A note on replication in (M,R)-systems

The condition which allows the existence of induced replication maps in (M,R)-systems is shown to place strong restrictions on the “richness” of the category from which these systems can be constructed. This condition also admits of a simple biological interpretation, which can be checked empirically, and which may offer insight into the physical and biological realizations of these abstract systems.     

Carotenoid synthesis in Streptomyces setonii ISP5395 is induced by the gene crtS, whose product is similar to a sigma factor

In many species of actinomycetes, carotenogenesis can be photoinduced. The capacity to respond to photoinduction is, however unstable and, in various strains of Streptomyces, is lost at a relatively high frequency. In Streptomyces setonii ISP5395, which normally produces no carotenoids, carotenoid-producing mutants can be obtained following protoplast regeneration. We report here the characterization of a gene, crtS, which was isolated from one such mutant and can confer on wild-type S. setonii ISP5395 cells the capacity to synthesize carotenoids. Sequence analysis of crtS reveals an open reading frame, which shows homology to genes that encode alternative sigma factors in Bacillus subtilis. We propose that crtS encodes a sigma factor which is necessary for the expression of a cryptic gene(s) for carotenoid biosynthesis in S. setonii ISP5395.     

Demiarcs,creaons and genons

Useful insights into the representation of natural systems can be gained by decomposing directed graphs (digraphs) into elementary components. Arcs of digraphs can be split into male demiarcs (outarcs) which leave vertices and female demiarcs (inarcs) which enter demiarcs. Likewise, a vertex can be split into an input perceiving side called the creaon and an output generating side called the genon. Digraphs can be regarded as being hierarchically organized because each vertex in a level-1 digraph can be expanded into a level-2 digraph. In general, each vertex of a level-i digraph can be expanded into a level-(i+1) digraph. Arcs of a level-i digraph can be regarded as bundles of level-(i + 1) arcs which are split at the vertex boundary. These elementary graphical components are shown to be useful for depicting input-output systems such as organisms, ecosystems and societies.     

Viable populations in a prey–predator system

 Lotka–Volterra equations are considered a dynamical game, where the phenotypes of the predator and of the prey can vary. This differs from the usual procedure of specifying as a priori laws according to which strategies are supposed to change. The question at stake is the survival of each of the species, instead of the maximization of a given pay-off by each player, as it is commonly discussed in games. The predator needs the prey, while the prey can survive without the predator. These obvious and simplistic constraints are enough to shape the regulation of the system: notably, the largest closed set of initial conditions can be delineated, from which there exists at least one evolutionary path where the population can avoid extinction forever. To these so-called viable trajectories, viable strategies are associated, respectively for the prey or for the predator. A coexistence set can then be defined. Within this set and outside the boundary, strategies can vary arbitrarily within given bounds while remaining viable, whereas on the boundary, only specific strategies can guarantee the viability of the system. Thus, the largest set can be determined, outside of which strategies will never be flexible enough to avoid extinction. Received 2 May 1995; received in revised form 15 August 1995     

Calcium signaling in pancreatic ductal epithelial cells: An old friend and a nasty enemy

Ductal epithelial cells of the exocrine pancreas secrete HCO₃⁻ rich, alkaline pancreatic juice, which maintains the intraluminal pH and washes the digestive enzymes out from the ductal system. Importantly, damage of this secretory process can lead to pancreatic diseases such as acute and chronic pancreatitis. Intracellular Ca²⁺ signaling plays a central role in the physiological regulation of HCO₃⁻ secretion, however uncontrolled Ca²⁺ release can lead to intracellular Ca²⁺ overload and toxicity, including mitochondrial damage and impaired ATP production. Recent findings suggest that the most common pathogenic factors leading to acute pancreatitis, such as bile acids, or ethanol and ethanol metabolites can evoke different types of intracellular Ca²⁺ signals, which can stimulate or inhibit ductal HCO₃⁻ secretion. Therefore, understanding the intracellular Ca²⁺ pathways and the mechanisms which can switch a good signal to a bad signal in pancreatic ductal epithelial cells are crucially important. This review summarizes the variety of Ca²⁺ signals both in physiological and pathophysiological aspects and highlight molecular targets which may strengthen our old friend or release our nasty enemy.     

Detecting overlapping coding sequences in virus genomes

Background  

Detecting new coding sequences (CDSs) in viral genomes can be difficult for several reasons. The typically compact genomes often contain a number of overlapping coding and non-coding functional elements, which can result in unusual patterns of codon usage; conservation between related sequences can be difficult to interpret – especially within overlapping genes; and viruses often employ non-canonical translational mechanisms – e.g. frameshifting, stop codon read-through, leaky-scanning and internal ribosome entry sites – which can conceal potentially coding open reading frames (ORFs).     

谷氨酸受体可逆磷酸化及其功能

谷氨酸受体(GluRs)C端区存在被多种蛋白激酶磷酸化的位点,同时又能被多种蛋白磷酸酶去磷酸化,磷酸化的结果可使Ca²⁺内流增加,增强GluRs功能;去磷酸化作用则相反.正常情况下GluRs可逆磷酸化处于一种动态平衡状态,在突触可塑性机制如长时程增强(LTP)中起重要作用,而在病理状态如缺血性脑损伤中,这种平衡失衡加重兴奋性神经元损伤.     

