Performance of Multiple Metagenomics Pipelines in Understanding Microbial Diversity of a Low-Biomass Spacecraft Assembly Facility

NASA planetary protection (PP) requires an assessment of the biological contamination of the potential microbial burden on spacecraft destined to explore planetary bodies that may harbor signs of life, like Mars and Europa. To help meet these goals, the performance of multiple metagenomic pipelines were compared and assessed for their ability to detect microbial diversity of a low-biomass clean room environment used to build spacecraft destined to these planetary bodies. Four vendors were chosen to implement their own metagenomic analysis pipeline on the shotgun sequences retrieved from environmental surfaces in the relevant environments at NASA's Jet Propulsion Laboratory. None of the vendors showed the same microbial profile patterns when analyzing same raw dataset since each vendor used different pipelines, which begs the question of the validity of a single pipeline to be recommended for future NASA missions. All four vendors detected species of interest, including spore-forming and extremotolerant bacteria, that have the potential to hitch-hike on spacecraft and contaminate the planetary bodies explored. Some vendors demonstrated through functional analysis of the metagenomes that the molecular mechanisms for spore-formation and extremotolerance were represented in the data. However, relative abundances of these microorganisms varied drastically between vendor analyses, questioning the ability of these pipelines to quantify the number of PP-relevant microorganisms on a spacecraft surface. Metagenomics offers tantalizing access to the genetic and functional potential of a microbial community that may offer NASA a viable method for microbial burden assays for planetary protection purposes. However, future development of technologies such as streamlining the processing of shotgun metagenome sequence data, long read sequencing, and all-inclusive larger curated and annotated microbial genome databases will be required to validate and translate relative abundances into an actionable assessment of PP-related microbes of interest. Additionally, the future development of machine learning and artificial intelligence techniques could help enhance the quality of these metagenomic analyses by providing more accurate identification of the genetic and functional potential of a microbial community.

Characterization of Spacesuit Associated Microbial Communities and Their Implications for NASA Missions

BACKGROUND

Crewed National Aeronautics and Space Administration (NASA) missions to other solar system bodies are currently being planned. One high-profile scientific focus during such expeditions would be life detection, specifically the discovery of past or present microbial life, if they exist. However, both humans and associated objects typically carry a high microbial burden. Thus, it is essential to distinguish between microbes brought with the expedition and those present on the exploring planets. Modern spacesuits are unique, customized spacecraft which provide protection, mobility and life support to crew during spacewalks, yet they vent, and the mobility of microbes through spacesuits has not been studied.

RESULTS

To evaluate the microbial colonization of spacesuits, NASA used an Extravehicular Activity swab kit to examine viable microbial populations of 48 samples from spacesuits using both traditional microbiological methods and molecular sequencing methods. The cultivable microbial population ranged from below the detection limit to 9 × 102 colony forming units per 25 cm2 of sample and also significantly varied by the location. The cultivable microbial diversity was dominated by members of Bacillus, Arthrobacter, and Ascomycota. However, 16S rRNA-based viable bacterial burden ranged from 105 to 106 copies per 25 cm2 of sample. Shotgun metagenome sequencing revealed the presence of a diverse microbial population on the spacesuit surfaces, including Curtobacterium and Methylobacterium from across all sets of spacesuits in high abundance. Among bacterial species identified, higher abundance of Cutibacterium acnes, Methylobacterium oryzae, and M. phyllosphaerae reads were documented.

CONCLUSION

The results of this study provide evidence that identical microbial strains may live on the wrist joint, inner gauntlet, and outer gauntlet of spacesuits. This raises the possibility, but does not confirm that microbial contaminants on the outside of the suits could contaminate planetary science operations unless additional measures are taken. Overall, these data provide the first estimate of microbial distribution associated with spacesuit surfaces, which will help future mission planners develop effective planetary protection strategies.

Comparative transcriptome analyses revealed different heat stress responses in pigeonpea (Cajanus cajan) and its crop wild relatives

