Spectroscopic and dosimetric comparison of tooth enamel separation methods for EPR retrospective dosimetry.

Precise estimation of individual radiation dose utilizing biomaterials (fingernail, bone, and tooth) is very challenging due to their complex sample processing. Despite, tooth enamel, the most mineralized tissue of tooth is used for this purpose due to its high radiation sensitivity and ability to produce radiation induced long lived CO2- radicals. However, human teeth are not always available, and invasive nature of sample collection adds to the complexity making dose estimation difficult. In such cases, animal teeth (goat, cow, and moose) can be used as a substitute for human teeth due to comparable enamel sensitivity. Moreover, separation of enamel from dentine is a crucial step towards accurate dose estimation from irradiated teeth. In this work, Indian goat teeth were used as it was readily available to us and the comparison of goat enamel sensitivity to radiation was found to be within ∼7.4 % that of human. The enamel samples were separated following two chemical methods; (1) density separation using sodium polytungstate, (2) alkaline denaturation using NaOH and the quality was compared based on their purity and radiation sensitivity. Combined results of spectroscopic characterization using X-ray diffraction (XRD), Fourier transform infrared (FTIR), and Raman analysis authenticated the crystallinity and purity of the separated enamel samples. The radiation sensitivity of separated enamel samples was compared by electron paramagnetic resonance (EPR) analysis as a part of dosimetric characterization. The suitability of both the samples for retrospective dosimetry and epidemiological studies was checked by validating the dose estimated from separated enamel samples with standard alanine/EPR dosimeter.

The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics.

BACKGROUND: Chloroplast genomes provide insufficient phylogenetic information to distinguish between closely related sugarcane cultivars, due to the recent origin of many cultivars and the conserved sequence of the chloroplast. In comparison, the mitochondrial genome of plants is much larger and more plastic and could contain increased phylogenetic signals. We assembled a consensus reference mitochondrion with Illumina TruSeq synthetic long reads and Oxford Nanopore Technologies MinION long reads. Based on this assembly we also analyzed the mitochondrial transcriptomes of sugarcane and sorghum and improved the annotation of the sugarcane mitochondrion as compared with other species. METHODS: Mitochondrial genomes were assembled from genomic read pools using a bait and assemble methodology. The mitogenome was exhaustively annotated using BLAST and transcript datasets were mapped with HISAT2 prior to analysis with the Integrated Genome Viewer. RESULTS: The sugarcane mitochondrion is comprised of two independent chromosomes, for which there is no evidence of recombination. Based on the reference assembly from the sugarcane cultivar SP80-3280 the mitogenomes of four additional cultivars (R570, LCP85-384, RB72343 and SP70-1143) were assembled (with the SP70-1143 assembly utilizing both genomic and transcriptomic data). We demonstrate that the sugarcane plastome is completely transcribed and we assembled the chloroplast genome of SP80-3280 using transcriptomic data only. Phylogenomic analysis using mitogenomes allow closely related sugarcane cultivars to be distinguished and supports the discrimination between Saccharum officinarum and Saccharum cultum as modern sugarcane's female parent. From whole chloroplast comparisons, we demonstrate that modern sugarcane arose from a limited number of Saccharum cultum female founders. Transcriptomic and spliceosomal analyses reveal that the two chromosomes of the sugarcane mitochondrion are combined at the transcript level and that splice sites occur more frequently within gene coding regions than without. We reveal one confirmed and one potential cytoplasmic male sterility (CMS) factor in the sugarcane mitochondrion, both of which are transcribed. CONCLUSION: Transcript processing in the sugarcane mitochondrion is highly complex with diverse splice events, the majority of which span the two chromosomes. PolyA baited transcripts are consistent with the use of polyadenylation for transcript degradation. For the first time we annotate two CMS factors within the sugarcane mitochondrion and demonstrate that sugarcane possesses all the molecular machinery required for CMS and rescue. A mechanism of cross-chromosomal splicing based on guide RNAs is proposed. We also demonstrate that mitogenomes can be used to perform phylogenomic studies on sugarcane cultivars.

Whole chloroplast genome and gene locus phylogenies reveal the taxonomic placement and relationship of Tripidium (Panicoideae: Andropogoneae) to sugarcane.

