Excellence in Research and Innovation for Humanity

International Science Index

Commenced in January 1999 Frequency: Monthly Edition: International Abstract Count: 49738

Biotechnology and Bioengineering

589
86378
Epigenetic Modification Observed in Yeast Chromatin Remodeler Ino80p
Abstract:
The packaging of DNA into nucleosomes is critical to genomic compaction, yet it can leave gene promoters inaccessible to activator proteins or transcription machinery and thus prevents transcriptional initiation. Both chromatin remodelers and histone acetylases (HATs) are the two main transcription co-activators that can reconfigure chromatin structure for transcriptional activation. Ino80p is the core component of the INO80 remodeling complex. Recently, it was shown that Ino80p dissociates from the yeast INO1 promoter after induction. However, when certain HATs were deleted or mutated, Ino80p accumulated at the promoters during gene activation. This suggests a link between HATs’ presence and Ino80p’s dissociation. However, it has yet to be demonstrated that Ino80p can be acetylated. To determine if Ino80p can be acetylated, wild-type Saccharomyces cerevisiae cells carrying Ino80p engineered with a double FLAG tag (MATa INO80-FLAG his3∆200 leu2∆0 met15∆0 trp1∆63 ura3∆0) were grown to mid log phase, as were non-tagged wild type (WT) (MATa his3∆200 leu2∆0 met15∆0 trp1∆63 ura3∆0) and ino80∆ (MATa ino80∆::TRP1 his3∆200 leu2∆0 met15∆0 trp1∆63 ura3∆0) cells as controls. Cells were harvested, and the cell lysates were subjected to immunoprecipitation (IP) with α-FLAG resin to isolate Ino80p. These eluted IP samples were subjected to SDS-PAGE and Western blot analysis. Subsequently, the blots were probed with the α-FLAG and α-acetyl lysine antibodies, respectively. For the blot probed with α-FLAG, one prominent band was shown in the INO80-FLAG cells, but no band was detected in the IP samples from the WT and ino80∆ cells. For the blot probed with the α-acetyl lysine antibody, we detected acetylated Ino80p in the INO80-FLAG strain while no bands were observed in the control strains. As such, our results showed that Ino80p can be acetylated. This acetylation can explain the co-activator’s recruitment patterns observed in current gene activation models. In yeast INO1, it has been shown that Ino80p is recruited to the promoter during repression, and then dissociates from the promoter once de-repression begins. Histone acetylases, on the other hand, have the opposite pattern of recruitment, as they have an increased presence at the promoter as INO1 de-repression commences. This Ino80p recruitment pattern significantly changes when HAT mutant strains are studied. It was observed that instead of dissociating, Ino80p accumulates at the promoter in the absence of functional HATs, such as Gcn5p or Esa1p, under de-repressing processes. As such, Ino80p acetylation may be required for its proper dissociation from the promoters. The remodelers’ dissociation mechanism may also have a wide range of implications with respect to transcriptional initiation, elongation, or even repression as it allows for increased spatial access to the promoter for the various transcription factors and regulators that need to bind in that region. Our findings here suggest a previously uncharacterized interaction between Ino80p and other co-activators recruited to promoters. As such, further analysis of Ino80p acetylation not only will provide insight into the role of epigenetic modifications in transcriptional activation, but also gives insight into the interactions occurring between co-activators at gene promoters during gene regulation.
Digital Article Identifier (DAI):
588
84149
Fermentation of Wood Waste by Treating with H₃PO₄-Acetone for Bioethanol Production
Abstract:
Wood waste is a potentially significant resource for economic and environment-friendly recycling. Wood waste represents a key sustainable source of biomass for transformation into bioethanol. Unfortunately, wood waste is highly recalcitrant for biotransformation, which limits its use and prevents economically viable conversion into bioethanol. As a result, an effective pretreatment is necessary to degrade cellulose of the wood waste, which improves the accessibility of cellulase. In this work, a H₃PO₄-acetone pretreatment was selected among the various pretreatment methods and used to dissolve cellulose and lignin. When the H₃PO₄ and acetone were used, 5–6% of the wood waste was found to be very appropriate for saccharification. Also, when the enzymatic saccharification was conducted in the mixture of the wood waste and 0.05 M citrate buffer solution, glucose and xylose were measured to be 80.2 g/L and 9.2 g/L respectively. Furthermore, ethanol obtained after 70 h of fermentation by S. cerevisiae was 30.4 g/L. As a result, the conversion yield from wood waste to bioethanol was calculated to be 57.4%. These results show that the pretreated wood waste can be used as good feedstocks for bioethanol production and that the H₃PO₄-acetone pretreatment can effectively increase the yield of ethanol production.
Digital Article Identifier (DAI):
587
84089
Development of Gold Nanoparticles-Antibody System for the Selective Photothermal Destruction of Multidrug Resistant Bacteria
Abstract:
Antimicrobial resistance, which threatens the efficacy of the existing antibiotics represents a worldwide public health issue. At the current time, vancomycin is the only responsive treatment although has significant cytotoxicity, is partially effective and it is poorly retained by infected tissues. From a clinical point of view, attractive alternative approaches for treating such Meticillin-Resistant Staphylococcus Aureus (MRSA) strains would be using agents that cause physical damage to the bacteria. Modular nanopharmaceuticals systems are being designed to address all of these multifunctional capabilities for the ideal bacterial treatment, with the ability to mix and match appropriate functions. Here we present a novel method of selective laser photothermal ablation of MRSA bacteria mediated by gold nanoparticles bound to PBP antibody against PBP protein located on the MRSA surface.
