Cis-regulatory control of mammalian Trps1 gene expression.

TRPS1 serves as the causative gene for tricho-rhino phalangeal syndrome, known for its craniofacial and skeletal abnormalities. The Trps1 gene encodes a protein that represses Wnt signaling through strong interactions with Wnt signaling inhibitors. The identification of genomic cis-acting regulatory sequences governing Trps1 expression is crucial for understanding its role in embryogenesis. Nevertheless, to date, no investigations have been conducted concerning these aspects of Trps1. To identify deeply conserved noncoding elements (CNEs) within the Trps1 locus, we employed a comparative genomics approach, utilizing slowly evolving fish such as coelacanth and spotted gar. These analyses resulted in the identification of eight CNEs in the intronic region of the Trps1 gene. Functional characterization of these CNEs in zebrafish revealed their regulatory potential in various tissues, including pectoral fins, heart, and pharyngeal arches. RNA in-situ hybridization experiments revealed concordance between the reporter expression pattern induced by the identified set of CNEs and the spatial expression pattern of the trps1 gene in zebrafish. Comparative in vivo data from zebrafish and mice for CNE7/hs919 revealed conserved functions of these enhancers. Each of these eight CNEs was further investigated in cell line-based reporter assays, revealing their repressive potential. Taken together, in vivo and in vitro assays suggest a context-dependent dual functionality for the identified set of Trps1-associated CNE enhancers. This functionally characterized set of CNE-enhancers will contribute to a more comprehensive understanding of the developmental roles of Trps1 and can aid in the identification of noncoding DNA variants associated with human diseases.

Identification of ancestral gnathostome Gli3 enhancers with activity in mammals.

Abnormal expression of the transcriptional regulator and hedgehog (Hh) signaling pathway effector Gli3 is known to trigger congenital disease, most frequently affecting the central nervous system (CNS) and the limbs. Accurate delineation of the genomic cis-regulatory landscape controlling Gli3 transcription during embryonic development is critical for the interpretation of noncoding variants associated with congenital defects. Here, we employed a comparative genomic analysis on fish species with a slow rate of molecular evolution to identify seven previously unknown conserved noncoding elements (CNEs) in Gli3 intronic intervals (CNE15-21). Transgenic assays in zebrafish revealed that most of these elements drive activities in Gli3 expressing tissues, predominantly the fins, CNS, and the heart. Intersection of these CNEs with human disease associated SNPs identified CNE15 as a putative mammalian craniofacial enhancer, with conserved activity in vertebrates and potentially affected by mutation associated with human craniofacial morphology. Finally, comparative functional dissection of an appendage-specific CNE conserved in slowly evolving fish (elephant shark), but not in teleost (CNE14/hs1586) indicates co-option of limb specificity from other tissues prior to the divergence of amniotes and lobe-finned fish. These results uncover a novel subset of intronic Gli3 enhancers that arose in the common ancestor of gnathostomes and whose sequence components were likely gradually modified in other species during the process of evolutionary diversification.

Exploration of natural colourant of (Solanum melongena L.) brinjal plant residues for fabric dyeing: a novel approach towards textile processing.

Natural products have become the main focus of mankind due to increasing environmental pollution. The current study was concerned with brinjal plant residues as a source of bio colourant for cotton dyeing. Various media have been employed for the extraction of colourant. Present studies illustrated that excellent colourant yield was obtained in 4% acidified methanol. Cotton fabric was dyed at 50 °C, for 55 min and showed optimised dyeing conditions. Varying chemicals and bio-mordants have been used to achieve elegant shade. Chemical mordanting results revealed that 2% FeSO4as pre-mordant, and 6% TA as post-mordant while in bio- mordanting, 8% of pomegranate peel extract as pre-mordant and 2% pomegranate peel extract as post-mordant indicated a darker shade to mordanted fabrics. Bio-mordanting gave darker shade, and fastness which revealed that bio-mordants have improved the fastness characteristics. FTIR results revealed the confirmation of flavonoids as a colourant for cotton dyeing.

Pediatric Acute Lymphoblastic Leukemia: Clinical Characteristics, Treatment Outcomes, and Prognostic Factors: 10 Years' Experience From a Low- and Middle-Income Country.

