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In-vitro inhibition of growth of some seedling blight inducing pathogens by compost-inhabiting microbes
S. Muhammad, N. A. Amusa
African Journal of Biotechnology , 2003,
Abstract: Compost-inhabiting bacteria were studied for their effect on seedling blight inducing pathogens. Aspergillus niger, Trichoderma harzianum, Bacillus cereus and Bacillus subtilis were the microbes found associated with cow dung, sawdust and rice husk composted soils. Sclerotium rolfsii, Fusarium oxysporum, Pythium aphanidermatum and Macrophomina phaseolina were isolated from blighted seedlings of Cowpea, while S. rolfsii, P. aphanidermatum, Helminthosporium maydis and Rhizoctonia solani were isolated from blighted maize seedlings. When these compost-inhabiting microbes were paired with the seedling blight inducing pathogens, T. harzianum grew on the mycelia of all the test fungal pathogens. B. cereus reduced the mycelia growth of Sclerotium rolfsii, F. oxysporum, P. aphanidermatum, H. maydis and R. solani, with inhibitory zones ranging from 35.5% to 53.3%. B. subtilis in culture also inhibited the mycelia growth of all tested pathogenic fungi with inhibitory zones of between 40.0% to 57.8%. The inhibitory activities of the compost-inhabiting microbes might partly be responsible for the efficacy of compost in reducing seedling blight diseases of crops. (African Journal of Biotechnology: 2003 2(6): 161-164)
Profiling Cellular Protein Complexes by Proximity Ligation with Dual Tag Microarray Readout  [PDF]
Maria Hammond, Rachel Yuan Nong, Olle Ericsson, Katerina Pardali, Ulf Landegren
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0040405
Abstract: Patterns of protein interactions provide important insights in basic biology, and their analysis plays an increasing role in drug development and diagnostics of disease. We have established a scalable technique to compare two biological samples for the levels of all pairwise interactions among a set of targeted protein molecules. The technique is a combination of the proximity ligation assay with readout via dual tag microarrays. In the proximity ligation assay protein identities are encoded as DNA sequences by attaching DNA oligonucleotides to antibodies directed against the proteins of interest. Upon binding by pairs of antibodies to proteins present in the same molecular complexes, ligation reactions give rise to reporter DNA molecules that contain the combined sequence information from the two DNA strands. The ligation reactions also serve to incorporate a sample barcode in the reporter molecules to allow for direct comparison between pairs of samples. The samples are evaluated using a dual tag microarray where information is decoded, revealing which pairs of tags that have become joined. As a proof-of-concept we demonstrate that this approach can be used to detect a set of five proteins and their pairwise interactions both in cellular lysates and in fixed tissue culture cells. This paper provides a general strategy to analyze the extent of any pairwise interactions in large sets of molecules by decoding reporter DNA strands that identify the interacting molecules.
Detection of Human Papillomaviruses by Polymerase Chain Reaction and Ligation Reaction on Universal Microarray  [PDF]
Jarmo Ritari, Jenni Hultman, Rita Fingerroos, Jussi Tarkkanen, Janne Pullat, Lars Paulin, Niina Kivi, Petri Auvinen, Eeva Auvinen
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0034211
Abstract: Sensitive and specific detection of human papillomaviruses (HPV) in cervical samples is a useful tool for the early diagnosis of epithelial neoplasia and anogenital lesions. Recent studies support the feasibility of HPV DNA testing instead of cytology (Pap smear) as a primary test in population screening for cervical cancer. This is likely to be an option in the near future in many countries, and it would increase the efficiency of screening for cervical abnormalities. We present here a microarray test for the detection and typing of 15 most important high-risk HPV types and two low risk types. The method is based on type specific multiplex PCR amplification of the L1 viral genomic region followed by ligation detection reaction where two specific ssDNA probes, one containing a fluorescent label and the other a flanking ZipCode sequence, are joined by enzymatic ligation in the presence of the correct HPV PCR product. Human beta-globin is amplified in the same reaction to control for sample quality and adequacy. The genotyping capacity of our approach was evaluated against Linear Array test using cervical samples collected in transport medium. Altogether 14 out of 15 valid samples (93%) gave concordant results between our test and Linear Array. One sample was HPV56 positive in our test and high-risk positive in Hybrid Capture 2 but remained negative in Linear Array. The preliminary results suggest that our test has accurate multiple HPV genotyping capability with the additional advantages of generic detection format, and potential for high-throughput screening.
Stimulation of fungi originated from Wamena Biological Garden on maturity of compost nutrient and the number of phosphate solubilizing and nitrogen fixing microbes
Biodiversitas , 2005,
Abstract: The aims of the research was to know ability of fungi catalisator, i.e. Aspergillus niger, Trichoderma viridae, and Chaetomium sp. to increase composting process and decrease C/N ratio content. The experiments used grass as carbon source, cow dung as nitrogen source, and A. niger, T. viridae, and Chaetomium sp. as catalisator. The result showed that the activators accelerated the compost maturity process. The compost was contained phosphate solubilizing fungi (± 109 cell/g), phosphate solubilizing bacteria (± 109 cell/g), and nitrogen fixing bacteria (± 108 cell/g). The C/N ratio of compost was 8.90.
