On the origin of three base periodicity in genomes

Genomes of almost all organisms have been found to exhibit several periodicities, the most prominent one is the three base periodicity. It is more pronounced in the gene coding regions and has been exploited to identify the segments of a genome that code for a protein. The reason for this three base periodicity in the gene-coding region has been attributed to inhomogeneous nucleotide compositions in the three codon positions. However, this reason cannot explain the three base periodicity present at the level of the whole genome where the codon concept is not applicable. Even though the distribution of each nucleotide is uniform at the positions 0(mod 3), 1(mod 3) and 2(mod 3) when the whole genome data is considered, our analysis reveals that the three base periodicity is arising because of higher correlations among the nucleotides separated by three bases.     

On RecA protein-mediated homologous alignment of two DNA molecules. Three strands versus four strands

The recA protein from Escherichia coli can homologously align two duplex DNA molecules; however, this interaction is much less efficient than the alignment of a single strand and a duplex. Three strand paranemic joints are readily detected. In contrast, duplex-duplex pairing is detected only when the incoming (second) duplex is negatively supercoiled, and even here the pairing is inefficient. The recA protein-promoted four strand exchange reaction is initiated in a three strand region, with efficiency increasing with the length of potential three strand pairing available for initiation. This indicates that a paranemic joint involving three DNA strands may be an important intermediate in all recA protein-mediated DNA strand exchange reactions and that the presence of three strands rather than four is a fundamental structural parameter of paranemic joints.     

Comparative structure analysis of proteinase inhibitors from the desert locust, Schistocerca gregaria.

The solution structure of three small serine proteinase inhibitors, two natural and one engineered protein, SGCI (Schistocerca gregaria chymotrypsin inhibitor), SGCI[L30R, K31M] and SGTI (Schistocerca gregaria trypsin inhibitor), were determined by homonuclear NMR-spectroscopy. The molecules exhibit different specificities towards target proteinases, where SGCI is a good chymotrypsin inhibitor, its mutant is a potent trypsin inhibitor, and SGTI inhibits both proteinases weakly. Interestingly, SGTI is a much better inhibitor of insect proteinases than of the mammalian ones used in common assays. All three molecules have a similar fold composed from three antiparallel beta-pleated sheets with three disulfide bridges. The proteinase binding loop has a somewhat distinct geometry in all three peptides. Moreover, the stabilization of the structure is different in SGCI and SGTI. Proton-deuterium exchange experiments are indicative of a highly rigid core in SGTI but not in SGCI. We suggest that the observed structural properties play a significant role in the specificity of these inhibitors.     

The computation of structure from fixed-axis motion: rigid structures

We show that three distinct orthographic views of three points in a rigid configuration are compatibel with at most 64 interpretations of the three-dimensional structure and motion of the points. If, in addition, one assumes that the three points spin about a fixed axis over the three views, then with probability one there is a unique three-dimensional interpretation (plus a reflection). Moreover the probability of false targets is zero. In the special case that the axis of rotation is parallel to the image plane three views of the three points are sufficient to obtain at most two interpretations (plus reflections)-unless one assumes the angular velocity about the axis is constant, in which case three views of two points are sufficient to determine a unique interpretation. Closed form solutions are obtained for each of these cases. The systems of equations studied here are in each case overconstraining (i.e. there are more independent equations than unknowns) and are amenable to solution by nonlinear programming. These two properties make possible the construction of noise insensitive algorithms for computer vision systems. Our uniqueness proofs employ the Principle of upper semicontinuity, a principle which underlies a general mathematical framework for the analysis of solutions to overconstraining systems of equations.     

The community matrix in three species community models

The explicit function of the community matrix of a three dimensional Lotka-Volterra model is delineated by a set of necessary and sufficient conditions for a positive equilibrium to be asymptotically stable. In the special case that the community matrix is quasi weakly diagonally dominant, it is shown that a positive determinant for the community matrix is not only necessary but is also sufficient for stability. The results are specific to three dimensional models and do not extend to communities of dimension greater than three.     

