101 research outputs found
Genome-wide analysis of wheat calcium ATPases and potential role of selected ACAs and ECAs in calcium stress
No full textBackground:P2- type calcium ATPases (ACAs-auto inhibited calcium ATPases and ECAs-endoplasmic reticulum calcium ATPases) belong to the P- type ATPase family of active membrane transporters and are significantly involved in maintaining accurate levels of Ca2+, Mn2+ and Zn2+ in the cytosol as well as playing a very important role in stress signaling, stomatal opening and closing and pollen tube growth. Here we report the identification and possible role of some of these ATPases from wheat.Results:In this study, ACA and ECA sequences of six species (belonging to Poaceae) were retrieved from different databases and a phylogenetic tree was constructed. A high degree of evolutionary relatedness was observed among P2 sequences characterized in this study. Members of the respective groups from different plant species were observed to fall under the same clade. This pattern highlights the common ancestry of P2− type calcium ATPases. Furthermore, qRT-PCR was used to analyse the expression of selected ACAs and ECAs from Triticum aestivum (wheat) under calcium toxicity and calcium deficiency. The data indicated that expression of ECAs is enhanced under calcium stress, suggesting possible roles of these ATPases in calcium homeostasis in wheat. Similarly, the expression of ACAs was significantly different in plants grown under calcium stress as compared to plants grown under control conditions. This gives clues to the role of ACAs in signal transduction during calcium stress in wheat.Conclusion:Here we concluded that wheat genome consists of nine P2B and three P2A -type calcium ATPases. Moreover, gene loss events in wheat ancestors lead to the loss of a particular homoeolog of a gene in wheat. To elaborate the role of these wheat ATPases, qRT-PCR was performed. The results indicated that when plants are exposed to calcium stress, both P2A and P2B gene expression get enhanced. This further gives clues about the possible role of these ATPases in wheat in calcium management. These findings can be useful in future for genetic manipulations as well as in wheat genome annotation process.<br/
Investigations on Aspergillus fumigatus double-stranded RNAs and their effects on the fungus
No full textThe aim of this research was to assess the incidence of dsRNA mycoviruses in the
opportunistic human pathogenic fungus Aspergillus fumigatus, where previously no dsRNA
viruses had been reported and to investigate the effects of any dsRNAs on the growth and
pathogenicity of the fungus. Thus far 366 isolates (clinical and environmental) have been
screened, 24 of which posses dsRNA elements. Successful efforts were made to completely
characterise the two dsRNA segments of the isolate 88, partitivirus to obtain novel sequence
information.
Fungal viruses or mycoviruses are widespread and they usually infect their hosts persistently
without any detectable phenotypic effects. They have been however linked with both
hypovirulence and hypervirulence but are normally cryptic. To obtain information on the effect
of the dsRNAs on their respective hosts, efforts were made to ‘cure’ isolate 88 of its dsRNA
infection by cycloheximide treatment. However, following cycloheximide treatment, a
sensitive reverse transcription polymerase chain reaction (RT-PCR) amplification assay
showed that the dsRNA elements, whilst being reduced in amount, were not eliminated
completely and that high levels of cycloheximide also interfered with spore production,
pigmentation and overall growth of the isolate. In further experiments attempts were made to
mobilise the dsRNAs from 4 isolates viz. A-56, A-54, A-78 and isolate 88 into isolate Af-273y,
which is hygromycin resistant and yellow in colour, by hyphal tip fusion, protoplast fusion and
protoplast transfection with purified virus. Protoplast fusion and viral transfection experiments
were successful for some isolates, as assessed by the RT-PCR assay and small scale extractions
of nucleic acids. Subsequently comparative growth experiments by radial growth assay and
mycelial weight measurements between isolate Af-273y and Af-273y transfected with isolate
88 partitivirus in essentially the same genetic background were performed. These experiments
showed that the partitivirus infection resulted in a sectored phenotype and significantly lowered
the growth of the fungus. All efforts to initiate the molecular characterisation of
uncharacterised dsRNA elements found in isolates A-54, A-78 and isolate-66 have thus far
proven unsuccessful but a new approach (cDNA library construction) is proposed for the
characterisation of these dsRNAs
A comprehensive computational mutation structurefunction approach for determining potential drug target sites in poliovirus 2A protease
No full textA comprehensive computational mutation structurefunction approach for determining potential drug target sites in poliovirus 2A protease
