Evaluation of the flow-dialysis technique for analysis of protein-ligand interactions: an experimental and a monte carlo study

Flow dialysis has found widespread use in determining the dissociation constant (KD) of a protein-ligand interaction or the amount of available binding sites (E0). This method has the potency to measure both these parameters in a single experiment and in this article a method to measure simultaneously the KD and E0 is presented, together with an extensive error analysis of the method. The flow-dialysis technique is experimentally simple to perform. However, a number of practical aspects of this method can have a large impact on the outcome of KD and E0. We have investigated all sources of significant systematic and random errors, using the interaction between mannitol and its transporter from Escherichia coli as a model. Monte Carlo simulations were found to be an excellent tool to assess the impact of these errors on the binding parameters and to define the experimental conditions that allow their most accurate estimation.     

非线性种群反应扩散系统奇摄动ROBIN问题

研究了一类具有非线性种群反应扩散系统奇摄动Robin初始边值问题.在适当的条件下,利用微分不等式理论,讨论了问题解的存在性和渐近性态.     

The spring development of phytoplankton in Lake Erken: species composition,biomass, primary production and nutrient conditions — a review

Relative abundance and within-lake distributions of three fishes, northern redbelly dace (Phoxinus eos), finescale dace (Phoxinus neogaeus), and central mudminnow (Umbra limi), were examined using minnow traps in Tuesday Lake, a small bog lake in the Upper Peninsula, Michigan. For these species, catches in minnow traps placed at the perimeter of the lake were 21 to 52 times higher than catches in midlake traps. Variance: mean ratios of perimeter trap catches indicated that both dace species were highly aggregated while the distribution of mudminnows was less aggregated or random. Over an 11 day period during which all fish caught were removed from the lake, catch per unit effort (CPUE) of both dace species declined in response to fish removal. In contrast, CPUE for mudminnows was low initially, increased to an asymptote and then declined only in the last 5 days of the fish removal. The patterns of CPUE for mudminnows indicated that mudminnow trapability and/or activity was reduced in the presence of high densities of dace. The low abundance of dace in traps with many mudminnows suggested mudminnows avoided traps already containing dace. Throughout the removal period, CPUE provided an accurate index of dace abundance, whereas this was true for mudmnnows only after dace populations had been reduced drastically. Therefore, in any use of minnow traps to estimate populations, both spatial distributions and relative species abundance of small fishes must be taken into account.     

Improvement of a crystallization process for the purification of vancomycin

We evaluated the effects of the sample feeding and mixing methods on the efficiency of vancomycin crystallization and developed a method to dramatically shorten the time required for crystal formation by increasing the available surface area inside the reactor. The highest purity (97%) and yield (99%) of vancomycin could be obtained with an initial one-step feeding and mixing method, resulting in the formation and growth of spherical fan-shaped crystals. The yield of vancomycin increased when the surface area per working volume (S/V) was increased to 0.428 mm⁻¹ using glass beads (0.5 mm), the cation exchange resin Amberlite 200, or the anion exchange resin Amberlite IRA-400. In particular, most of the vancomycin (>99%) could be recovered after 6 h of crystallization using Amberlite 200, resulting in a dramatic reduction in the time required for crystallization. On the other hand, increasing S/V had almost no effect on vancomycin purity and crystal size.     

Intimate coupling of creatine phosphokinase and myofibrillar adenosinetriphosphatase

ATPase and creatine phosphokinase (CPK) activities of isolated cardiac myofibrils were determined with ³²P γ-labeled ATP alone and with the addition of phosphorylcreatine (PC). With ATP and PC as substrates the label in the inorganic phosphate formed is greatly diluted indicating that the ATP formed by PC through CPK can reach the ATPase active site more readily than labeled ATP from the medium. The tight coupling of the ATPase and CPK activities further strengthens our view that PC serves an important role as high energy carrier between the energy producing sites (mitochondria) and the energy utilizing sites (myofibrils).     