BACKGROUND: For over 50 years, attempts have been made to introgress agronomically useful traits from Erianthus sect. Ripidium (Tripidium) species into sugarcane based on both genera being part of the 'Saccharum Complex', an interbreeding group of species believed to be involved in the origins of sugarcane. However, recent low copy number gene studies indicate that Tripidium and Saccharum are more divergent than previously thought. The extent of genus Tripidium has not been fully explored and many species that should be included in Tripidium are still classified as Saccharum. Moreover, Tripidium is currently defined as incertae sedis within the Andropogoneae, though it has been suggested that members of this genus are related to the Germainiinae. RESULTS: Eight newly-sequenced chloroplasts from potential Tripidium species were combined in a phylogenetic study with 46 members of the Panicoideae, including seven Saccharum accessions, two Miscanthidium and three Miscanthus species. A robust chloroplast phylogeny was generated and comparison with a gene locus phylogeny clearly places a monophyletic Tripidium clade outside the bounds of the Saccharinae. A key to the currently identified Tripidium species is presented. CONCLUSION: For the first time, we have undertaken a large-scale whole plastid study of eight newly assembled Tripidium accessions and a gene locus study of five Tripidium accessions. Our findings show that Tripidium and Saccharum are 8 million years divergent, last sharing a common ancestor 12 million years ago. We demonstrate that four species should be removed from Saccharum/Erianthus and included in genus Tripidium. In a genome context, we show that Tripidium evolved from a common ancestor with and extended Germainiinae clade formed from Germainia, Eriochrysis, Apocopis, Pogonatherum and Imperata. We re-define the 'Saccharum complex' to a group of genera that can interbreed in the wild and extend the Saccharinae to include Sarga along with Sorghastrum, Microstegium vimineum and Polytrias (but excluding Sorghum). Monophyly of genus Tripidium is confirmed and the genus is expanded to include Tripidium arundinaceum, Tripidium procerum, Tripidium kanashiroi and Tripidium rufipilum. As a consequence, these species are excluded from genus Saccharum. Moreover, we demonstrate that genus Tripidium is distinct from the Germainiinae.

A novel approach for intra-operative shape acquisition of the tibio-femoral joints using 3D laser scanning in computer assisted orthopaedic surgery.

BACKGROUND: Image registration (IR) is an important process of developing a spatial relationship between pre-operative data and the physical patient in the operation theatre. Current IR techniques for Computer Assisted Orthopaedic Surgery (CAOS) are time consuming and costly. There is a need to automate and accelerate this process. METHODS: Bespoke quick, cost effective, contactless and automated 3D laser scanning techniques based on the DAVID Laserscanner method were designed. 10 cadaveric knee joints were intra-operatively laser scanned and were registered with the pre-operative MRI scans. The results are supported with a concurrent validity study. RESULTS: The average absolute errors between scan models were systematically less than 1 mm. Errors on femoral surfaces were higher than tibial surfaces (P<0.05). Additionally, scans acquired through the large exposure produced higher errors than the smaller exposure (P<0.05). CONCLUSION: This study has provided proof of concept for a novel automated shape acquisition and registration technique for CAOS.

Herbicide targets and detoxification proteins in sugarcane: from gene assembly to structure modelling.

In a genome context, sugarcane is a classic orphan crop, in that no genome and only very few genes have been assembled. We have devised a novel exome assembly methodology that has allowed us to assemble and characterize 49 genes that serve as herbicide targets, safener interacting proteins, and members of herbicide detoxification pathways within the sugarcane genome. We have structurally modelled the products of each of these genes, as well as determining allelic, genomic, and RNA-Seq based polymorphisms for each gene. This study provides the largest collection of sugarcane structures modelled to date. We demonstrate that sugarcane genes are highly polymorphic, revealing that each genotype is evolving both uniquely and independently. In addition, we present an exome assembly system for orphan crops that can be executed on commodity infrastructure, making exome assembly practical for any group. In terms of knowledge about herbicide modes of action and detoxification, we have advanced sugarcane from a crop where no information about any herbicide-associated gene was available to the situation where sugarcane is now a species with the single largest collection of known and annotated herbicide-associated genes.

Role of oxygen functional groups in reduced graphene oxide for lubrication.

