• Amniotic Fluid Infection in Preterm Pregnancies with-taliem-ir

    Amniotic Fluid Infection in Preterm Pregnancies with Intact Membranes


    Intra-amniotic infection (IAI) is a major cause of preterm labor and adverse neonatal outcome. We evaluated amniotic fluid (AF) proteolytic cascade forming biomarkers in relation to microbial invasion of the amniotic cavity (MIAC) and IAI in preterm pregnancies with intact membranes. Material and Methods. Amniocentesis was made to 73 women with singleton pregnancies; 27 with suspected IAI; and 46 controls. AF biomarkers were divided into three cascades: Cascade 1: matrix metalloproteinase-8 (MMP-8), MMP-9, myeloperoxidase (MPO), and interleukin-6; Cascade 2: neutrophil elastase (HNE), elafn, and MMP-9; Cascade 3: MMP-2, tissue inhibitor of matrix  etalloproteinases-1 (TIMP-1), MMP-8/TIMP-1 molar ratio, and Creactive protein(CRP). MMP-8 was measured by an immunoenzymometric assay and the others were measured by ELISA. Standard biochemical methods, molecular microbiology, and culture techniques were used. Results. MMP-8, MMP-9, MPO, elafn, and TIMP-1 concentrations were higher in IAI suspected cases compared to controls and also in IAI suspected cases with MIAC compared to those without MIAC when adjusted by gestational age at amniocentesis. All biomarkers except elafn and MMP-2 had the sensitivity of 100% with thresholds based on ROC-curve. Odd ratios of biomarkers for MIAC were 1.2-38 and 95% confdential intervals 1.0-353.6. Conclusions. Neutrophil based AF biomarkers were associated with IAI and MIAC.


  • Animals as sources of food-borne pathogens-taliem-ir

    Animals as sources of food-borne pathogens: A review


    Food-producing animals are the major reservoirs for many foodborne pathogens such as Campylobacter species, non-Typhi serotypes of Salmonella enterica, Shiga toxin- producing strains of Escherichia coli, and Listeria monocytogenes. The zoonotic potential of foodborne pathogens and their ability to produce toxins causing diseases or even death are sufficient to recognize the seriousness of the situation. This manuscript reviews the evidence that links animals as vehicles of the foodborne pathogens Salmonella, Campylobacter, Shiga toxigenic E. coli, and L. monocytogenes, their impact, and their current status. We conclude that these pathogenic bacteria will continue causing outbreaks and deaths throughout the world, because no effective interventions have eliminated them from animals and food.


  • Bats of the Philippine Islands—A review of research-taliem-ir

    Bats of the Philippine Islands—A review of research directions and relevance to national-level priorities and targets


     Effective science-based conservation priorities and policies are crucially important to effectively maintain biodiversity into the future. For many threatened species and systems insufficient information exists to generate priorities, or the mechanisms needed to effectively conserve species into the future, and this is especially important in megadiversity countries like the Philippines, threatened by rapid rates of development and with few overarching strategies to maintain their biodiversity. Here, using a bibliographic approach to indicate research strengths and priorities, we summarised scientific information on Philippine bats from 2000- 2017. We examine relationships between thematic areas and effort allocated for each species bat guild, and conservation status. We found that an average of 7.9 studies was published annually with the majority focused on diversity and community surveys. However, research effort is not even between taxonomic groups, thematic areas or species, with disproportionate effort focusing on ‘taxonomy and systematics’ and  ‘ecology’. Species effort allocation betweenthreatened and less threatened species does not show a significant difference, though this may be because generalist species are found in many studies, whereas rarer species have single species studies devoted to them. A growing collaborative effort in bat conservation initiativesin the Philippines has focused on the protection of many endemic and threatened species (e.g., flying foxes) and their habitats. The implementation of conservation relevant policies, outreach programs, capacity building, and mainstreaming of evidence-based conservation are encouraged to strengthen bat conservation in the Philippines.


  • Big genetic data and its big data protection-taliem-ir

    Big genetic data and its big data protection challenges


    The use of various forms of big data have revolutionised scientifc research. This includes research in the feld of genetics in areas ranging from medical research to anthropology. Developments in this area have inter alia been  characterised by the ability to sequence genomewide sequences (GWS) cheaply, the ability to share and combine with other forms of complimentary data and ever more powerful processing techniques that have become possible given tremendous increases in computing power. Given that many if not most of these techniques will make use of personal data it is necessary to take into account data protection law. This article looks at challenges for researchers that will be presented by the EU’s General Data Protection Regulation, which will be in effect from May 2018. The very nature of research with big data in general and genetic data in particular means that in many instances compliance will be onerous, whilst in others it may even be diffcult to envisage how compliance may be possible. Compliance concerns include issues relating to ‘purpose limitation’, ‘data minimisation’ and ‘storage limitation’. Other requirements, including the need to facilitate data subject rights and potentially conduct a Data Protection Impact Assessment (DPIA) may provide further complications for researchers. Further critical issues to consider include the choice of legal base: whether to opt for what is often seen as the ‘default option’ (i.e.  consent) or to process under the so called ‘scientifc research exception’.Each presents its own challenges (including the likely need to gain ethical approval) and opportunities that will have to be considered according to the particular context in question.


