A qPCR method to characterize the sex type of the cell strains from rats

A simple and fast method was established to identify the sex types of the rat-derived cell strains. The single copy X-chromosome-linked gene AR and the single copy Y-chromosome-linked gene Sry were both detected with qPCR for the rat genomic DNA sample and the AR/Sry ratio was calculated. According to the law of the AR/Sry ratio, a new method to identify the sex types of the rat-derived cell strains was developed. The new assay was proved effective. The new assay showed advantages over the traditional sex type identification PCR methods, which detected only the Sry gene. Moreover, the new method was used to identify the sex types of two rat-derived cell strains unknown for the sex types and the results were confirmed with the in situ hybridization. Finally, the problem of the cross contamination between the female and the male samples was addressed and discussed extensively.     

Unbiased estimation of the rates of synonymous and nonsynonymous substitution

Summary The current convention in estimating the number of substitutions per synonymous site (K _S ) and per nonsynonymous site (K _A ) between two protein-coding genes is to count each twofold degenerate site as one-third synonymous and two-thirds nonsynonymous because one of the three possible changes at such a site is synonymous and the other two are nonsynonymous. This counting rule can considerably overestimate theK _S value because transitional mutations tend to occur more often than transversional mutations and because most transitional mutations at twofold degenerate sites are synonymous. A new method that gives unbiased estimates is proposed. An application of the new and the old method to 14 pairs of mouse and rat genes shows that the new method gives aK _S value very close to the number of substitutions per fourfold degenerate site whereas the old method gives a value 30% higher. Both methods give aK _A value close to the number of substitutions per nondegenerate site.     

Mapping of the Mod-1 locus on mouse Chromosome 9

A new method for typing the Mod-1 locus on mouse Chromosome (Chr) 9 was developed, based on restriction fragment length polymorphism (RFLP) within a polymerase chain reaction (PCR)-amplified fragment. The new method led us to revise the strain distribution pattern (SDP) of Mod-1 in the BXD (C57BL/6JxDBA/2J) and AKXD (AKR/J x DBA/2J) recombinant inbred (RI) strains. The new SDP eliminates several previously reported examples of double recombination events between Mod-1 and the closest flanking loci in the BXD and AKXD strains. In the BXD strains, the revised SDP of Mod-1 was identical to that of the Mod-1-related D9Rtil locus. Thus, the identity of D9Rtil as a Mod-1-related locus rather than Mod-1 itself is in question. The method was also applied to an interspecific backcross panel between an inbred strain of Mus musculus molossinus (MSM/Ms) and C57BL/6J to map Mod-1 with respect to surrounding microsatellite loci, defining the proximal localization of Mod-1 with respect to D9Mit10 with a genetic distance of 0.6±0.6 cM.     

The Chemical Potential of Dense Liquids by the Coupled Test Particle Method

Abstract

A new method for chemical potential estimation is proposed which is based on the coupled particle approach. The coupled particle method defines an attractive solution to the weighting function problem in umbrella sampling, bridging the gap between f and g distributions at high density. A way of eliminating the origin singularity is suggested, which is similar in spirit to the restricted umbrella sampling of Shing and Gubbins, but which is based on geometric rather than energetic criteria.

The method is illustrated on the Lennard-Jones system up to a reduced density ρ? = 1.1 along the isotherm T? = 1.2 and results are compared with the test particle insertion method and empirical equations of state. The new method is particularly useful at high liquid densities where it is superior to the other methods relying on the degree of overlap of f and g distributions. It gives reliable estimates of the chemical potential in the whole range of liquid densities.     

A New Enzymatic Method for the Measurement of Creatinine Involving a Novel ATP-dependent Enzyme,N-Methylhydantoin Amidohydrolase

A new enzymatic method for the measurement of serum and urine creatinine is described. The method is based on a novel microbial creatinine degradation pathway via N-methylhydantoin [Shimizu et al., Clin. Chim. Acta, 185, 241–252 (1989)]. By using two novel enzymes, N-methylhydantoin amidohydrolase and N-carbamoylsarcosine amidohydrolase, as key enzymes, coupled with a colorimetric procedure for hydrogen peroxide detection, the creatinine level can be measured. The results obtained for human serum and urine show good correlation with those obtained by a standard chemical method based on the Jaffe reaction. The new method is simple and specific, and shows excellent sensitivity and reliability.     

salmonnb: a program for computing cohort‐specific effective population sizes (Nb) in Pacific salmon and other semelparous species using the temporal method

We describe a new method and a computer program salmonn b to calculate the effective number of breeders (N_b) per year in semelparous species with variable age at maturity. The existing temporal method for the ‘salmon’ life history produces an estimate of the harmonic mean N_b in the two sampled years. salmonn b reads genotypic data in standard formats and computes yearly N_b values by combining information from pairwise comparisons of samples taken in 3 or more years. Simulations show that the new method produces unbiased estimates of yearly N_b, and precision is inversely proportional to true effective size.     