Mutational analysis of the mitochondrial copper metallochaperone Cox17

The copper metallochaperone Cox17 is proposed to shuttle Cu(I) ions to the mitochondrion for the assembly of cytochrome c oxidase. The Cu(I) ions are liganded by cysteinyl thiolates. Mutational analysis on the yeast Cox17 reveals three of the seven cysteinyl residues to be critical for Cox17 function, and these three residues are present in a Cys-Cys-Xaa-Cys sequence motif. Single substitution of any of these three cysteines with serines results in a nonfunctional cytochrome oxidase complex. Cells harboring such a mutation fail to grow on nonfermentable carbon sources and have no cytochrome c oxidase activity in isolated mitochondria. Wild-type Cox17 purified as untagged protein binds three Cu(I) ions/molecule. Mutant proteins lacking only one of these critical Cys residues retain the ability to bind three Cu(I) ions and are imported within the mitochondria. In contrast, Cox17 molecules with a double Cys --> Ser mutation exhibit no Cu(I) binding but are still localized to the mitochondria. Thus, mitochondrial uptake of Cox17 is not restricted to the Cu(I) conformer of Cox17. COX17 was originally cloned by virtue of complementation of a mutant containing a nonfunctional Cys --> Tyr substitution at codon 57. The mutant C57Y Cox17 fails to accumulate within the mitochondria but retains the ability to bind three Cu(I) ions. A C57S Cox17 variant is functional, and a quadruple Cox17 mutant with C16S/C36S/C47S/C57S substitutions binds three Cu(I) ions. Thus, only three cysteinyl residues are important for the ligation of three Cu(I) ions. A novel mode of Cu(I) binding is predicted.     

Role of weak interactions in thermal stability of proteins

A database analysis was done to study the role of weak interactions such as CHcdots, three dots, centeredO, CHcdots, three dots, centeredPI(m) and NHcdots, three dots, centeredPI(m) in the thermal stability of proteins. The CHcdots, three dots, centeredO and CHcdots, three dots, centeredPI(m) interactions are more in the case of thermophilic proteins as compared to mesophiles. Amino acid analysis showed that hydrophobic amino acids like Val and Ile, and Cys contribute more to CHcdots, three dots, centeredO hydrogen bonds where as Pro and Gly contribute more to CHcdots, three dots, centeredPI(m) interactions. Though NHcdots, three dots, centeredPI(m) interactions are dominated by Lys and Arg in thermophiles and mesophiles, the Arg contribution is significantly higher in thermophiles. Interestingly, Glycine is a predominant contributor to all the weak interactions. The number of aromatic amino acids in the thermophiles is more and hence a large number of aromatic clusters were observed in this class. Thus, a cumulative effect of weak interactions seems to be important in thermal stability of proteins. The study also shows that introduction of Gly, Arg, Phe, Pro, and Tyr may enhance the thermal stability.     

Study on binding modes between cellobiose and β-glucosidases from glycoside hydrolase family 1

The hydrolysis of cellobiose by β-glucodisases is an important step of cellulose biodegradation. However, the interactive mechanism between cellobiose and β-glucosidases is still unclear until now. Thus, in this study, we explored the binding modes between cellobiose and three β-glucosidases from glycoside hydrolase family 1 by means of molecular docking. The three β-glucosidases were named as TmGH1 (from bacterium Thermotoga), SsGH1 (from archaea Sulfolobus solfataricus) and TrGH1 (from fungus Trichoderma reesei) respectively, according to the monophyletic groups they belong to. Molecular dockings were performed between cellobiose and the three β-glucosidases, resulting in three optimum docking complexes, that is TmGH1-cellobiose, SsGH1-cellobiose and TrGh1-cellobiose complexes. Our docking results indicated that there were non-bonded interactions between cellobiose and the three β-glucosidases. The binding affinities of the three complexes were -13.6669kJ/mol, -13.2973kJ/mol and -18.6492kJ/mol, respectively. Then the detailed interactions were investigated, which revealed the key amino acid residues interacted with cellobiose by hydrogen bonds (H-bonds) or hydrophobic interactions. It was observed that most of the key residues involved in the non-bonded interactions were equivalent and conserved for the three complexes, and these residues were a glutamine, a histidine, a tyrosine, a phenylalanine, three glutamics, and four tryptophans. This information is of great importance for designing β-glucosidase with higher cellobiose-hydrolyzing efficiency.     