  • Biological control of soil transmitted helminths-taliem-ir

    Biological control of soil transmitted helminths (STHs) in a zoological park by using saprophytic fungi


    Toxascaris leonina and Trichuris sp. are soil-transmitted helminths (STHs) infecting domestic and wild mammals. The antagonistic effect of the saprophytic filamentous fungi Mucor circinelloides and Verticillium sp. was examined on eggs of T. leonina passed in the feces of captive lynxes (Lynx lynx) kept in a zoological park. The activity of M. circinelloides and Trichoderma atrobrunneum was tested on eggs of Trichuris sp. shed by captive dromedaries (Camelus dromedarius). The parasiticide activity was assessed by measuring the ovistatic   (delayed development)and ovicidal (non-viability) effects on eggs placed in Petri plates, and by spraying spores directly onto fecal samples. Based on the observation of that hyphae of M. circinelloides, Verticillium sp. and T. atrobrunneum adhered to the eggshells, penetrated and destroyed the inner embryo, an ovicidal type 3 effect was concluded. Development of eggs of T. leonina and Trichuris sp.  in the feces was delayed in the presence of all fungi, and onethird remained at the stage of zygote. A significant reduction of T. leonina viable eggs was recorded in the feces sprayed spores of M. circinelloides (58%) or Verticillium sp. (67%). Fifty percent of the eggs of Trichuris sp. became into non-viable by 30 days after the exposure to either M. circinelloides or T. atrobrunneum. It is concluded that  distribution of the filamentous fungi M. circinelloides, Verticillium sp. and T. atrobrunneum constitutes a novelapproach to conduct the biological control of the STHs (T. leonina and Trichuris sp.) affecting wild animals captive in a zoological park.


  • Brief Overview of a Decade of Genome-Wide-taliem-ir

    Brief Overview of a Decade of Genome-Wide Association Studies on Primary Hypertension


    Hypertension is highly prevalent globally. The estimated number of people with uncontrolled hypertension is nearly 1 billion (around 15% of the world population), with the number predicted to increase to 1.56 billion by the year 2025 . Due to its high prevalence, hypertension is the leading risk factor for cardiovascular disease, stroke, and endstage kidney diseases. The increased risk of cardiovascular mortality and morbidity has led to the estimation that hypertension causes 13% of all deaths (around 7.5 million deaths worldwide). Patients are considered to have hypertension when their systolic blood pressure is 140 mmHg and/or their diastolic blood pressure is 90 mmHg . However, raised blood pressure, even within the normal range, is positively and continuously related to mortality and morbidityeach increment of 20 (systolic)/10 (diastolic) mmHg of blood pressure doubles the risk of  ardiovascular diseases Hence, the number of people at risk is higher as the prevalence of raised blood pressure for .adults (aged 25 years) is around 40%


  • Citrus limon from Tunisia Phytochemical-taliem.ir

    Citrus limon from Tunisia: Phytochemical and Physicochemical Properties and Biological Activities


    Natural plant extracts contain a variety of phenolic compounds which are assigned various biological activities. Our  work aimsto make a quantitative and qualitative characterization of the Zest (ZL) and the Flesh (FL) of lemon (Citrus limon), to valorize the pharmacological uses of lemon, by evaluating in vitro activities (DPPH, free radical  scavenging and reducing power). Te antibacterial, antifungal, and antiproliferative activities were sought in the ability of Citrus limon extracts to protect DNA and protein. We found that the ZL contains high amounts of phenolics responsible for the important antioxidant properties of the extract. However, the FL is richer in flavonoids than the ZL. Te FL extract was also found to be more effective than the ZL in protecting plasmid DNA against the strand breakage induced by hydroxyl radicals. We also concluded that the FL extract exhibited potent antibacterial activity unlike ZL. Analysis by LC/MS-MS identifed 6 compounds (Caffeoyl N-Tryptophan, Hydroxycinnamoyl-Oglucoside acid, Vicenin 2, Eriocitrin, Kaempferol-3-O- rutinoside, and Quercetin-3-rutinoside). Tese preliminary results showed that Citrus limon has antibacterial and antioxidant activity in vitro. It would be interesting to  conduct further studies to evaluate the in vivo potential in an animal model.


