Genome-Wide Comparative Analysis of Five Amaranthaceae Species Reveals a Large Amount of Repeat Content.

Amaranthus is a genus of C4 dicotyledonous herbaceous plant species that are widely distributed in Asia, Africa, Australia, and Europe and are used as grain, vegetables, forages, and ornamental plants. Amaranth species have gained significant attention nowadays as potential sources of nutritious food and industrial products. In this study, we performed a comparative genome analysis of five amaranth species, namely, Amaranthus hypochondriacus, Amaranthus tuberculatus, Amaranthus hybridus, Amaranthus palmeri, and Amaranthus cruentus. The estimated repeat content ranged from 54.49% to 63.26% and was not correlated with the genome sizes. Out of the predicted repeat classes, the majority of repetitive sequences were Long Terminal Repeat (LTR) elements, which account for about 13.91% to 24.89% of all amaranth genomes. Phylogenetic analysis based on 406 single-copy orthologous genes revealed that A. hypochondriacus is most closely linked to A. hybridus and distantly related to A. cruentus. However, dioecious amaranth species, such as A. tuberculatus and A. palmeri, which belong to the subgenera Amaranthus Acnida, have formed their distinct clade. The comparative analysis of genomic data of amaranth species will be useful to identify and characterize agronomically important genes and their mechanisms of action. This will facilitate genomics-based, evolutionary studies, and breeding strategies to design faster, more precise, and predictable crop improvement programs.

Genetic diversity, transcript heterogeneity and allele mining of TaSKP1-6B-4 gene variants across diverse genotypes under terminal heat stress and genome wide characterization of TaSKP1 gene family from bread wheat (Triticum aestivum L.).

SKP1 (S-phase kinase protein1) is an essential regulatory component of SCF (Skp1-cullin-F-box) E3 ubiquitin ligases involved in maintenance of cellular protein homeostasis through ubiquitin mediated proteasome system (UPS). UPS play a key role in stress response and grain yield. Earlier, we isolated TaSKP1-6B-4, highly induced in flag leaf tissues (Accession No. KJ830759.1) of developing wheat caryopses under heat stress. To further assess the functional role of SKP1, genetic variability analysis was carried out in a panel of 25 contrasting germplasm through extensive phenotyping and transcript profiling of TaSKP1-6B-4 during anthesis under ambient and terminal heat stress (THS) in field experiments for two consecutive years. The analysis of variance revealed significant variations for all the traits studied. Higher H2(%), GCV, PCV, GA and GA% mean observed in tiller number per plant (23.81, 17.65, 5.71, 28, 30.86%) and grain number per head (30.27, 82.79, 60.16, 105.00, 108.64%) under THS over ambient temperature. Higher fold induction of TaSKP1-6B-4 transcripts was recorded in 10 genotypes viz. HD2967 (9.9), IC145456 (6.18) in flag leaf; while C-306 (15.88), RAJ3765 (8.37) in ear head. Allele mining of SKP1-6B-4 showed genotypic sequence variations. Whole genome wide search of SKP1 gene family identified 95 SKP1 genes which were structurally characterized. Grain yield, leaf senescence and other agronomic-morpho-physiological parameters combined with transcript profiling, cvHD2967, was found to be the best positively responsive to THS which by pedigree was not heat tolerant. We report a novel 2 year comprehensive field based analysis on collective genetic variability and SKP1/UPS modulation under a natural environmental setting. The data reveals potential functional role of UPS under THS and tolerant cultivars can be further utilized for clarifying the role of UPS mechanistically at the molecular level and for developing terminal heat stress tolerant wheat.

Assessment of air pollution tolerance and anticipated performance index of roadside trees in urban and semi-urban regions.

