International Science Index

International Journal of Bioengineering and Life Sciences

Emergency Treatment of Methanol Poisoning: A Mathematical Approach
Every year a considerable number of people die due to methyl alcohol poisoning, in which most of them die even before proper treatment. This work gives a simple and cheap first aid to those affected individuals by the administration of activated charcoal. In this article, we emphasise on the adsorption capability of activated charcoal for the treatment of poisoning and use an impulsive differential equation to study the effect of activated charcoal during adsorption. We also investigate the effects of various parameters on the adsorption which are incorporated in the model system.
I-Optimal Design of 3D Scaffolds for Bone Tissue Engineering
Porous 3D scaffolds act as templates for tissue regeneration and provide a temporary mechanical support in the implantation site. This paper presents the design of 3D scaffolds made of poly(lactic-co-glycolic) acid (PLGA)/nanohydroxyapatite (nHA) produced by thermally induced phase separation (TIPS). This method is desirable as it generates interconnected micropores for nutrient supply, while it allows a certain level of control on pore size by manipulating the experimental factors (TIPS temperature, PLGA%, and nHA%). We have used a split-plot I-optimal design of experiments (DOE) to find the optimal set of the hard-to-change and easy-to-change factors that produce a scaffold porosity over 75%. The ultimate goal of this study is to fine-tune the macro/micro-architecture of these composite porous constructs and maximize bone formation. Further optimization of the scaffold architecture is underway by generating interconnected microchannels within the microporous matrix. These new hierarchical scaffolds are anticipated to provide an ideal environment for cell migration and future in vivo vascularization.
Modulating the Architecture of 3D Scaffolds in Melt Extrusion Additive Manufacturing
The tissue engineering approach often uses three-dimensional (3D) porous scaffolds for the regeneration or repair of injured and diseased tissues and organs. In recent years, advanced additive manufacturing (AM) has assisted researchers in producing 3D porous scaffolds with custom-designed internal architectures. In some cases, organic solvents have been used to dissolve the biomaterial prior to processing it into a 3D porous construct. Solvent toxicity may not be considered critical in in vitro studies; however, the use of potentially toxic solvents may be subject to scrutiny when the porous scaffolds are intended for clinical trials. On the other hand, optimizing the internal architecture of 3D scaffolds produced by melt extrusion additive manufacturing is highly challenging, mainly due to the pronounced variations in the deposited fiber diameter during the manufacturing process. Variations in polymer viscoelasticity and experimental factors of the fabrication process can influence the scaffold architecture due to extrudate swell. An I-optimal, split-plot designed experiment has been used in this study to investigate the extrudate swell in melt extrusion additive manufacturing. We have used the fitted regression relationships to simultaneously optimize three responses (extrudate swell, scaffold density, and scaffold modulus). We wanted to estimate the full quadratic response surface model, in order to consider possible optimal factor levels in the interior of the design space. To this end, we constructed a 24-run I-optimal, split-plot design in JMP software. The swell response was constrained to be close to 1 while targeting a desired modulus and the lowest density for the scaffold. To the extent of the model’s validity, we have been able to eliminate the effect of extrudate swell in 3D scaffold design, while enabling a desired range of porosity and modulus for bone tissue engineering scaffolds. The result of this optimization was a predicted modulus greater than 10 MPa and a predicted porosity of over 70%. These predicted responses corresponded to factor levels of 2 mm/s for the dispensing speed, a needle diameter of 0.6 μm diameter, a plotting pressure of 2.5 bar, and a melt temperature of 114°C for polycaprolactone (PCL).
Effects of Conversion of Indigenous Forest to Plantation Forest on the Diversity of Macro-Fungi in Kereita Forest, Kikuyu Escarpment, Kenya
Tropical forests harbor a wide range of biodiversity and rich macro-fungi diversity compared to the temperate regions in the World. However, biodiversity is facing the threat of extinction following the rate of forest loss taking place before proper study and documentation of macrofungi is achieved. The present study was undertaken to determine the effect of converting indigenous habitat to plantation forest on macrofungi diversity. To achieve the objective of this study, an inventory focusing on macro-fungi diversity was conducted within Kereita block in Kikuyu Escarpment forest which is on the southern side of Aberdare mountain range. The macrofungi diversity was conducted in the indigenous forest and in more than 15 year old Patula plantation forest , during the wet (long rain season, December 2014) and dry (Short rain season, May, 2015). In each forest type, 15 permanent (20m x 20m) sampling plots distributed across three (3) forest blocks were used. Both field and laboratory methods involved recording abundance of fruiting bodies, taxonomic identity of species and analysis of diversity indices and measures in terms of species richness, density and diversity. R statistical program was used to analyze for species diversity and Canoco 4.5 software for species composition. A total number of 76 genera in 28 families and 224 species were encountered in both forest types. The most represented taxa belonged to the Agaricaceae (16%), Polyporaceae (12%), Marasmiaceae, Mycenaceae (7%) families respectively. Most of the recorded macro-fungi were saprophytic, mostly colonizing the litter 38% and wood 34% based substrates, which was followed by soil organic dwelling species (17%). Ecto-mycorrhiza fungi (5%) and parasitic fungi (2%) were the least encountered. The data established that indigenous forests (native ecosystems) hosts a wide range of macrofungi assemblage in terms of density (2.6 individual fruit bodies / m2), species richness (8.3 species / plot) and species diversity (1.49/ plot level) compared to the plantation forest. The Conversion of native forest to plantation forest also interfered with species composition though did not alter species diversity. Seasonality was also shown to significantly affect the diversity of macro-fungi and 61% of the total species being present during the wet season. Based on the present findings, forested ecosystems in Kenya hold diverse macro-fungi community which warrants conservation measures.
