Miracle-dz/UniFAR-FTUs huggingface dataset:
Changes in signal cross-talking in Mycobacterium smegmatis infected murine macrophages in presence of aqueous garlic extract

Tuberculosis (TB), an infectious disease caused by Mycobacterium tuberculosis, still continues to be the biggest infectious threat to mankind. The present havoc due to global resurgence of TB, and the emergence of multi-drug resistant (MDR)-TB in India makes the search for alternative anti-tubercular phytomedicines an absolute mandate. As a fresh preparation of crude aqueous garlic extract (AGE) was earlier found to be bactericidal against M. smegmatis having similar cell-wall structure-composition as the pathogenic M. tuberculosis at a minimal bactericidal concentration (MBC) of 60 mg/ml, and the same confirmed by biochemical assays and micro-RNA (mi-RNA) expression studies, the present work involves immuno-molecular studies on the differential expression of NF-κB, a transcription factor involved in cellular immunobiological responses to foreign stimuli such as bacterial and viral antigens, in murine peritoneal-macrophages infected respectively with untreated, alive M. smegmatis (positive control) and M. smegmatis treated with crude AGE (at 60 mg/ml) (experimental) by SDS PAGEWestern Blot techniques. Significantly, a prominent band of NF-κB was observed in the lane of macrophages infected with untreated, alive M. smegmatis, indicating up-regulation of NF-κB gene expression there following the pathogen invasion, as compared to the macrophages infected with crude AGE-treated (at 60 mg/ml) M. smegmatis, thus confirming the mycobactericidal potency of aqueous garlic extract. Data obtained out of biochemical assays carried out for the determination of specific activities of inducible nitric oxide synthase (iNOS) and superoxide dismutase (SOD) enzymes from the same set of macrophage samples, which showed prominent induction of these two enzymes in case of macrophages infected with untreated, alive M. smegmatis with respect to macrophages infected with crude AGE-treated (at 60 mg/ml) M. smegmatis, also substantiated the same.
Potential of seed dusts of Jatropha curcas L., Thevetia peruviana (Pers.), and Piper guineense Schumach. against the maize weevil, Sitophilus zeamais (Motschulsky, 1855) (Coleoptera: Curculionidae) in storage of corn grain

Abstract A laboratory evaluation was carried out to determine the efficacy and phytochemical composition of powdered seeds of Physic nut Jatropha curcas, Yellow oleander Thevetia peruviana and West African black pepper Piper guineense at different dosages (2.5, 5.0, 7.5 and 10.0 g) for the management of Sitophilus zeamais. Treatments were mixed with 50 g of maize and infested with 10 adult S. zeamais in 200 ml air-tight glass vials and kept under ambient conditions (25-30°C and 70-90 RH) for a period of 28 days in August 2015. The trial was laid out in a completely randomized design in four replicates. Results from data analyses showed that treated maize grains in storage recorded significantly (P < 0.05) higher mean mortality levels of adult S. zeamais than the untreated controls. However, there were no significant differences in mean mortality of the weevil at 7, 14, 21 and 28 DAT, except on those stored only for 1 DAT. Batches treated with higher doses (10.0, 7.5, 5.0 g) suffered a higher total mortality of adult S. zeamais; this was significantly (P < 0.05) higher compared with treatments using smaller dosages (2.5 and 0.0 g). Phytochemical analysis of treatments revealed high levels of alkaloids, tannins and phenols in all the plant extracts. The flavonoid contents were also high in Piper guineense and Permethrin, but lower in Jatropha curcas and Thevetia peruviana. These compounds are known to possess insecticidal properties that may have been responsible for the mortality of Sitophilus zeamais.
Effect of Processing Method of Sesame ( Sesam um indicum Linn.) Seeds on the Growth Performance and Nutrient Utilization of Broiler Chicks