No full textPurpose: To investigate a computational approach for analysing the structure-function relationship of poliovirus 2A protease using various bioinformatics tools. Methods: The three-dimensional structure of 2Apro was modelled and analyzed using the crystal structure of coxsakievirus B4 as a template to understand the function of this protein. Structural validation programs, VADAR and QMEAN, were used to verify the 2Apro model. Analysis of protein stability changes in poliovirus 2A protease-mutated sequences using various servers was also performed. Furthermore, mutation pattern, intrinsic disorder regions (IDRs), hydrophobic regions, drug binding sites (DBS) and subcellular localization were identified. Results: Hydrophobicity results confirmed the suitability and reliability of 2A protease as a potential drug target. Less IDRs were observed in the protein. Moreover, the results showed the presence of various important drug binding targets among conserved regions of the protease. The predicted drug binding sites indicate their suitability for the inhibition and development of anti-viral drugs against poliovirus 2A protease. Conclusion: The current study resulted in the detection of important ligand interactions with respect to the binding site of the targeted protein. Thus, these compounds may be potent drug candidates and their potency may be increased against poliovirus 2A protease with relatively simple structural changes. Keywords: 2A Protease, Computational analysis, Drug binding sites, Intrinsic disorder regions, Hydrophobicit
Investigations on Aspergillus fumigatus double-stranded RNAs and their effects on the fungus
No full textThe aim of this research was to assess the incidence of dsRNA mycoviruses in the opportunistic human pathogenic fungus Aspergillus fumigatus, where previously no dsRNA viruses had been reported and to investigate the effects of any dsRNAs on the growth and pathogenicity of the fungus. Thus far 366 isolates (clinical and environmental) have been screened, 24 of which posses dsRNA elements. Successful efforts were made to completely characterise the two dsRNA segments of the isolate 88, partitivirus to obtain novel sequence information. Fungal viruses or mycoviruses are widespread and they usually infect their hosts persistently without any detectable phenotypic effects. They have been however linked with both hypovirulence and hypervirulence but are normally cryptic. To obtain information on the effect of the dsRNAs on their respective hosts, efforts were made to ‘cure’ isolate 88 of its dsRNA infection by cycloheximide treatment. However, following cycloheximide treatment, a sensitive reverse transcription polymerase chain reaction (RT-PCR) amplification assay showed that the dsRNA elements, whilst being reduced in amount, were not eliminated completely and that high levels of cycloheximide also interfered with spore production, pigmentation and overall growth of the isolate. In further experiments attempts were made to mobilise the dsRNAs from 4 isolates viz. A-56, A-54, A-78 and isolate 88 into isolate Af-273y, which is hygromycin resistant and yellow in colour, by hyphal tip fusion, protoplast fusion and protoplast transfection with purified virus. Protoplast fusion and viral transfection experiments were successful for some isolates, as assessed by the RT-PCR assay and small scale extractions of nucleic acids. Subsequently comparative growth experiments by radial growth assay and mycelial weight measurements between isolate Af-273y and Af-273y transfected with isolate 88 partitivirus in essentially the same genetic background were performed. These experiments showed that the partitivirus infection resulted in a sectored phenotype and significantly lowered the growth of the fungus. All efforts to initiate the molecular characterisation of uncharacterised dsRNA elements found in isolates A-54, A-78 and isolate-66 have thus far proven unsuccessful but a new approach (cDNA library construction) is proposed for the characterisation of these dsRNAs.EThOS - Electronic Theses Online ServiceHigher Education Commission of PakistanGBUnited Kingdo
Building antifragile manufacturing systems through strategic technology integration
No full textPurpose – This study develops and validates, through expert consensus, a framework for achieving antifragilityin manufacturing by strategically integrating modern digital technologies with capabilities that enableorganizations to grow stronger through disruption. It moves beyond traditional resilience-focused approaches byemphasizing continuous adaptability, sustained growth and competitive advantage in an environmentcharacterized by volatility and rapid technological change. Design/methodology/approach – Grounded in the dynamic capability perspective, the study synthesizesinsights from an extensive literature review with the results of a Delphi study involving a panel of 14 industryand academic experts. The process identified and refined a set of critical supporting capabilities, including cross-functional governance, interoperability assessment and risk-responsive integration, that enable the alignment ofdigital transformation initiatives with antifragile objectives. Findings – Antifragility is positioned as a higher-order dynamic capability that transforms volatility into a driverof innovation and strategic renewal. The resulting expert-based framework maps emerging technologies such asartificial intelligence, the Internet of Things and big data analytics to specific sensing, seizing and transformingcapabilities, providing