A Novel Control Module for Heat Stress Memory in Plants
Plants have the capacity to 'memorize' stressful events and protect themselves from future stresses. Furthermore, they are able to 'reset' or 'forget' memories of certain stressful situations, which helps to maximize growth after returning to non-stress conditions. A delicate balance between the consolidation of stress memory and the degree of forgetfulness is critical for plant growth and productivity under changing environmental conditions. Here we report a novel control module for heat stress memory (thermomemory) in plants. Recently we identified HSP21, a chloroplast-localized small heat shock protein, as a crucial component of thermomemory. Variation in HSP21 protein level contributes to the differential thermomemory performance of Arabidopsis accessions, indicating a strong link between protein abundance of HSP21 and enhanced thermomemory capacity. Employing a combined pharmacological/genomics approach, we discovered a plastid-localised metalloprotease, FtsH6, for which no previous in vivo function was reported, as a protease involved in the initial degradation of HSP21 during the memory phase in Col-0. Furthermore, we showed that in addition to FtsH6, autophagy contributes to the selective degradation of HSP21 at later stages of the thermomemory phase. Our results thus reveal the presence of a novel HSP21- a plastidial protease – autophagy control module for thermomemory in plants and hold a great promise for understanding how plants grow and reproduce in highly dynamic environments with many predictable and unpredictable variables.
Morphology, Chromosome Numbers and Molecular Evidences of Three New Species of Begonia Section Baryandra (Begoniaceae) from Panay Island, Philippines
The flora of Panay Island is under-collected compared with the other islands of the Philippines. In a joint expedition to the island, botanists from Taiwan and the Philippines found three unknown Begonia and compared them with potentially allied species. The three species are clearly assignable to Begonia section Baryandra which is largely endemic to the Philippines. Studies of literature, herbarium specimens, and living plants support the recognition of the three new species: Begonia culasiensis, Begonia merrilliana, and Begonia sykakiengii. Somatic chromosomes at metaphase were determined to be 2n=30 for B. culasiensis and 2n=28 for both B. merrilliana and B. sykakiengii, which are congruent with those of most species in sect. Baryandra. Molecular phylogenetic evidence is consistent with B. culasiensis being a relict from the late Miocene, and with B. merrilliana and B. sykakiengii being younger species of Pleistocene origin. The continuing discovery of endemic Philippine species means the remaining fragments of both primary and secondary native vegetation in the archipelago are of increasing value in terms of natural capital. A secure future for the species could be realized through ex-situ conservation collections and raising awareness with community groups.
Protective Role of Curcumin against Ionising Radiation of Gamma Ray
Curcumin, a dietary antioxidant has been identified as a wonder molecule to possess therapeutic properties protecting the cellular macromolecules from oxidative damage. In our experimental study, we have explored the effectiveness of curcumin in protecting the structural paradigm of Human Serum Albumin (HSA) when exposed to gamma irradiation. HSA, being an important transport protein of the circulatory system, is involved in binding of variety of metabolites, drugs, dyes and fatty acids due to the presence of hydrophobic pockets inside the structure. HSA is also actively involved in the transportation of drugs and metabolites to their targets, because of its long half-life and regulation of osmotic blood pressure. Gamma rays, in its increasing concentration, results in structural alteration of the protein and superoxide radical generation. Curcumin, on the other hand, mitigates the damage, which has been evidenced in the following experiments. Our study explores the possibility for protection by curcumin during the molecular and conformational changes of HSA when exposed to gamma irradiation. We used a combination of spectroscopic methods to probe the conformational ensemble of the irradiated HSA and finally evaluated the extent of restoration by curcumin. SDS - PAGE indicated the formation of cross linked aggregates as a consequence of increasing exposure of gamma radiation. CD and FTIR spectroscopy inferred significant decrease in alpha helix content of HSA from 57% to 15% with increasing radiation doses. Steady state and time resolved fluorescence studies complemented the spectroscopic measurements when lifetime decay was significantly reduced from 6.35 ns to 0.37 ns. Hydrophobic and bityrosine study showed the effectiveness of curcumin for protection against radiation induced free radical generation. Moreover, bityrosine and hydrophobic profiling of gamma irradiated HSA in presence and absence of curcumin provided light on the formation of ROS species generation and the protective (magical) role of curcumin. The molecular mechanism of curcumin protection to HSA from gamma irradiation is yet unknown, though a possible explanation has been proposed in this work using Thioflavin T assay. It was elucidated, that when HSA is irradiated at low dose of gamma radiation in presence of curcumin, it is capable of retaining the native characteristic properties to a greater extent indicating stabilization of molecular structure. Thus, curcumin may be utilized as a therapeutic strategy to protect cellular proteins.
Shrinking Domestic Chickens Leads to Increased Genomic Diversity and Evolution of Genotypes
Since domestication, chickens (Gallus gallus domesticus) have experienced intensive anthropomorphic evolution and selection. In the Netherlands, bantamized variants have, over the past few decades, become popular alternatives to large fowls of traditional breeds, because they are easily housed in a hobby setting. Making these new bantam breeds is done by crossing a large breed with a small chicken breed, with subsequent selection to retain the exterior phenotype of the large donor breed and the small size of the bantam donor breed. However, while backcrossing for phenotype selection is threatening the long-term existence and genetic makeup of most neo-bantams, genetic exchange between breeders may also generate genetic diversity in these new breeds. In this study, high-density SNP arrays were used to characterize the genetic diversity and demographic history of 37 traditional Dutch chicken breeds, comprising large fowls (n=17 breeds), true bantams (n=4), and neo-bantams (n=16). In particular, genetic relationship, admixture patterns, and level of inbreeding of neo-bantams were investigated to assess their contribution to the national chicken genetic diversity. Large fowls and neo-bantams showed slightly similar polymorphism, though neo-bantams were the most inbred of the traditional breeds. Principal component analysis (PCA) and distance-based neighbor-joining (NJ) tree revealed high genotypic similarities between large fowls and neo-bantams while identifying signatures of recent genetic introgression during neo-bantams development. Population admixture analysis supported these findings, along with revealing ongoing changes in the bantamising trend of most neo-bantams. Traditional breeds showed remarkable variation in the run of homozygosity (ROH) profile, which was characterized by a low number of long homozygous segments. Despite that, long ROHs covered a significant proportion of the genome, particularly of neo-bantams. The genetic variation we observed within breeds is explained by the metapopulation structure comprising small farmer-based breeding units, whose genetic diversity is strongly influenced by breeding practices and selection preferences of individual breeders and breed associations. Results show that a small flock size and gene flow of varying extent have divergent consequences on the genetic diversity of large fowls and neo-bantams. We observed that the bantamising trend has changed over time towards an increased development of new phenotypes or breeder’s decision to establish new small size varieties. We showed that extensive gene flow contributes to the neo-bantams genetic diversity. However, sequential backcrossing derived from the lack of information of the degree of recent inbreeding. Hence, rapid genetic changes are expected to particularly affect neo-bantams, due to their smaller founder size and unstructured selection for morphological standards. The present study confirms the importance of using genotype data to inform genetic management and conservation priority of traditional breeds to preserve genetic diversity. We conclude that neo-bantams are reservoirs of emerging quantitative traits and phenotypes, suggesting that the bantamising breeding strategy can generate and maintain genetic diversity. However, such exceptional diversity can be preserved in the near future only with proper genetic information and structured breeding programmes.
