A mixed-flow model for heterogeneous vehicles enforcing a movement control protocol utilizing a vehicular size-based equilibrium speed function.

This work addressed the effect of heterogeneous vehicle sizes on traffic flow fields by introducing a movement control protocol. Considering a continuum traffic model, a new equilibrium velocity function that is dependent on traffic density was introduced to account for the effect of vehicle size. The established model showed a quantitative comparison between the Optimal Velocity and Full Velocity Difference models. A neutral stability test was carried out to evaluate the model's capability of neutralizing flow fields. The density wave behavior near a critical point was portrayed by deducing the Korteweg-de Vries-Burgers equation through a nonlinear analysis. A series of numerical simulations, the outcomes of which agreed well with the analytical results, was performed to observe the overall flow field scenario.

An improved microscopic traffic model for heterogeneous vehicles using the vehicle's mass effect.

This study aims to develop a traffic model for heterogeneous vehicle movement, which introduces the vehicle's heterogeneity by considering the internal mass effect. We explore the behavioral characteristics of the flow field generated by the proposed model and provide a comparative analysis of the conventional model. A linear stability condition is deduced to showcase the model's capacity to neutralize flow. Nonlinear analysis is employed to derive the modified Korteweg-de Vries (mKdV) equation and its corresponding analytical solution, enabling the observation of traffic flow behavior in proximity to the neutral stability condition. A numerical simulation is then conducted, considering cyclic boundary conditions. The results indicate that the mass effect tends to absorb traffic jams provided no time delay is imposed.

UV-Visible-NIR camouflage textiles with natural plant based natural dyes on natural fibre against woodland combat background for defence protection.

Woodland combat background (CB) is a common source of natural plant based natural dyes (NPND). Swietenia Macrophylla, Mangifera Indica, Terminalia Arjuna, Corchorus Capsularis, Camellia Sinensis, Azadirachta Indica, Acacia Acuminata, Areca Catechu and Cinnamomum Tamala were dried-grinded-powdered-extracted-polyaziridine encapsulated-dyed-coated-printed with leafy design on cotton fabric and tested against woodland CB under the reflection engineering of ultraviolet (UV)-visible (Vis)-near infrared (NIR) spectrums and photographic versus chromatic techniques of Vis imaging. The reflection properties of NPND treated and untreated cotton fabric were experimented by UV-Vis-NIR spectrophotometer from 220 to 1400 nm. Six segments of field trialling for NPND treated woodland camouflage textiles were also investigated for concealment, detection, recognition and identification of target signature against forest plants/herbs species; common tree of woodland CB such as Shorea Robusta Gaertn, Bamboo Vulgaris, Musa Acuminata; and a wooden bridge made by Eucalyptus Citriodora & Bamboo Vulgaris. The imaging properties such as CIE L*, a*, b* and RGB (red, green, blue) of NPND treated cotton-garments were captured by digital camera from 400 to 700 nm against tree stem/bark, dry leaves, green leaves and dry wood of woodland CB. Therefore, a colorful matching for concealment, detection, recognition and identification of target signature against woodland CB was verified by Vis camera imaging and UV-Vis-NIR reflection mechanism. UV-protection property of Swietenia Macrophylla treated cotton fabric was also investigated by diffuse reflection for defence clothing. Simultaneous 'camouflage textiles in UV-Vis-NIR' and 'UV-protective' property of Swietenia Macrophylla treated fabric have been investigated for NPND materials-based textiles coloration (dyeing-coating-printing) which is a new concept for camouflage formulation of NPND dyed-NPND mordanted-NPND coated-NPND printed textiles in terms of ecofriendly source of woodland camouflage materials. Therefore, technical properties of NPND materials and methodologies of camouflage textile assessment have been advanced in addition to coloration philosophy of natural dyed-coated-printed textiles.

A dynamical traffic flow model for a cognitive drivers' sensitivity in Lagrangian scope.

