Designing and expression of novel recombinant fusion protein for efficient antigen screening of SARS-CoV-2.

Corona virus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), claimed millions globally. After the report of the first incidence of the virus, variants emerged with each posing a unique threat than its predecessors. Though many advanced diagnostic assays like real-time PCR are available for screening of SARS-CoV-2, their applications are being hindered because of accessibility and cost. With the advent of rapid assays for antigenic screening of SARS-CoV-2 made diagnostics far easy as the assays are rapid, cost-effective and can be used at point-of-care settings. In the present study, a fusion construct was made utilising highly immunogenic B cell epitopes from the three important structural proteins of SARS-CoV-2. The protein was expressed; purified capture mAbs generated and rapid antigen assay was developed. Eight hundred and forty nasopharyngeal swab samples were screened for the evaluation of the developed assay which showed 37.14% positivity, 96.51% and 100% sensitivity and specificity respectively. The assay developed was supposed to identify SARS-CoV-2 wild-type as well as variants of concern and variants of importance in real-time conditions.

Impact of Climate Change on Altered Fruit Quality with Organoleptic, Health Benefit, and Nutritional Attributes.

As a consequence of global climate change, acute water deficit conditions, soil salinity, and high temperature have been on the rise in their magnitude and frequency, which have been found to impact plant growth and development negatively. However, recent evidence suggests that many fruit plants that face moderate abiotic stresses can result in beneficial effects on the postharvest storage characters of the fruits. Salinity, drought, and high temperature conditions stimulate the synthesis of abscisic acid (ABA), and secondary metabolites, which are vital for fruit quality. The secondary metabolites like phenolic acids and anthocyanins that accumulate under abiotic stress conditions have antioxidant activity, and therefore, such fruits have health benefits too. It has been noticed that fruits accumulate more sugar and anthocyanins owing to upregulation of phenylpropanoid pathway enzymes. The novel information that has been generated thus far indicates that the growth environment during fruit development influences the quality components of the fruits. But the quality depends on the trade-offs between productivity, plant defense, and the frequency, duration, and intensity of stress. In this review, we capture the current knowledge of the irrigation practices for optimizing fruit production in arid and semiarid regions and enhancement in the quality of fruit with the application of exogenous ABA and identify gaps that exist in our understanding of fruit quality under abiotic stress conditions.

Performance evaluation of in-house developed Covid-19 IgG/IgM antibody rapid diagnostic kit.

In the interest of preventing the Coronavirus Disease 2019 (COVID-19) pandemic from spreading, it is crucial to promptly identify and confine afflicted patients. Serological antibody testing is a significant diagnostic technique that is increasingly employed in clinics, however its clinical use is still being investigated. The present study was carried out to scrutinize how well Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) antibody testing using in-house developed rapid antibody assay worked against the chemiluminescence (CLIA) assay. Either IgG positive (IgG + IgM-) or IgM positive (IgM + IgG-); both IgG and IgM positive (IgM + IgG+); and negatives (IgM- IgG-) have been evaluated. A total of 300 samples with diverse age and sexual identity data were included. The combined sensitivities for IgG + IgM+, IgM + IgG-, IgG + IgM- and IgG-IgM- were evaluated. More accurate diagnostic results may be obtained using molecular diagnostic tools. The Antibody Rapid Diagnostic kit's (in-house developed) performance was satisfactory for determining the presence of Covid-19 infection with IgG and IgM positivity. The IgG and IgM positivity helped evaluate the immune response in the individual for the COVID-19 infection. These results lend support to the additional utilisation of serological antibody tests in the COVID-19 diagnosis.

Perspectives on Rapid Antigen Tests for Downstream Validation and Development of Theranostics.

Point-of-care SARS-CoV-2 rapid antigen tests have proven to be useful over the years and have become more apparent to the public eye during COVID-19 pandemic due to their ease of use, rapid processing and result times, and low cost. Here, we have assessed the effectiveness and accuracy of rapid antigen tests in comparison to the standard real-time polymerase chain reaction analyses of the same samples.

Machine Learning Heuristics on Gingivobuccal Cancer Gene Datasets Reveals Key Candidate Attributes for Prognosis.

