Metabolite profiles and growth characteristics of Rhizobium meliloti cultivated at different specific growth rates

Rhizobium meliloti (ATCC 55340) was grown at different specific growth rates in a chemostat apparatus. Metabolic products, relating to the Embden-Meyerhof-Parnas (EMP) pathway and the tricarboxylic acid (TCA) cycle, were measured and quantified to probe the influence of specific growth rate on the distribution of important metabolites. The detection of propionate in the fermentation broth implies that the imbalance of reducing equivalents of FADH(2) and NADH + H(+) resulted in a partially reductive operation of the TCA cycle. Additionally, experimental results show that the specific growth rate plays an essential role in modulating the biomass concentration, the specific substrate uptake rate, the cell length, the specific exopolysaccharide (EPS) production rate, the distribution of EPS molecular weight, and the profiles of carbohydrate and organic acid. The specific EPS production rate (varying from 13.3 to 111 mg EPS/g-DW/h) follows a growth-associated pattern at the specific growth rate ranging from 0.06 to 0.20 h(-1) and switches into non-growth-associated mode when the specific growth rate is over 0.20 h(-1).     

Single strand conformation of adenylate chains analysed by a specific photoreaction. Determination of structure by 5'' residue.

The photoreactivity was analysed in various oligo- and polyadenylates: 1) The quantum yields of the specific photoreaction in poly(dA) and dApdA decrease with increasing temperature, whereas the quantum yield of the photodegradation in poly(rA) increases. 2) The photoreactivities of poly(2'MeA) and poly(2'EtA) closely correspond to that of poly(rA). 3) The photodegradation of rApdA is very similar to that of rAprA, whereas dAprA shows the same specific photoreaction as observed for dApdA. These data support the view, that the specific photoreaction observed in oligo(dA) and poly(dA) is dependent upon a specific conformation, which is not accessible to oligo(rA), poly(rA), poly(2'MeA) and poly(2'EtA). The specific conformation is determined by the nucleotide, which carries the internucleotide bond in the 3'-position.     

ROOT AERENCHYMA DEVELOPMENT IN SPARTINA PATENS IN RESPONSE TO FLOODING

Root aerenchyma, developed in response to flooding, was measured as specific gravity in previously existing (old) and newly developed (new) roots of Spartina patens in a 25-day greenhouse experiment. Root specific gravity was related to porosity (fractional volume of aerenchyma): porosity = 1.026 – 0.969 × specific gravity, over a wide range of specific gravities (0.5 to 0.9). The specific gravity of flooded roots (new and old) decreased from 0.78 to 0.58 between day 5 and 25, while the specific gravity of old roots that remained drained did not change. After 5 days growth, newly produced roots were found to have less aerenchyma than their older counterparts, but after 25 days the specific gravity of new roots equaled that of old roots. In addition, flooding increased mortality of preexisting roots and inhibited growth of new roots.     

Over-expression of recombinant human interferon-gamma in high cell density fermentation of Escherichia coli

Human interferon-gamma (hIFN-gamma) was expressed in Escherichia coli BL21(DE3) under the control of the T7 promoter. Glucose was used as the sole source of carbon and energy with simple exponential feeding rate in fed-batch process. Cell density of recombinant E. coli was reached to 100 g dry wt l(-1) under both constant (0.12 h(-1)) and variable (0.12-0.52 h(-1)) specific growth rates. In the variable specific growth rate fed-batch process, plasmid stability and specific yield of rhIFN-gamma were greater than constant specific growth rate fed-batch process. The final specific yield and overall productivity of rhIFN-gamma were 0.35 +/- 0.02 g rhIFN-gamma g(-1) dry cell wt and 0.9 +/- 0.05 g rhIFN-gamma l(-1) h(-1) in the variable specific growth rate fed-batch process, respectively.     

The binding of the cyclic AMP receptor protein to synthetic DNA sites containing permutations in the consensus sequence TGTGA.

