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  • 1
    Publication Date: 2016-12-04
    Description: The nuclear pore complex (NPC) mediates nuclear transport of RNA and proteins into and out of the nucleus. Certain nucleoporins have additional functions in chromatin organization and transcription regulation....
    Electronic ISSN: 1756-8935
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 2
    Publication Date: 2013-08-16
    Description: Background: Adaptations to different habitats across the globe and consequent genetic variation within rice have resulted in more than 120,000 diverse accessions including landraces, which are vital genetic resources for agronomic and quality traits. In India the rice landraces of the states West Bengal, Assam, Mizoram, Manipur and Nagaland are worthy candidates for genetic assessment. Keeping the above in view, the present study was conducted with the aim to (i) calculate the genetic distances among the accessions of 83 landraces collected from these states along with 8 check accessions (total 91 accessions) using 23 previously mapped SSR markers and (ii) examine the population structure among the accessions using model-based clustering approach. Results: Among the 91 accessions, 182 alleles were identified which included 51 rare and 27 null alleles. The average PIC value was 0.7467/marker. The non-aromatic landraces from West Bengal was most diverse with 154 alleles and an average PIC value of 0.8005/marker, followed by the aromatic landraces from West Bengal with 118 alleles and an average PIC value of 0.6524/marker, while the landraces from North East ranked third with 113 alleles and an average PIC value of 0.5745/marker. In the dendrogram distinct clusters consisting of predominantly aromatic landraces and predominantly North East Indian landraces were observed. The non-aromatic landraces from West Bengal were interspersed within these two clusters. The accessions were moderately structured, showing four sub-populations (A-D) with an Fst value of 0.398, 0.364, 0.206 and 0.281, respectively. The assigned clustering of accessions was well in agreement in both distance-based and model-based approaches. Conclusions: Each of the accessions could be identified unequivocally by the SSR profiles. Genetically the non aromatic landraces from West Bengal were most diverse followed by the aromatic landraces from the same state. The North Eastern accessions ranked third. Further, grouping of accessions based on their agronomic traits may serve as a resource for future studies, leading to the improvement of rice. Moreover in-situ preservation of the landraces is also a means of protection of biodiversity and cultural heritage.
    Electronic ISSN: 1471-2156
    Topics: Biology
    Published by BioMed Central
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  • 3
    Publication Date: 2013-07-23
    Description: Background: Homologous recombination is the key process that generates genetic diversity and drives evolution. SPO11 protein triggers recombination by introducing DNA double stranded breaks at discreet areas of the genome called recombination hotspots. The hotspot locations are largely determined by the DNA binding specificity of the PRDM9 protein in human, mice and most other mammals. In budding yeast Saccharomyces cerevisae, which lacks a Prdm9 gene, meiotic breaks are formed opportunistically in the regions of accessible chromatin, primarily at gene promoters. The genome-wide distribution of hotspots in this organism can be altered by tethering Spo11 protein to Gal4 recognition sequences in the strain expressing Spo11 attached to the DNA binding domain of the Gal4 transcription factor. To establish whether similar re-targeting of meiotic breaks can be achieved in PRDM9-containing organisms we have generated a Gal4BD-Spo11 mouse that expresses SPO11 protein joined to the DNA binding domain of yeast Gal4. Results: We have mapped the genome-wide distribution of the recombination initiation sites in the Gal4BD-Spo11 mice. More than two hundred of the hotspots in these mice were novel and were likely defined by Gal4BD, as the Gal4 consensus motif was clustered around the centers in these hotspots. Surprisingly, meiotic DNA breaks in the Gal4BD-Spo11 mice were significantly depleted near the ends of chromosomes. The effect is particularly striking at the pseudoautosomal region of the X and Y chromosomes -- normally the hottest region in the genome. Conclusions: Our data suggest that specific, yet-unidentified factors influence the initiation of meiotic recombination at subtelomeric chromosomal regions.