Inter‐laboratory validation of a rapid assay for the detection and quantification of Legionella spp. in water samples

Aims: To compare the standard culture method with a new, rapid test (ScanVIT‐Legionella?) using fluorescently labelled gene probes for the detection and enumeration of Legionella spp. The new technique was validated through experiments conducted on both artificially and naturally contaminated water and through an inter‐laboratory comparison. Methods and Results: All samples were processed by the ScanVIT test according to the manufacturer’s instructions and by a culture method (ISO 11731). ScanVIT detected significantly more positive samples, although concentrations were similar and a strong positive correlation between the two methods was observed (r = 0·888, P < 0·001). The new test was more accurate in identifying the co‐presence of Legionella pneumophila and Leg. non‐pneumophila. ScanVIT showed a slightly higher Legionella recovery from water samples artificially contaminated with Leg. pneumophila alone or together with Pseudomonas aeruginosa. Lastly, the inter‐laboratory comparison revealed that the ScanVIT test exhibits a lower variability than the traditional culture test (mean coefficient of variation 8·7 vs 16·1%). Conclusions: The results confirmed that the ScanVIT largely overlaps the reference method and offers advantages in terms of sensitivity, quantitative reliability and reduced assay time. Significance and Impact of the Study: The proposed method may represent a useful validated alternative to traditional culture for the rapid detection and quantification of Legionella spp. in water.     

The Enamel Microstructure of the Early Eocene Pantodont Coryphodonand the Nature of the Zigzag Enamel

An additional method for the investigation of the microstructure of enamel is described using the teeth of Coryphodon, Uintatherium, Entelodon, and Crocuta. Under low magnification natural surfaces or sections of teeth display details of the enamel microstructure when the light guide effect of prisms is used. Under the same low magnification even more details were obtained from sputter-coated surfaces of sections. The method is of particular significance for the investigation of large teeth with thick enamels when structures are somewhat irregular. The new method provides a better general survey, where scanning electron microscope images often show confusing details. The enamel of Coryphodon shows oblique lines of nested chevrons that are similar, to some degree, to the zigzag enamel in Crocuta, but a distinct asymmetry between ascending and descending lineaments was observed. This specific Coryphodon -enamel was also found in Uintatherium and Entelodon. This enamel type, which evolved several times in parallel, cannot be attributed to a specific diet, but must be regarded as one of the several ways to strengthen the enamel against breakage.     

Linked Lists and the Method of Lights in Molecular Dynamics Simulation - Search for the Best Method of Forces Evaluation in Sequential MD Codes

Abstract

In this paper two methods of forces evaluation used in the MD codes are presented and compared against the classical linked lists algorithm [3,4] and its modified version [5]. The first algorithm, so called the method of lights is a sequential version of the CYBER 205 vector oriented code [6]. A new algorithm of forces evaluation is also proposed, which incorporates advantages of the method of lights and the linked lists technique.     

An easier method to identify the individual genomic composition of allopolyploid complexes

A new method for the fast identification of the genomic composition of the cyprinid Squalius alburnoides is presented. The method is based on a length polymorphism detected in the β‐actin gene, which serves as the basis for the development of a semi‐quantitative PCR.     

