2,163 research outputs found
How promising are endophytic fungi as alternative sources of plant secondary metabolites?
In this article the authors discusses the use of endophytic fungi as substitute of plant secondary metabolites. It states that endophytic fungi exist internally in plants and enhance the plants' ability to tolerate abiotic and biotic stresses. Endophytic fungi if cultured outside their host can produce secondary metabolites such as anti-cancer, anti-fungal, anti-diabetic and immunosuppressant compounds
Transcriptome analysis of stem wood of Nothapodytes nimmoniana (Graham) Mabb. identifies genes associated with biosynthesis of camptothecin, an anti-carcinogenic molecule
Camptothecin (CPT), a monoterpene indole alkaloid, is a potent inhibitor of DNA topoisomerase I and has applications in treating ovarian, small lung and refractory ovarian cancers. Stem wood tissue of Nothapodytes nimmoniana (Graham) Mabb. (family Icacinaceae) is one of the richest sources of CPT. Since there is no genomic or transcriptome data available for the species, the present work sequenced and analysed transcriptome of stem wood tissue on an Illumina platform. From a total of 77,55,978 reads, 9,187 transcripts were assembled with an average length of 255 bp. Functional annotation and categorization of these assembled transcripts unraveled the transcriptome
architecture and also a total of 13 genes associated with CPT biosynthetic pathway were identified in the stem wood
tissue. Four genes of the pathway were cloned to full length by RACE to validate the transcriptome data. Expression analysis of 13 genes associated with CPT biosynthetic pathway in 11 different tissues vis-à-vis CPT content analysis suggested an important role of NnPG10H, NnPSLS and NnPSTR genes in the biosynthesis of CPT. These results indicated that CPT might be synthesized in the leaves and then perhaps exported to stem wood tissue for storage
Adaptation of in vitro cytoadherence assay to Plasmodium knowlesi field isolates
P. knowlesi was the first Plasmodium species in which
antigenic variation was observed. Variation was due to
schizont infected cell agglutination (SICAvar) antigens
expressed by the parasite and transported to the
exposed surface of the host erythrocyte [1]. PfEMP1 is
P. falciparum’s orthologue of P. knowlesi’s SICA proteins
[2]. In P. falciparum PfEMP1 is associated with infected
erythrocytes binding to receptors such as ICAM-1
expressed on the endothelial cells of the host microvasculature.
Here, we use a static protein assay [3] to determine
if naturally occurring human P. knowlesi infections
can cause erythrocytes to bind to ICAM-1, VCAM-1
and CD36
A Functional Henipavirus Envelope Glycoprotein Pseudotyped Lentivirus Assay System
<p>Abstract</p> <p>Background</p> <p>Hendra virus (HeV) and Nipah virus (NiV) are newly emerged zoonotic paramyxoviruses discovered during outbreaks in Queensland, Australia in 1994 and peninsular Malaysia in 1998/9 respectively and classified within the new <it>Henipavirus </it>genus. Both viruses can infect a broad range of mammalian species causing severe and often-lethal disease in humans and animals, and repeated outbreaks continue to occur. Extensive laboratory studies on the host cell infection stage of HeV and NiV and the roles of their envelope glycoproteins have been hampered by their highly pathogenic nature and restriction to biosafety level-4 (BSL-4) containment. To circumvent this problem, we have developed a henipavirus envelope glycoprotein pseudotyped lentivirus assay system using either a luciferase gene or green fluorescent protein (GFP) gene encoding human immunodeficiency virus type-1 (HIV-1) genome in conjunction with the HeV and NiV fusion (F) and attachment (G) glycoproteins.</p> <p>Results</p> <p>Functional retrovirus particles pseudotyped with henipavirus F and G glycoproteins displayed proper target cell tropism and entry and infection was dependent on the presence of the HeV and NiV receptors ephrinB2 or B3 on target cells. The functional specificity of the assay was confirmed by the lack of reporter-gene signals when particles bearing either only the F or only G glycoprotein were prepared and assayed. Virus entry could be specifically blocked when infection was carried out in the presence of a fusion inhibiting C-terminal heptad (HR-2) peptide, a well-characterized, cross-reactive, neutralizing human mAb specific for the henipavirus G glycoprotein, and soluble ephrinB2 and B3 receptors. In addition, the utility of the assay was also demonstrated by an examination of the influence of the cytoplasmic tail of F in its fusion activity and incorporation into pseudotyped virus particles by generating and testing a panel of truncation mutants of NiV and HeV F.</p> <p>Conclusions</p> <p>Together, these results demonstrate that a specific henipavirus entry assay has been developed using NiV or HeV F and G glycoprotein pseudotyped reporter-gene encoding retrovirus particles. This assay can be conducted safely under BSL-2 conditions and will be a useful tool for measuring henipavirus entry and studying F and G glycoprotein function in the context of virus entry, as well as in assaying and characterizing neutralizing antibodies and virus entry inhibitors.</p
