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Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an emerging infectious disease. We present the complete genome sequences of these organisms along with comparisons to other organisms in the Rickettsiales order. Ehrlichia spp. and Anaplasma spp. display a unique large expansion of immunodominant outer membrane proteins facilitating antigenic variation. All Rickettsiales have a diminished ability to synthesize amino acids compared to their closest free-living relatives. Unlike members of the Rickettsiaceae family, these pathogenic Anaplasmataceae are capable of making all major vitamins, cofactors, and nucleotides, which could confer a beneficial role in the invertebrate vector or the vertebrate host. Further analysis identified proteins potentially involved in vacuole confinement of the Anaplasmataceae, a life cycle involving a hematophagous vector, vertebrate pathogenesis, human pathogenesis, and lack of transovarial transmission. These discoveries provide significant insights into the biology of these obligate intracellular pathogens. © 2006 Dunning Hotopp.

A hyperspectral microscope imaging (HMI) method, which provides both spatial and spectral information of bacterial cells, was developed for foodborne pathogen detection. The AOTF-basedhyperspectral microscope imaging system can be effective for characterizing spectral properties of biofilms formed by Salmonella enteritidis as well as Escherichia coli. The intensity of spectral images and the pattern of intensity distribution of spectra varied with system parameters (integration time as well as gain) of the HMI system. Preliminary results demonstrated that determination of optimum parameter values of the HMI system and the integration time, which must be no more than 250 ms, are important for quality image acquisition from biofilms formed by S. enteritidis. Among the 89 contiguous spectral images between 450 and 800 nm, the intensity of images at 458, 494, 522, 550, 574, 590, and 670 nm were distinctive for biofilm o/S. enteritidis, whereas the intensity of spectral images at 546 nm was distinctive for E. coli with dark-field illumination with a metal halide light source. For more accurate comparison of intensity from spectral images, a calibration protocol of quantitative intensity comparison needs to be developed to standardize image acquisition using neutral-density filters and multiple exposures. For the identification or classification of unknown foodborne pathogen samples, ground truth region-of-interest pixels need to be selected for "spectrally pure fingerprints 'from various foodborne pathogens such as E. coli and Salmonella species. [ABSTRACT FROM AUTHOR]

Near-infrared (NIR) spectroscopy was used to measure the moisture content (MC) of in-shell Virginia and Valencia type peanuts. NIR spectral data from 400 to 2500 nm were collected on calibration samples from Virginia type peanuts ranging in moisture from 6% to 22%. Calibration models to estimate MC were developed using raw and derivative data, and an appropriate model was selected based on parameters such as standard error of calibration and prediction. The ability to predict MC in different types of in-shell peanuts with a single calibration model would save time and labor, otherwise needed for multiple calibrations, and could be useful in developing a commercial instrument. [ABSTRACT FROM AUTHOR]

Peanuts are indeterminate crops and do not mature evenly. Thus, it is difficult to decide the optimal time of harvest. Pod maturity is currently determined by the hull scrape method in conjunction with the maturity profile board (MPB) for estimating the "days until digging". The method is based on the known correlation between maturity level and pod mesocarp color, which is a subjective assessment. The objective of this research was to develop visible (Vis; 400 to 750 nm) and/or visible plus shortwave near-infrared (Vis/NIR; 400 to 1100 nm) reflectance models to predict maturity classes on a pod-by-pod basis. This would allow estimation of the optimum days to dig the crop. Peanuts ('Georgia Green') were harvested on five dates in 2008 and analyzed by the hull scrape method and Vis/NIR reflectance spectroscopy. Spectra from the side of the pod basal segment (N = 754) and from the saddle of the dorsal segment (N = 625) of each pod were analyzed in the Vis and Vis/NIR regions. Partial least squares regression was used to regress MPB maturity column numbers on spectra of pods from three sampling dates. Calibration regression error for MPB class column number was higher for saddle spectra. Based on the calibrations, placement of the pods on the profile board could differ by 1.5 columns, which could alter the estimate of days until digging by ±3 days. Validations of all spectroscopic models were equal to and/or 3 to 7 days longer than the corresponding MPB estimates of days until digging. Separation of the maturity classes was primarily due to the broad and increasing absorbance at 640 nm as the pod matures. [ABSTRACT FROM AUTHOR]

