The Role of Protein Interactions in Mediating Essentiality and Synthetic Lethality

Genes are characterized as essential if their knockout is associated with a lethal phenotype, and these “essential genes” play a central role in biological function. In addition, some genes are only essential when deleted in pairs, a phenomenon known as synthetic lethality. Here we consider genes displaying synthetic lethality as “essential pairs” of genes, and analyze the properties of yeast essential genes and synthetic lethal pairs together. As gene duplication initially produces an identical pair or sets of genes, it is often invoked as an explanation for synthetic lethality. However, we find that duplication explains only a minority of cases of synthetic lethality. Similarly, disruption of metabolic pathways leads to relatively few examples of synthetic lethality. By contrast, the vast majority of synthetic lethal gene pairs code for proteins with related functions that share interaction partners. We also find that essential genes and synthetic lethal pairs cluster in the protein-protein interaction network. These results suggest that synthetic lethality is strongly dependent on the formation of protein-protein interactions. Compensation by duplicates does not usually occur mainly because the genes involved are recent duplicates, but is more commonly due to functional similarity that permits preservation of essential protein complexes. This unified view, combining genes that are individually essential with those that form essential pairs, suggests that essentiality is a feature of physical interactions between proteins protein-protein interactions, rather than being inherent in gene and protein products themselves.     

Concordance of cranial and dental morphological traits and evidence for endogamy in ancient Egypt

A biological affinities study based on frequencies of cranial nonmetric traits in skeletal samples from three cemeteries at predynastic Naqada, Egypt, confirms the results of a recent nonmetric dental morphological analysis. Both cranial and dental traits analyses indicate that the individuals buried in a cemetery characterized archaeologically as high status are significantly different from individuals buried in two other, apparently nonelite cemeteries and that the nonelite samples are not significantly different from each other. A comparison with neighbouring Nile Valley skeletal samples suggests that the high status cemetery represents an endogamous ruling or elite segment of the local population at Naqada, which is more closely related to populations in northern Nubia than to neighbouring populations in southern Egypt. © 1996 Wiley-Liss, Inc.     

Are non-functional, unfolded proteins ('junk proteins') common in the genome?

It has recently been shown that many proteins are unfolded in their functional state. In addition, a large number of stretches of protein sequences are predicted to be unfolded. It has been argued that the high frequency of occurrence of these predicted unfolded sequences indicates that the majority of these sequences must also be functional. These sequences tend to be of low complexity. It is well established that certain types of low-complexity sequences are genetically unstable, and are prone to expand in the genome. It is possible, therefore, that in addition to these well-characterised functional unfolded proteins, there are a large number of unfolded proteins that are non-functional. Analogous to 'junk DNA' these protein sequences may arise due to physical characteristics of DNA. Their high frequency may reflect, therefore, the high probability of expansion in the genome. Such 'junk proteins' would not be advantageous, and may be mildly deleterious to the cell.     

Recovery and analysis of formyltetrahydrofolate synthetase gene sequences from natural populations of acetogenic bacteria

Primers for PCR amplification of partial (1,102 of 1,680 bp) formyltetrahydrofolate synthetase (FTHFS) gene sequences were developed and tested. Partial FTHFS sequences were successfully amplified from DNA from pure cultures of known acetogens, from other FTHFS-producing organisms, from the roots of the smooth cordgrass, Spartina alterniflora, and from fresh horse manure. The amplimers recovered were cloned, their nucleotide sequences were determined, and their translated amino acid sequences were used to construct phylogenetic trees. We found that FTHFS sequences from homoacetogens formed a monophyletic cluster that did not contain sequences from nonhomoacetogens and that FTHFS sequences appear to be informative regarding major physiological features of FTHFS-producing organisms.     

Physiological Diversity of Rhizoplane Diazotrophs of the Saltmeadow Cordgrass,Spartina patens: Implications for Host Specific Ecotypes

Diazotrophic bacteria are important contributors to salt marsh productivity, but the biotic and abiotic factors that influence their distributions and function and the extent of their diversity cannot be understood in the absence of physiological information. Here we examine the physiological diversity and distribution patterns of diazotrophic bacteria associated with the rhizoplane of the saltmeadow cordgrass, Spartina patens, in comparison with diazotrophs from other intertidal grasses (tall and short form Spartina alterniflora and Juncus roemerianus) from the same salt marsh. S. patens plants were collected from two distinct habitats, and a total of 115 strains (111 Gram negative and 4 Gram positive strains) were isolated into pure culture by stab inoculating roots and rhizomes into combined nitrogen-free semisolid media. Most strains were microaerophilic and approximately one-half were motile. API test strips were used to eliminate redundancy within the culture collection, resulting in 21 physiologically different API groups (17 Gram negative and 4 Gram positive groups). A representative strain from each API group was selected for dot blot hybridization with a nifH specific probe and 16 strains (13 Gram negative and 3 Gram positive) were scored as positive. The nifH positive API group representative strains were characterized further using BIOLOG test plates. Substrate utilization potentials defined two S. patens strain clusters, and only one S. patens strain was physiologically similar to any other strain from a different host plant origin. No distinctions could be made based on the different S. patens habitats, suggesting that the host plant may have a greater impact than abiotic environmental conditions on the distributions of the rhizoplane diazotrophs recovered.     

