An improved protocol for efficient transformation and regeneration of diverse indica rice cultivars

Background

Common bean (Phaseolus vulgaris L.) is a crop of economic and nutritious importance in many parts of the world. The lack of genomic resources have impeded the advancement of common bean genomics and thereby crop improvement. Although concerted efforts from the "Phaseomics" consortium have resulted in the development of several genomic resources, functional studies have continued to lag due to the recalcitrance of this crop for genetic transformation.

Results

Here we describe the use of a bean pod mottle virus (BPMV)-based vector for silencing of endogenous genes in common bean as well as for protein expression. This BPMV-based vector was originally developed for use in soybean. It has been successfully employed for both protein expression and gene silencing in this species. We tested this vector for applications in common bean by targeting common bean genes encoding nodulin 22 and stearoyl-acyl carrier protein desaturase for silencing. Our results indicate that the BPMV vector can indeed be employed for reverse genetics studies of diverse biological processes in common bean. We also used the BPMV-based vector for expressing the green fluorescent protein (GFP) in common bean and demonstrate stable GFP expression in all common bean tissues where BPMV was detected.

Conclusions

The availability of this vector is an important advance for the common bean research community not only because it provides a rapid means for functional studies in common bean, but also because it does so without generating genetically modified plants. Here we describe the detailed methodology and provide essential guidelines for the use of this vector for both gene silencing and protein expression in common bean. The entire VIGS procedure can be completed in 4-5 weeks.     

Tagging: on the use of passive integrated transponder (PIT) tags for the identification of fish

To determine the efficacy of passive integrated transponder (PIT) tags for marking rohu Labeo rohita (Ham.) in the selective breeding programme, a series of experiments has been carried out at the Central Institute of Freshwater Aquaculture (CIFA) under the Indo–Norwegian project of ‘Selective breeding of rohu’. Six groups of rohu fingerlings with weight ranging from 2 g to 20 g were tagged with PIT tags to determine a suitable size range for tagging. Fingerlings weighing 8–15 g were found to be quite suitable for tagging with a PIT tag. Recovery of the PIT tag depends upon the survival of tagged fish under field conditions. Rejection of the PIT tag by rohu was observed to be only 0.05%. Through effective management practice, the survival of tagged fish increased up to 95%, and thus tag loss was minimized.     

Structural aspects of alkali treated sisal fiber — A SAXS investigation

The present work emphasizes the effect of alkali (NaOH) solution on macromolecular parameters of sisal fiber. The macromolecular parameters of alkali treated sisal fiber were computed along with air-dried sisal fiber by treating fiber as a non-ideal two-phase system characterized by continuous variation of electron density at the phase boundary. Small angle Xray scattering (SAXS) technique was employed to evaluate the macromolecular parameters, using correlation functions, applying the theories of Vonk, Ruland and Misra et al. The finite value of width of transition layer suggests to treat the fiber to be a non-ideal two-phased system. The evaluated macromolecular parameters are: transversal periodicity, specific inner surface, volume fractions of matter and void phases, transversal lengths in both phases, range of inhomogeneity, volume fraction of transition layer and length of coherence.     

Bacteriocins and their applications for the treatment of bacterial diseases in aquaculture: a review

Aquaculture is one of the fastest growing food producing sectors in the world. The increase in the world population requires faster growth in aquaculture for better food availability and to overcome malnutrition. But this worldwide growth of aquaculture is overwhelmed by catastrophic fish diseases and spoilage during cultivation and preservation problems caused by pathogenic bacteria. Various remedies are available for food preservation and also from the bacterial diseases in the fish production. Due to the emergence of antibiotic resistance and adverse effects, an alternative to antibiotic is the need of the hour. The proteins such as bacteriocins, i.e. ribosomally synthesized antimicrobial peptides (AMPs) and possess antagonistic against closely related and other bacteria. These proteins are produced by most lineages of bacteria which are playing key roles in recognition and possess a cognate immunity system for self‐protection as well as host protection from infections. These proteins are potent immunomodulators with broad spectrum inhibition properties which are further used as novel therapeutic agents. In this review, we have tried to summarize the bacteriocins on the basis of their classifications, structural and functional attributes, mode of actions, bacteriocins isolated from fish and gut microbiota and presence of beneficiary bacteria in the fish gut. Further, this study highlighted where further research is a prerequisite to increase our basic understanding and search for novel bacteriocins to elucidate the proteins/peptides having antimicrobial properties for disease control in aquaculture as an alternative to antibiotics.     