Delayed cancer detection is one of the common causes of poor prognosis in the case of many cancers, including cancers of the oral cavity. Despite the improvement and development of new and efficient gene therapy treatments, very little has been carried out to algorithmically assess the impedance of these carcinomas. In this work, from attributes or NCBI's oral cancer datasets, viz. (i) name, (ii) gene(s), (iii) protein change, (iv) condition(s), clinical significance (last reviewed). We sought to train the number of instances emerging from them. Further, we attempt to annotate viable attributes in oral cancer gene datasets for the identification of gingivobuccal cancer (GBC). We further apply supervised and unsupervised machine learning methods to the gene datasets, revealing key candidate attributes for GBC prognosis. Our work highlights the importance of automated identification of key genes responsible for GBC that could perhaps be easily replicated in other forms of oral cancer detection.

Comparative performance of different antigens on the lateral flow assay (LFA) platform for the rapid serodiagnosis of paratuberculosis.

Paratuberculosis is a globally prevalent disease, that adversely affects the economy of livestock farming. Control is largely based on early detection followed by 'Test and Cull' or 'Test and Segregate' Policy. Implementation of paratuberculosis control is a special challenge due to the non-availability of point of care diagnostics (PoCD). Therefore, the present study aimed to optimize and evaluate a lateral flow assay (LFA) for the rapid serodiagnosis of paratuberculosis in ruminant species, especially in the view of the resource-limited areas. Performance of three different antigenic preparations including native purified protoplasmic antigen (nPPA-LFA), commercial purified protoplasmic antigen (cPPA-LFA), and a cocktail of recombinant secretory proteins (RP-LFA) was evaluated as detection reagents for coating LFA strips. Comparative performance of the optimized LFA was also evaluated with gold standard tissue culture, fecal PCR (polymerase chain reaction), and plate ELISA. In addition, the onsite testing of animals belonging to different farms (endemic), species, and regions using optimized LFA was also done to highlight the on-farm testing approach. Findings revealed recombinant secretory proteins based LFA (RP-LFA) had a higher sensitivity of detection compared to other antigens. RP-LFA had a sensitivity of 77.7%, 75.44%, and 75.16% in comparison to gold standard tissue culture, fecal PCR, and plate ELISA, respectively. The specificity of RP-LFA was 100% with all reference tests. In comparison to plate ELISA, RP-LFA had a detection limit of 100% when the S/P ratio of the serum sample is ≥1.0 and 80% when the S/P ratio range of 0.8-1.0. Using RP-LFA, on-farm testing of 608 animals was done and 283 (46.5%) were found positive. Kappa analysis of present RP-LFA revealed 'good strength of agreement' with gold standard tissue culture, fecal PCR, and plate ELISA. Optimized RP-LFA had no cross-reactivity with bovine tuberculosis (bovine TB). The RP-LFA was found reproducible, user-friendly and test results can be interpreted within five minutes. In conclusion, the findings of the present study advocate the huge potential of LFA-based PoCD in the rapid diagnosis and control of paratuberculosis.

The Omic Insights on Unfolding Saga of COVID-19.

The year 2019 has seen an emergence of the novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease of 2019 (COVID-19). Since the onset of the pandemic, biological and interdisciplinary research is being carried out across the world at a rapid pace to beat the pandemic. There is an increased need to comprehensively understand various aspects of the virus from detection to treatment options including drugs and vaccines for effective global management of the disease. In this review, we summarize the salient findings pertaining to SARS-CoV-2 biology, including symptoms, hosts, epidemiology, SARS-CoV-2 genome, and its emerging variants, viral diagnostics, host-pathogen interactions, alternative antiviral strategies and application of machine learning heuristics and artificial intelligence for effective management of COVID-19 and future pandemics.

SARS-CoV-2 transgressing LncRNAs uncovers the known unknowns.

SARS-CoV-2 harbors many known unknown regions in the form of hypothetical open reading frames (ORFs). Although the mechanisms underlying the disease pathogenesis are not clearly understood, molecules such as long noncoding RNAs (lncRNAs) play a key regulatory role in the viral pathogenesis from endocytosis. We asked whether or not the lncRNAs in the host are associated with the viral proteins and argue that lncRNA-mRNAs molecules related to viral infection may regulate SARS-CoV-2 pathogenesis. Toward the end of the perspective, we provide challenges and insights into investigating these transgression pathways.

Improvement of small seed for big nutritional feed.

