Intra and Inter-Molecular Communications Through Protein Structure Network

Communication within and across proteins is crucial for the biological functioning of proteins. Experiments such as mutational studies on proteins provide important information on the amino acids, which are crucial for their function. However, the protein structures are complex and it is unlikely that the entire responsibility of the function rests on only a few amino acids. A large fraction of the protein is expected to participate in its function at some level or other. Thus, it is relevant to consider the protein structures as a completely connected network and then deduce the properties, which are related to the global network features. In this direction, our laboratory has been engaged in representing the protein structure as a network of non-covalent connections and we have investigated a variety of problems in structural biology, such as the identification of functional and folding clusters, determinants of quaternary association and characterization of the network properties of protein structures. We have also addressed a few important issues related to protein dynamics, such as the process of oligomerization in multimers, mechanism on protein folding, and ligand induced communications (allosteric effect). In this review we highlight some of the investigations which we have carried out in the recent past. A review on protein structure graphs was presented earlier, in which the focus was on the graphs and graph spectral properties and their implementation in the study of protein structure graphs/networks (PSN). In this article, we briefly summarize the relevant parts of the methodology and the focus is on the advancement brought out in the understanding of protein structure-function relationships through structure networks. The investigations of structural/biological problems are divided into two parts, in which the first part deals with the analysis of PSNs based on static structures obtained from x-ray crystallography. The second part highlights the changes in the network, associated with biological functions, which are deduced from the network analysis on the structures obtained from molecular dynamics simulations.

The crystal structure of the amino-terminal pentapeptide of suzukacillin. Occurrence of a four-fold peptide helix

The monohydrate of the protected amino-terminal pentapeptide of suzukacillin, t-butoxycarbonyl--aminoisobutyryl-L-prolyl-L-valyl--aminoisobutyryl-L-valine methyl ester, C29H51N5O8, crystallizes in the orthorhombic space group P212121 with a= 10.192, b= 10.440, c= 32.959 Å, and Z= 4. The structure has been solved by direct methods and refined to an R value of 0.101 for 1 827 observed reflections. The molecule exists as a four-fold helix with a pitch of 5.58 Å. The helix is stabilised by N–H O hydrogen bonds, two of the 51 type (corresponding to the -helix) and the third of the 41 type (310 helix). The carbonyl oxygen of the amino-protecting group accepts two hydrogen bonds, one each from the amide NH groups of the third (41) and fourth (51) residues. The remaining 51 hydrogen bond is between the two terminal residues. The lone water molecule in the structure is hydrogen bonded to carbonyl oxygens of the prolyl residue in one molecule and the non-terminal valyl residue in a symmetry-related molecule.

Female Reproductive Biology and Spawning Periodicity of Two Species of King Prawns, Penaeus longistylus Kubo and Penaeus latisulcatus Kishinouye, from Queensland's East Coast Fishery

In the coastal region of central Queensland female red-spot king prawns, P. longistylus, and the western or blue-leg king prawns, P. latisulcatus, had high mean ovary weights and high proportions of advanced ovary development during the winter months of July and August of 1985 and 1986. On the basis of insemination, both species began copulating at the size of 26-27 mm CL, but P. longistylus matured and spawned at a smaller size than P. latisulcatus. Abundance of P. longistylus was generally three to four times greater than that of P. latisulcatus but the latter was subject to greater variation in abundance. Low mean ovary weight and low proportions of females with advanced ovaries were associated with the maximum mean bottom sea-water temperature (28.5ºC) for both species. Population fecundity indices indicated that peaks in yolk or egg production (a) displayed a similar pattern for both species, (b) varied in timing from year to year for both species and (c) were strongly influenced by abundance. Generally, sample estimates of abundance and commercial catch rates (CPUE) showed similar trends. Differences between the two may have been due to changes in targeted commercial effort in this multi-species fishery.

