The surface layer (S-layer) glycoprotein of Geobacillus stearothermophilus NRS 2004/3a. Analysis of its glycosylation.

Geobacillus stearothermophilus NRS 2004/3a possesses an oblique surface layer (S-layer) composed of glycoprotein subunits as the outermost component of its cell wall. In addition to the elucidation of the complete S-layer glycan primary structure and the determination of the glycosylation sites, the structural gene sgsE encoding the S-layer protein was isolated by polymerase chain reaction-based techniques. The open reading frame codes for a protein of 903 amino acids, including a leader sequence of 30 amino acids. The mature S-layer protein has a calculated molecular mass of 93,684 Da and an isoelectric point of 6.1. Glycosylation of SgsE was investigated by means of chemical analyses, 600-MHz nuclear magnetic resonance spectroscopy, and matrix-assisted laser desorption ionization-time of flight mass spectrometry. Glycopeptides obtained after Pronase digestion revealed the glycan structure [-->2)-alpha-L-Rhap-(1-->3)-beta-L-Rhap-(1-->2)-alpha-L-Rhap-(1-->](n = 13-18), with a 2-O-methyl group capping the terminal trisaccharide repeating unit at the non-reducing end of the glycan chains. The glycan chains are bound via the disaccharide core -->3)-alpha-l-Rhap-(1-->3)-alpha-L-Rhap-(L--> and the linkage glycose beta-D-Galp in O-glycosidic linkages to the S-layer protein SgsE at positions threonine 620 and serine 794. This S-layer glycoprotein contains novel linkage regions and is the first one among eubacteria whose glycosylation sites have been characterized.     

Fox-2 splicing factor binds to a conserved intron motif to promote inclusion of protein 4.1R alternative exon 16

Activation of protein 4.1R exon 16 (E16) inclusion during erythropoiesis represents a physiologically important splicing switch that increases 4.1R affinity for spectrin and actin. Previous studies showed that negative regulation of E16 splicing is mediated by the binding of heterogeneous nuclear ribonucleoprotein (hnRNP) A/B proteins to silencer elements in the exon and that down-regulation of hnRNP A/B proteins in erythroblasts leads to activation of E16 inclusion. This article demonstrates that positive regulation of E16 splicing can be mediated by Fox-2 or Fox-1, two closely related splicing factors that possess identical RNA recognition motifs. SELEX experiments with human Fox-1 revealed highly selective binding to the hexamer UGCAUG. Both Fox-1 and Fox-2 were able to bind the conserved UGCAUG elements in the proximal intron downstream of E16, and both could activate E16 splicing in HeLa cell co-transfection assays in a UGCAUG-dependent manner. Conversely, knockdown of Fox-2 expression, achieved with two different siRNA sequences resulted in decreased E16 splicing. Moreover, immunoblot experiments demonstrate mouse erythroblasts express Fox-2. These findings suggest that Fox-2 is a physiological activator of E16 splicing in differentiating erythroid cells in vivo. Recent experiments show that UGCAUG is present in the proximal intron sequence of many tissue-specific alternative exons, and we propose that the Fox family of splicing enhancers plays an important role in alternative splicing switches during differentiation in metazoan organisms.     

Molecular characterization of acquired tolerance of tumor cells to picropodophyllin (PPP)

Background

Picropodophyllin (PPP) is a promising novel anti-neoplastic agent that efficiently kills tumor cells in vitro and causes tumor regression and increased survival in vivo. We have previously reported that PPP treatment induced moderate tolerance in two out of 10 cell lines only, and here report the acquired genomic and expression alterations associated with PPP selection over 1.5 years of treatment.

Methodology/Principal Findings

Copy number alterations monitored using metaphase and array-based comparative genomic hybridization analyses revealed largely overlapping alterations in parental and maximally tolerant cells. Gain/ amplification of the MYC and PVT1 loci in 8q24.21 were verified on the chromosome level. Abnormalities observed in connection to PPP treatment included regular gains and losses, as well as homozygous losses in 10q24.1-q24.2 and 12p12.3-p13.2 in one of the lines and amplification at 5q11.2 in the other. Abnormalities observed in both tolerant derivatives include amplification/gain of 5q11.2, gain of 11q12.1-q14.3 and gain of 13q33.3-qter. Using Nexus software analysis we combined the array-CGH data with data from gene expression profilings and identified genes that were altered in both inputs. A subset of genes identified as downregulated (ALDH1A3, ANXA1, TLR4 and RAB5A) or upregulated (COX6A1, NFIX, ME1, MAPK and TAP2) were validated by siRNA in the tolerant or parental cells to alter sensitivity to PPP and confirmed to alter sensitivity to PPP in further cell lines.

Conclusions

Long-term PPP selection lead to altered gene expression in PPP tolerant cells with increase as well as decrease of genes involved in cell death such as PTEN and BCL2. In addition, acquired genomic copy number alterations were observed that were often reflected by altered mRNA expression levels for genes in the same regions.     

