Selected reaction monitoring for quantitative proteomics: a tutorial

Systems biology relies on data sets in which the same group of proteins is consistently identified and precisely quantified across multiple samples, a requirement that is only partially achieved by current proteomics approaches. Selected reaction monitoring (SRM)—also called multiple reaction monitoring—is emerging as a technology that ideally complements the discovery capabilities of shotgun strategies by its unique potential for reliable quantification of analytes of low abundance in complex mixtures. In an SRM experiment, a predefined precursor ion and one of its fragments are selected by the two mass filters of a triple quadrupole instrument and monitored over time for precise quantification. A series of transitions (precursor/fragment ion pairs) in combination with the retention time of the targeted peptide can constitute a definitive assay. Typically, a large number of peptides are quantified during a single LC‐MS experiment. This tutorial explains the application of SRM for quantitative proteomics, including the selection of proteotypic peptides and the optimization and validation of transitions. Furthermore, normalization and various factors affecting sensitivity and accuracy are discussed.     

Impact of Iron,Copper, and Nickel Ions Introduced into the Soil Separately and in Various Combinations on Soil Microbiota

Biology Bulletin - Abstract—In a long-term model experiment, the abundance dynamics of soil microorganisms was studied as affected by the pollution of southern chernozem soils with various...     

草鱼种无机盐需要量之研究

应用正交法设计进行了三批草鱼种对钙、磷、镁、铁等无机盐元素需要量饲养试验.在此基础上又设计进行了两批以三池平行为一组的鉴别试验.经数理统计分析,获得了草鱼种饲料适宜混合无机盐含量,草鱼种对钙、磷等13种无机盐元素的适宜需要量,以及适宜比例.取得了比哈尔佛Halver氏鱼类营养盐(美国药典U.S.P.Ⅻ.No.2营养盐加哈尔佛微量元素)更适于草鱼种生长需要的新型混合无机盐.试验表明,对草鱼种生长影响比较大的无机盐元素是钙、磷、铁、硫、镁和钴.适宜的混合无机盐对草鱼种生长具有显著的促进作用,不适宜的混合无机盐或缺乏无机盐则草鱼种食欲差,生长缓慢,蛋白质效率低,出现营养缺乏症状.草鱼种对无机盐的需要表明,它不同于已有报道的大鳞大马哈鱼、斑点叉尾鮰、虹鳟、鲤、红海鲷、日本鳗、溪红点鲑,以及非鲫等.所作鱼体背肌、脊柱和血液的生化成分分析表明,第四、五批试验所养草鱼种与常规用草饲养的草鱼种基本一致.       

Introduction to “Moral (and Other) Laboratories”

“Moral (and other) laboratories” is a special issue that draws on Cheryl Mattingly’s notion of the “moral laboratory” to explore the uncanny interface between laboratory ethnography and moral anthropology, and to examine the relationship between experience and experiment. We ask whether laboratory work may provoke new insights about experimental practices in other social spaces such as homes, clinics, and neighborhoods, and conversely, whether the study of morality may provoke new insights about laboratory practices as they unfold in the day-to-day interactions between test tubes, animals, apparatuses, scientists, and technicians. The papers in this collection examine issues unique to authors’ individual projects, but as a whole, they share a common theme: moral experimentation—the work of finding different ways of relating—occurs in relation to the suffering of something or someone, or in response to some kind of moral predicament that tests cultural and historically shaped “human values.” The collection as a whole intends to push for the theoretical status of not merely experience itself, but also of possibility, in exploring uncertain border zones of various kinds—between the human and the animal, between codified ethical rules and ordinary ethics, and between “real” and metaphorical laboratories.     

HOST LIFE HISTORY AND THE EVOLUTION OF PARASITE VIRULENCE

Abstract.— We present a general epidemiological model of host‐parasite interactions that includes various forms of superinfection. We use this model to study the effects of different host life‐history traits on the evolution of parasite virulence. In particular, we analyze the effects of natural host death rate on the evolutionarily stable parasite virulence. We show that, contrary to classical predictions, an increase in the natural host death rate may select for lower parasite virulence if some form of superinfection occurs. This result is in agreement with the experimental results and the verbal argument presented by Ebert and Mangin (1997). This experiment is discussed in the light of the present model. We also point out the importance of superinfections for the effect of nonspecific immunity on the evolution of virulence. In a broader perspective, this model demonstrates that the occurrence of multiple infections may qualitatively alter classical predictions concerning the effects of various host life‐history traits on the evolution of parasite virulence.     