Exploding global population, rapid urbanization, salinization of soils, decreasing arable land availability, groundwater resources, and dynamic climatic conditions pose impending damage to our food security by reducing the grain quality and quantity. This issue is further compounded in arid and semi-arid regions due to the shortage of irrigation water and erratic rainfalls. Millets are gluten (a family of proteins)-free and cultivated all over the globe for human consumption, fuel, feed, and fodder. They provide nutritional security for the under- and malnourished. With the deployment of strategies like foliar spray, traditional/marker-assisted breeding, identification of candidate genes for the translocation of important minerals, and genome-editing technologies, it is now tenable to biofortify important millets. Since the bioavailability of iron and zinc has been proven in human trials, the challenge is to make such grains accessible. This review encompasses nutritional benefits, progress made, challenges being encountered, and prospects of enriching millet crops with essential minerals.

Development of rELISA using novel markers for the diagnosis of paratuberculosis.

Paratuberculosis is one of the complex livestock infections whose control has largely been hampered due to the lack of efficacious diagnostics. Present study optimized plate ELISA assay for the diagnosis and screening of paratuberculosis using recombinant secretory proteins. Five secretory antigens (2677c, 3547c, 4308c, 1693c, and 2168c) were produced in the recombinant system using the E. coli host and used for the optimization of the assay. These proteins were selected because of their prior proven specificity and antigenicity as humoral immunity markers. The assay was first optimized using traditional ELISA reader and then the performance was evaluated using a handheld ELISA reader. Findings were identical in both traditional ELISA reader as well as handheld ELISA reader. Optimized ELISA was found reproducible using different batches of the recombinant antigens as well as in terms of the inter and intra assay %CV values. The present ELISA has a sensitivity and specificity of 91.6% and 100%, respectively. Also, rELISA revealed AUCROC and Youden index J of 0.95 and 0.91, respectively. In conclusion, assay conditions of MAP-recombinant protein-based ELISA were optimized and the optimized ELISA ODs can be read using portable handheld ELISA reader. Thereby, opening a future window to develop assay for onsite testing.

Molecular docking and dynamics studies of curcumin with COVID-19 proteins.

Coronavirus disease 2019 (COVID-19) is caused by a Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2), which is a positive-strand RNA virus. The SARS-CoV-2 genome and its association to SAR-CoV-1 vary from ca. 66 to 96% depending on the type of betacoronavirideae family members. With several drugs, viz. chloroquine, hydroxychloroquine, ivermectin, artemisinin, remdesivir, azithromycin considered for clinical trials, there has been an inherent need to find distinctive antiviral mechanisms of these drugs. Curcumin, a natural bioactive molecule has been shown to have therapeutic potential for various diseases, and its effect on COVID-19 is also currently being explored. In this study, we show the binding potential of curcumin targeted to a variety of SARS-CoV-2 proteins, viz. spike glycoproteins (PDB ID: 6VYB), nucleocapsid phosphoprotein (PDB ID: 6VYO), spike protein-ACE2 (PDB ID: 6M17) along with nsp10 (PDB ID: 6W4H) and RNA dependent RNA polymerase (PDB ID: 6M71) structures. Furthermore, representative docking complexes were validated using molecular dynamics simulations and mechanistic studies at 100 ns was carried on nucleocapsid and nsp10 proteins with curcumin complexes which resulted in stable and efficient binding energies and correlated with that of docked binding energies of the complexes. Both the docking and simulation studies indicate that curcumin has the potential as an antiviral against COVID-19.

Overexpression of RNA-binding bacterial chaperones in rice leads to stay-green phenotype, improved yield and tolerance to salt and drought stresses.

Genes encoding bacterial cold shock proteins A (CspA, 213 bp) and B (CspB, 216 bp) were isolated from Escherichia coli strain K12, which showed 100% homology with gene sequences isolated from other bacterial species. In silico domain, analysis showed eukaryotic conserved cold shock domain (CSD) and ribonuclease-binding domain (RBD) indicating that they bind to RNA and are involved in temperature stress tolerance. Overexpression of these two genes in E. coli resulted in higher growth in presence of 200 mM NaCl and 300 mM mannitol. Western blot confirmed the translational products of the two genes. Seedlings of indica rice were transformed with Agrobacterium tumefaciens containing pCAMBIA1301 CspA and CspB genes. Transgene integration was confirmed by ß-glucuronidase (GUS) histochemical assay, polymerase chain reaction (PCR) amplification, and gene copy number by Southern blotting. Chlorophyll, proline, Na+ , and K+ contents were higher in transgenics exposed to 150 mM NaCl and drought (imposed by withholding water) stresses during floral initiation stage. Catalase (CAT), superoxide dismutase (SOD), and guaiacol peroxidase (GPX) activities increased, while malondialdehyde (MDA) content was low in transgenics. Transgenics displayed increased root, shoot, and panicle lengths, root dry mass, and a distinct stay-green (SGR) phenotype. Higher transcript levels of CspA, CspB, SGR, chlorophyllase, isopentenyl adenine transferase 1 (IPT1), 9-cis-epoxycarotenoid dioxygenase (NCED), SOD, and sirtuin 1 (SIRT1) genes were observed in transgenics compared to wild type plants (WT) under multiple stresses. Present work indicates that bacterial chaperone proteins are capable of imparting SGR phenotype, salt and drought stress tolerance alongside grain improvement.