Enhanced Botrytis cinerea Resistance of Arabidopsis Plants Grown in Compost May Be Explained by Increased Expression of Defense-Related Genes, as Revealed by Microarray Analysis  [PDF]
Guillem Segarra, Gabriel Santpere, Georgina Elena, Isabel Trillas
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0056075
Abstract: Composts are the products obtained after the aerobic degradation of different types of organic matter waste and can be used as substrates or substrate/soil amendments for plant cultivation. There is a small but increasing number of reports that suggest that foliar diseases may be reduced when using compost, rather than standard substrates, as growing medium. The purpose of this study was to examine the gene expression alteration produced by the compost to gain knowledge of the mechanisms involved in compost-induced systemic resistance. A compost from olive marc and olive tree leaves was able to induce resistance against Botrytis cinerea in Arabidopsis, unlike the standard substrate, perlite. Microarray analyses revealed that 178 genes were differently expressed, with a fold change cut-off of 1, of which 155 were up-regulated and 23 were down-regulated in compost-grown, as against perlite-grown plants. A functional enrichment study of up-regulated genes revealed that 38 Gene Ontology terms were significantly enriched. Response to stress, biotic stimulus, other organism, bacterium, fungus, chemical and abiotic stimulus, SA and ABA stimulus, oxidative stress, water, temperature and cold were significantly enriched, as were immune and defense responses, systemic acquired resistance, secondary metabolic process and oxireductase activity. Interestingly, PR1 expression, which was equally enhanced by growing the plants in compost and by B. cinerea inoculation, was further boosted in compost-grown pathogen-inoculated plants. Compost triggered a plant response that shares similarities with both systemic acquired resistance and ABA-dependent/independent abiotic stress responses.
Optimised padlock probe ligation and microarray detection of multiple (non-authorised) GMOs in a single reaction
Theo W Prins, Jeroen P van Dijk, Henriek G Beenen, AM Angeline Van Hoef, Marleen M Voorhuijzen, Cor D Schoen, Henk JM Aarts, Esther J Kok
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-584
Abstract: In this paper we present an innovative method for detecting (approved) GMOs as well as the potential presence of NAGs in complex DNA samples containing different crop species. An optimised protocol has been developed for padlock probe ligation in combination with microarray detection (PPLMD) that can easily be scaled up. Linear padlock probes targeted against GMO-events, -elements and -species have been developed that can hybridise to their genomic target DNA and are visualised using microarray hybridisation.In a tenplex PPLMD experiment, different genomic targets in Roundup-Ready soya, MON1445 cotton and Bt176 maize were detected down to at least 1%. In single experiments, the targets were detected down to 0.1%, i.e. comparable to standard qPCR.Compared to currently available methods this is a significant step forward towards multiplex detection in complex raw materials and derived products. It is shown that the PPLMD approach is suitable for large-scale detection of GMOs in real-life samples and provides the possibility to detect and/or identify NAGs that would otherwise remain undetected.In recent years there have been a number of incidents in which not (yet) EU-approved GMO varieties were present in shipments imported into the EU. Examples are Bt10 maize [1], LL601 rice [2] and Bt63 rice [3]. As a result the EU has formulated additional regulations in the case of the Bt10 maize and Bt63 and LL601 rice varieties that stipulate that in specific shipments it needs to be certified that the named unapproved varieties are not present [1-3]. With the increasing complexity of world trade networks, asynchronous approval of GMO varieties in different parts of the world leads to the increased possibility that non-authorised GMOs (NAGs) are present in EU import batches.Producers of new GM crop varieties to be marketed within the EU need to supply an event-specific method for the new variety as well as the related positive and negative reference materials [4,5]. As a result
Pakistan Journal of Botany , 2008,
Abstract: In the present study compost was prepared from waste fruit and vegetables and enriched with 25% (44 kg ha-1) of full dose (175 kg ha-1) of N fertilizer for maize. Pure auxin, indole 3-acetic acid (IAA) and L-TRP (precursor) were blended with respective batches @ 10 mg kg-1 compost for the value addition of N-enriched compost (NEC). Comparative effectiveness of IAA or L-TRP-blended NEC was studied, in the presence or absence of 50% (88 kg N ha-1) of full dose of N fertilizer, through pot and field trials. Compost was applied @ 300 kg ha-1. Results indicated that IAA-blended NEC supplemented with half dose of N fertilizer was as effective as NEC in improving growth and yield of maize. However, precursor (L-TRP)-blended NEC was found better than pure auxin (IAA)-blended, when both were compared with NEC. It significantly improved growth, yield and nutrient uptakes (up to 8.4, 8.6 and 11% respectively) of maize over NEC in the presence of 88 kg N ha-1. The technology bears its promise not only to improve crop yield on sustainable basis but also reduce huge piles of organic wastes causing environmental pollution.