NIR spectroscopy was used to measure the moisture content (MC) of Virginia and Valencia type in-shell peanuts. Peanuts were conditioned to various moisture levels between 7% and 26% (wet basis), and the MC was verified using the standard oven method. Sample from the various moisture levels were separated into two groups, as calibration and validation. NIR absorption spectral data from 400 nm to 2500 nm were collected using peanuts within the calibration and validation sample sets. Measurements were obtained on 30 replicates within each moisture level. Partial least squares (PLS) analysis was performed on the calibration set, and models were developed using the raw spectral data and its derivative function data. The standard error of calibration (SEC) and R² of the calibration models were calculated to select the best calibration model for each peanut market type. Both Valencia and Virginia types gave an R² value of 0.99 for the derivative spectral data treatment as well as for the raw data. The selected models were used to predict the moisture content of peanuts in the validation sample set. Predicted and reference moisture contents were compared. Relative percent deviation (RPD) and standard error of prediction (SEP) were calculated to validate the goodness of fit of the prediction model The raw reflectunce spectra model gave an RPD of 5.55 with a corresponding SEP of O.97 for Valencia type peanuts, which is an indicator that the model is good for quality control and analysis. For Virginia type peanuts, the derivative reflectance spectra model gave the highest RPD value of 5. 75 and the lowest SEP of O. 771. Thus, these two models were selected for the respective peanut types as the best models for prediction of moisture content. [ABSTRACT FROM AUTHOR]

Objectives: Capsaicin (CAP) is the chief pungent principle found in the hot red peppers and the chili peppers that have long been used as spices, food additives and drugs. This study investigated the anticancer potential of CAP through its ability to modify extracellular matrix components and proteases during mice lung carcinogenesis. Methods: Swiss albino mice were treated with benzo(a) pyrene (50 mg/kg body weight dissolved in olive oil) orally twice a week for four successive weeks to induce lung cancer at the end of 14th week. CAP was administrated (10 mg/kg body weight dissolved in olive oil) intraperitoneally. Extracellular matrix components were assayed; Masson’s trichome staining of lung tissues was performed. Western blot analyses of matrix metalloproteases 2 and 9 were also carried out. Results: In comparison with the control animals, animals in which benzo(a)pyrene had induced lung cancer showed significant increases in extracellular matrix components such as collagen (hydroxy proline), elastin, uronic acid and hexosamine and in glycosaminoglycans such as hyaluronate, chondroitin sulfate, keratan sulfate and dermatan sulfate. The above alterations in extracellular matrix components were effectively counteracted in benzo(a)pyrene along with CAP supplemented animals when compared to benzo(a) pyrene alone supplemented animals. The results of Masson’s trichome staining for collagen and of, immunoblotting analyses of matrix metalloproteases 2 and 9 further supported the biochemical findings. Conclusion: The apparent potential of CAP in modulating extracellular matrix components and proteases suggests that CAP plays a chemomodulatory and anti- cancer role working against experimentally induced lung carcinogenesis.

The occurrence of dipteran fly, Chrysomya megacephala (Fabricius, 1794) is reported for the first time from Royapuram fishing harbour (Chennai), Tamil Nadu, South East India. The fully grown third instar larvae of C. megacephala were collected from decaying fishes near Royapuram fishing harbour. This site is found to be the regular breeding site for C. megacephala. Larvae were reared under laboratory condition and freshly emerged adult flies from pupae were collected and identified by morphological features and molecular tools. Molecular identification through generation of DNA barcoding using mitochondrial COI gene of C. megacephala is appended.

