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Signal transduction networks are crucial for inter- and intra-cellular signaling. Signals are often transmitted via covalent modification of protein structure, with phosphorylation/dephosphorylation as the primary example. In this paper, we apply a recently described method of computational algebra to the modeling of signaling networks, based on time-course protein modification data. Computational algebraic techniques are employed to construct next-state functions. A Monte Carlo method is used to approximate the Deegan-Packel Index of Power corresponding to the respective variables. The Deegan-Packel Index of Power is used to conjecture dependencies in the cellular signaling networks. We apply this method to two examples of protein modification time-course data available in the literature. These experiments identified protein carbonylation upon exposure of cells to sub-lethal concentrations of copper. We demonstrate that this method can identify protein dependencies that might correspond to regulatory mechanisms to shut down glycolysis in a reverse, step-wise fashion in response to copper-induced oxidative stress in yeast. These examples show that the computational algebra approach can identify dependencies that may outline signaling networks involved in the response of glycolytic enzymes to the oxidative stress caused by copper.

Analysis of assembled random shotgun sequence data from a low-diversity, subsurface acid mine drainage (AMD) biofilm revealed a single nif operon. This was found on a genome fragment belonging to a member of Leptospirillum group III, a lineage in the Nitrospirae phylum with no cultivated representatives. Based on the prediction that this organism is solely responsible for nitrogen fixation in the community, we pursued a selective isolation strategy to obtain the organism in pure culture. An AMD biofilm sample naturally abundant in Leptospirillum group III cells was homogenized, filtered, and serially diluted into a nitrogen-free liquid medium. The resulting culture in the terminal dilution grew autotrophically to a maximum cell density of approximately 10(6) cells/ml, oxidizing ferrous iron as the sole energy source. 16S rRNA-internal transcribed spacer region clone library analysis confirmed that the isolate is a member of Leptospirillum group III and that the culture is axenic. We propose the name Leptospirillum ferrodiazotrophum sp. nov. for this iron-oxidizing, free-living diazotroph. This study highlights how environmental sequence data can provide insights for culturing previously uncultured microorganisms.

It is possible to reconstruct near-complete, and possibly complete, genomes of the dominant members of microbial communities from DNA that is extracted directly from the environment. Genome sequences from environmental samples capture the aggregate characteristics of the strain population from which they were derived. Comparison of the sequence data within and among natural populations can reveal the evolutionary processes that lead to genome diversification and speciation. Community genomic datasets can also enable subsequent gene expression and proteomic studies to determine how resources are invested and functions are distributed among community members. Ultimately, genomics can reveal how individual species and strains contribute to the net activity of the community.

Microbial communities are vital in the functioning of all ecosystems; however, most microorganisms are uncultivated, and their roles in natural systems are unclear. Here, using random shotgun sequencing of DNA from a natural acidophilic biofilm, we report reconstruction of near-complete genomes of Leptospirillum group II and Ferroplasma type II, and partial recovery of three other genomes. This was possible because the biofilm was dominated by a small number of species populations and the frequency of genomic rearrangements and gene insertions or deletions was relatively low. Because each sequence read came from a different individual, we could determine that single-nucleotide polymorphisms are the predominant form of heterogeneity at the strain level. The Leptospirillum group II genome had remarkably few nucleotide polymorphisms, despite the existence of low-abundance variants. The Ferroplasma type II genome seems to be a composite from three ancestral strains that have undergone homologous recombination to form a large population of mosaic genomes. Analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment.

Marine unicellular cyanobacteria are responsible for an estimated 20-40% of chlorophyll biomass and carbon fixation in the oceans. Here we have sequenced and analysed the 2.4-megabase genome of Synechococcus sp. strain WH8102, revealing some of the ways that these organisms have adapted to their largely oligotrophic environment. WH8102 uses organic nitrogen and phosphorus sources and more sodium-dependent transporters than a model freshwater cyanobacterium. Furthermore, it seems to have adopted strategies for conserving limited iron stores by using nickel and cobalt in some enzymes, has reduced its regulatory machinery (consistent with the fact that the open ocean constitutes a far more constant and buffered environment than fresh water), and has evolved a unique type of swimming motility. The genome of WH8102 seems to have been greatly influenced by horizontal gene transfer, partially through phages. The genetic material contributed by horizontal gene transfer includes genes involved in the modification of the cell surface and in swimming motility. On the basis of its genome, WH8102 is more of a generalist than two related marine cyanobacteria.

