Effects of photosynthetic inhibitors and light-dark regimes on the replication of cyanophage SM-2

The effects of photosynthetic inhibitors and light-dark regimes on the replication of cyanophage SM-2 in its host cyanobacteria (Synechococcus elongatus UTEX 563 and Microcystis aeruginosa NRC-1, Synechococcus NRC-1 UTEX 1937) have been investigated. Photoassimilation of CO₂ by infected cells was enhanced and remained elevated until late in the infection cycle. Photosynthetic inhibitors and the removal of light suppressed viral replication. SM-2, like other cyanophage of unicellular cyanobacteria, is highly dependent on host photosynthetic metabolism for the energy required in replication.Abbreviations DCMU 3-(3,4-dichlorophenyl)-1,1-dimethylurea - CCCP carbonyl-cyanide m-chlorophenyl hydrazone - MMH Modified Modified Hughes Medium     

A revised equation relating DNA buoyant density to guanine plus cytosine content

An equation relating DNA buoyant density of CsCl to G + C content is given which uses the correct density value of Escherichia coli DNA as the reference. This is done to eliminate the current confusion brought about by two references states.     

FramePlot: a new implementation of the Frame analysis for predicting protein-coding regions in bacterial DNA with a high G+C content

FramePlot is a web-based tool for predicting protein-coding regions in bacterial DNA with a high G + C content, such as Streptomyces. The graphical output provides for easy distinction of protein-coding regions from non-coding regions. The plot is a clickable map. Clicking on an ORF provides not only the nucleotide sequence but also its deduced amino acid sequence. These sequences can then be compared to the NCBI sequence database over the Internet. The program is freely available for academic purposes at http://www.nih.go.jp/jun/cgi-bin/frameplot.pl.     

The effects of guanine and cytosine variation on dinucleotide frequency and amino acid composition in the human genome

Summary One hundred twelve human DNA sequences were analyzed with respect to dinucleotide frequency and amino acid composition. The variation in guanine and cytosine (G+C) content revealed: (1) at 2–3 and 3-1 doublet positions CG discrimination is attenuated at high G+C, but TA disfavor is enhanced, and (2) several amino acids are subject to G+C change. These findings have been reported in part for collections of sequences from various species. The present study confirms that in a single organism-the human-the G+C effects do exist. Aspects of the argument that connects G+C with protein thermal stability are also discussed.     

The evaluation of an average nucleotide composition from melting curves

A new formula has been derived for the calculation of the average G + C content - X of DNAs from different origins using thermal melting data. As compared to existing formulas the new method gives highly accurate results, although being much easier to use than similar equations.     

细菌ncRNA基因预测工具的评估

<正>细菌非编码RNA(ncRNA)在RNA的转录调节、染色体复制、RNA加工与修饰、m RNA翻译与稳定性、蛋白质降解与转运以及细菌感染等许多过程中都发挥着重要作用[1]。目前,基于实验鉴定的细菌ncRNA,已开发出不同的生物信息学预测方法[3-6],其中比较基因组学和转录单元预测方法是目前最常用的方法。比较基因组学和转录单元预测方法的结合使用,具有较高的特异性,但大多数方法的普适性较低,不     

Modulation of succinate transport in Hep G2 cell line by PKC

The cellular uptake of the tricarboxylic acid cycle (TCA) intermediates is very important for cellular metabolism. However, the transport pathways for these intermediates in liver cells are not well characterized. We have examined the transport of succinate and citrate in the human hepatoma cell line Hep G2 and found that it exhibited a higher rate of succinate compared to citrate transport, which was sodium dependent. Comparison of the transport properties of Hep G2 to that of human retinal pigment epithelial (HRPE) cells transfected with human sodium dicarboxylate transporters, hNaDC-1, hNaDC-3, and hNaCT indicated that Hep G2 cells express a combination of hNaDC-3 and hNaCT. Short period activation of protein kinase C (PKC) by phorbol 12-myristate, 13-acetate (PMA) and α-adrenergic receptor agonist, phenylephrine (PE), downregulated sodium-dependent succinate transport presumably via hNaDC-3. The inhibition by PMA was partially prevented by cytochalasin D, suggesting that PKC reduces the hNaDC-3 activity, at least in part, by increased endocytosis. In contrast, activation of PKA by both forskolin and epidermal growth factor (EGF) had no effect on succinate transport. Our results suggest that Hep G2 cells provide a useful model for studies of di- and tricarboxylate regulation of human liver.     