Lysine, Lysine-Rich, Serine, and Serine-Rich Proteins: Link Between Metabolism, Development, and Abiotic Stress Tolerance and the Role of ncRNAs in Their Regulation.

Lysine (Lys) is indispensable nutritionally, and its levels in plants are modulated by both transcriptional and post-transcriptional control during plant ontogeny. Animal glutamate receptor homologs have been detected in plants, which may participate in several plant processes through the Lys catabolic products. Interestingly, a connection between Lys and serotonin metabolism has been established recently in rice. 2-Aminoadipate, a catabolic product of Lys appears to play a critical role between serotonin accumulation and the color of rice endosperm/grain. It has also been shown that expression of some lysine-methylated proteins and genes encoding lysine-methyltransferases (KMTs) are regulated by cadmium even as it is known that Lys biosynthesis and its degradation are modulated by novel mechanisms. Three complex pathways co-exist in plants for serine (Ser) biosynthesis, and the relative preponderance of each pathway in relation to plant development or abiotic stress tolerance are being unfolded slowly. But the phosphorylated pathway of L-Ser biosynthesis (PPSB) appears to play critical roles and is essential in plant metabolism and development. Ser, which participates indirectly in purine and pyrimidine biosynthesis and plays a pivotal role in plant metabolism and signaling. Also, L-Ser has been implicated in plant responses to both biotic and abiotic stresses. A large body of information implicates Lys-rich and serine/arginine-rich (SR) proteins in a very wide array of abiotic stresses. Interestingly, a link exists between Lys-rich K-segment and stress tolerance levels. It is of interest to note that abiotic stresses largely influence the expression patterns of SR proteins and also the alternative splicing (AS) patterns. We have checked if any lncRNAs form a cohort of differentially expressed genes from the publicly available PPSB, sequence read archives of NCBI GenBank. Finally, we discuss the link between Lys and Ser synthesis, catabolism, Lys-proteins, and SR proteins during plant development and their myriad roles in response to abiotic stresses.

Comparative evaluation of Mycobacterium avium subspecies paratuberculosis (MAP) recombinant secretory proteins as DTH marker for paratuberculosis.

Delayed type hypersensitivity (DTH) based skin test is an important onsite animal herd screening procedure for detecting the early stages of the chronic mycobacterial infections. DTH testing plays a vital role in the diagnosis of paratuberculosis infection. However, there are questions over the specificity of this test due to cross-reactive epitopes present on the purified protein derivative (PPD) prepared from the whole cell secretory proteins. PPD may contain proteins shared with other mycobacteria especially environmental species. Therefore, it is needed to test alternate paratuberculosis specific secretory antigens. Present study explored the potential of recombinant secretory proteins (MAP2168c, MAP1693c, MAP3547c, MAP4308c and MAP2677c) as DTH markers. The published literature shows that these proteins as strong cell mediated markers with specificity to paratuberculosis bacilli. To determine the positive skin thickness cutoff, herds of farm animals with history of endemic paratuberculosis were selected and thickness of >2.0 mm was reported as the positive cutoff. Preliminary findings on pilot scale animals report the usefulness of recombinant secretory proteins as DTH markers over traditional Johnin assay. Traditional Johnin reported more false positives and negatives compared to gold standard fecal PCR and field reference plate ELISA test. Present findings encourage and demand further research.

Development and evaluation of LAMP-coupled lateral flow device for the detection of MAP in livestock at point of care resource-limited areas.