Numerical dominance and phylotype diversity of marine Rhodobacter species during early colonization of submerged surfaces in coastal marine waters as determined by 16S ribosomal DNA sequence analysis and fluorescence in situ hybridization

Early stages of surface colonization in coastal marine waters appear to be dominated by the marine Rhodobacter group of the alpha subdivision of the division Proteobacteria (alpha-Proteobacteria). However, the quantitative contribution of this group to primary surface colonization has not been determined. In this study, glass microscope slides were incubated in a salt marsh tidal creek for 3 or 6 days. Colonizing bacteria on the slides were examined by fluorescence in situ hybridization by employing DNA probes targeting 16S or 23S rRNA to identify specific phylogenetic groups. Confocal laser scanning microscopy was then used to quantify and track the dynamics of bacterial primary colonists during the early stages of surface colonization and growth. More than 60% of the surface-colonizing bacteria detectable by fluorescence staining (Yo-Pro-1) could also be detected with the Bacteria domain probe EUB338. Archaea were not detected on the surfaces and did not appear to participate in surface colonization. Of the three subdivisions of the Proteobacteria examined, the alpha-Proteobacteria were the most abundant surface-colonizing organisms. More than 28% of the total bacterial cells and more than 40% of the cells detected by EUB338 on the surfaces were affiliated with the marine Rhodobacter group. Bacterial abundance increased significantly on the surfaces during short-term incubation, mainly due to the growth of the marine Rhodobacter group organisms. These results demonstrated the quantitative importance of the marine Rhodobacter group in colonization of surfaces in salt marsh waters and confirmed that at least during the early stages of colonization, this group dominated the surface-colonizing bacterial assemblage.     

Overcoming the constraints of long range radio telemetry from animals: getting more useful data from smaller packages

Many species carry out their most interesting activities wherethey cannot readily be observed or monitored. Marine mammalsare extreme among this group, accomplishing their most astoundingactivities both distant from land and deep in the sea. Collection,storage and transmission of data about these activities areconstrained by the energy requirements and size of the recordingloggers and transmitters. The more bits of information collected,stored and transmitted, the more battery is required and thelarger the tag must be. We therefore need to be selective aboutthe information we collect, while maintaining detail and fidelity.To accomplish this in the study of marine mammals, we have designed"intelligent" data logger/transmitters that provide context-drivendata compression, data relay, and automated data base storage.We later combine these data with remotely sensed environmentalinformation and other oceanographic data sets to recreate theenvironmental context for the animal's activity, and we displaythe combined data using computer animation techniques. In thisway, the system can provide near real time "observation" ofanimal behavior and physiology from the remotest parts of theglobe.     

Effect of Rainbow Trout Growth Hormone Complementary DNA on Body Shape,Carcass Yield,and Carcass Composition of F1 and F2 Transgenic Common Carp (Cyprinus carpio

The effect of rainbow trout growth hormone complementary DNA on body shape, dress-out yield, and body composition were assessed in the F1 and F2 generations of transgenic common carp (Cyprinus carpio). All measurements were compared with those for nontransgenic full-sibling common carp in their respective families, and the fish were communally evaluated in earthen ponds. The body weight and length were highly correlated (P <0.01) in both genotypes in all the families. Head morphometrics were negatively correlated (P <0.05) to weight and length of the fish. Various head, body, and caudal traits grew disproportionately faster in transgenic fish in both generations. The altered body shape of transgenic fish resulted in improved dressing percentage in the F2 generation. The carcass composition of transgenic muscle had a lower percentage of (P <0.01) moisture and lipids and higher (P <0.01) percentage of protein in both generations. Six of the 18 amino acids analyzed in F1 transgenic common carp muscle were higher F1 (P <0.05) than the control genotype; however, amino acid ratios were minimally changed. Also, the fatty acid profiles of both genotypes were minimally altered. Higher histidine and lysine ratios in the diet are recommended for maximum growth and health of transgenic common carp in intensive culture systems on the basis of essential amino acid ratios.     

Decreased thioredoxin and increased thioredoxin reductase levels in Alzheimer's disease brain

Increasing evidence supports the role of reactive oxygen species (ROS) in the pathogenesis of Alzheimer's disease (AD). Both in vivo and in vitro studies demonstrate that thioredoxin (Trx) and thioredoxin reductase (TR), the enzyme responsible for reduction of oxidized Trx, have protective roles against cytotoxicity mediated by the generation of ROS. The present study measured levels of Trx protein and activities of TR in the brain in AD compared with control subjects, and evaluated the possible protective role of TR and Trx against amyloid beta-peptide (Abeta) toxicity in neuronal cultures. Analysis of Trx protein levels in 10 AD and 10 control subjects demonstrated a general decrease in all AD brain regions studied, with statistically significant decreases in the amygdala (p <.05), hippocampus/parahippocampal gyrus (p <.05), and marginally significant (p <.10) depletions in the superior and middle temporal gryi. Thioredoxin reductase activity levels were increased in all AD brain regions studied with statistically significant increases occurring in AD amygdala (p =.01) and cerebellum (p =.007). To investigate the protective effects of Trx and TR against Abeta-induced toxicity, primary hippocampal cultures were treated with Trx or TR in combination with toxic doses of Abeta. Treatment of cultures with Trx led to a statistically significant concentration-dependent enhancement in cell survival against Abeta-mediated toxicity as did treatment with TR. Together, these data suggest that, although TR is protective against Abeta-mediated toxicity, the increase observed in AD brain offers no protection due to the significant decrease in Trx levels. This decrease in the antioxidant Trx-TR system may contribute to the increased oxidative stress and subsequent neurodegeneration observed in the brain in AD.