Discovering riboswitches: the past and the future.

Riboswitches are structured noncoding RNA domains used by many bacteria to monitor the concentrations of target ligands and regulate gene expression accordingly. In the past 20 years over 55 distinct classes of natural riboswitches have been discovered that selectively sense small molecules or elemental ions, and thousands more are predicted to exist. Evidence suggests that some riboswitches might be direct descendants of the RNA-based sensors and switches that were likely present in ancient organisms before the evolutionary emergence of proteins. We provide an overview of the current state of riboswitch research, focusing primarily on the discovery of riboswitches, and speculate on the major challenges facing researchers in the field.

The discovery of novel noncoding RNAs in 50 bacterial genomes.

Structured noncoding RNAs (ncRNAs) contribute to many important cellular processes involving chemical catalysis, molecular recognition and gene regulation. Few ncRNA classes are broadly distributed among organisms from all three domains of life, but the list of rarer classes that exhibit surprisingly diverse functions is growing. We previously developed a computational pipeline that enables the near-comprehensive identification of structured ncRNAs expressed from individual bacterial genomes. The regions between protein coding genes are first sorted based on length and the fraction of guanosine and cytidine nucleotides. Long, GC-rich intergenic regions are then examined for sequence and structural similarity to other bacterial genomes. Herein, we describe the implementation of this pipeline on 50 bacterial genomes from varied phyla. More than 4700 candidate intergenic regions with the desired characteristics were identified, which yielded 44 novel riboswitch candidates and numerous other putative ncRNA motifs. Although experimental validation studies have yet to be conducted, this rate of riboswitch candidate discovery is consistent with predictions that many hundreds of novel riboswitch classes remain to be discovered among the bacterial species whose genomes have already been sequenced. Thus, many thousands of additional novel ncRNA classes likely remain to be discovered in the bacterial domain of life.

8-oxoguanine riboswitches in bacteria detect and respond to oxidative DNA damage.

Riboswitches rely on structured aptamer domains to selectively sense their target ligands and regulate gene expression. However, some riboswitch aptamers in bacteria carry mutations in their otherwise strictly conserved binding pockets that change ligand specificities. The aptamer domain of a riboswitch class originally found to selectively sense guanine forms a three-stem junction that has since been observed to exploit numerous alterations in its ligand-binding pocket. These rare variants have modified their ligand specificities to sense other purines or purine derivatives, including adenine, 2'-deoxyguanosine (three classes), and xanthine. Herein, we report the characteristics of a rare variant that is narrowly distributed in the Paenibacillaceae family of bacteria. Known representatives are always associated with genes encoding 8-oxoguanine deaminase. As predicted from this gene association, these variant riboswitches tightly bind 8-oxoguanine (8-oxoG), strongly discriminate against other purine derivatives, and function as genetic "ON" switches. Following exposure of cells to certain oxidative stresses, a representative 8-oxoG riboswitch activates gene expression, likely caused by the accumulation of 8-oxoG due to oxidative damage to G nucleobases in DNA, RNA, and the nucleotide pool. Furthermore, an engineered version of the variant aptamer was prepared that exhibits specificity for 8-oxoadenine, further demonstrating that RNA aptamers can acquire mutations that expand their ability to detect and respond to oxidative damage.

Multiple in vivo roles for the C-terminal domain of the RNA chaperone Hfq.

Hfq, a bacterial RNA chaperone, stabilizes small regulatory RNAs (sRNAs) and facilitates sRNA base-pairing with target mRNAs. Hfq has a conserved N-terminal domain and a poorly conserved disordered C-terminal domain (CTD). In a transcriptome-wide examination of the effects of a chromosomal CTD deletion (Hfq1-65), the Escherichia coli mutant was most defective for the accumulation of sRNAs that bind the proximal and distal faces of Hfq (Class II sRNAs), but other sRNAs also were affected. There were only modest effects on the levels of mRNAs, suggesting little disruption of sRNA-dependent regulation. However, cells expressing Hfq lacking the CTD in combination with a weak distal face mutation were defective for the function of the Class II sRNA ChiX and repression of mutS, both dependent upon distal face RNA binding. Loss of the region between amino acids 66-72 was critical for this defect. The CTD region beyond amino acid 72 was not necessary for distal face-dependent regulation, but was needed for functions associated with the Hfq rim, seen most clearly in combination with a rim mutant. Our results suggest that the C-terminus collaborates in various ways with different binding faces of Hfq, leading to distinct outcomes for individual sRNAs.