Digital Article Identifier (DAI):
586
84088
Nanotechnology-Based Treatment of Klebsiella pneumoniae Infections
Abstract:
We present method of nanoparticle enhanced laser thermal ablation of Klebsiella pneumoniae infections, using gold nanoparticles combined with a specific growth factor and demonstrate its selective therapeutic efficacy. Ab (antibody solution) bound to GNPs (gold nanoparticles) was administered in vitro and determined the specific delivery of the nano-bioconjugate into the microorganism. The extent of necrosis was considerable following laser therapy, and at the same time, normal cells were not seriously affected. The selective photothermal ablation of the infected tissue was obtained after the selective accumulation of Ab bound to GNPs into bacteria following perfusion. These results may represent a major step in antibiotherapy treatment using nanolocalized thermal ablation by laser heating.
Digital Article Identifier (DAI):
585
82449
Synthesis of a Hybrid of PEG-b-PCL and G1-PEA Dendrimer Based Six-Armed Star Polymer for Nano Delivery of Vancomycin
Abstract:
Treatment of infections is compromised by limitations of conventional dosage forms and drug resistance. Nanocarrier system is a strategy to overcome these challenges and improve therapy. Thus, the development of novel materials for drug delivery via nanocarriers is essential. The aim of the study was to synthesize a multi-arm polymer (6-mPEPEA) for enhanced activity of vancomycin (VM) against susceptible and resistant Staphylococcus aureus (MRSA). The synthesis steps of the star polymer followed reported procedures. The synthesized 6-mPEPEA was characterized by FTIR, ¹H and ¹³CNMR and MTT assays. VM loaded micelles were prepared from 6-mPEPEA and characterized for size, polydispersity index (PI) and surface charge (ZP) (Dynamic Light Scattering), morphology by TEM, drug loading (UV Spectrophotometry), drug release (dialysis bag), in vitro and in vivo efficacy against sensitive and resistant S. aureus. 6-mPEPEA was synthesized, and its structure was confirmed. MTT assays confirmed its nontoxic nature with a high cell viability (77%-85%). Unimolecular spherical micelles were prepared. Size, PI, and ZP was 52.48 ± 2.6 nm, 0.103 ± 0.047, -7.3 ± 1.3 mV, respectively and drug loading was 62.24 ± 3.8%. There was a 91% drug release from VCM-6-mPEPEA after 72 hours. In vitro antibacterial test revealed that VM-6-mPEPEA had 8 and 16-fold greater activity against S. aureus and MRSA when compared to bare VM. Further investigations using flow cytometry showed that VM-6-mPEPEA had 99.5% killing rate of MRSA at the MIC concentration. In vivo antibacterial activity revealed that treatment with VM-6-mPEPEA had a 190 and a 15-fold reduction in the MRSA load in untreated and VM treated respectively. These findings confirmed the potential of 6-mPEPEA as a promising bio-degradable nanocarrier for antibiotic delivery to improve treatment of bacterial infections.
Digital Article Identifier (DAI):
584
80739
All-or-None Principle and Weakness of Hodgkin-Huxley Mathematical Model
Abstract:
Mathematical and computational modellings are the necessary tools for reviewing, analysing, and predicting processes and events in the wide spectrum range of scientific fields. Therefore, in a field as rapidly developing as neuroscience, the combination of these two modellings can have a significant role in helping to guide the direction the field takes. The paper combined mathematical and computational modelling to prove a weakness in a very precious model in neuroscience. This paper is intended to analyse all-or-none principle in Hodgkin-Huxley mathematical model. By implementation the computational model of Hodgkin-Huxley model and applying the concept of all-or-none principle, an investigation on this mathematical model has been performed. The results clearly showed that the mathematical model of Hodgkin-Huxley does not observe this fundamental law in neurophysiology to generating action potentials. This study shows that further mathematical studies on the Hodgkin-Huxley model are needed in order to create a model without this weakness.
Digital Article Identifier (DAI):
583
78646
Insights into Archaeological Human Sample Microbiome Using 16S rRNA Gene Sequencing
Abstract:
Human body is inhabited by a vast number of microorganisms, collectively known as the human microbiome, and there is a tremendous interest in evolutionary changes in human microbial ecology, diversity and function. The field of paleomicrobiology, study of ancient human microbiome, is powered by modern techniques of Next Generation Sequencing (NGS), which allows extracting microbial genomic data directly from archaeological sample of interest. One of the major techniques is 16S rRNA gene sequencing, by which certain 16S rRNA gene hypervariable regions are being amplified and sequenced. However, some limitations of this method exist including the taxonomic precision and efficacy of different regions used. The aim of this study was to evaluate the phylogenetic sensitivity of different 16S rRNA gene hypervariable regions for microbiome studies in the archaeological samples. Towards this aim, archaeological bone samples and corresponding soil samples from each burial environment were collected in Medieval cemeteries in Latvia. The Ion 16S™ Metagenomics Kit targeting different 16S rRNA gene hypervariable regions was used for library construction (Ion Torrent technologies). Sequenced data were analysed by using appropriate bioinformatic techniques; alignment and taxonomic representation was done using Mothur program. Sequences of most abundant genus were further aligned to E. coli 16S rRNA gene reference sequence using MEGA7 in order to identify the hypervariable region of the segment of interest. Our results showed that different hypervariable regions had different discriminatory power depending on the groups of microbes, as well as the nature of samples. On the basis of our results, we suggest that wider range of primers used can provide more accurate recapitulation of microbial communities in archaeological samples. Acknowledgements. This work was supported by the ERAF grant Nr. 1.1.1.1/16/A/101.
