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Markov models have frequently been used in genetic sequence analysis. The number of parameters of a Markov model increases exponentially with model order, so it is often recommended that the order be chosen based on the size of data being modeled, lower orders for small and higher orders for large dataset sizes. Approaches based on model selection criterion have also been proposed. An important problem in microbiology and evolutionary biology is to decipher chimeric genomes of microbes, particularly, identify segments of distinct ancestries in genomes and reconstruct the plausible evolutionary scenarios that might have shaped the chimeric genomes in the microbial world. In this study, we assessed a Markov model-based segmentation method for its ability to detect compositionally disparate segments in chimeric sequence constructs as a function of model order, sequence length, and phylogenetic divergence. Our results show that the choice of Markov model order depends on both sequence size and composition. Higher order Markov models were found to be more effective in delineating sequence segments arising from closely related organisms in longer constructs; on the other hand, lower order Markov models were found to be more appropriate in delineating sequence segments arising from distantly related organisms in shorter constructs. These findings are important and timely, with broad implications in fields such as epidemiology that has to deal with the emergence of novel pathogenic chimeras that arise by foreign DNA acquisition, and ecology where chimeric structures may arise in various ecosystems, necessitating more robust approaches for their deconstruction and interpretation.

Background Molecular characterization of late-onset Alzheimer’s disease (LOAD), the leading cause of age-related dementia, has revealed transcripts, proteins, and pathway alterations associated with disease. Assessing these postmortem signatures of LOAD in experimental model systems can further elucidate their relevance to disease origins and progression. Model organisms engineered with human genetic factors further link these signatures to disease-associated variants, especially when studies are designed to leverage homology across species. Here we assess differential gene splicing patterns in aging mouse models carrying humanized APOE4 and/or the Trem2*R47H variant on a C57BL/6J background. We performed a differential expression of gene (DEG) and differential splicing analyses on whole brain transcriptomes at multiple ages. To better understand the difference between differentially expressed and differentially spliced genes, we evaluated enrichment of KEGG pathways and cell-type specific gene signatures of the adult brain from each alteration type. To determine LOAD relevance, we compared differential splicing results from mouse models with multiple human AD splicing studies. Results We found that differentially expressed genes in Trem2*R47H mice were significantly enriched in multiple AD-related pathways, including immune response, osteoclast differentiation, and metabolism, whereas differentially spliced genes were enriched for neuronal related functions, including GABAergic synapse and glutamatergic synapse. These results were reinforced by the enrichment of microglial genes in DEGs and neuronal genes in differentially spliced genes in Trem2*R47H mice. We observed significant overlap between differentially spliced genes in Trem2*R47H mice and brains from human AD subjects. These effects were absent in APOE4 mice and suppressed in APOE4.Trem2*R47H double mutant mice relative to Trem2*R47H mice. Conclusions The cross-species observation that alternative splicing observed in LOAD are present in Trem2*R47H mouse models suggests a novel link between this candidate risk gene and molecular signatures of LOAD in neurons and demonstrates how deep molecular analysis of new genetic models links molecular disease outcomes to a human candidate gene.

BackgroundCurrent models to study Alzheimer’s disease (AD) include cell cultures and animal models. Human diseases, however, are often poorly reproduced in animal models. Developing techniques to differentiate human brain cells from induced pluripotent stem cells (iPSCs) provides a novel approach to studying AD. Three-dimensional (3D) cultures to model AD are represented by organoids, neurospheroids, and scaffold-based cultures. Some AD-related phenotypes have been identified across 3D models [1]. However, to our knowledge, none of these studies could recapitulate several AD-related hallmarks in one single model and establish a temporal relation among them. Furthermore, to date, the transcriptomic features of these 3D models have not been compared with those of human AD brains. These data are, in our opinion, key to understanding the pertinency of these models for studying AD-related pathomechanisms over time.MethodsWe developed a 3D bioengineered model of iPSC-derived neural tissue that combines a porous scaffold composed of silk fibroin protein with an intercalated collagen hydrogel to support the growth of neurons and glial cells into complex and functional networks. This biomaterial scaffold, designed to match the mechanical properties of brain tissue, can support 3D neural cultures for an extended time without necrosis, a fundamental requisite for aging studies.We have optimized our protocol by seeding neural precursor cells (NPCs) into these scaffolds. NPC-derived cultures were generated from iPSC lines obtained from two subjects carrying the familial AD (FAD) APP London mutation, two well-studied control lines, and an isogenic control. Cultures were analyzed at 2 and 4.5 months.ResultsAn elevated Aβ42/40 ratio was detected in conditioned media from FAD cultures at both time points, as previously reported in 2D cultures derived from the same FAD lines. However, extracellular Aβ42 deposition and enhanced neuronal excitability were observed in FAD culture only at 4.5 months. The increased excitability of FAD cultures correlated with extracellular Aβ42 deposition but not with soluble Aβ42/40 ratio levels, as they were similar at both time points. These data suggest that extracellular Aβ deposition may trigger enhanced network activity. Notably, neuronal hyperexcitability has been described in AD patients early in the disease. Transcriptomic analysis revealed the deregulation of multiple gene sets in FAD samples. Notably, such alterations were similar to those observed in human AD brains in a large study that performed a co-expression meta-analysis of harmonized data from Accelerating Medicines Partnership for Alzheimer’s Disease (AMP-AD) across three independent cohorts.ConclusionsOur 3D tissue model supports the differentiation of healthy iPSC-derived cultures in a porous silk-collagen composite sponge with an optically clear central region. This design facilitates nutrient delivery to meet the metabolic demand of long-term cultures. These data provide evidence that our bioengineered model from patient-derived FAD iPSCs develops time-dependent AD-related phenotypes and establishes a temporal relation among them. Furthermore, FAD iPSC-derived neuronal tissue recapitulates transcriptomic features of AD patients. Thus, our bioengineered neural tissue represents a unique tool to model AD-related pathomechanisms over time, with several advantages compared to the existing models.