PURPOSE: Acute lymphoblastic leukemia (ALL) represents around 70% of pediatric leukemia. In high-income countries, the 5-year survival is above 90%, but survival in low- and middle-income countries is inferior. This study documents the treatment outcome and prognostic factors of pediatric ALL in Pakistan. MATERIALS AND METHODS: In this prospective cohort study, all newly diagnosed patients with ALL/lymphoblastic lymphoma from age 1 to 16 years enrolled between January 1, 2012, and December 31, 2021, were included. The treatment was based on the standard arm of the UKALL2011 protocol. RESULTS: Data from 945 patients with ALL, including 597 males (63.2%), were analyzed. The mean age at diagnosis was 5.73 ± 3.51 years. Pallor was the commonest presentation in 95.2% followed by fever in 84.2% of patients. The mean WBC count was 56.6 ± 103.4 × 109/L. Neutropenic fever followed by myopathy was the most common complication during induction. In univariate analysis, the high WBC count (P ≤ 0.001), intensive chemotherapy (P ≤ 0.001), malnutrition (P = .007), poor response to induction chemotherapy (P = .001), delayed presentation (P = .004), and use of steroids before chemotherapy (P = .023) significantly adversely affected overall survival (OS). The delayed presentation was the most significant prognostic factor in the multivariate analysis (P ≤ .002). After a median follow-up of 54.64 ± 33.80 months, the 5-year OS and disease-free survival (DFS) were 69.9% and 67.8%, respectively. CONCLUSION: In this largest cohort of childhood ALL from Pakistan, a high WBC count, malnutrition, delayed presentation, previous steroids use, intensive chemotherapy, and poor response to the induction chemotherapy were associated with decreased OS and DFS rates.

Evolutionary relevance of single nucleotide variants within the forebrain exclusive human accelerated enhancer regions.

BACKGROUND: Human accelerated regions (HARs) are short conserved genomic sequences that have acquired significantly more nucleotide substitutions than expected in the human lineage after divergence from chimpanzees. The fast evolution of HARs may reflect their roles in the origin of human-specific traits. A recent study has reported positively-selected single nucleotide variants (SNVs) within brain-exclusive human accelerated enhancers (BE-HAEs) hs1210 (forebrain), hs563 (hindbrain) and hs304 (midbrain/forebrain). By including data from archaic hominins, these SNVs were shown to be Homo sapiens-specific, residing within transcriptional factors binding sites (TFBSs) for SOX2 (hs1210), RUNX1/3 (hs563), and FOS/JUND (hs304). Although these findings suggest that the predicted modifications in TFBSs may have some role in present-day brain structure, work is required to verify the extent to which these changes translate into functional variation. RESULTS: To start to fill this gap, we investigate the SOX2 SNV, with both forebrain expression and strong signal of positive selection in humans. We demonstrate that the HMG box of SOX2 binds in vitro with Homo sapiens-specific derived A-allele and ancestral T-allele carrying DNA sites in BE-HAE hs1210. Molecular docking and simulation analysis indicated highly favourable binding of HMG box with derived A-allele containing DNA site when compared to site carrying ancestral T-allele. CONCLUSION: These results suggest that adoptive changes in TF affinity within BE-HAE hs1210 and other HAR enhancers in the evolutionary history of Homo sapiens might. have brought about changes in gene expression patterns and have functional consequences on forebrain formation and evolution. METHODS: The present study employ electrophoretic mobility shift assays (EMSA) and molecular docking and molecular dynamics simulations approaches.

Transformation and expressional studies of GaZnF gene to improve drought tolerance in Gossypium hirsutum.