Reproductive Biology and Spawning Periodicity of Endeavour Shrimps Metapenaeus endeavouri (Schmitt, 1926) and Metapenaeus ensis (de Haan, 1850) from a Central Queensland (Australia) Fishery

Metapenaeus endeavouri and M. ensis from coastal trawl fishing grounds off central Queensland, Australia, have marked seasonal reproductive cycles. Female M. endeavouri grew to a larger size than female M. ensis and occurred over a wider range of sites and depths. Although M. ensis was geographically restricted in distribution to only the shallowest sites it was highly abundant. Mating activity in these open thelycum species, indicated by the presence or absence of a spermatophore, was relatively low and highly seasonal compared with closed thelyeum shrimps. Seasonal variation in spermatophore insemination can be used as an independent technique to study spawning periodicity in open thelycum shrimps. Data strongly suggest an inshore movement of M. endeavouri to mature and spawn. This differs from most concepts of Penaeus species life cycles, but is consistent with the estuarine significance in the life cycle of Metapenaeus species. Monthly population fecundity indices suggest summer spawning for both species, which contrasts with the winter spawning of other shrimps from the same multispecies fishery.

The fishery and reproductive biology of Barking crayfish, Linuparus trigonus (Von Siebold, 1824) along Queenslands east coast

This paper describes the fishery and reproductive biology for Linuparus trigonus obtained from trawl fishermen operating off Queensland’s east coast, Australia. The smallest mature female lobster measured 59.8 mm CL, however, 50% maturity was reached between 80 and 85 mm CL. Brood fecundity (BF) was size dependent and ranged between 19,287 and 100,671 eggs in 32 females from 59.8 to 104.3 mm CL. The relationship was best described by the power equation BF = 0.1107*CL to the power of 2.9241 (r to the power of 2 = 0:74). Egg size ranged from 0.96 to 1.12 mm in diameter (mean = 1:02 (+or-) 0:01 mm). Egg weight and size were independent of lobster size. Length frequencies displayed multi-modal distributions.The percentage of female to male lobsters was relatively stable for small size classes (30 to 70 mm CL; 50.0 to 63.6% females), but female proportions rose markedly between 75 and 90 mm (72.2 to 85.4%) suggesting that at the onset of sexual maturity female growth rates are reduced. In size classes greater than 95 mm, males were numerically dominant. A description of the L. trigonus fishery in Queensland is also detailed.

On Systems Thinking, Systems Biology, and the in Silico Plant

The recent summary report of a Department of Energy Workshop on Plant Systems Biology (P.V. Minorsky [2003] Plant Physiol 132: 404-409) offered a welcomed advocacy for systems analysis as essential in understanding plant development, growth, and production. The goal of the Workshop was to consider methods for relating the results of molecular research to real-world challenges in plant production for increased food supplies, alternative energy sources, and environmental improvement. The rather surprising feature of this report, however, was that the Workshop largely overlooked the rich history of plant systems analysis extending over nearly 40 years (Sinclair and Seligman, 1996) that has considered exactly those challenges targeted by the Workshop. Past systems research has explored and incorporated biochemical and physiological knowledge into plant simulation models from a number of perspectives. The research has resulted in considerable understanding and insight about how to simulate plant systems and the relative contribution of various factors in influencing plant production. These past activities have contributed directly to research focused on solving the problems of increasing biomass production and crop yields. These modeling approaches are also now providing an avenue to enhance integration of molecular genetic technologies in plant improvement (Hammer et al., 2002).