Objective: This research was conducted to investigate the effect of feeding processed sesame seed (Sesamum indicum) on the performance and nutrient utilization of broiler chicks. Method: 400 day old (Anak, 2000) white strain unsexed broiler chicks were allocated to four treatments with each treatment having two replicates in a completely randomized design (CRD). Each treatment contained 100 chicks with 50 chicks per replicate. A control diet, which served as treatment 1 had full fat soya bean, whereas the cooked, pre-pressed and de-hulled seed based diets served as treatments 2, 3 and 4 respectively. Feed and water were supplied ad libitum. Result: The pre-pressed Sesame seeds had significantly (P 0.05) differences in the means of the other treatments. The mean values for mean weekly feed intake of the birds fed de-hulled and pre-pressed (291.21 g) and de-hulled (292.21 g) were significantly (P<0.05) higher than that of the control (335.96 g), which was significantly lower than cooked (260.92 g). The results for body weight gain and FCR follow the same trend. The digestibility of crude fibre in the pre-pressed seeds (40.80%) is significantly (P<0.05) higher, and least in the cooked (31.02%) and control treatment. A cooked Sesame seed give better feed conversion ratio than other processing methods but does not necessarily correspond to the best performance. Conclusion: Arising from this study, the three processing methods show promise as feed for broiler chicks. As a result, all three processing methods are commended for the different objectives for which they perform optimally but the pre-pressed proved to be the best method of processing sesame seeds for appreciable result on crude protein levels.
Channel crosstalk correction in suspension and imaging mass cytometry

Mass cytometry enables simultaneous analysis of over 40 proteins and their modifications in single cells through use of metal-tagged antibodies. Compared to fluorescent dyes, the use of pure metal isotopes strongly reduces spectral overlap among measurement channels. Crosstalk still exists, however, caused by isotopic impurity, oxide formation, and mass cytometer properties. Spillover effects can be minimized, but not avoided, by following a set of constraining rules when designing an antibody panel. Generation of such low crosstalk panels requires considerable expert knowledge, knowledge of the abundance of each marker and substantial experimental effort. Here we describe a novel bead-based compensation workflow that includes R-based software and a web tool, which enables correction for interference between channels. We demonstrate utility in suspension mass cytometry and show how this approach can be applied to imaging mass cytometry. Our approach greatly simplifies the development of new antibody panels, increases flexibility for antibody-metal pairing, improves overall data quality, thereby reducing the risk of reporting cell phenotype and function artifacts, and greatly facilitates analysis of complex samples for which antigen abundances are unknown.
Molecular physiological responses and acclimation of the seagrass species Z. muelleri to light limitation

Seagrasses are marine ecosystem engineers that are currently declining in abundance at an alarming rate due to both natural and anthropogenic disturbances in ecological niches. Despite reports on the morphological and physiological adaptations of seagrasses to extreme environments, little is known of the molecular mechanisms underlying photo-acclimation and/or tolerance in these marine plants. This study applies the two-dimensional isoelectric focusing (2D-IEF) proteomics approach to identify photo-acclimation/tolerance proteins in the marine seagrass Zostera muelleri. For this, Z. muelleri was exposed for 10 days in laboratory mesocosms to saturation (control, 200 μmol photons m-2 s-1), supersaturation (SSL, 600 μmol photons m-2 s-1), and light limitation (LL, 20 μmol photons m-2 s-1). Using LC-MS/MS analysis, 93 and 40 protein spots were differentially regulated under SSL and LL conditions, respectively, when compared to the control. In contrast to the LL condition, Z. muelleri robustly tolerated super-saturation light than control conditions, evidenced by their higher relative electron transport rate and half-saturation of photosynthetic rate values. Proteomic analyses revealed up-regulation and/or appearances of proteins belonging to the Calvin-Benson and Krebs cycle, glycolysis, the glycine cleavage system of photorespiration, and the antioxidant system. These proteins, together with those from the inter-connected glutamate-proline-GABA pathway, shaped Z. muelleri photosynthesis and growth under super-saturation light conditions. In contrast, the LL condition negatively impacted the metabolic activities of Z. muelleri by downregulating key metabolic enzymes for photosynthesis and the metabolism of carbohydrates and amino acids, which is consistent with the observation with lower photosynthetic performance under LL condition. This study provides novel insights into the underlying molecular photo-acclimation mechanisms in Z. muelleri, in addition to identifying protein-based biomarkers that could be used as early indicators to detect acute/chronic light stress in seagrasses to monitor seagrass health.
ADIPOSE-DERIVED STEM CELLS AND PLATELET-RICH PLASMA: INPUTS FOR REGENERATIVE MEDICINE