基于窖泥微生物相对定量与绝对定量联用的窖泥老熟特征分析

[目的] 基于传统的相对定量法,在总DNA提取过程中加入内标菌,探索不同老熟程度下窖泥微生物菌群组成特征。[方法] 通过添加外源菌丙酮丁醇梭菌（Clostridium acetobutylicum）作为内标菌,利用16S rRNA基因扩增子测序技术,基于相对丰度与绝对丰度解析不同老熟程度窖泥内的菌群结构和理化差异。[结果] 相对定量分析表明,随着窖泥老熟,窖泥微生物群落的多样性增加,己酸菌属（Caproiciproducens）、甲烷杆菌属（Methanobacterium）、甲烷八叠球菌属（Methanosarcina）和互营单胞菌属（Syntrophomonas）等菌的相对丰度显著增高。结合绝对丰度分析,老熟窖泥内的生物量分别是新窖泥与趋老熟窖泥的600倍与28倍。不同于相对定量分析,乳杆菌属（Lactobacillus）的绝对丰度在老熟窖泥内并未降低,为新窖泥的20倍。己酸菌属在老窖泥中的绝对丰度为新窖泥的25000倍;其他功能微生物包括甲烷杆菌属、甲烷八叠球菌属、甲烷短杆菌属（Methanobrevibacter）、互营单胞菌属的绝对丰度也随着窖龄的增加而显著增加。菌群结构的绝对定量动态分析表明,新窖泥转变为老熟窖泥的过程是一个菌群组成多样性不断提高、生物量也逐步增加的过程,老窖泥中己酸菌属、互营单胞菌属、多种甲烷菌等微生物绝对量的增加,推测对降低窖泥内的乳酸含量和形成窖泥稳态环境具有重要作用。[结论] 绝对定量方法的引入,可观测不同窖龄窖泥微生物生物量的差异,解析不同老熟阶段窖泥功能微生物绝对丰度的动态变化,为窖泥菌群结构和代谢功能的定量化和因果关系研究提供了新的策略。     

Improved method for the dynamic measurement of mass transfer coefficient for application to solid–substrate fermentation

A new method has been developed for the measurement of overall volumetric mass transfer coefficient (K_L a) in gas-liquid-solid systems. This method is based on the examination of gas phase dynamics in a three-phase contactor and consists of measuring continuously the response of the outlet gas composition to a step input change of CO₂ in the inlet gas stream. The advantages and limitations of the new method are presented and its sensitivity is discussed on the basis of model predictions. Preliminary results on the implementation of the CO₂ method are also reported. Experimental data obtained in a nonviscous electrolyte solution show that the proposed method compares favorably with the conventional dissolved oxygen technique, provided that a correction is made to take account of the difference in diffusivity of oxygen and carbon dioxide.     

New chorological data for flora of the Pannonian region of Serbia

The northern part of Serbia, known as Pannonian Serbia, is a lowland region. The autochthonous (indigenous) flora is classified as either steppe, forest-steppe, sand dune or salt flat. Most of the area has been developed agriculturally, thereby reducing the amount of land containing preserved habitats. The flora of this region was collected over a period of several years, supplying new data on the distribution of numerous plant species. The first data on the distribution of flora in Pannonian Serbia for Humulus scandens and Ophris scolopax subsp. Cornuta is presented in this study. The local regions cited were the first time precisely recorded regions were made after a period of over 100 years, for Cardamine impatiens, Monotropa hypopitys subsp. hypopitys, Ononis pusilla, Globularia punctata, Gymnadenia odoratissima and Carex brevicollis. The groups, Peucedanum carvifola and Galium tenuissimum, quite rare in the northern part of Serbia, were found at new localities. In order to present the data, the authors used the method of indirect mapping on UTM grid, with 10 × 10 km as the basic unit. This method is compatible with the edition Atlas Florae Europaeae.     

A modified method for the cultivation of phototrophic bacteria

Simplified anaerobic media and a convenient method for the cultivation of Rhodospirillaceae, Chlorobiaceae, Chloroflexaceae and Chromatiaceae are described. The modified conditions assure almost complete anaerobiosis for media, growth and maintenance.Strains representing several species of Rhodospirillaceae, Chlorobiaceae and Chromatiaceae were successfully grown within relatively short times with full pigmentation, indicating that the new media and cultivation conditions were most suited for photoautotrophic growth.     

Use of Quantitative Real-Time PCR to Investigate the Dynamics of the Red Tide Dinoflagellate Lingulodinium polyedrum

A new method based on quantitative real-time polymerase chain reaction (qPCR) was developed and applied to quantify the red tide dinoflagellate Lingulodinium polyedrum in natural seawater samples and in laboratory cultures. The method uses a Molecular Beacon™ approach to target a species-specific region of the small subunit ribosomal RNA gene. The accuracy of the method was verified by microscopical counts using cultures of the dinoflagellate isolated from coastal waters near Los Angeles, CA, and with natural water samples spiked with cultured L. polyedrum. The method was applied to document the pattern and timing of vertical migration by the dinoflagellate in a 2-m water column on an 11:13 h light/dark photoperiod established in the laboratory. Positive phototaxis of L. polyedrum resulted in dense aggregations of the dinoflagellate within the top few centimeters of the water column during the light period. This pattern of distribution was readily established by both methods, although abundances of L. polyedrum determined using qPCR were higher than abundances determined by microscopy in the morning and lower in the afternoon and evening. These differences may have been a consequence of variability in the DNA content per cell because of synchrony of cell division. Counts using both methods to analyze natural samples collected from coastal waters in the Long Beach–Los Angeles area and adjacent San Pedro Channel were in close agreement. However, the qPCR method exhibited greater sensitivity than the microscopical method when L. polyedrum was present at low abundances, and qPCR had a much higher rate of sample throughput than microscopy. The development of this new approach for enumerating L. polyedrum provides a useful tool for studying the ecology of this important red tide species.     