Inconsistent Effects of Landscape Heterogeneity on Animal Diversity in an Agricultural Mosaic: A Multi-Scale and Multi-Taxon Investigation
A key challenge for the developing world is reconciling biodiversity conservation with the growing demand for food. In these regions, agriculture is typically interspersed among other land-uses creating heterogeneous landscapes. A primary hypothesis for promoting biodiversity in agricultural landscapes is the habitat heterogeneity hypothesis. While there is evidence that landscape heterogeneity positively influences biodiversity, the application of this hypothesis is hindered by a need to determine which components of landscape heterogeneity drive these effects and at what spatial scale(s). Additionally, whether diverse taxonomic groups are similarly affected is central for determining the applicability of this hypothesis as a general conservation strategy in agricultural mosaics. Two major components of landscape heterogeneity are compositional and configurational heterogeneity. Disentangling the roles of each component is important for biodiversity conservation because each represents different mechanisms underpinning variation in biodiversity. We identified a priori independent gradients of compositional and configurational landscape heterogeneity within an extensive agricultural mosaic in north-eastern Swaziland. We then tested how bird, dung beetle, ant and meso-carnivore diversity responded to compositional and configurational heterogeneity across six different spatial scales. To determine if a general trend could be observed across multiple taxa, we also tested which component and spatial scale was most influential across all taxonomic groups combined, Compositional, not configurational, heterogeneity explained diversity in each taxonomic group, with the exception of meso-carnivores. Bird and ant diversity was positively correlated with compositional heterogeneity at fine spatial scales < 1000 m, whilst dung beetle diversity was negatively correlated to compositional heterogeneity at broader spatial scales > 1500 m. Importantly, because of these contrasting effects across taxa, there was no effect of either component of heterogeneity on the combined taxonomic diversity at any spatial scale. The contrasting responses across taxonomic groups exemplify the difficulty in implementing effective conservation strategies that meet the requirements of diverse taxa. To promote diverse communities across a range of taxa, conservation strategies must be multi-scaled and may involve different strategies at varying scales to offset the contrasting influences of compositional heterogeneity. A diversity of strategies are likely key to conserving biodiversity in agricultural mosaics, and we have demonstrated that a landscape management strategy that only manages for heterogeneity at one particular scale will likely fall short of management objectives.
Balancing Biodiversity and Agriculture: A Broad-Scale Analysis of the Land Sparing/Land Sharing Trade-off for South African Birds
Modern agriculture has revolutionised the planet’s capacity to support humans, yet has simultaneously had a greater negative impact on biodiversity than any other human activity. Balancing the demand for food with the conservation of biodiversity is one of the most pressing issues of our time. Biodiversity-friendly farming (‘land sharing’), or alternatively, separation of conservation and production activities (‘land sparing’), are proposed as two strategies for mediating the trade-off between agriculture and biodiversity. However, there is much debate regarding the efficacy of each strategy, as this trade-off has typically been addressed by short term studies at fine spatial scales. These studies ignore processes that are relevant to biodiversity at larger scales, such as meta-population dynamics and landscape connectivity. Therefore, to better understand species response to agricultural land-use and provide evidence to underpin the planning of better production landscapes, we need to determine the merits of each strategy at larger scales. In South Africa, a remarkable citizen science project - the South African Bird Atlas Project 2 (SABAP2) – collates an extensive dataset describing the occurrence of birds at a 5-min by 5-min grid cell resolution. We use these data, along with fine-resolution data on agricultural land-use, to determine which strategy optimises the agriculture-biodiversity trade-off in a southern African context, and at a spatial scale never considered before. To empirically test this trade-off, we model bird species population density, derived for each 5-min grid cell by Royle-Nicols single-species occupancy modelling, against both the amount and configuration of different types of agricultural production in the same 5-min grid cell. In using both production amount and configuration, we can show not only how species population densities react to changes in yield, but also describe the production landscape patterns most conducive to conservation. Furthermore, the extent of both the SABAP2 and land-cover datasets allows us to test this trade-off across multiple regions to determine if bird populations respond in a consistent way and whether results can be extrapolated to other landscapes. We tested the land sparing/sharing trade-off for 281 bird species across three different biomes in South Africa. Overall, a higher proportion of species are classified as losers, and would benefit from land sparing. However, this proportion of loser-sparers is not consistent and varies across biomes and the different types of agricultural production. This is most likely because of differences in the intensity of agricultural land-use and the interactions between the differing types of natural vegetation and agriculture. Interestingly, we observe a higher number of species that benefit from agriculture than anticipated, suggesting that agriculture is a legitimate resource for certain bird species. Our results support those seen at smaller scales and across vastly different agricultural systems, that land sparing benefits the most species. However, our analysis suggests that land sparing needs to be implemented at spatial scales much larger than previously considered. Species persistence in agricultural landscapes will require the conservation of large tracts of land, and is an important consideration in developing countries, which are undergoing rapid agricultural development.