Abstract Regenerative medicine and tissue engineering have the aim of restoring function due to tissue damage or organ failure. This goal can be achieved either by stimulating endogenous stem cells or by providing exogenous stem cells along with appropriate biomimetic scaffold and growth factors. Among the different sources and types of stem cells, particular attention has been given to adipose tissue-derived mesenchymal stromal cells (ADSCs). The use of ADSCs as source of adult stem cells offers numerous advantages: the collection technique is easier and less invasive than with bone marrow; these stem cells show a high proliferative rate in vitro and are endowed with multi-differentiative capability and tissue repair properties. On the other hand, therapies implying the use of growth factors for tissue regeneration are widely based on platelets: these anucleated cells are a rich source of growth factors and are physiologically involved in hemostasis, wound healing and tissue repair. Platelet-rich plasma (PRP) is an autologous platelet concentrate with antibacterial and anti-inflammatory properties and a vehicle and source of growth factors. Due to these properties, PRP is increasingly used for regenerative medicine purposes, especially in the field of wound healing and osteoarthritis. In this review article, we give an overview of the combined action of ADSCs and PRP in therapeutic applications for these pathological conditions.
Are biochemical composition parameters of sediment good tools for assessing the environmental quality of estuarine areas in tropical systems?

The present study aims to assess the environmental quality of six estuaries in north-eastern Brazil, using biochemical composition and quantity of organic matter in tropical sediments. Samples were collected monthly during spring low tide from August 2011 to July 2012, in the mid-littoral. Concentrations of organic matter and its biochemical composition reflected the degree of anthropogenic pressure. Although total concentrations of proteins and carbohydrates were similar among estuaries with contrasting levels of anthropogenic pressure, the protein to carbohydrates (PRT : CHO) ratio effectively reflected the trophic state of these areas. PRT : CHO ratios >1 were observed in all studied areas suggesting eutrophic conditions or an initial stage of eutrophication in all of them. Low Chl-a/Phaeo ratios may be associated with the level of eutrophication of each area, however it may also reflect the natural productivity or the presence of mangrove debris. These results were compared with those obtained in previous environmental assessments of the same estuarine areas using the AZTI Marine Biotic Index and monitoring reports showing good agreement. The present study confirmed for the first time in tropical estuarine areas that the biochemical approach can be successfully used to assess the trophic state of the benthic compartment.
Leaf, panicle and fruit blight of litchi (Litchi chinensis) caused by Alternaria alternata in Bihar state, India

Abstract India is one of the leading litchi (Litchi chinensis Sonn.) producing countries in the world. A leaf blight on litchi was observed in April 2012 on nursery plants at Muzaffarpur, Bihar, India. Light to dark brown necrosis starting from leaf tips resulted in complete drying of leaves. Blighting of panicles and fruits were also noticed during April–June, 2014. Panicles dried out as a result of necrosis, while necrosis of pedicels led to complete drying of the rind of developing fruits. Infected tissues collected from different sites in diseased fields were cultured on potato dextrose agar (PDA), and the pathogen was identified as Alternaria alternata (Fr.) Keissler on the basis of morphological and cultural characteristics. The fungus produced greyish-black colonies on PDA with obclavate or obpyriform conidia in chains. Conidia had 1–4 transverse and 0–3 longitudinal septa, and measured 16–40 × 4–13 μm. Morphological identification was confirmed by sequencing the internal transcribed spacer (ITS) region of rDNA using ITS1 and ITS4 primers. Pathogenicity tests indicated that A. alternata infected and caused blights of the leaves, panicles and fruit of litchi. Alternaria alternata has been reported to cause post-harvest decay of litchi fruit, but this is the first report of A. alternata causing blights of leaves, panicles and fruit in the field.
Local and regional stressors interact to drive a salinization‐induced outbreak of predators on oyster reefs

