Mutant U2AF1-induced alternative splicing of H2afy (macroH2A1) regulates B-lymphopoiesis in mice.

Somatic mutations in spliceosome genes are found in ∼50% of patients with myelodysplastic syndromes (MDS), a myeloid malignancy associated with low blood counts. Expression of the mutant splicing factor U2AF1(S34F) alters hematopoiesis and mRNA splicing in mice. Our understanding of the functionally relevant alternatively spliced target genes that cause hematopoietic phenotypes in vivo remains incomplete. Here, we demonstrate that reduced expression of H2afy1.1, an alternatively spliced isoform of the histone H2A variant gene H2afy, is responsible for reduced B cells in U2AF1(S34F) mice. Deletion of H2afy or expression of U2AF1(S34F) reduces expression of Ebf1 (early B cell factor 1), a key transcription factor for B cell development, and mechanistically, H2AFY is enriched at the EBF1 promoter. Induced expression of H2AFY1.1 in U2AF1(S34F) cells rescues reduced EBF1 expression and B cells numbers in vivo. Collectively, our data implicate alternative splicing of H2AFY as a contributor to lymphopenia induced by U2AF1(S34F) in mice and MDS.

Plasma metagenomic sequencing to detect and quantify bacterial DNA in ICU patients suspected of sepsis: A proof-of-principle study.

BACKGROUND: Timely recognition of sepsis and identification of pathogens can improve outcomes in critical care patients but microbial cultures have low accuracy and long turnaround times. In this proof-of-principle study, we describe metagenomic sequencing and analysis of nonhuman DNA in plasma. We hypothesized that quantitative analysis of bacterial DNA (bDNA) levels in plasma can enable detection and monitoring of pathogens. METHODS: We enrolled 30 patients suspected of sepsis in the surgical trauma intensive care unit and collected plasma samples at the time of diagnostic workup for sepsis (baseline), and 7 days and 14 days later. We performed metagenomic sequencing of plasma DNA and used computational classification of sequencing reads to detect and quantify total and pathogen-specific bDNA fraction. To improve assay sensitivity, we developed an enrichment method for bDNA based on size selection for shorter fragment lengths. Differences in bDNA fractions between samples were evaluated using t test and linear mixed-effects model, following log transformation. RESULTS: We analyzed 72 plasma samples from 30 patients. Twenty-seven samples (37.5%) were collected at the time of infection. Median total bDNA fraction was 1.6 times higher in these samples compared with samples with no infection (0.011% and 0.0068%, respectively, p < 0.001). In 17 patients who had active infection at enrollment and at least one follow-up sample collected, total bDNA fractions were higher at baseline compared with the next sample (p < 0.001). Following enrichment, bDNA fractions increased in paired samples by a mean of 16.9-fold. Of 17 samples collected at the time when bacterial pathogens were identified, we detected pathogen-specific DNA in 13 plasma samples (76.5%). CONCLUSION: Bacterial DNA levels in plasma are elevated in critically ill patients with active infection. Pathogen-specific DNA is detectable in plasma, particularly after enrichment using selection for shorter fragments. Serial changes in bDNA levels may be informative of treatment response. LEVEL OF EVIDENCE: Epidemiologic/Prognostic, Level V.

A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing.

Virtually all tumors are genetically heterogeneous, containing mutationally-defined subclonal cell populations that often have distinct phenotypes. Single-cell RNA-sequencing has revealed that a variety of tumors are also transcriptionally heterogeneous, but the relationship between expression heterogeneity and subclonal architecture is unclear. Here, we address this question in the context of Acute Myeloid Leukemia (AML) by integrating whole genome sequencing with single-cell RNA-sequencing (using the 10x Genomics Chromium Single Cell 5' Gene Expression workflow). Applying this approach to five cryopreserved AML samples, we identify hundreds to thousands of cells containing tumor-specific mutations in each case, and use the results to distinguish AML cells (including normal-karyotype AML cells) from normal cells, identify expression signatures associated with subclonal mutations, and find cell surface markers that could be used to purify subclones for further study. This integrative approach for connecting genotype to phenotype is broadly applicable to any sample that is phenotypically and genetically heterogeneous.