Stimulation of Ca efflux from fura-2-loaded platelets activated by thrombin or phorbol myristate acetate

We investigated the restoration of [Ca²⁺]_i in fura-2-loaded human platelets following discharge of internal Ca²⁺ stores in the absence of external Ca²⁺. After stimulation by thrombin [Ca²⁺]_i returned from a peak level of 0.6 μM to resting levels within 4 min. When ionomycin discharged the internal stores the recovery was slower with [Ca²⁺]_i still elevated at around 0.5 μM after 5 min. Thrombin added shortly after ionomycin could accelerate the recovery of [Ca²⁺]_i and restore resting levels within 5 min, an effect that was mimicked by phorbol-12-myristate-13-acetate (PMA). Since the continued presence of ionomycin precluded reuptake into the internal stores we conclude that thrombin and PMA stimulate Ca²⁺ efflux, perhaps via protein kinase C actions on a plasma membrane Ca²⁺ pump.     

Kinetic Characterization of Ca2+ Transport in Synaptic Membranes

Lysed synaptosomal membranes were prepared from brain cortices of HA/ICR Swiss mice, and the ATP-stimulated Ca2+ uptake, Ca2+-stimulated Mg2+-dependent ATPase activity, and the Ca2+-stimulated acyl phosphorylation of these membranes were studied. The Km values for free calcium concentrations ([Ca2+]f) for these processes were 0.50 microM, 0.40 microM, and 0.31 microM, respectively. Two kinetically distinct binding sites for ATP were observed for the ATP-stimulated Ca2+ uptake and the Ca2+-stimulated Mg2+-ATPase activity. The high-affinity Km values for ATP for these two processes were 16.3 microM and 28 microM, respectively. These results indicate that the processes studied operate in similar physiological concentration ranges for the substrates [Ca2+]f and ATP under identical assay conditions and, further, that these processes may be functionally coupled in the membrane.     

Analysis of nucleotide distribution in the genome of Streptomyces coelicolor A3(2) using the Z curve method

The nucleotide distribution of all 33 527 open reading frames (ORFs) (≥300 bp) in the genome of Streptomyces coelicolor A3(2) has been analyzed using the Z curve method. Each ORF is mapped onto a point in a 9-dimensional space. To visualize the distribution of mapping points, the points are projected onto the principal plane based on principal component analysis. Consequently, the distribution pattern of the 33 527 points in the principal plane shows a flower-like shape, in which there are seven distinct regions. In addition to the central region, there are six petal-like regions around the center, one of which corresponds to 7172 coding sequences. The central region and the remaining five petal-like regions correspond to the intergenic sequences and out-of-frame non-coding ORFs, respectively. It is shown that selective pressure produces a remarkable bias of the G+C content among three codon positions, resulting in the interesting phenomenon observed. A similar phenomenon is also observed for other bacterial genomes with high genomic G+C content, such as Pseudomonas aeruginosa PA01 (G+C=66.6%). However, for the genomes of Bacillus subtilis (G+C=43.5%) and Clostridium perfringens (G+C=28.6%), no similar phenomenon was observed. The finding presented here may be useful to improve the gene-finding algorithms for genomes with high G+C content. A set of supplementary materials including the plots displaying the base distribution patterns of ORFs in 12 prokaryotes is provided on the website http://tubic.tju.edu.cn/highGC/.     

