs). It is shown that some neurons that belong to a subclass of class I, when coupled by GJs, exhibit extensive spatiotemporal chaos in some parameter regions. This subclass is called class I* and is characterized by a phase plane structure with a narrow channel. We can tune our circuit to be class I, I*, or II by changing the resistance values. We show PSpice simulation results for a circuit implemented with discrete elements. A GJ-coupled network consisting of 20 such neurons is shown to generate itinerant dynamics with spatiotemporal chaos similar to class I* GJ-couple systems. The circuitry is compatible with standard complementary metal-oxide semiconductor (CMOS) processes. Hence, it can be implemented in an analog very-large-scale integrated circuit (VLSI) and the construction of a relatively large network is possible.

Update of the standard numbering scheme for class B beta-lactamases.

Update of the standard numbering scheme for class B beta-lactamases.

Expression of the Novel Basic Helix-Loop-Helix Gene eHAND in Neural Crest Derivatives and Extraembryonic Membranes during Mouse Development

We employed the yeast two-hybrid technique to screen a mouse embryo cDNA library for novel tissue-specific Class B basic helix-loop-helix (bHLH) transcription factors, which heterodimerize with the ubiquitously expressed Class A bHLH protein E12. From this screen, we cloned a novel bHLH protein, which we named eHAND. Its low sequence identity with other bHLH family members and unique expression pattern during development suggest that eHAND defines a new subclass of Class B bHLH proteins. eHAND was expressed at high levels in trophoblast cells and extraembryonic membranes throughout development. The first site of eHAND expression in embryos was the heart, where it was expressed at high levels between 8.5 and 10.5 days post coitum (d.p.c.), after which transcript levels declined abruptly. By 13.5 d.p.c., eHAND expression in the heart was localized to regions of valve formation. Expression in other regions of the embryo was confined to tissues with a substantial neural crest component. eHAND was expressed in the first branchial arch and its derivatives, in the sympathoadrenal lineage, and in the enteric system. The expression pattern of eHAND during development is distinct from that of other bHLH genes and suggests that it has a role in formation of extraembryonic tissues, heart, and neural crest derivatives.

Architectures of class-defining and specific domains of glutamyl-tRNA synthetase.

The crystal structure of a class I aminoacyl-transfer RNA synthetase, glutamyl-tRNA synthetase (GluRS) from Thermus thermophilus, was solved and refined at 2.5 A resolution. The amino-terminal half of GluRS shows a geometrical similarity with that of Escherichia coli glutaminyl-tRNA synthetase (GlnRS) of the same subclass in class I, comprising the class I-specific Rossmann fold domain and the intervening subclass-specific alpha/beta domain. These domains were found to have two GluRS-specific, secondary-structure insertions, which then participated in the specific recognition of the D and acceptor stems of tRNA(Glu) as indicated by mutagenesis analyses based on the docking properties of GluRS and tRNA. In striking contrast to the beta-barrel structure of the GlnRS carboxyl-terminal half, the GluRS carboxyl-terminal half displayed an all-alpha-helix architecture, an alpha-helix cage, and mutagenesis analyses indicated that it had a role in the anticodon recognition.