A Systematic Map of Systematic Reviews in Pediatric Dentistry—What Do We Really Know?

ObjectivesTo identify, appraise and summarize existing knowledge and knowledge gaps in practice-relevant questions in pediatric dentistry.MethodsA systematic mapping of systematic reviews was undertaken for domains considered important in daily clinical practice. The literature search covered questions in the following domains: behavior management problems/dental anxiety; caries risk assessment and caries detection including radiographic technologies; prevention and non-operative treatment of caries in primary and young permanent teeth; operative treatment of caries in primary and young permanent teeth; prevention and treatment of periodontal disease; management of tooth developmental and mineralization disturbances; prevention and treatment of oral conditions in children with chronic diseases/developmental disturbances/obesity; diagnosis, prevention and treatment of dental erosion and tooth wear; treatment of traumatic injuries in primary and young permanent teeth and cost-effectiveness of these interventions. Abstracts and full text reviews were assessed independently by two reviewers and any differences were solved by consensus. AMSTAR was used to assess the risk of bias of each included systematic review. Reviews judged as having a low or moderate risk of bias were used to formulate existing knowledge and knowledge gaps.ResultsOut of 81 systematic reviews meeting the inclusion criteria, 38 were judged to have a low or moderate risk of bias. Half of them concerned caries prevention. The quality of evidence was high for a caries-preventive effect of daily use of fluoride toothpaste and moderate for fissure sealing with resin-based materials. For the rest the quality of evidence for the effects of interventions was low or very low.ConclusionThere is an urgent need for primary clinical research of good quality in most clinically-relevant domains in pediatric dentistry.     

EST-based gene discovery in pig: virtual expression patterns and comparative mapping to human

A molecular understanding of porcine reproduction is of biological interest and economic importance. Our Midwest Consortium has produced cDNA libraries containing the majority of genes expressed in major female reproductive tissues, and we have deposited into public databases 21,499 expressed sequence tag (EST) gene sequences from the 3 end of clones from these libraries. These sequences represent 10,574 different genes, based on sequence comparison among these data, and comparison with existing porcine ESTs and genes indicate as many as 4652 of these EST clusters are novel. In silico analysis identified sequences that are expressed in specific pig tissues or organs and confirmed the broad expression in pig for many genes ubiquitously expressed in human tissues. Furthermore, we have developed computer software to identify sequence similarity of these pig genes with their human counterparts, and to extract the mapping information of these human homologues from genome databases. We demonstrate the utility of this software for comparative mapping by localizing 61 genes on the porcine physical map for Chromosomes (Chrs) 5, 10, and 14. The following Accession numbers were assigned to our deposited sequences: BF701840 – BF704551, BF708383, BF708386 – BF713604, BG322266 – BG322271, BI398567 – BI405235, BQ597354 – BQ605166.     

Right Ventricular Function Quantification in Takotsubo Cardiomyopathy Using Two-Dimensional Strain Echocardiography

Aims

This study sought to characterize global and regional right ventricular (RV) myocardial function in patients with Takotsubo cardiomyopathy (TC) using 2D strain imaging.

Methods

We compared various parameters of RV and left ventricular (LV) systolic function between 2 groups of consecutive patients with TC at initial presentation and upon follow-up. Group 1 had RV involvement and group 2 did not have RV involvement.

Results

At initial presentation, RV peak systolic longitudinal strain (RVPSS) and RV fractional area change (RVFAC) were significantly lower in group 1 (−13.2±8.6% vs. −21.8±5.4%, p = 0.001; 30.7±9.3% vs. 43.5±6.3%, p = 0.001) and improved significantly upon follow-up. Tricuspid annular plane systolic excursion (TAPSE) did not differ significantly at initial presentation between both groups (14.8±4.1 mm vs. 17.9±3.5 mm, p = 0.050). Differences in regional systolic RV strain were only observed in the mid and apical segments. LV ejection fraction (LVEF) and LV global strain were significantly lower in group 1 (36±8% vs. 46±10%, p = 0.006 and −5.5±4.8% vs. −10.2±6.2%, p = 0.040) at initial presentation. None of the parameters were significantly different between the 2 groups upon follow-up. A RVPSS cut-off value of >−19.1% had a sensitivity of 85% and a specificity of 71% to discriminate between the 2 groups.

Conclusion

In TC, RVFAC, RVPSS, LVEF and LV global strain differed significantly between patients with and without RV dysfunction, whereas TAPSE did not. 2 D strain imaging was feasible for the assessment of RV dysfunction in TC and could discriminate between patients with and without RV involvement in a clinically meaningful way.     