The binding of the cyclic AMP receptor protein (CRP) to symmetrical synthetic DNA-binding sites was investigated with a gel-retardation assay. A set of ten different sequences was employed, comprising all base permutations at positions 2, 4, and 5 of the consensus sequence 5'(TGTGA)3'. We show that: (i) CRP has a higher affinity for the completely symmetrical site than towards the lac wild-type site; (ii) base substitutions at position 2 lead to either a complete loss of specific CRP binding (G----C), a reduction in specific CRP binding (G----A) or only marginal effects on specific CRP binding (G----T); (iii) changes at position 4 abolish (G----C; G----A) or reduce (G----T) specific CRP binding; and (iv) base permutations at position 5 reduce specific CRP binding, but never completely abolish it. Thus position 4, and to a lesser extent position 2, in the DNA consensus sequence are the most crucial ones for specific binding by CRP.     

Differences in tissue expressions of enzyme activities in interspecific sunfish (Centrarchidae) hybrids and their backcross progeny

The extent of naturally occurring variations of enzyme locus expression was determined for three tissues (liver, muscle, and eye) in two species of sunfish (Centrarchidae), the green sunfish (Lepomis cyanellus) and the redear sunfish (L. microlophus). The genetic basis for species differences in tissue enzyme specific activities of malate dehydrogenase (EC 1.1.1.37), lactate dehydrogenase (EC 1.1.1.27), phosphoglucomutase (EC 2.7.5.1), and glucosephosphate isomerase (EC 5.3.1.9) was investigated by determining enzyme specific activities in the tissues of the reciprocal F1 hybrids and of their backcross progenies. The specific activities for most enzymes in hybrids were intermediate between those of the parental species. Significant differences in enzyme specific activity were detected among the F1 progeny as well as those of backcrosses. Variations in specific activity levels in one tissue were often independent of variations in specific activities in a different tissue. However, the changes in the specific activities of different enzymes within the same tissue were often positively correlated. The tissue glucosephosphate isomerase activity differences appear not to be due to different functional contributions of the glucosephosphate isomerase allelic isozymes. Cluster analysis of distributions of specific activities revealed no simple Mendelian pattern of inheritance for control of tissue enzyme activity. Our results suggest a polygenic control of tissue enzyme specific activity levels.     

Eicosanoid biosynthesis is activated via Toll, but not Imd signal pathway in response to fungal infection

Phospholipase A(2) (PLA(2)) catalyzes hydrolysis of phospholipids at sn-2 position and usually releases arachidonic acid, which is oxygenated into various eicosanoids that mediate innate immune responses in insects. PLA(2) activities were measured in both immune-associated tissues of hemocyte and fat body in the beet armyworm, Spodoptera exigua. Upon challenge of an entomopathogenic fungus, Beauveria bassiana, the PLA(2)s were significantly activated in both hemocyte and fat body. The fungal infection also induced gene expression of antimicrobial peptides (AMPs), such as two attacins, cecropin, gallerimycin, gloverin, hemolin, and transferrin of S. exigua. RNA interference of Toll or Imd signal pathway using double-stranded RNAs (dsRNAs) specific to SeToll or SeRelish suppressed specific AMP gene expressions, in which dsRNA specific to SeToll suppressed two attacins, cecropin, gallerimycin, gloverin, hemolin, and transferrin I, while dsRNA specific to SeRelish suppressed only cecropin. Interestingly, dsRNA specific to SeToll also significantly inhibited the activation of PLA(2) in response to the fungal infection, but dsRNA specific to SeRelish did not. Eicosanoid-dependent hemocyte nodulation was inhibited by dsRNA specific to SeToll but was not by dsRNA specific to SeRelish. These results suggest that eicosanoid biosynthesis is activated via Toll, but not Imd signal pathway in response to fungal infection in S. exigua.     

