02477nas a2200325 4500008004100000022001400041245009500055210006900150260005700219300001400276490000700290520142400297653001201721653002001733653001501753653001101768653002001779100002001799700002001819700001701839700002501856700002101881700002001902700002201922700001901944700002501963700002101988700002202009856012002031 2014 eng d a0175-759800aProteomics of arsenic stress in the gram-positive organism Exiguobacterium sp PS NCIM 54630 aProteomics of arsenic stress in the grampositive organism Exiguo a233 SPRING ST, NEW YORK, NY 10013 USAbSPRINGERcAUG a6761-67730 v983 a

The general responses of microorganisms to environmental onslaughts are modulated by altering the gene expression pattern to reduce damage in the cell and produce compensating stress responses. The present study attempts to unravel the response of the Gram-positive Exiguobacterium sp. PS NCIM 5463 in the presence of [As(III)] and arsenate [As(V)] using comparative proteomics via two-dimension gel electrophoresis (2-DE) coupled with identification of proteins using matrix-assisted laser desorption/ionisation (MALDI-TOF/MALDI-TOF/TOF). Out of 926 Coomassie-stained proteins, 45 were differentially expressed (p < 0.05). Considering the resolution and abundance level, 24 spots (peptides) were subjected to MALDI analysis, identified and categorised into several functional categories, viz., nitrogen metabolism, energy and stress regulators, carbohydrate metabolism, protein synthesis components and others. A functional role of each protein is discussed in Exiguobacterium sp. PS 5463 under arsenic stress and validated at their transcript level using a quantitative real-time polymerase chain reaction. Unlike previous reports that unravel the responses toward arsenic stress in Gram-negative organisms, the present study identified new proteins under arsenic stress in a Gram-positive organism, Exiguobacterium sp. PS NCIM 5463, which could elucidate the physiology of organisms under arsenic stress.

10aArsenic10aExiguobacterium10aproteomics10aStress10aTranscriptomics1 aSacheti, Poonam1 aPatil, Rajendra1 aDube, Ankita1 aBhonsle, Hemangi, S.1 aThombre, Dipalee1 aMarathe, Sayali1 aVidhate, Ravindra1 aWagh, Priyanka1 aKulkarni, Mahesh, J.1 aRapole, Srikanth1 aGade, Wasudeo, N. uhttps://library.ncl.res.in/content/proteomics-arsenic-stress-gram-positive-organism-exiguobacterium-sp-ps-ncim-546301875nas a2200265 4500008004100000022001400041245008900055210006900144260007400213300001400287490000700301520096100308653002101269653001601290653002601306653002301332653001901355653002001374100001401394700002601408700002101434700001901455700001701474856011801491 2015 eng d a0141-549200aCell line development for biomanufacturing processes: recent advances and an outlook0 aCell line development for biomanufacturing processes recent adva aVAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDSbSPRINGERcAUG a1553-15640 v373 a

At the core of a biomanufacturing process for recombinant proteins is the production cell line. It influences the productivity and product quality. Its characteristics also dictate process development, as the process is optimized to complement the producing cell to achieve the target productivity and quality. Advances in the past decade, from vector design to cell line screening, have greatly expanded our capability to attain producing cell lines with certain desired traits. Increasing availability of genomic and transcriptomic resources for industrially important cell lines coupled with advances in genome editing technology have opened new avenues for cell line development. These developments are poised to help biosimilar manufacturing, which requires targeting pre-defined product quality attributes, e.g., glycoform, to match the innovator's range. This review summarizes recent advances and discusses future possibilities in this area.