Clinical Profile and Outcome of Posterior Reversible Encephalopathy Syndrome in Hemodialysis Patients.

Posterior reversible encephalopathy syndrome (PRES) is a clinico-radiologic entity characterized by headache, altered level of consciousness, seizures, visual disturbances, and reversible vasogenic subcortical edema. Hypertension and renal failure are well known principal risk factors for the development of PRES. However, risk factors and outcome of PRES has not been studied in patients on maintenance hemodialysis (MHD). The objective of this study is to characterize the factors predisposing to the development of PRES in patients on MHD. We performed a retrospective analysis in patients of MHD who were diagnosed with PRES between August 1, 2013, and July 31, 2015. Those with a history of cerebrovascular accidents/stroke, and epilepsy were excluded. We analyzed the clinical details, course, and laboratory data. One year follow-up data were noted in recurrence of PRES and mortality. A total of 18 patients were included for the final analysis. Of these, 13 (72%) patients were males. Majority of these patients were young and mean age was 21.1 years (6-50 years). Most of the PRES episodes developed shortly after initiation of MHD with mean duration of 2 months after initiation of MHD (1 month-3 years). All 18 patients had resistant hypertension. Eight (45%) patients had infection at the time of PRES episodes. Four patients had catheter-related bloodstream infection, 1 had pneumonia and 3 patients were recently diagnosed with pulmonary tuberculosis. Four (22%) patients developed recurrence of PRES and all these episodes developed within 2 months of index event. Seven (39%) patients underwent renal transplantation, and all received triple immune suppression and had uncontrolled hypertension in the perioperative period. However, none of these patients developed PRES after transplantation. All these patients had been maintaining stable graft function in the follow-up. All episodes of PRES were of generalized tonic-clonic seizure type and 6 of them presented as status epilepticus. None of them had any neurological sequel and no mortality at the end of 1 year. PRES is not uncommon in patients on MHD. Uncontrolled hypertension and infection are common predisposing factors. Renal transplantation is safe and not adversely affected by prior episodes of PRES in MHD.

Lernaea cyprinacea infection in a new host Puntius pulchellus in intensive culture system and its control by doramectin.

The present study explored the susceptibility of Puntius pulchellus subadults to Lernaea cyprinacea infection subsequent upon their first introduction to an intensive culture system that had a previous history of Lernaea infection and evaluated the efficacy of doramectin against the parasite. All the P. pulchellus introduced to the culture pond got infected demonstrating 100 % susceptibility of this species to Lernaea infection. Pathological changes caused by the parasite as evidenced by the extensive hemorrhage and tissue necrosis of the host at the point of parasite attachment was most severe in P. pulchellus. On the contrary, among the fish species already present in the pond and were previously exposed to the infection before the start of the present study, only Labeo fimbriatus developed mild to moderate infection. Cirrhinus mrigala, Ctenopharyngodon idella and Cyprinus carpio from the same culture pond did not develop Lernaea infection. Doramectin administration at 1 mg/kg b.wt. of fish incorporated in feed and given orally for 10 days or by a single intramuscular injection at 200 µg/kg b.wt. was found to be effective in controlling L. cyprinacea adult parasite infection in P. pulchellus. Doramectin hastened healing of the wounds caused by L. cyprinacea and did not cause any noticeable adverse reactions or toxicity to the fish host during the present study. In conclusion, P. pulchellus was observed to be highly susceptible to L. cyprinacea upon its first exposure to the infective stages of the parasite and a single intramuscular injection of doramectin at 200 µg/kg b.wt. was more effective than oral administration of the drug in controlling L. cyprinacea infection.

DHA and EPA Content and Fatty Acid Profile of 39 Food Fishes from India.