Digital Article Identifier (DAI):
582
78173
Effect of Low Temperature on Structure and RNA Binding of E.coli CspA: A Molecular Dynamics Based Study
Abstract:
Cold shock protein A (CspA) is major cold inducible protein present in Escherichia coli. The protein is involved in stabilizing secondary structure of RNA by working as chaperone during cold temperature. Two RNA binding motifs play key role in the stabilizing activity. This study aimed to investigate implications of low temperature on structure and RNA binding activity of E. coli CspA. Molecular dynamics simulations were performed to compare the stability of the protein at 37°C and 10 °C. The protein was mutated at RNA binding motifs and docked with RNA to assess the stability of both complexes. Results suggest that CspA as well as CspA-RNA complex is more stable at low temperature. It was also confirmed that RNP1 and RNP2 play key role in RNA binding.
Digital Article Identifier (DAI):
581
76882
Effect of Black Cumin (Nigella sativa) Extract on Damaged Brain Cells
Abstract:
The nervous system is made up of complex delicate structures such as the spinal cord, peripheral nerves and the brain. These are prone to various types of injury ranging from neurodegenerative diseases to trauma leading to diseases like Parkinson's, Alzheimer's, multiple sclerosis, amyotrophic lateral sclerosis (ALS), multiple system atrophy etc. Unfortunately, because of the complicated structure of nervous system, spontaneous regeneration, repair and healing is seldom seen due to which brain damage, peripheral nerve damage and paralysis from spinal cord injury are often permanent and incapacitating. Hence, innovative and standardized approach is required for advance treatment of neurological injury. Nigella sativa (N. sativa), an annual flowering plant native to regions of southern Europe and Asia; has been suggested to have neuroprotective and anti-seizures properties. Neuroregeneration is found to occur in damaged cells when treated using extract of N. sativa. Due to its proven health benefits, lots of experiments are being conducted to extract all the benefits from the plant. The flowers are delicate and are usually pale blue and white in color with small black seeds. These seeds are the source of active components such as 30–40% fixed oils, 0.5–1.5% essential oils, pharmacologically active components containing thymoquinone (TQ), ditimoquinone (DTQ) and nigellin. In traditional medicine, this herb was identified to have healing properties and was extensively used Middle East and Far East for treating diseases such as head ache, back pain, asthma, infections, dysentery, hypertension, obesity and gastrointestinal problems. Literature studies have confirmed the extract of N. sativa seeds and TQ have inhibitory effects on inducible nitric oxide synthase and production of nitric oxide as well as anti-inflammatory and anticancer activities. Experimental investigation will be conducted to understand which ingredient of N. sativa causes neuroregeneration and roots to its healing property. An aqueous/ alcoholic extract of N. sativa will be made. Seed oil is also found to have used by researchers to prepare such extracts. For the alcoholic extracts, the seeds need to be powdered and soaked in alcohol for a period of time and the alcohol must be evaporated using rotary evaporator. For aqueous extracts, the powder must be dissolved in distilled water to obtain a pure extract. The mobile phase will be the extract while the suitable stationary phase (substance that is a good adsorbent e.g. silica gels, alumina, cellulose etc.) will be selected. Different ingredients of N. sativa will be separated using High Performance Liquid Chromatography (HPLC) for treating damaged cells. Damaged brain cells will be treated individually and in different combinations of 2 or 3 compounds for different intervals of time. The most suitable compound or a combination of compounds for the regeneration of cells will be determined using DOE methodology. Later the gene will also be determined and using Polymerase Chain Reaction (PCR) it will be replicated in a plasmid vector. This plasmid vector shall be inserted in the brain of the organism used and replicated within. The gene insertion can also be done by the gene gun method. The gene in question can be coated on a micro bullet of tungsten and bombarded in the area of interest and gene replication and coding shall be studied. Investigation on whether the gene replicates in the organism or not will be examined.
Digital Article Identifier (DAI):
580
76141
An Android Application for ECG Monitoring and Evaluation Using Pan-Tompkins Algorithm
Abstract:
Parallel to the fast worldwide increase of elderly population and spreading unhealthy life habits, there is a significant rise in the number of patients and health problems. The supervision of people who have health problems and oversight in detection of people who have potential risks, bring a considerable cost to health system and increase workload of physician. To provide an efficient solution to this problem, in the recent years mobile applications have shown their potential for wide usage in health monitoring. In this paper we present an Android mobile application that records and evaluates ECG signal using Pan-Tompkins algorithm for QRS detection. The application model includes an alarm mechanism that is proposed to be used for sending message including abnormality information and location information to health supervisor.