Resistance against Fracture in Teeth Managed by Root Canal Treatment on Restoring with Onlays, Inlays, and Endocrowns: A Comparative Analysis.

AIM AND OBJECTIVE: To compare the fracture resistance in teeth managed by root canal treatment after restoring with different types of onlays, inlays, and endocrowns prepared with hybrid ceramics and pulp chambers restored with fiber-reinforced composite and resin composite that were radiopaque, light-cured, and flowable. MATERIALS AND METHODS: The present study was carried out on 252 extracted mandibular molars. All the specimens were divided into six groups randomly. Each group consisted of 42 specimens. Group 1 consisted of intact teeth without any access cavity. It was the control group. Group 2 consisted of teeth with endocrown and empty pulp chamber. Group 3 consisted of teeth with mesio-occlusal-distal (MOD) onlay prepared with hybrid ceramics and pulp chamber filled with flowable, light-cured, radiopaque resin composite. Group 4 consisted of teeth with MOD onlay and pulp chamber filled with fiber-reinforced composite. Group 5 consisted of teeth with MOD inlay and pulp chamber filled with flowable, light-cured, radiopaque resin composite. Group 6 consisted of teeth with MOD inlay and pulp chamber filled with fiber-reinforced composite. Inlay, onlay, and endocrowns were prepared with computer-aided design (CAD) and computer-aided machine (CAM) using hybrid ceramics. Universal testing machine was used for the measurement of the fracture resistance of each specimen. Inferential statistics were performed by applying Fisher's exact test and chi-square test. RESULTS: Fracture strength was found to be maximum in the intact teeth group followed by the endocrown. The fracture strength was minimum in the inlay group. The fracture strength was intermediate in the onlay groups. CONCLUSION: Endocrown showed maximum fracture resistance as compared to the inlay and onlay restorations. CLINICAL SIGNIFICANCE: Proper management of root canal-treated teeth is one of the greatest challenges for endodontists. It has been observed that tooth preparation design and the material used for the restoration of root canal-treated teeth play a vital role in the resistance against fracture in the teeth.

C-terminal domain of the RNA chaperone Hfq drives sRNA competition and release of target RNA.

The bacterial Sm protein and RNA chaperone Hfq stabilizes small noncoding RNAs (sRNAs) and facilitates their annealing to mRNA targets involved in stress tolerance and virulence. Although an arginine patch on the Sm core is needed for Hfq's RNA chaperone activity, the function of Hfq's intrinsically disordered C-terminal domain (CTD) has remained unclear. Here, we use stopped flow spectroscopy to show that the CTD of Escherichia coli Hfq is not needed to accelerate RNA base pairing but is required for the release of dsRNA. The Hfq CTD also mediates competition between sRNAs, offering a kinetic advantage to sRNAs that contact both the proximal and distal faces of the Hfq hexamer. The change in sRNA hierarchy caused by deletion of the Hfq CTD in E. coli alters the sRNA accumulation and the kinetics of sRNA regulation in vivo. We propose that the Hfq CTD displaces sRNAs and annealed sRNA⋅mRNA complexes from the Sm core, enabling Hfq to chaperone sRNA-mRNA interactions and rapidly cycle between competing targets in the cell.

Screening of phytochemicals against protease activated receptor 1 (PAR1), a promising target for cancer.