Functionalized and fully characterized graphene-based lubricant additives are potential 2D materials for energy-efficient tribological applications in machine elements, especially at macroscopic contacts. Two different reduced graphene oxide (rGO) derivatives, terminated by hydroxyl and epoxy-hydroxyl groups, were prepared and blended with two different molecular weights of polyethylene glycol (PEG) for tribological investigation. Epoxy-hydroxyl-terminated rGO dispersed in PEG showed significantly smaller values of the friction coefficient. In this condition, PEG chains intercalate between the functionalized graphene sheets, and shear can take place between the PEG and rGO sheets. However, the friction coefficient was unaffected when hydroxyl-terminated rGO was coupled with PEG. This can be explained by the strong coupling between graphene sheets through hydroxyl units, causing the interaction of PEG with the rGO to be non- effective for lubrication. On the other hand, antiwear properties of hydroxyl-terminated rGO were significantly enhanced compared to epoxy-hydroxyl functionalized rGO due to the integrity of graphene sheet clusters.

Electrospun cellulose acetate phthalate nanofibrous scaffolds fabricated using novel solvent combinations biocompatible for primary chondrocytes and neurons.

Electrospun nanofibres have been shown to exhibit extracellular matrix (ECM)-like characteristics required for tissue engineering in terms of porosity, flexibility, fibre organization and strength. This study focuses on developing novel cellulose acetate phthalate (CAP) scaffolds by electrospinning for establishing 3-D chondrocyte and neuronal cultures. Five solvent combinations were employed in fabricating the fibres, namely, acetone/ethanol (9:1), dimethylformamide/tetrahydrofuran/acetone (3:3:4), tetrahydrofuran/acetone (1:1), tetrahydrofuran/ethanol (1:1) and chloroform/methanol (1:1). The electrospun fibres were characterized by scanning electron microscopy (SEM) analysis and confirmed to be within the nanometre range. Based on the morphology of the fibers from SEM results, two solvent combinations such as acetone/ethanol and dimethylformamide/tetrahydrofuran/acetone were selected for stabilization as CAP exhibits a pH dependent solubility. Fourier-Transform Infrared (FTIR) analysis revealed the hydrolysis of CAP which was overcome by EDC [1-ethyl-3-(3-dimethylaminopropyl) carbodiimide] and EDC/NHS (N-hydroxysuccinimide) cross-linking resulting in its stability (pH of 7.2) for three months. MTT [3-(4, 5-dimethylthiazol-2-yl)-1, 5-diphenyltetrazolium bromide] assay performed using L6 myoblast confirmed the biocompatibility of the scaffolds. 3-D primary chondrocyte and neuronal cultures were established on the scaffolds and maintained for a period of 10 days. H&E staining and SEM analysis showed the attachment of the chondrocytes and neurons on CAP scaffolds prepared using dimethylformamide/tetrahydrofuran/acetone and acetone/ethanol respectively.

Elucidating modes of activation and herbicide resistance by sequence assembly and molecular modelling of the Acetolactate synthase complex in sugarcane.

Acetolactate synthase (ALS) catalyzes the first portion of the biosynthetic pathway leading to the generation of branched-chain amino acids. As such it is essential for plant health and is a major target for herbicides. ALS is a very poorly characterized molecule in sugarcane. The enzyme is activated and inhibited by a regulatory subunit (known as VAT1 in plants) whose mode of action is entirely unknown. Using Saccharum halepense as a template we have assembled the ALS gene of sugarcane (Saccharum hybrid) and have modelled the structure of ALS based on an Arabidopsis template (the first ALS model for a monocot). We have also assembled the ALS regulatory proteins (VAT1 and VAT2) from sugarcane and show that VAT2 is specific to true grasses. Employing a bacterial model, we have generated a structural model for VAT1, which explains why the separate domains of the proteins bind to either leucine or valine but not both. Using co-evolution studies we have determined molecular contacts by which we modelled the docking of VAT1 to ALS. In conclusion, we demonstrate how the binding of VAT1 to ALS activates ALS and show how VAT1 can also confer feedback inhibition to ALS. We validate our ALS model against biochemical data and employ this model to explain the function of a novel herbicide binding mutant in sugarcane.

Vitamin D Supplementation in Adults with Vitamin D Deficiency and Its Effect on Metabolic Syndrome - A Randomized Controlled Study.