Reproductive biology of the red throat emperor Lethrinus miniatus (Pisces : Lethrinidae) from the southern Great Barrier Reef, Australia

The reproductive biology of the red throat emperor, Lethrinus miniatus (Schneider, 1801) was examined in the southern Great Barrier Reef (GBR), Australia. The species was found to display the characteristics of an incomplete metagynous hermaphrodite based on histological evidence and size frequency information. Over 95% of functional males possessed a remnant lumen, but there was no evidence of oocytes in the testes of males. A single transitional fish was sampled which had both ovarian and testicular tissue present in its gonad. Size frequency data showed that females dominated the smaller size classes with the majority of fish < 40 cm being females. Lethrinus miniatus had an extended spawning season from July-November, although spawning was more pronounced during the spring. Spawning was initiated earlier at lower latitudes. There was no particular size or age when sex change occurred since females older than 20 and males as young as 2-yrs old were sampled.

The use of a synthetic prostaglandin e1 analogue (misoprostol) as an adjunct to pancreatic enzyme replacement in cystic fibrosis

Eleven cystic fibrosis children (mean age, 9.6 years) were chosen at random to participate in a study to observe the effects of concurrently stimulating gastric/duodenal bicarbonate secretion and inhibiting gastric acid secretion, using a methylated prostaglandin E1 analogue in patients with pancreatic insufficiency and taking pancreatic enzymes. Percentage fat absorption in 3-day stool collections were calculated before and after commencing therapy with misoprostol, 400 μg/day in divided doses. We found a significant reduction in fat output (14.7 ± 11.7 versus 7.5 ± 3.5 g/day, p < 0.05) in the study group as a whole and a significant reduction in steatorrhoeic level as a percentage of fat intake in all of the patients with abnormal base-line collections (23.1% versus 9.2% p < 0.002). We conclude that misoprostol should be considered in cystic fibrosis patients with steatorrhoea as a means of improving nutrient absorption. © 1988 Informa UK Ltd All rights reserved: reproduction in whole or part not permitted.

Trap Design Effect on the Capture of Carpophilus spp. (Coleoptera: Nitidulidae) Using Synthetic Aggregation Pheromones and a Coattractant

In a series of experiments conducted in stone fruit orchards in southern Australia, water-based funnel-type traps baited with synthetic aggregation pheromone and fermenting bread dough, trapped 3- to 7-fold as many Carpophihus beetles (primarily C. dauidsoni) than wind-oriented pipe traps or dry funnel traps. The efficacy of dry funnel traps but not pipe traps, appeared to be improved by using water-filled collecting bottles. The potential for using water-based funnel traps in population suppression of Carpophilus spp. in stone fruit orchards through mass trapping is discussed.

Biology of Plant Rhabdoviruses

The Rhabdoviridae, whose members collectively infect invertebrates, animals, and plants, form a large family that has important consequences for human health, agriculture, and wildlife ecology. Plant rhabdoviruses can be separated into the genera Cytorhabdovirus and Nucleorhabdovirus, based on their sites of replication and morphogenesis. This review presents a general overviewof classical and contemporary findings about rhabdovirus ecology, pathology, vector relations, and taxonomy. The genome organization and structure of several recently sequenced nucleorhabdoviruses and cytorhabdoviruses is integrated with new cell biology findings to provide a model for the replication of the two genera. A prospectus outlines the exciting opportunities for future research that will contribute to a more detailed understanding of the biology, biochemistry, replication and host interactions of the plant rhabdoviruses.

The use of a synthetic prostaglandin-E1 analog (misoprostol) as an adjunct to pancreatic-enzyme replacement in cystic-fibrosis

Eleven cystic fibrosis children (mean age, 9.6 years) were chosen at random to participate in a study to observe the effects of concurrently stimulating gastric/duodenal bicarbonate secretion and inhibiting gastric acid secretion, using a methylated prostaglandin E1 analogue in patients with pancreatic insufficiency and taking pancreatic enzymes. Percentage fat absorption in 3-day stool collections were calculated before and after commencing therapy with misoprostol, 400 μg/day in divided doses. We found a significant reduction in fat output (14.7 ± 11.7 versus 7.5 ± 3.5 g/day, p < 0.05) in the study group as a whole and a significant reduction in steatorrhoeic level as a percentage of fat intake in all of the patients with abnormal base-line collections (23.1% versus 9.2%, p < 0.002). We conclude that misoprostol should be considered in cystic fibrosis patients with steatorrhoea as a means of improving nutrient absorption.