Obesity is recognized as a significant risk factor for Alzheimer’s disease (AD). Studies have supported the notion that obesity accelerates AD-related pathophysiology in mouse models of AD. The majority of studies, to date, have focused on the use of early-onset AD models. Here, we evaluate the impact of genetic risk factors on late-onset AD (LOAD) in mice fed with a high fat/high sugar diet (HFD). We focused on three mouse models created through the IU/JAX/PITT MODEL-AD Center. These included a combined risk model with APOE4 and a variant in triggering receptor expressed on myeloid cells 2 (Trem2R47H). We have termed this model, LOAD1. Additional variants including the M28L variant in phospholipase C Gamma 2 (Plcg2M28L) and the 677C > T variant in methylenetetrahydrofolate reductase (Mthfr677C >T) were engineered by CRISPR onto LOAD1 to generate LOAD1.Plcg2M28L and LOAD1.Mthfr677C >T. At 2 months of age, animals were placed on an HFD that induces obesity or a control diet (CD), until 12 months of age. Throughout the study, blood was collected to assess the levels of cholesterol and glucose. Positron emission tomography/computed tomography (PET/CT) was completed prior to sacrifice to image for glucose utilization and brain perfusion. After the completion of the study, blood and brains were collected for analysis. As expected, animals fed a HFD, showed a significant increase in body weight compared to those fed a CD. Glucose increased as a function of HFD in females only with cholesterol increasing in both sexes. Interestingly, LOAD1.Plcg2M28L demonstrated an increase in microglia density and alterations in regional brain glucose and perfusion on HFD. These changes were not observed in LOAD1 or LOAD1.Mthfr677C >T animals fed with HFD. Furthermore, LOAD1.Plcg2M28L but not LOAD1.Mthfr677C >T or LOAD1 animals showed transcriptomics correlations with human AD modules. Our results show that HFD affects the brain in a genotype-specific manner. Further insight into this process may have significant implications for the development of lifestyle interventions for the treatment of AD.

Transcriptomic analysis of the mammalian retinal pigment epithelium (RPE) aims to identify cellular networks that influence ocular development, maintenance, function, and disease. However, available evidence points to RPE cell heterogeneity in the native tissue, which adds complexity to transcriptomic analysis. Here, to assess cell heterogeneity, we performed single-cell RNA sequencing of RPE cells from two young adult male C57BL/6J mice. Following quality control to ensure robust transcript identification limited to cell singlets, we detected 13,858 transcripts among 2,667 and 2,846 RPE cells, respectively. Dimensional reduction by principal component analysis and uniform manifold approximation and projection revealed six distinct cell popu-lations. All clusters expressed transcripts typical of RPE cells; the smallest (C1, containing 1–2% of total cells) exhibited hallmarks of stem and/or progenitor cells. Placing C1–6 along a pseudotime axis suggested a relative decrease in melanogenesis and stem/progenitor gene expression, and a corresponding increase in visual cycle gene expression upon RPE maturation. K-means testing of all detected transcripts identified additional expression patterns that may advance understanding of RPE stem/pro-genitor cell maintenance and the evolution of cellular metabolic networks during development. This work provides new insights into the transcriptome of the mouse RPE and a baseline for identifying experimentally induced transcriptional changes in future studies of this tissue.

IntroductionAlzheimer's disease (AD) is the most common form of dementia. Beta-secretase (BACE) inhibitors have been proposed as potential therapeutic interventions; however, initiating treatment once disease has significantly progressed has failed to effectively stop or treat disease. Whether BACE inhibition may have efficacy when administered prophylactically in the early stages of AD has been under-investigated. The present studies aimed to evaluate prophylactic treatment of the BACE inhibitor verubecestat in an AD mouse model using the National Institute on Aging (NIA) resources of the Model Organism Development for Late-Onset Alzheimer's Disease (MODEL-AD) Preclinical Testing Core (PTC) Drug Screening Pipeline.Methods5XFAD mice were administered verubecestat ad libitum in chow from 3 to 6 months of age, prior to the onset of significant disease pathology. Following treatment (6 months of age), in vivo imaging was conducted with 18F-florbetapir (AV-45/Amyvid) (18F-AV45) and 18-FDG (fluorodeoxyglucose)-PET (positron emission tomography)/MRI (magnetic resonance imaging), brain and plasma amyloid beta (Aβ) were measured, and the clinical and behavioral characteristics of the mice were assessed and correlated with the pharmacokinetic data.ResultsProphylactic verubecestat treatment resulted in dose- and region-dependent attenuations of 18F-AV45 uptake in male and female 5XFAD mice. Plasma Aβ40 and Aβ42 were also dose-dependently attenuated with treatment. Across the dose range evaluated, side effects including coat color changes and motor alterations were reported, in the absence of cognitive improvement or changes in 18F-FDG uptake.DiscussionProphylactic treatment with verubecestat resulted in attenuated amyloid plaque deposition when treatment was initiated prior to significant pathology in 5XFAD mice. At the same dose range effective at attenuating Aβ levels, verubecestat produced side effects in the absence of improvements in cognitive function. Taken together these data demonstrate the rigorous translational approaches of the MODEL-AD PTC for interrogating potential therapeutics and provide insight into the limitations of verubecestat as a prophylactic intervention for early-stage AD.

The application of a mixture of pesticides to the agricultural field may adversely affect the health of non-target organisms besides the target ones. In the present study, the antagonistic effect o...