10aBiomanufacturing10aBiosimilars10aCell line development10aCHO cells genomics10aGenome editing10aTranscriptomics1 aLe, Huong1 aVishwanathan, Nandita1 aJacob, Nitya, M.1 aGadgil, Mugdha1 aHu, Wei-Shou uhttps://library.ncl.res.in/content/cell-line-development-biomanufacturing-processes-recent-advances-and-outlook-002560nas a2200313 4500008004100000022001400041245010100055210006900156260000800225300001100233490000800244520153800252653002601790653001201816653001201828653003301840653001401873653002801887653001701915653002901932653002001961100002001981700002502001700001902026700001802045700003302063700002002096856013002116 2020 eng d a0031-942200aBiosynthesis and tissue-specific partitioning of camphor and eugenol in Ocimum kilimandscharicum0 aBiosynthesis and tissuespecific partitioning of camphor and euge cSEP a1124510 v1773 a

In Ocimum kilimandscharicum, the relative volatile composition of camphor in leaves was as high as 55%, while that of eugenol in roots was 57%. These metabolites were differentially partitioned between the aerial and root tissues. Global metabolomics revealed tissue-specific biochemical specialization, evident by the differential distribution of 2588 putative metabolites across nine tissues. Next-generation sequencing analysis indicated differential expression of 51 phenylpropanoid and 55 terpenoid pathway genes in aerial and root tissues. By integrating metabolomics with transcriptomics, the camphor biosynthesis pathway in O. kilimandscharicum was elucidated. In planta bioassays revealed the role of geranyl diphosphate synthase (gpps) and borneol dehydrogenase (bdh) in camphor biosynthesis. Further, the partitioning of camphor was attributed to tissue-specific gene expression of both the pathway entry point (gpps) and terminal (bdh) enzyme. Unlike camphor, eugenol accumulated more in roots; however, absence of the eugenol synthase gene in roots indicated long distance transport from aerial tissues. In silico co-expression analysis indicated the potential involvement of ATP-binding cassette, multidrug and toxic compound extrusion, and sugar transporters in eugenol transport. Similar partitioning was evident across five other Ocimum species. Overall, our work indicates that metabolite partitioning maybe a finely regulated process, which may have implications on plant growth, development, and defense.

10aBorneol dehydrogenase10aCamphor10aEugenol10aGeranyl diphosphate synthase10aLamiaceae10aMetabolite partitioning10aMetabolomics10aOcimum kilimandscharicum10aTranscriptomics1 aSingh, Priyanka1 aKalunke, Raviraj, M.1 aShukla, Anurag1 aTzfadia, Oren1 aThulasiram, Hirekodathakallu1 aGiri, Ashok, P. uhttps://library.ncl.res.in/content/biosynthesis-and-tissue-specific-partitioning-camphor-and-eugenol-ocimum-kilimandscharicum02526nas a2200277 4500008004100000022001400041245010300055210006900158260000800227300000700235490000700242520162300249653001801872653001301890653001301903653002301916653002001939653002701959100001601986700002302002700002402025700002502049700002102074700002702095856012602122 2023 eng d a0137-588100aRole of ions and their transporters in combating salt stress in Pandanus odorifer (Forssk.) Kuntze0 aRole of ions and their transporters in combating salt stress in  cMAY a660 v453 a

Soil salinity is a major environmental constraint causing huge losses in crop production. Pandanus odorifer (Forssk.) Kuntze is an aromatic monocot plant species belonging to the family Pandanaceae, which grows naturally on the saline soils along the coasts of Asia, Southeast Asia, and Polynesia. The plants are dioecious and highly fertile, and the consistent saline sprays, strong winds, and severe soil salinity hardly affect their growth and fertility. Hence, understanding the mechanism of high salinity tolerance in P. odorifer could provide major advances in overcoming salinity stress in crop plants. In the present study, we analyzed control (0 M NaCl) and treated (1 M NaCl treatment for 3 weeks) plants of P. odorifer to understand the role of ion distribution, ion transport, and related mechanisms under salt stress. Using a combination of ionomics and transcriptomics approaches, we identified the molecular mechanisms contributing to the high salinity stress in P. odorifer. Under NaCl stress, there was a significant increase in Na, Cl, and other ions in leaves, while the concentrations of Si, Fe, Ni, and Ti decreased. Similarly, in roots, the levels of Na, Mg, Cd, and Cr were significantly high, while the levels of other ions decreased. Most of the genes related to ion transport and homeostasis, such as NHX1, CLC-C, SOS1, HAK, and ABC transporters, were upregulated in 1 M NaCl stress conditions. This study revealed that vacuolar sequestration of Na+ and the distribution of ions in the roots and shoots play significant roles in the salt-stress tolerance mechanism of P. odorifer.