Improving the Bioprocess Phenotype of Chinese Hamster Ovary Cells Using CRISPR/Cas9 and Sponge Decoy Mediated MiRNA Knockdowns
Chinese Hamster Ovary (CHO) cells are the prominent cell line used in biopharmaceutical production. To improve yields and find beneficial bioprocess phenotypes genetic engineering plays an essential role in recent research. The miR-23 cluster, specifically miR-24 and miR-27, was first identified as differentially expressed during hypothermic conditions suggesting a role in proliferation and productivity in CHO cells. In this study, we used sponge decoy technology to stably deplete the miRNA expression of the cluster. Furthermore, we implemented the CRISPR/Cas9 system to knockdown miRNA expression. Sponge constructs were designed for an imperfect binding of the miRNA target, protecting from RISC mediated cleavage. GuideRNAs for the CRISPR/Cas9 system were designed to target the seed region of the miRNA. The expression of mature miRNA and precursor were confirmed using RT-qPCR. For both approaches stable expressing mixed populations were generated and characterised in batch cultures. It was shown, that CRISPR/Cas9 can be implemented in CHO cells with achieving high knockdown efficacy of every single member of the cluster. Targeting of one miRNA member showed that its genomic paralog is successfully targeted as well. The stable depletion of miR-24 using CRISPR/Cas9 showed increased growth and specific productivity in a CHO-K1 mAb expressing cell line. This phenotype was further characterized using quantitative label-free LC-MS/MS showing 186 proteins differently expressed with 19 involved in proliferation and 26 involved in protein folding/translation. Targeting miR-27 in the same cell line showed increased viability in late stages of the culture compared to the control. To evaluate the phenotype in an industry relevant cell line; the miR-23 cluster, miR-24 and miR-27 were stably depleted in a Fc fusion CHO-S cell line which showed increased batch titers up to 1.5-fold. In this work, we highlighted that the stable depletion of the miR-23 cluster and its members can improve the bioprocess phenotype concerning growth and productivity in two different cell lines. Furthermore, we showed that using CRISPR/Cas9 is comparable to the traditional sponge decoy technology.
Unicellular to Multicellular: Some Empirically Parsimoniously Plausible Hypotheses
Possibly a slime mold somehow mutated or already was mutated at progeniture and so stayed as a metazoan when it developed into the fruiting stage and so the slime mold(s) we are evolved and similar to are genetically differ from the slime molds in existence now. This may be why there are genetic links between humans and other metazoa now alive and slime molds now alive but we are now divergent branches of the evolutionary tree compared to the original slime mold, or perhaps slime mold-like organisms, that gave rise to metazoan animalia and perhaps algae and plantae as slime molds were undifferentiated enough in many ways that could allow their descendants to evolve into these three separate phylogenetic categories. Or it may be a slime mold was born or somehow progenated as multicellular, as the particular organism was mutated enough to have say divided in a a 'pseudo-embryonic' stage, and this could have happened for algae, plantae as well as animalia or all the branches may be from the same line but the missing link might be covered in 'phylogenetic sequence comparison noise'.
Protective Effect of Aframomun chrysanthum Seed Aqueous Extract in Acetaminophen-Induced Liver Toxicity in Rats
Owing to the outbreak of different diseases and microbial resistance to some available drugs, proper identification, and evaluation of plants have been encouraged. There have been claims worldwide by the traditional system that some plants possessed medicinal properties. Plants and their components have been said to be source of large amount of drugs which comprise of distinct groups such as antispasmodics, anticancer and antimicrobials. Researchers have reported that chemicals in plants are responsible for the medicinal uses of plants. Thus this study evaluated the protective effect of Aframomun chrysanthum seed aqueous extract in acetaminophen-induced liver toxicity in rats. A suspension of 750 mg/kg acetaminophen was administered once every 72 hours to induce toxicity in the rats. Oral administration of 500, 1000 and 2000 mg/kg body weight of the extract and 100 mg/kg of silymarin (reference drug) were administered for 10 days. Biochemical analysis showed significant (p < 0.05) increase in the activities of aspartate aminotransferase (AST), alanine aminotransferase (ALT)and alkaline phosphatase (ALP)as well as the concentrations of albumin (ALB) and total bilirubin (T.B.) levels in rats administered with acetaminophen only. The levels of these parameters were significantly (p < 0.05) decreased in the groups pretreated with the extract.
Effect of Radiation on Magnetohydrodynamic Two Phase Stenosed Arterial Blood Flow with Heat and Mass Transfer
In blood, the concentration of red blood cell varies with the arterial diameter. In the case of narrow arteries, red blood cells concentrate around the center of the artery and there exists a cell-free plasma layer near the arterial wall due to Fahraeus-Lindqvist effect. Due to non- uniformity of the fluid in the narrow arteries, it is preferable to consider the two-phase model of the blood flow. In the present article, coupled nonlinear differential equations have been developed for momentum, energy and concentration of two phase model of the blood flow assuming the Newtonian fluid in both central core and cell free plasma layer and the exact solutions have been found for the problem. For having an adequate insight into the stenosed arterial two-phase blood flow, major components of the flow as flow resistance, total flow rate, and wall shear stress have been estimated for different values of magnetic and radiation parameter. Results show that the increase in the effects of magnetic field decreases the velocity of both cores as well as plasma regions. This result can be helpful to control the blood flow in narrow arteries during surgical process. Temperature of core as well plasma regions decrease as value of radiation parameter increases. The present result is implemented in the form of radiation therapy which is very helpful for cancer patients.
A Mathematical Analysis of a Model in Capillary Formation: The Roles of Endothelial, Pericyte and Macrophages in the Initiation of Angiogenesis
Our model is based on the theory of reinforced random walks coupled with Michealis-Menten mechanisms which view endothelial cell receptors as the catalysts for transforming both tumor and macrophage derived tumor angiogenesis factor (TAF) into proteolytic enzyme which in turn degrade the basal lamina. The model consists of two main parts. First part has seven differential equations (DE’s) in one space dimension over the capillary, whereas the second part has the same number of DE’s in two space dimensions in the extra cellular matrix (ECM). We connect these two parts via some boundary conditions to move the cells into the ECM in order to initiate capillary formation. But, when does this movement begin? To address this question we estimate the thresholds that activate the transport equations in the capillary. We do this by using steady-state analysis of TAF equation under some assumptions. Once these equations are activated endothelial, pericyte and macrophage cells begin to move into the ECM for the initiation of angiogenesis. We do believe that our results play an important role for the mechanisms of cell migration which are crucial for tumor angiogenesis. Furthermore, we estimate the long time tendency of these three cells, and find that they tend to the transition probability functions as time evolves. We provide our numerical solutions which are in good agreement with our theoretical results.
Identifying Promoters and Their Types Based on a Two-Layer Approach
Prokaryotic promoter, consisted of two short DNA sequences located at in -35 and -10 positions, is responsible for controlling the initiation and expression of gene expression. Different types of promoters have different functions, and their consensus sequences are similar. In addition, their consensus sequences may be different for the same type of promoter, which poses difficulties for promoter identification. Unfortunately, all existing computational methods treat promoter identification as a binary classification task and can only identify whether a query sequence belongs to a specific promoter type. It is desired to develop computational methods for effectively identifying promoters and their types. Here, a two-layer predictor is proposed to try to deal with the problem. The first layer is designed to predict whether a given sequence is a promoter and the second layer predicts the type of promoter that is judged as a promoter. Meanwhile, we also analyze the importance of feature and sequence conversation in two aspects: promoter identification and promoter type identification. To the best knowledge of ours, it is the first computational predictor to detect promoters and their types.