CONTEXT: Drug resistance and drug-associated toxicity are the primary causes for withdrawal of many drugs, although patient recovery is satisfactory in many instances. Interestingly, the use of phytochemicals in the treatment of cancer as an alternative to synthetic drugs comes with a host of advantages; minimum side effects, good human absorption and low toxicity to normal cells. Protease activated receptor 1 (PAR1) has been established as a promising target in many diseases including various cancers. Strong evidences suggest its role in metastasis also. OBJECTIVE: There are no natural compounds known to inhibit its activity, so we aimed to identify phytochemicals with antagonist activity against PAR1. METHODS: We screened phytochemicals from Naturally Occurring Plant-based Anticancer Compound-Activity-Target database (NPACT, http://crdd.osdd.net/raghava/npact/ ) against PAR1 using virtual screening workflow of Schrödinger software. It analyzes pharmaceutically relevant properties using Qikprop and calculates binding energy using Glide at three accuracy levels (high-throughput virtual screening, standard precision and extra precision). RESULTS AND CONCLUSION: Our study led to the identification of phytochemicals, which showed interaction with at least one experimentally determined active site residue of PAR1, showed no violations to Lipinski's rule of five along with predicted high human absorption. Furthermore, structural interaction fingerprint analysis indicated that the residues H255, D256, E260, S344, V257, L258, L262, Y337 and S344 may play an important role in the hydrogen bond interactions of the phytochemicals screened. Of these residues, H255 and L258 residues were experimentally proved to be important for antagonist binding. The residues Y183, L237, L258, L262, F271, L332, L333, Y337, L340, A349, Y350, A352, and Y353 showed maximum hydrophobic interactions with the phytochemicals screened. The results of this work suggest that phytochemicals Reissantins D, 24,25-dihydro-27-desoxywithaferin A, Isoguaiacin, 20-hydroxy-12-deoxyphorbol angelate, etc. could be potential antagonist of PAR1. However, further experimental studies are necessary to validate their antagonistic activity against PAR1.

Sequence-structure based phylogeny of GPCR Class A Rhodopsin receptors.

Current methods of G protein coupled receptors (GPCRs) phylogenetic classification are sequence based and therefore inappropriate for highly divergent sequences, sharing low sequence identity. In this study, sequence structure profile based alignment generated by PROMALS3D was used to understand the GPCR Class A Rhodopsin superfamily evolution using the MEGA 5 software. Phylogenetic analysis included a combination of Neighbor-Joining method and Maximum Likelihood method, with 1000 bootstrap replicates. Our study was able to identify potential ligand association for Class A Orphans and putative/unclassified Class A receptors with no cognate ligand information: GPR21 and GPR52 with fatty acids; GPR75 with Neuropeptide Y; GPR82, GPR18, GPR141 with N-arachidonylglycine; GPR176 with Free fatty acids, GPR10 with Tachykinin & Neuropeptide Y; GPR85 with ATP, ADP & UDP glucose; GPR151 with Galanin; GPR153 and GPR162 with Adrenalin, Noradrenalin; GPR146, GPR139, GPR142 with Neuromedin, Ghrelin, Neuromedin U-25 & Thyrotropin-releasing hormone; GPR171 with ATP, ADP & UDP Glucose; GPR88, GPR135, GPR161, GPR101with 11-cis-retinal; GPR83 with Tackykinin; GPR148 with Prostanoids, GPR109b, GPR81, GPR31with ATP & UTP and GPR150 with GnRH I & GnRHII. Furthermore, we suggest that this study would prove useful in re-classification of receptors, selecting templates for homology modeling and identifying ligands which may show cross reactivity with other GPCRs as signaling via multiple ligands play a significant role in disease modulation.

Epigallocatechin gallate regulates the myeloid-specific transcription factor PU.1 in macrophages.