Digital Article Identifier (DAI):
579
75660
Selective Recovery and Molecular Identification of Laccase-Producing Bacteria from Selected Terrestrial and Aquatic Milieu in the Eastern Cape, South Africa: Toward the Production of Environmentally Relevant Biocatalysts
Abstract:
Laccase is constantly gaining status as important biocatalyst in biotechnology. The illimitable potential of its industrial applications and the corresponding aggressive need for phenomenal volumes of extracellularly secreted laccases have called for its interminable production from sources which are able to meet this demand within a relatively short period of time, preferably bacteria. In response to this call, this study was designed to source for laccase-producing bacteria from different environmental matrices. Three sampling environments were chosen such as wastewater treatment plants, University of Fort Hare vicinity and the Hogback woodland, all within the Eastern Cape, South Africa. Samples such as effluents, sediments, leaf litters, degrading wood and rock scrapings were selectively enriched with some model aromatic compounds and were further screened qualitatively and quantitatively on five phenolic substrates ABTS (2,2’-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid), Guaiacol, 1-Naphthol, Potassium Ferric Cyanide and Syringaldazine). Basis for selection was their ability to elicit a colour change on at least three of the above mentioned agar based assay substrates. The choice isolates were further identified based on 16S rRNA molecular identification techniques. 33 isolates were screened out of the 40 representative distinct colonies during the qualitative plate screens, while quantitative screens selected out 11 bacterial isolates. They were, based on molecular identification, desginated as members of the genera Pseudomonas, Stenotrophomonas and Citrobacter of the gammaproteobacteria and Bordetalla and Achromobacter of the betaproteobacteria respectively. We therefore conclude based on our outcomes that we may have isolated efficient laccase-producing bacteria, which might be of beneficial significance in catalysis and biotechnology.
Digital Article Identifier (DAI):
578
75369
De Novo Assembly and Characterization of the Transcriptome during Seed Development, and Generation of Genic-SSR Markers in Pomegranate (Punica granatum L.)
Abstract:
Pomegranate (Punica granatum L.) is known to be one of the oldest edible fruit tree species, with a wide geographical global distribution. Fruits from the two defined varieties (Hicaznar and 33N26) were taken at intervals after pollination and fertilization at different sizes. Seed samples were used for transcriptome sequencing. Primary sequencing was produced by Illumina Hi-Seq™ 2000. Firstly, we had raw reads, and it was subjected to quality control (QC). Raw reads were filtered into clean reads and aligned to the reference sequences. De novo analysis was performed to detect genes expressed in seeds of pomegranate varieties. We performed downstream analysis to determine differentially expressed genes. We generated about 27.09 gb bases in total after Illumina Hi-Seq sequencing. All samples were assembled together, we got 59,264 Unigenes, the total length, average length, N50, and GC content of Unigenes are 84.547.276 bp, 1.426 bp, 2,137 bp, and 46.20 %, respectively. Unigenes were annotated with 7 functional databases, finally, 42.681(NR: 72.02%), 39.660 (NT: 66.92%), 30.790 (Swissprot: 51.95%), 20.212 (COG: 34.11%), 27.689 (KEGG: 46.72%), 12.328 (GO: 20.80%), and 33,833 (Interpro: 57.09%) Unigenes were annotated. With functional annotation results, we detected 42.376 CDS, and 4.999 SSR distribute on 16.143 Unigenes.
Digital Article Identifier (DAI):
577
75348
The Role and Importance of Genome Sequencing in Prediction of Cancer Risk
Abstract:
The role and relative importance of intrinsic and extrinsic factors in the development of complex diseases such as cancer still remains a controversial issue. Determining the amount of variation explained by these factors needs experimental data and statistical models. These models are nevertheless based on the occurrence and accumulation of random mutational events during stem cell division, thus rendering cancer development a stochastic outcome. We demonstrate that not only individual genome sequencing is uninformative in determining cancer risk, but also assigning a unique genome sequence to any given individual (healthy or affected) is not meaningful. Current whole-genome sequencing approaches are therefore unlikely to realize the promise of personalized medicine. In conclusion, since genome sequence differs from cell to cell and changes over time, it seems that determining the risk factor of complex diseases based on genome sequence is somewhat unrealistic, and therefore, the resulting data are likely to be inherently uninformative.
Digital Article Identifier (DAI):
576
75206
Cr³⁺/SiO₄⁴⁻ Codoped Hydroxyapatite Nanorods: Fabrication and Microstructure Analysis
Abstract:
In this study, nanorods of Cr³⁺/SiO₄⁴⁻ codoped hydroxyapatite (Cr³⁺/SiO₄⁴⁻-HA) were synthesized successfully and rapidly through microwave irradiation technique, using (Ca(NO₃)₂•4H₂O), ((NH₄)₂HPO₄), (SiC₈H₂₀O₄) and (Cr(NO₃)₃.9H₂O) as source materials for Ca²⁺, PO₄³⁻, SiO₄⁴⁻ and Cr³⁺ ions, respectively. The impact of dopants on the phase formation and microstructure of the powders were investigated by means of X-ray diffraction (XRD), Fourier transform infrared spectrum analysis (FT-IR) and Field emission electron microscopy (FESEM) techniques. XRD analysis showed that with an incorporation of Cr³⁺/SiO₄⁴⁻ ions into HA structure resulted in peak broadening and reduced peak height due to the amorphous nature and reduced crystallinity of the resulting HA powder. FTIR spectroscopy revealed the existence of the different vibrational modes matching to phosphates and hydroxyl groups. The FESEM analysis showed a change in the crystal shape from spherical to rod shaped particles upon Cr³⁺ doping into the crystal structure. Acknowledgments: This study was supported by Karabük University (Project no. KBÜBAP-17-YD-144). The authors would like to thank for support.