Mutations in MTHFR Gene Associated with Mental Retardation and Cerebral Palsy Combined with Mental Retardation in Erbil City
Folate metabolism plays a crucial role in the normal development of the neonatal central nervous system. It is regulated by MTHFR gene polymorphism. Any factors, which will affect this metabolism either by hereditary or gene mutation will lead to many mental disorders. The purpose of this study was to investigate whether MTHFR gene mutation contributes to the development of mental retardation and CP combined with mental retardation in Erbil city. DNA was isolated from the peripheral blood samples of 40 cases suffering from mental retardation (MR) and CP combined with MR were recruited, sequence the 4, 6, 7, 8 exons of the MTHFR gene were done to identify the variants. Exons were amplified by PCR technique and then sequenced according to Sanger method to show the differences with MTHFR reference sequences. We observed (14) mutations in 4, 6, 7, 8 exons in the MTHFR gene associated with Cerebral Palsy combined with mental retardation included deletion, insertion, Substitution. The current study provides additional evidence that multiple variations in the MTHFR gene are associated with mental retardation and Cerebral Palsy.
Thermal Stabilisation of Poly(a)•Poly(U) by TMPyP4 and Zn(X)TMPyP4 Derivatives in Aqueous Solutions
The duplex Poly(A)-Poly(U) denaturation in an aqueous solutions in mixtures with the tetracationic MeTMPyP4 (Me = 2H, Zn(II); TMPyP4 is 5,10,15,20-tetrakis(N-methylpyridinium-4-yl)porphyrin), was investigated by monitoring the changes in the UV-Vis absorbance spectrum with increasing temperatures from 20°С to 70°С (рН 7.0, I=0.15M). The absorbance data matrices were analyzed with a versatile chemometric procedure that provides the melting profile (distribution of species) and the pure spectrum for each chemical species present along the heating experiment. As revealed by the increase of Tm, the duplex structure was stabilized by these porphyrins. The values of stabilization temperature ΔTm in the presence of these porphyrins are relatively large, 1.2-8.4 °C, indicating that the porphyrins contribute differently in stabilizing the duplex Poly(A)-Poly(U) structure. Remarkable is the fact that the porphyrin TMPyP4 was less effective in the stabilization of the duplex structure than the metalloporphyrin Zn(X)TMPyP4 which suggests that metallization play an important role in porphyrin-RNA binding. Molecular Dynamics Simulations has been used to illustrate melting of the duplex dsRNA bound with a porphyrin molecule.
Ex vitro Rescue, Physiochemical Evaluation, Secondary Metabolite Production and Assessment of Genetic Stability Using DNA Based Molecular Markers in Regenerated Plants of Decalepis salicifolia (Bedd. Ex hook.f.) Venter
Decalepis salicifolia (Bedd. ex Hook.f.) Venter (family- Apocynaceae) is a new source of drug to cure tuberculosis, asthma and intestinal disorders being used extensively in both traditional and modern medicines. Due to ever increasing demands, the over collection leads to the loss of habitats which creates a thrust on natural population of the plant and thus listed to critically endangered categories. To ensure replenishment, a refine protocol for micropropagation was developed using mature nodal explants for D. salicifolia. A high frequency shoot regeneration system was obtained on nutrient medium comprised of Murashige and Skoog (MS) + 6- benzyladenine (BA) (5.0 µM) + α- naphthalene acetic acid (NAA) (0.5 µM) + adenine sulphate (ADS) (30.0 µM) corresponds to a highest mean number of 9.97 ± 0.01 shoots per explants with maximum shoot length of 6.46 ± 0.1 cm. Successful rooting in microshoots was achieved when reduced nutrient supply was used i.e. half strength MS medium fortified with indole-3-butyric acid (IBA) (2.5 µM). A maximum of 6.10 ± 0.07 roots per microshoot with average root length of 2.30 ± 0.06 cm was obtained. As much as 90 % survival of plantlets was reached where SoilriteTM was used as substrate and finally established in soil without any casualty and morphological variation. Acclimatized plantlets were screened for pigment content, net photosynthetic rate (PN), stomatal conductance (Gs) and transpiration rate (E) during subsequent days of acclimatization as well as the changes in antioxidant was evaluated. A steady rise was observed in the activity of superoxide dismutase (SOD) for initial 21 days and then after a decrease was found showing improved acclimatization efficiency of the plant. Similarly, the activities of catalase (CAT), ascorbate peroxidase (APX) and glutathione reductase (GR) enzyme shows reliable increase as the days of acclimatization advanced which play their precautionary role against oxidative damage to the plant. The genetic fidelity of the in vitro raised plantlets with that of mother plant was further confirmed using random amplified polymorphic DNA (RAPD) and interns simple sequence repeats (ISSR) analysis. The remarkable monomorphism affirms the genetic uniformity of micro propagated clones. Additionally, the effect of acclimatization on the biosynthesis of 2-hydroxy-4-methoxybenzaldehyde (2H4MB) in the root system was also evaluated in relation to their biomass production. Maximum fresh weight (4.9 g/plant), dry weight (0.65 g/plant) of roots and 2H4MB content (6.8 µg/ml of root extract) was obtained after 10 weeks of acclimatization. Accelerated multiplication rate with the stability of genetic virtue, physiological and biochemical parameter assure the efficacy of the protocol developed for the propagation of this critically endangered medicinal plant.
NUX: A Lightweight Block Cipher for Security at Wireless Sensor Node Level
This paper proposes an ultra-lightweight cipher NUX. NUX is a generalized Feistel network. It supports 128/80 bit key length and block length of 64 bit. For 128 bit key length, NUX needs only 1022 GEs which is less as compared to all existing cipher design. NUX design results into less footprint area and minimal memory size. This paper presents security analysis of NUX cipher design which shows cipher’s resistance against basic attacks like Linear and Differential Cryptanalysis. Advanced attacks like Biclique attack is also mounted on NUX cipher design. Two different F function in NUX cipher design results in high diffusion mechanism which generates large number of active S-boxes in minimum number of rounds. NUX cipher has total 31 rounds. NUX design will be best-suited design for critical application like smart grid, IoT, wireless sensor network, where memory size, footprint area and the power dissipation are the major constraints.