Hepatogenic polyglobulinemias and polycythemias]

The authors distinguish three kinds of hepatogenous polyglobulia: Polycythaemia caused by Budd-Chiari syndrome, polycythaemia caused by a Mosse syndrome (cirrhosis without liver venous thrombosis) and polyglobulia caused by liver tumours. In all three cases the same mechanism is likely to induce polycythaemia or polyglobulia respectively. In addition to the three cases of the Mosse syndrome published in 1966, the present paper deals with three cases of Budd-Chiari syndrome. Twice the Budd-Chiari syndrome was followed by a polycythaemia, once a Budd-Chiari syndrome was developed in the course of a polycythaemia vera.     

Transitional forms between the three domains of life and evolutionary implications

The question as to the origin and relationship between the three domains of life is lodged in a phylogenetic impasse. The dominant paradigm is to see the three domains as separated. However, the recently characterized bacterial species have suggested continuity between the three domains. Here, we review the evidence in support of this hypothesis and evaluate the implications for and against the models of the origin of the three domains of life. The existence of intermediate steps between the three domains discards the need for fusion to explain eukaryogenesis and suggests that the last universal common ancestor was complex. We propose a scenario in which the ancestor of the current bacterial Planctomycetes, Verrucomicrobiae and Chlamydiae superphylum was related to the last archaeal and eukaryotic common ancestor, thus providing a way out of the phylogenetic impasse.     

The pattern of expression of the Xenopus laevis tadpole alpha-globin genes and the amino acid sequence of the three major tadpole alpha-globin polypeptides

We have isolated cDNA clones derived from three tadpole alpha-globin mRNAs of Xenopus laevis. The entire nucleotide sequence of the three mRNAs has been determined from the cDNA clones and is presented together with the deduced amino acid sequence of the encoded polypeptides. Two of the three polypeptide sequences are 96% homologous whilst the third sequence is highly diverged, with only a 72% homology. The three tadpole alpha-globin genes are all similarly diverged from the two X. laevis adult alpha-globin genes with which they display approximately 50% homology. Analysis of several independent clones from each class of tadpole alpha-globin sequence reveals a very high degree of coding region polymorphism for each of the three corresponding genes. Using the cloned DNA sequences as hybridisation probes, we have analysed the expression of the corresponding genes during larval development. We show that all three genes are activated simultaneously early in development and that thereafter all three are expressed at an approximately equivalent level. A fourth tadpole alpha-globin mRNA sequence, for which we do not have a cDNA clone, accumulates co-ordinately with the three major mRNA sequences but to a much lower concentration. This pattern of gene expression differs significantly from that of the tadpole beta-globin genes of X. laevis, despite the two classes of genes being closely linked in the genome.     

The taxonomy, biogeography and host plant relationships of jumping plant-lice (Hemiptera: Psyllidae) associated with creosote bushes (Larrea spp., Zygophyllaceae)

Abstract.  The Neotropical genus Panisopelma (Psyllidae: Aphalaroidinae) is revised and its internal phylogeny analysed. The constituent species, including five new ones, are described and illustrated. Keys are provided for the adults and the last instar larvae. Eight species are associated with creosote bushes ( Larrea , Zygophyllaceae): five with L. nitida and three with L. divaricata . There is evidence that another three species, the larvae of which are unknown, also develop on L. divaricata . Seven species are restricted to Argentina, one to Bolivia and three to Chile. The cladistic analysis based on male, female and larval morphological characters yielded a single most-parsimonious tree. The species associated with L. nitida form a monophyletic clade, those on L. divaricata , by contrast, are paraphyletic. One clade with three species is restricted to Argentina, but three clades each contain a species from Argentina and Chile. Although a close association exists between Panisopelma and Larrea , there is no evidence for cospeciation, but rather an initial shift from an unknown host to L. divaricata and a second shift from L. divaricata to L. nitida . In three species pairs of Panisopelma , the distribution patterns suggest geographical vicariance between Argentina and Chile.     