Comparative transcriptome analyses accompanied by biochemical assays revealed high variability in heat stress response in Cajanus species. Among the studied species, C. scarabaeoides was the most thermotolerant followed by C. cajanifolius, C. cajan, and C. acutifolius. Pigeonpea is one of the climate-resilient grain legumes. Though the optimum temperature for cultivated pigeonpea is ~ 25-35 °C, its wild relatives grow in temperatures ranging between 18 and 45 °C. To gain insight into molecular mechanisms responsible for the heat stress tolerance in pigeonpea, we conducted time-series transcriptome analysis of one pigeonpea cultivar (Cajanus cajan) and two wild relatives, Cajanus acutifolius, and Cajanus scarabaeoides subjected to heat stress at 42 ± 2 ºC for 30 min and 3 h. A total of 9521, 12,447, and 5282 identified transcripts were differentially expressed in C. cajan, C. acutifolius, and C. scarabaeoides, respectively. In this study, we observed that a significant number of genes undergo alternative splicing in a species-specific pattern during heat stress. Gene expression profiling analysis, histochemical assay, chlorophyll content, and electrolyte leakage assay showed that C. scarabaeoides has adaptive features for heat stress tolerance. The gene set enrichment analyses of differentially expressed genes in these Cajanus species during heat stress revealed that oxidoreductase activity, transcription factor activity, oxygen-evolving complex, photosystem-II, thylakoid, phenylpropanoid biosynthetic process, secondary metabolic process, and flavonoid biosynthetic process were highly affected. The histochemical assay showed more lipid peroxidation in C. acutifolius compared to other Cajanus species inferring the presence of higher quantities of polyunsaturated fatty acids in the plasma membrane which might have led to severe damage of membrane-bound organelles like chloroplast, and high electrolyte leakage during heat stress. This study paves the way for the identification of candidate genes, which can be useful for the development of thermo-tolerant pigeonpea cultivars.

Methylobacterium ajmalii sp. nov., Isolated From the International Space Station

Four strains belonging to the family of Methylobacteriaceae were isolated from different locations on the International Space Station (ISS) across two consecutive flights. Of these, three were identified as Gram-negative, rod-shaped, catalase-positive, oxidase-positive, motile bacteria, designated as IF7SW-B2^T, IIF1SW-B5, and IIF4SW-B5, whereas the fourth was identified as Methylorubrum rhodesianum. The sequence similarity of these three ISS strains, designated as IF7SW-B2^T, IIF1SW-B5, and IIF4SW-B5, was <99.4% for 16S rRNA genes and <97.3% for gyrB gene, with the closest being Methylobacterium indicum SE2.11^T. Furthermore, the multi-locus sequence analysis placed these three ISS strains in the same clade of M. indicum. The average nucleotide identity (ANI) values of these three ISS strains were <93% and digital DNA-DNA hybridization (dDDH) values were <46.4% with any described Methylobacterium species. Based on the ANI and dDDH analyses, these three ISS strains were considered as novel species belonging to the genus Methylobacterium. The three ISS strains showed 100% ANI similarity and dDDH values with each other, indicating that these three ISS strains, isolated during various flights and from different locations, belong to the same species. These three ISS strains were found to grow optimally at temperatures from 25 to 30°C, pH 6.0 to 8.0, and NaCl 0 to 1%. Phenotypically, these three ISS strains resemble M. aquaticum and M. terrae since they assimilate similar sugars as sole carbon substrate when compared to other Methylobacterium species. Fatty acid analysis showed that the major fatty acid produced by the ISS strains are C_18:1−ω7c and C_18:1−ω6c. The predominant quinone was ubiquinone 10, and the major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, and an unidentified lipid. Therefore, based on genomic, phylogenetic, biochemical, and fatty acid analyses, strains IF7SW-B2^T, IIF1SW-B5, and IIF4SW-B5, are assigned to a novel species within the genus Methylobacterium, and the name Methylobacterium ajmalii sp. nov. is proposed. The type strain is IF7SW-B2^T (NRRL B-65601^T and LMG 32165^T).

Assessment of Remineralization Capacity of Various Remineralizing Agents on Artificial Enamel Lesions Using Confocal Laser Scanning Microscope: An In Vitro Study

AIM AND OBJECTIVE

The present study aimed at evaluating the effectiveness of diverse remineralizing agents on artificial enamel lesion using confocal laser scanning microscope (CLSM).

MATERIALS AND METHODS

Totally 80 mandibular premolars which were single rooted were included. All teeth were suspended in a demineralizing solution to create artificial enamel lesions on the exposed enamel. The samples were separated randomly into four groups (20 each) depending on the application of the remineralizing agents as follows: group 1: control; group 2: calcium sucrose phosphate (CaSP); group 3: fluoride varnish; and group 4: casein phosphopeptides-amorphous calcium phosphate (CPP-ACP). The samples in individual group were treated with the corresponding remineralizing agent (except for the control group) two times a day for 14 days. The experimental and control groups were exposed to CLSM assessment to analyze the data of remineralization and demineralization.

RESULTS

The mean depth of remineralization of fluoride varnish group was slightly more compared to other groups. The highest mean depth of remineralization was found in the fluoride varnish group (122.26 ± 0.28) followed by CaSP (110.58 ± 1.34), CPP-ACP (107.08 ± 0.48), and control (157.78 ± 0.46) groups. The different comparisons among the remineralization material groups showed a statistically significant difference (p < 0.05) in almost all groups except group 2 vs group 4.