Omega-3 polyunsaturated fatty acids (PUFAs) such as eicosapentaenoic acid (20:5n-3; EPA) and docosahexaenoic acid (22:6n-3; DHA) have been shown to be of major importance in the promotion of cardiovascular health, proper human development and the prevention of some cancers. A high proportion of bacterial isolates from low-temperature and high-pressure marine environments produce EPA or DHA. This paper presents the sequence of a 33 kbp locus from the deep-sea bacterium Photobacterium profundum strain SS9 which includes four of the five genes required for EPA biosynthesis. As with other bacterial pfa (polyunsaturated fatty acid) genes, the deduced amino acid sequences encoded by the SS9 genes reveal large multidomain proteins that are likely to catalyse EPA biosynthesis by a novel polyketide synthesis mechanism. RNase protection experiments separated the SS9 pfa genes into two transcriptional units, pfaA-C and pfaD. The pfaA transcriptional start site was identified. Cultivation at elevated hydrostatic pressure or reduced temperature did not increase pfa gene expression despite the resulting increase in percentage composition of EPA under these conditions. However, a regulatory mutant was characterized which showed both increased expression of pfaA-D and elevated EPA percentage composition. This result suggests that a regulatory factor exists which coordinates pfaA-D transcription. Additional consideration regarding the activities required for PUFA synthesis is provided together with comparative analyses of bacterial pfa genes and gene products.

Education of our children is arguably society's most important task, profoundly shaping the communities in which we all live. Achievement and success in many facets of our culture depend critically on formal education. Education is widely perceived as the only viable weapon against the poverty, drug abuse, crime and teenage pregnancy that derail many citizens, particularly in the inner cities, from realizing their productive human potential. Beyond its value to individuals, education is the cornerstone of societal advancement.

To more fully explore the role of unsaturated fatty acids in high-pressure, low-temperature growth, the fabF gene from the psychrotolerant, piezophilic deep-sea bacterium Photobacterium profundum strain SS9 was characterized and its role and regulation were examined. An SS9 strain harboring a disruption in the fabF gene (strain EA40) displayed growth impairment at elevated hydrostatic pressure concomitant with diminished cis-vaccenic acid (18:1) production. However, growth ability at elevated pressure could be restored to wild-type levels by the addition of exogenous 18:1 to the growth medium. Transcript analysis did not indicate that the SS9 fabF gene is transcriptionally regulated, suggesting that the elevated 18:1 levels produced in response to pressure increase result from posttranscriptional changes. Unlike many pressure-adapted bacterial species such as SS9, the mesophile Escherichia coli did not regulate its fatty acid composition in an adaptive manner in response to changes in hydrostatic pressure. Moreover, an E. coli fabF strain was as susceptible to elevated pressure as wild-type cells. It is proposed that the SS9 fabF product, beta-ketoacyl-acyl carrier protein synthase II has evolved novel pressure-responsive characteristics which facilitate SS9 growth at high pressure.

There is considerable evidence correlating the production of increased proportions of membrane unsaturated fatty acids (UFAs) with bacterial growth at low temperatures or high pressures. In order to assess the importance of UFAs to microbial growth under these conditions, the effects of conditions altering UFA levels in the psychrotolerant piezophilic deep-sea bacterium Photobacterium profundum SS9 were investigated. The fatty acids produced by P. profundum SS9 grown at various temperatures and pressures were characterized, and differences in fatty acid composition as a function of phase growth, and between inner and outer membranes, were noted. P. profundum SS9 was found to exhibit enhanced proportions of both monounsaturated (MUFAs) and polyunsaturated (PUFAs) fatty acids when grown at a decreased temperature or elevated pressure. Treatment of cells with cerulenin inhibited MUFA but not PUFA synthesis and led to a decreased growth rate and yield at low temperature and high pressure. In addition, oleic acid-auxotrophic mutants were isolated. One of these mutants, strain EA3, was deficient in the production of MUFAs and was both low-temperature sensitive and high-pressure sensitive in the absence of exogenous 18:1 fatty acid. Another mutant, strain EA2, produced little MUFA but elevated levels of the PUFA species eicosapentaenoic acid (EPA; 20:5n-3). This mutant grew slowly but was not low-temperature sensitive or high-pressure sensitive. Finally, reverse genetics was employed to construct a mutant unable to produce EPA. This mutant, strain EA10, was also not low-temperature sensitive or high-pressure sensitive. The significance of these results to the understanding of the role of UFAs in growth under low-temperature or high-pressure conditions is discussed.