Massive fish kills within the Nyanza Gulf of Lake Victoria,Kenya

The morphometry and hydrology of the Nyanza Gulf of Lake Victoria can be greatly affected by violent storms. This can result in a condition in which nutrient-rich bottom mud is mixed with the sediment-laden runoff water from neighbouring marshes and rivers. This situation can lead to massive fish kills. It is such an event in 1984 which will be described that caused the sudden death of over 400 000 fish weighing over 2400 tonnes.The unusually low precipitation in the catchment area during that year resulted in a drop in the lake level from 12.4 to 11.8 m. This low water level, combined with a severe storm created the conditions which caused this large fish kill. The species affected were Lates niloticus and Oreochromis niloticus. Mortality was attributed to several factors which included high levels of suspended material in the water column (detritus and algae) which clogged the gills of the fish, low dissolved oxygen, low pH, and high concentrations of algae.     

A continuous spectrophotometric assay for Escherichia coli alanyl-transfer RNA synthetase

A new continuous spectrophotometric assay is demonstrated for Escherichia coli alanyl-tRNA synthetase. It involves β-γ adenylyl imidophosphate as a substitute for ATP in the pyrophosphate exchange reaction. The net conversion of β-γ adenylyl imidophosphate to ATP can be linked to NADP reduction by hexokinase and glucose-6-P dehydrogenase catalyzed reactions, which can be monitored at 340 nm. This assay can be extended to other aminoacyl-tRNA synthetases which can use β-γ nonhydrolyzable analogs of ATP as an ATP substitute.     

Mapping quantitative trait loci (QTLs) for fatty acid composition in an interspecific cross of oil palm

Background  

Marker Assisted Selection (MAS) is well suited to a perennial crop like oil palm, in which the economic products are not produced until several years after planting. The use of DNA markers for selection in such crops can greatly reduce the number of breeding cycles needed. With the use of DNA markers, informed decisions can be made at the nursery stage, regarding which individuals should be retained as breeding stock, which are satisfactory for agricultural production, and which should be culled. The trait associated with oil quality, measured in terms of its fatty acid composition, is an important agronomic trait that can eventually be tracked using molecular markers. This will speed up the production of new and improved oil palm planting materials.     

Transposon mutagenesis of nuclear photosynthetic genes in Zea mays

The discovery of a new maize (Zea mays L.) transposon system, Mutator, and the cloning of the 1.4 kilobase transposon, Mul, have made feasible the isolation of nuclear photosynthetic genes which are recognized only by their mutant phenotype. Mutant maize plants which express a high chlorophyll fluorescent (hcf) phenotype due to a defect in the electron transport or photophosphorylation apparatus have been isolated following mutagenesis with an active Mutator stock. The affected genes and their products in these mutants are inaccessible to classical methods of analysis. However, mutagenesis with the Mutator transposon makes it possible to isolate these genes.Although the PSII-deficient mutant hcf3 has been thoroughly studied by classical photo-biological methods, the nature of the lesion which results in the observed phenotype has not been established. A Mutator-induced allele of hcf3 has been isolated. A fragment of genomic DNA has been identified which is homologous to Mul and co-segregates with the mutant phenotype. This fragment is expected to contain a portion of the hcf3 locus which will be used to clone the normal gene. Direct study of the gene can provide insight into the nature and function of its polypeptide product.This approach can be used to study any photosynthetic gene which has been interrupted by a transposon. The isolation of more than 100 different chemically-induced hcf mutants, most of which can not be fully characterized using classical means, indicates the wealth of information which can be obtained using a transposon tagging technique.     

Nuclear mRNA Export Requires Complex Formation between Mex67p and Mtr2p at the Nuclear Pores

We have identified between Mex67p and Mtr2p a complex which is essential for mRNA export. This complex, either isolated from yeast or assembled in Escherichia coli, can bind in vitro to RNA through Mex67p. In vivo, Mex67p requires Mtr2p for association with the nuclear pores, which can be abolished by mutating either MEX67 or MTR2. In all cases, detachment of Mex67p from the pores into the cytoplasm correlates with a strong inhibition of mRNA export. At the nuclear pores, Nup85p represents one of the targets with which the Mex67p-Mtr2p complex interacts. Thus, Mex67p and Mtr2p constitute a novel mRNA export complex which can bind to RNA via Mex67p and which interacts with nuclear pores via Mtr2p.     

Carotenoid synthesis in Streptomyces setonii ISP5395 is induced by the gene crtS,whose product is similar to a sigma factor

In many species of actinomycetes, carotenogenesis can be photoinduced. The capacity to respond to photoinduction is, however unstable and, in various strains of Streptomyces, is lost at a relatively high frequency. In Streptomyces setonii ISP5395, which normally produces no carotenoids, carotenoid-producing mutants can be obtained following protoplast regeneration. We report here the characterization of a gene, crtS, which was isolated from one such mutant and can confer on wild-type S. setonii ISP5395 cells the capacity to synthesize carotenoids. Sequence analysis of crtS reveals an open reading frame, which shows homology to genes that encode alternative sigma factors in Bacillus subtilis. We propose that crtS encodes a sigma factor which is necessary for the expression of a cryptic gene(s) for carotenoid biosynthesis in S. setonii ISP5395.     