Leucine pools in normal and dystrophic chicken skeletal muscle cells in culture

The specific radioactivity of [3H]Leu in the extracellular, intracellular, and Leu-tRNA pools of normal (white leghorn) and dystrophic (line 307) embryonic chick breast muscle cultures was analyzed as a function of equilibration time and extracellular Leu concentration (0.05-5 mM). The primary results were the following 1) [3H]Leu equilibrated to a constant specific radioactivity in the intracellular and Leu-tRNA pools within 2 min after addition to both normal and dystrophic cultures. 2) After equilibration, the extracellular [3H] Leu specific radioactivity in dystrophic cell culture medium was lower than that of medium exposed to normal cells (especially at low Leu concentrations), probably because of increased release of unlabeled Leu from the dystrophic cells as a result of faster protein breakdown. Accordingly, the specific radioactivities in the intracellular and the Leu-tRNA pools were also lower in dystrophic cells. 3) At 5 mM extracellular Leu, the specific radioactivity in the Leu-tRNA pool was approximately 40% lower than the specific radioactivity in the intracellular pool in both normal and dystrophic cells. Thus, high concentrations of extracellular Leu cannot be used to "flood out" reutilization of unlabeled Leu (released by protein degradation) during protein synthesis. 4) At 5.0 mM extracellular Leu, the specific radioactivity of [3H]Leu in the intracellular pool was comparable to that in the extracellular pool in normal and dystrophic cells; however, the specific radioactivity of Leu-tRNA (i.e. the immediate precursor to protein synthesis) was only 55-65% of the extracellular specific radioactivity in normal and dystrophic cells. In conclusion, reutilization of Leu from protein degradation is higher in dystrophic muscle cell cultures than in normal muscle cell cultures, and accurate rates of protein synthesis in cell cultures can only be obtained if specific radioactivity of amino acid in tRNA is measured.     

Expansion of symmetric exon-bordering domains does not explain evolution of lineage specific genes in mammals

In order to examine the evolution of lineage specific genes, we analyzed intron phase distributions and exon-bordering domains in primate and rodent specific genes. We found that the expansion of symmetric exon-bordering domains could not explain the evolution of lineage specific genes. Rather internal intron loss of a domain can partially explain the excess of class 1–1 intron phases in the lineage specific genes. We suggest the event that led to excess of symmetric exons in lineage specific genes had little bearing on shaping the phenotypes specific to the individual lineage. Instead, Kruppel-associated box (KRAB) proteins associated with zinc finger C2H2 (zf-C2H2) type are likely to be responsible for the lineage specific function.     

Survivin特异性SiRNA提高鼻咽癌移植瘤放射敏感性

目的：研究Survivin特异性SiRNA（small interfering RNA）对鼻咽癌移植瘤的放疗增敏作用,探索提高鼻咽癌疗效的新方法。方法：Survivin特异性SiRNA转染鼻咽癌5-8F细胞系,培养48h后,采用RT-PCR、流式细胞仪（flow cytometry,FCM）分别检测Survivin mRNA和蛋白在5-8F细胞中表达。将Survivin基因特异性SiRNA转染5-8F细胞,培养24h后,用剂量为6GY的放射线处理,培养6h后,收集细胞,进行裸鼠皮下接种,50d后处死裸鼠,对移植瘤进行分析。结果：Survivin特异性SiRNA能有效抑制5-8F细胞中Survivin表达。Survivin特异性SiRNA组,Survivin表达阳性率12.37±1.86%,与对照组阳性率91.93±1.3%和阴性对照组阳性率92.43±2.34%比较,差别具有显著性（p〈0.01）。特异性SiRNA加放射组移植瘤（0.03±0.03g）显著小于特异性SiRNA组（0.28±0.02g,p〈0.01）与阴性SiRNA加放射组（0.17±0.02g,p〈0.01）。结论：Survivin特异性SiRNA增强了鼻咽癌5-8F细胞移植瘤的放射敏感性。     

Genetic sex assignment in wild populations using genotyping‐by‐sequencing data: A statistical threshold approach