Rapid urbanization and rising vehicular population are the main precursors in increasing air pollutants concentration which negatively influences the surrounding ecosystem. Roadside plants are frequently used as the barrier against traffic emissions to minimize the effects of air pollution. They are, however, vulnerable to various contaminants, and their tolerance capacity varies. This necessitates a scientific inquiry into the role of roadside plantations in improved urban sprawl planning and management, where chosen trees could be cultivated to reduce air pollution. The present study assesses biochemical and physiological characteristics to evaluate the air pollution tolerance index (APTI) in Ranchi, Jharkhand. The anticipated performance index (API) was assessed based on calculated APTI and socioeconomic characteristics of a selected common tree species along the roadside at different sites. According to APTI, Mangifera indica and Eugenia jambolana were the most tolerant species throughout all the sites, while Ficus benghalensis and Ficus religiosa were intermediately tolerant towards air pollution. The one-way ANOVA shows no significant variation in APTI throughout all the sites. The regression plot shows the positive correlation of APTI with ascorbic acid among all the parameters. According to API, the Mangifera indica, Eugenia jambolana Ficus religiosa and Ficus benghalensis were excellent and best performers among all the sites. So, the air pollution-resistant tree species can be recommended for roadside plantations for the development of green belt areas in urban regions.

Amaranth Genomic Resource Database: an integrated database resource of Amaranth genes and genomics.

Amaranth (Amaranthus L.) is native to Mexico and North America, where it was cultivated thousands of years ago, but now amaranth is grown worldwide. Amaranth is one of the most promising food crops with high nutritional value and belongs to the family Amaranthaceae. The high-quality genome assembly of cultivated amaranth species (A. hypochondriacus, A. cruentus) and wild/weedy species (A. tuberculatus, A. hybridus, and A. palmeri) has already been reported; therefore, we developed an Amaranth Genomic Resource Database (AGRDB) to provide access to all the genomic information such as genes, SSRs, SNPs, TFs, miRNAs, and transporters in one place. The AGRDB database contains functionally annotated gene information with their sequence details, genic as well as genomic SSRs with their three sets of primers, transcription factors classified into different families with their sequence information and annotation details, putative miRNAs with their family, sequences, and targeted gene details, transporter genes with their superfamily, trans-membrane domain details, and details of genic as well as nongenic SNPs with 3' and 5' flanking sequence information of five amaranth species. A database search can be performed using the gene ID, sequence ID, sequence motif, motif repeat, family name, annotation keyword, scaffold or chromosome numbers, etc. This resource also includes some useful tools, including JBrowse for the visualization of genes, SSRs, SNPs, and TFs on the respective amaranth genomes and BLAST search to perform a BLAST search of the user's query sequence against the amaranth genome as well as protein sequences. The AGRDB database will serve as a potential platform for genetic improvement and characterization of this futuristic crop. The AGRDB database will be accessible via the link: http://www.nbpgr.ernet.in:8080/AmaranthGRD/.

De Novo Transcriptome Profiling for the Generation and Validation of Microsatellite Markers, Transcription Factors, and Database Development for Andrographis paniculata.

Andrographis paniculata belongs to the family Acanthaceae and is known for its medicinal properties owing to the presence of unique constituents belonging to the lactones, diterpenoids, diterpene glycosides, flavonoids, and flavonoid glycosides groups of chemicals. Andrographolide, a major therapeutic constituent of A. paniculata, is extracted primarily from the leaves of this plant and exhibits antimicrobial and anti-inflammatory activities. Using 454 GS-FLX pyrosequencing, we have generated a whole transcriptome profile of entire leaves of A. paniculata. A total of 22,402 high-quality transcripts were generated, with an average transcript length and N50 of 884 bp and 1007 bp, respectively. Functional annotation revealed that 19,264 (86%) of the total transcripts showed significant similarity with the NCBI-Nr database and were successfully annotated. Out of the 19,264 BLAST hits, 17,623 transcripts were assigned GO terms and distributed into three major functional categories: molecular function (44.62%), biological processes (29.19%), and cellular component (26.18%) based on BLAST2GO. Transcription factor analysis showed 6669 transcripts, belonging to 57 different transcription factor families. Fifteen TF genes that belong to the NAC, MYB, and bHLH TF categories were validated by RT PCR amplification. In silico analysis of gene families involved in the synthesis of biochemical compounds having medicinal values, such as cytochrome p450, protein kinases, heat shock proteins, and transporters, was completed and a total of 102 different transcripts encoding enzymes involved in the biosynthesis of terpenoids were predicted. Out of these, 33 transcripts belonged to terpenoid backbone biosynthesis. This study also identified 4254 EST-SSRs from 3661 transcripts, representing 16.34% of the total transcripts. Fifty-three novel EST-SSR markers generated from our EST dataset were used to assess the genetic diversity among eighteen A. paniculata accessions. The genetic diversity analysis revealed two distinct sub-clusters and all accessions based on the genetic similarity index were distinct from each other. A database based on EST transcripts, EST-SSR markers, and transcription factors has been developed using data generated from the present study combined with available transcriptomic resources from a public database using Meta transcriptome analysis to make genomic resources available in one place to the researchers working on this medicinal plant.