Mothers' perceptions of child weight status and the subsequent weight gain of their children : a population based longitudinal study
BACKGROUND: There is a plethora of cross sectional work on maternal perceptions of child weight status showing that mothers typically do not classify their overweight child as being overweight according to commonly used clinical criteria. Awareness of overweight in their child is regarded as an important prerequisite for mothers to initiate appropriate action. The gap in the literature is determining whether, if mothers do classify their overweight child's weight status correctly, this is associated with a positive outcome for the child's body mass index (BMI) at a later stage. OBJECTIVE: To explore longitudinal perceptions of child weight status from mothers of a contemporary population-based birth cohort (Gateshead Millennium Study) and relationships of these perceptions with future child weight gain. METHODS: Data collected in the same cohort at 7, 12 and 15 years of age: mothers' responses to two items concerning their child's body size; child's and mother's BMI; pubertal maturation; demographic information. RESULTS: Mothers' perceptions of whether their child was overweight did not change markedly over time. Child BMI was the only significant predictor of mothers' classification of overweight status, and it was only at the extreme end of the overweight range and in the obese range that mothers reliably described their child as overweight. Even when mothers did appropriately classify their child as overweight at an earlier stage, this was not related to relatively lower child BMI a few years later. CONCLUSIONS: Mothers tend to classify their child as overweight in only more extreme cases. It is an important finding that no beneficial impact was shown on later child BMI in overweight children whose mothers classified their child's weight status as overweight at an earlier stage.International Journal of Obesity accepted article preview online, 25 January 2017. doi:10.1038/ijo.2017.20
Estimating sleep parameters using an accelerometer without sleep diary
This is the final version. Available from the publisher via the DOI in this record.Wrist worn raw-data accelerometers are used increasingly in large-scale population research. We examined whether sleep parameters can be estimated from these data in the absence of sleep diaries. Our heuristic algorithm uses the variance in estimated z-axis angle and makes basic assumptions about sleep interruptions. Detected sleep period time window (SPT-window) was compared against sleep diary in 3752 participants (range = 60–82 years) and polysomnography in sleep clinic patients (N = 28) and in healthy good sleepers (N = 22). The SPT-window derived from the algorithm was 10.9 and 2.9 minutes longer compared with sleep diary in men and women, respectively. Mean C-statistic to detect the SPT-window compared to polysomnography was 0.86 and 0.83 in clinic-based and healthy sleepers, respectively. We demonstrated the accuracy of our algorithm to detect the SPT-window. The value of this algorithm lies in studies such as UK Biobank where a sleep diary was not used.Medical Research Council (MRC)National Institute of Health (NIH
Chapter 7: Grading a Body of Evidence on Diagnostic Tests
10.1007/s11606-012-2021-9Journal of General Internal Medicine27SUPPL.1S47-S55JGIM
Of cattle, sand flies and men : a systematic review of risk factor analyses for South Asian visceral leishmaniasis and implications for elimination
Background: Studies performed over the past decade have identified fairly consistent epidemiological patterns of risk
factors for visceral leishmaniasis (VL) in the Indian subcontinent.
Methods and Principal Findings: To inform the current regional VL elimination effort and identify key gaps in knowledge,
we performed a systematic review of the literature, with a special emphasis on data regarding the role of cattle because
primary risk factor studies have yielded apparently contradictory results. Because humans form the sole infection reservoir,
clustering of kala-azar cases is a prominent epidemiological feature, both at the household level and on a larger scale.
Subclinical infection also tends to show clustering around kala-azar cases. Within villages, areas become saturated over a
period of several years; kala-azar incidence then decreases while neighboring areas see increases. More recently, post kalaazar
dermal leishmaniasis (PKDL) cases have followed kala-azar peaks. Mud walls, palpable dampness in houses, and peridomestic
vegetation may increase infection risk through enhanced density and prolonged survival of the sand fly vector.