Horizontal gene transfer (HGT) or lateral gene transfer (LGT), the exchange of genetic materials among organisms by means of other than parent-to-offspring (vertical) inheritance, plays a major role in prokaryotic genome evolution, facilitating adaptation of prokaryotes to changes in the environment. Phylogenetic methods have been frequently invoked to catalog horizontally acquired genes; however, these methods are often constrained by the paucity of sequenced genomes of close relatives (and even distant relatives) for a robust analysis and reliable inference. In this chapter, we describe a HGT quantification protocol that exploits the complementary strengths of the integrative segmentation and clustering method and the comparative genomics approach to identify foreign genes. Users can use this pipeline in combination with phylogenetic tree reconstruction to identify foreign genes that are supported by multiple lines of evidence, that is, atypical composition, atypical distribution in close relatives, and aberrant phylogenetic pattern.

Horizontal gene transfer (HGT) or lateral gene transfer (LGT), the exchange of genetic materials among organisms by means of other than parent-to-offspring (vertical) inheritance, plays a major role in prokaryotic genome evolution, facilitating adaptation of prokaryotes to changes in the environment. Phylogenetic methods have been frequently invoked to catalog horizontally acquired genes; however, these methods are often constrained by the paucity of sequenced genomes of close relatives (and even distant relatives) for a robust analysis and reliable inference. In this chapter, we describe a HGT quantification protocol that exploits the complementary strengths of the integrative segmentation and clustering method and the comparative genomics approach to identify foreign genes. Users can use this pipeline in combination with phylogenetic tree reconstruction to identify foreign genes that are supported by multiple lines of evidence, that is, atypical composition, atypical distribution in close relatives, and aberrant phylogenetic pattern.

Transcriptomic analysis of the mammalian retinal pigment epithelium (RPE) aims to identify cellular networks that influence ocular development, maintenance, function, and disease. However, available evidence points to RPE cell heterogeneity within native tissue, which adds complexity to global transcriptomic analysis. Here, to assess cell heterogeneity, we performed single-cell RNA sequencing of RPE cells from two young adult male C57BL/6J mice. Following quality control to ensure robust transcript identification limited to cell singlets, we detected 13,858 transcripts among 2667 and 2846 RPE cells. Dimensional reduction by principal component analysis and uniform manifold approximation and projection revealed six distinct cell populations. All clusters expressed transcripts typical of RPE cells; the smallest (C1, containing 1–2% of total cells) exhibited the hallmarks of stem and/or progenitor (SP) cells. Placing C1–6 along a pseudotime axis suggested a relative decrease in melanogenesis and SP gene expression and a corresponding increase in visual cycle gene expression upon RPE maturation. K-means clustering of all detected transcripts identified additional expression patterns that may advance the understanding of RPE SP cell maintenance and the evolution of cellular metabolic networks during development. This work provides new insights into the transcriptome of the mouse RPE and a baseline for identifying experimentally induced transcriptional changes in future studies of this tissue.

Late-onset Alzheimer’s disease (AD; LOAD) is the most common human neurodegenerative disease, however, the availability and efficacy of disease-modifying interventions is severely lacking. Despite exceptional efforts to understand disease progression via legacy amyloidogenic transgene mouse models, focus on disease translation with innovative mouse strains that better model the complexity of human AD is required to accelerate the development of future treatment modalities. LOAD within the human population is a polygenic and environmentally influenced disease with many risk factors acting in concert to produce disease processes parallel to those often muted by the early and aggressive aggregate formation in popular mouse strains. In addition to extracellular deposits of amyloid plaques and inclusions of the microtubule-associated protein tau, AD is also defined by synaptic/neuronal loss, vascular deficits, and neuroinflammation. These underlying processes need to be better defined, how the disease progresses with age, and compared to human-relevant outcomes. To create more translatable mouse models, MODEL-AD (Model Organism Development and Evaluation for Late-onset AD) groups are identifying and integrating disease-relevant, humanized gene sequences from public databases beginning with APOEε4 and Trem2*R47H, two of the most powerful risk factors present in human LOAD populations. Mice expressing endogenous, humanized APOEε4 and Trem2*R47H gene sequences were extensively aged and assayed using a multi-disciplined phenotyping approach associated with and relative to human AD pathology. Robust analytical pipelines measured behavioral, transcriptomic, metabolic, and neuropathological phenotypes in cross-sectional cohorts for progression of disease hallmarks at all life stages. In vivo PET/MRI neuroimaging revealed regional alterations in glycolytic metabolism and vascular perfusion. Transcriptional profiling by RNA-Seq of brain hemispheres identified sex and age as the main sources of variation between genotypes including age-specific enrichment of AD-related processes. Similarly, age was the strongest determinant of behavioral change. In the absence of mouse amyloid plaque formation, many of the hallmarks of AD were not observed in this strain. However, as a sensitized baseline model with many additional alleles and environmental modifications already appended, the dataset from this initial MODEL-AD strain serves an important role in establishing the individual effects and interaction between two strong genetic risk factors for LOAD in a mouse host.

The ability to investigate therapeutic interventions in animal models of neurodegenerative diseases depends on extensive characterization of the model(s) being used. There are numerous models that have been generated to study Alzheimer’s disease (AD) and the underlying pathogenesis of the disease. While transgenic models have been instrumental in understanding AD mechanisms and risk factors, they are limited in the degree of characteristics displayed in comparison with AD in humans, and the full spectrum of AD effects has yet to be recapitulated in a single mouse model. The Model Organism Development and Evaluation for Late-Onset Alzheimer’s Disease (MODEL-AD) consortium was assembled by the National Institute on Aging (NIA) to develop more robust animal models of AD with increased relevance to human disease, standardize the characterization of AD mouse models, improve preclinical testing in animals, and establish clinically relevant AD biomarkers, among other aims toward enhancing the translational value of AD models in clinical drug design and treatment development. Here we have conducted a detailed characterization of the 5XFAD mouse, including transcriptomics, electroencephalogram, in vivo imaging, biochemical characterization, and behavioral assessments. The data from this study is publicly available through the AD Knowledge Portal.