Environmental impacts of air pollution and its abatement by plant species: A comprehensive review.

Air pollution is one of the major global environmental issues urgently needed attention for its control through sustainable approaches. The release of air pollutants from various anthropogenic and natural processes imposes serious threats to the environment and human health. The green belt development using air pollution-tolerant plant species has become popular approach for air pollution remediation. Plants' biochemical and physiological attributes, especially relative water content, pH, ascorbic acid, and total chlorophyll content, are taken into account for assessing air pollution tolerance index (APTI). In contrast, anticipated performance index (API) is assessed based on socio-economic characteristics including "canopy structure, type, habit, laminar structure, economic value and APTI score" of plant species. Based on previous work, plants with high dust-capturing capacity are identified in Ficus benghalensis L. (0.95 to 7.58 mg/cm2), and highest overall PM accumulation capacity was observed in Ulmus pumila L. (PM10 = 72 µg/cm2 and PM2.5 = 70 µg/cm2) in the study from different regions. According to APTI, the plant species such as M. indica (11 to 29), Alstonia scholaris (L.) R. Br. (6 to 24), and F. benghalensis (17 to 26) have been widely reported as high air pollution-tolerant species and good to best performer in terms of API at different study sites. Statistically, previous studies show that ascorbic acid (R2 = 0.90) has good correlation with APTI among all the parameters. The plant species with high pollution tolerance capacity can be recommended for future plantation and green belt development.

Optical Microscope Based Universal Parameter for Identifying Layer Number in Two-Dimensional Materials.

Optical contrast is the most common preliminary method to identify layer number of two-dimensional (2D) materials, but it is seldom used as a confirmatory technique. We explain the reason for variation of optical contrast between imaging systems, motivating system-independent measurement of optical contrast as a critical need. We describe a universal method to quantify the layer number using the RGB (red-green-blue) and RAW optical images. For RGB images, the slope of 2D flake (MoS2, WSe2, graphene) intensity vs substrate intensity is extracted from optical images with varying lamp power. The intensity slope identifies layer number and is system independent. For RAW images, intensity slopes and intensity ratios are completely system and intensity independent. Intensity slope (for RGB) and intensity ratio (for RAW) are thus universal parameters for identifying layer number. The RAW format is not present in all imaging systems, but it can confirm layer number using a single optical image, making it a rapid and system-independent universal method. A Fresnel-reflectance-based optical model provides an excellent match with experiments. Furthermore, we have created a MATLAB-based graphical user interface that can identify layer number rapidly. This technique is expected to accelerate the preparation of heterostructures and to fulfill a prolonged need for universal optical contrast method.

TinoTranscriptDB: A Database of Transcripts and Microsatellite Markers of Tinospora cordifolia, an Important Medicinal Plant.

Tinospora cordifolia, commonly known as "Giloe" in India, is a shrub belonging to the family Menispermaceae. It is an important medicinal plant known for its antipyretic, anti-inflammatory, antispasmodic, and antidiabetic properties and is used in the treatment of jaundice, gout, and rheumatism. Despite its economic importance, the limited information related to its genomic resources prohibits its judicious exploitation through molecular breeding or biotechnological approaches. In this study, we generated a meta-transcriptome assembly of 43,090 non-redundant transcripts by merging the RNASeq data obtained from Roche 454 GS-FLX, and Illumina platforms, and report the first transcriptome-based database for simple sequence repeats and transcription factors ("TinoTranscriptDB" (Tinospora cordifolia Transcriptome Database)). We annotated 26,716 (62%) of the total transcripts successfully from National Center for Biotechnology Information non-redundant protein (NCBI-NR), gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Swiss-Prot, and Pfam databases. This database contains information of 2620 perfect simple sequence repeats (P-SSRs) with a relative abundance of 340.12 (loci/Mb), and relative density of 6309.29 (bp/Mb). Excluding mono-nucleotides, the most abundant SSR motifs were tri-nucleotides (54.31%), followed by di-nucleotides (37.51%), tetra-nucleotides (4.54%), penta-nucleotides (3.16%) and hexa-nucleotides (0.45%). Additionally, we also identified 4,311 transcription factors (TFs) and categorized them into 55 sub-families. This database is expected to fill the gap in genomic resource availability in T. cordifolia and thus accelerate molecular breeding and related functional and other applied studies aimed towards genetic improvements of T. cordifolia and related species.

