Draft genome sequence of Sclerospora graminicola, the pearl millet downy mildew pathogen:Genome sequence of pearl millet downy mildew pathogen

Sclerospora graminicola pathogen is one of the most important biotic production constraints of pearl millet worldwide. We report a de novo whole genome assembly and analysis of pathotype 1. The draft genome assembly contained 299,901,251 bp with 65,404 genes. Pearl millet [Pennisetum glaucum (L.) R. Br.], is an important crop of the semi-arid and arid regions of the world. It is capable of growing in harsh and marginal environments with highest degree of tolerance to drought and heat among cereals (1). Downy mildew is the most devastating disease of pearl millet caused by Sclerospora graminicola (sacc. Schroet), particularly on genetically uniform hybrids. Estimated annual grain yield loss due to downy mildew is approximately 10?80 % (2-7). Pathotype 1 has been reported to be the highly virulent pathotype of Sclerospora graminicola in India (8). We report a de novo whole genome assembly and analysis of Sclerospora graminicola pathotype 1 from India. A susceptible pearl millet genotype Tift 23D2B1P1-P5 was used for obtaining single-zoospore isolates from the original oosporic sample. The library for whole genome sequencing was prepared according to the instructions by NEB ultra DNA library kit for Illumina (New England Biolabs, USA). The libraries were normalised, pooled and sequenced on Illumina HiSeq 2500 (Illumina Inc., San Diego, CA, USA) platform at 2 x100 bp length. Mate pair (MP) libraries were prepared using the Nextera mate pair library preparation kit (Illumina Inc., USA). 1 ?g of Genomic DNA was subject to tagmentation and was followed by strand displacement. Size selection tagmented/strand displaced DNA was carried out using AmpureXP beads. The libraries were validated using an Agilent Bioanalyser using DNA HS chip. The libraries were normalised, pooled and sequenced on Illumina MiSeq (Illumina Inc., USA) platform at 2 x300 bp length. The whole genome sequencing was performed by sequencing of 7.38 Gb with 73,889,924 paired end reads from paired end library, and 1.15 Gb with 3,851,788 reads from mate pair library generated from Illumina HiSeq2500 and Illumina MiSeq, respectively. The sequences were assembled using various assemblers like ABySS, MaSuRCA, Velvet, SOAPdenovo2, and ALLPATHS-LG. The assembly generated by MaSuRCA (9) algorithm was observed superior over other algorithms and hence used for scaffolding using SSPACE. Assembled draft genome sequence of S. graminicola pathotype 1 was 299,901,251 bp long, with a 47.2 % GC content consisting of 26,786 scaffolds with N50 of 17,909 bp with longest scaffold size of 238,843 bp. The overall coverage was 40X. The draft genome sequence was used for gene prediction using AUGUSTUS. The completeness of the assembly was investigated using CEGMA and revealed 92.74% proteins completely present and 95.56% proteins partially present, while BUSCO fungal dataset indicated 64.9% complete, 12.4% fragmented, 22.7% missing out of 290 BUSCO groups. A total of 52,285 predicted genes were annotated using BLASTX and 38,120 genes were observed with significant BLASTX match. Repetitive element analysis in the assembly revealed 8,196 simple repeats, 1,058 low complexity repeats and 5,562 dinucleotide to hexanucleotide microsatellite repeats.publishersversionPeer reviewe

Dysregulated miRNAome and Proteome of PPRV Infected Goat PBMCs Reveal a Coordinated Immune Response

In this study, the miRNAome and proteome of virulent Peste des petits ruminants virus (PPRV) infected goat peripheral blood mononuclear cells (PBMCs) were analyzed. The identified differentially expressed miRNAs (DEmiRNAs) were found to govern genes that modulate immune response based on the proteome data. The top 10 significantly enriched immune response processes were found to be governed by 98 genes. The top 10 DEmiRNAs governing these 98 genes were identified based on the number of genes governed by them. Out of these 10 DEmiRNAs, 7 were upregulated, and 3 were downregulated. These include miR-664, miR-2311, miR-2897, miR-484, miR-2440, miR-3533, miR-574, miR-210, miR-21-5p, and miR-30. miR-664 and miR-484 with proviral and antiviral activities, respectively, were upregulated in PPRV infected PBMCs. miR-210 that inhibits apoptosis was downregulated. miR-21-5p that decreases the sensitivity of cells to the antiviral activity of IFNs and miR-30b that inhibits antigen processing and presentation by primary macrophages were downregulated, indicative of a strong host response to PPRV infection. miR-21-5p was found to be inhibited on IPA upstream regulatory analysis of RNA-sequencing data. This miRNA that was also highly downregulated and was found to govern 16 immune response genes in the proteome data was selected for functional validation vis-a-vis TGFBR2 (TGF-beta receptor type-2). TGFBR2 that regulates cell differentiation and is involved in several immune response pathways was found to be governed by most of the identified immune modulating DEmiRNAs. The decreased luciferase activity in Dual Luciferase Reporter Assay indicated specific binding of miR-21-5p and miR-484 to their target thus establishing specific binding of the miRNAs to their targets.This is the first report on the miRNAome and proteome of virulent PPRV infected goat PBMCs

Impact of delayed prosthetic treatment of velopharyngeal insufficiency on quality of life