Docosahexaenoic acid (DHA) is the principal constituent of a variety of cells especially the brain neurons and retinal cells and plays important role in fetal brain development, development of motor skills, and visual acuity in infants, lipid metabolism, and cognitive support and along with eicosapentaenoic acid (EPA) it plays important role in preventing atherosclerosis, dementia, rheumatoid arthritis, Alzheimer's disease, and so forth. Being an essential nutrient, it is to be obtained through diet and therefore searching for affordable sources of these ω-3 polyunsaturated fatty acids (PUFA) is important for consumer guidance and dietary counseling. Fish is an important source of PUFA and has unique advantage that there are many food fish species available and consumers have a wide choice owing to availability and affordability. The Indian subcontinent harbors a rich fish biodiversity which markedly varies in their nutrient composition. Here we report the DHA and EPA content and fatty acid profile of 39 important food fishes (including finfishes, shellfishes, and edible molluscs from both marine water and freshwater) from India. The study showed that fishes Tenualosa ilisha, Sardinella longiceps, Nemipterus japonicus, and Anabas testudineus are rich sources of DHA and EPA. Promotion of these species as DHA rich species would enhance their utility in public health nutrition.

Micronutrient Composition of 35 Food Fishes from India and Their Significance in Human Nutrition.

The micronutrients (vitamins and minerals) are required in small amounts but are essential for health, development, and growth. Micronutrient deficiencies, which affect over two billion people around the globe, are the leading cause of many ailments including mental retardation, preventable blindness, and death during childbirth. Fish is an important dietary source of micronutrients and plays important role in human nutrition. In the present investigation, micronutrient composition of 35 food fishes (includes both finfishes and shellfishes) was investigated from varying aquatic habitats. Macrominerals (Na, K, Ca, Mg) and trace elements (Fe, Cu, Zn, Mn, Se) were determined by either atomic absorption spectroscopy (AAS) or inductively coupled plasma mass spectrometry (ICP-MS)/atomic emission spectrometry (ICP-AES). Phosphorus content was determined either spectrophotometrically or by ICP-AES. Fat-soluble vitamins (A, D, E, K) were analyzed by high-performance liquid chromatography (HPLC). The analysis showed that, in general, the marine fishes were rich in sodium and potassium; small indigenous fishes (SIFs) in calcium, iron, and manganese; coldwater fishes in selenium; and the brackishwater fishes in phosphorous. The marine fishes Sardinella longiceps and Epinephelus spp. and the SIFs were rich in all fat-soluble vitamins. All these recommendations were made according to the potential contribution (daily value %) of the species to the recommended daily allowance (RDA). Information on the micronutrients generated would enhance the utility of fish in both community and clinical nutrition.

Multiphysics modelling, quantum chemistry and risk analysis for corrosion inhibitor design and lifetime prediction.

Organic corrosion inhibitors can provide an effective means to extend the life of equipment in aggressive environments, decrease the environmental, economic, health and safety risks associated with corrosion failures and enable the use of low cost steels in place of corrosion resistant alloys. To guide the construction of advanced models for the design and optimization of the chemical composition of organic inhibitors, and to develop predictive tools for inhibitor performance as a function of alloy and environment, a multiphysics model has been constructed following Staehle's principles of "domains and microprocesses". The multiphysics framework provides a way for science-based modelling of the various phenomena that impact inhibitor efficiency, including chemical thermodynamics and speciation, oil/water partitioning, effect of the inhibitor on multiphase flow, surface adsorption and self-assembled monolayer formation, and the effect of the inhibitor on cathodic and anodic reaction pathways. The fundamental tools required to solve the resulting modelling from a first-principles perspective are also described. Quantification of uncertainty is significant to the development of lifetime prediction models, due to their application for risk management. We therefore also discuss how uncertainty analysis can be coupled with the first-principles approach laid out in this paper.

Amino Acid compositions of 27 food fishes and their importance in clinical nutrition.

Proteins and amino acids are important biomolecules which regulate key metabolic pathways and serve as precursors for synthesis of biologically important substances; moreover, amino acids are building blocks of proteins. Fish is an important dietary source of quality animal proteins and amino acids and play important role in human nutrition. In the present investigation, crude protein content and amino acid compositions of important food fishes from different habitats have been studied. Crude protein content was determined by Kjeldahl method and amino acid composition was analyzed by high performance liquid chromatography and information on 27 food fishes was generated. The analysis showed that the cold water species are rich in lysine and aspartic acid, marine fishes in leucine, small indigenous fishes in histidine, and the carps and catfishes in glutamic acid and glycine. The enriched nutrition knowledge base would enhance the utility of fish as a source of quality animal proteins and amino acids and aid in their inclusion in dietary counseling and patient guidance for specific nutritional needs.

