Genetic analysis of agronomic and biochemical variables among different tomato (Solanum lycopersicum L.) accessions

In the present study, thirty accessions of tomato were evaluated for estimation of correlation and path analysis among various quantitative and qualitative characters related to fruit yield. There were highly significant differences among the accessions for all the characters studied as per the analysis of variance. Genotypic correlation coefficients were generally similar in nature and higher in magnitude than the corresponding phenotypic correlation coefficients. The results revealed that the fruit yield plant-1 was significantly and positively correlated with number of fruits plant-1 (0.3119 and 0.3184) followed by fruit set percentage (0.2434 and 0.2499), fruit weight (0.6766 and 0.6731), polar diameter of fruit (0.4687 and 0.4635) at genotypic and phenotypic level, respectively, indicating that effective improvement in fruit yield plant-1 through these characters could be achieved. Fruit weight showed positive and significant genotypic and phenotypic correlation with fruit yield plant-1 by having greatest positive direct effect (1.1298 and 1.1116) on fruit yield plant-1 at both levels, indicating the true relationship between them and the feasibility to exploit the potentiality of this trait for effective direct selection to improve fruit yield plant-1

Mechanism of Mg 2+ -accompanied product release in sugar nucleotidyltransferases

The nucleotidyl transfer reaction, catalyzed by sugar nucleotidyltransferases (SNTs), is assisted by two active site Mg 2+ ions. While studying this reaction using X-ray crystallography, we captured snapshots of the pyrophosphate (product) as it exits along a pocket. Surprisingly, one of the active site Mg 2+ ions remains coordinated to the exiting pyrophosphate. This hints at the participation of Mg 2+ in the process of product release, besides its role in catalyzing nucleotidyl transfer. These observations are further supported by enhanced sampling molecular dynamics simulations. Free energy computations suggest that the product release is likely to be rate limiting in SNTs, and the origin of the high free energy barrier for product release could be traced back to the “slow” conformational change of an Arg residue at the exit end of the pocket. These results establish a dual role for Mg 2+, and propose a general mechanism of product release during the nucleotidyl transfer by SNTs

Substrate-bound crystal structures reveal features unique to Mycobacterium tuberculosis N-acetyl-glucosamine 1-phosphate uridyltransferase and a catalytic mechanism for acetyl transfer

N-Acetyl-glucosamine-1-phosphate uridyltransferase (GlmU), a bifunctional enzyme involved in bacterial cell wall synthesis is exclusive to prokaryotes. GlmU, now recognized as a promising target to develop new antibacterial drugs, catalyzes two key reactions: acetyl transfer and uridyl transfer at two independent domains. Hitherto, we identified GlmU from Mycobacterium tuberculosis (GlmUMtb) to be unique in possessing a 30-residue extension at the C terminus. Here, we present the crystal structures of GlmUMtb in complex with substrates/products bound at the acetyltransferase active site. Analysis of these and mutational data, allow us to infer a catalytic mechanism operative in GlmUMtb. In this SN2 reaction, His-374 and Asn-397 act as catalytic residues by enhancing the nucleophilicity of the attacking amino group of glucosamine 1-phosphate. Ser-416 and Trp-460 provide important interactions for substrate binding. A short helix at the C-terminal extension uniquely found in mycobacterial GlmU provides the highly conserved Trp-460 for substrate binding. Importantly, the structures reveal an uncommon mode of acetyl-CoA binding in GlmUMtb; we term this the U conformation, which is distinct from the L conformation seen in the available non-mycobacterial GlmU structures. Residues, likely determining U/L conformation, were identified, and their importance was evaluated. In addition, we identified that the primary site for PknB-mediated phosphorylation is Thr-418, near the acetyltransferase active site. Down-regulation of acetyltransferase activity upon Thr-418 phosphorylation is rationalized by the structures presented here. Overall, this work provides an insight into substrate recognition, catalytic mechanism for acetyl transfer, and features unique to GlmUMtb, which may be exploited for the development of inhibitors specific to GlmU

Design and synthesis of and π-stacked conjugated oligomers and polymers

Interchain interactions between π-systems have a strong effect on the properties of conjugated organic materials that find application in devices such as light emitting diodes (OLEDs), organic photovoltaics (OPVs), and field effect transistors (FETs). We have prepared covalently-stacked oligo(1,4-phenylene ethynylene)s and oligo(1,4-phenylene vinylene)s to study the influence of chain-chain interactions on the electronic structure of closely packed conjugated units. These serve as models for segments of conjugated materials in thin film devices. Extension of this concept has allowed us to prepare multi-tiered systems that display the influence of pi-stacking. The stacked architectures were prepared by multi-step synthesis of the scaffolds, followed by metal-catalyzed cross coupling reactions (Sonogashira, Heck, Suzuki couplings) to incorporate the conjugated oligomers. The optical and electrochemical properties of these stacked compounds and polymers were compared to their unstacked linear counterparts. These studies provide a platform for the exploration of the nature of charge carriers and excitons in a broad class of materials that have significant potential in addressing challenges in power generation, lighting and electronics.PhDCommittee Chair: Collard, David; Committee Member: Beckham, Haskell; Committee Member: France, Stefan; Committee Member: Srinivasarao, Mohan; Committee Member: Tolbert, Lare

Phytochemicals in the treatment of inflammation-associated diseases: the journey from preclinical trials to clinical practice

Advances in biomedical research have demonstrated that inflammation and its related diseases are the greatest threat to public health. Inflammatory action is the pathological response of the body towards the external stimuli such as infections, environmental factors, and autoimmune conditions to reduce tissue damage and improve patient comfort. However, when detrimental signal-transduction pathways are activated and inflammatory mediators are released over an extended period of time, the inflammatory process continues and a mild but persistent pro-inflammatory state may develop. Numerous degenerative disorders and chronic health issues including arthritis, diabetes, obesity, cancer, and cardiovascular diseases, among others, are associated with the emergence of a low-grade inflammatory state. Though, anti-inflammatory steroidal, as well as non-steroidal drugs, are extensively used against different inflammatory conditions, they show undesirable side effects upon long-term exposure, at times, leading to life-threatening consequences. Thus, drugs targeting chronic inflammation need to be developed to achieve better therapeutic management without or with a fewer side effects. Plants have been well known for their medicinal use for thousands of years due to their pharmacologically active phytochemicals belonging to diverse chemical classes with a number of these demonstrating potent anti-inflammatory activity. Some typical examples include colchicine (alkaloid), escin (triterpenoid saponin), capsaicin (methoxy phenol), bicyclol (lignan), borneol (monoterpene), and quercetin (flavonoid). These phytochemicals often act via regulating molecular mechanisms that synergize the anti-inflammatory pathways such as increased production of anti-inflammatory cytokines or interfere with the inflammatory pathways such as to reduce the production of pro-inflammatory cytokines and other modulators to improve the underlying pathological condition. This review describes the anti-inflammatory properties of a number of biologically active compounds derived from medicinal plants, and their mechanisms of pharmacological intervention to alleviate inflammation-associated diseases. The emphasis is given to information on anti-inflammatory phytochemicals that have been evaluated at the preclinical and clinical levels. Recent trends and gaps in the development of phytochemical-based anti-inflammatory drugs have also been included