Targeted proteomic study of the cyclin-Cdk module

The cell division cycle of the yeast S. cerevisiae is driven by one Cdk (cyclin-dependent kinase), which becomes active when bound to one of nine cyclin subunits. Elucidation of Cdk substrates and other Cdk-associated proteins is essential for a full understanding of the cell cycle. Here, we report the results of a targeted proteomics study using affinity purification coupled to mass spectrometry. Our study identified numerous proteins in association with particular cyclin-Cdk complexes. These included phosphorylation substrates, ubiquitination-degradation proteins, adaptors, and inhibitors. Some associations were previously known, and for others, we confirmed their specificity and biological relevance. Using a hypothesis-driven mass spectrometric approach, we also mapped in vivo phosphorylation at Cdk consensus motif-containing peptides within several cyclin-associated candidate Cdk substrates. Our results demonstrate that this approach can be used to detect a host of transient and dynamic protein associations within a biological module.     

Isolation and characterization of subnuclear compartments from Trypanosoma brucei. Identification of a major repetitive nuclear lamina component

Protozoan parasites of the order Kinetoplastida are responsible for a significant proportion of global morbidity and economic hardship. These organisms also represent extremely distal points within the Eukarya, and one such organism, Trypanosoma brucei, has emerged as a major system for the study of evolutionary cell biology. Significant technical challenges have hampered the full exploitation of this organism, but advances in genomics and proteomics provide a novel approach to acquiring rapid functional data. However, the vast evolutionary distance between trypanosomes and the higher eukaryotes presents significant problems with functional assignment based on sequence similarity, and frequently homologues cannot be identified with sufficient confidence to be informative. Direct identification of proteins in isolated organelles has the potential of providing robust functional insight and is a powerful approach for initial assignment. We have selected the nucleus of T. brucei as a first target for protozoan organellar proteomics. Our purification methodology was able to reliably provide both nuclear and subnuclear fractions. Analysis by gel electrophoresis, electron microscopy, and immunoblotting against trypanosome subcellular markers indicated that the preparations are of high yield and purity, maintain native morphology, and are well resolved from other organelles. Minor developmental differences were observed in the nuclear proteome for the bloodstream and procyclic stages, whereas significant morphological alterations were visible. We demonstrate by direct sequencing that the NUP-1 nuclear envelope antigen is a coiled coil protein, containing approximately 20 near-perfect copies of a 144-amino acid sequence. Immunoelectron microscopy localized NUP-1 to the inner face of the nuclear envelope, suggesting that it is a major filamentous component of the trypanosome nuclear lamina.     

In vitro manipulation and propagation of medicinal plants

Well developed techniques are currently available to help growers meet the demand of the pharmaceutical industry in the next century. These protocols are designed to provide optimal levels of carbohydrates, organic compounds (vitamins), mineral nutrients, environmental factors (e.g. light, gaseous environment, temperature, and humidity) and growth regulators required to obtain high regeneration rates of many plant species in vitro and thereby facilitate commercially viable micropropagation. Well-defined cell culture methods have also been developed for the production of several important secondary products. An overview of the regeneration of medicinal plants by direct and indirect organogenesis and by somatic embryogenesis from various types of explants is presented, and the use of these techniques combined with other biotechnological approaches to improve medicinal plants through somaclonal variation and genetic transformation is reviewed.     