Late-onset Alzheimer’s disease (LOAD) is the most common human neurodegenerative disease. Legacy amyloidogenic mouse models have been useful for understanding disease progression, however in the face of failing human trials more focus on disease translation with new mouse strains that better model human Alzheimer’s disease (AD) is required. MODEL-AD (Model Organism Development and Evaluation for Late-onset AD) groups are identifying and integrating disease-relevant, humanized gene sequences from public databases to create more translatable mouse models for therapy development. Mice expressing strong genetic risk factors for LOAD, APOEe4 and Trem2*R47H, were extensively aged and assayed using a multi-disciplined phenotyping approach associated with and relative to human AD pathology. Behavioral, transcriptomic, metabolic, and neuropathological assays identified sex and age as the main sources of variation between genotypes including age-specific enrichment of AD-related processes in the absence of mouse amyloid plaque formation. These data provide an important, baseline understanding of the individual effects and interaction between two strong genetic risk factors for LOAD. These two alleles together form a sensitized, background strain (B6.APOE4.Trem2*R47H, which we have termed ‘LOAD1’) necessary to examine how important underlying risk factors interact with any subsequent genetic or environmental cues to drive pathology.

Industrial effluents reaching to the aquatic ecosystem is one of the major causes of environmental pollution. Heteropneustes fossilis, one of the most common edible fish if exposed to industrial effluents containing harmful substances may be a serious threat to human health. Therefore, the present study aimed to study the impact of fertilizer industry effluent on H. fossilis. Fish were exposed to treated and untreated fertilizer industry effluent (LC50 ​= ​2.35% v/v) for 96 ​h along with a proper control. The physico-chemical parameters such as turbidity, biological oxygen demand (BOD) and chemical oxygen demand (COD) of both treated and untreated fertilizer industry effluent were also analyzed as these parameters were not in range as per guidelines. Hematological parameters such as Red Blood cells (RBC), Haemoglobin (% Hb), Mean corpuscular volume (MCV), Mean Corpuscular Hemoglobin (MCH) and Mean Corpuscular Hemoglobin Concentration (MCHC) showed significant decrease while there was sharp increase in differential leucocyte count (DLC) especially the neutrophil count. Distinct alteration in the architecture of gills, liver and kidney was observed besides significant increase in the level of lipid peroxidation (LPO), alanine aminotransferase (ALT), aspartate aminotransferase (AST), acid phosphatases (ACP) and alkaline phosphatase (ALP) while the level of superoxide dismutase (SOD), catalase (CAT), glutathione s-transferase (GST) and reduced glutathione (GSH) activity decreased in metabolically active tissues like brain, liver, kidney, gills and muscles. The results indicate that industrial effluent has potent oxidative stress inducers on one hand and histoarchitectural and physiological altering contaminants on the other. This condition may adversely affect the health of aquatic organisms, the fish and ultimately the human beings.

Industrial revolution is a good indicator of economic development of a country; however, it can be a threat to the flora and fauna if the untreated effluent of an industry is discharged. The present study is aimed to assess the comparative toxicological impacts of treated and untreated industrial effluents on acetylcholinesterase (AChE) activity in Heteropneustes fossilis and Labeo rohita, the most common edible fishes having diverse characters which include differences in morphology, habitat, food and feeding, etc. The physico-chemical parameters such as pH, electrical conductivity (EC), alkalinity, hardness, dissolved oxygen (DO), phosphate, sulphate, nitrate, free ammonia, chloride, zinc, iron, chromium and potassium of both untreated and treated effluent from the fertilizer industry were also analyzed as these parameters were not in range as per ISO guidelines. The LC50 value for untreated effluent was 2.34% (v/v) and 0.80% (v/v) for 96 h in H. fossilis and L. rohita, respectively, while no mortality was recorded in the treated effluent. The AChE activity in both fish species was found to decline in metabolically responsive organs like brain, muscle and gills through exposure to sub-lethal concentrations (1/15th, 1/10th and 1/5th of LC50 value) of the untreated effluent for 96 h. Further studies on biochemical and molecular aspects may reveal the mechanism of their action.

C-lignin is a linear polymer of caffeyl alcohol, found in the seed coats of several exotic plant species, with promising properties for generation of carbon fibers and high value chemicals. In the ornamental plant Cleome hassleriana, guaiacyl (G) lignin is deposited in the seed coat for the first 6-12 days after pollination, after which G-lignin deposition ceases and C-lignin accumulates, providing an excellent model system to study C-lignin biosynthesis. We performed RNA sequencing of seed coats harvested at 2-day intervals throughout development. Bioinformatic analysis identified a complete set of lignin biosynthesis genes for Cleome. Transcript analysis coupled with kinetic analysis of recombinant enzymes in Escherichia coli revealed that the switch to C-lignin formation was accompanied by down-regulation of transcripts encoding functional caffeoyl CoA- and caffeic acid 3-O-methyltransferases (CCoAOMT and COMT) and a form of cinnamyl alcohol dehydrogenase (ChCAD4) with preference for coniferaldehyde as substrate, and up-regulation of a form of CAD (ChCAD5) with preference for caffealdehyde. Based on these analyses, blockage of lignin monomer methylation by down-regulation of both O-methyltransferases (OMTs) and methionine synthase (for provision of C1 units) appears to be the major factor in diversion of flux to C-lignin in the Cleome seed coat, although the change in CAD specificity also contributes based on the reduction of C-lignin levels in transgenic Cleome with down-regulation of ChCAD5. Structure modeling and mutational analysis identified amino acid residues important for the preference of ChCAD5 for caffealdehyde.