Our previous research demonstrated that PU.1 regulates expression of the genes involved in inflammation in macrophages. Selective knockdown of PU.1 in macrophages ameliorated LPS-induced acute lung injury (ALI) in bone marrow chimera mice. Inhibitors that block the transcriptional activity of PU.1 in macrophages have the potential to mitigate the pathophysiology of LPS-induced ALI. However, complete inactivation of PU.1 gene disrupts normal myelopoiesis. Although the green tea polyphenol Epigallocatechin gallate (EGCG) has been shown to regulate inflammatory genes in various cell types, it is not known if EGCG alters the transcriptional activity of PU.1 protein. Using Schrodinger Glide docking, we have identified that EGCG binds with PU.1 protein, altering its DNA-binding and self-dimerization activity. In silico analysis shows that EGCG forms Hydrogen bonds with Glutamic Acid 209, Leucine 250 in DNA binding and Lysine 196, Tryptophan 193, and Leucine 182 in the self-dimerization domain of the PU.1 protein. Experimental validation using mouse bone marrow-derived macrophages (BMDM) confirmed that EGCG inhibits both DNA binding by PU.1 and self-dimerization. Importantly, EGCG had no impact on expression of the total PU.1 protein levels but significantly reduced expression of various inflammatory genes and generation of ROS. In summary, we report that EGCG acts as an inhibitor of the PU.1 transcription factor in macrophages.

Cis-9-octadecenoic acid from the rhizospheric bacterium Stenotrophomonas maltophilia BJ01 shows quorum quenching and anti-biofilm activities.

Quorum quenching (QQ) is an effective approach for the prevention of bacterial infections involving biofilms. This study reports the QQ and anti-biofilm activities of a rhizospheric bacterium identified as Stenotrophomonas maltophilia BJ01. The QQ activity was demonstrated using Chromobacterium violaceum CV026 as a biosensor. A maximum of 95% reduction in violacein production, a quorum sensing-regulated behavior, was observed. Gas chromatography-mass spectroscopy of the extract showed that the active compound was cis-9-octadecenoic acid, which was confirmed by electronspray ionization-mass spectroscopy data. The extract also inhibited biofilm formation of Pseudomonas aeruginosa ATCC 9027 without affecting its growth. Scanning electron and atomic force microscopy showed architectural disruption of the biofilm when treated with the extract. This is the first report of the QQ and anti-biofilm activities of cis-9-octadecenoic acid isolated from any bacterium. It may have the potential to combat detrimental infections with P. aeruginosa. Further validation is required for any possible medical application.

Quorum sensing inhibition by Asparagopsis taxiformis, a marine macro alga: separation of the compound that interrupts bacterial communication.

The majority of the marine algal species, though completing their life cycle in seawater, are rarely susceptible to fouling, making them an important source of quorum sensing (QS) inhibitory substances. The separation and characterization of QS inhibitors are crucial for any potential application. Thirty marine macroalgae were tested for QS inhibition activity by using Chromobacterium violaceum CV026 as the reporter strain, and among them, Asparagopsis taxiformis showed antibacterial, as well as antiquorum, sensing activities. Cinnamaldehyde (75 mM) and methanol were used as positive and negative controls, respectively. The antiquorum sensing activity of A. taxiformis was further confirmed using the sensor strain, Serratia liquefaciens MG44, having green fluorescent protein (gfp). Methanolic extract of the alga was fractionated by solid phase extraction (SPE), and each fraction was tested for QS inhibition. Two types of activities were observed-zone of clearance (antibacterial activity) and zone of inhibition with or without finger-like projections (QS inhibition). Out of five SPE cartridges, Bond Elut PH showed clear separation of these two fractions. The Ion Cyclotron Resonance Fourier Transformation Mass Spectrometer (ICR-FT/MS) analysis of the fractions further supported the bioassay results. The presence of strong QS inhibitory compound in A. taxiformis indicates its potential use in antifouling preparations.

A conserved uORF in the ilvBNC mRNA of Corynebacterium species regulates ilv operon expression.