Anaerobic Digestion Batch Study of Taxonomic Variations in Microbial Communities during Adaptation of Consortium to Different Lignocellulosic Substrates Using Targeted Sequencing
Anaerobic digestion has been widely used for production of methane from different biowastes. However, the complexity of microbial communities involved in the process is poorly understood. The performance of biogas production process concerning the process productivity is closely coupled to its microbial community structure and syntrophic interactions amongst the community members. The present study aims at understanding taxonomic variations occurring in any starter inoculum when acclimatised to different lignocellulosic biomass (LBM) feedstocks relating to time of digestion. The work underlines use of high throughput Next Generation Sequencing (NGS) for validating the changes in taxonomic patterns of microbial communities. Biomethane Potential (BMP) batches were set up with different pretreated and non-pretreated LBM residues using the same microbial consortium and samples were withdrawn for studying the changes in microbial community in terms of its structure and predominance with respect to changes in metabolic profile of the process. DNA of samples withdrawn at different time intervals with reference to performance changes of the digestion process, was extracted followed by its 16S rRNA amplicon sequencing analysis using Illumina Platform. Biomethane potential and substrate consumption was monitored using Gas Chromatography(GC) and reduction in COD (Chemical Oxygen Demand) respectively. Taxonomic analysis by QIIME server data revealed that microbial community structure changes with different substrates as well as at different time intervals. It was observed that biomethane potential of each substrate was relatively similar but, the time required for substrate utilization and its conversion to biomethane was different for different substrates. This could be attributed to the nature of substrate and consequently the discrepancy between the dominance of microbial communities with regards to different substrate and at different phases of anaerobic digestion process. Knowledge of microbial communities involved would allow a rational substrate specific consortium design which will help to reduce consortium adaptation period and enhance the substrate utilisation resulting in improved efficacy of biogas process.
A Kernel-Based Method for MicroRNA Precursor Identification
MicroRNAs (miRNAs) are small non-coding RNA molecules, functioning in transcriptional and post-transcriptional regulation of gene expression. The discrimination of the real pre-miRNAs from the false ones (such as hairpin sequences with similar stem-loops) is necessary for the understanding of miRNAs’ role in the control of cell life and death. Since both their small size and sequence specificity, it cannot be based on sequence information alone but requires structure information about the miRNA precursor to get satisfactory performance. Kmers are convenient and widely used features for modeling the properties of miRNAs and other biological sequences. However, Kmers suffer from the inherent limitation that if the parameter K is increased to incorporate long range effects, some certain Kmer will appear rarely or even not appear, as a consequence, most Kmers absent and a few present once. Thus, the statistical learning approaches using Kmers as features become susceptible to noisy data once K becomes large. In this study, we proposed a Gapped k-mer approach to overcome the disadvantages of Kmers, and applied this method to the field of miRNA prediction. Combined with the structure status composition, a classifier called imiRNA-GSSC was proposed. We show that compared to the original imiRNA-kmer and alternative approaches. Trained on human miRNA precursors, this predictor can achieve an accuracy of 82.34 for predicting 4022 pre-miRNA precursors from eleven species.
High-Throughput Biomolecular Interaction Studies Using Label-Free Microarrays
Precise characterization of biomolecular interactions providing information on thermodynamic and kinetic constants like affinity and on/off rates is mandatory for many life-science applications. Also, the knowledge about specific sequence of the binding site as well as competition between different proteins towards this epitope provides important data for the discovery and development of new therapeutics, vaccines, and diagnostic applications. Label-free technologies are suitable for obtaining all the above-mentioned data. However, current techniques suffer from low throughput and thus require a lot of subsequent measurements, which are time, material and cost consuming. A novel label-free microarray assay using SCORE technology (single colour reflectometry) allows a high-throughput workflow that is compatible with standard microarrays used e.g. in fluorescence applications. Up to 22,500 interactions of an analyte to its targets can be analysed within on single measurement run within some few minutes making it suitable for fast protein-protein interaction characterisation. To demonstrate the versatility of label-free microarrays, an epitope mapping, as well as an epitope binning, were performed on the Biametrics b-screen device and the related advantages compared to common approaches. Epitope mapping was performed on variations of the FLAG epitope on a high-density peptide array. For the epitope binning study, a set of 7 antibody fabs and their spatial epitope arrangement has been investigated. Also, the label-free readout of high-density peptide microarrays using SCORE technology was shown. The binding affinities of the protein Grb2, which is an adaptor protein involved in signal transduction/cell communication and represents an interesting target for anti-tumor agents, to more than 500 target peptides on the microarray, was analysed. Label-free microarrays are an ideal tool for analysing high-density arrays of any kind of biomolecular interactions, ranging from peptides to (recombinant) proteins and antibodies up to whole cells. They are compatible with standard microarrays and printing technologies.
Temperature as a Tool to Enhance Biofuel Characteristics of Indigeneous Chlorella Sorokiniana Integrated with Phycoremediation
All anthropogenic activities generate liquid or gaseous waste which when discharged into the environment, causes pollution of natural resources. Phycoremediation is the process of removing pollutants from aqua-waste using algae which is safe for the environment as well as can be used for recovery of bioresources. The microalgae have an ability to rapidly divide and accumulate lipids while removing nutrient from wastewater and remediating it. The biomass from photosynthetic microalga is a potential feedstock for producing biodiesel. We have screened an indigenous fast growing oleaginous microalga from the wastewater of Neela-Hauz Lake, New Delhi which is a sewage fed urban water body. The strain identity was discerned using the 16S and 18S rDNA and named as Chlorella sorokiniana-I (ICGEB) based on the DNA sequence homology with C. sorokiniana species. The growth kinetics of C. sorokiniana-I was evaluated using different parameters such as dry cell weight, total lipid content and fatty acid methyl ester (FAME) over a range of temperatures and nutrient media. The biomass and fatty acid profiles were observed to vary with variations in growth temperatures and culture media. C. sorokiniana-I showed tolerance to higher temperatures along with significant alterations in the fatty acid profiles. When grown in wastewater, the indigenous C. sorokiniana-I has efficiently removed TN (77%), TP (81%), Fe (67%), Ca (42%), and reduced the chemical oxygen demand (COD) and biological oxygen demand (BOD) and alkalinity by 48%, 47%, 15%, respectively from it. C. sorokiniana-I thrives well at continuous temperatures of 37°C and 40°C and accumulated about 52% higher lipid and two fold higher FAME using wastewater when compared to commercial medium tris acetate phosphate (TAP), which makes it amenable for economic biodiesel feedstock production coupled with remediation of the wastewater.