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
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  • 4
    Publication Date: 2012-06-22
    Description: Background: The three-dimensional structure of a protein can be described as a graph where nodes represent residues andthe strength of non-covalent interactions between them are edges. These protein contact networks can beseparated into long and short-range interactions networks depending on the positions of amino acids inprimary structure. Long-range interactions play a distinct role in determining the tertiary structure of aprotein while short-range interactions could largely contribute to the secondary structure formations. Inaddition, physico chemical properties and the linear arrangement of amino acids of the primary structure ofa protein determines its three dimensional structure. Here, we present an extensive analysis of proteincontact subnetworks based on the London van der Waals interactions of amino acids at different lengthscales. We further subdivided those networks in hydrophobic, hydrophilic and charged residues networksand have tried to correlate their influence in the overall topology and organization of a protein. Results: The largest connected component (LCC) of long (LRN)-, short (SRN)- and all-range (ARN) networks withinproteins exhibit a transition behaviour when plotted against different interaction strengths of edges amongamino acid nodes. While short-range networks having chain like structures exhibit highly cooperativetransition; long- and all-range networks, which are more similar to each other, have non-chain like structuresand show less cooperativity. Further, the hydrophobic residues subnetworks in long- and all-range networkshave similar transition behaviours with all residues all-range networks, but the hydrophilic and chargedresidues networks don't. While the nature of transitions of LCC's sizes is same in SRNs for thermophilesand mesophiles, there exists a clear difference in LRNs. The presence of larger size of interconnectedlong-range interactions in thermophiles than mesophiles, even at higher interaction strength between aminoacids, give extra stability to the tertiary structure of the thermophiles. All the subnetworks at different lengthscales (ARNs, LRNs and SRNs) show assortativity mixing property of their participating amino acids.While there exists a significant higher percentage of hydrophobic subclusters over others in ARNs andLRNs; we do not find the assortative mixing behaviour of any the subclusters in SRNs. The clusteringcoefficient of hydrophobic subclusters in long-range network is the highest among types of subnetworks.There exist highly cliquish hydrophobic nodes followed by charged nodes in LRNs and ARNs; on the otherhand, we observe the highest dominance of charged residues cliques in short-range networks. Studies on theperimeter of the cliques also show higher occurrences of hydrophobic and charged residues' cliques. Conclusions: The simple framework of protein contact networks and their subnetworks based on London van der Waalsforce is able to capture several known properties of protein structure as well as can unravel several newfeatures. The thermophiles do not only have the higher number of long-range interactions; they also havelarger cluster of connected residues at higher interaction strengths among amino acids, than their mesophiliccounterparts. It can reestablish the significant role of long-range hydrophobic clusters in protein folding andstabilization; at the same time, it shed light on the higher communication ability of hydrophobicsubnetworks over the others. The results give an indication of the controlling role of hydrophobicsubclusters in determining protein's folding rate. The occurrences of higher perimeters of hydrophobic andcharged cliques imply the role of charged residues as well as hydrophobic residues in stabilizing the distantpart of primary structure of a protein through London van der Waals interaction.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
    Published by BioMed Central
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  • 5
    Publication Date: 2015-02-13
    Description: Background: Fusarium oxysporum f. sp. ciceris (Foc), the causal agent of Fusarium wilt is a devastating pathogen of chickpea. In chickpea, various soil borne pathogens produce (s) similar symptoms, therefore cannot be distinguished easily at field level. There is real need for a rapid, inexpensive, and easy to operate and maintain genotyping tool to facilitate accurate disease diagnosis and surveillance for better management of Fusarium wilt outbreaks. Results: In this study, we developed a loop-mediated isothermal amplification (LAMP) assay targeting the elongation factor 1 alpha gene sequence for visual detection of Foc. The LAMP reaction was optimal at 63?C for 60?min. When hydroxynaphthol blue (HNB) was added before amplification, samples with Foc DNA developed a characteristic sky blue colour but those without DNA or with the DNA of six other plant pathogenic fungi did not. Results obtained with LAMP and HNB were confirmed when LAMP products were subjected to gel electrophoresis. The detection limit of this LAMP assay for Foc was 10?fg of genomic DNA per reaction, while that of conventional PCR was 100?pg. Conclusions: In conclusion, it was found that a LAMP assay combined with HNB is simple, rapid, sensitive, and specific. The LAMP assay does not require specialized equipment, hence can be used in the field for the rapid detection of Foc. This is the first report of the use of LAMP assay for the detection of Foc. The presented LAMP method provides a specific, sensitive and rapid diagnostic tool for the distinction of Foc, with the potential to be standardized as a detection method for Foc in endemic areas and will be very useful for monitoring the disease complex in the field further suggesting the management strategies.