Computational methods can be used to identify putative structured noncoding RNAs (ncRNAs) in bacteria, which can then be validated using various biochemical and genetic approaches. In a search for ncRNAs in Corynebacterium pseudotuberculosis, we observed a conserved region called the ilvB-II motif located upstream of the ilvB gene that is also present in other members of this genus. This gene codes for an enzyme involved in the production of branched-chain amino acids (BCAAs). The ilvB gene in some bacteria is regulated by members of a ppGpp-sensing riboswitch class, but previous and current data suggest that the ilvB-II motif regulates expression by a transcription attenuation mechanism involving protein translation from an upstream open reading frame (uORF or leader peptide). All representatives of this RNA motif carry a start codon positioned in-frame with a nearby stop codon, and the peptides resulting from translation of this uORF are enriched for BCAAs, suggesting that expression of the ilvB gene in the host cells is controlled by attenuation. Furthermore, recently discovered RNA motifs also associated with ilvB genes in other bacterial species appear to carry distinct uORFs, suggesting that transcription attenuation by uORF translation is a common mechanism for regulating ilvB genes.

3D Bioprinting: A Systematic Review for Future Research Direction.

Purpose: 3D bioprinting is capable of rapidly producing small-scale human-based tissue models, or organoids, for pathology modeling, diagnostics, and drug development. With the use of 3D bioprinting technology, 3D functional complex tissue can be created by combining biocompatible materials, cells, and growth factor. In today's world, 3D bioprinting may be the best solution for meeting the demand for organ transplantation. It is essential to examine the existing literature with the objective to identify the future trend in terms of application of 3D bioprinting, different bioprinting techniques, and selected tissues by the researchers, it is very important to examine the existing literature. To find trends in 3D bioprinting research, this work conducted an systematic literature review of 3D bioprinting. Methodology: This literature provides a thorough study and analysis of research articles on bioprinting from 2000 to 2022 that were extracted from the Scopus database. The articles selected for analysis were classified according to the year of publication, articles and publishers, nation, authors who are working in bioprinting area, universities, biomaterial used, and targeted applications. Findings: The top nations, universities, journals, publishers, and writers in this field were picked out after analyzing research publications on bioprinting. During this study, the research themes and research trends were also identified. Furthermore, it has been observed that there is a need for additional research in this domain for the development of bioink and their properties that can guide practitioners and researchers while selecting appropriate combinations of biomaterials to obtain bioink suitable for mimicking human tissue. Significance of the Research: This research includes research findings, recommendations, and observations for bioprinting researchers and practitioners. This article lists significant research gaps, future research directions, and potential application areas for bioprinting. Novelty: The review conducted here is mainly focused on the process of collecting, organizing, capturing, evaluating, and analyzing data to give a deeper understanding of bioprinting and to identify potential future research trends.

Identification of Multi-kinase Allosteric Inhibitors of Oncogenic Targets EGFR1, PI3K, and BRAF Kinase.

AIM: This study aimed to identify promising allosteric inhibitors with the potential to inhibit EGFR1, PI3K, and BRAF kinases as a single agent or in a combination of existing drugs, thus acting as a therapeutic option when traditional drugs fail to give a beneficial response in disease pathology. BACKGROUND: Upregulation of EGFR1 activates several downstream signaling pathways, resulting in pathophysiological alterations that contribute to cancer. The RAS/RAF/MEK/ERK (MAPK) and PI3K/Akt/mTOR (PI3K/Akt/mTOR) pathways are major downstream signalling partners induced by EGFR1 activation. Despite their vast importance, allosteric FDA-approved drugs targeting EGFR1 and these pathways are not available. OBJECTIVE: The objective of the study is to identify novel multi-kinase small molecules with the potential to inhibit major sites of amplification of cancer signalling pathways, i.e., EGFR1, PI3K/Akt/mTOR, and RAS/RAF/MEK/ERK (MAPK) signalling pathways targeting allosteric sites. METHODS: In silico methods were used to identify the potential inhibitors using EGFR1, PI3, and BRAF crystal structures complexed with allosteric inhibitors. The potential novel molecules were confirmed for their drug-likeness. Their stability of binding was also confirmed using molecular dynamics simulation studies. To eliminate false negatives, this study used a pharmacophore and structure-based targeting method. RESULTS: The current study was effective in identifying drug-like small molecules, such as ZINC38783966, ZINC01456629, ZINC01456628, and 124173751, 137352549, 137353176, 137352399, 132020316 from ZINC and PubChem database, respectively, with a potential to bind EGFR1 (6DUK), PI3 (4A55) and BRAF (6P3D) at allosteric sites. A 50 ns molecular dynamics investigation also revealed that these potential novel multitarget kinase allosteric inhibitors exhibited stable binding. CONCLUSION: Alterations in EGFR1, PI3K/Akt/mTOR, and RAS/RAF/MEK/ERK (MAPK) signalling pathways are observed in cancers in high frequency and are also used by viral and environmental toxicants for pathologic purposes. These multi-kinase allosteric inhibitors will provide insight into allosteric drug discovery and deepen our understanding of targeting these pathways, either individually or in combination with orthosteric inhibitors.