BACKGROUND: Inverse relationship between metabolic syndrome (MetS) and 25-hydroxyvitamin D (25(OH) D) levels is controversial. Hypovitaminosis-D has long been suspected as a risk factor for glucose intolerance. AIM: A randomized double blind placebo controlled study to evaluate effects of vitamin D supplementation on insulin resistance in subjects with hypovitaminosis-D and MetS. MATERIALS AND METHODS: Subjects were randomized to receive either oral 25(OH) D3 supplement (60000 (IU) per week for 8 weeks followed by 60,000 IU monthly for 4 months) or a placebo for six months. The parameters measured were blood pressure, vitamin D, fasting blood sugar (FBS), insulin, homeostasis model assessment (HOMA), quantitative insulin sensitivity check index (QUICKI), body mass index (BMI), and waist circumference (WC). RESULTS: There were no significant changes in parameters of vitamin-D group compared to placebo group except serum vitamin-D was significantly increased in vitamin-D group (p < 0.0001). In vitamin-D group, mean WC at baseline was 95.9 ± 6.66, which significantly changed to 94.6 ± 7.47 (p = 0.001). Mean BMI at baseline was 29.1 ± 4.06 which significantly changed to 28.5 ± 4.16 (p = 0.001). The mean vitamin-D concentration at baseline was 15.4 ± 9.03 which significantly (p < .0001) increased to 26.1 ± 11.8. In placebo group mean insulin levels was 10.7 ± 4.81IU / L which increased significantly (p = 0.03) to 15.4 ± 14.0. Mean QUICKI at baseline was 0.34 ± 0.03 which decreased significantly (p = 0.02) to 0.32 ± 0.03. CONCLUSION: In this study the relationship between vitamin D supplementation and MetS or IR was not established. Whether achieving vitamin D sufficiency in large population-based trials with a longer duration would produce more favorable results needs to be assessed.

A mechanical model of the cornea considering the crimping morphology of collagen fibrils.

PURPOSE: To develop a mechanical model with which to investigate the relationship between the crimping morphology of collagen fibrils and the nonlinear mechanical behavior of the cornea. METHODS: Uniaxial tensile experiments were performed with corneal strips to test their mechanical behavior. A constitutive model was constructed based on the Gaussian-distributed morphology of crimped collagen fibrils. The parameters that represent the micro characteristics of collagen fibrils were determined by fitting the experimental data to the constitutive model. Transmission electron microscopy (TEM) was used to visualize the crimping morphology of collagen fibrils in the stroma. A quantitative analysis of fibril crimping degrees in the TEM images was conducted to test the parameters predicted by the constitutive model. RESULTS: The parameters were derived using a fitting method that included the expectation for the distribution of fibril crimping degrees, µ = 1.063; the standard deviation, σ = 0.0781; the elastic modulus of collagen fibrils, E = 52.74 MPa; and the fibril ultimate strain, εb = 0.1957. TEM images showed a variation of the fibril crimping morphology when the cornea was subjected to different tensile loads. A good agreement was found between the parameters derived by the constitutive model and the data quantified from the TEM images. CONCLUSIONS: The nonlinear mechanical behavior of the cornea is closely correlated with the crimping morphology of collagen fibrils. The findings are expected to guide further research of corneal pathologies related to the abnormal microstructure of collagen fibrils.

Quantitative analysis of sodium carbonate and sodium bicarbonate in solid mixtures using Fourier transform infrared spectroscopy (FT-IR).

An analytical methodology is proposed based on constant ratio and absorbance correction methods to quantify sodium carbonate, Na2CO3 (1450 cm⁻¹), and sodium bicarbonate, NaHCO3 (1000 cm⁻¹, 1923 cm⁻¹), in solid mixtures using Fourier transform infrared (FT-IR) spectroscopy. Potassium ferricyanide, K3Fe(CN)6 (2117cm⁻¹), was used as an internal standard to get characteristic parameters. NaHCO3 was quantified using the constant ratio method. Spectral interference of NaHCO3 in Na2CO3 (1450 cm⁻¹) was corrected using the absorbance correction method. The corrected absorbance was successfully applied to quantify Na2CO3 (1450 cm⁻¹) in the mixture using the constant ratio method. The results obtained for simulated samples were satisfactory (relative standard deviation less than 7%) for all samples.