A Clinical and Radiographic Evaluation of Periodontal Regenerative Potential of PerioGlas®: A Synthetic, Resorbable Material in Treating Periodontal Infrabony Defects.

BACKGROUND: Study of the clinical application of bioactive glass in treating periodontal defects has been gaining momentum. Studies in the past have hypothesized that bioactive glass resulted in an improvement of bony lesion when compared with open flap debridement. Considering that there were very few studies in the Indian dental literature involving the analysis of PerioGlas®- A particulate Bioglass in intrabony defects, the present clinical trial aimed to clinically and radiographically evaluate the efficacy of PerioGlas® and compare it to open debridement as control in the treatment of human periodontal osseous (three and two wall) defects in South Indian population. MATERIALS AND METHODS: Ten patients with chronic periodontitis within the age group of 30-45 years having at least two pockets with depth of ≥6 mm exhibiting vertical osseous defects were selected for the study. A total of 20 defect sites were randomly assigned to one of the two treatment modalities such that 10 sites (experimental) received PerioGlas® material after open flap debridement and 10 sites with open flap debridement (controls). Plaque index and gingival index (GI) were recorded at baseline, 6 weeks, 3 months, 6 months and 9 months, whereas probing pocket depth (PPD), clinical attachment level and gingival recession (GR) were recorded at baseline, 6 and 9 months postoperatively. Linear radiographic measurements were carried out at baseline, 6 and 9 months to evaluate the defect fill, defect resolution and change in the alveolar crest height (ACH). RESULTS: Both experimental and control site showed a significant reduction in plaque and GI, and a slight increase in GR. The mean reduction in PPD for experimental and control site was 4.4 ± 0.34 mm and 3.2 ± 0.1 mm, respectively. Gain in clinical attachment at experimental and control site was 4.4 ± 0.21 and 3.4 ± 0.11, respectively which on comparison was statistically non-significant for both sites. The radiographic mean defect fill for experimental site was 1.73 mm. The mean defect resolution was 46.5% and 15.3% for the experimental group and control group, respectively, with a slight increase in the ACH at the experimental site. CONCLUSION: Comparison of experimental and control sites revealed a statistically significant improvement in both clinical and radiographic parameters, but experimental sites showed better results when compared with control. How to cite the article: Chacko NL, Abraham S, Rao HN, Sridhar N, Moon N, Barde DH. A clinical and radiographic evaluation of periodontal regenerative potential of PerioGlas®: A synthetic, resorbable material in treating periodontal infrabony defects. J Int Oral Health 2014;6(3):20-6.

An In Vitro Study on Effect of Ceramic Thickness and Multiple Firings on Colour of Metal Ceramic Restorations.

Preparation of porcelain restorations that match the natural dentition has been a subject of great concern for many years. An understanding of the process by which the colour and translucency of fixed restorations are planned and obtained so as to replicate the colour of its adjacent teeth is important for achieving an esthetic restoration. This study was done to study the effect of fabrication procedures such as ceramic thickness and number of firing cycles on the colour of metal ceramic restorations. Metal ceramic samples with three different ceramic thicknesses; 0.5, 1 and 1.5 mm (N = 30, n = 10 per group) were fabricated. A3 shade of [VMK 95, VITA Zahnfabrik, Bad Sackingen, Germany] ceramic was used for the fabrication of samples. Samples were subject to multiple firing cycles and colour was measured after 2nd, 3rd, 4th, 6th, 8th and 10th firing cycle. Colour measurement was done objectively using spectrolino (Gretag Macbeth Inc., Germany) spectrophotometer. 'Repeated measures ANOVA' test was used for doing statistical analysis. No significant change was noticed in any of the four colour parameters between the baseline reading after second firing uptil the tenth firing for any of the three groups with different ceramic thicknesses. There was a consistent rise in L* or lightness of colour as the thickness of ceramic increased. Between group I and group III there was a consistent shift of a* axis towards the blue green side and there was a consistent shift in b* axis towards purple-blue with an increase in ceramic thickness. It was observed that there was a change in ΔE with a change in ceramic thickness. There was a change of about two units between group I and group II and a change of about one unit between group II and group III. Change in ΔE between group I and group III was the most significant, being about three units. It was concluded from the study that multiple firing cycles during fabrication of metal ceramic restorations do not have any effect on colour while colour varies with change in ceramic thickness.