Bed net use, sleeping on a cot and indoor residual spraying are generally associated with decreased risk. Poor micronutrient
status increases the risk of progression to kala-azar. The presence of cattle is associated with increased risk in some studies
and decreased risk in others, reflecting the complexity of the effect of bovines on sand fly abundance, aggregation, feeding
behavior and leishmanial infection rates. Poverty is an overarching theme, interacting with individual risk factors on multiple
levels.
Conclusions: Carefully designed demonstration projects, taking into account the complex web of interconnected risk
factors, are needed to provide direct proof of principle for elimination and to identify the most effective maintenance
activities to prevent a rapid resurgence when interventions are scaled back. More effective, short-course treatment
regimens for PKDL are urgently needed to enable the elimination initiative to succeed
Analysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in pigeonpea (Cajanus spp.)
<p>Abstract</p> <p>Background</p> <p>Pigeonpea [<it>Cajanus cajan </it>(L.) Millsp.] is an important legume crop of rainfed agriculture. Despite of concerted research efforts directed to pigeonpea improvement, stagnated productivity of pigeonpea during last several decades may be accounted to prevalence of various biotic and abiotic constraints and the situation is exacerbated by availability of inadequate genomic resources to undertake any molecular breeding programme for accelerated crop improvement. With the objective of enhancing genomic resources for pigeonpea, this study reports for the first time, large scale development of SSR markers from BAC-end sequences and their subsequent use for genetic mapping and hybridity testing in pigeonpea.</p> <p>Results</p> <p>A set of 88,860 BAC (bacterial artificial chromosome)-end sequences (BESs) were generated after constructing two BAC libraries by using <it>Hin</it>dIII (34,560 clones) and <it>Bam</it>HI (34,560 clones) restriction enzymes. Clustering based on sequence identity of BESs yielded a set of >52K non-redundant sequences, comprising 35 Mbp or >4% of the pigeonpea genome. These sequences were analyzed to develop annotation lists and subdivide the BESs into genome fractions (e.g., genes, retroelements, transpons and non-annotated sequences). Parallel analysis of BESs for microsatellites or simple sequence repeats (SSRs) identified 18,149 SSRs, from which a set of 6,212 SSRs were selected for further analysis. A total of 3,072 novel SSR primer pairs were synthesized and tested for length polymorphism on a set of 22 parental genotypes of 13 mapping populations segregating for traits of interest. In total, we identified 842 polymorphic SSR markers that will have utility in pigeonpea improvement. Based on these markers, the <it>first </it>SSR-based genetic map comprising of 239 loci was developed for this previously uncharacterized genome. Utility of developed SSR markers was also demonstrated by identifying a set of 42 markers each for two hybrids (ICPH 2671 and ICPH 2438) for genetic purity assessment in commercial hybrid breeding programme.</p> <p>Conclusion</p> <p>In summary, while BAC libraries and BESs should be useful for genomics studies, BES-SSR markers, and the genetic map should be very useful for linking the genetic map with a future physical map as well as for molecular breeding in pigeonpea.</p
Machine-Part cell formation through visual decipherable clustering of Self Organizing Map
Machine-part cell formation is used in cellular manufacturing in order to
process a large variety, quality, lower work in process levels, reducing
manufacturing lead-time and customer response time while retaining flexibility
for new products. This paper presents a new and novel approach for obtaining
machine cells and part families. In the cellular manufacturing the fundamental
problem is the formation of part families and machine cells. The present paper
deals with the Self Organising Map (SOM) method an unsupervised learning
algorithm in Artificial Intelligence, and has been used as a visually
decipherable clustering tool of machine-part cell formation. The objective of
the paper is to cluster the binary machine-part matrix through visually
decipherable cluster of SOM color-coding and labelling via the SOM map nodes in
such a way that the part families are processed in that machine cells. The
Umatrix, component plane, principal component projection, scatter plot and
histogram of SOM have been reported in the present work for the successful
visualization of the machine-part cell formation. Computational result with the
proposed algorithm on a set of group technology problems available in the
literature is also presented. The proposed SOM approach produced solutions with
a grouping efficacy that is at least as good as any results earlier reported in
the literature and improved the grouping efficacy for 70% of the problems and
found immensely useful to both industry practitioners and researchers.Comment: 18 pages,3 table, 4 figure
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