Identification of novel allosteric binding sites and multi-targeted allosteric inhibitors of receptor and non-receptor tyrosine kinases using a computational approach.

EGFR1, VEGFR2, Bcr-Abl and Src kinases are key drug targets in non-small cell lung cancer (NSCLC), bladder cancer, pancreatic cancer, CML, ALL, colorectal cancer, etc. The available drugs targeting these kinases have limited therapeutic efficacy due to novel mutations resulting in drug resistance and toxicity, as they target ATP binding site. Allosteric drugs have shown promising results in overcoming drug resistance, but the discovery of allosteric drugs is challenging. The allosteric binding pockets are difficult to predict, as they are generally associated with high energy conformations and regulate protein function in yet unknown mechanisms. In addition, the discovery of drugs using conventional methods takes long time and goes through several challenges, putting the lives of many cancer patients at risk. Therefore, the aim of the present work was to apply the most successful, drug repurposing approach in combination with computational methods to identify kinase inhibitors targeting novel allosteric sites on protein structure and assess their potential multi-kinase binding affinity. Multiple crystal structures belonging to EGFR1, VEGFR2, Bcr-Abl and Src tyrosine kinases were selected, including mutated, inhibitor bound and allosteric conformations to identify potential leads, close to physiological conditions. Interestingly the potential inhibitors identified were peptides. The drugs identified in this study could be used in therapy as a single multi-kinase inhibitor or in a combination of single kinase inhibitors after experimental validation. In addition, we have also identified new hot spots that are likely to be druggable allosteric sites for drug discovery of kinase-specific drugs in the future.Communicated by Ramaswamy H. Sarma.

In vitro Evaluation of Laser vs. Handpiece for Tooth Preparation.

Background: The erbium-doped yttrium aluminium garnet (Er:YAG) laser has been revealed to effectively ablate dental hard tissues, and its utilisation to caries eradication and cavity preparation is envisaged. Nevertheless, only a limited research has been performed on the Er:YAG laser's capacity to treat caries. Aim and Objectives: The efficiency of caries elimination with an Er:YAG laser in vitro was equated to that of traditional mechanical therapy in this study. Methodology: The investigation made use of teeth that had suffered from root caries. The Er:YAG laser was used to treat half of each tooth, while the other half was either removed with a conventional bur or left untouched as a control. Each therapy was evaluated in terms of how long it took to remove cavities, histological examinations of decalcified serial sections, scanning electron microscopy (SEM) analyses and the density of the dentin. Result: A longer treatment time was required for the Er:YAG laser to completely eradicate carious dentin because of its precise irradiation strategy. However, the Er:YAG laser was effective in removing diseased and softening carious dentin with little heat injury to neighbouring intact dentin, much as the bur treatment. It was also shown that the Er:YAG laser treatment had a lower amount of vibration than other methods. The SEM study of the lased dentin surface revealed characteristic micro-irregularities. Conclusion: The Er:YAG laser system appears to be a potential novel technical option for caries therapy, based on our findings.