Similarities and differences between the responses induced in human phagocytes through activation of the medium chain fatty acid receptor GPR84 and the short chain fatty acid receptor FFA2R

GPR84 is a recently de-orphanized member of the G-protein coupled receptor (GPCR) family recognizing medium chain fatty acids, and has been suggested to play important roles in inflammation. Due to the lack of potent and selective GPR84 ligands, the basic knowledge related to GPR84 functions is very limited. In this study, we have characterized the GPR84 activation profile and regulation mechanism in human phagocytes, using two recently developed small molecules that specifically target GPR84 agonistically (ZQ16) and antagonistically (GLPG1205), respectively. Compared to our earlier characterization of the short chain fatty acid receptor FFA2R which is functionally expressed in neutrophils but not in monocytes, GPR84 is expressed in both cell types and in monocyte-derived macrophages. In neutrophils, the GPR84 agonist had an activation profile very similar to that of FFA2R. The GPR84-mediated superoxide release was low in naïve cells, but the response could be significantly primed by TNFα and by the actin cytoskeleton disrupting agent Latrunculin A. Similar to that of FFA2R, a desensitization mechanism bypassing the actin cytoskeleton was utilized by GPR84. All ZQ16-mediated cellular responses were sensitive to GLPG1205, confirming the GPR84-dependency. Finally, our data of in vivo transmigrated tissue neutrophils indicate that both GPR84 and FFA2R are involved in neutrophil recruitment processes in vivo.In summary, we show functional similarities but also some important differences between GPR84 and FFA2R in human phagocytes, thus providing some mechanistic insights into GPR84 regulation in blood neutrophils and cells recruited to an aseptic inflammatory site in vivo.     

Mapping QTLs for seed yield and drought susceptibility index in soy-bean（Glycine max L.） across different environments

Drought stress has long been a major constraint in maintaining yield stability of soybean （Glycine max （L.） Merr.） in rainfed ecosystems. The identification of consistent quantitative trait loci （QTL） involving seed yield per plant （YP） and drought susceptibility index （DSI） in a population across different environments would therefore be important in molecular marker-assisted breeding of soybean cultivars suitable for rainfed regions. The YP of a recombinant line population of 184 F2：7：11 lines from a cross of Kefengl and Nannong1138-2 was studied under water-stressed （WS） and well-watered （WW） conditions in field （F） and greenhouse （G） trials, and DSI for yield was calculated in two trials. Nineteen QTLs associated with YP-WS and YP-WW, and 10 QTLs associated with DSI, were identi- fied. Comparison of these QTL locations with previous findings showed that the majority of these regions control one or more traits re- lated to yield and other agronomic traits. One QTL on molecular linkage group （MLG） K for YP-F, and two QTLs on MLG C2 for YP-G, remained constant across different water regimes. The regions on MLG C2 for YP-WW-F and MLG H for YP-WS-F had a pleiotropic effect on DSI-F, and MLG A1 for YP-WS-G had a pleiotropic effect on DSI-G. The identification of consistent QTLs for YP and DSI across different environments will significantly improve the efficiency of selecting for drought tolerance in soybean.     

Molecular cloning of the gene for dihydrofolate reductase from Lactobacillus casei

The Lactobacillus casei gene for dihydrofolate reductase has been cloned in Escherichia coli using the multicopy vector pBR322. A restriction map of the cloned DNA has been prepared. The cloned DNA directs the synthesis of L. casei dihydrofolate reductase in E. coli and confers trimethoprim and methotrexate resistance.     

Phosphorus nutrition-mediated effects of arbuscular mycorrhiza on leaf morphology and carbon allocation in perennial ryegrass

The aim of this work was to disentangle phosphorus status-dependent and -independent effects of arbuscular mycorrhizal fungus (AMF) on leaf morphology and carbon allocation in perennial ryegrass (Lolium perenne). To this end, we assessed the P-response function of morphological components in mycorrhizal and nonmycorrhizal plants of similar size. AMF (Glomus hoi) stimulated relative P-uptake rate, decreased leaf mass per area (LMA), and increased shoot mass ratio at low P supply. Lower LMA was caused by both decreased tissue density and thickness. Variation in tissue density was almost entirely caused by variations in soluble C, while that in thickness involved structural changes. All effects of AMF were indistinguishable from those mediated by increases in relative P-uptake rate through higher P-supply rates. Thus the relationships between relative P-uptake rate, leaf morphology and C allocation were identical in mycorrhizal and nonmycorrhizal plants. No evidence was found for AMF effects not mediated by changes in plant P status.