Prevalence and severity of periodontal disease in type 2 diabetes mellitus (non-insulin-dependent diabetes mellitus) patients in Bangalore city: An epidemiological study.

BACKGROUND: Our objective was to study the prevalence and severity of periodontal disease in type 2 diabetes mellitus (DM) patients in Bangalore city. MATERIALS AND METHODS: Four hundred and eight type 2 DM patients (Study Group) and 100 non-diabetic patients (Control Group) among the age group of 35-75 years were included in the study. The study group was divided based on Glycated hemoglobin levels into well, moderately and poorly controlled. Relevant information regarding age, oral hygiene habits and personal habits was obtained from the patients. Diabetic status and mode of anti-diabetic therapy of the study group was obtained from the hospital records with consent from the patient. Community periodontal index (CPI) was used to assess the periodontal status. The results were statistically evaluated. RESULTS: The mean CPI score and the number of missing teeth was higher in diabetics compared with non-diabetics, and was statistically significant (P=0.000), indicating that prevalence and extent of periodontal disease was more frequent and more severe in diabetic patients. The risk factors like Glycated hemoglobin, duration of diabetes, fasting blood sugar, personal habits and oral hygiene habits showed a positive correlation with periodontal destruction, whereas mode of anti-diabetic therapy showed a negative correlation according to the multiple regression analysis. The odds ratio of a diabetic showing periodontal destruction in comparison with a non-diabetic was 1.97, 2.10 and 2.42 in well, moderately and poorly controlled diabetics, respectively. CONCLUSION: Our study has made an attempt to determine the association between type 2 DM (NIDDM) and periodontal disease in Bangalore city. It was found that type 2 DM (non-insulin-dependent diabetes mellitus [NIDDM]) subjects manifested relatively higher prevalence and severity of periodontal disease as compared with non-diabetics.

Comparative study to evaluate the accuracy of polyether occlusal bite registration material and occlusal registration wax as a guide for occlusal reduction during tooth preparation.

INTRODUCTION: The use of different materials and techniques has been studied to decide the safest quantum of reduction of the occlusal surfaces. However, these methods provide limited information as to the actual amount of reduction with limitations in accuracy, accessibility and complexity. OBJECTIVE: The objective of this study was to compare and evaluate the reliability of the most commonly used occlusal registration wax that with polyether bite registration material as a guide for occlusal reduction required during tooth preparations. MATERIALS AND METHODS: For the purpose of this study, 25 abutment teeth requiring tooth preparation for fixed prosthesis were selected and tooth preparations carried out. Modeling wax strips of specific dimensions were placed onto the cast of prepared tooth, which was mounted on maximum intercuspation on the articulator and the articulator was closed. The thickness of the wax registration was measured at three zones namely two functional cusps and central fossa. Similar measurements were made using the polyether bite registration material and prosthesis at the same zones. The data was tabulated and was subjected to statistical analysis using anova test and Tukey honestly significant difference test. RESULTS: The differences in thickness between wax record and prosthesis by 0.1346 mm, whereas the difference between polyether and prosthesis was 0.02 mm with a P value of 0.042, which is statistically significant. This means that the wax record was 8.25% larger than the prosthesis while polyether was just 1.27% larger than the prosthesis. CONCLUSION: The clinical significance of the above analysis is that Ramitec polyether bite registration material is most suitable material when compared with commonly used modeling wax during the tooth preparation.

Horizontal ridge augmentation using a combination approach.