10aIon transport10aIonomics10aPandanus10aSalinity tolerance10aTranscriptomics10aVacuolar sequestration1 aRashmi, Deo1 aAnsari, Waquar, A.1 aKadoo, Narendra, Y.1 aBarvkar, Vitthal, T.1 aDeshmukh, Rupesh1 aNadaf, Altafhusain, B. uhttps://library.ncl.res.in/content/role-ions-and-their-transporters-combating-salt-stress-pandanus-odorifer-forssk-kuntze02505nas a2200265 4500008004100000022001400041245016800055210006900223260000800292300001200300490000700312520152900319653003101848653001101879653002501890653002201915653002001937100003701957700003801994700002202032700001802054700002002072700002202092856012502114 2023 eng d a1479-262100aTargeted metabolite profiling and de novo transcriptome sequencing reveal the key terpene synthase genes in medicinally important plant, Couroupita guianensis Aubl0 aTargeted metabolite profiling and de novo transcriptome sequenci cDEC a558-5700 v213 a

The Lecythidaceae family tree, Couroupita guianensis Aubl, popularly known as Nagpushpa, is a widely cultivated ornamental tree with several uses in traditional medicine. The tree is revered as highly sacred in Indian traditional culture due to its uniquely shaped, fragrant flowers. Considering the significance, we were prompted to carry out the metabolite and transcriptome analysis of Nagapushpa. The flower, petals, stamen, stem and leaf of C. guianensis were metabolically profiled, and it was discovered that the flower tissue contained the highest terpenoid reservoir. A number of terpenoid pathway transcripts were also found in the flower tissue after transcriptome profiling. KEGG pathway mapping was carried out to correlate transcript sequences with the biosynthesis of different types of terpenes. We were able to clone three full-length terpene synthase gene candidates, i.e. monoterpene ocimene synthase, diterpene ent-kaurene synthase and sesquiterpene farnesene synthase. The transcript expression of selected terpene synthase genes was also verified in flower tissue. These cloned sequences were used for in silico structural investigations and protein function prediction at the level of 3D structure. The data presented in this study provide a comprehensive resource for the metabolic and transcriptomic profiles of C. guianensis. The study paves the way towards the elucidation of terpene biosynthetic pathway in C. guianensis and heterologous production of useful terpenoids in the future.

10aCouroupita guianensis Aubl10aflower10aMetabolite profiling10aterpene synthases10aTranscriptomics1 aThulasiram, Hirekodathakallu, V.1 aKaregaonkar, Shrikant, Jagannathr1 aSharma, Poojadevi1 aKumar, Ashish1 aRamkumar, Sudha1 aPandreka, Avinash uhttps://library.ncl.res.in/content/targeted-metabolite-profiling-and-de-novo-transcriptome-sequencing-reveal-key-terpene00772nas a2200229 4500008004100000022001400041245010200055210006900157260000900226300000700235490000700242653002200249653001200271653001700283653002000300653001400320653001800334100002200352700002000374700001800394856013000412 2024 eng d a0250-599100aTrehalase inhibition in Helicoverpa armigera activates machinery for alternate energy acquisition0 aTrehalase inhibition in Helicoverpa armigera activates machinery cJUL  a740 v4910aEnergy metabolism10aglucose10aMetabolomics10aTranscriptomics10atrehalase10avalidamycin A1 aTellis, Meenakshi1 aMohite, Sharada1 aJoshi, Rakesh uhttps://library.ncl.res.in/content/trehalase-inhibition-helicoverpa-armigera-activates-machinery-alternate-energy-acquisition02891nas a2200229 4500008004100000022001400041245011200055210006900167260000800236300000800244490000800252520211300260653000902373653001202382653002002394653001802414653003302432653002002465100002002485700002402505856013202529 2025 eng d a0032-093500aIntegrative multi-omics and computer-aided biofungicide design approach to combat fusarium wilt of chickpea0 aIntegrative multiomics and computeraided biofungicide design app cSEP a1070 v2623 a