Recent advances in the molecular biology of Leifsonia xyli subsp. xyli, causal organism of ratoon stunting disease

Twelve years ago our understanding of ratoon stunting disease (RSD) was confined almost exclusively to diagnosis of the disease and control via farm hygiene, with little understanding of the biology of the interaction between the causal agent (Leifsonia xyli subsp. xyli) and the host plant sugarcane (Saccharum spp. hybrids). Since then, research has focused on developing the molecular tools to dissect L. xyli subsp. xyli, so that better control strategies can be developed to prevent losses from RSD. Within this review, we give a brief overview of the progression in research on L. xyli subsp. xyli and highlight future challenges. After a brief historical background on RSD, we discuss the development of molecular tools such as transformation and transposon mutagenesis and discuss the apparent lack of genetic diversity within the L. xyli subsp. xyli world population. We go on to discuss the sequencing of the genome of L. xyli subsp. xyli, describe the key findings and suggest some future research based on known deficiencies that will capitalise on this tremendous knowledge base to which we now have access.

Yield of synthetic backcross-derived lines in rainfed environments of Australia

Wheat is one of the major food crops in the world. It is Australia's largest crop and most important agricultural commodity. In Australia the crop is grown under rainfed conditions with inherently important regional environmental differences; wheat growing areas are characterized by winter dominant rainfall in southern and western Australia and summer rainfall in northern Australia. Maximizing yield potential across these diverse regions is dependent upon managing, either genetically or agronomically, those factors in the environment that limit yield. The potential of synthetic backcross lines (SBLs) to increase yield in the diverse agroecological zones of Australia was investigated. Significant yield advantages were found for many of the SBLs across diverse environments. Depending on the environment, the yield of the SBLs ranged from 8% to 30% higher than the best local check in Australia. Apart from adaptation to semiarid water stressed conditions, some SBLs were also found to be significantly higher yielding under more optimal (irrigated) conditions. The four testing environments were classified into two groups, with the northern and southern environments being in separate groups. An elite group of SBLs was identified that exhibited broad adaptation across all diverse Australian environments included in this study. Other SBLs showed specific adaptation to either northern or southern Australia. This study showed that SBLs are likely to provide breeders with the opportunity to significantly improve wheat yield beyond what was previously possible in a number of diverse production environments.

Spatial patterns in the biology of the chokka squid, Loligo reynaudii on the Agulhas Bank, South Africa

Although migration patterns for various life history stages of the chokka squid (Loligo reynaudii) have been previously presented, there has been limited comparison of spatial variation in biological parameters. Based on data from research surveys; size ranges of juveniles, subadults and adults on the Agulhas Bank were estimated and presented spatially. The bulk of the results appear to largely support the current acceptance of the life cycle with an annual pattern of squid hatching in the east, migrating westwards to offshore feeding grounds on the Central and Western Agulhas Bank and the west coast and subsequent return migration to the eastern inshore areas to spawn. The number of adult animals in deeper water, particularly in autumn in the central study area probably represents squid spawning in deeper waters and over a greater area than is currently targeted by the fishery. The distribution of life history stages and different feeding areas does not rule out the possibility that discrete populations of L. reynaudii with different biological characteristics inhabit the western and eastern regions of the Agulhas Bank. In this hypothesis, some mixing of the populations does occur but generally squid from the western Agulhas Bank may occur in smaller numbers, grow more slowly and mature at a larger size. Spawning occurs on the western portion of the Agulhas Bank, and juveniles grow and mature on the west coast and the central Agulhas Bank. Future research requirements include the elucidation of the age structure of chokka squid both spatially and temporally, and a comparison of the statolith chemistry and genetic characterisation between adults from different spawning areas across the Agulhas Bank.