a structured pathway for operationalizing antifragility in manufacturing contexts. Practical implications – The framework offers manufacturers a structured approach for aligning technology investments with antifragile objectives, ensuring that digital transformation enhances rather than undermines adaptability and growth. It encourages a phased, resource-aware implementation strategy that leverages disruptions as strategic assets, fostering both business continuity and long-term competitiveness. Originality/value – This research conceptualizes antifragility as a distinct and advanced capability in manufacturing and demonstrates how it can be purposefully developed through strategic technology integration. By combining theoretical grounding with expert validation, it bridges the gap between digital transformation and antifragility, offering a practical roadmap for turning uncertainty and variability into sources of competitive advantage.CC BY 4.0© Morteza Ghobakhloo, Behzad Foroughi, Masood Fathi, Mostafa Al-Emran, Mohammed A. Al-Sharafiand Muhammad Faraz Mubarak.Corresponding author Morteza Ghobakhloo can be contacted at: [email protected]</p
Comprehensive Analyses of NAC Transcription Factor Family in Almond (Prunus dulcis) and Their Differential Gene Expression during Fruit Development
No full textAs plant specific transcription factors, NAC (NAM, ATAF1/2, CUC2) domain is involved in the plant development and stress responses. Due to the vitality of NAC gene family, BLASTp was performed to identify NAC genes in almond (Prunus dulcis). Further, phylogenetic and syntenic analyses were performed to determine the homology and evolutionary relationship. Gene duplication, gene structure, motif, subcellular localization, and cis-regulatory analyses were performed to assess the function of PdNAC. Whereas RNA-seq analysis was performed to determine the differential expression of PdNAC in fruits at various developmental stages. We identified 106 NAC genes in P. dulcis genome and were renamed according to their chromosomal distribution. Phylogenetic analysis in both P. dulcis and Arabidopsis thaliana revealed the presence of 14 subfamilies. Motif and gene structure followed a pattern according to the PdNAC position in phylogenetic subfamilies. Majority of NAC are localized in the nucleus and have ABA-responsive elements in the upstream region of PdNAC. Differential gene expression analyses revealed one and six PdNAC that were up and down-regulated, respectively, at all development stages. This study provides insights into the structure and function of PdNAC along with their role in the fruit development to enhance an understanding of NAC in P. dulcis
A versatile dataset for intrinsic plagiarism detection, text reuse analysis, and author clustering in Urdu
No full textPlagiarism detection (PD) is a process of identifying instances where someone has presented another person's work or ideas as their own. Plagiarism detection is categorized into two types (i) Intrinsic plagiarism detection primarily concerns the assessment of authorship consistency within a single document, aiming to identify instances where portions of the text may have been copied or paraphrased from elsewhere within the same document. Author clustering, closely related to intrinsic plagiarism detection, involves grouping documents based on their stylistic and linguistic characteristics to identify common authors or sources within a given dataset. On the other hand, (ii) extrinsic plagiarism detection delves into the comparative analysis of a suspicious document against a set of external source documents, seeking instances of shared phrases, sentences, or paragraphs between them, which is often referred to as text reuse or verbatim copying. Detection of plagiarism from documents is a long-established task in the area of NLP with remarkable contributions in multiple applications. A lot of research has already been conducted in the English and other foreign languages but Urdu language needs a lot of attention especially in intrinsic plagiarism detection domain. The major reason is that Urdu is a low resource language and unfortunately there is no high-quality benchmark corpus available for intrinsic plagiarism detection in Urdu language. This study presents a high-quality benchmark Corpus comprising 10,872 documents. The corpus is structured into two granularity levels: sentence level and paragraph level. This dataset serves multifaceted purposes, facilitating intrinsic plagiarism detection, verbatim text reuse identification, and author clustering in the Urdu language. Also, it holds significance for natural language processing researchers and practitioners as it facilitates the development of specialized plagiarism detection models tailored to the Urdu language. These models can play a vital role in education and publishing by improving the accuracy of plagiarism detection, effectively addressing a gap and enhancing the overall ability to identify copied content in Urdu writing
Hallmark Attributes of Plant Transcription Factors and Potentials of WRKY, MYB and NAC in Abiotic Stresses
No full textComplete nucleotide sequences of two dsRNAs associated with a new partitivirus infecting Aspergillus fumigatus
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