Hydrothermal Liquefaction for Astaxanthin Extraction from Wet Algae
Algal biomass is not only a potential source for biocrude but also for high value chemicals like carotenoids, fatty acids, proteins, polysaccharides, vitamins etc. Astaxanthin is one such high value vital carotenoid which has extensive applications in pharmaceutical, aquaculture, poultry and cosmetic industries and expanding as dietary supplement to humans. Green microalgae Haematococcus pluvialis is identified as the richest natural source of astaxanthin and is the key source of commercial astaxanthin. Several extraction processes from wet and dry Haematococcus pluvialis biomass have been explored by researchers. Extraction with supercritical CO₂ and various physical disruption techniques like mortar and pestle, homogenization, ultrasonication and ball mill from dried algae are widely used extraction methods. However, these processes require energy intensive drying of biomass that escalates overall costs notably. From the process economics perspective, it is vital to utilize wet processing technology in order to eliminate drying costs. Hydrothermal liquefaction (HTL) is a thermo-chemical conversion process that converts wet biomass containing over 80% water to bio-products under high temperature and high pressure conditions. Astaxanthin is a lipid soluble pigment and is usually extracted along with lipid component. Mild HTL at 200°C and 60 bar has been demonstrated by researchers in a microfluidic platform achieving near complete extraction of astaxanthin from wet biomass. There is very limited work done in this field. An integrated approach of sequential HTL offers cost-effective option to extract astaxanthin/lipid from wet algal biomass without drying algae and also recovering water, minerals and nutrients. This paper reviews past work and evaluates the astaxanthin extraction processes with focus on hydrothermal extraction.
Estimation of Viscoelastic Properties of Thin Film by Numeric Method and Its Application on Estimation of Flattened Cardiac Cells by Atomic Force Microscopy-Based Creep Tests
Nanoindentation technology has proven an effective method to investigate the viscoelastic properties of biological cells, and atomic force microscope is frequently to realize nanoindentation application in biological cells. The experimental data obtained by AFM-based nanoindentation are frequently interpreted by Hertz contact model. However, in order to facilitate the application of Hertz contact model, the indented sample cell is assumed to be semi-infinite such that the substrate does not affect the indentation. However, this assumption does not always hold due to the fact that cell might change their morphology after being removed from their native environment. Most of the popular contact models do not include the correction needed due to stiff bottom substrate influence on the measure properties. Although restricting indentation to the thicker region or apply lower force would result in small indentation depth (within 10% of the sample height) in macro scope, there exists a limit to the minimum force which can be applied in AFM below which the obtained AFM data become unreliable due to low signal to noise ratio. If not accounted for, bottom substrate effect would lead to over-estimation of the measured properties. In this study, a rigorous contact model based upon linear elasticity is developed for the interpretation of indentation tests of flattened cells which represent a factual morphology. The cell, normally bonded to the petri dish, is initially treated as an elastic layer of finite thickness perfectly bonded to a rigid substrate, and the conic indenter is assumed to be frictionless. The theory of linear elasticity is utilized to describe this contact issue which is finally converted into the solution of the Fredholm integral equation of the second kind. To solve this equation, numeric method is utilized, and a semi-analytical solution is developed. The solutions are then extended to viscoelastic situation which is regarded as a good indicator for mechanical properties of biological cells. To apply the present model, an AFM-based creep test is conducted on living myocardial cell (H9C2(2-1) cell) and its colchicine-treated counterpart. The result indicates that the present model could not only describe very well the creep behavior of H9C2(2-1)cells but can also curb overestimation of the mechanical properties due to substrate effect. The semi-analytical expression of the model can help in estimating more realistic biomechanical properties of cells from atomic force microscopy based indentation technique. Moreover, the present model could identify the difference between the control and treated H9C2(2-1) cells in terms of the extracted viscoelastic parameters, suggesting its biomechanics potential in revealing the biomechanical effects of colchicine-like drug treatment on cardiac cells.
Study of Biomechanical Model for Smart Sensor Based Prosthetic Socket Design System
Prosthetic socket is a component that connects the residual limb of an amputee with an artificial prosthesis. It is widely recognized as the most critical component that determines the comfort of a patient when wearing the prosthesis in his/her daily activities. Through the socket, the body weight and its associated dynamic load are distributed and transmitted to the prosthesis during walking, running or climbing. In order to achieve a good-fit socket for an individual amputee, it is essential to obtain the biomechanical properties of the residual limb. In current clinical practices, this is achieved by a touch-and-feel approach which is highly subjective. Although there have been significant advancements in prosthetic technologies such as microprocessor controlled knee and ankle joints in the last decade, the progress in designing a comfortable socket has been rather limited. This means that the current process of socket design is still very time-consuming, and highly dependent on the expertise of the prosthetist. Supported by the state-of-the-art sensor technologies and numerical simulations, a new socket design system is being developed to help prosthetists achieve rapid design of comfortable sockets for above knee amputees. This paper reports the research work related to establishing biomechanical models for socket design. Through numerical simulation using finite element method, comprehensive relationships between pressure on residual limb and socket geometry were established. This allowed local topological adjustment for the socket so as to optimize the pressure distributions across the residual limb. When the full body weight of a patient is exerted on the residual limb, high pressures and shear forces between the residual limb and the socket occur. During numerical simulations, various hyperplastic models, namely Ogden, Yeoh and Mooney-Rivlin, were used, and their effectiveness in representing the biomechanical properties of soft tissues of the residual limb was evaluated. This also involved reverse engineering, which resulted in an optimal representative model under compression test. To validate the simulation results, a range of silicone models were fabricated. They were tested by an indentation device which yielded the force-displacement relationships. Comparisons of results obtained from FEA simulations and experimental tests showed that the Ogden model did not fit well the soft tissue material indentation data, while the Yeoh model gave the best representation of the soft tissue mechanical behavior under indentation. Compared with hyperplastic model, the result showed that elastic model also had significant errors. In addition, normal and shear stress distributions on the surface of the soft tissue model were obtained. The effect of friction in compression testing and the influence of soft tissue stiffness and testing boundary conditions were also analyzed. All these have contributed to the overall goal of designing a good-fit socket for individual above knee amputees.