The Mycobacterium avium subspecies paratuberculosis (MAP) causes paratuberculosis (Johne's disease), a systemic and chronic inflammation of intestine that affects bovine, small ruminants like goat and sheep. The disease has a greater economic importance in cattle and in small ruminants. But its effective control is impeded due to lack of rapid and accurate diagnostics. The present study is aimed at developing a LAMP-coupled lateral flow device (LFD) for rapid detection of paratuberculosis in livestock animal species such as cattle and in small ruminants at resource-limited areas. LAMP primers with biotin and FITC end tags were designed for IS900 gene specific for MAP. To determine sensitivity of LAMP assay, 10-fold serial dilutions were made from 10 ng/µl MAP stock DNA and were compared with PCR. The detection limits of LAMP-coupled LFD were defined and reactions were repeated for reproducibility. The specificity was evaluated using other infectious bacteria such as M. bovis, M. tuberculosis, Brucella abortus, Leptospira interrogan, Yersinia enterocolitica, Salmonella typhimurium, Listeria monocytogens, and Staphylococcus aureus. A total of 95 samples turned positive for LAMP-coupled LFD out of 389 fecal samples. All the cultural-positive and PCR-positive samples showed positive in LAMP-coupled LFD. Nine samples with negative cultures turned positive in LAMP assay. The overall sensitivity and specificity of the LAMP-coupled LFD assays were 100% and 97.02% respectively in comparison with the culture as the gold standard method. The sensitivity detection limit of developed assay was 10 fg/µl and specificity was 100%. This assay successfully detected MAP not only by using bacterial DNA but also in clinical fecal samples. The clear band formation at control and test positions was observed on LAMP-coupled LFD. The developed assay is a simple, rapid, easy to perform, and is very useful in early diagnosis of Mycobacterium avium subsp. paratuberculosis at point of care resource-limited areas.

Selecting better diagnostic kits for diagnosis of malarial parasites at point of care.

Malaria is a fatal life-threatening parasitic infection and a leading cause of morbidity and mortality. The present study was aimed to evaluate simple, inexpensive, accurate, reliable, easily available better diagnostic for rapid detection of malaria at point of care (POC). The study includes 1403 samples collected from the patients, of which 1227 were clinically suspected cases and 176 from consecutive feverish patients. Among the suspected cases only 338 samples were confirmed positive and 889 samples were negative for Plasmodium species by PCR. All the 889 samples showed negative result for plasmodium species by microscopy, Malarial Ag rapid kits but only 867 samples were confirmed negative with malarial Ab rapid kits. Of the 338 PCR positive samples, 337 samples were confirmed positive by microscopy and Malarial Ag rapid kits, but only 284 samples were confirmed positive using malarial Ab rapid kits. Overall the microscopy and the malaria antigen-based lateral flow assay exhibited similar sensitivity, specificity, PPV, NPV and efficiency, respectively, whereas the PCR assay had 100% sensitivity, specificity, PPV, NPV and efficiency. But the evolutionary data for malaria antibody lateral flow assay has 92.81% sensitivity, 94.13% specificity, 84.02% PPV, 97.52% NPV and 93.80% efficiency. The developed Malaria pf/pv antigen and antibody field-deployable kits are simple, rapid, accurate, reliable, inexpensive, user friendly, POC. In addition the kits are highly sensitive and species-specific. The pf/pv antigen kit is found to be more accurate with 99.7% sensitivity and 100% specificity than to Malaria pf/pv antibody rapid kits. Of the two rapid kits developed, Malaria pf/pv antigen kit is found be more accurate with 99.7% sensitivity and 100% specificity than to Malaria pf/pv antibody rapid kits.

Development of Loop-Mediated Isothermal Amplification-Based Lateral Flow Device Method for the Detection of Malaria.

The present study aims to develop a method for rapid diagnosis of malaria using loop-mediated isothermal amplification (LAMP) combined with a lateral flow device (LFD). By adding the biotin-labeled and fluorescein amidite-labeled loop primers to the LAMP reaction solution, the end product can be visualized on a LFD. The entire procedure takes approximately 42 minutes to complete, LAMP assay exhibited high sensitivity, as the detection limit was 0.01 pg/µL for all five Plasmodium species. It was demonstrated that all Plasmodium knowlesi (N = 90) and Plasmodium vivax (N = 56) were positively amplified by LAMP-LFD assay, whereas healthy donor samples (N = 8) were negative. However, not all mixed infections were positive, and other infected nonmalaria samples were negative. Loop-mediated isothermal amplification-LFD represents a robust approach with potential suitability for use in resource-constrained laboratories. We believe that LAMP-LFD has a potential to be developed as point-of-care diagnostic tool in future.

