Screening and investigation of dye decolorization activities of basidiomycetes

ArticleJOURNAL OF BIOSCIENCE AND BIOENGINEERING. 105(1): 69-72 (2008)journal articl

DNA-guided establishment of canonical nucleosome patterns in a eukaryotic genome [preprint]

A conserved hallmark of eukaryotic chromatin architecture is the distinctive array of well-positioned nucleosomes downstream of transcription start sites (TSS). Recent studies indicate that trans-acting factors establish this stereotypical array. Here, we present the first genome-wide in vitro and in vivo nucleosome maps for the ciliate Tetrahymena thermophila. In contrast with previous studies in yeast, we find that the stereotypical nucleosome array is preserved in the in vitro reconstituted map, which is governed only by the DNA sequence preferences of nucleosomes. Remarkably, this average in vitro pattern arises from the presence of subsets of nucleosomes, rather than the whole array, in individual Tetrahymena genes. Variation in GC content contributes to the positioning of these sequence-directed nucleosomes, and affects codon usage and amino acid composition in genes. We propose that these ‘seed’ nucleosomes may aid the AT-rich Tetrahymena genome – which is intrinsically unfavorable for nucleosome formation – in establishing nucleosome arrays in vivo in concert with trans-acting factors, while minimizing changes to the coding sequences they are embedded within

Reconstruction of Cortical and Cancellous Bone in Tibia with Osteogenesis Imperfecta

Osteogenesis Imperfecta (OI) is the bone fragility disorder that leads to long bone bowing. Finite Element Analysis (FEA) has become the tool of choice to assess behaviour structural within bones. Currently, the FEA performed on the tibia is based on the bone constructed without considering different components of the bone, where the bone was created as a single material. In an attempt to further investigate the bone with OI, the present study was conducted to investigate the mechanical stress distribution using finite element model of the OI affected tibia. The model was reconstructed from the CT images composed of cortical and cancellous bones obtained from Osirix database. The segmentation of the cortical and cancellous of the tibia was performed on 346 images using two different methods which are global thresholding and the selection of the binary object. The segmented images were used to develop a three-dimensional model of the tibia using VOXELCON software. The boundary conditions were set to the meshed model in preparation for the finite element analysis using the same software. Displacements ranging from 5 mm to 35 mm were assigned to a point in between the proximal and distal of the tibia model. In the coronal plane, the highest stress levels were recorded on the medial side of the cortical bone, whereas in the sagittal plane, the highest stress levels were recorded on the anterior side of the cortical bone when the model was subjected to 35 mm displacement. The cancellous bone, however, showed lower stress levels on both planes when subjected to similar displacement. With each increment of displacement, the model experienced more stress and caused the higher percentage volume of individual cortical and cancellous that exceed critical stress of 115 MPa. There were no significant differences in the percentage volume of voxels affected between the cortical and cancellous bones for both coronal and sagittal planes with the pvalue of 0.29 and 0.32 respectively (p > 0.05). There was no significant difference obtained for the percentage volume of voxels affected between the coronal and sagittal planes with the p-value is 0.13 (p > 0.05)

Extraction of parabens from cosmetic and environmental water samples coupled with uv-visible spectroscopy

An effective and fast vortex-assisted dispersive liquid–liquid extraction method was developed for the extraction of paraben in cosmetic samples and water samples. The paraben was determined and quantifi ed using ultraviolet-visible (UV-Vis) spectrometry. A response surface methodology (RSM) based on the central composite design was used for the optimization of factors (composition of the extractant, volume of extractant, extraction time, centrifugation time, and centrifugation velocity) affecting the extraction effi ciency of the procedure. The optimum parameters for vortexassisted dispersive liquid–liquid extraction (VA-DLLE) are: chloroform used as the extractant solvent, 5 ml volume of extractant, 3 min extraction time, 5 min centrifugation time, and 2400 rpm centrifugation velocity. The limit of detection (LOD) and the limit of quantifi cation (LOQ) for paraben are 0.0476 and 0.1442 μg/mL, respectively. Spiked cosmetic samples have the extraction recoveries in the range of 81.2–96.8%, whereas spiked water sample extraction recoveries were in the range of 88.8–100.63%. Each sample was repeated (n = 2), with a relative standard deviation of <5.74% for cosmetic samples and <9.03% for water samples. In conclusion, this extraction method is fast and inexpensive for the extraction of paraben

Microautophagy of the Nucleus Coincides with a Vacuolar Diffusion Barrier at Nuclear–Vacuolar Junctions

Nuclear-vacuolar (NV) junctions are organelle contact sites in yeast. They exclude nuclear pores from the organelle interface. On the vacuolar side, a lipid-dependent process excludes specific membrane proteins, such as V-ATPase, from the contact site. This suggests that NV junctions establish selective diffusion barriers

PRPF8-mediated dysregulation of hBrr2 helicase disrupts human spliceosome kinetics and 5\ub4-splice-site selection causing tissue-specific defects

\ua9 The Author(s) 2024.The carboxy-terminus of the spliceosomal protein PRPF8, which regulates the RNA helicase Brr2, is a hotspot for mutations causing retinitis pigmentosa-type 13, with unclear role in human splicing and tissue-specificity mechanism. We used patient induced pluripotent stem cells-derived cells, carrying the heterozygous PRPF8 c.6926 A &gt; C (p.H2309P) mutation to demonstrate retinal-specific endophenotypes comprising photoreceptor loss, apical-basal polarity and ciliary defects. Comprehensive molecular, transcriptomic, and proteomic analyses revealed a role of the PRPF8/Brr2 regulation in 5’-splice site (5’SS) selection by spliceosomes, for which disruption impaired alternative splicing and weak/suboptimal 5’SS selection, and enhanced cryptic splicing, predominantly in ciliary and retinal-specific transcripts. Altered splicing efficiency, nuclear speckles organisation, and PRPF8 interaction with U6 snRNA, caused accumulation of active spliceosomes and poly(A)+ mRNAs in unique splicing clusters located at the nuclear periphery of photoreceptors. Collectively these elucidate the role of PRPF8/Brr2 regulatory mechanisms in splicing and the molecular basis of retinal disease, informing therapeutic approaches