A new microscopic traffic flow model is established based on heterogeneous driver's sensitivity; in this new model, the driver's sensitivity is defined as being dependent on the headway distances to the preceding vehicle, similar to Bando's optimal velocity function. We introduce the formulation of this cognitive driver's sensitivity utilizing a modified form of Bando's optimal velocity function. A simple methodology, which is used for improving Bando's optimal velocity function, has been implemented for developing the cognitive driver's sensitivity function, which establishes a correlation between the flow field's density and human drivers' responses. The model is highly advanced for introducing a human-driven traffic flow field considering the driver's mental behavioral activity. Using the linear stability condition, we elucidate a neutral stability condition. A series of numerical simulations indicates how the present model describes dynamics that differ from the conventional model, which assumes a constant driver's sensitivity.

Characterization and expression in Pichia pastoris of a raw starch degrading glucoamylase (GA2) derived from Aspergillus flavus NSH9.

The Aspergillus flavus NSH9 gene, encoding a pH and thermostable glucoamylase with a starch binding domain (SBD), was expressed in Pichia pastoris to produce recombinant glucoamylase (rGA2). The full-length glucoamylase gene (2039 bp), and cDNA (1839 bp) encode a 612 amino acid protein most similar to glucoamylase from Aspergillus oryzae RIB40; the first 19 amino acids are presumed to be a signal peptide for secretion, and the SBD is at the C-terminal. The cDNA was successfully secreted by Pichia at 8.23 U mL-1, and the rGA2 was found to be: a 80 kDa monomer, stable from pH 3.0-9.0, with optimum catalytic activity at pH 5.0, active at temperatures up to 80°C (rGA2 retained 58% of its activity after 60 min of incubation at 70°C), and metal ions such as Na+, K+, Ca++ and Mg++ enhanced rGA2 enzyme activity. The starch degrading ability of rGA2 was also observed on raw sago starch and where prolonged incubation generated larger, deeper, holes on the starch granules, indicating rGA2 is an excellent candidate for industrial starch processing applications.

Molecular characterization of second tomato α1,3/4-fucosidase (α-Fuc'ase Sl-2), a member of glycosyl hydrolase family 29 active toward the core α1,3-fucosyl residue in plant N-glycans.

In a previous study, we molecular-characterized a tomato (Solanum lycopersicum) α1, 3/4-fucosidase (α-Fuc'ase Sl-1) encoded in a tomato gene (Solyc03g006980), indicating that α-Fuc'ase Sl-1 is involved in the turnover of Lea epitope-containing N-glycans. In this study, we have characterized another tomato gene (Solyc11g069010) encoding α1, 3/4-fucosidase (α-Fuc'ase Sl-2), which is also active toward the complex type N-glycans containing Lea epitope(s). The baculovirus-insect cell expression system was used to express that α-Fuc'ase Sl-2 with anti-FLAG tag, and the expression product (rFuc'ase Sl-2), was found as a 65 kDa protein using SDS-PAGE and has an optimum pH of around 5.0. Similarly to rFuc'ase Sl-1, rFuc'ase Sl-2 hydrolyzed the non-reducing terminal α1, 3-fucose residue on LNFP III and α1, 4-fucose residues of Lea epitopes on plant complex type N-glycans, but not the core α1, 3-fucose residue on Manß1-4GlcNAcß1-4(Fucα1-3)GlcNAc or Fucα1-3GlcNAc. However, we found that both α-Fuc'ases Sl-1 and Sl-2 were specifically active toward α1, 3-fucose residue on GlcNAcß1-4(Fucα1-3)GlcNAc, indicating that the non-substituted ß-GlcNAc linked to the proximal GlcNAc residue of the core tri-saccharide moiety of plant specific N-glycans must be a pre-requisite for α-Fuc'ase activity. A 3 D modelled structure of the catalytic sites of α-Fuc'ase Sl-2 suggested that Asp192 and Glu236 may be important for binding to the α1, 3/4 fucose residue.

Molecular characterization of tomato α1,3/4-fucosidase, a member of glycosyl hydrolase family 29 involved in the degradation of plant complex type N-glycans.