An In Vitro study to Compare Dental Laser with other Treatment Modalities on Biofilm Ablation from Implant and Tooth Surfaces.

Background: Periodontal and peri-implant disorders are etiologically linked to bacterial biofilms. The researchers wanted to see how well the erbium-doped yttrium aluminum garnet (Er:YAG) laser removed bacterial biofilms along with attached epithelial cells (EC), gingival fibroblasts (GF), in addition to osteoblast-like cells (OC) dentin along with titanium surfaces compared to previous therapy methods. Methodology: 3.5 days were spent growing bacterial biofilms on standardized dentin and also titanium samplings using a sand-blasted along with the acid-etched surface. Following that, the specimens were positioned into pockets that had been formed artificially. The following approaches were used to remove biofilm: (1) Er:YAG, (2) photodynamic therapy (PDT), and (3) curette (CUR) along with supplementary PDT (CUR/PDT). The remaining biofilms' colony forming units (CFUs) were determined, as well as the attachment of EC, GF, in addition to OC. Analysis of variance with a posthoc least significant difference was utilized in the statistical analysis. Results: When compared to untreated dentin and titanium surfaces, all therapy strategies reduced total CFUs in statistically significant biofilms (p = 0.001). On the dentin, Er:YAG was as effective as CUR and PDT, but not as effective as CUR/PDT (p = 0.005). The application of Er:YAG on titanium surfaces leads to statistically significantly improved biofilm eradication equated to the supplementary three therapies (all p = 0.001). On untouched infested dentin and titanium surfaces, the counts of attached EC, GF, and OC were the lowermost. Atop the dentin, increased EC counts were detected after CUR/PDT (p = 0.006). On titanium, all cleaning procedures increased the counts of attached EC by a statistically significant amount (p = 0.001), with no variations between groups. After Er:YAG decontamination, there were statistically substantially elevated amounts of GF (p = 0.024) and OC (p = 0.001) than on untreated surfaces. Conclusion: The usage of Er:YAG laser to ablate subgingival biofilms and, specifically, to decontaminate titanium implant surfaces appears to be a promising strategy that needs further research.

Brachybacterium saurashtrense sp. nov., a halotolerant root-associated bacterium with plant growth-promoting potential.

A Gram-positive-staining, aerobic, non-motile, coccoid shaped, halotolerant bacterium (strain JG 06(T)) was isolated from the roots of Salicornia brachiata, an extreme halophyte. Phylogenetic analysis based on 16S rRNA gene sequence showed that the novel strain had sequence similarities of 99.2% to Brachybacterium paraconglomeratum JCM 11608(T), 99.0% to Brachybacterium conglomeratum DSM 10241 and 98.2% to Brachybacterium faecium DSM 4810(T). DNA-DNA hybridization with B. paraconglomeratum DSM 46341(T), B. conglomeratum DSM 10241(T), B. faecium DSM 4810(T), Brachybacterium tyrofermentans DSM 10673(T), Brachybacterium alimentarium DSM 10672(T), Brachybacterium fresconsis DSM 14564(T), Brachybacterium sacelli DSM 14566(T) and Brachybacterium muris DSM 15460(T) resulted in reassociation values of 36.2%, 36.5%, 35.8%, 27.6%, 27.9%, 28.2%, 28.7% and 11.2%, respectively. The peptidoglycan type of strain JG 06(T) was variant A4γ. The menaquinone content was MK7 (100%). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, monogalactosyl diglyceride, three unidentified phospholipids and three glycolipids. The predominant fatty acid was anteiso-C(15:0) (52.07%); significant amounts of iso-C(16:0)(12.38%), iso-C(15:0 )(8.59%) and anteiso-C(17:0)(10.03%) were also present. The G+C content of the DNA was 73.0 mol%. The strain formed a growth pellicle in nitrogen-free semisolid NFb medium containing NaCl at levels of up to 4% (w/v) and reduced acetylene to ethylene, a result indicative of N(2) fixation. In nutrient broth medium the novel strain grew at NaCl concentrations up to 15% (w/v). It also had the ability to produce indole-3-acetic acid (IAA) and siderophores, utilized 1-aminocyclopropane-1-carboxylate (ACC) as a sole source of nitrogen and possessed the ACC deaminase enzyme. On the basis of physiological, biochemical data and phylogenetic analyses, strain JG 06(T) should be placed in the genus Brachybacterium. Strain JG 06(T) represents a novel species of the genus Brachybacterium for which the name Brachybacterium saurashtrense sp. nov. is proposed (type strain JG 06(T)=DSM 23186(T)=IMCC 252(T)).