Digital Article Identifier (DAI):
575
74869
Characterization of Articular Cartilage Based on the Response of Cartilage Surface to Loading/Unloading
Abstract:
Articular cartilage is a fluid-swollen tissue of synovial joints that functions by providing a lubricated surface for articulation and to facilitate the load transmission. The biomechanical function of this tissue is highly dependent on the integrity of its ultrastructural matrix. Any alteration of articular cartilage matrix, either by injury or degenerative conditions such as osteoarthritis (OA), compromises its functional behaviour. Therefore, the assessment of articular cartilage is important in early stages of degenerative process to prevent or reduce further joint damage with associated socio-economic impact. Therefore, there has been increasing research interest into the functional assessment of articular cartilage. This study developed a characterization parameter for articular cartilage assessment based on the response of cartilage surface to loading/unloading. This is because the response of articular cartilage to compressive loading is significantly depth-dependent, where the superficial zone and underlying matrix respond differently to deformation. In addition, the alteration of cartilage matrix in the early stages of degeneration is often characterized by PG loss in the superficial layer. In this study, it is hypothesized that the response of superficial layer is different in normal and proteoglycan depleted tissue. To establish the viability of this hypothesis, samples of visually intact and artificially proteoglycan-depleted bovine cartilage were subjected to compression at a constant rate to 30 percent strain using a ring-shaped indenter with an integrated ultrasound probe and then unloaded. The response of articular surface which was indirectly loaded was monitored using ultrasound during the time of loading/unloading (deformation/recovery). It was observed that the rate of cartilage surface response to loading/unloading was different for normal and PG-depleted cartilage samples. Principal Component Analysis was performed to identify the capability of the cartilage surface response to loading/unloading, to distinguish between normal and artificially degenerated cartilage samples. The classification analysis of this parameter showed an overlap between normal and degenerated samples during loading. While there was a clear distinction between normal and degenerated samples during unloading. This study showed that the cartilage surface response to loading/unloading has the potential to be used as a parameter for cartilage assessment.
Digital Article Identifier (DAI):
574
74777
In vitro Plant Regeneration of Gonystylus Bancanus (Miq) Kurz. Through Direct Organogenesis
Abstract:
Plant regeneration was achieved from shoot tip and nodal segment of Gonystylus bancanus (Miq) Kurz. cultured in Murashige and Skoog’s medium supplemented with various concentrations of 6-benzylaminopurine (BAP). The most optimum concentration of BAP for shoot initiation is 10.0 mgl⁻¹ with approximately 10% of shoot tip and 15% of nodal segment produced single shoot after 28 and 15 days of culture incubation respectively. Rooting was achieved when shoots were transferred into MS medium supplemented with 5.0 mgl⁻¹ Naphthalene acetic acid (NAA). Synthesizing results developed through this research can be a starting point for the upscalling and optimization process in future.
Digital Article Identifier (DAI):
573
74687
Milk Yield and Fingerprinting of Beta-Casein Precursor (CSN2) Gene in Some Saudi Camel Breeds
Abstract:
Camels are substantial providers of transport, milk, sport, meat, shelter, fuel, security and capital in many countries, particularly Saudi Arabia. Identification of animal breeds has progressed rapidly during the last decade. Advanced molecular techniques are playing a significant role in breeding or strain protection laws. On the other hand, fingerprinting of some molecular markers related to some productive traits in farm animals represents most important studies to our knowledge, which aim to conserve these local genetic resources, and to the genetic improvement of such local breeds by selective programs depending on gene markers. Milk records were taken two days in each week from female camels of Majahem, Safara, Wathaha, and Hamara breeds, respectively from different private farms in northern Jeddah, Riyadh and Alwagh governorates and average weekly yields were calculated. DNA sequencing for CSN2 gene was used for evaluating the genetic variations and calculating the genetic distance values among four Saudi camel populations which are Hamra(R), Safra(Y), Wadha(W) and Majaheim(M). In addition, this marker was analyzed for reconstructing the Neighbor joining tree among evaluating camel breeds. In respect to milk yield during winter season, result indicated that average weekly milk yield of Safara camel breed (30.05 Kg/week) is significantly (p < 0.05) lower than the other 3 breeds which ranged from 39.68 for Hamara to 42.42 Kg/week for Majahem, while there are not significant differences between these three breeds. The Neighbor Joining analysis that re-constructed based on DNA variations showed that samples are clustered into two unique clades. The first clade includes Y (from Y4 to Y18) and M (from M1, to M9). On the other hand, the second cluster is including all R (from R1 to R6) and W (from W1 to W6). The genetic distance values were equal 0.0068 (between the groups M&Y and R&W) and equal 0 (within each group).
Digital Article Identifier (DAI):
572
74636
Validation of a Fluid-Structure Interaction Model of an Aortic Dissection versus a Bench Top Model
Authors:
Abstract:
The aim of this investigation was to validate the fluid-structure interaction (FSI) model of type B aortic dissection with our experimental results from a bench-top-model. Another objective was to study the relationship between the size of a septectomy that increases the outflow of the false lumen and its effect on the values of the differential of pressure between true lumen and false lumen. FSI analysis based on Galerkin&rsquo;s formulation was used in this investigation to study flow pattern and hemodynamics within a flexible type B aortic dissection model using boundary conditions from our experimental data. The numerical results of our model were verified against the experimental data for various tear size and location. Thus, CFD tools have a potential role in evaluating different scenarios and aortic dissection configurations.
Digital Article Identifier (DAI):
571
74607
Construction of the Large Scale Biological Networks from Microarrays
Authors:
Abstract:
One of the sustainable goals of the system biology is understanding gene-gene interactions. Hence, gene regulatory networks (GRN) need to be constructed for understanding the disease ontology and to reduce the cost of drug development. To construct gene regulatory from gene expression we need to overcome many challenges such as data denoising and dimensionality. In this paper, we develop an integrated system to reduce data dimension and remove the noise. The generated network from our system was validated via available interaction databases and was compared to previous methods. The result revealed the performance of our proposed method.