Abstract Background A goal of the Bovine Genome Database (BGD; http://BovineGenome.org) has been to support the Bovine Genome Sequencing and Analysis Consortium (BGSAC) in the annotation and analysis of the bovine genome. We were faced with several challenges, including the need to maintain consistent quality despite diversity in annotation expertise in the research community, the need to maintain consistent data formats, and the need to minimize the potential duplication of annotation effort. With new sequencing technologies allowing many more eukaryotic genomes to be sequenced, the demand for collaborative annotation is likely to increase. Here we present our approach, challenges and solutions facilitating a large distributed annotation project. Results and Discussion BGD has provided annotation tools that supported 147 members of the BGSAC in contributing 3,871 gene models over a fifteen-week period, and these annotations have been integrated into the bovine Official Gene Set. Our approach has been to provide an annotation system, which includes a BLAST site, multiple genome browsers, an annotation portal, and the Apollo Annotation Editor configured to connect directly to our Chado database. In addition to implementing and integrating components of the annotation system, we have performed computational analyses to create gene evidence tracks and a consensus gene set, which can be viewed on individual gene pages at BGD. Conclusions We have provided annotation tools that alleviate challenges associated with distributed annotation. Our system provides a consistent set of data to all annotators and eliminates the need for annotators to format data. Involving the bovine research community in genome annotation has allowed us to leverage expertise in various areas of bovine biology to provide biological insight into the genome sequence.

Abstract Background The decrease in cost for sequencing and improvement in technologies has made it easier and more common for the re-sequencing of large genomes as well as parallel sequencing of small genomes. It is possible to completely sequence a small genome within days and this increases the number of publicly available genomes. Among the types of genomes being rapidly sequenced are those of microbial and viral genomes responsible for infectious diseases. However, accurate gene prediction is a challenge that persists for decoding a newly sequenced genome. Therefore, accurate and efficient gene prediction programs are highly desired for rapid and cost effective surveillance of RNA viruses through full genome sequencing. Results We have developed VIGOR (Viral Genome ORF Reader), a web application tool for gene prediction in influenza virus, rotavirus, rhinovirus and coronavirus subtypes. VIGOR detects protein coding regions based on sequence similarity searches and can accurately detect genome specific features such as frame shifts, overlapping genes, embedded genes, and can predict mature peptides within the context of a single polypeptide open reading frame. Genotyping capability for influenza and rotavirus is built into the program. We compared VIGOR to previously described gene prediction programs, ZCURVE_V, GeneMarkS and FLAN. The specificity and sensitivity of VIGOR are greater than 99% for the RNA viral genomes tested. Conclusions VIGOR is a user friendly web-based genome annotation program for five different viral agents, influenza, rotavirus, rhinovirus, coronavirus and SARS coronavirus. This is the first gene prediction program for rotavirus and rhinovirus for public access. VIGOR is able to accurately predict protein coding genes for the above five viral types and has the capability to assign function to the predicted open reading frames and genotype influenza virus. The prediction software was designed for performing high throughput annotation and closure validation in a post-sequencing production pipeline.

Macrophages are primary immune cells that mediate a wide range of inflammatory diseases through their polarization potential. In this study, phytol isolated from Scoparia dulcis has been explored against 7-ketocholesterol and bacterial lipopolysaccharide-induced macrophage polarization in IC-21 cells. Isolated phytol has been characterized using GC-MS, TLC, HPTLC, FTIR, 1 H-NMR, and HPLC analyses. The immunomodulatory effects of viable concentrations of phytol were tested on oxidative stress, arginase activity, nuclear and mitochondrial membrane potentials in IC-21 cells in addition to the modulation of calcium and lipids. Further, gene and protein expression of atherogenic markers were studied. Results showed that the isolated phytol at a viable concentration of 400 µg/ml effectively reduced the production of nitric oxide, superoxide anion (ROS generation), calcium and lipid accumulation, stabilized nuclear and mitochondrial membranes, and increased arginase activity. The atherogenic markers including iNOS, COX-2, IL-6, IL-1β, MMP-9, CD36, and NF-κB were significantly downregulated at the levels of gene and protein expression, while macrophage surface and nuclear receptor markers (CD206, CD163, and PPAR-γ) were significantly upregulated by phytol pre-treatment in macrophages. Therefore, the present pharmacognostic study supports the role of phytol isolated from Scoparia dulcis in preventing M2-M1 macrophage polarization under inflammatory conditions, making it a promising compound., Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-024-03924-9., Competing Interests: Conflict of interestThe authors declare that they have no conflict of interest in the publication., (© King Abdulaziz City for Science and Technology 2024. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.)

