Efficient regeneration protocol for callus and shoot induction from recalcitrant Phaseolus vulgaris L. explants under optimum growth conditions

Callus is the most significant morphogenic response obtained in plant tissue culture studies. It can be used for micropropagation or to create transgenic lines. Phaseolus vulgaris L. (common bean) is one of the economically important crops with a great nutritional value. However, very little effort has been made to regenerate callus from P. vulgaris explants. Six explants were used namely root tip, leaves, plumule, radicle, cotyledon and embryo to develop a callus from P. vulgaris. The minimum days for callus induction was 10 days in plumule, radicle and embryo explants, while the maximum was 15 days in cotyledon explants with the callus induction percentage of 75%. The largest callus was found to be 2.77 gm in weight and 2.5 cm in diameter in MS medium. Medium with different concentrations of plant growth regulators (PGRs) showed different growth pattern in callus induction. Culture medium with 1.50 mg/l of BAP, 0.50 mg/l of 2, 4-D and 0.10 mg/l of NAA showed the best result in callus induction. Higher concentration of BAP (2.00 mg/l), along with 0.25 mg/l of 2, 4-D was ideal for shoot regeneration and maturation. Shoot induction medium along with 2.00 mg/l of NAA concentrations were found to be best for rooting. It was found that plumule and radicle favor callus induction, however, they are also potent for shoot and root induction. Knowledge gained in this study will be useful in developing a standard protocol for plant regeneration from P. vulgaris explants and will also be useful in creating transgenic line of P. vulgaris

Expression study of an Amino Acid Permease-like gene in Phaseolus vulgaris L.

Amino acid permease-like (AAP-like) gene plays a critical role in absorbing amino acids through roots in plants. A number of studies have been done on amino acids uptake in plants but till date there is no report about the expression of AAP gene in Phaseolus under field allied condition. The aim of this study is to measure the expression of AAP-like gene on alanine, glycine and proline amino acid uptake capacity in Phaseolus vulgaris at field relevant concentrations. Amongst three amino acids, a drastic significant increase of 63.15 fold in expression of AAP-like gene is observed in 50 µM alanine at 2 hr. At 50 µM of proline and 25 µM of alanine, AAP-like gene expression also shows high expression of 43.71 fold at 2 hr and 42.50 fold at 1 hr respectively. This study elucidated the dose dependent relationship of glycine, alanine and proline with the expression of AAP-like gene in amino acid transport in natural conditions in roots of P. vulgaris. Additionally, this research is also useful in identification of plants needing less surplus nitrogen additions and helpful in optimizing fertilizers by tailoring AAP gene expression to match plant uptake capacities in agriculture

Identification of new strain of mungbean yellow mosaic virus infecting french bean (Phaseolus vulgaris L.) in Santiniketan

113-117Outbreak of yellow mosaic diseases emerged during 2017 in French bean (Phaseolus vulgaris L.) growing region of Santiniketan, Bolpur, West Bengal, India. Yellow mosaic disease was characterized by bright yellow mosaic spots on leaves. Amplification of an expected 598 bp DNA band has been done by polymerase chain reaction (PCR) using primers specific to Santiniketan coat protein (AV1) gene (HQ221570.1) of mungbean yellow mosaic India virus (MYMIV). Comparison of sequences obtained from PCR products with corresponding nucleotide sequences in GenBank, confirmed association of causative agent with mungbean yellow mosaic India virus. Nucleotide sequence analyses of MYMIV- Santiniketan isolates of French bean showed high sequence similarities (> 95%) with others isolates present world-wide. A close relationship of coat protein gene isolate of Santiniketan with DNA-A of Pant Nagar, Uttarakhand (DQ389152.1) of mungbean yellow mosaic India virus has been established on phylogenetic tree analysis. This report provides an evidence of MYMIV infections in French bean in Santiniketan