Digital Article Identifier (DAI):
570
73792
Hemodynamics of a Cerebral Aneurysm under Rest and Exercise Conditions
Abstract:
Physiological flow under rest and exercise conditions in patient-specific cerebral aneurysm models is numerically investigated. A finite-volume based code with BiCGStab as the linear equation solver is used to simulate unsteady three-dimensional flow field through the incompressible Navier-Stokes equations. Flow characteristics are first established in a healthy cerebral artery for both physiological conditions. The effect of saccular aneurysm on cerebral hemodynamics is then explored through a comparative analysis of the velocity distribution, nature of flow patterns, wall pressure and wall shear stress (WSS) against the reference configuration. The efficacy of coil embolization as a potential strategy of surgical intervention is also examined by modelling coil as a homogeneous and isotropic porous medium where the extended Darcy’s law, including Forchheimer and Brinkman terms, is applicable. The Carreau-Yasuda non-Newtonian blood model is incorporated to capture the shear thinning behavior of blood. Rest and exercise conditions correspond to normotensive and hypertensive blood pressures respectively. The results indicate that the fluid impingement on the outer wall of the arterial bend leads to abnormality in the distribution of wall pressure and WSS, which is expected to be the primary cause of the localized aneurysm. Exercise correlates with elevated flow velocity, vortex strength, wall pressure and WSS inside the aneurysm sac. With the insertion of coils in the aneurysm cavity, the flow bypasses the dilatation, leading to a decline in flow velocities and WSS. Particle residence time is observed to be lower under exercise conditions, a factor favorable for arresting plaque deposition and combating atherosclerosis.
Digital Article Identifier (DAI):
569
73720
Metagenomics Analysis of Bacteria in Sorghum Using next Generation Sequencing
Abstract:
Sorghum is an important cereal crop in the world. In particular, it has attracted breeders due to capacity to serve as food, feed, fiber and bioenergy crop. Like any other plant, sorghum hosts a variety of microbes, which can either, have a neutral, negative and positive influence on the plant. In the current study, regions (V3/V4) of 16 S rRNA were targeted to extensively assess bacterial multitrophic interactions in the phyllosphere of sorghum. The results demonstrated that the presence of a pathogen has a significant effect on the endophytic bacterial community. Understanding these interactions is key to develop new strategies for plant protection.
Digital Article Identifier (DAI):
568
73657
Europium Chelates as a Platform for Biosensing
Abstract:
Rare earth nanotechnology has gained a considerable amount of interest in the field of biosensing due to the unique luminescence properties of lanthanides. Chelating rare earth ions plays a significant role in biological labelling applications including medical diagnostics, due to their different excitation and emission wavelengths, variety of their spectral properties, sharp emission peaks and long fluorescence lifetimes. We aimed to develop a platform for biosensors based on Europium (Eu³⁺) chelates against biomarkers of cardiac injury (heart-type fatty acid binding protein; H-FABP3) and stroke (glial fibrillary acidic protein; GFAP). Additional novelty in this project is the use of synthetic binding proteins (Affimers), which could offer an excellent alternative targeting strategy to the existing antibodies. Anti-GFAP and anti-HFABP3 Affimer binders were modified to increase the number of carboxy functionalities. Europium nitrate then incubated with the modified Affimer. The luminescence characteristics of the Eu³⁺ complex with modified Affimers and antibodies against anti-GFAP and anti-HFABP3 were measured against different concentrations of the respective analytes on excitation wavelength of 395nm. Bovine serum albumin (BSA) was used as a control against the IgG/Affimer Eu³⁺ complexes. The emission spectrum of Eu³⁺ complex resulted in 5 emission peaks ranging between 550-750 nm with the highest intensity peaks were at 592 and 698 nm. The fluorescence intensity of Eu³⁺ chelates with the modified Affimer or antibodies increased significantly by 4-7 folder compared to the emission spectrum of Eu³⁺ complex. The fluorescence intensity of the Affimer complex was quenched proportionally with increased analyte concentration, but this did not occur with antibody complex. In contrast, the fluorescence intensity for Eu³⁺ complex increased slightly against increased concentration of BSA. These data demonstrate that modified Affimers Eu³⁺ complexes can function as nanobiosensors with potential diagnostic and analytical applications.
Digital Article Identifier (DAI):
567
73249
Optimization of Lead Bioremediation by Marine Halomonas sp. ES015 Using Statistical Experimental Methods
Abstract:
Bioremediation technology is now used for treatment instead of traditional metal removal methods. A strain was isolated from Marsa Alam, Red sea, Egypt showed high resistance to high lead concentration and was identified by the 16S rRNA gene sequencing technique as Halomonas sp. ES015. Medium optimization was carried out using Plackett-Burman design, and the most significant factors were yeast extract, casamino acid and inoculums size. The optimized media obtained by the statistical design raised the removal efficiency from 84% to 99% from initial concentration 250 ppm of lead. Moreover, Box-Behnken experimental design was applied to study the relationship between yeast extract concentration, casamino acid concentration and inoculums size. The optimized medium increased removal efficiency to 97% from initial concentration 500 ppm of lead. Immobilized Halomonas sp. ES015 cells on sponge cubes, using optimized medium in loop bioremediation column, showed relatively constant lead removal efficiency when reused six successive cycles over the range of time interval. Also metal removal efficiency was not affected by flow rate changes. Finally, the results of this research refer to the possibility of lead bioremediation by free or immobilized cells of Halomonas sp. ES015. Also, bioremediation can be done in batch cultures and semicontinuous cultures using column technology.