Biochemical parameters in rats with an applied model of sepsis (cecal ligation and puncture) with pure and mixed bacterial culture
Stojanovi? Dragica,Velhner Maja,Stojanov I.,Petrovi? Jelena
Acta Veterinaria , 2012, DOI: 10.2298/avb1206543s
Abstract: The goal of this work was to induce clinical sepsis in rats in order to measure the following biochemical parameters (glucoses, triglycerides, cholesterol, total proteins, albumins and creatinine). The experiments were done on 104 male Wistar rats, body weight 190 to 240 g. The rats were divided in four groups. Treated groups consisted of 28 animals while in the control groups there were 20 animals. Animals were observed and sacrificed at 12, 24, 72 and 120 hours after surgery. In this model of sepsis (cecal ligation and puncture - CLP) with pure and mixed bacterial cultures, significant changes were noticed in all biochemical parameters. Significant hypoglycemia, hypercholesterolemia, decreased concentration of urea and increased concentration of creatinine were found in the first half of the experiment in all groups of rats with sepsis (at 12 and 24 hours). Hyperproteinemia and hypotriglyceridemia reached statistically significant values at 24 h in the groups of rats in which sepsis was induced with pure bacteria culture. In the other half of the experiment significant hypoalbuminemia was found in all rats with sepsis (at 71 and 120 h). [Projekat Ministarstva nauke Republike Srbije, br. TR 31071]
Substitution of Deoxyinosine as Universal Base in Oligonucleotides for DNA Ligation  [PDF]
Zhiliang Yu
Engineering (ENG) , 2013, DOI: 10.4236/eng.2013.510B090

Oligonucleotides libraries have been developed for various applications, but the library size of oligonucleotide increases dramatically with the addition of oligonucleotide length. To assess the possibility of shortening library size by using universal base, deoxyinosine (dITP), the effect of single/multiple dITP substituted in oligonucleotide on ligation was investigated. It was found that different pairs with dITP had different ligation patterns and pairs with dITP at different locations also showed different ligation patterns. With the departure of substitution position from ligation site, the ligation yield increased. Single dITP substitution at ligation site did extremely hurt the ligation efficiency, except for I:C pair. On the other hand, single substitution at two bases or more apart from ligation site, there is no obvious effect on ligation. Multiple dITP substitutions can more or less affect the ligation, besides I:C pair. This research demonstrated that dITP can be applied to reduce oligonucleotide library size after substitution.

Assessment of MRI issues at 3-Tesla for metallic surgical implants: findings applied to 61 additional skin closure staples and vessel ligation clips
Amreeta Gill, Frank G Shellock
Journal of Cardiovascular Magnetic Resonance , 2012, DOI: 10.1186/1532-429x-14-3
Abstract: A skin closure staple (Visistat Skin Stapler, staple, Polytetrafluoroethylene, PTFE, coated 316L/316LVM stainless steel; Teleflex Medical, Durham, NC) and a vessel ligation clip (Hemoclip Traditional, stainless steel; Teleflex Medical, Durham, NC) that represented the largest metallic sizes made from materials with the highest magnetic susceptibilities (i.e., based on material information) among 61 other surgical implants (52 metallic implants, 9 nonmetallic implants) underwent evaluation for magnetic field interactions, MRI-related heating, and artifacts using standardized techniques. MRI-related heating was assessed by placing each implant in a gelled-saline-filled phantom with MRI performed using a transmit/receive RF body coil at an MR system reported, whole body averaged SAR of 2.9-W/kg for 15-min. Artifacts were characterized using T1-weighted, SE and GRE pulse sequences.Each surgical implant showed minor magnetic field interactions (20- and 27-degrees, which is acceptable from a safety consideration). Heating was not substantial (highest temperature change, ≤ 1.6°C). Artifacts may create issues if the area of interest is in the same area or close to the respective surgical implant.The results demonstrated that it would be acceptable for patients with these metallic surgical implants to undergo MRI at 3-Tesla or less. Because of the materials and dimensions of the surgical implants that underwent testing, these findings pertain to 61 additional similar implants.Surgical staples are specialized implants used in surgery in place of sutures and are commonly used to close skin wounds, as well as to connect or remove anatomic areas such as the bowels or lungs [1]. The use of staples is often preferred because it is considered to be faster than suturing by hand and tends to be more accurate and consistent, while creating less tissue trauma [1]. In skin closure, particularly those where aesthetics are not of great concern (e.g., the scalp), the use of skin staples is
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