CONCLUSION

This study concluded that improved remineralization of artificial enamel lesion could be achieved with the fluoride varnish group when compared to the CaSP and CPP-ACP groups.

CLINICAL SIGNIFICANCE

Remineralization as a treatment technique has received a lot of consideration from clinicians. The process of remineralization and demineralization is considered an active process categorized by the movement of calcium and phosphate in and out of the enamel. Presently, the attention has changed toward increasing the resistance of the tooth by applying remineralizing agents topically, which has led to the notable fall in dental caries.

Structural insight of two 4-Coumarate CoA ligase (4CL) isoforms in Leucaena suggests targeted genetic manipulations could lead to better lignin extractability from the pulp

4-Coumarate: coenzyme A ligase (4CL) is a key enzyme involved in the early steps of the monolignol biosynthetic pathway. It is hypothesized to modulate S and G monolignol content in the plant. Lignin removal is imperative to the paper industry and higher S/G ratio governs better extractability of lignin and economics of the pulping process. This background prompted us to predict 3D structure of two isoforms of 4CL in Leucaena leucocephala and evaluate their substrate preferences. The 3D structure of Ll4CL1 and Ll4CL2 protein were created by homology modeling and further refined by loop refinement. Molecular docking studies suggested differential substrate preferences of both the isoforms. Ll4CL1 preferred sinapic acid (- 4.91 kcal/mole), ferulic acid (- 4.84 kcal/mole), hydroxyferulic acid (- 4.72 kcal/mole), and caffeic acid (- 4.71 kcal/mole), in their decreasing order. Similarly, Ll4CL2 preferred caffeic acid (- 6.56 kcal/mole, 4 H bonds), hydroxyferulic acid (- 6.56 kcal/mole, 3 H bonds), and ferulic acid (- 6.32 kcal/mole) and sinapic acid (- 5.00 kcal/mole) in their decreasing order. Further, active site residues were identified in both the isoforms and in silico mutation and docking analysis was performed. Our analysis suggested that ASP228, TYR262, and PRO326 for Ll4CL1 and SER165, LYS247 and PRO315 for Ll4CL2 were important for their functional activity. Based on differential substrate preferences of the two isoforms, as a first step towards genetically modified Leuaena having the desired phenotype, it can be proposed that over-expression of Ll4CL1 gene and/or down-regulation of Ll4CL2 gene could yield higher S/G ratio leading to better extractability of lignin.

Validating an Automated Nucleic Acid Extraction Device for Omics in Space Using Whole Cell Microbial Reference Standards

NASA has made great strides in the past five years to develop a suite of instruments for the International Space Station in order to perform molecular biology in space. However, a key piece of equipment that has been lacking is an instrument that can extract nucleic acids from an array of complex human and environmental samples. The Omics in Space team has developed the μTitan (simulated micro(μ) gravity tested instrument for automated nucleic acid) system capable of automated, streamlined, nucleic acid extraction that is adapted for use under microgravity. The μTitan system was validated using a whole cell microbial reference (WCMR) standard comprised of a suspension of nine bacterial strains, titrated to concentrations that would challenge the performance of the instrument, as well as to determine the detection limits for isolating DNA. Quantitative assessment of system performance was measured by comparing instrument input challenge dose vs recovery by Qubit spectrofluorometry, qPCR, Bioanalyzer, and Next Generation Sequencing. Overall, results indicate that the μTitan system performs equal to or greater than a similar commercially available, earth-based, automated nucleic acid extraction device. The μTitan system was also tested in Yellowstone National Park (YNP) with the WCMR, to mimic a remote setting, with limited resources. The performance of the device at YNP was comparable to that in a laboratory setting. Such a portable, field-deployable, nucleic extraction system will be valuable for environmental microbiology, as well as in health care diagnostics.

Description of Chloramphenicol Resistant Kineococcus rubinsiae sp. nov. Isolated From a Spacecraft Assembly Facility