In this study, we identified a gene in tomato that encodes an acidic α-fucosidase (LOC101254568 or Solyc03g006980, α-Fuc'ase S1-1), which may be involved in the turnover of plant complex-type N-glycans. Recombinant α-Fuc'ase S1-1 (rFuc'ase S1-1) was expressed using a baculovirus-insect cell expression system. rFuc'ase Sl-1 is 55 kDa in size and has an optimum pH around 4.5. It substantially hydrolyzed the non-reducing terminal α1,3-fucose residue on LNFP III and α1,4-fucose residues of Lea epitopes on plant complex-type N-glycans, but not the α1,2-fucose residue on LNFP I or the α1,3-fucose residue on pyridylaminated Fucα1-3GlcNAc. Furthermore, we found that this tomato α-Fuc'ase S1-1 was inactive toward the core penta-oligosaccharide unit [Manß1-4(Xylß1-2)GlcNAcß1-4(Fucα1-3)GlcNAc-PA] of plant complex-type N-glycans. Molecular 3D modelling of α-Fuc'ase Sl-1 and structure/sequence interpretation based on comparison with a homologous α-fucosidase from Bifidobacterium longum subsp. infantis (Blon_2336) indicated that residues Asp193 and Glu237 might be important for substrate binding.

Molecular And 3D-Structural Characterization Of Fructose-1,6-Bisphosphate Aldolase Derived From Metroxylon Sagu

ABSTRACT Fructose-1,6-bisphosphate aldolase (FBAld) is an enzyme that catalyzes the cleavage of D-fructose-1,6-phosphate (FBP) to D-glyceraldehyde-3-phosphate (G3P) and dihydroxyacetone phosphate (DHAP), and plays vital role in glycolysis and gluconeogenesis. However, molecular characterization and functional roles of FBAld remain unknown in sago palm. Here we report a modified CTAB-RNA extraction method was developed for the isolation of good quality RNA (RIN>8) from sago leaves and the isolation of FBAld cDNA from sago palm. The isolated sago FBAld (msFBAld) cDNA has total length of 1288 bp with an open reading frame of 1020 bp and a predicted to encode for a protein of 340 amino acid resides. The predicted protein shared a high degree of homology with Class-I FBAld from other plants. Meanwhile, the msFBAld gene spanned 2322 bp and consisted of five exons. Conserved domain search identified fifteen catalytically important amino acids at the active site and phylogenetic tree revealed localization of msFBAld in the chloroplast. A molecular 3D-structure of msFBAld was generated by homology modeling and a Ramachandran plot with 86.7% of the residues in the core region, 13.4% in the allowed region with no residues in the disallowed region. The modeled structure is a homotetramer containing an (/(-TIM-barrel at the center. Superimposition of the model with Class-I aldolases identified a catalytic dyad, Lys209-Glu167, which could be involved in the Schiff's base formation and aldol condensation. Apart from that, overproduction of the recombinant msFBAld in Escherichia coli resulted in increased tolerance towards salinity.

Heterologous, Expression, and Characterization of Thermostable Glucoamylase Derived from Aspergillus flavus NSH9 in Pichia pastoris.

A novel thermostable glucoamylase cDNA without starch binding domain (SBD) of Aspergillus flavus NSH9 was successfully identified, isolated, and overexpressed in Pichia pastoris GS115. The complete open reading frame of glucoamylase from Aspergillus flavus NSH9 was identified by employing PCR that encodes 493 amino acids lacking in the SBD. The first 17 amino acids were presumed to be a signal peptide. The cDNA was cloned into Pichia pastoris and the highest expression of recombinant glucoamylase (rGA) was observed after 8 days of incubation period with 1% methanol. The molecular weight of the purified rGA was about 78 kDa and exhibited optimum catalytic activity at pH 5.0 and temperature of 70°C. The enzyme was stable at higher temperature with 50% of residual activity observed after 20 min at 90°C and 100°C. Low concentration of metal (Mg(++), Fe(++), Zn(++), Cu(++), and Pb(++)) had positive effect on rGA activity. This rGA has the potential for use and application in the saccharification steps, due to its thermostability, in the starch processing industries.