Palatopharyngeal dysfunction may take place when palatopharyngeal valve is unable to perform its own closing due to a lack of tissue (palatopharyngeal insufficiency) or lack of proper movement (palatopharyngeal incompetence). Palatopharyngeal insufficiency induces nasal regurgitation of liquids, hypernasal speech, nasal escape, disarticulations and impaired speech intelligibility. Prosthetic management of palatopharyngeal insufficiency requires a close co-operation between an otolaryngologist and a speech pathologist. As a result, the patient can be socially and physically rehabilitated with the improved speech quality as well as prevention of leakage of liquids

The art of managing various ocular defects in different clinical scenarios: A case series

The absence of eye and irradiation post-enucleation may result in problems like dryness of the eye sockets, itching and crusting. This may lead to poor prosthesis adaptation and a lack of patient acceptance of the prosthesis. To combat the most common problem of dryness, patients are advised artificial tears to use as teardrops or ocular prostheses along with a tear reservoir. This case series describes methods of fabricating ocular prosthesis indicated in different scenarios: the modified stock ocular and a custom-made ocular prosthesis when tearing secretion is enough in the eye socket and an ocular prosthesis with a tear reservoir in cases showing reduced tear secretion. A novel technique of fabricating hollow lightweight ocular prostheses having the sustained prolonged release of artificial tears has been described

Quantitative analysis of leaching of different metals in human saliva from dental casting alloys: An in vivo study

Background: The issue of biomaterial-derived ionic release in various sites of the human body has attracted the interest of many investigators because of the possibility that debris or degradation products elicit a foreign body reaction or have a role in the induction of pathological processes. Purpose: The purpose was to evaluate the saliva of denture wearers after insertion of the prosthesis for leaching of metals from metallic denture. Materials and Methods: Total 20 subjects of age group of 40-60 years including both males (10) and females (10) were selected for the study. Total subjects were divided into 2 groups each containing 10 subjects, Group I (control group): Subjects having dentition intact up to second molar and free of any dental restoration; Group II (study group): Partially edentulous subjects rehabilitated with cast-metal removable partial denture. Saliva samples were taken at three stages that is, 1 h, 24 h and 72 h after the denture insertion from subjects of study group as well as from the control group. Atomic absorption spectroscopy (AAS) was used to estimate the concentration of elemental ions. Obtained data′s were analyzed using SPSS (Statistical Package for Social Sciences) version 15.0 statistical analysis software. The values were represented in a number (%) and mean ± standard deviation. Results: At 1 h, 24 h and 72 h after the denture insertion in study group, chromium (Cr) had statistically significant higher mean concentration as compared to manganese (Mn) (P < 0.001). Cr had maximum concentration (0.1479 + 0.0052) immediately after denture insertion while maximum concentration of Mn (0.1479 + 0.0052) was found 24 h after denture insertion. Conclusion: Metal-based dentures show maximum leaching immediately after wearing of the prosthesis which decreased significantly over the period of 3 days. Cr and Mn were the metal ions mainly found in saliva of cast partial denture wearer. No concentration of cobalt, molybdenum (Mo) and iron (Fe) was found in saliva of metal base denture wearer. There was a significant change in concentration of elutes in saliva in first 72 h/3 days making time an effective variable was observed

Implant-assisted removable partial denture: An approach to switch Kennedy Class I to Kennedy Class III

The Kennedy Class I and II distal extension situation poses a challenge to the prosthodontist as it inherently possesses a lack of stability, which may be attributed to the difference in compressibility of the mucosa and the periodontal ligament surrounding the distal-most abutment tooth. This results in a rotational tendency of the prosthesis around the line connecting its terminal abutments. Placement of osseointegrated dental implants in the posterior edentulous regions, distal to the terminal abutment provides improved vertical support to the distal extension removable partial denture, effectively converting its intraoral performance from a Kennedy Class I to a Class III situation, thereby resulting in improved stability of the prosthesis and consequently, enhanced patient satisfaction. This case report describes such an approach to the restoration of a Kennedy Class I partially edentulous situation

Comparative sequence analysis of morbillivirus receptors and its implication in host range expansion

SLAM (CD150) and nectin-4 are the major morbillivirus receptors responsible for virus pathogenesis and host range expansion. Recently, morbillivirus infections have been reported in unnatural hosts, including endangered species, posing a threat to their conservation. To understand the host range expansion of morbilliviruses, we generated the full-length sequences of morbillivirus receptors (goat, sheep, and dog SLAM, and goat nectin-4) and tried to correlate their role in determining host tropism. A high level of amino acid identity was observed between the sequences of related species, and phylogenetic reconstruction showed that the receptor sequences of carnivores, marine mammals, and small ruminants grouped separately. Analysis of the ligand binding region (V region; amino acid residues 52–136) of SLAM revealed high amino acid identity between small ruminants and bovine SLAMs. Comparison of canine SLAM with ruminants and non-canids SLAM revealed appreciable changes, including charge alterations. Significant differences between feline SLAM and canine SLAM have been reported. The binding motifs of nectin-4 genes (FPAG motif and amino acid residues 60, 62, and 63) were found to be conserved in sheep, goat, and dog. The differences reported in the binding region may be responsible for the level of susceptibility or resistance of a species to a particular morbillivirus.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author