A Gram-positive, coccoid, motile, aerobic bacterium, designated strain B12T was isolated from a Jet Propulsion Laboratory spacecraft assembly cleanroom, Pasadena, CA, United States. Strain B12T was resistant to chloramphenicol (100 μg/mL), and is a relatively slow grower (3-5 days optimal). Strain B12T was found to grow optimally at 28 to 32°C, pH 7 to 8, and 0.5% NaCl. Fatty acid methyl ester analysis showed that the major fatty acid of the strain B12T was anteiso C15 : 0 (66.3%), which is also produced by other Kineococcus species. However, arachidonic acid (C20 : 4 ω6,9,12,16c) was present in strain B12T and Kineococcus glutinatus YIM 75677T but absent in all other Kineococcus species. 16S rRNA analysis revealed that strain B12T was 97.9% similar to Kineococcus radiotolerans and falls within the Kineococcus clade. Low 16S rRNA gene sequence similarities (<94%) with other genera in the family Kineosporiaceae, including Angustibacter (93%), Kineosporia (94% to 95%), Pseudokineococcus (93%), Quadrisphaera (93%), and Thalassiella (94%) demonstrated that the strain B12T does not belong to these genera. Phylogenetic analysis of the gyrB gene show that all known Kineococcus species exhibited <86% sequence similarity with B12T. Multi-locus sequence and whole genome sequence analyses confirmed that B12T clades with other Kineococcus species. Average nucleotide identity of strain B12T were 75-78% with other Kineococcus species, while values ranged from 72-75% with species from other genera within family Kineosporiaceae. Average amino-acid identities were 66-72% with other Kineococcus species, while they ranged from 50-58% with species from other genera. The dDDH comparison of strain B12T genome with members of genera Kineococcus showed 20-22% similarity, again demonstrating that B12T is distantly related to other members of the genus. Furthermore, analysis of whole proteome deduced from WGS places strain B12T in order Kineosporiales, confirming that strain B12T is a novel member of family Kineosporiaceae. Based on these analyses and other genome characteristics, strain B12T is assigned to a novel species within the genus Kineococcus, and the name Kineococcus rubinsiae sp. nov., is proposed. The type strain is B12T (=FJII-L1-CM-PAB2T; NRRL B-65556T, DSM 110506T).

A Bayesian framework to unravel food, groundwater, and climate linkages: A case study from Louisiana

Advancing our understanding of the connections among groundwater, food, and climate is critical to meet global food demands while optimizing water resources usage. However, our understanding of the linkages among groundwater, food, and climate is still limited. Here, we offer a Bayesian framework to simulate crop yield at a regional scale and quantify its relationships and associated uncertainty with climate, groundwater, agricultural, and energy-related variables. We implemented the framework in the rice-producing regions of Louisiana from 1960-2015. To build a parsimonious model, we used a probability-based variable selection approach to detect the key drivers of rice yield. Rice yield increased, groundwater declined, and area planted declined or did not change over 56yrs. The number of irrigation wells, groundwater level, air temperature, and area planted were found to be the key drivers of rice yield. The regression coefficients showed that rice yield was positively related to groundwater level, and negatively related to area planted and the number of irrigation wells. The limited influence of N fertilizer was noted on rice yield for the period when fertilizer data were available. The inverse relationship between rice yield and area planted pointed to the adaption of efficient crop management practices that maintained or increased yield, despite the decline in area planted. The farmers' ability to install irrigation wells during droughts sustained the yields over long-term but not short-term. This decline in rice yield in response to drought over the short-term might explain the negative relation between yield and irrigation wells. Overall, this work highlighted the uncertainty in relationships between rice yield and key drivers and quantified the intimate connection between food and groundwater. This work may have implications for managing two highly competing commodities (i.e., groundwater and food) in agricultural regions.

Identification and characterization of Dicer-like genes in leaf rust pathogen (Puccinia triticina) of wheat

Puccinia triticina (P. triticina) is one of the most devastating fungal pathogens of wheat which causes significant annual yield loss to the crop. Understanding the gene regulatory mechanism of the biotrophic pathogen is one of the important aspects of host-pathogen interaction studies. Dicer-like genes are considered as important mediators of RNAi-based gene regulation. In this study, we report the presence of three Dicer-like genes (Pt-DCL1, Pt-DCL2, Pt-DCL3) in P. triticina genome identified through computational and biological analyses. Quantitative real-time PCR studies revealed an increase in the expression of these genes in germinating spore stages. Heterologous expression combined with mass spectrometry analysis of Pt-DCL2 confirmed the presence of a canonical Dicer-like gene in P. triticina. Phylogenetic analysis of the Pt-DCLs with the Dicer-like proteins from other organisms showed a distinct cluster of rust pathogens from the order Pucciniales. The results indicated a species-specific duplication of Dicer-like genes within the wheat rust pathogens. This study, for the first time, reports the presence of Dicer-dependent RNAi pathway in P. triticina that may play a role in gene regulatory mechanism of the pathogen during its development. Our study serves as a vital source of information for further RNAi-based molecular studies for better understanding and management of the wheat leaf rust disease.