Plasmodium berghei, P. chabaudi, and P. falciparum: similarities in phosphoproteins and protein kinase activities and their stage specific expression

Phosphoproteins from Plasmodium berghei, P. chabaudi, and P. falciparum are compared. A major phosphoprotein of 46 kDa is found in all three species. Peptide mapping indicates that this protein is indeed the same in all three cases and is phosphorylated at similar sites in all three species. Monoclonal antibodies were raised against three other P. berghei phosphoproteins. All three monoclonal antibodies recognize both P. berghei and P. chabaudi proteins. Only one of the monoclonal antibodies crossreacts with a P. falciparum protein of 36 kDa, whereas the equivalent P. berghei and P. chabaudi proteins are 34 and 32 kDa, respectively. The highest rate of synthesis of the phosphoproteins is observed during the early trophozoite stage, whereas the highest rate of phosphorylation is observed during the late trophozoite stage.     

Disulfide scrambling of interleukin-2: HPLC resolution of the three possible isomers

Native interleukin-2 (IL-2) contains three cysteines; two exist in a disulfide bridge (Cys-58 and Cys-105) and the third Cys-125 is a free sulfhydryl. In the presence of 6 M guanidine hydrochloride at alkaline pH, IL-2 is converted into three isomers. Each isomer represents one of the three possible disulfide-linked forms that can be generated from three cysteines. These three isomers were resolved on a C4 reverse-phase HPLC system. The identity of each of the three forms was determined by carboxymethylation of the free cysteines in each isomer with [3H]iodoacetic acid followed by determination of the labelled cysteines by tryptic peptide mapping. Tryptic peptide mapping of the more predominant of the two scrambled peaks showed it to be the Cys-105-S-S-Cys-125 linked form of IL-2. A Ser-125 construction of IL-2, which lacks a free cysteine, did not scramble under these conditions. These experiments demonstrate the utility of reverse-phase HPLC in studies of protein folding and disulfide bond structure.     

Photolysis and excitation in vertebrate photoreceptors

The proposal (Leibovic and Kurtz, 1975; Leibovic, 1975) that the physiological response of a vertebrate photoreceptor can be analyzed in terms of three stages of pigment photolysis is examined in relation to a possible transmitter acting on sodium channels in the outer segment membrane. One of the three stages is proposed to be a precursor for the transmitter. The functional significance of the three stages is considered in terms of visual adaption and the different needs of responding to light at low and at high levels of illumination.     

A SIMULATION OF WRIGHT'S SHIFTING-BALANCE PROCESS: MIGRATION AND THE THREE PHASES

Wright partitioned the shifting-balance process into three phases. Phase one is the shift of a deme within a population to the domain of a higher adaptive peak from that of the historical peak. Phase two is mass selection within a deme towards that higher peak. Phase three is the conversion of additional demes to the higher peak. The migration rate between demes is critical for the existence of phases one and three. Phase one requires small effective population sizes, hence low migration rates. Phase three is optimal under high migration rates that spread the most-fit genotype from deme to deme. Thus, a population-wide peak shift requires intermediate levels of migration. By altering the rates of phases one and three, migration affects the predominant direction of mass selection within a population. This study examines the degree to which migration, through its effects on phases one and three, determines the probability of a simulated population arriving at its genotypic optimum after 12,000 generations. These simulations reveal that there is a range of migration rates for which an entire population might be expected to shift to a higher peak. Below m = 0.001 peak shifts occur frequently (phases I and II) but are not successfully exported out of subpopulations (phase III), and above 0.01 peak shifts within demes (phase I and II), required to initiate phase III, become increasingly uncommon. Because it is unlikely that real populations will have uniform migration rates from generation to generation, the probable effects of varying migration rates on broadening the range of conditions producing peak shifts are discussed.     

Chronosexuality of Plasmodium species of Central African Muridae.