Simple, rapid, inexpensive platform for the diagnosis of malaria by loop mediated isothermal amplification (LAMP).

We attempted to improve the loop-mediated isothermal amplification (LAMP) method for malaria diagnosis by using a simple DNA extraction procedure, and a portable device performing both the amplification and detection of LAMP in one platform. Additionally, the device served as a heating block for the DNA preparation. We refer this method as LAMP-Tube scanner, and evaluated using 209 microscopically positive malaria samples and compared them to RDTs and LAMP-Thermocycler. Two most common human infecting Plasmodium species were detected. The LAMP-Tube scanner method is found to be simple and allowed real-time detection of DNA amplification. The time to amplification varied but was closely less than 60 min. Sensitivity and specificity of LAMP-Tube scanner in detecting Plasmodium falciparum were 95% and 93.3%, compared to microscopy and 98.3% and 100% respectively, compared to standard LAMP-Thermocycler. In addition, it showed a detection limit of 10 and 40 copies of the parasitemia for Plasmodium vivax and P. falciparum. Accordingly, in comparison to the results obtained by microscopy, the LAMP-Tube scanner had a less divergence in sensitivity and specificity, and yielded results similar to those of LAMP-Thermocycler. This method has the great potential as a field usable molecular tool for the diagnosis of malaria and is an alternative to conventional PCR-based diagnostic methods for field use.

Increased severity of alcoholic liver injury in female verses male rats: a microarray analysis.

Alcoholic liver disease (ALD) is an increasingly recognized condition that may progress to end-stage liver disease. In addition to alcohol consumption, genetic factors, dietary fatty acids, gender and viral infection potentiate the severity of alcoholic liver injury. In humans, significant gender differences in susceptibility to ALD are observed. In the intragastric infusion rat model of ALD, female rats developed more severe liver injury than males. To understand the effect of gender on the development of more severe ALD in female rats, we performed a microarray based expression profiling of genes in rats fed with fish oil and ethanol diet. A large number of genes showed significant changes in female livers compared to males. The upregulated genes in female liver were involved in proteosome endopeptidase activity, catalytic activity, lipid metabolism, alcohol metabolism, mitochondrial and oxidoreductase activity. The downregulated genes were involved in oxidoreductase activity, chaperone activity, and electron transport activity in the female liver as demonstrated by biological theme analysis. Ingenuity computational pathway analysis tools were used to identify specific regulatory networks of genes operative in promoting liver injury. These networks allowed us to identify a large cluster of genes involved in lipid metabolism, development, cellular growth and proliferation, apoptosis, carcinogenesis and various signaling pathways. Genes listed in this article that were significantly increased or decreased (expression two fold or more) were assigned to pathological functional groups and reviewed for relevance to establish hypotheses of potential mechanisms involved in ALD in female liver injury.

Transcriptional networks in a rat model for nonalcoholic fatty liver disease: a microarray analysis.

BACKGROUND: Nonalcoholic fatty liver disease (NAFLD) is a common hepatic condition that may progress to end-stage liver disease. High-fat diets in animals reproduce many of the features found in nonalcoholic steatohepatitis. OBJECTIVE: To understand how various dietary or genetic factors influence the development of fatty liver and consequently NAFLD, we performed microarray-based expression profiling of genes, induced by fish oil and dextrose diet, a putative mediator of alcohol-like effects on the liver of the female rat. DESIGN: Male and age-matched female rats were fed fish oil and dextrose for 4 weeks. Hepatic RNA from each sample was extracted and used for microarray analysis. RESULTS: A large number of genes underwent significant changes in the female liver as compared to male controls. In the female rat liver, biological theme analysis demonstrated a shift in the transcriptional program which included upregulation of genes involved in lipid metabolism, chaperone activity, mitochondrial and oxidoreductase activity combined with downregulation of genes involved in nucleic acid metabolism. The differential expression of genes of interest identified by microarray technique was validated by real-time reverse transcription-polymerase chain reaction. Ingenuity computational pathway analysis tools were used to identify specific regulatory networks of genes operative in promoting liver injury. CONCLUSIONS: The use of networks stated above allowed us to identify genes involved in cell death, apoptosis, peroxisome proliferator-activated receptor alpha-regulated lipid metabolism and mitogen-activated protein kinase signaling pathways.