Comparative analysis of chromosome 2A molecular organization in diploid and hexaploid wheat

Diploid A genome wheat species harbor immense genetic variability which has been targeted and proven useful in wheat improvement. Development and deployment of sequence-based markers has opened avenues for comparative analysis, gene transfer and marker assisted selection (MAS) using high throughput cost effective genotyping techniques. Chromosome 2A of wheat is known to harbor several economically important genes. The present study aimed at identification of genic sequences corresponding to full length cDNAs and mining of SSRs and ISBPs from 2A draft sequence assembly of hexaploid wheat cv. Chinese Spring for marker development. In total, 1029 primer pairs including 478 gene derived, 501 SSRs and 50 ISBPs were amplified in diploid A genome species Triticum monococcum and T. boeoticum identifying 221 polymorphic loci. Out of these, 119 markers were mapped onto a pre-existing chromosome 2A genetic map consisting of 42 mapped markers. The enriched genetic map constituted 161 mapped markers with final map length of 549.6 cM. Further, 2A genetic map of T. monococcum was anchored to the physical map of 2A of cv. Chinese Spring which revealed several rearrangements between the two species. The present study generated a highly saturated genetic map of 2A and physical anchoring of genetically mapped markers revealed a complex genetic architecture of chromosome 2A that needs to be investigated further.

Expressivity of the key genes associated with seed and pod development is highly regulated via lncRNAs and miRNAs in Pigeonpea

Non-coding RNA’s like miRNA, lncRNA, have gained immense importance as a significant regulatory factor in different physiological and developmental processes in plants. In an effort to understand the molecular role of these regulatory agents, in the present study, 3019 lncRNAs and 227 miRNAs were identified from different seed and pod developmental stages in Pigeonpea, a major grain legume of Southeast Asia and Africa. Target analysis revealed that 3768 mRNAs, including 83 TFs were targeted by lncRNAs; whereas 3060 mRNA, including 154 TFs, were targeted by miRNAs. The targeted transcription factors majorly belong to WRKY, MYB, bHLH, etc. families; whereas the targeted genes were associated with the embryo, seed, and flower development. Total 302 lncRNAs interact with miRNAs and formed endogenous target mimics (eTMs) which leads to sequestering of the miRNAs present in the cell. Expression analysis showed that notably, Cc_lncRNA-2830 expression is up-regulated and sequestrates miR160h in pod leading to higher expression of the miR160h target gene, Auxin responsive factor-18. A similar pattern was observed for SPIKE, Auxin signaling F-box-2, Bidirectional sugar transporter, and Starch synthetase-2 eTMs. All the identified target mRNAs code for transcription factor and genes are involved in the processes like cell division, plant growth and development, starch synthesis, sugar transportation and accumulation of storage proteins which are essential for seed and pod development. On a combinatorial basis, our study provides a lncRNA and miRNA based regulatory insight into the genes governing seed and pod development in Pigeonpea.

MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an important class of natural products that contain antibiotics and a variety of other bioactive compounds. The existing methods for discovery of RiPPs by combining genome mining and computational mass spectrometry are limited to discovering specific classes of RiPPs from small datasets, and these methods fail to handle unknown post-translational modifications. Here, we present MetaMiner, a software tool for addressing these challenges that is compatible with large-scale screening platforms for natural product discovery. After searching millions of spectra in the Global Natural Products Social (GNPS) molecular networking infrastructure against just eight genomic and metagenomic datasets, MetaMiner discovered 31 known and seven unknown RiPPs from diverse microbial communities, including human microbiome and lichen microbiome, and microorganisms isolated from the International Space Station.

A Granger causality analysis of groundwater patterns over a half-century

Groundwater depletion in many areas of the world has been broadly attributed to irrigation. However, more formal, data-driven, causal mechanisms of long-term groundwater patterns have not been assessed. Here, we conducted the first Granger causality analysis to identify the “causes” of groundwater patterns using the rice-producing parishes of Louisiana, USA, as an example. Trend analysis showed a decline of up to 6 m in groundwater level over 51 years. We found that no single cause explained groundwater patterns for all parishes. Causal linkages were noted between groundwater and area harvested, number of irrigation wells, summer precipitation totals, and drought. Bi-directional linkages were noted between groundwater and rice yield, suggesting feedback between both time series. Causal linkages were absent between groundwater and many drivers where significant correlations were noted, highlighting the importance of using robust causal relationships over illusive correlations to detect the cause. These results advance our understanding of groundwater dynamics and can reveal a key connection between food and groundwater.

Changes in middle ear transmission characteristics secondary to altered bone remodelling

Alteration in the process of bone remodelling results in conditions like osteopenia and osteoporosis in which the bones become susceptible to fracture. The functioning of middle ear bones in such individuals were assessed in this study and it was found that the middle ear bones are equally susceptible to micro-fractures and can cause reduction in the transmission of sound energy.

INTRODUCTION

Alteration in the process of bone remodelling or increase in the number of osteoclasts cells as it occurs in osteoporosis and osteopenia are likely to affect the middle ear bones in the same way it affects the skeletal bones. Whether these micro-structural changes occurring at the level of the middle ear secondary to altered bone remodelling cause any significant impairment in its functioning is not explored. Thus, the present study aimed at assessing the different aspects of middle ear functioning in individuals with reduced BMD.