Cadherins: cellular adhesive molecules serving as signalling mediators

The single pass, transmembrane proteins of the cadherin family have been appreciated as important proteins that regulate intercellular adhesion. In addition to this critical function, cadherins contribute to important signalling events that control cellular homeostasis. Many examples exist of classical, desmosomal and atypical cadherins participating in the regulation of signalling events that control homeostatic functions in cells. Much of the work on cadherin mediated signalling focuses on classical cadherins or on specific disease states such as pemphigus vulgaris. Cadherin mediated signalling has been shown to play critical roles during development, in proliferation, apoptosis, disease pathobiology and beyond. It is becoming increasingly clear that cadherins operate through a range of molecular mechanisms. The diversity of pathways and cellular functions regulated by cadherins suggests that we have only scratched the surface in terms of the roles that these versatile proteins play in signalling and cellular function.Modalities of cadherin mediated signalling. Cadherins have been shown to participate in many diverse signalling pathways and mechanisms. Not only is the range of functional outcomes that cadherins regulate wide, the number of different types of mechanisms that cadherins participate in to mediate their signalling is also impressive. Many times cadherins themselves act as scaffolds for important signalling events and the ability of the cadherin to participate in these signalling mechanisms is often dependent upon their participation in cadherin mediated adhesion (A). Other mechanisms requiring cadherin mediated adhesion include cadherin protein association with other transmembrane signalling proteins and receptors (B). There are several reports of cadherin mediated signalling that requires the formation of stable cadherin protein fragments via regulated proteolytic cleavage (C and D). Most of these mechanisms require cadherin extracellular fragment generation and often both stimulate receptor signalling pathways and interfere with cadherin mediated adhesion (C). There are, however, multiple studies describing cadherin intracellular protein fragment generation (D). These mechanisms often entail binding of the intracellular fragment to a cytoplasmic signalling partner, nuclear re‐localization, and regulation of gene transcription.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/145515/1/tjp13128.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/145515/2/tjp13128_am.pd

The UPF3B gene, implicated in intellectual disability, autism, ADHD and childhood onset schizophrenia regulates neural progenitor cell behaviour and neuronal outgrowth

HMG Advance Access published July 2, 2013Loss-of-function mutations in UPF3B result in variable clinical presentations including intellectual disability (ID, syndromic and non-syndromic), autism, childhood onset schizophrenia and attention deficit hyperactivity disorder. UPF3B is a core member of the nonsense-mediatedmRNAdecay (NMD) pathway that functions to rapidly degrade transcripts with premature termination codons (PTCs). Traditionally identified in thousands of human diseases, PTCs were recently also found to be part of 'normal' genetic variation in human populations. Furthermore, many human transcripts have naturally occurring regulatory features compatible with 'endogenous'PTCsstrongly suggesting roles ofNMDbeyondPTCmRNAcontrol. In this study,weinvestigated the role of Upf3b andNMD in neural cells.Weprovide evidence that suggests Upf3b-dependentNMD(Upf3b-NMD) is regulated at multiple levels during development including regulation of expression and sub-cellular localization of Upf3b. Furthermore, complementary expression of Upf3b, Upf3a and Stau1 stratify the developing dorsal telencephalon, suggesting that alternativeNMD,andthe related Staufen1-mediatedmRNAdecay (SMD) pathways are differentially employed. A loss of Upf3b-NMD in neural progenitor cells (NPCs) resulted in the expansion of cell numbers at the expense of their differentiation. In primary hippocampal neurons, loss of Upf3b-NMD resulted in subtle neurite growth effects. Our data suggest that the cellular consequences of loss of Upf3b-NMD can be explained in-part by changes in expression of key NMD-feature containing transcripts, which are commonly deregulated also in patients with UPF3B mutations. Our research identifies novel pathological mechanisms of UPF3B mutations and at least partly explains the clinical phenotype of UPF3B patients.Lachlan A. Jolly, Claire C. Homan, Reuben Jacob, Simon Barry and Jozef Gec

Comparative transcriptome profiling of a resistant vs. susceptible Vigna mungo cultivar in response to Mungbean yellow mosaic India virus infection reveals new insight into MYMIV resistance

