Molecular identification and evolutionary relationships between the subspecies of Musa by DNA barcodes

BACKGROUND

The banana (Musa sp., AAA) genome is constantly increasing due to high-frequency of somaclonal variations. Due to its large diversity, a conventional numerical and morphological based taxonomic identification of banana cultivars is laborious, difficult and often leads to subject of disagreements.

RESULTS

Hence, in the present study, we used universal DNA barcode ITS2 region to identify and to find the genetic relationship between the cultivars and varieties of banana. Herein, a total of 16 banana cultivars were PCR amplified using ITS2 primer pair. In addition, 321 sequences which were retrieved from GenBank, USA, were used in this study. The sequences were then aligned using Clustal W and genetic distances were computed using MEGA V5.1. The study showed significant divergence between the intra- and inter-specific genetic distances in ITS2 region. BLAST1 and Distance methods proved that ITS2 DNA barcode region successfully identified and distinguished the cultivar and varieties of banana.

CONCLUSION

Thus, from the results of the present study, it is clear that ITS2 is not only an efficient DNA barcode to identify the banana species but also a potential candidate for enumerating the phylogenetic relationships between the subspecies and cultivars. This is the first comprehensive study to categorically distinguish the economically important banana subspecies and varieties using DNA barcodes and to understand its evolutionary relationship.

Corrigendum to: In silico characterisation and functional validation of chilling tolerant divergence 1 (COLD1) gene in monocots during abiotic stress

The G protein-coupled receptor is one of the major transmembrane proteins in plants. It consists of an α subunit, a β subunit and three γ subunits. Chilling tolerant divergence 1 (COLD1) includes a Golgi pH receptor (GPHR) domain, which maintains cell membrane organisation and dynamics, along with abscisic acid linked G protein-coupled receptor (ABA_GPCR) that regulates the signalling pathways during cold stress. In the present study, we performed characterisation of a homologous COLD1 from the economically important monocot species Oryza sativa L., Zea mays L., Sorghum bicolor (L.)Moench and Erianthus arundinaceus (L.) Beauv. IK 76-81, a wild relative of Saccharum. COLD1 was isolated from E. arundinaceus IK 76-81, analysed for its evolution, domain, membrane topology, followed by prediction of secondary, tertiary structures and functionally validated in all four different monocots. Gene expression studies of COLD1 revealed differential expression under heat, drought, salinity and cold stresses in selected monocots. This is the first study on regulation of native COLD1 during abiotic stress in monocots, which has opened up new leads for trait improvement strategies in this economically important crop species.

In silico characterisation and functional validation of chilling tolerant divergence 1 (COLD1) gene in monocots during abiotic stress

The G protein-coupled receptor is one of the major transmembrane proteins in plants. It consists of an α subunit, a β subunit and three γ subunits. Chilling tolerant divergence 1 (COLD1) includes a Golgi pH receptor (GPHR) domain, which maintains cell membrane organisation and dynamics, along with abscisic acid linked G protein-coupled receptor (ABA_GPCR) that regulates the signalling pathways during cold stress. In the present study, we performed characterisation of a homologous COLD1 from the economically important monocot species Oryza sativa L., Zea mays L., Sorghum bicolor (L.)Moench and Erianthus arundinaceus (L.) Beauv. IK 76-81, a wild relative of Saccharum. COLD1 was isolated from E. arundinaceus IK 76-81, analysed for its evolution, domain, membrane topology, followed by prediction of secondary, tertiary structures and functionally validated in all four different monocots. Gene expression studies of COLD1 revealed differential expression under heat, drought, salinity and cold stresses in selected monocots. This is the first study on regulation of native COLD1 during abiotic stress in monocots, which has opened up new leads for trait improvement strategies in this economically important crop species.

A nanocrystalline CdS thin film as a heterogeneous, recyclable catalyst for effective synthesis of dihydropyrimidinones and a new class of carbazolyl dihydropyrimidinones via an improved Biginelli protocol

An improved Biginelli protocol for the efficient synthesis of a new class of carbazolyl dihydropyrimidinones mediated by CdS thin film nanoparticles deposited on the inner walls of a glass reactor as a recyclable, heterogeneous catalyst.

[Advances in Molecular Cloning]

"Molecular cloning" meaning creation of recombinant DNA molecules has impelled advancement throughout life sciences. DNA manipulation has become easy due to powerful tools showing exponential growth in applications and sophistication of recombinant DNA technology. Cloning genes has become simple what led to an explosion in the understanding of gene function by seamlessly stitching together multiple DNA fragments or by the use of swappable gene cassettes, maximizing swiftness and litheness. A novel archetype might materialize in the near future with synthetic biology techniques that will facilitate quicker assembly and iteration of DNA clones, accelerating the progress of gene therapy vectors, recombinant protein production processes and new vaccines by in vitro chemical synthesis of any in silico-specified DNA construct. The advent of innovative cloning techniques has opened the door to more refined applications such as identification and mapping of epigenetic modifications and high-throughput assembly of combinatorial libraries. In this review, we will examine the major breakthroughs in cloning techniques and their applications in various areas of biological research that have evolved mainly due to easy construction of novel expression systems.