A new value for mol percent guanine + cytosine of DNA for the salmonid fish pathogen Renibacterium salmoninarum

The mol% G + C of DNA extracted from seven different isolates of Renibacterium salmoninarum was determined. Organisms studied were from selected geographical areas (U.S.A., Canada, England and France) and were isolated from five different species of salmonid fish. The mol% G + C was determined to be 55.5, higher than the currently reported value of 53.     

Ca2+-Dependent and Ca2+-Independent Protein Kinase C Changes in the Brains of Patients with Alzheimer's Disease

Abstract: We examined protein kinase C (PKC) activity in Ca²⁺-dependent PKC (Ca²⁺-dependent PKC activities) and Ca²⁺-independent PKC (Ca²⁺-independent PKC activities) assay conditions in brains from Alzheimer's disease (AD) patients and age-matched controls. In cytosolic and membranous fractions, Ca²⁺-dependent and Ca²⁺-independent PKC activities were significantly lower in AD brain than in control brain. In particular, reduction of Ca²⁺-independent PKC activity in the membranous fraction of AD brain was most enhanced when cardiolipin, the optimal stimulator of PKC-ε, was used in the assay; whereas Ca²⁺-independent PKC activity stimulated by phosphatidylinositol, the optimal stimulator of PKC-δ, was not significantly reduced in AD. Further studies on the protein levels of Ca²⁺-independent PKC-δ, PKC-ε, and PKC-ζ in AD brain revealed reduction of the PKC-ε level in both cytosolic and membranous fractions, although PKC-δ and PKC-ζ levels were not changed. These findings indicated that Ca²⁺-dependent and Ca²⁺-independent PKC are changed in AD, and that among Ca²⁺-independent PKC isozymes, the alteration of PKC-ε is a specific event in AD brain, suggesting its crucial role in AD pathophysiology.     

散斑壳属两近似种的表型性状和ITS序列分析比较研究

对针叶树散斑壳Lophodermium conigenum与其近似种南方散斑壳L.australe的形态学特征及生态习性等进行了比较研究,同时对这两个种8个菌株的rDNA-ITS区进行了PCR扩增和序列测定,结合GenBank中16个相关ITS序列构建了系统发育树。结果表明,L.conigenum与L.australe有着非常密切的关系。L.conigenum除子囊果形状、子座基部层、线纹和寄生性外,其余特征与L.australe基本相同。L.conigenum的ITS序列的G+C含量(51.0%)小于L.australe的G+C含量(54.0%)。在系统发育树中,此二种形成两个明显独立的分支,支持了依据形态学等表型性状的分类。二者种间及种内的遗传差异与寄主有较大的相关性,而与产地无明显关联。通过表型性状和ITS序列的分析与比较,可准确地将L.conigenum与L.australe鉴别开来。     

Multi-Shell Copper Catalysts for Selective Electroreduction of CO2 to Multicarbon Chemicals

Electrocatalytic CO₂ reduction (CO₂R) coupled with renewable electricity has been considered as a promising route for the sustainability transition of energy and chemical industries. However, the unsatisfactory yield of desired products, particularly multicarbon (C₂₊) products, has hindered the implementation of this technology. This work describes a strategy to enhance the yield of C₂₊ product formation in CO₂R by utilizing spatial confinement effects. The finite element simulation results suggest that increasing the number of shells in the catalyst wil lead to a high local concentration of *CO and promotes the formation of C₂₊ products. Inspired by this, Cu nanoparticles are synthesized with desired hollow multi-shell structures. The CO₂ reduction results confirm that as the number of shells increase, the hollow multi-shell copper catalysts exhibit improved selectivity toward C₂₊ products. Specifically, the Cu catalyst with 4.4-shell achieved a high selectivity of over 80% toward C₂₊ at a current density of 900 mA cm⁻². Evidence from in situ attenuated total reflection surface-enhanced infrared absorption spectroscopy unveils that the multi-shell Cu catalyst exhibits an enhanced *CO_atop coverage and the stronger interaction with *CO_atop compared to commercial Cu, confirming the simulation results. Overall, the work promises an effective approach for boosting CO₂R selectivity toward value-added chemicals.     