Isolation and physico-chemical characterisation of extracellular polymeric substances produced by the marine bacterium Vibrio parahaemolyticus.

A marine bacterial strain identified as Vibrio parahaemolyticus by 16S rRNA gene (HM355955) sequencing and gas chromatography (GC) coupled with MIDI was selected from a natural biofilm by its capability to produce extracellular polymeric substances (EPS). The EPS had an average molecule size of 15.278 µm and exhibited characteristic diffraction peaks at 5.985°, 9.150° and 22.823°, with d-spacings of 14.76661, 9.29989 and 3.89650 Å, respectively. The Fourier-transform infrared spectroscopy (FTIR) spectrum revealed aliphatic methyl, primary amine, halide groups, uronic acid and saccharides. Gas chromatography mass spectrometry (GCMS) confirmed the presence of arabinose, galactose, glucose and mannose. (1)HNMR (nuclear magnetic resonance) revealed functional groups characteristic of polysaccharides. The EPS were amorphous in nature (CI(xrd) 0.092), with a 67.37% emulsifying activity, thermostable up to 250°C and displayed pseudoplastic rheology. MALDI-TOF-TOF analysis revealed a series of masses, exhibiting low-mass peaks (m/z) corresponding to oligosaccharides and higher-mass peaks for polysaccharides consisting of different ratios of pentose and hexose moieties. This is the first report of a detailed characterisation of the EPS produced by V. parahaemolyticus, which could be further explored for biotechnological and industrial use.

Predictors and prevalence of periodontitis among pregnant women of slum areas of Patna, India: An opportunity for oral health promotion.

BACKGROUND: There is abundant documentation in literature that presence of maternal periodontal infections has been attributed to serious health problem to the mother and the child. Regular evaluation of any illness burden is required for planning preventive and treatment strategies and fills the existing health gap. There is a lack of literature about the predictors and prevalence of periodontal diseases in expectant women in the slum areas of Patna. MATERIALS AND METHODS: It was a cross-sectional study conducted on pregnant women of slum areas of Patna, Bihar, by convenience sampling method. Using a questionnaire, data collection was carried for demographic and oral hygiene habits information. Periodontal examination was done using modified community periodontal index criteria (WHO, 2013) by recording bleeding on probing (BoP), periodontal pockets (PD) and loss of attachment (LoA). The prevalence of potential predictors was estimated and bivariate analysis was performed with BoP, PD, and LoA and then to explore the prevalence of odds ratio (ORs) multivariate logistic regression framework was employed. The level of significance was kept at P < 0.05. RESULTS: A higher level of BoP and PD was observed among women who had the habit of cleaning their teeth once daily a day than those who cleaned their teeth with brush twice a day. Oral cleanliness (hygiene) frequency established the maximum OR of 2.77 (2.07-3.71) for BoP. Gingival bleeding robustly was related with PD. Among all multivariate framework of predictors of LoA, BoP, and PD came as the firmest predictors. CONCLUSION: Teaching correctly how to maintain oral hygiene and periodic periodontal check-up can improvise the general well-being and adverse pregnancy outcomes can be lessened.