The acute toxicity of three formula grade pesticides namely, triazophos (an organophosphate, OP), deltamethrin (a pyrethroid) and combined pesticide (triazophos + deltamethrin) was determined in ea...

Multiple chromosomes in bacteria are designated as a larger primary chromosome (CI) and smaller accessory chromosomes (CII and CIII). Although previous studies examined multiple chromosomes in several bacterial species, the evolutionary mechanisms for the origin of CIIs still remain unclear. In this study, the four following hypotheses were tested. 1) CIIs exhibit lower sequence conservation and sequence divergence compared to their corresponding CIs across species of Proteobacteria. 2) The differential sequence divergence of CI and CII depends on pathogenic and non-pathogenic lifestyles. 3) CIIs harbor a higher level of horizontal gene transfers (HGTs) than CIs. 4) Orthologs located on CIIs experience less purifying selection than their corresponding orthologs on CIs. Results reveal a higher level of sequence conservation of CIs than the sequence conservation of CIIs. There is no significant difference in HGT estimates between CIs and CIIs. A majority of orthologous genes of CIs and CIIs experience purifying selection; however, genes on CIIs were significantly less constrained than the corresponding ones on CIs. This finding is true for both pathogenic and non-pathogenic bacteria, but the selective constraints for non-pathogenic bacteria are relatively less constrained. It was concluded that the differential selective constraint is a potent driving force for the rapid evolution of CII. Therefore, gene expression analysis at the transcriptome and proteome levels may shed light on the gene regulation mechanisms that might affect the sequence divergence between CI and CII.

Recurrent application of chemical pesticides in the agricultural fields have adverse impact on flora and fauna of soil ecosystem. Earthworms immensely contribute in increasing the fertility of soil. They may act as a bioindicator for the ecotoxicological analysis of pesticide induced soil pollution. Earthworms, Eudrilus eugeniae were exposed to different concentrations of pesticides chlorpyrifos (OP), cypermethrin (a pyrethroid) and their combination for 48 h by paper contact toxicity method. The LC50 for commercial grade of chlorpyrifos, cypermethrin and combined pesticides were determined as 0.165, 0.066 and 0.020 μg/cm2, respectively. To assess the sub-lethal effect of these pesticides, E. eugeniae were exposed to 5% and 10% of LC50 of the pesticides for 48 h. Variation in morpho-behavioural changes such as coiling, clitellar swelling, mucus release, bleeding and body fragmentation in earthworms were observed after exposure of both pesticides and their combination. Various biochemical estimations such as specific activity of acetylcholinesterase (AChE), superoxide dismutase (SOD), catalase (CAT), glutathione -S-transferase (GST); levels of lipid peroxidation (LPO) and reduced glutathione (GSH) were carried out in different body segments. Significant changes in these stress markers were observed at low and high sub-acute concentration of pesticides exposed earthworm, Eudrilus eugeniae. Such changes indicate potential health risk to E. eugeniae if exposed to the high concentrations of these pesticides accumulated in soil. Keywords: AChE activity, Stress markers, Chlorpyrifos, Cypermethrin, Chlorpyrifos + Cypermethrin, Eudrilus eugeniae

Background: Late-onset Alzheimer’s Disease (AD) (LOAD) is the most common neurodegenerative disease. Despite extensive efforts to understand disease progression there are currently no approved disease modifying interventions to delay or reverse neurodegeneration caused by AD. Repeated failures in human trials, despite promising preclinical results in amyloidogenic mouse models, highlight the need for animals that better model human AD. MODEL-AD (Model organism development and evaluation for late-onset AD) are identifying and integrating disease-relevant, humanized gene sequences identified from public AD data repositories to create more translatable mouse models relevant to AD.Methods: Strong risk factors for LOAD, APOEε4 and Trem2*R47H, were expressed alone or in combination on a congenic C57BL/6J (B6) background, in cohorts of mice established on multiple sites and aged to between 4-24 months. A deep phenotyping approach was employed to assess phenotypes relative to human AD. Results: The LOAD1 mouse strain, expressing humanized APOEε4 and Trem2*R47H alleles, was designed to elucidate the disease state of animals expressing the two strongest genetic risk factors of LOAD at endogenous levels. Robust analytical pipelines measured behavioral, transcriptomic, metabolic, and neuropathological phenotypes in cross-sectional cohorts for progression of disease hallmarks at all life stages. In vivo PET/MRI neuroimaging revealed regional alterations in glycolytic metabolism and vascular perfusion. Transcriptional profiling by RNA-Seq of brain hemispheres identified sex and age as the main sources of variation between genotypes including age-specific enrichment of AD-related processes. Similarly, age, but not genotype, was the strongest determinant of behavioral change. In the absence of mouse amyloid plaque formation, many of the hallmarks of AD were not observed in this strain. However, these two alleles together form a sensitized, background strain which will serve as a platform for the characterization of additional genetic and environmental LOAD risk factors. Conclusions: Comprehensive phenotyping provided key insights into genetic and environmental effects aimed at modeling human disease, critical to understand the complex intergenic interactions and subsequent molecular signaling cascades. The data provided by these assays are important for understanding the relative contributions of subsequent risk factors amended to LOAD1.