Let R = Q[x1, x2,..., xn] and R* denote the quotient of R by the ideal generated by the elementary symmetric functions. R*, under the action of Sn, yields a graded version of the left regular representation. Procesi asked for a basis of R* consisting of homogeneous polynomials Gamma[S, C] indexed by pairs of tableaux, with S standard and C cocharge, that exhibits the decomposition of R* into its irreducible components. Procesi also suggested a way to construct the Gamma[S, C]. Using Rota's straightening algorithm, I show that certain polynomials [S, C] closely related to the Gamma[S, C] terms yield the desired basis. Parallel to the ring R* there is a family of Sn-modules R that have recently been studied by Garsia and Procesi. These modules have a graded character that is closely related to the q-Kostka-Foulkes polynomials Klambdamu(q). The [S, C] can be shown to yield also a basis when restricted to a given R. Through this connection the work reported here leads to an additional way of proving the charge interpretation for the polynomials Klambdamu(q).

The [14C]2-deoxyglucose (2-DG) technique was used to study patterns of neural activity associated with the species-typical courtship behavior of male red-sided garter snakes (Thamnophis sirtalis parietalis). Males in this species court females intensely during the first month following spring emergence from their prolonged winter hibernation. Autoradiographic methods were used to measure the accumulation of radioactive label in various regions through the brains of male garter snakes that courted females, males that failed to court females, and males not exposed to females. Male garter snakes that actively courted females showed a pronounced increase in 2-DG accumulation, and therefore presumably neural activity, in the region of the anterior hypothalamus/preoptic area, relative to males that did not actively court females. Males exposed to females (regardless of whether they courted or not) showed widespread, non-specific increases in 2-DG uptake relative to males not exposed to females. The results indicate the utility of the 2-DG technique for studying complex, species-typical behaviors in vertebrates.

Immunoassay kits for urine cocaine (and metabolite) screening, obtained from two commercial sources, were examined for correlation of their results, expressed in terms of equivalent benzoylecgonine concentration, with the gas chromatography/mass spectrometry (GC/MS) concentration of benzoylecgonine. The correlation coefficients obtained, based on 62 (out of a total sample population of 3295) highly relevant samples, were 0.467 and 0.766 for Abuscreen (ARIA) and TDx (TDX), respectively. The preliminary screen cutoff values, which correspond to 150 ng/mL benzoylecgonine (as determined by GC/MS), were calculated based on the resulting regression equations and found to be 380 and 190 ng/mL for ARIA and TDX, respectively. With these cutoff values, ARIA generates 5 false negatives and 16 unconfirmed presumptive positives, while TDX results in 3 false negatives and 6 unconfirmed presumptive positives.

Because norepinephrine (NE) reuptake inhibitors have been reported to block 6-hydroxydopamine (6-OHDA) induced NE depletion, we wondered whether a reuptake inhibitor would block 6-OHDA's effects on visual cortical plasticity. We found, however, that desmethylimipramine (DMI) did not reduce 6-OHDA-induced NE depletion at 6-OHDA doses sufficient to prevent the effects of monocular deprivation. We also found that DMI itself induced transient NE depletion. We used this last result to further examine the NE hypothesis of depletion. In contrast to 6-OHDA-induced NE depletion, DMI-induced NE depletion was not accompanied by changes in visual cortical plasticity.