Establishing the sex of individuals in wild systems can be challenging and often requires genetic testing. Genotyping‐by‐sequencing (GBS) and other reduced‐representation DNA sequencing (RRS) protocols (e.g., RADseq, ddRAD) have enabled the analysis of genetic data on an unprecedented scale. Here, we present a novel approach for the discovery and statistical validation of sex‐specific loci in GBS data sets. We used GBS to genotype 166 New Zealand fur seals (NZFS, Arctocephalus forsteri) of known sex. We retained monomorphic loci as potential sex‐specific markers in the locus discovery phase. We then used (i) a sex‐specific locus threshold (SSLT) to identify significantly male‐specific loci within our data set; and (ii) a significant sex‐assignment threshold (SSAT) to confidently assign sex in silico the presence or absence of significantly male‐specific loci to individuals in our data set treated as unknowns (98.9% accuracy for females; 95.8% for males, estimated via cross‐validation). Furthermore, we assigned sex to 86 individuals of true unknown sex using our SSAT and assessed the effect of SSLT adjustments on these assignments. From 90 verified sex‐specific loci, we developed a panel of three sex‐specific PCR primers that we used to ascertain sex independently of our GBS data, which we show amplify reliably in at least two other pinniped species. Using monomorphic loci normally discarded from large SNP data sets is an effective way to identify robust sex‐linked markers for nonmodel species. Our novel pipeline can be used to identify and statistically validate monomorphic and polymorphic sex‐specific markers across a range of species and RRS data sets.     

Quantitative Assessment of Specificity in Immunoelectron Microscopy

In immunoelectron microscopy (immuno-EM) on ultrathin sections, gold particles are used for localization of molecular components of cells. These particles are countable, and quantitative methods have been established to estimate and evaluate the density and distribution of “raw” gold particle counts from a single uncontrolled labeling experiment. However, these raw counts are composed of two distinct elements: particles that are specific (specific labeling) and particles that are not (nonspecific labeling) for the target component. So far, approaches for assessment of specific labeling and for correction of raw gold particle counts to reveal specific labeling densities and distributions have not attracted much attention. Here, we discuss experimental strategies for determining specificity in immuno-EM, and we present methods for quantitative assessment of (1) the probability that an observed gold particle is specific for the target, (2) the density of specific labeling, and (3) the distribution of specific labeling over a series of compartments. These methods should be of general utility for researchers investigating the distribution of cellular components using on-section immunogold labeling. (J Histochem Cytochem 58:917–927, 2010)     

Correlation of phenylalanine hydroxylase activity with cell density in cultured hepatoma cells.

We have found that the specific activity of phenylalanine hydroxylase varies over at least a forty-fold range during the growth cycle of Reuber hepatoma (H4) cells growing in monolayer culture. The variation has three phases: (1) a very rapid drop in specific activity upon subculturing to a low cell density; (2) a region of low specific activity and (3) after confluency, a rise to a high specific activity. All the results indicate that the cell density in the culture dish is primarily responsible for this fall and rise in activity. Neither conditioning of the growth medium, the rate of cell division, nor enzyme leakage from the cells appear to play a major role in the changes observed. Lactic dehydrogenase specific activity was determined in all experiments; a much smaller, but still cell density-dependent variation was observed for this enzyme.     

Interplay between minor and major groove-binding transcription factors Sox2 and Oct1 in translocation on DNA studied by paramagnetic and diamagnetic NMR