Organic alloys of room temperature liquids thiophenol and selenophenol

The first examples of organic alloys of two room temperature liquids, obtained and characterizedvia in situcryo-crystallography, are presented. Thiophenol and selenophenol, which exhibit isostructurality and similar modes of S⋯S and Se⋯Se homo-chalcogen interactions along with weak and rare S–H⋯S and Se–H⋯Se hydrogen bonds, are shown to form solid solutions exhibiting Veggard's law-like trends.

Contrasting emission behaviour of phenanthroimidazole with ZnO nanoparticles

A new fluorophore 2-(4-fluorophenyl)-1-phenyl-1H-phenanthro [9,10-d]imidazole has been synthesized and characterized by spectroscopic techniques. Nanoparticulate ZnO enhances the fluorescence of the synthesised fluorophore. The absorption, fluorescence, lifetime, cyclic voltammetry and infrared studies reveal that fluorophore is attached to the surface of ZnO semiconductor. Photo-induced electron transfer (PET) explains the enhancement of fluorescence by nanoparticulate ZnO and the apparent binding constant has been obtained. Adsorption of the fluorophore on ZnO nanoparticle lowers the HOMO and LUMO energy levels of the fluorophore. The strong adsorption of the phenanthrimidazole derivative on the surface of ZnO nanocrystals is likely due to the chemical affinity of the nitrogen atom of the organic molecule to the zinc ion on the surface of nanocrystal.

1-(4-Meth-oxy-phen-yl)-2-[4-(tri-fluoro-meth-yl)phen-yl]-1H-phenanthro[9,10-d]imidazole

In the title compound, C29H19F3N2O, a phenanthroline-fused imidazole tetra-cyclic system, the fused benzene rings deviate slightly from the central ring and make dihedral angles with this ring of 3.47 (8) and 3.05 (8)°. The tri-fluoro-methyl-phenyl ring is roughly coplanar with the phenanthroline-fused imidazole tetra-cyclic system [dihedral angle = 11.02 (6)°], while the meth-oxy-phenyl ring is almost perpendicular [dihedral angle = 87.65 (6)°]. There are intra-molecular C-H ⋯π inter-actions involving the meth-oxy-phenyl ring and the central phenanthroline ring, as well as an inter-molecular C-H⋯π inter-action involving the phenanthroline ring. In addition, there is an inter-molecular π-π inter-action involving the central phenanthroline ring and the tri-fluoro-methyl-phenyl ring [centroid-centroid distance = 3.685 (2) Å], as well as C-H⋯N inter-actions linking the mol-ecules into dimers.

Fluorescence quenching of bovine serum albumin by NNMB

A new type of fluorophore 2-(naphthalen-1-yl)-1-((naphthalen-1-yl)methyl)-1H-benzimidazole (NNMB) has been prepared and characterized by (1)H NMR, (13)C NMR, mass and IR spectral analysis. Absorption, fluorescence and synchronous fluorescence spectral studies have been made for the mutual interaction of NNMB with bovine serum albumin (BSA). Absorption spectroscopy proved the formation of a ground state BSA…NNMB complex. Fluorescence spectrum of BSA in the presence of NNMB clearly shows that NNMB acts as a quencher. Based on the theory of Forester's non-radiation energy transfer (FRET) binding distance has been deduced. The Stern-Volmer quenching constant (KSV), binding site number (n), apparent binding constant (KA) and corresponding thermodynamic parameters (ΔG, ΔH and ΔS) were determined.

1-(4-Methyl-phen-yl)-2-[4-(trifluoro-methyl)phen-yl]-1H-phenanthro[9,10-d]imida-zole

In the title compound, C29H19F3N2, the tetra-cyclic ring system is essentially planar [maximum deviation from the best plane = 0.076 (1) Å] and makes dihedral angles of 78.10 (5) and 33.71 (4)° with the methyl-phenyl and fluoro-phenyl rings, respectively. An intra-molecular C-H⋯π inter-action occurs. In the crystal, pairs of C-H⋯π inter-actions link inversion-related mol-ecules.

2-(4-Fluoro-phen-yl)-1-(4-meth-oxy-phen-yl)-1H-phenanthro[9,10-d]imidazole

In the title compound, C28H19FN2O, the phenanthrene fused with an imidazole ring, constituting an essentially planar tetra-cyclic system [maximum deviation = 0.032 (2) Å], makes dihedral angles of 60.83 (4) and 80.55 (4)° with the fluoro-benzene and meth-oxy-benzene rings, respectively. The dihedral angle between the the meth-oxy-benzene and fluoro-benzene rings is 69.45 (6)°. In the crystal, C-H⋯O hydrogen bonds connect the mol-ecules into infinite strands along the b axis. The crystal structure is further consolidated by C-H⋯π inter-actions.