Under some circumstances intraventricular administration of 6-OHDA decreases visual cortical plasticity of kittens; the mechanism for this change is not known, but depletion of norepinephrine (NE) is not the entire explanation. We have examined the effects of 6-OHDA treatment on beta adrenergic receptor binding in kitten visual cortex. Subjects were given vehicle solution alone, a low dose of 6-OHDA which depleted cortical NE without affecting visuocortical plasticity, or a higher dose of 6-OHDA which depleted cortical NE and decreased visuocortical plasticity. Drugs were administered in single daily injections via intraventricular cannulas. Saturation assays were performed on homogenates of visual cortical tissue using 125I-pindolol (30-400 pM) along w/ isoproterenol (237 microM) as a cold competitor. We measured radioactivity bound to tissue and retained on filters and analyzed the data using the EBDA computer program (McPherson 1983, 1985); we determined the affinity constant (Kd) and receptor density (Bmax) in multiple assays for each animal. Despite 75-90% NE depletion in both experimental groups, only the group receiving the lower dose of 6-OHDA showed any evidence of supersensitivity. The Kds did not differ among the groups. The data suggest that the effects of 6-OHDA on visuocortical plasticity are not secondary to beta adrenergic supersensitivity.

The organization of thalamic input to functionally characterized zones in primary somatosensory cerebral cortex (S-I) of macaque monkeys (Macaca mulatta) was investigated using the method of labelling by retrograde transport of horseradish peroxidase (HRP). It was found that the cell columns positioned at the posterior margin of the band of cortex representing a given body region receive thalamic input from a posterior level of the ventroposterior thalamic nucleus (VP), and that cell columns at successively more anterior positions within that band receive input from successively more anterior levels of VP. The extreme posterior and anterior margins of the S-I hand, foot and face areas receive input from neuron populations which are not as widely separated in the anteroposterior dimension of VP as the neurons projecting to the extreme anterior and posterior margins of the proximal limb and trunk representations in S-I. These characteristics of the organization of the projections from VP to S-I are consistent with the view that the body representations in VP and S-I have the same connectivity and differential submodality distribution; and with the idea that thalamocortical conncetions only exist between functionally equivalent neuron populations in VP and S-I.

We recorded from the visual cortex of 4 groups of monocularly deprived kittens. Three groups were treated with intraventricular 6-hydroxydopamine (6-OHDA) at different times relative to monocular deprivation (MD). One group received only vehicle solution and MD. 6-OHDA caused the greatest decrease in plasticity in the kittens receiving 6-OHDA throughout the deprivation period; that is, these kittens were the least affected by MD. 6-OHDA caused a smaller decrease in plasticity in kittens receiving 6-OHDA just prior to eyelid suture and a still smaller decrease in kittens waiting a week between 6-OHDA treatment and eyelid suture. The kittens in all groups receiving 6-OHDA were equally depleted of norepinephrine (NE). We conclude that 6-OHDA decreases plasticity in the visual cortex; however, the time course of this decrease is better related to the time course of the 6-OHDA treatment than to the time course of NE depletion.

Unilateral visual stimulation following 2-deoxyglucose injection was used to delineate functional visual pathways in red-sided garter snakes (Thamnophis sirtalis parietalis) and whiptail lizards (Cnemidophorus inornatus and C. uniparens). Stimulation enhanced both overall uptake and particularly uptake in visual pathways contralateral to the side of stimulation. Bilaterally symmetrical uptake was observed in retinae, septum, nucleus sphericus, and brainstem nuclei. Overall uptake and lateralization of uptake were consistently greater in garter snakes than in whiptail lizards.

Spectral sensitivity of the cichlid fish Haplochromis burtoni was measured under both scotopic and photopic conditions using a two-choice, food reward, operant conditioning paradigm. The highest absolute sensitivity (scotopic) is one quantum for every 5 to 50 rods measured at 475 nm (equivalent to a corneal irradiance of 3.8 x 10(6) Q s-1 cm-2). A P500(1) photopigment apparently mediates spectral sensitivity over most of the visible spectrum; microspectrophotometric studies of rods had previously shown them to contain this photopigment. However, the scotopic behavioral action spectrum shows a sensitivity to short wavelength light higher than is consistent with a P500(1) photopigment alone mediating the scotopic visual process. Determinations made under photopic conditions reveal a behavioral action spectrum broader than that found under scotopic conditions and consistent with mediation by interaction of the three known cone types in an opponent processing manner. The calculated photopic threshold value of approximately 10(4) Q s-1 (receptor)-1 is in agreement with results from other species and corresponds to a corneal irradiance of about 7 x 10(10) Q s-1 cm-2.