Chemical cues modify species interactions: the ecological consequences of predator avoidance by freshwater snails

Chemical signals released by predators or injured prey often induce shifts in the traits of prey species, which may in turn affect species interactions. Here we investigate the role that chemical cues play in mediating species interactions in the littoral food web of lakes. Previous studies have shown that predators induce shifts in the morphology, life history, and behavior of the freshwater snail Physella, but the ecological consequences of developing these inducible defenses are not well documented. We observed habitat use of the freshwater snail Physella gyrina along a depth gradient in a natural lake, and found they increased their use of covered habitats with increasing depth. We hypothesized that this habitat shift was due to changes in the level and type of predation risk, and that the habitat shift would affect periphyton standing crops. These hypotheses were tested in a mesocosm experiment in which we manipulated the presence of molluscivorous fish and crayfish. Predators were confined to cages and snail density was identical in all treatments, so any effects of predators were mediated through trait shifts induced by chemical cues. In the presence of fish, Physella moved under cover, but in the presence of crayfish, Physella avoided cover and moved to the water surface. These non‐lethal effects of predators on snail habitat use influenced the interaction between snails and their periphyton resources. In the presence of fish, periphyton standing crop in covered habitats was reduced to just 8% of periphyton in the absence of fish. Crayfish had no significant effect on periphyton in covered habitats, but they reduced periphyton in near‐surface habitats to 39% of the standing crop in the absence of crayfish. The combined effects of fish and crayfish were generally intermediate to their individual effects. We conclude that because chemical cues often have strong effects on individual traits and trophic interactions are sensitive to trait values, chemical cues may play an important role in shaping the structure and dynamics of food webs.     

Anti-herpesvirus bovine type 5 activities of extracts obtained from Plocamium brasiliense

Bovine herpesvirus type 5 (BoHV-5) is an important etiologic agent of meningoencephalitis in cattle and has been frequently identified in outbreaks of neurological disease in bovine in the southern hemisphere including Brazil. This study aimed to evaluate the cytotoxic effect and the antiviral properties of extracts obtained from Plocamium brasiliense (Greville) Howe and Taylor in BoHV-5 RJ42/01 replication. The cytotoxic effects were measured in Madin-Darbin bovine kidney cells (MDBK) and cytotoxic concentration (CC₅₀) values have been determined for acyclovir (ACV) (223 μg?±?2.0), ethyl acetate extract from P. brasiliense (2,109 μg?±?10), hexane extract from P. brasiliense (7.181 μg?±?5), dichloromethane extract from P. brasiliense (2.356 μg?±?6.5), and hydroalcoholic extract from P. brasiliense (1.408 μg?±?5.8). As a first approach to characterize the action of these extracts on BoHV-5 RJ42/01, a virucidal assay activity was performed. A virus suspension containing 1?×?10⁵ plaque-forming units (PFU) of the BoHV-5 RJ42/01 was mixed with 600 μg of extract and acyclovir and kept at room temperature (24 °C) for 3 h. Meanwhile, a control of untreated infected virus was performed in the same conditions. Then, treated virus suspension and untreated control were diluted, and percentage of inhibition of infectivity was determined by plaque assay: ethyl acetate extract (99 %), hexane extract (90 %), dichloromethane extract (99 %), and hydroalcoholic extract (27 %). Acyclovir had a slight virucidal activity on viral particle. The inhibition of attachment was performed in MDBK cells inoculated with 100 PFU of BoHV-5 RJ42/01 in the presence or absence of various concentrations of extracts (0.3, 0.9, and 1.5 μg mL^?1). Acyclovir was also assayed at 2.8 and 11.25 μg mL^?1. The inhibition of adsorption was also tested in MDBK cells treated with the same concentrations of the extracts before virus inoculation. Results: hexane extracts inhibited virus attachment in pre-treated cell 0.9 μg (55 %) and 1.5 μg (71 %) and untreated MDBK cell only with 1.5 μg (63 %). Ethyl acetate extract on cell pre-treated with 0.3 μg (67 %), 0.9 μg (81 %), and 1.5 μg (91 %). Ethyl acetate extract on pre-treated cell 0.3 μg (67 %), 0.9 μg (81 %), and 1.5 (91 %) but discrete inhibition on cell untreated. Dichloromethane extract and acyclovir slightly inhibited virus binding on MDBK cell.     

Canadian polar bear population structure using genome‐wide markers

Predicting the consequences of environmental changes, including human‐mediated climate change on species, requires that we quantify range‐wide patterns of genetic diversity and identify the ecological, environmental, and historical factors that have contributed to it. Here, we generate baseline data on polar bear population structure across most Canadian subpopulations (n = 358) using 13,488 genome‐wide single nucleotide polymorphisms (SNPs) identified with double‐digest restriction site‐associated DNA sequencing (ddRAD). Our ddRAD dataset showed three genetic clusters in the sampled Canadian range, congruent with previous studies based on microsatellites across the same regions; however, due to a lack of sampling in Norwegian Bay, we were unable to confirm the existence of a unique cluster in that subpopulation. These data on the genetic structure of polar bears using SNPs provide a detailed baseline against which future shifts in population structure can be assessed, and opportunities to develop new noninvasive tools for monitoring polar bears across their range.