Drought stress is the major limiting factor in plant growth and production. Cotton is a significant crop as textile fiber and oilseed, but its production is generally affected by drought stress, mainly in dry regions. This study aimed to investigate the expression of Zinc finger transcription factor's gene (GaZnF) to enhance the drought tolerance in Gossypium hirsutum. Sequence features of the GaZnF protein were recognized through different bioinformatics tools like multiple sequence alignment analysis, phylogenetic tree for evolutionary relationships, Protein motifs, a transmembrane domain, secondary structure and physio-chemical properties indicating that GaZnF is a stable protein. CIM-482, a local Gossypium hirsutum variety was transformed with GaZnF through Agrobacterium-mediated transformation method with 2.57% transformation efficiency. The integration of GaZnF was confirmed through Southern blot showing 531 bp, and Western blot indicated a 95 kDa transgene-GUS fusion band in transgenic plants. The normalized real-time expression analysis revealed the highest relative fold spatial expression of cDNA of GaZnF within leaf tissues at vegetative and flowering stages under drought stress. Morphological, physiological and biochemical parameters of transgenic cotton plants at 05- and 10-day drought stress was higher than those of non-transgenic control plants. The values of fresh and dry biomass, chlorophyll content, photosynthesis, transpiration rate, and stomatal conductance reduced in GaZnF transgenic cotton plants at 05- and 10-day drought stress, but their values were less low in transgenic plants than those of non-transgenic control plants. These findings showed that GaZnF gene expression in transgenic plants could be a valuable source for the development of drought-tolerant homozygous lines through breeding.

Environmental friendly silk and cotton dyeing using natural colorant of Bougainvillea (Bougainvillea glabra) flowers: the sustainable approach towards textile industry.

For the current study, Bougainvillea flowers as environment friendly sustainable source of plant-based natural dye have been selected as an alternative to toxic synthetic dyes for dyeing of cotton and silk. Natural colorant from Bougainvillea flowers (Bougainvillea glabra) was extracted using aqueous and acidic extraction media. Maximum colorant was extracted in aqueous medium, and further it was used for cotton and silk dyeing. The optimum values of the dyeing parameters including dyeing time, dye to liquor ratio and salt level as exhausting agent were found to be 30 min, 35-mL liquor ratio and 3.0 g for cotton and for silk 45 min dyeing time, 45-mL liquor ratio and 3.0 g exhausting agent in aqueous dye extract. Bio mordanting has been applied to attain a variety of color shades. The utilization of 3% of henna, 4% of turmeric for silk pre-mordanting and for post-mordanting turmeric at 3% and henna at 4% for silk gave a darker shade. For cotton bio mordanting, 2% turmeric rhizome powder, 3% henna leaves powder extract as pre-mordant and 2% turmeric, 3% henna as post-mordant has developed a variety of shade. Overall, it has been found that natural colorant from Bougainvillea flowers is the new dye source for bio-coloration of natural fabrics, and addition of bio mordants has made the process more calming and eco-friendly.

Environmental friendly pollution free bio-dyeing of wool with haar singhar (Coral Jasmine) flower extract.

The world's move towards revival of eco-labelled products has created a huge urge to explore new means which are healthier for the global community. Among such means, plant-based bio-pigments for coloration of matrix are gaining worldwide fame, particularly in the textile sector. For the purpose of appraising new source of eco-friendly dyes, using microwave irradiation techniques, Coral Jasmine flowers have been explored for the bio-dyeing of wool. The colorant was extracted in acidic medium owing to nature of fabric, and both stuffs have been exposed to microwave treatment up to 5 min. Bio-coloration of MW irradiated and unirradiated wool was done using MW irradiated and unirradiated extract for observing high yield. Central composite design (CCD) as statistical method was utilized to see the significance of dyeing parameters chosen for mordanting to develop colorfast shades. Different concentrations of sustainable chemicals and bio-mordants as per weight of fabric were employed to introduce new shades with improved colorfastness properties. International standard textile methods determining shade permanency (fastness) have been employed onto selected dyed-mordanted fabrics. Good yield of colorant was observed when MW irradiated wool fabric was dyed at 75 °C for 45 min with extract of 7 pH, having 1.5g/100 mL of salt solution; the promising color yield was observed. As per gray scale ratings observed after ISO standard methods, pine nut as bio-mordant and iron salt as chemical mordant have developed colorfast shades. Conclusively, it can be recommended that methods for the isolation of colorants from new dye yielding plants, MW heating method as suitable clean technology and medicinal-based bio-mordants should be employed for getting permanent gamutes.

Disentangling the effects of traits with shared clustered genetic predictors using multivariable Mendelian randomization.