Momordica charantia seed lectin: toxicity, bacterial agglutination and antitumor properties.

In last three decades, several studies were carried out on the D-galactose-specific lectin of Momordica charantia seeds (MCL). In the present study, in vitro growth inhibition (8-23 %) at different concentrations (6-24 µg/ml) of MCL was observed against Ehrlich ascites carcinoma (EAC) cells by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. MCL also showed 28, 45, and 75 % growth inhibitions against EAC cells when administered 1.2, 2.0, and 2.8 mg/kg/day (i.p.), respectively for five consequent days in vivo in mice. After lectin treatment, the level of red blood cell and hemoglobin was increased significantly with the decrease of white blood cell and maintained the normal level when compared with EAC-bearing control and normal mice without EAC cells. Although MCL caused cell cycle arrest at G0/G1 phase of EAC cells, any irregular shape or apoptotic morphological alterations in the lectin-treated EAC cells was not observed by an optical and fluorescence microscope. Lectin showed toxicity against brine shrimp nauplii with an LC50 value of 49.7 µg/ml. Four out of seven pathogenic bacteria were agglutinated by MCL in the absence of inhibitory sugar D-lactose/D-galactose. In conclusion, MCL showed strong cytotoxic effect and therefore can be used as a potent anticancer chemotherapeutic agent.

Genetic transformation of Metroxylon sagu (Rottb.) cultures via Agrobacterium-mediated and particle bombardment.

Sago palm (Metroxylon sagu) is a perennial plant native to Southeast Asia and exploited mainly for the starch content in its trunk. Genetic improvement of sago palm is extremely slow when compared to other annual starch crops. Urgent attention is needed to improve the sago palm planting material and can be achieved through nonconventional methods. We have previously developed a tissue culture method for sago palm, which is used to provide the planting materials and to develop a genetic transformation procedure. Here, we report the genetic transformation of sago embryonic callus derived from suspension culture using Agrobacterium tumefaciens and gene gun systems. The transformed embryoids cells were selected against Basta (concentration 10 to 30 mg/L). Evidence of foreign genes integration and function of the bar and gus genes were verified via gene specific PCR amplification, gus staining, and dot blot analysis. This study showed that the embryogenic callus was the most suitable material for transformation as compared to the fine callus, embryoid stage, and initiated shoots. The gene gun transformation showed higher transformation efficiency than the ones transformed using Agrobacterium when targets were bombarded once or twice using 280 psi of helium pressure at 6 to 8 cm distance.

Changes in biochemical characteristics and activities of ripening associated enzymes in mango fruit during the storage at different temperatures.

As a part of the study to explore the possible strategy for enhancing the shelf life of mango fruits, we investigated the changes in biochemical parameters and activities of ripening associated enzymes of Ashwina hybrid mangoes at 4-day regular intervals during storage at -10°C, 4°C, and 30 ± 1°C. Titratable acidity, vitamin C, starch content, and reducing sugar were higher at unripe state and gradually decreased with the increasing of storage time at all storage temperatures while phenol content, total soluble solid, total sugar, and nonreducing sugar contents gradually increased. The activities of amylase, α-mannosidase, α-glucosidase, and invertase increased sharply within first few days and decreased significantly in the later stage of ripening at 30 ± 1°C. Meanwhile polyphenol oxidase, ß-galactosidase, and ß-hexosaminidase predominantly increased significantly with the increasing days of storage till later stage of ripening. At -10°C and 4°C, the enzymes as well as carbohydrate contents of storage mango changed slightly up to 4 days and thereafter the enzyme became fully dormant. The results indicated that increase in storage temperature and time correlated with changes in biochemical parameters and activities of glycosidases suggested the suppression of ß-galactosidase and ß-hexosaminidase might enhance the shelf life of mango fruits.