Decoding the genome of superior chapatti quality Indian wheat variety 'C 306' unravelled novel genomic variants for chapatti and nutrition quality related genes.

An Indian wheat variety, 'C 306' has good chapatti quality, which is controlled by multiple genes that have not been explored. We report the high quality de novo assembled genome of 'C 306' by combining short and long read sequencing data. The hybrid assembly covered 93% of gene space and identified about 142 K coding genes, 34% repetitive DNA and ~ 501 K SSR motifs. The phylogenetic analysis of about 83 K orthologous protein groups suggested the closest relationship with T. turgidum, T. aestivum and Ae. tauschii. Genome wide analysis annotated 69,217,536 genomic variants. Out of them, 1423 missense and 117 deleterious variants identified in processing, nutrition, and chapatti quality related genes such as alpha- and beta-gliadin, SSI, SSIII, SUT1, SBEI, CHS, YSL, DMAS, and NAS encoded proteins. These variants may affect quality genes. The genomic data will be potential genomic resources in wheat breeding programs for quality improvement.

Twist Angle-Dependent Interlayer Exciton Lifetimes in van der Waals Heterostructures.

In van der Waals (vdW) heterostructures formed by stacking two monolayers of transition metal dichalcogenides, multiple exciton resonances with highly tunable properties are formed and subject to both vertical and lateral confinement. We investigate how a unique control knob, the twist angle between the two monolayers, can be used to control the exciton dynamics. We observe that the interlayer exciton lifetimes in MoSe_{2}/WSe_{2} twisted bilayers (TBLs) change by one order of magnitude when the twist angle is varied from 1° to 3.5°. Using a low-energy continuum model, we theoretically separate two leading mechanisms that influence interlayer exciton radiative lifetimes. The shift to indirect transitions in the momentum space with an increasing twist angle and the energy modulation from the moiré potential both have a significant impact on interlayer exciton lifetimes. We further predict distinct temperature dependence of interlayer exciton lifetimes in TBLs with different twist angles, which is partially validated by experiments. While many recent studies have highlighted how the twist angle in a vdW TBL can be used to engineer the ground states and quantum phases due to many-body interaction, our studies explore its role in controlling the dynamics of optically excited states, thus, expanding the conceptual applications of "twistronics".

Evolutionary Understanding of Metacaspase Genes in Cultivated and Wild Oryza Species and Its Role in Disease Resistance Mechanism in Rice.

Metacaspases (MCs), a class of cysteine-dependent proteases found in plants, fungi, and protozoa, are predominately involved in programmed cell death processes. In this study, we identified metacaspase genes in cultivated and wild rice species. Characterization of metacaspase genes identified both in cultivated subspecies of Oryza sativa, japonica, and indica and in nine wild rice species was performed. Extensive computational analysis was conducted to understand gene structures, phylogenetic relationships, cis-regulatory elements, expression patterns, and haplotypic variations. Further, the haplotyping study of metacaspase genes was conducted using the whole-genome resequencing data publicly available for 4726 diverse genotype and in-house resequencing data generated for north-east Indian rice lines. Sequence variations observed among wild and cultivated rice species for metacaspase genes were used to understand the duplication and neofunctionalization events. The expression profiles of metacaspase genes were analyzed using RNA-seq transcriptome profiling in rice during different developmental stages and stress conditions. Real-time quantitative PCR analysis of candidate metacaspase genes in rice cultivars Pusa Basmati-1 in response to Magnaporthe oryzae infection indicated a significant role in the disease resistance mechanism. The information provided here will help to understand the evolution of metacaspases and their role under stress conditions in rice.

Growth Kinetics and Atomistic Mechanisms of Native Oxidation of ZrSxSe2-x and MoS2 Crystals.