The pathways whereby Sox2 scans DNA to locate its specific binding site are investigated by NMR in specific and nonspecific Sox2·DNA complexes and in a specific ternary complex with Oct1 on the Hoxb1 regulatory element. Direct transfer of Sox2 between nonspecific sites on different DNA molecules occurs without dissociation into free solution at a rate of ～10(6) M(-1) s(-1), whereas one-dimensional sliding proceeds with a diffusion constant of ≥0.1 μm(2)·s(-1). Translocation of Sox2 from one specific DNA site to another occurs via jumping, involving complete dissociation into free solution (k(d) ～5-6 s(-1)) followed by reassociation (k(a) ～5 × 10(8) M(-1) s(-1)). In the presence of Oct1 bound to an adjacent specific site, k(d) is reduced by more than 10-fold. Paramagnetic relaxation measurements, however, demonstrate that sparsely populated (<1%), transient states involving nonspecifically bound Sox2 in rapid exchange with specifically bound Sox2 are sampled in both binary Sox2·DNA- and ternary Oct1·Sox2·Hoxb1-DNA-specific complexes. Moreover, Sox2 modulates the mechanism of translocation of Oct1. Both Sox2 and the Oct1 POU(HD) domain are transiently released from the specific ternary complex by sliding to an adjacent nonspecific site, followed by direct transfer to another DNA molecule, whereas the Oct1 POU(S) domain is fixed to its specific site through direct interactions with Sox2. Intermolecular translocation of POU(HD) results in the formation of a bridged intermediate spanning two DNA molecules, enhancing the probability of complete intermolecular translocation of Oct1. By way of contrast, in the specific Oct1·DNA binary complex, POU(S) undergoes direct intermolecular translocation, whereas POU(HD) scans the DNA by sliding.     

Protein binding to brush borders of enterocytes from the jejunum of the neonatal rat

The specific binding of IgG to jejunal brush borders was greatest at acidic pH, at neutral pH no specific binding occurred. Specific binding declined with age-no specific binding occurred in borders from 20-and 24-day-old animals. There was no specific binding of IgG to borders from ileal enterocytes. Human transferrin and bovine serum albumin did not bind specifically to borders. The affinity of binding (-Ka) and the receptors site numbers per border estimated for rat IgG were 18.64 X 10(6) M-1 to 3.53 X 10(6) sites; for human IgG, 25.06 X 10(6) M-1 to 3.30 X 10(6) sites; for bovine IgG, 10.48 X 10(6) M-1 to 2.11 X 10(6) sites and for sheep IgG, 7.26 X 10(6) M-1 to 2.34 X 10(6) sites.     

Regulation of the nicotinamide adenine dinucleotide- and nicotinamide adenine dinucleotide phosphate-dependent glutamate dehydrogenases of Saccharomyces cerevisiae

Saccharomyces cerevisiae contains two distinct l-glutamate dehydrogenases. These enzymes are affected in a reciprocal fashion by growth on ammonia or dicarboxylic amino acids as the nitrogen source. The specific activity of the nicotinamide adenine dinucleotide phosphate (NADP) (anabolic) enzyme is highest in ammonia-grown cells and is reduced in cells grown on glutamate or aspartate. Conversely, the specific activity of the nicotinamide adenine dinucleotide (NAD) (catabolic) glutamate dehydrogenase is highest in cells grown on glutamate or aspartate and is much lower in cells grown on ammonia. The specific activity of both enzymes is very low in nitrogen-starved yeast. Addition of the ammonia analogue methylamine to the growth medium reduces the specific activity of the NAD-dependent enzyme and increases the specific activity of the NADP-dependent enzyme.     

大鼠胸腺细胞糖皮质激素受体结合与糖皮质激素效应的定量关系

本文通过糖皮质激素拮抗剂 RU486阻断不同分数的糖皮质激素受体(GR)后,GR 结合与糖皮质激素(GC)效应的比较,研究于两者的量的关系。在地塞米松(Dex)10_(-9)—10_(-5)mol/L浓度范围内,Dex 和大鼠胸腺细胞 GR 的特异结合与 Dex 抑制细胞尿嘧啶核苷(Urd)参入效应呈正向平行趋势。用 RU486阻断5×10_(-8)mol/L 浓度的 Dex与 GR 结合的不同分数,比较 Dex 特异结合与抑制效应的关系,发现两者表现为线性正相关(P<0.01)。将 Dex 结合-效应直线外推,结果提示 GR 有约20%的占领阈但几乎没有备用受体。     