Identification of MDP (muramyl dipeptide)-binding key domains in NOD2 (nucleotide-binding and oligomerization domain-2) receptor of Labeo rohita

In lower eukaryotes-like fish, innate immunity contributed by various pattern recognition receptor (PRR) plays an essential role in protection against diseases. Nucleotide-binding and oligomerization domain (NOD)-2 is a cytoplasmic PRR that recognizes MDP (muramyl dipeptide) of the Gram positive and Gram negative bacteria as ligand and activates signalling to induce innate immunity. Hypothesizing a similar NOD2 signalling pathway of higher eukaryotes, the peripheral blood leucocytes (PBLs) of rohu (Labeo rohita) was stimulated with MDP. The data of quantitative real-time PCR (qRT-PCR) revealed MDP-mediated inductive expression of NOD2 and its down-stream molecule RICK/RIP2 (receptor-interacting serine-threonine protein kinase-2). This observation suggested the existence of MDP-binding sites in rohu NOD2 (rNOD2). To investigate it, 3D model of ligand-binding leucine-rich repeat (LRR) region of rNOD2 (rNOD2-LRR) was constructed following ab initio and threading approaches in I-TASSER web server. Structural refinement of the model was performed by energy minimization, and MD (molecular dynamics) simulation was performed in GROMACS (Groningen Machine for Chemical Simulations). The refined model of rNOD2-LRR was validated through SAVES, ProSA, ProQ, WHAT IF and MolProbity servers, and molecular docking with MDP was carried out in GOLD 4.1. The result of docking identified LRR3-7 comprising Lys820, Phe821, Asn822, Arg847, Gly849, Trp877, Trp901 and Trp931 as MDP-binding critical amino acids in rNOD2. This is the first study in fish to provide an insight into the 3D structure of NOD2-LRR region and its important motifs that are expected to be engaged in MDP binding and innate immunity.     

The immune response in rohu,Labeo rohita (Actinopterygii: Cyprinidae) to Argulus siamensis (Branchiura: Argulidae) infection: kinetics of immune gene expression and innate immune response

Argulus siamensis is a major pathogen in freshwater aquaculture. The immune responses of Indian major carp, Labeo rohita to experimental infection of A. siamensis was evaluated by quantitation of immune‐relevant gene expression in head kidney and skin, and serum innate immune parameters through the course of infection. In skin of infected fish, antioxidant genes like natural killer cell enhancing factor (NKEF‐B) and superoxide dismutase (MnSOD) were significantly up‐regulated in addition to lysozyme G and β₂ microglobulin (β₂M). Both tumour necrosis factor α (TNFα) and toll‐like receptor 22 (TLR22) genes were significantly down‐regulated in skin during early phases of the infection. Most of the genes exhibited significant down‐regulation in head kidney; immunoglobulin (IgM) and β₂M genes being the exceptions which were significantly up‐regulated at 12 h and 3 days post infection. Most of the innate immune parameters like serum complement activity and ceruloplasmin levels showed significant reduction in infected fish. The observed results are indicative of A. siamensis modulating the immune response of rohu by down‐regulation of many immune factors which may explain the susceptibility of rohu to A. siamensis infection. The interaction of this parasite with the host need to be further explored to understand its pathogenesis.     

Survival,male morphotypes,female and male proportion,female reproductive status and tag loss in crosses among three populations of freshwater prawn Macrobrachium rosenbergii (de Man) in India

The present study examined the variation in survival, proportion of male morphotypes, female and male proportion, female reproductive status and tag losses in nine crosses from a complete (3 × 3) diallel mating of three populations of Macrobrachium rosenbergii in India. The populations originated from Gujarat (north‐west), Kerala (south‐west) and Odisha (east), representing different agro‐ecological regions in India. Progeny from 60 families (4773 juveniles) were individually tagged and reared for 16–17 weeks in earthen ponds. Binary logistic regression was used to analyse the data. Survival rate was greatest (0.88) for Kerala × Odisha (KO; the first letter represents the sire), whereas it was lowest (0.75) for both Kerala × Kerala (KK) and Gujarat × Kerala (GK). Significantly greater proportions of large male morphotypes were observed in KK cross and in combinations involving Kerala population. The highest proportion of immature females, as well as of non‐berried females, was observed in the Odisha × Odisha (OO) cross. Tag loss was greatest for KK (0.35) and lowest for GG (0.19). We found significant variations among crosses for all studied traits suggesting the possibility of including them in genetic improvement programmes of this species.     

Comparative evaluation of hormonal protocol on the performance of crossbred cattle

A total of 60 animals (38 cows, 22 heifers) were selected and were divided into three groups of 20 animals each (containing both anoestrus and repeat breeder) in which treatment was performed for 60 days. Group I: control (farmer practice), T₁ group: group I?+?hormone (double synch), and T₂ group: group I?+?hormone (Estra double synch). The growth performances were measured in terms of body weight and average daily gain (ADG). Blood collection was done at the start and end of the experiment for assessment of blood biochemical, hematological, and reproductive status of the animals. Results revealed significant improvement in growth and reproductive performances in treatment group as compared to control group. Higher percentage of conception was achieved in group III (60%) followed by group II (55%). The least percentage was in group I (15%), i.e., in control group. So it was found that the effect of treating the reproductive-disordered animals with Estra double synch gave comparatively better result than double synch hormonal application.