A thorough understanding of native oxides is essential for designing semiconductor devices. Here, we report a study of the rate and mechanisms of spontaneous oxidation of bulk single crystals of ZrSxSe2-x alloys and MoS2. ZrSxSe2-x alloys oxidize rapidly, and the oxidation rate increases with Se content. Oxidation of basal surfaces is initiated by favorable O2 adsorption and proceeds by a mechanism of Zr-O bond switching, that collapses the van der Waals gaps, and is facilitated by progressive redox transitions of the chalcogen. The rate-limiting process is the formation and out-diffusion of SO2. In contrast, MoS2 basal surfaces are stable due to unfavorable oxygen adsorption. Our results provide insight and quantitative guidance for designing and processing semiconductor devices based on ZrSxSe2-x and MoS2 and identify the atomistic-scale mechanisms of bonding and phase transformations in layered materials with competing anions.

Left ventricular dissecting hematoma caused by tissue stabilizer

Abstract Coronary artery bypass grafting is a commonly performed procedure for coronary revascularization. We describe the successful management of left ventricular dissecting hematoma, caused by the tissue stabilizer, while performing off-pump coronary artery bypass graft procedure.

Primary mediastinal hydatid cyst causing diaphragmatic palsy

Abstract Hydatid cystic disease is a significant clinical problem in endemic countries. Hydatid cysts are most commonly located in the liver and lungs. Primary mediastinal hydatid cyst is a rare clinical entity. The diagnosis must be considered in a patient with a mediastinal mass, particularly in endemic regions. Mediastinal hydatid cysts causing paralysis of phrenic and recurrent laryngeal nerves have been rarely reported. We describe a rare case of primary mediastinal hydatid cyst associated with diaphragmatic palsy caused by compression of the left phrenic nerve, which was successfully treated with partial cystectomy and capitonnage with hemidiaphragmatic plication.

Left Ventricular Dissecting Hematoma Caused by Tissue Stabilizer.

Coronary artery bypass grafting is a commonly performed procedure for coronary revascularization. We describe the successful management of left ventricular dissecting hematoma, caused by the tissue stabilizer, while performing off-pump coronary artery bypass graft procedure.

Nitric oxide and hydrogen sulfide crosstalk during heavy metal stress in plants.

Gases such as ethylene, hydrogen peroxide (H2 O2 ), nitric oxide (NO), carbon monoxide (CO) and hydrogen sulfide (H2 S) have been recognized as vital signaling molecules in plants and animals. Of these gasotransmitters, NO and H2 S have recently gained momentum mainly because of their involvement in numerous cellular processes. It is therefore important to study their various attributes including their biosynthetic and signaling pathways. The present review provides an insight into various routes for the biosynthesis of NO and H2 S as well as their signaling role in plant cells under different conditions, more particularly under heavy metal stress. Their beneficial roles in the plant's protection against abiotic and biotic stresses as well as their adverse effects have been addressed. This review describes how H2 S and NO, being very small-sized molecules, can quickly pass through the cell membranes and trigger a multitude of responses to various factors, notably to various stress conditions such as drought, heat, osmotic, heavy metal and multiple biotic stresses. The versatile interactions between H2 S and NO involved in the different molecular pathways have been discussed. In addition to the signaling role of H2 S and NO, their direct role in posttranslational modifications is also considered. The information provided here will be helpful to better understand the multifaceted roles of H2 S and NO in plants, particularly under stress conditions.

Primary Mediastinal Hydatid Cyst Causing Diaphragmatic Palsy.

Hydatid cystic disease is a significant clinical problem in endemic countries. Hydatid cysts are most commonly located in the liver and lungs. Primary mediastinal hydatid cyst is a rare clinical entity. The diagnosis must be considered in a patient with a mediastinal mass, particularly in endemic regions. Mediastinal hydatid cysts causing paralysis of phrenic and recurrent laryngeal nerves have been rarely reported. We describe a rare case of primary mediastinal hydatid cyst associated with diaphragmatic palsy caused by compression of the left phrenic nerve, which was successfully treated with partial cystectomy and capitonnage with hemidiaphragmatic plication.

Understanding the Effect of Structural Diversity in WRKY Transcription Factors on DNA Binding Efficiency through Molecular Dynamics Simulation.