Resorption of alveolar bone - a common sequel of tooth loss jeopardizes the functional and esthetic outcome of treatment, especially in the maxillary anterior areas. Therefore, augmentation of deficient alveolar ridges is an important aspect of dental implant therapy. A case of severe maxillary ridge deficiency successfully treated with horizontal ridge augmentation to facilitate implant placement is described. Ridge augmentation was achieved using a combination of autogenous block graft, particulate grafting, and guided bone regeneration (GBR). Follow-up was done next day, after ten days, three months, and six months. Various approaches can be followed in order to achieve an increase in the ridge width. In our case, we used a combination of different techniques for ridge augmentation. A significant improvement in ridge width was noticed at six months thus facilitating the placement of implants.

Comparative susceptibility of carp fingerlings to Lernaea cyprinacea infection.

Study was conducted to find out the comparative susceptibility of fingerlings of seven species of carps (Labeo fimbriatus, L. rohita, L. calbasu, Catla catla, Ctenopharyngodon idella, Cyprinus carpio and Hypophthamichthys molitrix) grown under both mono and polyculture to Lernaea cyprinacea infection. Under monoculture, C. carpio, L. rohita and L. calbasu, did not acquire Lernaea infection and were thus considered resistant, whereas C. idella, H. molitrix, C. catla and L. fimbriatus were susceptible. Even challenge with higher infective doses of copepodids under monoculture did not result in infection in the resistant fish species. The resistance of L. rohita and C. carpio to Lernaea infection under monoculture was not sustained when these two fish species were maintained in polyculture along with susceptible fish species. Labeo calbasu, even under polyculture, however, did not acquire Lernaea infection indicating that this fish species is the most resistant and least preferred host for this parasite. Similarly, C. carpio, L. rohita and L. calbasu when grown together in polyculture and exposed to a higher infective dose (120 copepodids/fish) also did not develop the infection. The possible reasons for differences in susceptibility shown by these carp species in monoculture and the loss of resistance by rohu and common carp while in polyculture with susceptible species are discussed. The ability of resistant fish species to prevent establishment of anchor worms on them under monoculture can be utilized to control this parasitic infection commonly encountered in culture ponds.

Continued root-end growth and apexification using a calcium hydroxide and iodoform paste (Metapex®): three case reports.

AIM: The aim of these case reports is to present a treatment to promote root-end growth and apexification in nonvital immature permanent teeth in children. METHODS AND MATERIALS: Three cases were presented where the calcium hydroxide and iodoform paste Metapex® was placed in the root canals of immature permanent teeth using disposable plastic tips. The teeth involved were evaluated radiographically at regular intervals for the first 12 months after placement of the paste. At the end of 12 months all the cases showed continued root growth and apical closure (apexification) with no evidence of periapical pathology. Conventional endodontic treatment was then performed. RESULTS: In all three of the clinical cases presented, a combination of calcium hydroxide and iodoform paste (Metapex®) was used and showed promising results in inducing root-end growth and closure after 12 months. CONCLUSION: In these three clinical cases, the calcium hydroxide and iodoform paste Metapex® (Meta Biomed Co. Ltd., South Korea) was found to induce apical closure when assessed radiographically. Over a period of 12 months all the cases showed continued root growth. CLINICAL SIGNIFICANCE: The calcium hydroxide and iodoform paste Metapex® promoted continued root-end growth with apexification in the nonvital immature permanent teeth treated.

A comparative evaluation of DIAGNOdent with visual and radiography for detection of occlusal caries: an in vitro study.

BACKGROUND: The diagnosis of dental caries is fundamental to the practice of dentistry. Despite the fact that dental caries has declined considerably, it is still a problem of great importance. The reduction in caries prevalence has not occurred uniformly for all the surfaces. The greatest reduction was observed at lesions located on smooth surfaces, so that occlusal caries are most common in children. AIM: The purpose of this study is to determine the clinical efficacy of DIAGNOdent in detecting occlusal caries. MATERIALS AND METHODS: A total number of 50 teeth were subjected for visual, radiographic, and DIAGNOdent examinations. All the three methods were compared to histology which is a gold standard. RESULTS: The result obtained showed that DIAGNOdent is superior to visual and radiographic methods in diagnosing occlusal caries.