Mungbean yellow mosaic India virus (MYMIV), causal agent of the yellow mosaic disease (YMD) in leguminous crops, causes enormous fall in productivity of economically important legumes worldwide. Vigna mungo is severely affected by YMD. In this study, the transcriptional modifications in V. mungo during MYMIV resistance as well as susceptibility were studied and 145 and 109 differentially expressed transcripts were identified in resistant and susceptible plants, respectively through suppression subtractive hybridization. Selected transcripts were validated through RT-qPCR. In incompatible interaction, significant induced expression of genes present in jasmonic acid signalling pathway was observed. Moreover, in incompatible interaction the generation of physical barrier upon virus invasion and maintenance of reactive oxygen species homeostasis was also evidenced. In compatible interaction, the virus succeeded to manipulate the host machinery resulting in significant decrease in defense related gene expression leading to manifestation of disease symptoms. We have generated two hypothetical models of incompatible and compatible interactions based on the possible biological and molecular function of differentially expressed transcripts obtained from resistant and susceptible plants following MYMIV infection. Knowledge gained from these models will help in deciphering the mechanism of MYMIV resistance not only in V. mungo but also in other plant-pathogen interaction study. Keywords: Suppression subtractive hybridization (SSH), Vigna mungo, MYMIV, Differential expression, RT-qPCR, Incompatible and compatible interactio

Molecular modeling of protein–protein interaction to decipher the structural mechanism of nonhost resistance in rice

<div><p>Nonhost resistance (NHR) is the most common and durable form of plant resistance to disease-causing organisms. A successful example of NHR is the cloning of a maize <i>R</i> gene <i>Rxo1</i> in rice and validating its function in conferring bacterial streak resistance in transgenic rice lines. In order to understand the structural mechanism of NHR in rice, we built the model of the protein–protein interaction between the encoded <i>Rxo1</i> (RXO1) and AvrRXO1 (avirulence protein of rice pathogen, <i>Xanthomonas oryzae</i> pv. <i>oryzicola</i>). Interestingly, although a RXO1 homolog in rice (RHR) is present, it does not interact with AvrRXO1 in nature. We have confirmed that the specificity of RXO1–AvrRXO1 interaction originates from the structured leucine rich repeat (LRR) domain of RXO1, facilitating the recognition process, while the absence of such ordered LRR region makes RHR unfavorable to recognize AvrRXO1. We postulate that the RXO1–AvrRXO1 complex formation is a three step process where electrostatic interactions, shape complementarity and short-range interactions play an important role. The presence of the structural and physicochemical properties essential for the protein–protein recognition process empowers RXO1 to mediate NHR, which the host protein RHR lacks and consequently loses its specificity to bind with AvrRXO1. To the best of our knowledge, this is the first report on the understanding of NHR in rice from the structural perspective of protein–protein interaction.</p></div

Genome-wide identification of miRNAs and lncRNAs in Cajanus cajan

Abstract Background Non-coding RNAs (ncRNAs) are important players in the post transcriptional regulation of gene expression (PTGR). On one hand, microRNAs (miRNAs) are an abundant class of small ncRNAs (~22nt long) that negatively regulate gene expression at the levels of messenger RNAs stability and translation inhibition, on the other hand, long ncRNAs (lncRNAs) are a large and diverse class of transcribed non-protein coding RNA molecules (> 200nt) that play both up-regulatory as well as down-regulatory roles at the transcriptional level. Cajanus cajan, a leguminosae pulse crop grown in tropical and subtropical areas of the world, is a source of high value protein to vegetarians or very poor populations globally. Hence, genome-wide identification of miRNAs and lncRNAs in C. cajan is extremely important to understand their role in PTGR with a possible implication to generate improve variety of crops. Results We have identified 616 mature miRNAs in C. cajan belonging to 118 families, of which 578 are novel and not reported in MirBase21. A total of 1373 target sequences were identified for 180 miRNAs. Of these, 298 targets were characterized at the protein level. Besides, we have also predicted 3919 lncRNAs. Additionally, we have identified 87 of the predicted lncRNAs to be targeted by 66 miRNAs. Conclusions miRNA and lncRNAs in plants are known to control a variety of traits including yield, quality and stress tolerance. Owing to its agricultural importance and medicinal value, the identified miRNA, lncRNA and their targets in C. cajan may be useful for genome editing to improve better quality crop. A thorough understanding of ncRNA-based cellular regulatory networks will aid in the improvement of C. cajan agricultural traits

Additional file 1: Table S1. of Genome-wide identification of miRNAs and lncRNAs in Cajanus cajan

Predicted miRNAs of C. cajan. (PDF 955 kb