Melatonin-loaded PLA nanoparticles are nowadays important in biological system for its biodegradable nature for targeted drug delivery. Hence, aim of the study is to note applicability and toxicity of Mel-PLA nanoparticles in osteoporosis. Different concentrations of melatonin and PLA were prepared by dissolving in dichloromethane (DCM). The final dried nanoparticles were used for structural analysis by SEM, TEM, and FTIR. Toxicity and immunological impact of nanoparticles were evaluated on rats: control and nanoparticle treated (n = 5/group) for 7 days. Afterward animals were sacrificed and blood, liver, and kidney were collected. A fraction of blood was processed for TLC, DLC, and %LC, and the remaining was centrifuged at 3000x g at 4 °C for 30 min. Separated plasma was used for measurements of IL-2, IL-6, TNF-α, IFN-γ, IL-1β, urea, creatinine, and BUN. Both plasma and tissue homogenates were used for AST, ALT, ACP, and ALP estimations. We noted significantly high (p 0.05) or unaffected (IFN-γ, ACP, and ALP). From our preliminary study, we may conclude that we have synthesized Mel-PLA nanoparticles and their effects were nontoxic to animals.

Graphical abstract, Highlights • The pesticides have adverse effect on the health of aquatic biota including fishes. • Comparative acute toxicity of both pesticides was determined in the present study. • Both pesticides have affected the behavioural activities of C. punctatus. • Alteration of behavioural patterns may be due to strong inhibition of AChE activity. • Triazophos (organophosphate) is more neurotoxic than deltamethrin (pyrethroid)., Pesticides are applied to control the pests indoor and outdoor; however, their remarkable amount reaches to the aquatic system through various routes like run-off, leaching, spray-drift, effluent from factories. These are reported to have negative metabolic impact on different non-target aquatic organisms like fishes. Thus, present study is aimed to evaluate the acute toxicity of two groups of pesticides, organophosphate and pyrethroid, namely triazophos and deltamethrin, respectively. The test was conducted for 96 h period in a freshwater teleost, Channa punctatus. The LC50 values for triazophos and deltamethrin after 96 h treatment was found to be 0.069 mg/L and 7.33 μg/L. The deltamethrin was found to be about ten times more toxic than triazophos to the fish. In treated fish, alterations in various behavioural patterns were observed with increasing concentrations of both the pesticides as compared to control. Further, tissue specific as well as dose dependent inhibition in the acetylcholinesterase (AChE, EC 3.1.1.7) activity was found in brain, muscle and gills in Channa punctatus exposed to both the insecticides. However, the effect was more pronounced in triazophos treated fishes than the deltamethrin. A futuristic approach on biochemical and molecular studies may throw light on the mechanism of action of these pesticides.

In the present study, the acute toxicity of chlorpyrifos (an organophosphate, OP) and cypermethrin (a pyrethroid) pesticides was estimated for 96 h in Heteropneustes fossilis. The LC50 for ...

In the present study, the crude ethanol extracts of leaves of Calotropis procera and Annona squamosa have been screened for their insecticidal activities against Musca domestica (a housefly). The third instar larvae of housefly were exposed with two different concentrations of both the extracts for 48 h by dipping method. The effect of extract exposure was studied on the activities of alkaline phosphatase, acid phosphatase, glutamate oxaloacetate transaminases and glutamate pyruvate transaminase. The enzyme inhibitory effect of leaf extract of C. procera was more pronounced than that of A. squamosa. The data indicate that these extracts may be used as the probable candidates for the development of bioinsecticides as safer and economic alternatives to the synthetic insecticides to control the M. domestica population.

Background New genetic and genomic resources have identified multiple genetic risk factors for late-onset Alzheimer’s disease (LOAD) and characterized this common dementia at the molecular level. Experimental studies in model organisms can validate these associations and elucidate the links between specific genetic factors and transcriptomic signatures. Animal models based on LOAD-associated genes can potentially connect common genetic variation with LOAD transcriptomes, thereby providing novel insights into basic biological mechanisms underlying the disease. Methods We performed RNA-Seq on whole brain samples from a panel of six-month-old female mice, each carrying one of the following mutations: homozygous deletions of Apoe and Clu; hemizygous deletions of Bin1 and Cd2ap; and a transgenic APOEε4. Similar data from a transgenic APP/PS1 model was included for comparison to early-onset variant effects. Weighted gene co-expression network analysis (WGCNA) was used to identify modules of correlated genes and each module was tested for differential expression by strain. We then compared mouse modules with human postmortem brain modules from the Accelerating Medicine’s Partnership for AD (AMP-AD) to determine the LOAD-related processes affected by each genetic risk factor. Results Mouse modules were significantly enriched in multiple AD-related processes, including immune response, inflammation, lipid processing, endocytosis, and synaptic cell function. WGCNA modules were significantly associated with Apoe−/−, APOEε4, Clu−/−, and APP/PS1 mouse models. Apoe−/−, GFAP-driven APOEε4, and APP/PS1 driven modules overlapped with AMP-AD inflammation and microglial modules; Clu−/− driven modules overlapped with synaptic modules; and APP/PS1 modules separately overlapped with lipid-processing and metabolism modules. Conclusions This study of genetic mouse models provides a basis to dissect the role of AD risk genes in relevant AD pathologies. We determined that different genetic perturbations affect different molecular mechanisms comprising AD, and mapped specific effects to each risk gene. Our approach provides a platform for further exploration into the causes and progression of AD by assessing animal models at different ages and/or with different combinations of LOAD risk variants.