  • Coordinating Cell Walls and Cell Growth-taliem-ir

    Coordinating Cell Walls and Cell Growth: A Role for LRX Extensin Chimeras


    To regulate the addition of cell wall components as cells expand and to control changes in cell wall composition as cells differentiate, there must be a feedback system that senses the state of the cell wall and transmits this information. The mechanisms underlying cell wall-intracellular signaling remain enigmatic despite the fundamental importance of such a system for normal growth. Cell wall proteins must play a role in this process. The most abundant cell wall proteins are extensins, but their relatively simple structure and the fact that they are covalently  cross-linked within the cell wall suggests that they have a role in stabilization rather than signaling.The LRX (for Leu-rich extensin chimera) proteins contain a C-terminal extensin domain and are tightly bound to cell walls, but their N-terminal Leu-rich repeat (LRR) domain presumably recognizes a ligand, and this interaction may participate in a cell wall signaling system (Rubinstein et al., 1995a, 1995b; Ringli, 2010). Consistent with this idea, genetic and biochemical studies have linked LRX proteins to cell growth and cell wall composition in growing root hairs and in overall plant growth (Baumberger et al., 2001; Draeger, et al., 2015).  In this issue of Plant Physiology, Wang et al. (2018) and Fabrice et al. (2018) examine the role of LRX proteins in pollen tube growth. Pollen tubes growing in vitro constitute a powerful model system for probing cell wall signaling due to the ease of manipulating growth conditions and imaging pollen tube growth in real time. Both groups carefully analyzed triple and quadruple mutations in the four pollen-expressed LRX genes in Arabidopsis, LRX8, LRX9, LRX10, and LRX11. Their results clearly indicate that LRX proteins are required for pollen tube germination and growth, a conclusion also supported in a brief paper by Sede et al. (2018). Abnormalities in mutant pollen tube growth in vitro included pollen tube bulging, branching, and bursting, phenotypes congruent with defects in cell wall structure. Fabrice et al. delved deeper into mutant phenotypes, documenting abnormalities in pollen and pollen tube cell walls at the ultrastructural level, as well as abnormal vesicle dynamics in growing tubes, and a Ca21 spike just prior to pollen tube bursting.

  • Cow’s Milk and immune Function-taliem-ir

    Cow’s Milk and immune Function in the Respiratory Tract: Potential Mechanisms


    During the last decades, the world has witnessed a dramatic increase in allergy prevalence. Epidemiological evidence shows that growing up on a farm is a protective factor, which is partly explained by the consumption of raw cow’s milk. Indeed, recent studies show inverse associations between raw cow’s milk consumption in early life and asthma, hay fever, and rhinitis. A similar association of raw cow’s milk consumption with respiratory tract infections is recently found. In line with these fndings, controlled studies in infants with milk components such as lactoferrin, milk fat globule membrane, and colostrum IgG have shown to reduce respiratory infections. However, for ethical reasons, it is not possible to conduct controlled studies with raw cow’s milk in infants, so formal proof is lacking to date. Because viral respiratory tract infections and aeroallergen exposure in children may be causally linked to the development of asthma, it is of interest to investigate whether cow’s milk components can modulate human immune function in the respiratory tract and via which mechanisms. Inhaled allergens and viruses trigger local immune responses in the upper airways in both nasal and oral lymphoid tissue. The components present in raw cow’s milk are able to promote a local microenvironment in which mucosal immune responses are modifed and the epithelial barrier is enforced. In addition, such responses may also be triggered in the gut after exposure to allergens and viruses in the nasal cavity that become available in the GI tract after swallowing. However, these immune cells that come into contact with cow’s milk components in the gut must recirculate into the blood and home to the (upper and lower) respiratory tract to regulate immune responses locally. Expression of the tissue homing-associated markers α4β7 and CCR9 or CCR10 on lymphocytes can be influenced by vitamin A and vitamin D3, respectively. Since both vitamins are present in milk, we speculate that raw milk may influence homing of lymphocytes to the upper respiratory tract. This review focuses on potential mechanisms via which cow’s milk or its components can influence immune function in the intestine and the upper respiratory tract. Unraveling these complex mechanisms may contribute to the development of novel dietary approaches in allergy and asthma prevention.


