Gramene: a resource for comparative grass genomics

Gramene (http://www.gramene.org) is a comparative genome mapping database for grasses and a community resource for rice. Rice, in addition to being an economically important crop, is also a model monocot for understanding other agronomically important grass genomes. Gramene replaces the existing AceDB database ‘RiceGenes’ with a relational database based on Oracle. Gramene provides curated and integrative information about maps, sequence, genes, genetic markers, mutants, QTLs, controlled vocabularies and publications. Its aims are to use the rice genetic, physical and sequence maps as fundamental organizing units, to provide a common denominator for moving from one crop grass to another and is to serve as a portal for interconnecting with other web-based crop grass resources. This paper describes the initial steps we have taken towards realizing these goals.     

Fuzzy logic feedback control for fed-batch enzymatic hydrolysis of lignocellulosic biomass

A fuzzy logic feedback control system was developed for process monitoring and feeding control in fed-batch enzymatic hydrolysis of a lignocellulosic biomass, dilute acid-pretreated corn stover. Digested glucose from hydrolysis reaction was assigned as input while doser feeding time and speed of pretreated biomass were responses from fuzzy logic control system. Membership functions for these three variables and rule-base were created based on batch hydrolysis data. The system response was first tested in LabVIEW environment then the performance was evaluated through real-time hydrolysis reaction. The feeding operations were determined timely by fuzzy logic control system and efficient responses were shown to plateau phases during hydrolysis. Feeding of proper amount of cellulose and maintaining solids content was well balanced. Fuzzy logic proved to be a robust and effective online feeding control tool for fed-batch enzymatic hydrolysis.     

An improved Agrobacterium-mediated transformation of recalcitrant indica rice (Oryza sativa L.) cultivars

Agrobacterium-mediated transformation of indica rice varieties has been quite difficult as these are recalcitrant to in vitro responses. In the present study, we established a high-efficiency Agrobacterium tumefaciens-mediated transformation system of rice (Oryza sativa L. ssp. indica) cv. IR-64, Lalat, and IET-4786. Agrobacterium strain EHA-101 harboring binary vector pIG121-Hm, containing a gene encoding for β-glucuronidase (GUS) and hygromycin resistance, was used in the transformation experiments. Manipulation of different concentrations of acetosyringone, days of co-culture period, bacterial suspension of different optical densities (ODs), and the concentrations of l-cysteine in liquid followed by solid co-culture medium was done for establishing the protocol. Among the different co-culture periods, 5 days of co-culture with bacterial cells (OD_600 nm?=?0.5–0.8) promoted the highest frequency of transformation (83.04 %) in medium containing l-cysteine (400 mg l^?1). Putative transformed plants were analyzed for the presence of a transgene through genomic PCR and GUS histochemical analyses. Our results also suggest that different cultural conditions and the addition of l-cysteine in the co-culture medium improve the Agrobacterium-mediated transformation frequencies from an average of 12.82 % to 33.33 % in different indica rice cultivars.     

Ubiquitin Signaling Regulates RNA Biogenesis,Processing, and Metabolism

The fate of eukaryotic proteins, from their synthesis to destruction, is supervised by the ubiquitin–proteasome system (UPS). The UPS is the primary pathway responsible for selective proteolysis of intracellular proteins, which is guided by covalent attachment of ubiquitin to target proteins by E1 (activating), E2 (conjugating), and E3 (ligating) enzymes in a process known as ubiquitylation. The UPS can also regulate protein synthesis by influencing multiple steps of RNA (ribonucleic acid) metabolism. Here, recent publications concerning the interplay between the UPS and different types of RNA are reviewed. This interplay mainly involves specific RNA-binding E3 ligases that link RNA-dependent processes with protein ubiquitylation. The emerging understanding of their modes of RNA binding, their RNA targets, and their molecular and cellular functions are primarily focused on. It is discussed how the UPS adapted to interact with different types of RNA and how RNA molecules influence the ubiquitin signaling components.     

Pharmacophore and molecular dynamics based activity profiling of natural products for kinases involved in lung cancer

To determine the kinase inhibitory potential of natural products that could be utilized in lung cancer therapy in the near future, a pharmacophore-based activity profiling protocol using parallel pharmacophore-based virtual screening of ZINC—a natural product database—was employed. The work presented here is based on the previously explored fact that pharmacophore-based parallel screening is a reliable in silico protocol to predict the possible biological activities of any compound, or any compound library, by screening it with a number of pharmacophore models. The present study involves ligand-based pharmacophore modeling of various kinases, including EGFR (T790 M), cMET, ErbB2, FGFR and ALK, which are well established targets of normal as well resistant lung cancer. The generated pharmacophore models were then utilized for parallel and cross screening. The profiled molecules for each target were then validated using molecular docking and molecular dynamic simulations. The results show that kinase inhibitory activity profiling of some natural product molecules was successfully achieved.

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Graphical abstract Pharmacophore and activity profiling of natural products for kinases involved in lung cancer

     

Surface Engineering of TiO2 ETL for Highly Efficient and Hysteresis‐Less Planar Perovskite Solar Cell (21.4%) with Enhanced Open‐Circuit Voltage and Stability

Interfacial studies and band alignment engineering on the electron transport layer (ETL) play a key role for fabrication of high‐performance perovskite solar cells (PSCs). Here, an amorphous layer of SnO₂ (a‐SnO₂) between the TiO₂ ETL and the perovskite absorber is inserted and the charge transport properties of the device are studied. The double‐layer structure of TiO₂ compact layer (c‐TiO₂) and a‐SnO₂ ETL leads to modification of interface energetics, resulting in improved charge collection and decreased carrier recombination in PSCs. The optimized device based on a‐SnO₂/c‐TiO₂ ETL shows a maximum power conversion efficiency (PCE) of 21.4% as compared to 19.33% for c‐TiO₂ based device. Moreover, the modified device demonstrates a maximum open‐circuit voltage (V_oc) of 1.223 V with 387 mV loss in potential, which is among the highest reported value for PSCs with negligible hysteresis. The stability results show that the device on c‐TiO₂/a‐SnO₂ retains about 91% of its initial PCE value after 500 h light illumination, which is higher than pure c‐TiO₂ (67%) based devices. Interestingly, using a‐SnO₂/c‐TiO₂ ETL the PCE loss was only 10% of initial value under continuous UV light illumination after 30 h, which is higher than that of c‐TiO₂ based device (28% PCE loss).     

Annotation and De Novo Sequence Characterization of Extracellular β-Fructofuranosidase from <Emphasis Type="Italic">Penicillium chrysogenum</Emphasis> Strain HKF42

The genome of a fungal strain Penicillium chrysogenum strain HKF42, which can grow on 20% sucrose has been annotated for 7595 protein coding sequences. On mining of CAZymes, we could annotate a β-fructofuranosidase gene responsible for fructo-oligosaccharides (FOS) synthesis which is a known prebiotic. The enzyme activity was demonstrated and validated with the generation of FOS as kestose and nystose.