When genetic variants in a gene cluster are associated with a disease outcome, the causal pathway from the variants to the outcome can be difficult to disentangle. For example, the chemokine receptor gene cluster contains genetic variants associated with various cytokines. Associations between variants in this cluster and stroke risk may be driven by any of these cytokines. Multivariable Mendelian randomization is an extension of standard univariable Mendelian randomization to estimate the direct effects of related exposures with shared genetic predictors. However, when genetic variants are clustered, due to being located in a single genetic region, a Goldilocks dilemma arises: including too many highly-correlated variants in the analysis can lead to ill-conditioning, but pruning variants too aggressively can lead to imprecise estimates or even lack of identification. We propose multivariable methods that use principal component analysis to reduce many correlated genetic variants into a smaller number of orthogonal components that are used as instrumental variables. We show in simulations that these methods result in more precise estimates that are less sensitive to numerical instability due to both strong correlations and small changes in the input data. We apply the methods to demonstrate the most likely causal risk factor for stroke at the chemokine gene cluster is monocyte chemoattractant protein-1.

Inflammation and Brain Structure in Schizophrenia and Other Neuropsychiatric Disorders: A Mendelian Randomization Study.

Importance: Previous in vitro and postmortem research suggests that inflammation may lead to structural brain changes via activation of microglia and/or astrocytic dysfunction in a range of neuropsychiatric disorders. Objective: To investigate the relationship between inflammation and changes in brain structures in vivo and to explore a transcriptome-driven functional basis with relevance to mental illness. Design, Setting, and Participants: This study used multistage linked analyses, including mendelian randomization (MR), gene expression correlation, and connectivity analyses. A total of 20 688 participants in the UK Biobank, which includes clinical, genomic, and neuroimaging data, and 6 postmortem brains from neurotypical individuals in the Allen Human Brain Atlas (AHBA), including RNA microarray data. Data were extracted in February 2021 and analyzed between March and October 2021. Exposures: Genetic variants regulating levels and activity of circulating interleukin 1 (IL-1), IL-2, IL-6, C-reactive protein (CRP), and brain-derived neurotrophic factor (BDNF) were used as exposures in MR analyses. Main Outcomes and Measures: Brain imaging measures, including gray matter volume (GMV) and cortical thickness (CT), were used as outcomes. Associations were considered significant at a multiple testing-corrected threshold of P < 1.1 × 10-4. Differential gene expression in AHBA data was modeled in brain regions mapped to areas significant in MR analyses; genes were tested for biological and disease overrepresentation in annotation databases and for connectivity in protein-protein interaction networks. Results: Of 20 688 participants in the UK Biobank sample, 10 828 (52.3%) were female, and the mean (SD) age was 55.5 (7.5) years. In the UK Biobank sample, genetically predicted levels of IL-6 were associated with GMV in the middle temporal cortex (z score, 5.76; P = 8.39 × 10-9), inferior temporal (z score, 3.38; P = 7.20 × 10-5), fusiform (z score, 4.70; P = 2.60 × 10-7), and frontal (z score, -3.59; P = 3.30 × 10-5) cortex together with CT in the superior frontal region (z score, -5.11; P = 3.22 × 10-7). No significant associations were found for IL-1, IL-2, CRP, or BDNF after correction for multiple comparison. In the AHBA sample, 5 of 6 participants (83%) were male, and the mean (SD) age was 42.5 (13.4) years. Brain-wide coexpression analysis showed a highly interconnected network of genes preferentially expressed in the middle temporal gyrus (MTG), which further formed a highly connected protein-protein interaction network with IL-6 (enrichment test of expected vs observed network given the prevalence and degree of interactions in the STRING database: 43 nodes/30 edges observed vs 8 edges expected; mean node degree, 1.4; genome-wide significance, P = 4.54 × 10-9). MTG differentially expressed genes that were functionally enriched for biological processes in schizophrenia, autism spectrum disorder, and epilepsy. Conclusions and Relevance: In this study, genetically determined IL-6 was associated with brain structure and potentially affects areas implicated in developmental neuropsychiatric disorders, including schizophrenia and autism.