Predator outbreaks are predicted to increasingly decimate economically and ecologically important prey populations because global climate change and food-web modi ﬁ cations frequently facili-tate predators and stress prey. Natural systems are organized hierarchically, with processes operating at multiple scales giving rise to patterns of biodiversity, so predicting and managing outbreaks requires a framework that accounts for the effects of both local and regional stressors. Here, we used the comparative experimental approach to investigate whether the collapse of a nationally important oyster ﬁ shery in the Gulf of Mexico (Apalachicola Bay, Florida) could have been (1) caused proximally by a predator outbreak and (2) whether this outbreak was mediated by local- and/or regional-scale forces. During the ﬁ shery collapse, we paired experiments with monitoring in Apalachicola Bay and found elevated water salinity, high abundance of predatory snails, and intense oyster mortality due to predation. By repeating these experiments over 4 yr, we found that periods of reduced water salinity inhibited predation on oysters. To partition the in ﬂ uence of local-versus-regional factors on this predator outbreak, we simultaneously replicated the paired experiments and monitoring in a nearby bay (Ochlockonee Bay) that shares the same regional-scale rainfall conditions. Increasing freshwater withdrawals from the watershed that drains into Apalachicola Bay have increased salinities in that bay, but there have not been similar withdrawals in the Ochlockonee Bay watershed. Therefore, Apalachicola Bay experienced a localized anthropogenic stress, while both bays experienced regional stress from drought. In Ochlockonee Bay, our experiments demonstrated that the river maintained suf ﬁ ciently low salinity to provide ~ 50% of oyster reefs with a refuge from predation. In contrast, salinity-dependent predation in Apalachicola Bay extended up to the river mouth. Given the stark differences in upstream water withdrawals between these watersheds, it is reasonable to surmise that these withdrawals exacerbated the stress of regional drought, created the difference in predation between the two bays, and thus may have precipitated the oyster ﬁ shery collapse. Our study provides empirical support for recent theory about the hierarchical organization of ecosystems, which predicts that stressors will interact across scales to cause localized predator outbreaks.
Thermotherapy and chemotherapy to control citrus HLB in the field - eScholarship

Huanglongbing (HLB), a systemic and destructive disease of citrus, is associated with three species of α-proteobacteria, ‘Candidatus Liberibacter asiaticus’ (Las), ‘Ca. L. africanus’ and ‘Ca. L. americanus’. Previous studies have found distinct variations in temperature sensitivity and tolerance among these species1. Las, the most prevalent and heat-tolerant species, can thrive at temperatures as high as 35°C1. Our earlier work has shown that Las bacteria in potted HLB-affected citrus were significantly reduced or eliminated when exposed to continuous temperatures of 40 to 42°C for a minimum of 48 h2. To determine the feasibility and effectiveness of thermotherapy in the field, various portable greenhouses were placed over commercial and dooryard citrus exposing trees to higher temperatures through solarization. Within weeks after treatment, most trees responded with vigorous new growth. Flush post-treatment had significantly less Las DNA present in leaves one year after treatment and trees continued to grow well. Unlike with potted trees, exposure to high heat through solarization was not sufficient to eradicate the Las population in field conditions, most flush after treatment was qPCR positive for Las. This may be attributed to fluctuating day and night temperatures, and the citrus roots imbedded in the soil being inadequately exposed to heat (temperature and duration). To further combat the systemic infection, chemicals such as penicillin and streptomycin used in conjunction with thermotherapy were applied to HLB-affected trees in the field. Plants post-treatment were monitored and leaves and roots were periodically sampled and tested for Las. Preliminary results indicate some treatment regimes are promising.
Identification, characterisation and phylogenetic analysis of commensal bacteria isolated from human breast milk in Malaysia

Human breast milk microbiota is essential for infant immune system development, maturation and protection against infection. However, there is scarce information on the fluid’s microbiological composition from Malaysia. The objective of the study was to isolate, identify and characterise commensal bacterial population present in human breast milk from Malaysia. One hundred bacteria were isolated from the human breast milk of healthy lactating women (n=30). After preliminary screening, 20 isolates were characterised using both phenotypic and molecular techniques. The results indicated that most frequently identified bacteria in this study were E. faecalis and S. hominis. These organisms alongside E. cloacae were all metabolised D-Maltose, Sucrose, D-Turanose, α-D-Glucose, D-Fructose, D-Mannose, D-Galactose, D-sorbitol and D-Mannitol and were able to grow at pH 5 and 6, 1% sodium lactate, 1%, 2% and 8% NaCl. BLAST showed over 99% similarity to those deposited in Genbank. Phylogenetic-relatedness was depicted using neighbour-joining method and had two clades with 100% bootstrap. These findings provided insight into the nature, characteristics and also phylogenetic-relatedness of bacteria present in human milk from Malaysia. Isolation and identification of commensal bacteria from human milk are considered the first step for future studies on the benefit of these organisms towards human health.
An integrated, pipeline-based approach for cryo-EM structure determination and atomic model refinement in the cloud