  • DeepARG a deep learning approach for predicting-taliem-ir

    DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data


    Growing concerns about increasing rates of antibiotic resistance call for expanded and comprehensive global monitoring. Advancing methods for monitoring of environmental media (e.g., wastewater, agricultural waste, food, and water) is especially needed for identifying potential resources of novel antibiotic resistance genes (ARGs), hot spots for gene exchange, and as pathways for the spread of ARGs and human exposure. Next-generation sequencing now enables direct access and profiling of the total metagenomic DNA pool, where ARGs are typically  identified or predicted based on the best hitsof sequence searches against existing databases. Unfortunately, this approach produces a high rate of false negatives. To address such limitations, we propose here a deep learning approach, taking into account a dissimilarity matrix created using all known categories of ARGs. Two deep learning models, DeepARG-SS and DeepARGLS, were constructed for short read sequences and full gene length  sequences, respectively.Results: Evaluation of the deep learning models over 30 antibiotic resistance categories  demonstrates that the DeepARGmodels can predict ARGs with both high precision (> 0.97) and recall (> 0.90).  The models displayed an advantage overthe typical best hit approach, yielding consistently lower false negative rates and thus higher overall recall (> 0.9). As more data become available for under-represented ARG categories,  the DeepARG modelsperformance can be expected to befurther enhanced due to the nature of the underlying neural networks. Our newly developed ARG database, DeepARG-DB, encompasses ARGs predicted with a high degree of confidence and extensive manual inspection, greatly expanding current ARG repositories. Conclusions: The deep learning models developed here offer more accurate antimicrobial resistance annotation relative to current bioinformatics practice. DeepARG does not require strict cutoffs, which enables identification of a much broader diversity of ARGs. The DeepARG models and database are available as a command line .version and as a Web service  at http://bench.cs.vt.edu/deeparg

  • Effect of light and natural ventilation systems-taliem-ir

    Effect of light and natural ventilation systems on the growth parameters and carvacrol content in the in vitro cultures of Plectranthus amboinicus (Lour.) Spreng


    The aim of the current study is to investigate the influence of light intensity, quality of light and alternative membrane sytems on the growth and headspace-GC/ MS chemical analysis of Plectranthus amboinicus cultivated in vitro. Nodal segments were grown under light intensities (26, 51, 69, 94 and 130 µmol m-2 s-1) provided by cool-white fluorescent lamps. Apical segments were grown under light-emitting diodes blue; red; 1 blue/2.5 red; 2.5 blue/1 red; 1 blue/1 red and white fluorescent lamps. Apical and nodal segments were grown under alternative membrane and membrane-free systems. One, two or four PTFE membranes were used on the lid of the culture  vessel.The membranes provided natural ventilation and worked as flters. The results have shown signifcant differences in the growth and carvacrol content, as well as in the content of carvacrol precursors (γ-terpinene and p-cymene) in different treatments. Among all tested light intensities, the significant increase in the dry weight and in the carvacrol content of plantlets derived from the nodal segments was recorded at 69 µmol m-2 s-1. The monochromatic red led to greater shoot length and higher dry weight in plantlets derived from the apical segments, as well as to carvacrol accumulation greater than that provided by the fluorescent lamps. The culture vessel enclosure by one and two membranes led to higher dry weight in plantlets derived from the apical and nodal segments, respectively. They also showed higher carvacrol content. Thus, it is possible optimizing the rowth .and carvacrol content in P. amboinicus  ultivated in vitro by adjusting these environmental parameters


  • Effect of melatonin and gibberellic acid foliar-taliem-ir

    Effect of melatonin and gibberellic acid foliar application on the yield and quality of Jumbo blackberry species


    Not many chemical hormone studies does exist in our country especially in berry fruits. Foliar application of melatonin and gibberellic acid hormones was performed in 2016 and 2017 in order to analyze the effects of different doses of hormone applications on fruit quality and  yield. Pheonologic, pomological and some bioactive content analyses of these hormones were studied. According to the research results, while M + GA10 ppm (240.50; 3.9) and M + GA 5 ppm (226.50; 3.6) applications have the highest fruit number and weight (g), the highest fruit size was obtained from GA 5 ppm (21.21 mm fruit length, 16.56 mm fruit width) and M 10 ppm (21.10 mm fruit length, 16.20 mm fruit width) chemical applications in Jumbo blackberry species. The highest values in Ph, soluble solid content (SSC) and titratable acidity averages were obtained from GA 5 ppm (3.69; 10.80; 2.42) and GA 10 ppm (3.68; 10.70; 2.40) applications; the highest total antioxidant activity in bioactive characteristics averages was found in G 10 ppm 143.21 mg/g, the highest total phenolics was identified in .G 5 ppm 72.68 ppm/GAE and the highest total flavonoids was determined in G 10 ppm 4925.75 ppm/QE