A new family of yeast nuclear pore complex proteins

We have identified a novel family of yeast nuclear pore complex proteins. Three individual members of this family, NUP49, NUP100, and NUP116, have been isolated and then characterized by a combination of molecular genetics and immunolocalization. Employing immunoelectron and immunofluorescence microscopy on yeast cells, we found that the binding of a polyspecific monoclonal antibody recognizing this family was predominantly at the nuclear pore complexes. Furthermore, the tagging of NUP49 with a unique epitope enabled the immunolocalization of this protein to the nuclear pore complex by both fluorescence and electron microscopy. DNA sequence analysis has shown that the amino-terminal regions of NUP49, NUP100, and NUP116 share repeated "GLFG" motifs separated from each other by glutamine, asparagine, serine and threonine rich spacers. All three proteins lack a repetitive domain found in the two precisely described yeast nuclear pore complex proteins. Only NUP49 is essential for cell viability. NUP116-deficient cells grow very slowly and are temperature sensitive, whereas the lack of NUP100 has no detectable phenotype. NUP100 and NUP116 are homologous over their entire lengths. Interestingly, NUP100 and NUP116 are both flanked by a histidine tRNA gene and a transposon element suggesting that they may have arisen by gene duplication. We propose that subfamilies of pore complex proteins can be defined by their characteristic combinations of different modular domains.     

Proteomic elucidation of the targets and primary functions of the picornavirus 2A protease

Picornaviruses are small RNA viruses that hijack host cell machinery to promote their replication. During infection, these viruses express two proteases, 2A^pro and 3C^pro, which process viral proteins. They also subvert a number of host functions, including innate immune responses, host protein synthesis, and intracellular transport, by utilizing poorly understood mechanisms for rapidly and specifically targeting critical host proteins. Here, we used proteomic tools to characterize 2A^pro interacting partners, functions, and targeting mechanisms. Our data indicate that, initially, 2A^pro primarily targets just two cellular proteins: eukaryotic translation initiation factor eIF4G (a critical component of the protein synthesis machinery) and Nup98 (an essential component of the nuclear pore complex, responsible for nucleocytoplasmic transport). The protease appears to employ two different cleavage mechanisms; it likely interacts with eIF3L, utilizing the eIF3 complex to proteolytically access the eIF4G protein but also directly binds and degrades Nup98. This Nup98 cleavage results in only a marginal effect on nuclear import of proteins, while nuclear export of proteins and mRNAs were more strongly affected. Collectively, our data indicate that 2A^pro selectively inhibits protein translation, key nuclear export pathways, and cellular mRNA localization early in infection to benefit viral replication at the expense of particular cell functions.     

Enhanced CellClassifier: a multi-class classification tool for microscopy images

Background  

Light microscopy is of central importance in cell biology. The recent introduction of automated high content screening has expanded this technology towards automation of experiments and performing large scale perturbation assays. Nevertheless, evaluation of microscopy data continues to be a bottleneck in many projects. Currently, among open source software, CellProfiler and its extension Analyst are widely used in automated image processing. Even though revolutionizing image analysis in current biology, some routine and many advanced tasks are either not supported or require programming skills of the researcher. This represents a significant obstacle in many biology laboratories.     

Chemical composition and bioactivity of Boswellia serrata Roxb. essential oil in relation to geographical variation

Oleo–gum–resin of Boswellia serrata Roxb. (Burseraceae) was collected from Shivpuri forest situated in northwestern district of Madhya Pradesh, India. The commercial samples were purchased from Mandsaur and Neemuch districts (the major herbal markets of Madhya Pradesh) for comparative study of their essential oils. The average essential oil contents in the commercial Neemuch samples (11.1%) were much better as compared to the wild collection from Shivpuri (6.1%) as well as commercial collection from Mandsaur (6.9%). The commercial samples contained higher percentage of monoterpene hydrocarbons (81.9–88.1%) including α-thujene (61.4–69.8%) as the major compound. The wild habitat contained higher percentage of oxygenated monoterpenoids/benzenoids (15.7%) and sesquiterpenes (19.2%) including α-terpineol (7.8%), terpinyl isobutyrate (5.1%), and eudesmol (11.5%). Further, the antimicrobial activities of these collections showed remarkable variation among the essential oils. On the other hand, wild habitat contained improved percentage of semi-polar compounds (34.9%) which might be responsible for enhanced antibacterial activity. Similarly, the winter collection from Neemuch (BS-N2) showed significant antioxidant activity, whereas the wild habitat did not show any antioxidant activity. The higher percentage of monoterpene hydrocarbons in commercial samples, especially δ-3-carene, α-pinene, and α-thujene, might be responsible for enhanced antifungal and antioxidant activities. The Pearson correlation values justify the bioactivity relationship of the major compounds with different microbial strains. It also justified the interaction among the major individual compounds.     