Access to streamlined computational resources remains a significant bottleneck for new users of cryo-electron microscopy (cryo-EM). To address this, we have built upon our previous work (Cianfrocco & Leschziner 2015) to develop software tools that will submit cryo-EM analysis routines and atomic model building jobs directly to Amazon Web Services (AWS) from a local computer or laptop. These new software tools (“cryoem-cloud-tools”) have incorporated optimal data movement, security, and cost-saving strategies, giving novice users access to complex cryo-EM data processing pipelines. Integrating these tools into the RELION processing pipeline and graphical user interface we determined a 2.2 Å structure of ß-galactosidase in ~55 hours on AWS. We implemented a similar strategy to submit Rosetta atomic model building and refinement to AWS. These software tools dramatically reduce the barrier for entry of new users to cloud computing for cryo-EM and are freely available at cryoem-tools.cloud.
Growth Inhibition by Amino Acids in Saccharomyces cerevisiae

Amino acids are essential metabolites but can also be toxic when present at high levels intracellularly. Substrate-induced down-regulation of amino acid transporters in Saccharomyces cerevisiae is thought to be a mechanism to avoid this toxicity. It has been shown that unregulated uptake by the general amino acid permease Gap1 causes cells to become sensitive to amino acids. Here, we show that overexpression of eight other amino acid transporters (Agp1, Bap2, Can1, Dip5, Gnp1, Lyp1, Put4 or Tat2) also induces a growth defect when specific single amino acids are present at concentrations of 0.5–5 mM. We can now state that all proteinogenic amino acids, as well as the important metabolite ornithine, are growth inhibitory to S. cerevisiae when transported into the cell at high enough levels. Measurements of initial transport rates and cytosolic pH show that toxicity is due to amino acid accumulation and not to the influx of co-transported protons. The amino acid sensitivity phenotype is a useful tool that reports on the in vivo activity of transporters and has allowed us to identify new transporter-specific substrates.
The Role of the Coxsackie-adenovirus Receptor in the Pathogenesis of Heart Disease and Coxsackieviral Myocarditis

The coxsackie-adenovirus receptor (CAR) is a viral receptor for Group B coxsackieviruses (CVB). Physiologically, CAR is a cellular adhesion protein. I report that upregulation of cardiac CAR in the young adult mouse (CAR/MtTA ) caused a cardiomyopathy that was characterized by inflammation and hypertrophy. In the hearts of CAR/MtTA mice c-Jun N terminal kinase (JNK) was specifically activated. JNK activation is known to promote hypertrophy of cardiomyocytes, and disrupt proteins at the intercalated disc. CVB3-infected CAR/MtTA mice did not exhibit increased cardiac viral load or myocarditis severity, but did demonstrate a greater cardiac interferon-γ (IFN-γ) response when compared to littermate controls. CAR-induced expression of this antiviral cytokine may have prevented the increase in myocarditis susceptibility. Further investigation into the activation of protein kinase signaling, and antiviral signaling will provide better understanding of how CAR participates in the pathogenesis of both viral and non-viral heart diseases.
Endogenous levels of polyamines during cold storage of bird-ofparadise treated with biocides

This study aimed to analyse the endogenous levels of free polyamines putrescine (Put), spermidine (spd) and spermine (spm) under the effect of 8-HQC (8-hydroxyquinoline citrate) and chlorine during cold storage of bird-of-paradise floral scapes. Flowers were selected, labelled and randomly distributed in recipients for postharvest trials. The base of flower scapes was immersed with pulsing treatments (Control, 100 chlorine, 250 or 500 mg L-1 8-HQC) for 48 h, thereafter, stored at 10.5 °C and 90% relative humidity for a period of 12 days. Flower parts were sampled for polyamines analysis at day 0, 4, 8 and 12 days during storage. All samples had higher Put levels than the control. Treatment with 500 mg L-1 8-HQC showed the highest Spd levels in bracts, while chlorine treatment had the highest Spm levels in stems.