Digital Article Identifier (DAI):
566
73036
Association of Lipoprotein Lipase Gene (HindIII rs320) Polymorphisms with Moderate Hypertriglyceridemia Secondary to Metabolic Syndrome
Abstract:
Lipoprotein Lipase (LPL) is a key enzyme for lipid metabolism; its genetic polymorphism can be a candidate for modulating lipids parameters in metabolic syndrome. The objective of the present study was to determine whether lipoproteins lipase polymorphisMetS (LPL-HindIII) could be associated with moderate hypertriglyceridemia (secondary to metabolism syndrome). The polymorphism Hind III (rs320) was assessed by PCR-RFLP in 51 MetS patients and 17 healthy controls from the hospital in Tlemcen. The logistic regression analyses showed no significant association with Hind III genotype and hypertriglyceridemia (TG ≥ 1,5g/l or TG lower treatment) (P=0,455), metabolic syndrome (P=0,455), hypertension (P=0,802) and type 2 diabetes (P=0,144). In terms of plasma biomarkers, although not statistically significant, there was a difference in TG levels (P > 0,05), which was lowest among carriers of the homogenous mutant allele (H-). In this study, there was no association between the rare allele (H-) and disease protection, and between the frequent allele (H+) and disease prevalence (hypertriglyceridemia, metabolic syndrome, hypertension, type 2 diabetes).
Digital Article Identifier (DAI):
565
73031
Some Extreme Halophilic Microorganisms Produce Extracellular Proteases with Long Lasting Tolerance to Ethanol Exposition
Abstract:
Extremophiles constitute a potentially valuable source of proteases for the development of biotechnological processes; however, the number of available studies in the literature is limited compared to mesophilic counterparts. Therefore, in this study, Peruvian halophilic microorganisms were characterized to select suitable proteolytic strains that produce active proteases under exigent conditions. Proteolysis was screened using the streak plate method with gelatin or skim milk as substrates. After that, proteolytic microorganisms were selected for phenotypic characterization and screened by a semi-quantitative proteolytic test using a modified method of diffusion agar. Finally, proteolysis was evaluated using partially purified extracts by ice-cold ethanol precipitation and dialysis. All analyses were carried out over a wide range of NaCl concentrations, pH, temperature and substrates. Of a total of 60 strains, 21 proteolytic strains were selected, of these 19 were extreme halophiles and 2 were moderates. Most proteolytic strains demonstrated differences in their biochemical patterns, particularly in sugar fermentation. A total of 14 microorganisms produced extracellular proteases, 13 were neutral, and one was alkaline showing activity up to pH 9.0. Proteases hydrolyzed gelatin as the most specific substrate. In general, catalytic activity was efficient under a wide range of NaCl (1 to 4 M NaCl), temperature (37 to 55 °C) and after an ethanol exposition performed at -20 °C for 24 hours. In conclusion, this study reported 14 candidates extremely halophiles producing extracellular proteases capable of being stable and active on a wide range of NaCl, temperature and even long lasting ethanol exposition.
Digital Article Identifier (DAI):
564
72965
Treatment of Histopathological Symptoms in N-Nitrosopyrrolidine Induced Changes in Lung Tissue by Isolated Flavonoid from Indigofera tinctoria
Abstract:
N-nitrosopyrollidine or NPYR is a tobacco-specific nitrosamine which upon intoxicated causes abnormal production of Reactive Oxygen Species disrupt the endogenous antioxidant system. The study was designed to evaluate the histological changes in lung tissue of Mus musculus in NPYR administered lungs and effect of isolated flavonoid 3,6-dihydroxy-(3’,4’,7’-trimethoxyphenyl)-chromen-4-one-7-glucoside (ITC) from experimental plant Indigofera tinctorial. Post treatment with isolated compound significantly restored the abnormal symptoms and changes in pulmonary tissue. Transverse section of mouse lung in control animals appeared as a thin lace. Histologically, most of the lung was arranged as alveoli which were thin walled structures made up of single layered squamous epithelial cells. In the transverse section of lung at 100 X will clearly show the component of alveoli, surround by a thin layer of connective tissue and blood vessels. Smaller bronchioles were lined by cuboidal epithelial cells while larger bronchioles were lined by ciliated columnar epithelium layer while in NPYR intoxicated lungs signs of vast pulmonary damages and carcinogenesis as alveolar damage, necrosis, DADs or defused alveolar damages hyperplasia, metaplasia, dysplasia and next stage of carcinogenesis were revealed. Treatment with ITC showed the significant positive changes in the lung tissue due to the side hydroxyl and methoxy groups in its structure which help in combating oxidative injuries and give protection from the free radicals generated during the metabolism of NPYR in body. Thus, histopathological analysis confirms the development of the cancerous conditions in the lung tissue in mice model and the protective effects of ITC.