A host harbouring many parasite species of the same genus is a phenomenon frequently observed in numerous parasitic infections. This is the case for the Plasmodium parasites of Muridae in Central Africa, where three different parasite species are found in the same rodent host species. It is highly likely that these three Plasmodium species are transmitted simultaneously by the same vector. We and others have shown that the maturation periods of the various asexual and sexual stages in the rodent, differ amongst the three parasites. In this article we propose that these differences are the product of complex adaptations which result, for all three Plasmodium species, in a maximum peak of infectivity to the insect vector occurring around 3 a.m., the period of highest activity of the nocturnal host rodent.     

3个中山杉杂种无性系及其亲本的光合特性比较

对‘中山杉405’(Taxodium‘Zhongshanshan 405’)、‘中山杉406’(T.‘Zhongshanshan 406’)和‘中山杉407’(T.‘Zhongshanshan 407’)及其母本墨西哥落羽杉(T.mucronatum Tenore)和父本落羽杉〔T.distichum(L.)Rich.〕在7月份、9月份和10月份的光合参数进行了测定,并比较了3个无性系净光合速率(Pn)、气孔导度(Gs)、蒸腾速率(Tr)和水分利用效率(WUE)的杂种优势。结果显示:不同月份3个无性系及其亲本的Pn值有明显差异,导致光响应曲线明显不同,但3个无性系的光响应曲线基本一致;3个无性系的Pn值在不同月份都高于落羽杉,且‘中山杉405’的Pn值高于另2个无性系。3个无性系及其亲本的光补偿点总体上表现为7月份最高、10月份最低,其中7月份墨西哥落羽杉的光补偿点显著高于3个无性系及落羽杉(P<0.05);3个无性系和墨西哥落羽杉的光饱和点则为9月份最高、7月份最低,而落羽杉的光饱和点为9月份最高、10月份最低。7月份3个无性系与其亲本的Pn日变化曲线均呈不规则型,低谷出现在中午12:00左右;9月份和10月份3个无性系和墨西哥落羽杉的Pn日变化曲线均呈单峰型,峰值出现在上午10:00;落羽杉的Pn值从上午8:00开始呈持续降低的趋势,且全天都明显低于其他树种。不同月份3个无性系的Pn、Gs、Tr和WUE的杂种优势有明显差异,总体上看,‘中山杉405’的Pn、Gs和Tr在3个月份中均保持较高的杂种优势率,而‘中山杉406’9月份的杂种优势率最高,‘中山杉407’则在7月份杂种优势率最高;3个无性系的WUE仅在10月份有明显的杂种优势,且‘中山杉405’和‘中山杉406’的杂种优势率远高于‘中山杉407’;‘中山杉405’各项指标的杂种优势率总体上高于另2个无性系。研究结果表明:3个中山杉无性系的光合能力接近其母本墨西哥落羽杉、高于父本落羽杉,其中‘中山杉405’杂种优势明显。     

Treatment of Epilepsy

The main clinical types of epilepsy and their treatment are described. The treatment of choice in petit mal epilepsy is trimethadione (Trimedone) 0.3 g., three to six times a day, or acetazolamide (Diamox) 125-250 mg., three to four times a day. Phenobarbital is usually given as well to prevent grand mal seizures. Diphenylhydantoin sodium (Dilantin Sodium), 100 mg., and/or phenobarbital, 30-100 mg., three to four times a day, is recommended in patients with focal and grand mal epilepsy. Psychomotor automatisms are a form of focal seizure. Primidone (Mysoline), in doses of 125-250 mg. two to three times a day, is a very useful anticonvulsant in patients with myoclonic features, psychomotor automatisms and grand mal seizures. Primidone should be started in small doses. Drug reactions, especially cerebellar ataxia in the case of diphenylhydantoin and blood dyscrasias in the case of some drugs, should be recognized. Excessive drowsiness can be avoided by proper dosage and proper timing of drug administration. Patients should be seen regularly at least two to three times a year. The objective of treatment is to achieve optimum control of seizures by using the appropriate drug in adequate dosage. Social adaptation is good in the majority of patients, who should be encouraged to carry on their life independently, usually free to marry and have children. Attention to special occupational hazards has to be considered. Education of employers and employees is often necessary. Special work arrangements are occasionally indicated for selected patients. Patients should be seizure-free for two to three years before permission is given to drive an automobile.