The effect of shade on the photosynthetic pigments of needles on trees of Pinus sylvestris ssp. scotica grown under field conditions

Summary

Field data show that Pinus sylvestris ssp. scotica adapts its needle concentration to the prevailing shade conditions. A new method of determining the degree of shading in the field is described, and a new term, the Minimal Shade Factor, is defined. It is shown that chlorophyll b is more favoured than chlorophyll a at low light levels.     

Intracellular proliferation of clover yellow vein virus is unaffected by the recessive resistance gene cyv1 of Pisum sativum

The pea cyv1 gene is a yet-to-be-identified recessive resistance gene that inhibits the infection of clover yellow vein virus (ClYVV). Previous studies confirmed that the cell-to-cell movement of ClYVV is inhibited in cyv1-carrying pea plants; however, the effect of cyv1 on viral replication remains unknown. In this study, we developed a new pea protoplast transfection method to investigate ClYVV propagation at the single-cell level. Using this method, we revealed that ClYVV accumulates to similar levels in both ClYVV-susceptible and cyv1-carrying pea protoplasts. Thus, the cyv1-mediated resistance would not suppress intracellular ClYVV replication.     

In vivo observation of gold nanoparticles in the central nervous system of <Emphasis Type="Italic">Blaberus discoidalis</Emphasis>

Background  

Nanoparticles (NPs) are widely studied for biomedical applications. Understanding interactions between NPs and biomolecules or cells has yet to be achieved. Here we present a novel in vivo method to study interactions between NPs and the nervous system of the discoid or false dead-head roach, Blaberus discoidalis. The aims of this study were to present a new and effective method to observe NPs in vivo that opens the door to new methods of study to observe the interactions between NPs and biological systems and to present an inexpensive and easy-to-handle biological system.     

Specific PCR assays for the detection of <Emphasis Type="Italic">Trichoderma harzianum</Emphasis> causing green mold disease during mushroom cultivation

We have developed a polymerase chain reaction (PCR)-based detection method for Trichoderma harzianum, which causes green mold disease in mushroom cultivation fields and facilities. Based on the sequence data of the internal transcribed spacer (ITS) region of T. harzianum strains and several other species, six primers consisting of three forward and three reverse primers were designed. Among the nine possible combinations of these primers, PCR with the pair THITS-F2 and THITS-R3 distinguished most T. harzianum strains from other Trichoderma species. The optimal annealing temperature for detection of T. harzianum strains was from 62° to 63°C with this primer combination. We designed new primers derived from THITS-F2 and THITS-R3. Annealing temperatures to detect T. harzianum ranged from 64° to 67°C using the new primers. The detection limit of T. harzianum DNA was 50 fg by nested PCR with THITS-F1 and LR1-1 for the first PCR and the new primers for the second PCR. T. harzianum was readily detectable in contaminated cultures of Lentinula edodes by this method.     

Antifungal activity of essential oils of Croton species from the Brazilian Caatinga biome

Aims: To find new antifungal agents among essential oils from Brazilian Croton species. Methods and Results: Plant leaves were steam distilled and the obtained essential oils were analyzed by gas chromatography/mass spectroscopy. The main constituents were estragole and anethole for Croton zehntneri, methyl-eugenol and bicyclogermacrene for Croton nepetaefolius and spathulenol and bicyclogermacrene for Croton argyrophylloides. The antifungal activity of essential oils was evaluated against Candida albicans, Candida tropicalis and Microsporum canis by the agar-well diffusion method and the minimum inhibitory concentration (MIC) by the broth microdilution method. Essential oils of Croton species demonstrated better activity against M. canis. Among the three plants C. argyrophylloides showed the best results, with MIC ranging from 9 to 19 μg ml⁻¹. The acute administration of the essential oil up to 3 g kg⁻¹ by the oral route to mice was devoid of overt toxicity. Conclusions: The studied essential oils are active in vitro against the dermatophyte M. canis and present relative lack of acute toxicity in vivo. Significance and Impact of the Study: Because of its antifungal activity and low toxicity, the essential oils of studied Croton species are promising sources for new phytotherapeutic agents to treat dermatophytosis.