海岸桐的抗旱生物学特性

南沙群岛土壤主要以珊瑚砂为主,由于其光照强、土壤水分和养分贫瘠等环境条件,导致很少植物能够在岛上正常生长.为了快速恢复南沙岛礁的植被,需要筛选出抗旱性强的植物并进行引种.海岸桐(Guettarda speciosa)是一种典型的热带海岸植物,在海岛和海岸带防风固沙及植被生态恢复等方面发挥着重要作用.该文以西沙永兴岛自然...     

A temporal precedence based clustering method for gene expression microarray data

Background  

Time-course microarray experiments can produce useful data which can help in understanding the underlying dynamics of the system. Clustering is an important stage in microarray data analysis where the data is grouped together according to certain characteristics. The majority of clustering techniques are based on distance or visual similarity measures which may not be suitable for clustering of temporal microarray data where the sequential nature of time is important. We present a Granger causality based technique to cluster temporal microarray gene expression data, which measures the interdependence between two time-series by statistically testing if one time-series can be used for forecasting the other time-series or not.     

A new non-natural arginine-like amino acid derivative with a sulfamoyl group in the side-chain

Sulfamoylation of the l-ornithine methyl ester side-chain generates a non-natural arginine isostere which can be coupled with N-Fmoc-l-proline to synthesize analogues which maintain the structural characteristics of the biologically important Pro-Arg dipeptide sequence. As a probe of its biological importance, the sulfamoylated amino acid derivative was also incorporated as P1 residue in tripeptide structures matching the C-terminal subsequence of fibrinogen. The reported results demonstrate that the functionalization of l-ornithine side-chain with a neutral sulfamoyl group can generate an arginine bioisostere which can be used for the synthesis of prototypes of a new class of human thrombin inhibitors.     

Ultrastructural study of oocyte maturation in the polychaete annelid Sabellaria alveolata

Summary

Maturation begins by a cortical reaction, which resembles that of the sea urchin egg, but can precede fertilization. Complete vitelline membrane elevation necessitates the dissolution of the cortical granule matrix (which can be prevented by concanavalin A) and the retraction of the microvilli at the egg surface (which is inhibited by acid pH). Later on, an aster, with centrioles, develops near the nuclear envelope, which becomes undulated before disruption. In contrast to all other species so far studied, nuclear pores do not disappear and can even be observed several minutes later, in remmants of the nuclear envelope. The meiotic spindle has typical centrioles and, at metaphase I, chromosomes are surrounded by endoplasmic reticulum.     

组织酸化参与外周痛觉传递的离子通道机制

组织酸化可以导致痛觉的产生.初级感觉神经元可以通过离子通道来感受外周的组织酸化.已鉴定了几个离子通道家族可能参与了外周组织酸化的感受：a.酸敏感离子通道(ASICs)是可以被酸直接门控的阳离子通道;b.辣椒素受体(VR1)可被酸敏化,同时可被pH＜6.0直接激活;c.P2X2和P2X2/3受体通道反应被酸上调;d.TwIK相关的酸感受钾通道（TASK）是被酸关闭的双孔内向整流钾通道.这些通道被酸所调控的共同结果就是提高了神经元的兴奋性.因此,它们在介导了组织酸化所诱导的痛觉感受和传递中具有重要作用.     

Exploiting Lithium‐Depleted Cathode Materials for Solid‐State Li Metal Batteries

Solid‐state lithium metal batteries (SSLMBs) may become one of the high‐energy density storage devices for the next generation of electric vehicles. High safety and energy density can be achieved by utilizing solid electrolytes and Li metal anodes. Therefore, developing cathode materials which can match with Li metal anode efficiently is indispensable. In SSLMBs, Li metal anodes can afford the majority of active lithium ions, then lithium‐depleted cathode materials can be a competitive candidate to achieve high gravimetric energy density as well as save lithium resources. Li_0.33MnO₂ lithium‐depleted material is chosen, which also has the advantages of low synthesis temperature and low cost (cobalt‐free). Notably, solid‐state electrolyte can greatly alleviate the problem of manganese dissolution in the electrolyte, which is beneficial to improve the cycling stability of the battery. Thus, SSLMBs enable practical applications of lithium‐depleted cathode materials.     

Passive electrical properties of Halobacterium species

The electrical conductivity of suspensions of two species of Halobacterium was measured at low A. C. frequency. The results obtained fromHalobacterium halobium suspensions show that the bacteria act as non-conducting particles. In contrast, the cells of a Halobacterium obtained from the Dead Sea (Halobacterium marismortui) had an apparently high conductivity which can be explained partly in terms of the cell-membrane being pierced by pores through which ions can move freely and partly in terms of highly concentrated cell ions, all of which are mobile.