MAGNETIC FIELD STIMULATION OF HYBRIDOMA CELLS IN VITRO

Non-ionizing physical field interactions with cells, both in situ and in vitro, is of current interest globally. This is from various directions—starting from their abilities to induce permanent modifications in cell behavior in situ, through carcinogenesis and mutagenesis, to utilizing field effects for possibly enhancing the viable cell population in vitro. This results in parallel increase in some high-value, low-volume biochemical production. In the present study, screening experiments were carried out with a unique cell line—hybridoma (OKT3) (secreting monoclonal antibodies [MAbs] against T3 surface antigens of human peripheral CD₄⁺ cells)—for a possible enhancement in the yield of extremely high value product (MAb). Overall, in the absence of any such data globally, there is apparently an urgent need for screening of such “field effects” on various other cell types in vitro for various reasons; e.g., low cost of manipulation, nonpolluting nature of interactions, distinct possibility of enhancement of produced biochemical titers, etc. In the present study, we observed various responses of the cell population both to magnetic fields alone and in combination with other known chemical stimulants of viable biomass (mono- and poly-lysine). Fifty hertz, 0.8 mT magnetic field and below, in conjunction with bulkier poly-lysine molecules, needs to be investigated further for a possible resonance-induced anti-interaction between these known mitogens and their cell surface receptors, which possibly could be extrapolated to other growth factor-receptor interactions in magnetic field environments, in situ.     

Predictive modelling of Lactobacillus casei KN291 survival in fermented soy beverage

The aim of the study was to construct and verify predictive growth and survival models of a potentially probiotic bacteria in fermented soy beverage. The research material included natural soy beverage (Polgrunt, Poland) and the strain of lactic acid bacteria (LAB) — Lactobacillus casei KN291. To construct predictive models for the growth and survival of L. casei KN291 bacteria in the fermented soy beverage we design an experiment which allowed the collection of CFU data. Fermented soy beverage samples were stored at various temperature conditions (5, 10, 15, and 20°C) for 28 days. On the basis of obtained data concerning the survival of L. casei KN291 bacteria in soy beverage at different temperature and time conditions, two non-linear models (r ²= 0.68–0.93) and two surface models (r ²=0.76–0.79) were constructed; these models described the behaviour of the bacteria in the product to a satisfactory extent. Verification of the surface models was carried out utilizing the validation data — at 7°C during 28 days. It was found that applied models were well fitted and charged with small systematic errors, which is evidenced by accuracy factor — Af, bias factor — Bf and mean squared error — MSE. The constructed microbiological growth and survival models of L. casei KN291 in fermented soy beverage enable the estimation of products shelf life period, which in this case is defined by the requirement for the level of the bacteria to be above 10⁶ CFU/cm³. The constructed models may be useful as a tool for the manufacture of probiotic foods to estimate of their shelf life period.     

A new cryomacroscope device (Type III) for visualization of physical events in cryopreservation with applications to vitrification and synthetic ice modulators

The objective of the current study is to develop a new cryomacroscope prototype for the study of vitrification in large-size specimens. The unique contribution in the current study is in developing a cryomacroscope setup as an add-on device to a commercial controlled-rate cooler and in demonstration of physical events in cryoprotective cocktails containing synthetic ice modulators (SIM)—compounds which hinder ice crystal growth. Cryopreservation by vitrification is a highly complex application, where the likelihood of crystallization, fracture formation, degradation of the biomaterial quality, and other physical events are dependent not only upon the instantaneous cryogenic conditions, but more significantly upon the evolution of conditions along the cryogenic protocol. Nevertheless, cryopreservation success is most frequently assessed by evaluating the cryopreserved product at its end states—either at the cryogenic storage temperature or room temperature. The cryomacroscope is the only available device for visualization of large-size specimens along the thermal protocol, in an effort to correlate the quality of the cryopreserved product with physical events. Compared with earlier cryomacroscope prototypes, the new Cryomacroscope-III evaluated here benefits from a higher resolution color camera, improved illumination, digital recording capabilities, and high repeatability in tested thermal conditions via a commercial controlled-rate cooler. A specialized software package was developed in the current study, having two modes of operation: (a) experimentation mode to control the operation of the camera, record camera frames sequentially, log thermal data from sensors, and save case-specific information; and (b) post-processing mode to generate a compact file integrating images, elapsed time, and thermal data for each experiment. The benefits of the Cryomacroscope-III are demonstrated using various tested mixtures of SIMs with the cryoprotective cocktail DP6, which were found effective in preventing ice growth, even at significantly subcritical cooling rates with reference to the pure DP6.     