Sustainable natural coloring potential of bitter gourd (Momordica charantia L.) residues for cotton dyeing: innovative approach towards textile industry.

Natural products particularly natural colorants have attained worldwide importance and being eco-friendly can be considered an alternative to toxic dyes in order to reduce environmental pollution. The current study is based on the exploration of natural coloring behavior of bitter gourd leaves extract for cotton dyeing. Colorant was extracted using different extraction media like aqueous, alkali, organic, and acidic at different conditions. It has been found that on application of 50 ml of acidic extract having 6 g/100 ml of table salt for 55 min at 60 C°, maximum color yield has been obtained onto cotton. Upon using chemical and bio-mordants, new shade with good color fastness rating was obtained. FTIR analysis of extract showed the presence of flavonoids. It is concluded that under mild condition, bitter gourd leaves extract can be considered potential source of natural colorant for cotton dyeing and the presence of bio-mordant has made the process more soothing and sustainable in nature.

Sustainable isolation of licorice (Glycyrrhiza glabra L.)-based yellow natural colorant for dyeing of bio-mordanted cotton.

Sustainability in the utilization of products in all fields particularly food textiles, solar cells, etc. is of prime concern to the global community. In this study, licorice (Glycyrrhiza glabra L.) as a source of herbal-based coloring agent for cotton dyeing has been explored under the influence of ultrasonic (US) waves. Methanolic extract of licorice bark after US treatment for 20 min has shown excellent color depth (K/S) onto ultrasonically treated cotton fabric at 65°Cfor 45 min. Applying bio-mordants, it has been found that acacia extract (1%), henna (5%), and pomegranate and turmeric extracts (7%) as pre-bio-mordant, whereas acacia, turmeric, and henna extracts (7%) and pomegranate extract (5%) as post-bio-mordants, exhibited superb color strength. Salts of Al (7%) and salts of Fe (3%) as pre chemical mordants, while salts of Al (3%) and salts of Fe (5%) as post chemical mordants, have given good results. Overall, it has been found that salt of Fe (3%) as pre-chemical mordant and extract of turmeric (7%) as post bio-mordant have shown superb color strength. It can be concluded that US treatment being an environmentally safe means has only improved the color strength of colorant onto cotton fabric and the adding of bio-mordants has contrived the method more sustainable.

Sustainable application of Cassia obovata-based chrysophanic acid as potential source of yellow natural colorant for textile dyeing.

In the current pandemic scenario, sustainable green products particularly antiviral, antioxidant, and antibacterial in nature are gaining worldwide fame in almost every walk of life. Cassia obovata (C. obovata) has been valorized as a source of yellow natural dye for nylon dyeing. For the isolation of dye extracts and for surface tuning, nylon fabrics were treated with microwave rays up to 10 min. For getting new shades with good to excellent fastness characteristics, sustainable bio-mordants in comparison with chemical mordants have been used at 60 °C, 70 °C, and 80°C. It has been found that for getting effective colorant yield, acidic extract should be exposed to MW ray treatment up to 6 min, and for getting improved fastness rating, bio-mordants have given excellent color characteristics. Statistical optimization of dyeing variable shows that application of 40 mL of C. obovata acidic extract of RE of 6 pH containing 3 g/100 mL of salt when employed at 55 °C for 45 min has given excellent results onto irradiated nylon fabric (RNF). It is inferred that Cassia obovata has an excellent potential for coloration of surface-modified fabrics, where the application of low amount of bio-mordants under statistical optimized conditions has made process more ecological, economical, and sustainable.

Eco-friendly approach towards isolation of colorant from Esfand for bio-mordanted silk dyeing.