Industrijska revolucija je dobar pokazatelj gospodarskog razvoja države, međutim, može biti i prijetnja za floru i faunu ako se u prirodu ispuštaju nepročišćene otpadne vode industrije. Cilj ovog istraživanja je procijeniti toksikološke učinke pročišćenih i nepročišćenih industrijskih otpadnih voda na aktivnost acetilkolinesteraze (AChE) kod Heteropneustes fossilis i Labeo rohita, jestivih riba različitih karakteristika poput razlika u morfologiji, staništu, ishrani, itd. Analizirani su fizikalno-kemijski parametri otpadnih voda kao što su: pH, električna vodljivost (EC), alkalitet, tvrdoća, otopljeni kisik (DO), fosfati, sulfati, nitrati, slobodni amonijak, kloridi, cink, željezo, krom i kalij jer ti parametri nisu bili u rasponu prema ISO smjernicama. Vrijednost LC50 za nepročišćene vode iznosila je 2,34% (v/v) i 0,80% (v/v) tijekom 96 h kod H. fossilis i L. rohita. Smrtnost riba u obrađenim otpadnim vodama nije zabilježena. Tijekom izlaganja subletalnim koncentracijama (1/15, 1/(10 ), 1/5 LC50) kod obje vrste riba aktivnost AChE u metabolički osjetljivim organima (mozak, mišići, škrge) je bila smanjena. Daljnja istraživanja biokemijskih i molekularnih pokazatelja mogla bi približiti mehanizam njihovog djelovanja., Industrial revolution is a good indicator of economic development of a country; however, it can be a threat to the flora and fauna if the untreated effluent of an industry is discharged. The present study is aimed to assess the comparative toxicological impacts of treated and untreated industrial effluents on acetylcholinesterase (AChE) activity in Heteropneustes fossilisand Labeo rohita, the most common edible fishes having diverse characters which include differences in morphology, habitat, food and feeding, etc. The physico-chemical parameters such as pH, electrical conductivity (EC), alkalinity, hardness, dissolved oxygen (DO), phosphate, sulphate, nitrate, free ammonia, chloride, zinc, iron, chromium and potassium of both untreated and treated effluent from the fertilizer industry were also analyzed as these parameters were not in range as per ISO guidelines. The LC50 value for untreated effluent was 2.34% (v/v) and 0.80% (v/v) for 96 h in H. fossilis and L. rohita, respectively, while no mortality was recorded in the treated effluent. The AChE activity in both fish species was found to decline in metabolically responsive organs like brain, muscle and gills through exposure to sub-lethal concentrations (1/15th, 1/10th and 1/5th of LC50 value) of the untreated effluent for 96 h. Further studies on biochemical and molecular aspects may reveal the mechanism of their action.

Graphical abstract, Highlights • In the present study, co-exposed administered pesticides induced a higher level of toxicity to Eudrilus eugeniae. • Statistically significant changes were observed after 48 h exposure of CPF, cypermethrin and combination of the two, reflects the synergistic cumulative impact on the AChE and oxidative stress parameters in dose- dependent manner. • Significant changes were observed in different body segments (Pre-Clitellar, Clitellar and Post-Clitellar) of earthworm in tissue specific pattern., Recurrent application of chemical pesticides in the agricultural fields have adverse impact on flora and fauna of soil ecosystem. Earthworms immensely contribute in increasing the fertility of soil. They may act as a bioindicator for the ecotoxicological analysis of pesticide induced soil pollution. Earthworms, Eudrilus eugeniae were exposed to different concentrations of pesticides chlorpyrifos (OP), cypermethrin (a pyrethroid) and their combination for 48 h by paper contact toxicity method. The LC50 for commercial grade of chlorpyrifos, cypermethrin and combined pesticides were determined as 0.165, 0.066 and 0.020 μg/cm2, respectively. To assess the sub-lethal effect of these pesticides, E. eugeniae were exposed to 5% and 10% of LC50 of the pesticides for 48 h. Variation in morpho-behavioural changes such as coiling, clitellar swelling, mucus release, bleeding and body fragmentation in earthworms were observed after exposure of both pesticides and their combination. Various biochemical estimations such as specific activity of acetylcholinesterase (AChE), superoxide dismutase (SOD), catalase (CAT), glutathione -S-transferase (GST); levels of lipid peroxidation (LPO) and reduced glutathione (GSH) were carried out in different body segments. Significant changes in these stress markers were observed at low and high sub-acute concentration of pesticides exposed earthworm, Eudrilus eugeniae. Such changes indicate potential health risk to E. eugeniae if exposed to the high concentrations of these pesticides accumulated in soil.

Alzheimer’s Disease (AD) is characterized by multiple clinical phenotypes and molecular signatures at different stages of the disease and aging is the major risk factor for sporadic AD. Aging and AD are linked at molecular, cellular and systems level with commonalities in inflammation and associated immune response in the brain. Mouse models of AD were developed that mimic various aspects of aging-associated neurodegeneration and inflammation. Research in mouse models of AD showed that drugs and treatments designed for AD can decelerate aging phenotypes suggesting efficient utilization of these models in aging research. We analyzed RNA-Seq transcriptomic data from transgenic mouse models of familial AD (APP/PS1 and 5XFAD) and knock-in mouse models of late-onset AD (APOE and TREM2) at the ages between 4-months and 24-months. The number of differentially expressed genes between transgenic/knock-in and WT mice increased by age in all mouse models. Gene set enrichment analysis identified metabolic pathways, including oxidative phosphorylation, altered in an age and genotype related manner in the brain of APP/PS1 and 5XFAD mice that recapitulate major features of amyloid pathology. Immunity related pathways were enriched in APOE4 model carrying Trem2*R47H mutation at >12 months-old. We also mapped the transcriptional signatures to co-expression gene modules of human LOAD from the AMP-AD consortium and observed correlations specific to each mouse model. Our study provides a detailed view of how the aging interacts with AD-relevant pathologies at the transcriptome level and demonstrates potential translational relevance of the AD mouse models in the context of human aging.