METHODS

The study included 25 normal, 39 osteopenic and 40 osteoporotic participants. The participants underwent pure-tone audiometry, otoscopic examination, conventional immittance evaluation using a 226 Hz probe tone, multi-component and multi-frequency tympanometry and acoustic reflex threshold testing. None of the participants had any current or previous history of middle ear effusion.

RESULTS

A significantly higher proportion of participants in the clinical group had hearing loss compared to the normal group. The clinical group participants also had reduced middle ear resonance frequency, elevated static compliance values and elevated or absent acoustic reflexes compared to the normal participants. There was no difference among the three groups for the proportion of participants having conductive hearing loss.

CONCLUSIONS

There is a detrimental impact of reduction in bone mineral density on middle ear transmission characteristics which may go unnoticed initially. Treatment of osteoporosis may potentially mitigate hearing loss from middle ear fractures due to reduced bone mineral density. Absence of significant air-bone gap with the presence of reduced middle ear resonance frequency may be early signs of reduced BMD.

Analysis of genetic control and QTL mapping of essential wheat grain quality traits in a recombinant inbred population

Wheat cultivars are genetically crossed to improve end-use quality for traits as per demands of baking industry and broad consumer preferences. The processing and baking qualities of bread wheat are influenced by a variety of genetic make-ups, environmental factors and their interactions. Two wheat cultivars, WL711 and C306, derived recombinant inbred lines (RILs) with a population of 206, were used for phenotyping of quality-related traits. The genetic analysis of quality traits showed considerable variation for measurable quality traits, with normal distribution and transgressive segregation across the years. From the 206 RILs, few RILs were found to be superior to those of the parental cultivars for key quality traits, indicating their potential use for the improvement of end-use quality and suggesting the probability of finding new alleles and allelic combinations from the RIL population. Mapping analysis identified 38 putative QTLs for 13 quality-related traits, with QTLs explaining 7.9-16.8% phenotypic variation spanning over 14 chromosomes, i.e., 1A, 1B, 1D, 2A, 2D, 3B, 3D, 4A, 4B, 4D, 5D, 6A, 7A and 7B. In-silico analysis based on homology to the annotated wheat genes present in database, identified six putative candidate genes within QTL for total grain protein content, qGPC.1B.1 region. Major QTL regions for other quality traits such as TKW have been identified on 1B, 2A, and 7A chromosomes in the studied RIL population. This study revealed the importance of the combination of stable QTLs with region-specific QTLs for better phenotyping, and the QTLs presented in our study will be useful for the improvement of wheat grain and bread-making quality.

An In Vitro Evaluation of Apical Leakage in Gutta-percha/ AH Plus and Resilon/Epiphany-filled Root Canals Using Two Dye Penetration Techniques

AIM

Aim of the present study was to evaluate the apical leakage in gutta-percha/AH plus and resilon/epiphany filled root canals using two dye penetration techniques.

MATERIALS AND METHODS

Sixty freshly extracted human single-rooted teeth were collected. The crown portion of each tooth was sectioned from the cementoenamel junction using a diamond disk. The canals were instrumented using Step back technique up to a caliber of 40. The roots were randomly divided into four experimental groups of 15 sample units each. All the groups are obturated using lateral compaction technique. Samples were placed in India ink and stored in an incubator for 7 days after which they were thoroughly washed under tap water and dried. The roots were divided into longitudinal splitting technique with diamond disks and using clearing technique was checked for linear dye penetration using stereomicroscope. The surfaces were scanned and surfaces with greatest dye penetration were measured by using De winter Biowizard software system.

RESULTS

The mean leakage for groups I, II, III, and IV are 2.31980, 2.68140, 4.11567, and 4.21047 respectively. One-way ANOVA was applied to the mean leakage scores of different groups, found a significant difference between mean leakage scores. F value of 3.266 and it was found to be significant with a p value of 0.028. Significant differences were obtained for mean comparisons of groups I and III, groups I and IV and groups III and IV. Further, between groups I and II, groups II and III, and groups III and IV no significant differences were observed.

CONCLUSION

In conclusion, gutta-percha/AH Plus sealed root canals showed lesser leakage than the Resilon Epiphany groups and there was no significant difference in the two different methodologies used for dye penetration.

CLINICAL SIGNIFICANCE

Tightly adapted endodontic filling material is one of the goals in successful clinical endodontics and Improvements in the adhesive technology have fostered attempts to reduce apical and coronal leakage by bonding to the root canal walls to obtain a solid monoblock.