Sustainability in all applied fields particularly in textiles is to protect our globe, environment, and community, where green dyed products are playing their role. For the current study, Esfand (Peganum harmala) has been explored using a green isolation tool, i.e., ultrasonic (U.S.) rays, and applied onto fabric. Different dyeing parameters have been explored statistically through response surface methodology by employing temperature (50-80°C), time (25-65 min), extract volume (15-55 mL), salt (1-5 g/100 mL), and dye bath pH (4-7) through series of experiments. For developing new shades, green mordants such as elaichi, neem, turmeric, and zeera have been utilized. It has been found that exposure of 35 mL extract of 7 pH containing 3 g/100 mL of salt as exhausting agent to U.S. rays for 30 min for the dyeing of silk at 70°C for 45 min has given maximum color strength with reddish-yellow shades. Color characteristics obtained in the CIE Lab system reveal that 5% of turmeric as meta bio-mordant has given good quality reddish-yellow shades. It is found that U.S. rays have not only good potential to isolate colorant followed by dyeing of silk under reduced condition but also the application of bio-mordants have made the process more greener, sustainable, and cleaner.

Waste black tea leaves (Camelia sinensis) as a sustainable source of tannin natural colorant for bio-treated silk dyeing.

Environmentally friendly products are the need of the hour, particularly in this pandemic situation because synthetic products need such toxic chemicals for their formulation and finishing which are carcinogenic for the globe. The current study is the utilization of waste black tea leaf (BT)-based tannin brown natural colorant for silk dyeing using microwave treatment. Dye (tannin) has been isolated in various media before and after microwave treatment up to 6 min and applied at various conditions. It has been found that 30 mL of aqueous extract of 3.0 pH obtained from 6.0 g of powder containing 3.0 g/100 mL of salt as an exhausting agent after microwave treatment for 5 min, when employed at 55 °C for 45 min, has given good color yield onto silk. Iron (3%) and acacia extract (2%) as pre-chemical and bio mordant, iron (2%) and pomegranate extract (2%) as post chemical and bio-mordant, and Al (3 %) and pomegranate extract (3%) as meta chemical and bio-mordant have given new shades with good to excellent fastness ratings. It is inferred that waste black tea leaves (BTs) in an aqueous medium have an excellent potential to serve as a source of natural tannin brown dye for the coloration of surface-modified silk fabrics under the influence of cost, energy, and time-effective microwave treatment. Additionally, the utilization of a low amount of sustainable chemical and bio-mordants has valorized the dyeing of silk by developing soothing and sustainable shades with good fastness properties.

Genomic Epidemiology of SARS-CoV-2 in Pakistan.

COVID-19 has swept globally and Pakistan is no exception. To investigate the initial introductions and transmissions of the SARS-CoV-2 in Pakistan, we performed the largest genomic epidemiology study of COVID-19 in Pakistan and generated 150 complete SARS-CoV-2 genome sequences from samples collected from March 16 to June 1, 2020. We identified a total of 347 mutated positions, 31 of which were over-represented in Pakistan. Meanwhile, we found over 1000 intra-host single-nucleotide variants (iSNVs). Several of them occurred concurrently, indicating possible interactions among them or coevolution. Some of the high-frequency iSNVs in Pakistan were not observed in the global population, suggesting strong purifying selections. The genomic epidemiology revealed five distinctive spreading clusters. The largest cluster consisted of 74 viruses which were derived from different geographic locations of Pakistan and formed a deep hierarchical structure, indicating an extensive and persistent nation-wide transmission of the virus that was probably attributed to a signature mutation (G8371T in ORF1ab) of this cluster. Furthermore, 28 putative international introductions were identified, several of which are consistent with the epidemiological investigations. In all, this study has inferred the possible pathways of introductions and transmissions of SARS-CoV-2 in Pakistan, which could aid ongoing and future viral surveillance and COVID-19 control.

Genetic modification of Gossypium arboreum universal stress protein (GUSP1) improves drought tolerance in transgenic cotton (Gossypium hirsutum).