Brain-derived neurotrophic factor gene (BDNF) polymorphism among Moscow citizens

Recent studies showed that brain-derived neurotrophic factor (BDNF) can participate in pathogenesis of various CNS disorders, being connected with proliferation, differentiation, and survival of neurons. In present study, analysis of occurrence rate was performed for three single nucleotide polymorphisms (SNPs) located in BDNF gene (rs6267 (A/G) allele A—0.265; rs2049046 (A/T) allele A—0.407; rs11030107 (A/G) allele A—0.872) in randomized selection of Moscow citizens. Linkage disequilibrium of rs6165 and rs2049046 loci was shown. Differences in allele frequencies in studied selection and populations of other regions were discovered.     

Ecological effects of larval trematode infestation on littoral marine invertebrate populations

Evidence is presented that, contrary to common scientific “belief”, larva digeneans have profound effects on various components at various levels of the littoral marine ecosystem. Their ecological capacity includes: —Reduction of the breeding potential of host populations by “parasitic castration”; —Structural modification of host populations by generation of erratic growth patterns, size-class differential mortality and “negative growth”; —Induction of host-population mortality and control by increased susceptibility to environmental stress; —Induction of changes in community structure by removal of hosts from their normal trophic levels; —Interference with major energy-flow pathways by precocious removal of hosts from their normal food-web position; —Interference with host-biomass, production and turnover-rate estimations by by-passing of hostassimilated energy; —Interference with predator-prey systems by affecting either component(s) of such systems.The notorious neglect of these factors by marine ecologists and, even more, their total unawareness of the effects these factors produce, raise serious doubts about the validity of marine ecological data and concepts. For the parasitologist, on the other hand, the study of ecological aspects of marine parasite (digenean) biology may open new avenues of research. With a true synthesis of both scientific disciplines, we may eventually arrive at a point where “more complete knowledge of life cycles will permit more intelligent and more effective regulatory methods, the reduction of morbidity, the advancement of health, and the conservation of natural resources.”The latter statement has not been cited from a recent issue of a scientific journal; it has been written down as long as 46 (!) years ago by one of the most outstanding investigators of marine digenean life cycles—Horace W. Stunkard (1940, p 15), but has lost nothing of its actuality. It is hoped that Stunkard's far-sighted words might encourage parasitologists to devote some of their scientific power and skill to the study of marine ecoparasitological problems—for the sake of a better understanding of ecological processes and to the benefit of the endangered marine life.     

Influence of the unified state examination on the functional state in high school students

The results of a local comparative experiment are presented in the course of which physiological reactions to emotional and mental stress related to the situation of taking an examination in two forms—a traditional examination and the unified state examination (USE)—were compared. It was shown that the physiological stress during the USE is slightly higher than during the traditional examination.     

Changes of the serotonergic system activity in fish tissues during an increase of water salinity

Changes of environment parameters produce essential effects on the serotonergic system activity in the body tissues. This paper describes study of the serotonergic system activity in various tissues of half-migratory fish—the Caspian roach Rutilus rutilus caspicus and the bream Abramis brama orientalis—caught in the fresh and brackish water. Using the method of indirect solid-phase ELISA test, the serotonergic system activity was assessed by determining in the studied fish tissues of the amount of serotonin-modulating anticonsolidation protein (SMAP) that is in the linear correlation with serotonin level. A significant change of the SMAP level in the Caspian roach and bream brain was found under effect on increased water salinity. Analysis of the SMAP amount in the bream liver did not reveal any differences in the animals caught in the brackish and fresh water. At the same time, in the bream gill there was a small rise of the SMAP content in the fish caught in the brackish water. The revealed in this experiment elevation of the SMAP amount in the Caspian roach and bream brain reflecting a corresponding increase of the serotonergic system activity indicates involvement of adaptive readjustments in the animal body.     