Identification of horizontal gene transfers (HGTs) has primarily relied on phylogenetic tree based methods, which require a rich sampling of sequenced genomes to ensure a reliable inference. Because the success of phylogenetic approaches depends on the breadth and depth of the database, researchers usually apply stringent filters to detect only the most likely gene transfers in the genomes of interest. One such study focused on a highly conservative estimate of trans-domain gene transfers in the extremophile eukaryote, Galdieria sulphuraria (Galdieri) Merola (Rhodophyta), by applying multiple filters in their phylogenetic pipeline. This led to the identification of 75 inter-domain acquisitions from Bacteria or Archaea. Because of the evolutionary, ecological, and potential biotechnological significance of foreign genes in algae, alternative approaches and pipelines complementing phylogenetics are needed for a more comprehensive assessment of HGT. We present here a novel pipeline that uncovered 17 novel foreign genes of prokaryotic origin in G. sulphuraria, results that are supported by multiple lines of evidence including composition-based, comparative data, and phylogenetics. These genes encode a variety of potentially adaptive functions, from metabolite transport to DNA repair.

The importance of the earthworms in the agricultural practices is well known. The increasing applications of pesticides and chemicals in the agricultural farms have adversely influenced the flora and fauna of the soil. Earthworms which immensely contribute in increasing the quality and fertility of agricultural soil are reported be worst hit organisms under such conditions. Recent reports have indicated growing interests among researchers to explore biochemical and molecular markers as indicators of accumulation of pollutants in the soil in general and pesticides in particular. The varying levels of several biomolecules in different parts of the earthworm have been reported which are indicative of sensitivity of the organisms to different xenobiotics. However, the existing information lacks the literature displaying stock of information regarding the impact of pesticides on the levels of some key enzymes regulating many crucial functions in the earthworm at one place. Keeping in view this issue, it was envisaged to bring out a mini review which illustrates updated information available on the impact of pesticides on the activities of certain key enzymes reported to be responsible for catalysing metabolic pathways concerning the neurotransmission system, energy metabolism, oxidative stress and amino acids metabolism in different body parts of the earthworms, a prospective bioindicators of pesticides contamination in the soil.

In the present study, the acute toxicity of chlorpyrifos (an organophosphate, OP) and cypermethrin (a pyrethroid) pesticides was estimated for 96 h in

Carbofuran (2,3-dihydro-2,2-dimethyl-7-benzofuranol methylcarbamate), is known to induce oxidative stress and to cause inhibition of acetylcholinesterase activity. The present work was envisaged to evaluate the effect of carbofuran on redox indices and its interactions with hepatic markers in rat. The ameliorating effect ofCitrus limonfruit extract on carbofuran induced toxicity was also monitored. The results indicated that carbofuran treatment caused significant alterations in the levels of activities of AST, ALT, and LDH in liver tissues and serum. The levels of enzymatic oxidative stress markers such as SOD and catalase and nonenzymatic redox molecules such as total thiol, GSH, and protein thiol also showed significant perturbations in rat liver due to carbofuran treatment. The administration ofCitrus limonfruit extract, however, was able to markedly ameliorate the toxicity of carbofuran by protecting the levels of aforesaid biomarkers to near normal levels. The ameliorative effect ofCitrus limonfruit extract may be due to the presence of different antioxidants in it which may neutralize the ROS and RNS generated in the body tissue due to pesticide stress. These results suggested thatCitrus limonfruit extract may be utilized as a potential supplement in proper management of pesticide intoxication in association with relevant therapeutics.

Wise men of intellects know that the materialistic human body is genetically controlled, environmentally modulated and controlled by unknown deluding power (Maya) or ULTIMATE. In the current period of time, Lust, Anger, Greed, Pride, Jealous, duplicity, perversity, hypocrisy, malice, heresy, pride, infatuation, concupiscence and arrogance pervade the whole universe. All are unreal, even though remedy is unknown. In this presidential address, I am bringing the new insights of these invisible agents and their remedies in association with diseases of mind, brain and body to provide complete health, doctrine and peace to whole world. The available unfathomable universe (Spirit, Piety, Vedas, Puranas, Agamas, Modern Yoga and Science) has been churned out in the laboratory of Nature and nectar like medicine has been discovered in the form of Ayurvedic, Yoga, Devotion, Wisdom and Dispassion. In brief, the root cause of diseases is the unreal concept of universe that is duality. Where is duality? In real fact, this does not exist and we all are just sleeping in night of delusion. All the human beings are bound to live their life under three humors "Sattva, Rajas and Tamas" and three states "Awaken, Dream and Sound Sleep" under the management of nature as slave of Desire, Senses & Mind. Indeed, all are suffering by time; fate; merit; demerit or disposition, but exact reason is unknown. In this, my approach is to bring the hypothesis of evenness theory in scientific society as the time is constant, only the dangerous waves of ignorance are flowing in the current period of time in all over universe. Under steeped condition, I and other have studied the level of DNA, RNA and Protein that is visible. Thus, we believe science with complete confidence and faith. Is there any remedy available to eradicate these invincible factors of diseases? Yes! Interestingly, in the laboratories of Nature, I have developed the remedies for these invincible factors along with an Ayurvedic formulation for the treatment of Vitiligo. Considering the very limit of Nescience and tremendous grief of whole universe, I have worked little hard to developed some nectar type medicine and in stage to reframe the universe by providing Health, Doctrine & Peace.

In order to understand the level of health risk posed by pyrethroid insecticides with strong soil-binding properties to freshwater fish, specifically living in muddy region of aquatic bodies, changes were examined in different biochemical stress markers in a freshwater muddy fish, Clarias batrachus, exposed to pyrethroid insecticides, cypermethrin and λ-cyhalothrin, in low sub-acute concentrations parts per million (ppm) for 96 hr. Data showed significant increase in levels of lipid peroxidation and in activities of lactate dehydrogenase, acid, and alkaline phosphatases along with marked decline in the specific activity of acetylcholinesterase in a concentration-dependent manner. The marked alterations in stress biomarkers indicate that pyrethroids induce significant stress in C. batrachus. This risk assessment study draws attention towards the potential health risk of freshwater muddy fish, which are continuously being exposed to the high concentrations of such insecticides accumulated as runoff in the m...