Cotton crop suffers shortage of irrigation water at reproductive stage which reduces the yield and fibre quality. Universal stress proteins belong to Pfam00582 which enables several plants to cope with multiple stresses via ATP binding. GUSP1 (Gossypium arboreum USP) is one of such proteins; its amino acids were mutated after in silico simulations including homology modeling and molecular docking analysis. Transgenic cotton plants were developed through Agrobacterium mediated genetic transformation by using mutated pmGP1 and non mutated pGP1 constructs under CaMV35S promoter. PCR and semi-quantitative PCR analyses confirmed the amplification and expression of transgene in transgenic plants. It was revealed that leaf relative water content, total chlorophyll content, CO2 assimilation as net photosynthesis, stomatal conductance, total soluble sugars and proline content was significantly increased at P ≤ 0.0001 and P ≤ 0.001 in both the pmGP1 and pGP1 transgenic plants as compared to non transgenic control plants. Moreover, relative membrane permeability and the transpiration rate were reduced significantly at P ≤ 0.0001 and P ≤ 0.001 respectively in transgenic plants under drought stress. Furthermore, the T1 transgenic seedlings containing pmGP1 mutated construct showed longer roots under desiccation stress imposed by 5% PEG. Transgene inheritance into the T1 progeny plants was confirmed by amplification through PCR and integration through Southern blot. Hence, our results pave the way to utilize the mutagenized known genes for increasing endurance of plants under drought stress. This will help to increase our understanding of drought tolerance/ sensitivity in cotton plants at the molecular level. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-01048-5.

Molecular characterization and expression of cyclic nucleotide gated ion channels 19 and 20 in Arabidopsis thaliana for their potential role in salt stress.

Cyclic nucleotide gated ion channels (CNGCs) in plants have very important role in signaling and development. The study reports role of CNGC19 and CNGC20 in salt stress in A. thaliana. In-silico, genome wide analysis showed that CNGC19 and CNGC20 are related to salt stress with maximum expression after 6 h in A. thaliana. The position of inserted T-DNA was determined (in-vivo) through TAIL-PCR for activation tagged mutants of CNGC19 and CNGC20 under salt stress. The expression of AtCNGC19 and AtCNGC20 after cloning under 35S promoter of expression vectors pBCH1 and pEarleyGate100 was determined in A. thaliana by real-time PCR analysis. Genome wide analysis showed that AtCNGC11 had lowest and AtCNGC20 highest molecular weight as well as number of amino acid residues. In-vivo expression of AtCNGC19 and AtCNGC20 was enhanced through T-DNA insertion and 35S promoter in over-expressed plants under high salt concentration. AtCNGC19 was activated twice in control and about five times under 150 mM NaCl stress level, and expression value was also higher than AtCNGC20. Phenotypically, over-expressed plants and calli were healthier while knock-out plants and calli showed retarded growth under salinity stress. The study provides new insight for the role of AtCNGC19 and AtCNGC20 under salt stress regulation in A. thaliana and will be helpful for improvement of crop plants for salt stress to combat food shortage and security.

Surface-enhanced Raman spectroscopy for comparison of serum samples of typhoid and tuberculosis patients of different stages.

BACKGROUND: Surface-enhanced Raman spectroscopy (SERS) is a reliable tool for the identification and differentiation of two different human pathological conditions sharing the same symptomology, typhoid and tuberculosis (TB). OBJECTIVES: To explore the potential of surface-enhanced Raman spectroscopy for differentiation of two different diseases showing the same symptoms and analysis by principal component analysis (PCA) and partial least square discriminate analysis (PLS-DA). METHODS: Serum samples of clinically diagnosed typhoid and tuberculosis infected individuals were analyzed and differentiated by SERS using silver nanoparticles (Ag NPs) as a SERS substrate. For this purpose, the collected serum samples were analyzed under the SERS instrument and unique SERS spectra of typhoid and tuberculosis were compared showing notable spectral differences in protein, lipid and carbohydrates features. Different stages of the diseased class of typhoid (Early acute and late acute stage) and tuberculosis (Pulmonary and extra-pulmonary stage) were compared with each other and with healthy human serum samples, which were significantly separated. Moreover, SERS data was analyzed using multivariate data analysis techniques including principal component analysis (PCA) and partial least square discriminate analysis (PLS-DA) and differences were so prominent to observe. RESULTS: SERS Spectral data of typhoid and tuberculosis showed clear differences and were significantly separated using PCA. SERS spectral data of both stages of typhoid and tuberculosis were separated according to 1st principle component. Moreover, by analyzing data using partial least square discriminate analysis, differentiation of two disease classes were considered more valid with a 100% value of sensitivity, specificity and accuracy. CONCLUSION: SERS can be employed for identification and comparison of two different human pathological conditions sharing same symptomology.