Molecular phylogeny and predicted 3D structure of plant beta-D-N-acetylhexosaminidase.

beta-D-N-Acetylhexosaminidase, a family 20 glycosyl hydrolase, catalyzes the removal of ß-1,4-linked N-acetylhexosamine residues from oligosaccharides and their conjugates. We constructed phylogenetic tree of ß-hexosaminidases to analyze the evolutionary history and predicted functions of plant hexosaminidases. Phylogenetic analysis reveals the complex history of evolution of plant ß-hexosaminidase that can be described by gene duplication events. The 3D structure of tomato ß-hexosaminidase (ß-Hex-Sl) was predicted by homology modeling using 1now as a template. Structural conformity studies of the best fit model showed that more than 98% of the residues lie inside the favoured and allowed regions where only 0.9% lie in the unfavourable region. Predicted 3D structure contains 531 amino acids residues with glycosyl hydrolase20b domain-I and glycosyl hydrolase20 superfamily domain-II including the (ß/α)8 barrel in the central part. The α and ß contents of the modeled structure were found to be 33.3% and 12.2%, respectively. Eleven amino acids were found to be involved in ligand-binding site; Asp(330) and Glu(331) could play important roles in enzyme-catalyzed reactions. The predicted model provides a structural framework that can act as a guide to develop a hypothesis for ß-Hex-Sl mutagenesis experiments for exploring the functions of this class of enzymes in plant kingdom.

Purification and characterization of a Ca(2+)-dependent novel lectin from Nymphaea nouchali tuber with antiproliferative activities.

A lectin (termed NNTL) was purified from the extracts of Nymphaea nouchali tuber followed by anion-exchange chromatography on DEAE-cellulose, hydrophobic chromatography on HiTrap Phenyl HP and by repeated anion-exchange chromatography on HiTrap Q FF column. The molecular mass of the purified lectin was 27.0 ± 1.0 kDa, as estimated by SDS/PAGE both in the presence and in the absence of 2-mercaptoethanol. NNTL was an o-nitrophenyl ß-D-galactopyranoside sugar-specific lectin that agglutinated rat, chicken and different groups of human blood cells and exhibited high agglutination activity over the pH range 5-9 and temperatures of 30-60 °C. The N-terminal sequence of NNTL did not show sequence similarity with any other lectin and the amino acid analysis revealed that NNTL was rich in leucine, methionine and glycine residues. NNTL was a glycoprotein containing 8% neutral sugar and showed toxicity against brine shrimp nauplii with an LC(50) value of 120 ± 29 µg/ml and exerted strong agglutination activity against four pathogenic bacteria (Bacillus subtilis, Sarcina lutea, Shigella shiga and Shigella sonnei). In addition, antiproliferative activity of this lectin against EAC (Ehrlich ascites carcinoma) cells showed 56% and 76% inhibition in vivo in mice at 1.5 and 3 mg·kg(-1)·day(-1) respectively. NNTL was a divalent ion-dependent glycoprotein, which lost its activity markedly in the presence of denaturants. Furthermore, measurement of fluorescence spectra in the presence and absence of urea and CaCl(2) indicated the requirement of Ca(2+) for the stability of NNTL.

Molecular characterization of plant acidic alpha-mannosidase, a member of glycosylhydrolase family 38, involved in the turnover of N-glycans during tomato fruit ripening.

It has been reported that acidic α-mannosidase activity increases during tomato fruit ripening, suggesting the turnover of N-glycoproteins is deeply associated with fruit ripening. As part of a study to reveal the relationship between the plant α-mannosidase activity and fruit maturation at the molecular level, we have already purified and characterized an α-mannosidase from tomato fruit (Hossain et al., Biosci. Biotechnol. Biochem. 2009;73:140-146). In this article, we describe the identification and expression of the tomato acidic α-mannosidase gene using the yeast-expression system. The α-mannosidase-gene located at chomosome 6 is a 10 kb spanned containing 30 exons. The gene-encoded-protein is single polypeptide chain of 1,028 amino acids containing glycosyl hydrolase domain-38 with predicted molecular mass of 116 kDa. The recombinant enzyme showed maximum activity at pH 5.5, and was almost completely inhibited by both of 1-deoxymannojirimycin and swainsonine. The recombinant α-mannosidase, like the native enzyme, could cleave α1-2, 1-3 and 1-6 mannosidic linkage from both high-mannose and truncated complex-type N-glycans. A molecular 3D modelling shows that catalytically important residues of animal lysosomal α-mannosidase could be superimposed on those of tomato α-mannosidase, suggesting that active site conformation is highly conserved between plant acidic α-mannosidase and animal lysosomal α-mannosidase.