Insects possess cellulolytic system capable of producing variegate enzymes with multifarious specificities to break down complex lignocellulosic products. Astonishingly, endoglucanases, exoglucanases and β-glycosidases act sequentially in a synergistic system to facilitate the breakdown of cellulose to utilisable energy source glucose. In silico docking studies of endo-β-1,4-glucanase from 19 different insects belonging to six different orders identified that it possesses high affinity for all the six substrates, including CMC, cellulose, cellotriose, cellotetraose, cellopentose and cellohexaose. Additionally, β-glucosidase from nearly all the reported insect sources also showed considerable affinity towards cellobiose. Van der Waals, conventional hydrogen bonds and carbon-hydrogen bonds stabilise the interaction between the enzyme and different substrates. Molecular dynamics simulations also held up the stability of various complexes. Efficient breakdown of lignocelluloses-based substrates becoming a major focus of industrial and academic communities worldwide, this study can perhaps complement the propensity of insect cellulases for prospected applications.

Phenoloxidase (PO) is a significant biomolecule involved in humoral defence mechanism of invertebrates. Spontaneous melanization of insect haemolymph is the major hinderance for studying PO activity, as haemolymph was collected devoid of phenylthiourea. In the study, no visible melanization was observed in crude serum from the grub of Oryctes rhinoceros up to 30 min of incubation amongst crude haemolymph, diluted haemolymph, crude serum and diluted serum that were subjected to visual observation for spontaneous melanization reaction. Accordingly, crude serum was taken for evaluating PO activity. At the same time, as PO substrates tend to auto-oxidize and provide false optical density value, tris-buffered saline devoid of any substrates were used as blank for PO assays. The ideal wavelength at which maximum PO activity occurred for each substrate, namely, tyrosine, tyramine, dopamine, L-dopa, DL-dopa, catechol, protocatechuic acid and pyrogallol was determined as 407, 410, 429, 465, 403, 466, 428 and 400 nm, respectively. Additionally, time course of oxidation for each phenolic substrate by the serum PO were examined and DL-dopa was identified as the specific substrate for serum PO in the grub of O. rhinoceros . Furthermore, maximum PO activity was observed at 5 min of incubation for 10 mM of DL-dopa that was considered as optimum concentration. The ideal pH and temperature for serum PO activity was observed as 7.5 and 20°C, respectively. These results suggested that standardizing a suitable substrate is an essential prerequisite to evaluate the real PO activity of serum which might significantly fluctuate in each insect model.

Salmonella is commonly found on broiler chickens during processing. This study investigates the Salmonella detection method that reduces the necessary time for confirmation, by collecting surface-enhanced Raman spectroscopy (SERS) spectra from bacteria colonies, applied to a substrate of biopolymer encapsulated AgNO 3 nanoparticles. Chicken rinses containing Salmonella Typhimurium (ST) were analyzed by SERS and compared to traditional plating and PCR analyses. SERS spectra from confirmed ST and non-Salmonella colonies appear similar in spectra composition, but with different peak intensities. t-Test on the peak intensities showed that ST and non-Salmonella colonies were significantly different (α = 0.0045) at 5 peaks, 692 cm -1 , 718 cm -1 , 791 cm -1 , 859 cm -1 , and 1018 cm -1 . A support vector machine (SVM) classification algorithm was able to separate ST and non-Salmonella samples with an overall classification accuracy of 96.7 %., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Published by Elsevier B.V.)