Assessment of hydrologic vulnerability to urbanization and climate change in a rapidly changing watershed in the Southeast U.S

This study assessed the combined effects of increased urbanization and climate change on streamflow in the Yadkin-Pee Dee watershed (North Carolina, USA) and focused on the conversion from forest to urban land use, the primary land use transition occurring in the watershed. We used the Soil and Water Assessment Tool to simulate future (2050-2070) streamflow and baseflow for four combined climate and land use scenarios across the Yadkin-Pee Dee River watershed and three subwatersheds. The combined scenarios pair land use change and climate change scenarios together. Compared to the baseline, projected streamflow increased in three out of four combined scenarios and decreased in one combined scenario. Baseflow decreased in all combined scenarios, but decreases were largest in subwatersheds that lost the most forest. The effects of land use change and climate change were additive, amplifying the increases in runoff and decreases in baseflow. Streamflow was influenced more strongly by climate change than land use change. However, for baseflow the reverse was true; land use change tended to drive baseflow more than climate change. Land use change was also a stronger driver than climate in the most urban subwatershed. In the most extreme land use and climate projection the volume of the 1-day, 100 year flood nearly doubled at the watershed outlet. Our results underscore the importance of forests as hydrologic regulators buffering streamflow and baseflow from hydrologic extremes. Additionally, our results suggest that land managers and policy makers need to consider the implications of forest loss on streamflow and baseflow when planning for future urbanization and climate change adaptation options.

Unravelling the epigenomic interactions between parental inbreds resulting in an altered hybrid methylome in pigeonpea

DNA methylation is an important heritable landmark conferring epigenetic changes in hybrids and has fascinated biologists and plant-breeders over the years. Although epigenetic changes have been documented in rice and maize hybrids, such investigations have not been reported in pigeonpea. Here, we report genome-wide methylation profiles of pigeonpea sterile and fertile inbred lines and their fertile F1 hybrid at single base resolution. We found that pigeonpea genome is relatively enriched in CG methylation. Identification of differentially methylated regions (DMRs) in the sterile and fertile parent revealed remarkable differences between their methylation patterns. Investigation of methylation status of parental DMRs in hybrid revealed non-additive methylation patterns resulting from trans-chromosomal methylation and trans-chromosomal demethylation events. Furthermore, we discovered several DMRs negatively associated with gene expression in the hybrid and fertile parent. Interestingly, many of those DMRs belonged to transposable elements and genes encoding pentatricopeptide repeats associated proteins, which may mediate a role in modulating the genes impacting pollen fertility. Overall, our findings provide an understanding of two parental epigenomes interacting to give rise to an altered methylome in pigeonpea hybrids, from genome-wide point of view.

Simulating stream response to floodplain connectivity and revegetation from reach to watershed scales: Implications for stream management

Natural-infrastructures (e.g., floodplains) can offer multiple ecosystem services (ES), including flood-resilience and water quality improvement. In order to maintain these ES, state and non-profit organizations consider various stream interventions, including increased floodplain connectivity and revegetation. However, the effect of these interventions is rarely quantified. We build a hydraulic model to simulate the influence of above-mentioned interventions on stream power and water depth during 5 yr and 100 yr flood return-intervals for two watersheds in Vermont, USA. Simulated revegetation of floodplains increased water depth and decreased stream power, whereas increasing connectivity resulted in decline of both responses. Combination of increased connectivity and floodplain revegetation showed greatest reduction in stream-power suggesting that interventions may influence stream response in diverse ways. Across all three interventions, 14% and 48% of altered reaches showed increase in stream power and water depth over baseline, indicating that interventions may lead to undesirable outcomes and their apparent effectiveness can vary with the measure chosen for evaluation. Interventions also influenced up to 16% of unaltered reaches (i.e., in which no interventions were implemented), indicating the consequences of interventions can spread both up and downstream. Multivariate analysis showed that up to 50% of variance in stream response to interventions is attributable to characteristics of reaches, indicating that these characteristics could mediate the effectiveness of interventions. This study offers a framework to evaluate the potential ES provided by natural infrastructure. All stream interventions involve tradeoffs among responses and between target and non-target areas, so careful evaluation is therefore needed to compare benefits and costs among interventions. Such assessments can lead to more effective management of stream-floodplain ecosystems both in Vermont and elsewhere.

Molecular analysis of anthocyanin biosynthesis pathway genes and their differential expression in mango peel

Mango fruit is cherished by masses for its taste and nutrition, contributed by color, flavor, and aroma. Among these, peel color is an important trait contributing to fruit quality and market value. We attempted to elucidate the role of key genes of the anthocyanin biosynthesis pathway related to fruit peel color from the leaf transcriptome of mango cultivar Amrapali. A total of 108 mined transcript sequences were assigned to the phenylpropanoid-flavonoid pathway from which 15 contigs representing anthocyanin biosynthesis genes were annotated. Alternate splice variants were identified by mapping against genes of Citrus clementina and Vitis vinifera (closest relatives) and protein subcellular localization was determined. Phylogenetic analysis of these pathway genes clustered them into distinct groups aligning with homologous genes of Magnifera indica, C. clementina, and V. vinifera. Expression profiling revealed higher relative fold expressions in mature fruit peel of red-colored varieties (Arunika, Ambika, and Tommy Atkins) in comparison with the green-peeled Amrapali. MiCHS, MiCHI, and MiF3H alternate splice variants revealed differential gene expression. Functionally divergent variants indicate availability of an allelic pool programmed to play critical roles in peel color. This study provides insight into the molecular genetic basis of peel color and offers scope for development of biomarkers in varietal improvement programs.