Effects of patch size and position above the substratum during early succession of subtidal soft-bottom communities

Early macrobenthos succession in small, disturbed patches on subtidal soft bottoms is facilitated by the arrival of post-larval colonizers, in particular by active and passive dispersers along the seafloor or through the water column. Using a field experiment at two contrasting sites (protected vs. exposed to wave action), we evaluated the role of (a) active and passive dispersal through the water column and (b) the influence of small-scale spatial variability during succession of subtidal macrobenthic communities in northern Chile. Containers of two sizes (surface area: small—0.12?m² and large—0.28?m²) at two positions above the natural substratum (height: low—3?cm and high—26?cm) were filled with defaunated sediment, installed at two sandy sublittoral sites (7–9?m water depth) and sampled after 7, 15, 30, 60 and 90?days, together with the natural bottom sediment. The experiment took place during austral fall (from late March to early July 2010), when both larval and post-larval stages are abundant. At the exposed site, early succession was driven by similar proportions of active and passive dispersers. A sequence from early, late and reference communities was also evident, but container position and size affected the proportional abundance of dispersal types. At the protected site, the successional process started with abundant colonization of active dispersers, but toward the end of the experiment, the proportion of swimmer/crawlers increased, thus resembling the dispersal types found in the natural community. At this site, the position above the sediment affected the proportional abundance of dispersal types, but patch size had no effect. This study highlights that macrobenthic post-larvae can reach at least 26?cm high above the bottom (actively or passively, depending on site exposure), thus playing an important role during early succession of sublittoral soft bottoms. The active or passive use of the sediment–water interphase may also play an important role in the connectivity of benthic populations and in the recovery after large-scale disturbances of sublittoral habitats.     

太湖不同解有机磷菌株胞外碱性磷酸酶活性对蓝藻碎屑的响应

浮游细菌胞外碱性磷酸酶在湖泊磷循环过程中具有关键作用, 但其与生物可利用性磷和颗粒态有机质之间的关系尚未得到充分的研究。研究以从太湖沉积物分离的3 株解有机磷细菌(OPB)和东湖水中OPB菌群为实验对象, 以蓝藻干物质为颗粒态有机质, 系统分析了模拟条件下OPB 的数量、不同大小颗粒所表现的胞外碱性磷酸酶活性(APA)与不同形态磷的浓度及其相互关系。从总体上讲, APA 与OPB 数量显著正相关, 且明显反比于溶解反应性磷(SRP)浓度, 在模拟实验过程中, 不同菌株(群)所对应的SRP 浓度均显著不同, 故其解磷能力各异。从绝对活性及其在总活性中所占的比例来看, 各处理间小颗粒(0.22—3.0 μm)APA亦明显不同, 而大颗粒(>3.0 μm)APA和溶解态(8 CFU/mL), SRP 浓度逐渐增加。实验后期(20—33 d)细菌数量大幅度减少, 且伴随SRP 和溶解态有机磷浓度的显著升高。因此, 在缺磷且富含颗粒态有机质的条件下, OPB 将产生胞外碱性磷酸酶, 分解有机磷, 进而满足其大量生长的需要, 同时有效改变溶解态磷的形态与生物可利用性。       

Novel broad-spectrum bacteriophages against Xanthomonas oryzae and their biocontrol potential in rice bacterial diseases

Bacterial leaf blight (BLB) and bacterial leaf streak (BLS)—caused by Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), respectively—are two major bacterial diseases that threaten the safe production of rice, one of the most important food crops. Bacteriophages are considered potential biocontrol agents against rice bacterial pathogens, due to their host specificity and environmental safety. It is common for BLB and BLS to occur together in fields, which highlights the need for broad-spectrum phages capable of infecting both Xoo and Xoc. In this study, two lytic broad-spectrum phages (pXoo2106 and pXoo2107) that can infect various strains of Xoo and Xoc were assessed. Both phages belong to the class Caudoviricetes and one of them to the family Autographiviridae, while the other belongs to an unclassified family. Two phages alone or combined in a phage cocktail could effectively inhibit Xoo and Xoc growth in vitro. In an in vivo biocontrol experiment, the phage cocktail reduced the total CFU and significantly eased the symptoms caused by Xoo or Xoc. Our results suggest that pXoo2106 and pXoo2107 have a broad-spectrum host range targeting different X. oryzae strains, and have strong biocontrol potential in field applications against both BLB and BLS.     