The present study intended to decipher the anti-infective potential of bioactive phytocompounds, such as rosmarinic acid, morin, naringin, chlorogenic acid, and mangiferin, against aquatic and human bacterial pathogens using Artemia spp. nauplii and Caenorhabditis elegans as animal models, respectively. Initially, the test compounds were screened against the QS traits in Vibrio spp., such as bioluminescence production and biofilm formation. The test compounds effectively inhibited the bioluminescence in V. harveyi. Further, the confocal laser scanning microscopic analysis revealed that these natural compounds could efficiently reduce the clumping morphology, a characteristic biofilm formation in Vibrio spp., without inhibiting bacterial growth. The results of in vivo analysis showed a significant increase in the survival of Artemia spp. nauplii infected with Vibrio spp. upon exposure to these compounds. Moreover, the compounds used in this study were already proven and reported for their quorum sensing inhibitory efficacy against Pseudomonas aeruginosa. Hence, the anti-infective efficacy of these compounds against P. aeruginosa (PAO1) and its clinical isolates (AS1 and AS2) was studied using C. elegans as a live animal model system. The results of time-killing assay deciphered that rosmarinic acid and naringin are being the most effective ones in rescuing the animals from P. aeruginosa infection followed by morin, mangiferin, and chlorogenic acid. Further, the toxicity results revealed that these compounds did not show any lethal effect on C. elegans and Artemia spp. nauplii at the tested concentrations. In conclusion, the phytochemicals used in this study were effective in controlling the QS-regulated virulence traits in Vibrio spp. and P. aeruginosa infections in Artemia spp. nauplii and C. elegans animal model systems, respectively., (© 2023. The Author(s), under exclusive licence to Springer Nature B.V.)

Undesired aggregation and adsorption of therapeutic proteins during manufacturing and administration processes can significantly decrease the efficacy of protein drugs, especially when a quantitative treatment is critical. In this study, we investigate molecular interactions of recombinant factor VIII (rFVIII), a therapeutic protein for hemophilia A treatment, at a static liquid-glass interface. We quantitatively analyze the adsorption and aggregation of rFVIII using atomic force microscopy (AFM), dynamic light scattering (DLS) and UV-Vis spectroscopy. We also investigate how PEGylation, temperature, ionic strength and pH affect the rFVIII aggregation and adsorption at the interface over time. The aggregation and adsorption of rFVIII are significantly reduced by decreasing electrostatic attractions in the solution. We observed that the PEGylation endows rFVIII molecules with high stability at the liquid-glass interface in a wide range of temperature, ionic strength and pH. Our studies will help to understand the molecular interactions of how proteins aggregate and adsorb on the solid surface and prevent the undesired events in pharmaceutical applications., Competing Interests: Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Seung-Wuk Lee reports was provided by University of California Berkeley. Seung-Wuk Lee reports a relationship with UC Berkeley that includes:. Seung-Wuk Lee reports a relationship with University of California Berkeley that includes:. Seung-Wuk Lee has patent N/A pending to N/A. N/A., (Published by Elsevier Inc.)

Hepatocellular carcinoma is a well-known internal malignancy with increased worldwide mortality. The increased progression rate is closely associated with chronic liver diseases such as cirrhosis. Chemical carcinogens cause tumor advocacy over free radical metabolites to causes numerous biochemical and molecular changes that bring oxidative stress. In addition, inflammatory cells and its growth factor promotes the progression of liver cancer through deregulates the numerous cellular signaling pathways involved in normal cellular proliferation. Plant derived phytochemicals have a better complimentary potency to defend against a wide array of free radical mediated diseases such as cancer. More recently, we have evaluated the anticancer effect of Farnesol against DEN induced hepatocellular carcinoma in male wistar albino rats. However, the possible mechanism in which Farnesol attributes its anticancer effect against DEN induced liver cancer remains unknown. Hence in the present study, an attempt has been made to reduce the oxidative stress by appraise the antioxidant effect by Farnesol in DEN induced hepatocellular carcinoma. Elevated oxidative stress markers with concomitant decreased cellular antioxidants levels were observed in DEN induced hepatic tissues. Further, proliferating nuclei with increased proliferating cell nucleolar antigen (PCNA) and inflammatory mediator expression were observed in DEN induced rats. Oral supplementation of Farnesol to DEN induced rats significantly decrease the oxidative stress markers and increase the cellular antioxidant status. Moreover, Farnesol treatment decreases the argyrophilic nuclear organizer region and PCNA along with decreased expression of inflammatory mediators suggest that Farnesol treatment restores DEN induced hepatic abnormalities and protects liver from cancer progression., (© 2021 Wiley Periodicals LLC.)

Competing Interests: There are no conflicts of interest.