Analysis of the codon usage of the cephamycin C producer Nocardia lactamdurans

Abstract The G + C content in a sequenced region of 27 kb of the Nocardia lactamdurans genome is 70.4 and 70.6% in the 14 characterized ORFs, showing an extreme average G + C content (94.9%) in the third codon position. The codon usage parameters of the N. lactamdurans genes studied are closely related and depart weakly from the values of other species of the genus Nocardia . The homologies and differences in the codon usage between N. lactamdurans and Streptomyces sp. or other high-G + C Gram-positive genera are analysed.     

Regulation of the L-Type Ca2+ Channel Current in Rat Pinealocytes

Abstract : In the present study, the role of phosphoprotein phosphatase in the regulation of L-type Ca²⁺ channel currents in rat pinealocytes was investigated using the whole-cell version of the patch-clamp technique. The effects of three phosphatase inhibitors, calyculin A, tautomycin, and okadaic acid, were compared. Although all three inhibitors were effective in inhibiting the L-type Ca²⁺ channel current, calyculin A was more potent than either tautomycin or okadaic acid, suggesting the involvement of phosphoprotein phosphatase-1. To determine the kinase involved in the regulation of these channels, cells were pretreated with H7 (a nonspecific kinase inhibitor), H89 (a specific inhibitor of cyclic AMP-dependent kinase), KT5823 (a specific inhibitor of cyclic GMP-dependent kinase), or calphostin C (a specific inhibitor of protein kinase C). Pretreatment with either H7 or calphostin C decreased the inhibitory effect of calyculin A on the L-type Ca²⁺ channel current. In contrast, pretreatment with H89 or KT5823 had no effect on the inhibition caused by calyculin A. Based on these observations, we conclude that basal phosphatase activity, probably phosphoprotein phosphatase-1, plays an important role in the regulation of L-type Ca²⁺ channel currents in rat pinealocytes by counteracting protein kinase C-mediated phosphorylation.     

Intracellular redistribution of protein kinase D2 in response to G-protein-coupled receptor agonists

The protein kinase D (PKD) family consists of three serine/threonine protein kinases: PKC mu/PKD, PKD2, and PKC nu/PKD3. While PKD has been the focus of most studies to date, no information is available on the intracellular distribution of PKD2. Consequently, we examined the mechanism that regulates its intracellular distribution in human pancreatic carcinoma Panc-1 cells. Analysis of the intracellular steady-state distribution of fluorescent-tagged PKD2 in unstimulated cells indicated that this kinase is predominantly cytoplasmic. Cell stimulation with the G protein-coupled receptor agonist neurotensin induced a rapid and reversible plasma membrane translocation of PKD2 by a mechanism that requires PKC activity. In contrast to the other PKD isoenzymes, PKD2 activation did not induce its redistribution from the cytoplasm to the nucleus. Thus, this study demonstrates that the regulation of the distribution of PKD2 is distinct from other PKD isoenzymes, and suggests that the differential spatio-temporal localization of these signaling molecules regulates their specific signaling properties.     

DNA序列进化过程中核苷酸替代的非独立性研究

本文评述了DNA序列间核苷酸替代数的估计方法,并通过对七个物种中组蛋白基因的比较对DNA进化的模型进行了考察。发现H2A基因第三位点上的碱基组成在物种间变异很大,并且跟H2A基因第一位点、H4基因第一、三位点及H2A上游,下游序列中的碱基组成有强正相关,提示DNA序列进化过程中存在着物种特异的区域性约束力。可能的原因是高等真核生物中GC含量升高,或者是染色体重组使这些同源序列位于不同的等质区段,从而受到不同的选择突变压。密码内各位点上核苷酸替代的相关性分析表明不同位点的替代是非独立的,其原因可能是一次替代事件引起多个位点的变化。文中讨论了这些结果对进化树推断的意义。