鱼类双重荧光标记研究——以中华倒刺鲃幼鱼为例

为探究盐酸四环素(TCH)和茜素红S(ARS)对中华倒刺鲃(Spinibarbus sinensis Bleeker)的影响及标记效果, 丰富鱼类荧光标记模式, 研究使用TCH(100—500 mg/L)和ARS(100—300 mg/L)对中华倒刺鲃幼鱼进行双重浸染荧光标记, 实验共设置5个处理组和1个对照组, 浸染时间均为24h。结果显示, 经90d的养殖实验后, 标记鱼的耳石(包括矢耳石和星耳石)、倒刺、鳍条和鳍棘均能检测到双重荧光标记环, 且TCH产生的黄色荧光环比ARS产生的红色荧光环更接近骨质结构内部。较高浓度处理组的矢耳石(≥300 mg/L TCH和≥150 mg/L ARS)、星耳石(≥300 mg/L TCH 和 ≥200 mg/L ARS)和倒刺(400—500 mg/L TCH 和150—300 mg/L ARS)中均能检测到明显的标记环(n≥2), 但所有处理组的侧线鳞和非侧线鳞的荧光标记不明显(0≤n≤1)。经200—500 mg/L TCH和150—300 mg/L ARS处理的鳍条, 及经300—500 mg/L TCH和200—300 mg/L ARS处理的鳍棘中可以同时检测到明显的TCH和ARS的标记环(n≥2)。此外, 在整个实验中各处理组标记鱼与对照组相比, 在生长和存活率方面均无显著性差异(P>0.05)。结果表明, 使用TCH和ARS双重标记中华倒刺鲃幼鱼是可行的。双重荧光标记方法在水生生物标记回捕实验及实验性生物学研究方面具有潜在的应用前景。     

Benzoylcellulose derivatives as chiral stationary phases for open tubular column chromatography

The application of cellulose-based stationary phases for chiral separations has been extended to open tubular column chromatography. Efficient columns were obtained by coating the capillaries with mixtures of chiral cellulose materials and conventional achiral stationary phases for gas chromatography. In this study, various siloxane and polyethylene glycol polymers were used as achiral components and mixed with different substituted benzoylcellulose derivatives as chiral components. Systematic investigations were carried out to determine the optimal ratio for the components of the stationary phase. Depending on the chromatographic mode—gas chromatography (GC) or supercritical fluid chromatography (SFC)—the stationary phases were found to behave differently. The applicability of the technique was demonstrated by the resolution of various racemic compounds. © 1993 Wiley-Liss, Inc.     

Phosphorus addition increased carbon partitioning to autotrophic respiration but not to biomass production in an experiment with Zea mays

Plant carbon (C) partitioning—the relative use of photosynthates for biomass production, respiration, and other plant functions—is a key but poorly understood ecosystem process. In an experiment with Zea mays, with or without arbuscular mycorrhizal fungi (AMF), we investigated the effect of phosphorus (P) fertilization and AMF on plant C partitioning. Based on earlier studies, we expected C partitioning to biomass production (i.e., biomass production efficiency; BPE) to increase with increasing P addition due to reduced C partitioning to AMF. However, although plant growth was clearly stimulated by P addition, BPE did not increase. Instead, C partitioning to autotrophic respiration increased. These results contrasted with our expectations and with a previous experiment in the same set-up where P addition increased BPE while no effect on autotropic respiration was found. The comparison of both experiments suggests a key role for AMF in explaining these contrasts. Whereas in the previous experiment substantial C partitioning to AMF reduced BPE under low P, in the current experiment, C partitioning to AMF was too low to directly influence BPE. Our results illustrate the complex influence of nutrient availability and mycorrhizal symbiosis on plant C partitioning.     

Ubiquilin4 is an adaptor protein that recruits Ubiquilin1 to the autophagy machinery

Ubiquilins (Ubqlns)—a family of ubiquitin‐binding proteins—are involved in several protein degradation pathways and have been implicated in various neurodegenerative diseases. Ubqln1 regulates autophagosome maturation during autophagy‐mediated degradation. We now show that Ubqln4 mediates the interaction between Ubqln1 and the autophagy machinery by recruiting Ubqln1 to LC3. This targeting of Ubqln1 to autophagosomes requires the Ubqln4 UBL domain and the Ubqln1 UBA domain. This study identifies a new role for Ubqln4, expanding the role for Ubqlns in protein degradation.     

Specificity of action of piperidylcholine derivatives as substrates of cholinesterases of various origin

The review deals with study of enzymologic properties of a novel highly specific acetylcholinesterase substrate, N-(β-acetoxyethyl) piperidinium iodomethylate (“piperidylcholine”), and its 30 derivatives that were tested as effectors of cholinesterases of mammals and various species of Pacific squids. It was proven for the first time that responsible for specificity of action was structure of cyclic ammonium grouping of the alcohol part of molecule of the ester substrate. Analysis of specificity is performed based on enzymatic hydrolysis parameters—activity of catalytic center of cholinesterases and bimolecular constant of the reaction rate that are determined at optimal and low substrate concentrations. Among the specially synthesized group of thioester compounds there is revealed one more highly specific acetylcholinesterase substrate—N-(β-acetoxyethyl) piperidinium.