Designing and construction of simulated constructed wetland for treatment of sewage containing metals

A simulated horizontal flow constructed wetland (CW) has been designed with gravel medium and aquatic plants Typha latifolia and Polygonum hydropiper to assess its performance efficiency for sewage treatment. Monitoring of fully developed CW revealed a high removal of nutrients and metals from sewage after treatment at varying retention times. The percent (%) removal of biological oxygen demand, total dissolved solids, total suspended solids, PO₄-P and total nitrogen in CW planted with T. latifolia were 88.20, 61.9, 72.12, 74.23 and 66.78%; however, with P. hydropiper, reductions were 79.47, 53.47, 55.46, 60.40 and 52.87%, respectively, at 8 d retention time. In addition, T. latifolia and P. hydropiper accumulated substantial amount of metals in their tissues particularly in roots. T. latifolia root accumulated maximum amount of Zn (40.44 µg/g dw) followed by Cu (39.24 µg/g dw), Pb (37.78 µg/g dw) and Cr (19.95 µg/g dw) as compared to P. hydropiper, which was 17.85, 33.43, 36.19 and 9.67 µg/g dw, respectively. Further, plant-specific high translocation factor (>1) of metals were observed at different retention times. Results suggest that simulated CW may be applied as an ecofriendly and low-cost tool to treat sewage before discharge into a fresh water body.

Chemosensing of honeybee parasite, Varroa destructor: Transcriptomic analysis

Chemosensing is a primary sense in nature, however little is known about its mechanism in Chelicerata. As a model organism we used the mite Varroa destructor, a key parasite of honeybees. Here we describe a transcriptomic analysis of two physiological stages for the Varroa foreleg, the site of primary olfactory organ. The transcriptomic analysis revealed transcripts of chemosensory related genes belonging to several groups. These include Niemann-Pick disease protein, type C2 (NPC2), gustatory receptors (GRs), ionotropic receptors (IRs), sensory neuron membrane proteins (SNMPs) and odorant binding proteins (OBP). However, no insect odorant receptors (ORs) and odorant co-receptors (ORcos) were found. In addition, we identified a homolog of the most ancient IR co-receptor, IR25a, in Varroa as well as in other members of Acari. High expression of this transcript in the mite's forelegs, while not detectable in the other pairs of legs, suggests a function for this IR25a-like in Varroa chemosensing.

Differential characterization of myogenic satellite cells with linolenic and retinoic acid in the presence of thiazolidinediones from prepubertal Korean black goats

Objective

Myogenic satellite cells were isolated from semitendinosus muscle of prepubertal Korean black goat to observe the differential effect of linolenic and retinoic acid in thepresence of thiazolidinediones (TZD) and also to observe the production insulin sensitive preadipocyte.

Methods

Cells were characterized for their stemness with cluster of differentiation 34 (CD34), CD13, CD106, CD44, Vimentin surface markers using flow cytometry. Cells characterized themselves as possessing significant (p<0.05) levels of CD13, CD34, CD106, Vimentin revealing their stemness potential. Goat myogenic satellite cells also exhibited CD44, indicating that they possessed a % of stemness factors of adipose lineage apart from their inherent stemness of paxillin factors 3/7.

Results

Cells during proliferation stayed absolutely and firmly within the myogenic fate without any external cues and continued to show a significant (p<0.05) fusion index % to express myogenic differentiation, myosin heavy chain, and smooth muscle actin in 2% horse serum. However, confluent myogenic satellite cells were the ones easily turning into adipogenic lineage. Intriguingly, upregulation in adipose specific genetic markers such as peroxisome proliferation-activated receptor γ, adiponectin, lipoprotein lipase, and CCAAT/enhancer binding protein α were observed and confirmed in all given treatments. However, the amount of adipogenesis was found to be statistically significant (p<0.01) with linolenic acid as compared to retinoic acid in combination with TZD’s.

Conclusion

Retinoic acid was found to produce smaller preadipocytes which have been assumed to have insulin sensitization and hence retinoic acid could be used as a potential agent to sensitize tissues to insulin in combination with TZD’s to treat diabetic conditions in humans and animals in future.