1-(3,5-Dimethyl-phen-yl)-2-(4-fluoro-phen-yl)-1H-phenanthro[9,10-d]imidazole

In the title compound, C₂₉H₂₁FN₂, the phenanthro tricyclic ring system is essentially planar with a maximum deviation of 0.030 (2) Å and makes dihedral angles between of 77.96 (6) and 37.18 (7)° with the dimethyl­phenyl and fluoro­phenyl rings, respectively. The crystal packing features weak C—H⋯π inter­actions involving the dimethyl­phenyl and other phenyl rings.

Selective quenching of benzimidazole derivatives by Cu²+ metal ion

It is a very big challenge to develop a Cu(2+) selective fluorescent sensor with the ability to exclude the interference of some metal ions such as Fe(3+), Mg(2+), Ag(+), K(+) and Na(+). Herein, we report a fluorescence quenching of some benzimidazole derivatives (1-6) with Cu(2+) metal ion. These benzimidazole derivatives have been shown to bind copper ions resulting in quenching of its fluorescence. The response to Cu(2+) is rapid, selective and reversible upon addition of a copper chelator. These benzimidazole derivatives were characterized by (1)H, (13)C NMR mass and elemental analysis. XRD analysis was carried out for 1-(4-methylbenzyl)-2-p-tolyl-1H-benzo[d]imidazole.

2-(4-Fluorophenyl)-1-(4-methylphenyl)-1H-phenanthro[9,10-d]imidazole

The phenanthrene tricyclic ring system in the title mol­ecule, C₂₈H₁₉FN₂, is slightly skewed with a dihedral angle of 7.50 (6)° between the outer benzene rings. The p-tolyl and fluoro­benzene rings are twisted from the attached imidazole ring by 70.40 (7) and 28.33 (7)°, respectively. In the crystal, C—H⋯F hydrogen bonds link the mol­ecules into zigzag chains in [001], and weak C—H⋯π inter­actions further consolidate the crystal packing.

4-[(E)-(4-Fluoro-benzyl-idene)amino]-3-methyl-1H-1,2,4-triazole-5(4H)-thione

In the asymmetric unit of the title compound, C(10)H(9)FN(4)S, there are two independent mol-ecules in which the dihedral angles between the 1,2,4-triazole and benzene rings are 36.85 (10) and 7.81 (10)°. In the crystal, N-H⋯S inter-actions link pairs of independent mol-ecules into dimers. There are also π-π inter-actions between the triazole and benzene rings of inversion-related pairs of the more planar mol-ecule [centroid-centroid distance = 3.6430 (13) Å].

3-Ethyl-6-(4-fluorophenyl)-7H-1,2,4-triazolo[3,4-b][1,3,4]thiadiazine

In the title compound, C₁₂H₁₁FN₄S, the thia­diazine ring adopts a twist-boat conformation. The dihedral angle between the triazolothia­diazine system and the benzene ring is 10.54 (9)°. The crystal structure is characterized by C—H⋯N hydrogen bonds. The crystal packing also exhibits π–π inter­actions, with a centroid–centroid distance of 3.6348 (15) Å.

3-Ethyl-4-[(E)-(4-fluoro-benzyl-idene)amino]-1H-1,2,4-triazole-5(4H)-thione

In the title compound, C₁₁H₁₁FN₄S, the dihedral angle between the 1,2,4-triazole ring and the benzene ring is 25.04 (12)° and an intra­moleuclar C—H⋯S inter­action leads to an S(6) ring. In the crystal, inversion dimers linked by pairs of N—H⋯S hydrogen bonds generate R₂²(8) loops.

Mining of simple sequence repeats in the Genome of Gentianaceae

Simple sequence repeats (SSRs) or short tandem repeats are short repeat motifs that show high level of length polymorphism due to insertion or deletion mutations of one or more repeat types. Here, we present the detection and abundance of microsatellites or SSRs in nucleotide sequences of Gentianaceae family. A total of 545 SSRs were mined in 4698 nucleotide sequences downloaded from the National Center for Biotechnology Information (NCBI). Among the SSR sequences, the frequency of repeat type was about 429 -mono repeats, 99 -di repeats, 15 -tri repeats, and 2 --hexa repeats. Mononucleotide repeats were found to be abundant repeat types, about 78%, followed by dinucleotide repeats (18.16%) among the SSR sequences. An attempt was made to design primer pairs for 545 identified SSRs but these were found only for 169 sequences.

3-Benzyl-6-benzylamino-1-methyl-5-nitro-1,2,3,4-tetrahydropyrimidine

In the title compound, C₁₉H₂₂N₄O₂, the tetra­hydro­pyrimidine ring adopts an envelope conformation (with the N atom connected to the benzyl group representing the flap). This benzyl group occupies a quasi-axial position. The two benzyl groups lie over the tetra­hydro­pyridimidine ring. The amino group is a hydrogen-bond donor to the nitro group.