Selective adsorption of proteins to their ligands covalently immobilized onto microfibers

Following ozone oxidation of polyester microfibers of 3.5 mum average diameter and 0.83 m(2)/g specific area, the fiber surface was subjected to graft polymerization of acrylic acid and subsequently immobilized with serologically active proteins including Staphylococcus aureus protein A, a specific antigen, and a specific antibody. The immobilization reaction was mediated by a watersoluble carbodiimide, which allowed formation of a co-valent linkage between the ligand proteins and the grafted poly(acrylic acid)chains. The yields of the immobilized ligand proteins were of the order of 1 mg/g fiber. Their binding affinity and capacity to respective specific proteins were studied in vitro from a buffered solution and serum. It was found that the specific proteins were selectively adsorbed with dissociation constants as low as 1x 10(-6) M, suggesting the adsorption to take place through highly specific protein-protein interaction. An addition of serum albumin did not significantly affect the specific binding, regardless of the ligand proteins. The binding capacity ranged from 1 x 10(-13) to 1x 10(-11) mol/cm(2) primarily depending on the surface density of the immobilized ligands and the number of their binding sites per molecule. (c) 1995 John Wiley & Sons Inc.     

Direct access to CD4+ T cells specific for defined antigens according to CD154 expression

The direct assessment of T helper (T(H))-cell responses specific for antigens is essential to evaluate pathogenic and protective immunity. Presently, analysis and isolation of antigen-specific T(H) cells is restricted to cells that produce cytokines, or can be performed only with a rare selection of specific peptide major histocompatibility complex class II (MHC II) multimers. Here we report a new method that enables the assessment and isolation of T(H) cells specific for a defined antigen according to CD154 expression induced after stimulation in vitro. We show that antigen-induced CD154 expression is highly sensitive and specific for human and mouse antigen-specific T(H) cells. Moreover, the isolation of antigen-specific CD154(+) T(H) cells necessitates only surface staining with antibodies, thereby enabling the fast generation of antigen-specific T(H) cell lines. Our approach allows assessment of T(H) cells with a defined specificity for the combined quantitative and qualitative analysis of T(H)-cell immunity as well as for the isolation of specific T(H) cells for targeted cellular immunotherapies.     

Adhesomes: specific granules containing receptors for laminin, C3bi/fibrinogen, fibronectin, and vitronectin in human polymorphonuclear leukocytes and monocytes

We have localized several major extracellular matrix protein receptors in the specific granules of human polymorphonuclear (PMN) and monocytic leukocytes using double label immunoelectron microscopy (IEM) with ultrathin frozen sections and colloidal-gold conjugates. Rabbit antibodies to 67-kD human laminin receptor (LNR) were located on the inner surface of the specific granule membrane and within its internal matrix. LNR antigens co-distributed with lactoferrin, a marker of specific granules, but did not co-localize with elastase in azurophilic granules of PMNs. Further, CD11b/CD18 (leukocyte receptor for C3bi, fibrinogen, endothelial cells, and endotoxin), mammalian fibronectin receptor (FNR), and vitronectin receptor (VNR) antigens were also co- localized with LNR in PMN specific granules. A similar type of granule was found in monocytes which stained for LNR, FNR, VNR, CD18, and lysozyme. Activation of PMNs with either PMA, f-met-leu-phe (fMLP), tumor necrosis factor (TNF), or monocytic leukocytes with lipopolysaccharide (LPS), induced fusion of specific granules with the cell membrane and expression of both LNR and CD18 antigens on the outer cell surface. Further, stimulation led to augmented PMN adhesion on LN substrata, and six- to eightfold increases in specific binding of soluble LN that was inhibited by LNR antibody. These results indicate that four types of extracellular matrix receptors are located in leukocyte specific granules, and suggest that up-regulation of these receptors during inflammation may mediate leukocyte adhesion and extravasation. We have thus termed leukocyte specific granules adhesomes.