Molecular identification and characterization of an acidic peptide:N-glycanase from tomato (Lycopersicum esculentum) fruits.

Plant acidic peptide:N-glycanase (PNGase) is one of the deglycosylation enzymes and has been considered to be involved in the catabolism of glycoproteins in plant cells. However, the tangible physiological significance involved in plant differentiation or growth is yet unclear. In this study, as a first step to elucidate the physiological role of free N-glycans and the de-N-glycosylation machinery working in developing plant cells, we have succeeded in expressing a cDNA from tomato fruits in Pichia pastoris and identified an acidic peptide:N-glycanase in the culture supernatant. The PNGase-gene-encoded protein is a single polypeptide chain of 588 amino acids with a predicted molecular mass of 65.8 kDa. The deduced amino acid sequence showed 57.9% similarity with almond PNGase A. The recombinant tomato PNGase showed optimum activity at pH 4.5 and 40 degrees C. It did not require any metal ions for full enzymatic activity and could release the complex-type N-glycan from glycopeptides. Our phylogenetic analysis reveals that the plant acidic PNGase is completely different from the ubiquitous cytosolic PNGase and is involved in a different de-N-glycosylation mechanism associated with plant growth and development.

alpha-mannosidase involved in turnover of plant complex type N-glycans in tomato (Lycopersicum esculentum) fruits.

In this study, we purified and characterized an alpha-mannosidase to homogeneity from mature red tomato fruits. Purified alpha-mannosidase (alpha-Man LE-1) gave two separate bands, of molecular masses of 70 kDa (L-subunit) and 47 kDa (S-subunit), on SDS-PAGE under non-reducing and reducing conditions. On the other hand, the molecular weight was estimated to be 230 kDa by gel filtration, indicating that alpha-Man LE-1 functions in a tetrameric structure in plant cells. The N-terminal sequence of the L-subunit and the S-subunit were determined to be L-Y-M-V-Y-M-T-K-Q-G- and X-X-L-E-Q/K-S-F-S-Y-Y respectively. When pyridylaminated N-glycans were used as substrates, alpha-Man LE-1 showed optimum activity at about pH 6 and at 40 degrees C, and the activity was completely inhibited by both swainsonine and 1-deoxy-mannojirimycin. alpha-Man LE-1 hydrolyzed the alpha-mannosidic linkages from both high-mannose type and plant complex type N-glycan, but preferred a truncated plant complex type structure to high-mannose type N-glycans bearing alpha1-2 mannosyl residues.

Clinical value of Tubex and Typhidot rapid diagnostic tests for typhoid fever in an urban community clinic in Bangladesh.

Tubex and Typhidot, rapid tests for typhoid fever, performed well in evaluations conducted in hospital settings among patients with culture-confirmed typhoid fever. We evaluated these tests in a community clinic in Bangladesh. Blood samples were obtained from 867 febrile patients for culture, Typhidot and Tubex tests. Considering the 43 blood culture-confirmed cases of typhoid fever as typhoid positive and the 24 other confirmed bacteremia cases as typhoid negative, Tubex was 60% sensitive and 58% specific, with 90% positive and 58% negative predictive values (NPVs); Typhidot was 67% sensitive and 54% specific, with 85% positive and 81% NPVs. When blood culture-negative patients and other bacteremia cases together were considered typhoid negative, positive predictive values were only 14% for Tubex and 13% for Typhidot, increasing to only 38% and 20% when restricted to patients with > or = 7 days of fever. We conclude that the value of Tubex and Typhidot tests for typhoid fever diagnosis in a community clinic in urban Bangladesh is low.