    Electronic ISSN: 1756-0500
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 6
    Publication Date: 2014-12-12
    Description: Background: In order to assess genetic diversity of a set of 41 Caricaceae accessions, this study used 34 primer pairs designed from the conserved domains of bacterial leaf blight resistance genes from rice, in a PCR based approach, to identify and analyse resistance gene analogues from various accessions of Carica papaya, Vasconcellea goudotiana, V. microcarpa, V. parviflora, V. pubescens, V. stipulata and, V. quercifolia and Jacaratia spinosa. Results: Of the 34 primer pairs fourteen gave amplification products. A total of 115 alleles were identified from 41 accesions along with 12 rare and 11 null alleles. The number of alleles per primer pair ranged from 4 to 10 with an average of 8.21 alleles/ primer pair. The average polymorphism information content value was 0.75 / primer. The primers for the gene Xa1 did not give any amplification product. As a group, the Indian Carica papaya accessions produced a total of 102 alleles from 27 accessions. The similarity among the 41 accessions ranged from 1% to 53 %. The dendrogram made from Jaccard?s genetic similarity coefficient generated two major clusters showing that the alleles of Jacaratia spinosa and Vasconcellea accessions were distinctly different from those of Carica papaya accessions. All the alleles were sequenced and eleven of them were allotted accession numbers by NCBI. Homology searches identified similarity to rice BLB resistance genes and pseudogenes. Conserved domain searches identified gamma subunit of transcription initiation factor IIA (TFIIA), cytochrome P450, signaling domain of methyl-accepting chemotaxis protein (MCP), Nickel hydrogenase and leucine rich repeats (LRR) within the sequenced RGAs. Conclusions: The RGA profiles produced by the 14 primer pairs generated high genetic diversity. The RGA profiles identified each of the 41 accessions clearly unequivocally. Most of the DNA sequences of the amplified RGAs from this set of 41 accessions showed significant homology to the conserved regions of rice bacterial leaf blight resistance genes. These information can be used in future for large scale investigation of tentative disease resistance genes of Carica papaya and other Caricaceae genus specially Vasconcellea. Inoculation studies will be necessary to link the identified sequences to disease resistance or susceptibility.
    Electronic ISSN: 1471-2156
    Topics: Biology
    Published by BioMed Central
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  • 7
    Publication Date: 2017-07-07
    Description: Tea (Camellia sinensis, (L.) Kuntze) is considered as most popular drink across the world and it is widely consumed beverage for its several health-benefit characteristics. These positive traits primarily rely on...