Digital Article Identifier (DAI):
563
72943
In silico Analysis of Differentially Expressed Genes in High-Grade Squamous Intraepithelial Lesion and Squamous Cell Carcinomas Stages of Cervical Cancer
Abstract:
Cervical cancer is one of the women related cancers which starts from the pre-cancerous cells and a fraction of women with pre-cancers of the cervix will develop cervical cancer. Cervical pre-cancers if treated in pre-invasive stage can prevent almost all true cervical squamous cell carcinoma. The present study investigates the genes and pathways that are involved in the progression of cervical cancer and are responsible in transition from pre-invasive stage to other advanced invasive stages. The study used GDS3292 microarray data to identify the stage specific genes in cervical cancer and further to generate the network of the significant genes. The microarray data GDS3292 consists of the expression profiling of 10 normal cervices, 7 HSILs and 21 SCCs samples. The study identifies 70 upregulated and 37 downregulated genes in HSIL stage while 95 upregulated and 60 downregulated genes in SCC stages. Biological process including cell communication, signal transduction are highly enriched in both HSIL and SCC stages of cervical cancer. Further, the ppi interaction of genes involved in HSIL and SCC stages helps in identifying the interacting partners. This work may lead to the identification of potential diagnostic biomarker which can be utilized for early stage detection.
Digital Article Identifier (DAI):
562
72940
miCoRe: Colorectal Cancer miRNAs Database
Abstract:
Colorectal cancer (CRC) also refers as bowel cancer or colon cancer. It involves the development of abnormal growth of cells in colon or rectum part of the body. This work leads to the development of a miRNA database in colorectal cancer. We named this database- miCoRe. This database comprises of all validated colon-rectal cancer miRNAs information from various published literature with an effectual knowledge based information retrieval system. miRNAs have been collected from various published literature reports. MySQL is used for main-framework of miCoRe while the front-end was developed in PHP script. The aim of developing miCoRe is to create a comprehensive central repository of colorectal carcinoma miRNAs with all germane information of miRNAs and their target genes. The current version of miCoRe consists of 238 miRNAs which are known to be implicated in malignancy of CRC. Alongside with miRNA information, miCoRe also contains the information related to the target genes of these miRNA. miCoRe furnishes the information about the mechanism of incidence and progression of the disease, which would further help the researchers to look for colorectal specific miRNAs therapies and CRC specific targeted drug designing. Moreover, it will also help in development of biomarkers for the better and early detection of CRC and will help in better clinical management of the disease.
Digital Article Identifier (DAI):
561
72833
Fluorescing Aptamer-Gold Nanoparticle Complex for the Sensitive Detection of Bisphenol A
Abstract:
Bisphenol A (BPA) is one of the endocrine disruptors (EDCs), which have been suspected to be associated with reproductive dysfunction and physiological abnormality in human. Since the BPA has been widely used to make plastics and epoxy resins, the leach of BPA from the lining of plastic products has been of major concern, due to its environmental or human exposure issues. The simple detection of BPA based on the self-assembly of aptamer-mediated gold nanoparticles (AuNPs) has been reported elsewhere, yet the detection sensitivity still remains challenging. Here we demonstrate an improved AuNP-based sensor of BPA by using fluorescence-combined AuNP colorimetry in order to overcome the drawback of traditional AuNP sensors. While the anti-BPA aptamer (full length or truncated ssDNA) triggered the self-assembly of unmodified AuNP (citrate-stabilized AuNP) in the presence of BPA at high salt concentrations, no fluorescence signal was observed by the subsequent addition of SYBR Green, due to a small amount of free anti-BPA aptamer. In contrast, the absence of BPA did not cause the self-assembly of AuNPs (no color change by salt-bridged surface stabilization) and high fluorescence signal by SYBP Green, which was due to a large amount of free anti-BPA aptamer. As a result, the quantitative analysis of BPA was achieved using the combination of absorption of AuNP with fluorescence intensity of SYBR green as a function of BPA concentration, which represented more improved detection sensitivity (as low as 1 ppb) than did in the AuNP colorimetric analysis. This method also enabled to detect high BPA in water-soluble extracts from thermal papers with high specificity against BPS and BPF. We suggest that this approach will be alternative for traditional AuNP colorimetric assays in the field of aptamer-based molecular diagnosis.
Digital Article Identifier (DAI):
560
72824
Visualizing Matrix Metalloproteinase-2 Activity Using Extracellular Matrix-Immobilized Fluorescence Resonance Energy Transfer Bioprobe in Cancer Cells
Abstract:
Visualizing matrix metalloproteinases (MMPs) activity is necessary for understanding cancer metastasis because they are implicated in cell migration and invasion by degrading the extracellular matrix (ECM). While much effort has been made to sense the MMP activity, but extracellularly long-term monitoring of MMP activity still remains challenging. Here, we report a collagen-bound fluorescent bioprobe for the detection of MMP-2 activity in the extracellular environment. This bioprobe consists of ECM-immobilized part (including collagen-bound protein) and MMP-sensing part (including peptide substrate linked with fluorescence resonance energy transfer (FRET) coupler between donor green fluorescent protein (GFP) and acceptor TAMRA dye), which was constructed through intein-mediated self-splicing conjugation. Upon being immobilized on the collagen-coated surface, this bioprobe enabled efficient long-lasting observation of MMP-2 activity in the cultured cells without affecting cell growth and viability. As a result, the FRET ratio (acceptor/donor) decreased as the MMP2 activity increased in cultured cancer cells. Furthermore, unlike wild-type MMP-2, mutated MMP-2 expression (Y580A in the hemopexin region) gave rise to lowering the secretion of MMP-2 in HeLa. Conclusively, our method is anticipated to find applications for tracing and visualizing enzyme activity.
Digital Article Identifier (DAI):