Main conclusionIntegrating multi-omics and computer-aided drug discovery approaches can overcome the limitations of traditional methods and help develop highly effective, specific, and environmentally safe biofungicides to control crop diseases.AbstractChickpea is a valuable legume crop in terms of nutrition, food security, economic sustainability, and environmental benefits. Fusarium wilt caused by the soil-borne fungus Fusarium oxysporum f.sp. ciceri is one of the most important diseases affecting chickpea. Several disease management methods, including crop rotation, soil fumigation with chemical fungicides, soil solarization, etc., are practiced to manage the disease. However, these methods have various limitations and cannot completely control the disease. Moreover, chemical fungicides indiscriminately kill even the beneficial soil microbes, pollute groundwater, and enter the food chain. Hence, modern approaches emphasizing innovative strategies and technologies need to be explored to manage the disease effectively. In this review, we propose integrating multi-omics (genomics, proteomics, metabolomics, etc.) and computer-aided drug discovery (CADD) approaches to develop biofungicides targeting vital pathogen proteins. Multi-omics approaches can delve deeper into the plant-pathogen interaction and reveal essential pathogen genes or proteins. These proteins could be targeted using CADD to identify phytochemical-based potential biofungicides, either using structure- or ligand-based drug design approaches. The potential biofungicides can be subjected to the prediction of carcinogenicity, hepatotoxicity, mutagenicity, etc., to identify biofungicides that are safe to use and are highly specific to the target pathogen. In vivo and in vitro validation studies can be followed to establish the efficacy and safety of the identified biofungicides for their practical application. This integrated approach can reduce the time and cost compared to the traditional methods and accelerate the discovery of highly effective biofungicides to protect crops from various diseases.

10aCADD10adocking10aFungal diseases10aMD Simulation10aProtein structure prediction10aTranscriptomics1 aSahoo, Rosaleen1 aKadoo, Narendra, Y. uhttps://library.ncl.res.in/content/integrative-multi-omics-and-computer-aided-biofungicide-design-approach-combat-fusarium-wilt02482nas a2200277 4500008004100000022001400041245011000055210006900165260000800234300001200242490000700254520152400261653001801785653003101803653001301834653002601847653002001873100002301893700002401916700002001940700002701960700002901987700003302016700002402049856013102073 2025 eng d a0971-589400aTranscriptome analyses reveal TaWRKY41 as a potential candidate governing spot blotch resistance in wheat0 aTranscriptome analyses reveal TaWRKY41 as a potential candidate  cAPR a591-6080 v313 a

Spot blotch disease caused by Bipolaris sorokiniana poses a significant threat to wheat production. Cultivation of disease-resistant wheat genotypes appears to be the most practical approach to mitigate the impact of this devastating disease. However, the molecular responses of wheat plants during spot blotch disease progression remain poorly understood. This study employed RNA-sequencing to unravel the spatiotemporal molecular events underlying the resistance mechanism in the spot blotch susceptible and resistant wheat genotypes. This study further provides a comprehensive overview of differentially expressed transcripts through functional analysis and transcription factor identification, elucidating the biological mechanisms governing wheat-B. sorokiniana interaction. In the resistant genotype, the expression of one of the key transcription factors, TaWRKY41, was significantly induced upon pathogen inoculation. Computational studies, electrophoretic-mobility shift assay, and yeast one-hybrid assay confirmed the interaction of the recombinant TaWRKY41 protein with W-box elements present in the promoters of plant defense-related genes. Furthermore, co-expression network analyses identified downstream genes positively correlated with TaWRKY41, providing insights into their probable involvement in the defense response. Overall, our investigation suggests that TaWRKY41 contributes to spot blotch resistance in wheat. This knowledge can help develop new disease-resistant wheat varieties.

10aPlant defense10aplant-pathogen interaction10aTaWRKY4110aTranscription factors10aTranscriptomics1 aDayama, Bhakti, R.1 aMahadik, Varsha, A.1 aSomani, Deepika1 aShinde, Balkrishna, A.1 aKondhare, Kirtikumar, R.1 aKarthikeyan, Muthukumarasamy1 aKadoo, Narendra, Y. uhttps://library.ncl.res.in/content/transcriptome-analyses-reveal-tawrky41-potential-candidate-governing-spot-blotch-resistance