    Electronic ISSN: 1756-0500
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 8
    Publication Date: 2014-07-13
    Description: Background: Bacterial leaf blight (BLB) caused by the vascular pathogen Xanthomonas oryzae pv. oryzae (Xoo) is one of the most serious diseases leading to crop failure in rice growing countries. A total of 37 resistance genes against Xoo has been identified in rice. Of these, ten BLB resistance genes have been mapped on rice chromosomes, while 6 have been cloned, sequenced and characterized. Diversity analysis at the resistance gene level of this disease is scanty, and the landraces from West Bengal and North Eastern states of India have received little attention so far. The objective of this study was to assess the genetic diversity at conserved domains of 6 BLB resistance genes in a set of 22 rice accessions including landraces and check genotypes collected from the states of Assam, Nagaland, Mizoram and West Bengal. Results: In this study 34 pairs of primers were designed from conserved domains of 6 BLB resistance genes; Xa1, xa5, Xa21, Xa21(A1), Xa26 and Xa27. The designed primer pairs were used to generate PCR based polymorphic DNA profiles to detect and elucidate the genetic diversity of the six genes in the 22 diverse rice accessions of known disease phenotype. A total of 140 alleles were identified including 41 rare and 26 null alleles. The average polymorphism information content (PIC) value was 0.56/primer pair. The DNA profiles identified each of the rice landraces unequivocally. The amplified polymorphic DNA bands were used to calculate genetic similarity of the rice landraces in all possible pair combinations. The similarity among the rice accessions ranged from 18% to 89% and the dendrogram produced from the similarity values was divided into 2 major clusters. The conserved domains identified within the sequenced rare alleles include Leucine-Rich Repeat, BED-type zinc finger domain, sugar transferase domain and the domain of the carbohydrate esterase 4 superfamily. Conclusions: This study revealed high genetic diversity at conserved domains of six BLB resistance genes in a set of 22 rice accessions. The inclusion of more genotypes from remote ecological niches and hotspots holds promise for identification of further genetic diversity at the BLB resistance genes.
    Electronic ISSN: 1471-2156
    Topics: Biology
    Published by BioMed Central
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  • 9
    Publication Date: 2012-09-18
    Description: Background: Advanced stages of leprosy show T cell unresponsiveness and lipids of mycobacterial origin are speculated to modulate immune responses in these patients. Present study elucidates the role of phenolicglycolipid (PGL-1) and Mannose-capped lipoarabinomannan (Man-LAM) on TCR- and TCR/CD28- mediated signalling. Results: We observed that lipid antigens significantly inhibit proximal early signallling events like Zap-70 phosphorylation and calcium mobilization. Interestingly, these antigens preferentially curtailed TCR-triggered early downstream signalling events like p38 phosphorylation whereas potentiated that of Erk1/2. Further, at later stages inhibition of NFAT binding, IL-2 message, CD25 expression and T-cell blastogenesis by PGL-1 and Man-LAM was noted. Conclusion: Altogether, we report that Man-LAM and PGL-1 preferentially interfere with TCR/CD28-triggered upstream cell signalling events, leading to reduced IL-2 secretion and T-cell blastogenesis which potentially could lead to immunosupression and thus, disease exacerbation, as noted in disease spectrum.
    Electronic ISSN: 1476-511X
    Topics: Biology
    Published by BioMed Central
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  • 10
    Publication Date: 2012-09-21
    Description: Background: The effect of an herbal formulation LI85008F on weight loss in obese human subjects was evaluated in an 8-weeks randomized, double-blind, placebo-controlled study (Clinical Trial Registration no. ISRCTN37381706). Fifty obese subjects (Body mass index 30 to 40 kg/m2, 29.3% male; 70.7% female; ages 27--50 years) were randomized into two groups; placebo (n = 25) and LI85008F formulation (n = 25). The participants received either 900 mg/day of LI85008F formulation in three divided doses or three identical placebo capsules and all of them remained on a calorie-controlled diet (2000 cal/day) and 30 min walking for 5 days a week during the entire duration of the study.Results and discussionAt the end of the trial period, LI85008F supplemented group showed significant net reductions in body weight and Body Mass Index (BMI). The participants who received the herbal formulation, showed reduced fasting blood glucose, LDL, LDL/HDL ratio, and triglycerides. At the end of the study, LI85008F supplementation also provided 21.26% (p = 0.012) increase in serum adiponectin level, compared with the placebo group. No major adverse events were reported by the participants in the study duration. In addition, Adipokine profiling study in 3T3-L1 adipocytes demonstrates that LI85008F modulates key regulatory factors of adipogenic differentiation and insulin sensitivity, such as Adiponectin, Pref-1, and resistin. Conclusion: The herbal formulation LI85008F (Adipromin) is prepared from commonly used medicinal plants extracts, which provides useful and safe application for weight loss in obese humans. It also demonstrates potential promise in controlling healthy blood glucose level in obesity linked type 2 diabetes.
    Electronic ISSN: 1476-511X
    Topics: Biology
    Published by BioMed Central
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