  • Effects of melatonin treatment on the postharvest-taliem-ir

    Effects of melatonin treatment on the postharvest quality of strawberry fruit


    The effects of exogenous melatonin on postharvest life and quality in strawberry fruit after harvest were evaluated. To explore the optimum concentration of melatonin treatment, strawberry fruit were treated with 0, 0.01, 0.1, 1 and 10 mmol L1 melatonin for 5 min and then stored at 4 °C and 90% RH for 12 d. The results showed that application of melatonin at 0.1 or 1 mmol L1 was notably effective in reducing decay and weight loss of fruit. Senescence of strawberry fruit was clearly delayed by the 0.1 or 1 mmol L1 melatonin treatment, as disclosed by the color, firmness, the total soluble solids content and titratable acidity of the fruit. Melatonin treatment at 0.1 or 1 mmol L1 significantly reduced the accumulation of hydrogen peroxide (H2O2) and malondialdehyde (MDA), but increased the total phenolics and flavonoid contents, resulting in the higher  ntioxidant capacity. Nevertheless, melatonin treatment had a negative impact on the ascorbic acid content. The optimum concentration of melatonin for extending the postharvest life and improving the quality of strawberry fruit was 0.1 or 1 mmol L1. Moreover, melatonin treatment at 0.1 mmol L1 enhanced the expression of melatonin biosynthetic genes including FaTDC, FaT5H, FaSNAT, and FaASMT and consequently increased the content of endogenous melatonin. These findings suggested that melatonin treatment may be a useful technique to extend the postharvest life and improve quality in strawberry fruit.


  • Genetic characterization and modification-taliem-ir

    Genetic characterization and modification of a bioethanol-producing yeast strain


    Yeast Saccharomyces cerevisiae strains isolated from different sources generally show extensive genetic and phenotypic diversity. Understanding how genomic variations influence phenotypes is important for developing strategies with improved economic traits. The diploid S. cerevisiae strain NY1308 is used for cellulosic bioethanol production. Whole genome sequencing identified an extensive amount of single nucleotide variations and small insertions/deletions in the genome of NY1308 compared with the S288c genome. Gene annotation of the  assembled NY1308 genome showed that 43 unique genes are absent in the S288c genome. Phylogenetic analysis suggested most of the unique genes were obtained through horizontal gene transfer from other species. RNA-Seq revealed that some unique genes were not functional in NY1308 due to unidentified intron sequences. During bioethanol fermentation, NY1308 tends to flocculate when certain inhibitors (derived from the pretreatment of cellulosic feedstock) are present in the fermentation medium. qRT-PCR and genetic manipulation confirmed that the novel gene, NYn43, contributed to the flocculation ability of NY1308. Deletion of NYn43 resulted in a faster fermentation rate for NY1308. This work disclosed the genetic characterization of a bioethanol-producing S. cerevisiae strain and provided a useful paradigm showing how the genetic diversity of the yeast population would facilitate the personalized development of desirable traits.


  • Group Treatment Strategies for Animals-taliem-ir

    Group Treatment Strategies for Animals in a Zoologic Setting


    Providing care for groups of animals is a major part of practicing zoologic medicine. Herd health is key to the mindset of a zoo clinician no matter the species encountered, be it avian or artiodactylid. In addition to the classic examples of group treatment involving chemotherapeutics (discussed in detail later), zoo clinicians also practice herd health by preventing disease from entering the collection. Before traveling to a new institution, most animals undergo a preshipment examination, which serves as a screening tool for common infectious diseases specific to that taxa, and provides a snapshot of that individual’s health. Diagnostics commonly included in a preshipment  xamination are a complete blood count, serum or plasma biochemistry, imaging, and fecal examination. On arrival to a new institution, most animals undergo a quarantine period, often 30 to 90 days, in addition to another thorough examination. All of these precautionary measures are vital to ensure that infectious disease does not enter an institution, and also provide the opportunity for targeted therapy if needed, before the animal is placed within its new social group. It is highly recommended that all animals that die within a zoologic setting receive a thorough gross necropsy with histopathology to try and determine the cause of death. Then, if an infectious cause is diagnosed, therapy for the remaining group of animals is based on the pathology findings.  Another way that zoo clinicians can try to limit the need for group treatment is to have a working knowledge of which taxa can be safely housed together. In addition to such factors as size and potential for trauma, knowledge of how certain infectious diseases interact with various species can prevent future outbreaks. For example,  Entamoeba invadens is transmitted from clinically healthy herbivorous tortoises to snakes when they are housed together, causing the snakes to develop severe ulcerative colitis and hepatitis.1