Objective: To examine the role of carvacrol in modulating PI3K/AKT signaling involved in human breast cancer pathogenesis using in vitro experimental model MCF-7 cells., Methods: MTT and lactate dehydrogenase assays were performed with cells treated with different doses of carvacrol (0-250 p mol/L) at different time points (24 and 48 h). The nuclear morphology was assessed in MCF-7 cells with propidium iodide (PI) and acridine orange/ethidium bromide (AO/EB) staining and analyzed by fluorescence microscopy. Events like cell cycle arrest, apoptosis was observed by flow cytometric analysis and expressions of p-Rb, cyclin D1, cyclin-dependent kinase 4 (CDK4), CDK6, Bax, Bcl-2, PI3K/p-AKT was analyzed by immunoblot., Results: Carvacrol significantly reduced cell viability with the half maximal inhibitory concentration value of 200 µmol/L at 24 and 48 h (P<0.05). importantly, there was a significant increase in the accumulation of the G 0 /G 1 phase upon treatment with carvacrol in MCF-7 cells (P<0.05 or P<0.01). A remarkable decrease in protein expressions of p-Rb, cyclin D1, CDK4 and CDK6 denotes cell cycle arrest (P<0.05 or P<0.01). In addition, carvacrol treatment significantly inhibited PI3K/p-AKT protein expressions leading to induction of apoptosis mediated by decreased Bcl2 and increased Bax protein expressions. Further, Annexin V/PI staining by FACS analysis, dual staining by AO/EB and PI staining studies suggests induction of apoptosis by carvacrol through PI3K/Akt signaling pathway in MCF-7 cells., Conclusion: Carvacrol significantly inhibited the breast cancer MCF-7 cell proliferation and induced apoptosis via suppressing PI3/AKT signaling pathway., (© 2020. The Chinese Journal of Integrated Traditional and Western Medicine Press and Springer-Verlag GmbH Germany, part of Springer Nature.)

7-ketocholesterol, a toxic oxidative product of oxysterol is a causative agent of several diseases and disabilities concomitant to aging including cardiovascular diseases like atherosclerosis. Auto-oxidation of cholesterol esters present in low-density lipoprotein (LDL) deposits lead to the formation of oxidized LDL (Ox-LDL) along with its byproducts, namely 7KCh. It is predominantly found in atherosclerotic plaque and also found to be more atherogenic than cholesterol by being cytotoxic, interfering with cellular homeostasis. This makes it a serious threat by being the foremost cause of morbidity and mortality worldwide and is likely to become more serious during forth coming years. It involves in mediating inflammatory mechanisms characterized by the advancement of fibroatheroma plaques. The atherosclerotic lesion is composed of Ox-LDL along with fibrotic mass consisting of immune cells and molecules. Macrophages being the specialized phagocytic cells, contribute to removal of detrimental contents of the lesion along with accumulated lipids leading to alteration of its biology and functionality due to its plasticity. Here, we have explored the known as well as proposed mechanisms involved with 7KCh associated atherogenesis along with potential therapeutic strategies for targeting 7KCh as a diagnostic and target in medicine., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Gastric volvulus (GV) and wandering spleen (WS) associated with eventration of diaphragm share a common pathological cause of absence or laxity of intraperitoneal ligaments. We herein report a rare case of a 13-year-old child presenting with an acute GV, WS, diaphragmatic eventration and an ectopic ascended kidney managed with a laparoscopic approach., Competing Interests: Competing interests: None declared., (© BMJ Publishing Group Limited 2021. No commercial re-use. See rights and permissions. Published by BMJ.)

An 8-month-old male child presented with the complaint of two separate urinary streams from the penis. The child had no complaints of incontinence or recurrent UTI (urinary tract infection). Initial diagnosis of urethrocutaneous fistula was made and proceeded to micturating cystourethrography (MCU) and found to be having a urethral duplication. The duplicated urethra was excised and accessory urethra closed. Postoperatively, the child was followed up for 1 year and had no complaints of recurrence or incontinence. Through this case report, we learn about different classification systems and types of urethral duplication and their associated anomalies, and mode of management, which is mainly surgical. Further, management should be individualised to each patient based on their complaints and intraoperative findings., Competing Interests: Competing interests: None declared., (© BMJ Publishing Group Limited 2021. No commercial re-use. See rights and permissions. Published by BMJ.)