A precise understanding of the molecular mechanism involved in stress conditions has great importance for crop improvement. Biomolecules, such as WRKY proteins, which are the largest transcription factor family that is widely distributed in higher plants, plays a significant role in plant defense response against various biotic and abiotic stressors. In the present study, an extensive homology-based three-dimensional model construction and subsequent interaction study of WRKY DNA-binding domain (DBD) in CcWRKY1 (Type I), CcWRKY51 (Type II), and CcWRKY70 (Type III) belonging to pigeonpea, a highly tolerant crop species, was performed. Evaluation of the generated protein models was done to check their reliability and accuracy based on the quantitative and qualitative parameters. The final model was subjected to investigate the comparative binding analysis of different types of WRKY-DBD with DNA-W-box (a cis-acting element) by protein-DNA docking and molecular dynamics (MD) simulation. The DNA binding specificity with WRKY variants was scrutinized through protein-DNA interaction using the HADDOCK server. The stability, as well as conformational changes of protein-DNA complex, was investigated through molecular dynamics (MD) simulations for 100 ns using GROMACS. Additionally, the comparative stability and dynamic behavior of each residue of the WRKY-DBD type were analyzed in terms of root mean square deviation (RMSD), root mean square fluctuation (RMSF)values of the backbone atoms for each frame taking the minimized structure as a reference. The details of DNA binding activity of three different types of WRKY-DBD provided here will be helpful to better understand the regulation of WRKY gene family members in plants.

Dry Transfer of van der Waals Crystals to Noble Metal Surfaces To Enable Characterization of Buried Interfaces.

Two-dimensional (2D) transition-metal dichalcogenides (TMDCs) have been explored for many optoelectronic applications. Most of these applications require them to be on insulating substrates. However, for many fundamental property characterizations, such as mapping surface potential or conductance, insulating substrates are nonideal as they lead to charging and doping effects or impose the inhomogeneity of their charge environment on the atomically thin 2D layers. Here, we report a simple method of residue-free dry transfer of 2D TMDC crystal layers. This method is enabled via noble-metal (gold, silver) thin films and allows comprehensive nanoscale characterization of transferred TMDC crystals with multiple scanning probe microscopy techniques. In particular, intimate contact with underlying metal allows efficient tip-enhanced Raman scattering characterization, providing high spatial resolution (<20 nm) for Raman spectroscopy. Further, scanning Kelvin probe force microscopy allows high-resolution mapping of surface potential on transferred crystals, revealing their spatially varying structural and electronic properties. The layer-dependent contact potential difference is clearly observed and explained by charge transfer from contacts with Au and Ag. The demonstrated sample preparation technique can be generalized to probe many different 2D material surfaces and has broad implications in understanding of the metal contacts and buried interfaces in 2D material-based devices.

Understanding the Role of the WRKY Gene Family under Stress Conditions in Pigeonpea (Cajanus Cajan L.).

Pigeonpea (Cajanus cajan L.), a protein-rich legume, is a major food component of the daily diet for residents in semi-arid tropical regions of the word. Pigeonpea is also known for its high level of tolerance against biotic and abiotic stresses. In this regard, understanding the genes involved in stress tolerance has great importance. In the present study, identification, and characterization of WRKY, a large transcription factor gene family involved in numerous biological processes like seed germination, metabolism, plant growth, biotic and abiotic stress responses was performed in pigeonpea. A total of 94 WRKY genes identified in the pigeonpea genome were extensively characterized for gene-structures, localizations, phylogenetic distribution, conserved motif organizations, and functional annotation. Phylogenetic analysis revealed three major groups (I, II, and III) of pigeonpea WRKY genes. Subsequently, expression profiling of 94 CcWRKY genes across different tissues like root, nodule, stem, petiole, petal, sepal, shoot apical meristem (SAM), mature pod, and mature seed retrieved from the available RNAseq data identified tissue-specific WRKY genes with preferential expression in the vegetative and reproductive stages. Gene co-expression networks identified four WRKY genes at the center of maximum interaction which may play a key role in the entire WRKY regulations. Furthermore, quantitative real-time polymerase chain reaction (qRT-PCR) expression analysis of WRKY genes in root and leaf tissue samples from plants under drought and salinity stress identified differentially expressed WRKY genes. The study will be helpful to understand the evolution, regulation, and distribution of the WRKY gene family, and additional exploration for the development of stress tolerance cultivars in pigeonpea and other legumes crops.