Vice-anvil use in nut processing by two Corvus species

Woodpeckers and certain passerine species secure encased food in the environment in various ways to facilitate the extraction of the contents with their bills. They do this by securing the food items in locations such as crevices and holes, newly defined in this paper as ‘vice-anvils’. Here I report that free-living New Caledonian crows (Corvus moneduloides) and rooks (Corvus frugilegus, in New Zealand) also use vice-anvils to process candlenuts and walnuts, respectively. New Caledonian crows placed candlenut sections in vice-anvils to aid kernel extraction, after the candlenuts had been dropped onto an anvil to break them open. In contrast, rooks used vice-anvils to secure walnuts while they broke the shell with their bills. Long-term use by rooks of a vice-anvil in a tree had produced a ‘purpose-made’ nut-cracking site. My findings extend the persistent use of specific vice-anvils to Corvus species and further demonstrate their innovative and flexible foraging behaviour.     

Lipase production by Aspergillus terreus using mustard seed oil cake as a carbon source

An extracellular lipase-producing fungus was isolated from the garden soil of the Post Graduate Department of Botany, Utkal University, Bhubaneswar, Odisha, India and identified as Aspergillus terreus. The A. terreus strain isolated was found to be capable of producing lipase in both solid state culture and liquid static surface culture. Experiments aimed at evaluating and improving the production of lipase and at studying the culture conditions revealed that of the many different materials tested as substrates, mustard oil cake (MoC) was the best substrate for extracellular lipase production. A correlation was found between the lipase production profile and biomass development. In a study aimed at continuing this line of research, we have investigated the influence of various culture conditions, such as environmental (i.e. temperature and pH), nutritional (i.e. carbon, nitrogen, metal ions, vitamins, combined agro-wastes and growth regulators) and other factors (inoculum size and initial moisture content) on the production of lipase by A. terreus in solid state and liquid static surface cultures. We observed that optimum lipase biosynthesis occurred under the following conditions: initial pH of 6.0, 30 °C, a 96-h incubation, lactose and ammonium persulphate as the carbon and nitrogen source respectively and 80 % moisture content. Changes in the vitamins (vitamin C, riboflavin, folic acid and vitamin E) and growth regulators (gibberellic acid, kinetin, 6-benzylaminopurine and 2,4-dichlorophenoxyacetic acid) did not support enhanced lipase production. MoC and neem oil cake (NoC) added to the media at a ratio of 9:1 respectively, supported maximum lipase production. Based on these results, we concluded that controlling the various culture conditions, supplementing MoC as a substrate and nutrient source modification of the medium can spectacularly enhance lipase biosynthesis by A. terreus.     

Single point mutation induced alterations in the equilibrium structural transitions on the folding landscape of HIV-1 protease

Equilibrium folding–unfolding transitions are hard to study in HIV-1 protease (PR) because of its autolytic properties. Further, the protease exhibits many tolerant point mutations some of which also impart drug resistance to the protein. It is conceivable that the mutations affect protein's function by altering its folding characteristics; these would clearly depend on the nature of the mutations themselves. In this background, we report here NMR studies on the effects of D25?N mutation, which removes one negative charge from the protein at the active site, on the equilibrium folding behaviour of PR starting from its acetic acid denatured state. It is observed that in PR_D25N two slowly exchanging conformations are present at the N-terminal. One of them is similar to that of PR. Though the conformational and dynamics preferences of PR and PR_D25N are fairly similar in 9?M acetic acid, they seem to undergo different folding transitions when acetic acid concentration is reduced. The differences are seen in the active site, in the flap, and in the hinge of the flap regions. The present study suggests that such differences, though different in detail, would occur for other mutations as well, and also for different initial denatured states. These would have significant regulatory implications for the efficacy of protease function.