Bile Salt Induced Microstructural Changes of Gemini Surfactant Micelles
Microstructural evolution of a cationic gemini surfactant 12-4-12 micelles in the presence of bile salts has been investigated using different techniques. A negative value of interaction parameter evaluated from surface tension measurements is a signature of strong synergistic interaction between oppositely charged surfactants. Both the bile salts compete with each other in inducing the micellar transition of 12-4-12 micelles depending on their hydrophobicity. Viscosity measurements disclose that loading of bile salts induces morphological changes in 12-4-12 micelles; sodium deoxycholate is more efficient in altering the aggregation behaviour of 12-4-12 micelles compared to sodium cholate and presents pronounced increase in viscosity and micellar growth which is suppressed at elevated temperatures. A remarkable growth of 12-4-12 micelles in the presence of sodium deoxycholate at low pH has been ascribed to the solubilization of bile acids formed in acidic medium. Small angle neutron scattering experiments provided size and shape of 12-4-12/bile salt mixed micelles are explicated on the basis of hydrophobicity of bile salts. The location of bile salts in micelle was determined from nuclear overhauser effect spectroscopy. The present study characterizes 12-4-12 gemini-bile salt mixed systems which significantly enriches our knowledge, and such a structural transition provides an opportunity to use these bioamphiphiles as delivery vehicles and in some pharmaceutical formulations.
Reintroduction and in vitro Propagation of Declapeis arayalpathra: A Critically Endangered Plant of Western Ghats, India
The present studies describe a protocol for high frequency in vitro propagation through nodal segments and shoot tips in D. arayalpathra, a critically endangered medicinal liana of the Western Ghats, India. Nodal segments were more responsive than shoot tips in terms of shoot multiplication. Murashige and Skoog’s (MS) basal medium supplemented with 2.5 µM 6-benzyladenine (BA) was optimum for shoot induction through both the explants. Among different combinations of plant growth regulator (PGRs) and growth additive screened, MS medium supplemented with BA (2.5 µM) + indole-3-acetic acid (IAA) (0.25 µM) + adenine sulphate (ADS) (10.0 µM) induced a maximum of 9.0 shoots per nodal segment and 3.9 shoots per shoot tip with mean shoot length of 8.5 and 3.9 cm respectively. Half-strength MS medium supplemented with Naphthaleneacetic acid (NAA) (2.5 µM) was the best for in vitro root induction. After successful acclimatization in SoilriteTM, 92 % plantlets were survived in field conditions. Acclimatized plantlets were studied for chlorophyll and carotenoid content, net photosynthetic rate (PN) and related attributes such as stomatal conductance (Gs) and transpiration rate during subsequent days of acclimatization. The rise and fall of different biochemical enzymes (SOD, CAT, APX and GR) were also studies during successful days of acclimatization. Moreover, the effect of acclimatization on the synthesis of 2-hydroxy-4-methoxy benzaldehyde (2H4MB) was also studied in relation to the biomass production. Maximum fresh weight (2.8 gm/plant), dry weight (0.35 gm/plant) of roots and 2H4MB content (8.5 µg/ ml of root extract) were recorded after 8 weeks of acclimatization. The screening of in vitro raised plantlet root was also carried out by using GC-MS analysis which witnessed more than 25 compounds. The regenerated plantlets were also screened for homogeneity by using RAPD and ISSR. The proposed protocol surely can be used for the conservation and commercial production of the plant.
Molecular Characterization, Host Plant Resistance and Epidemiology of Bean Common Mosaic Virus Infecting Cowpea (Vigna unguiculata L. Walp)
The identification of virus in cowpea especially potyviruses is confusing. Even though there are several studies on viruses causing diseases in cowpea, difficult to distinguish based on symptoms and serological detection. The differentiation of potyviruses considering as a constraint, the present study is initiated for molecular characterization, host plant resistance and epidemiology of the BCMV infecting cowpea. The etiological agent causing cowpea mosaic was identified as Bean Common Mosaic Virus (BCMV) on the basis of RT-PCR and electron microscopy. An approximately 750bp PCR product corresponding to coat protein (CP) region of the virus and the presence of long flexuous filamentous particles measuring about 952 nm in size typical to genus potyvirus were observed under electron microscope. The characterized virus isolate genome had 10054 nucleotides, excluding the 3’ terminal poly (A) tail. Comparison of polyprotein of the virus with other potyviruses showed similar genome organization with 9 cleavage sites resulted in 10 functional proteins. The pairwise sequence comparison of individual genes, P1 showed most divergent, but CP gene was less divergent at nucleotide and amino acid level. A phylogenetic tree constructed based on multiple sequence alignments of the polyprotein nucleotide and amino acid sequences of cowpea BCMV and potyviruses showed virus is closely related to BCMV-HB. Whereas, Soybean variant of china (KJ807806) and NL1 isolate (AY112735) showed 93.8 % (5’UTR) and 94.9 % (3’UTR) homology respectively with other BCMV isolates. This virus transmitted to different leguminous plant species and produced systemic symptoms under greenhouse conditions. Out of 100 cowpea genotypes screened, three genotypes viz., IC 8966, V 5 and IC 202806 showed immune reaction in both field and greenhouse conditions. Single marker analysis (SMA) was revealed out of 4 SSR markers linked to BCMV resistance, M135 marker explains 28.2 % of phenotypic variation (R2) and Polymorphic information content (PIC) value of these markers was ranged from 0.23 to 0.37. The correlation and regression analysis showed rainfall, and minimum temperature had significant negative impact and strong relationship with aphid population, whereas weak correlation was observed with disease incidence. Path coefficient analysis revealed most of the weather parameters exerted their indirect contributions to the aphid population and disease incidence except minimum temperature. This study helps to identify specific gaps in knowledge for researchers who may wish to further analyse the science behind complex interactions between vector-virus and host in relation to the environment. The resistant genotypes identified are could be effectively used in resistance breeding programme.