Trials of large group teaching in Malaysian private universities: a cross sectional study of teaching medicine and other disciplines

<p>Abstract</p> <p>Background</p> <p>This is a pilot cross sectional study using both quantitative and qualitative approach towards tutors teaching large classes in private universities in the Klang Valley (comprising Kuala Lumpur, its suburbs, adjoining towns in the State of Selangor) and the State of Negeri Sembilan, Malaysia. The general aim of this study is to determine the difficulties faced by tutors when teaching large group of students and to outline appropriate recommendations in overcoming them.</p> <p>Findings</p> <p>Thirty-two academics from six private universities from different faculties such as Medical Sciences, Business, Information Technology, and Engineering disciplines participated in this study. SPSS software was used to analyse the data. The results in general indicate that the conventional instructor-student approach has its shortcoming and requires changes. Interestingly, tutors from Medicine and IT less often faced difficulties and had positive experience in teaching large group of students.</p> <p>Conclusion</p> <p>However several suggestions were proposed to overcome these difficulties ranging from breaking into smaller classes, adopting innovative teaching, use of interactive learning methods incorporating interactive assessment and creative technology which enhanced students learning. Furthermore the study provides insights on the trials of large group teaching which are clearly identified to help tutors realise its impact on teaching. The suggestions to overcome these difficulties and to maximize student learning can serve as a guideline for tutors who face these challenges.</p

A Novel Enzymatic System against Oxidative Stress in the Thermophilic Hydrogen-Oxidizing Bacterium Hydrogenobacter thermophilus

Rubrerythrin (Rbr) is a non-heme iron protein composed of two distinctive domains and functions as a peroxidase in anaerobic organisms. A novel Rbr-like protein, ferriperoxin (Fpx), was identified in Hydrogenobacter thermophilus and was found not to possess the rubredoxin-like domain that is present in typical Rbrs. Although this protein is widely distributed among aerobic organisms, its function remains unknown. In this study, Fpx exhibited ferredoxin:NADPH oxidoreductase (FNR)-dependent peroxidase activity and reduced both hydrogen peroxide (H2O2) and organic hydroperoxide in the presence of NADPH and FNR as electron donors. The calculated Km and Vmax values of Fpx for organic hydroperoxides were comparable to that for H2O2, demonstrating a multiple reactivity of Fpx towards hydroperoxides. An fpx gene disruptant was unable to grow under aerobic conditions, whereas its growth profiles were comparable to those of the wild-type strain under anaerobic and microaerobic conditions, clearly indicating the indispensability of Fpx as an antioxidant of H. thermophilus in aerobic environments. Structural analysis suggested that domain-swapping occurs in Fpx, and this domain-swapped structure is well conserved among thermophiles, implying the importance of structural stability of domain-swapped conformation for thermal environments. In addition, Fpx was located on a deep branch of the phylogenetic tree of Rbr and Rbr-like proteins. This finding, taken together with the wide distribution of Fpx among Bacteria and Archaea, suggests that Fpx is an ancestral type of Rbr homolog that functions as an essential antioxidant and may be part of an ancestral peroxide-detoxification system

Impact of a Plasmodium falciparum AMA1 Vaccine on Antibody Responses in Adult Malians

Apical Membrane Antigen 1 (AMA1) of Plasmodium falciparum merozoites is a leading blood-stage malaria vaccine candidate. Protection of Aotus monkeys after vaccination with AMA1 correlates with antibody responses.A randomized, controlled, double-blind phase 1 clinical trial was conducted in 54 healthy Malian adults living in an area of intense seasonal malaria transmission to assess the safety and immunogenicity of the AMA1-C1 malaria vaccine. AMA1-C1 contains an equal mixture of yeast-expressed recombinant proteins based on sequences from the FVO and 3D7 clones of P. falciparum, adsorbed on Alhydrogel. The control vaccine was the hepatitis B vaccine (Recombivax). Participants were enrolled into 1 of 3 dose cohorts (n = 18 per cohort) and randomized 2:1 to receive either AMA1-C1 or Recombivax. Participants in the first, second, and third cohorts randomized to receive AMA1-C1 were vaccinated with 5, 20 and 80 microg of AMA1-C1, respectively. Vaccinations were administered on days 0, 28, and 360, and participants were followed until 6 months after the final vaccination. AMA1-C1 was well tolerated; no vaccine-related severe or serious adverse events were observed. AMA1 antibody responses to the 80 microg dose increased rapidly from baseline levels by days 14 and 28 after the first vaccination and continued to increase after the second vaccination. After a peak 14 days following the second vaccination, antibody levels decreased to baseline levels one year later at the time of the third vaccination that induced little or no increase in antibody levels.Although the AMA1-C1 vaccine candidate was well-tolerated and induced antibody responses to both vaccine and non-vaccine alleles, the antibody response after a third dose given at one year was lower than the response to the initial vaccinations. Additionally, post-vaccination increases in anti-AMA1 antibody levels were not associated with significant changes in in vitro growth inhibition of P. falciparum.ClinicalTrials.gov NCT00343005