Application of solid-phase extraction to agar-supported fermentation

Agar-supported fermentation (Ag-SF), a variant of solid-state fermentation, has recently been improved by the development of a dedicated 2 m² scale pilot facility, Platotex. We investigated the application of solid-phase extraction (SPE) to Ag-SF in order to increase yields and minimize the contamination of the extracts with agar constituents. The selection of the appropriate resin was conducted on liquid-state fermentation and Diaion HP-20 exhibited the highest recovery yield and selectivity for the metabolites of the model fungal strains Phomopsis sp. and Fusarium sp. SPE applied to Ag-SF resulted in a particular compartmentalization of the culture. The mycelium that requires oxygen to grow migrates to the top layer and formed a thick biofilm. The resin beads intercalate between the agar surface and the mycelium layer, and trap directly the compounds secreted by the mycelium through a “solid–solid extraction” (SSE) process. The resin/mycelium layer is easily recovered by scraping the surface and the target metabolites extracted by methanol. Ag-SF associated to SSE represents an ideal compromise for the production of bioactive secondary metabolites with limited economic and environmental impact.     

Application of solvent extraction to ethanol fermentation

Summary The basic problems of applying solvent extraction to ethanol fermentation were investigated. The selection of solvents was based on the selectivity ratio, which was expressed as the ratio of the ethanol distribution coefficient to the water distribution coefficient. Solvents with high selectivity ratios of more than 50 were found mainly among the alcohols and esters. However, most of these solvents were toxic to ethanol-producing microorganisms. We tried to make a barrier to solvent molecules beneath the surface of gel beads immobilizing the cells as a protection against solvent toxicity. Porapack Q was found to be an effective barrier, and the ethanol production rate of immobilized cells protected with Porapack Q did not change event after the production of eight batches in medium saturated with sec-octanol, which was the most toxic solvent used in our experiments.     

Determination of metformin in plasma using a new ion pair solid phase extraction technique and ion pair liquid chromatography

This article describes the development of the first ion pair solid phase extraction technique (IPSPE), which has been applied to the extraction of metformin from plasma samples. In addition an ion pair chromatographic method was developed for the specific HPLC determination of metformin. Several extraction and HPLC methods have been described previously for metformin, however, most of them did not solve the problems associated with the high polarity of this drug. Drug recovery in the developed method was found to be more than 98%. The limit of detection and limit of quantification was 3 and 5 ng/ml, respectively. The intraday and interday precision (measured by coefficient of variation, CV%) was always less than 9%. The accuracy (measured by relative error, R.E.%) was always less than 6.9%. Stability analysis showed that metformin is stable for at least 3 months when stored at -70 degrees C. The method has been applied to 150 patient samples as part of a medication adherence study.     

Dynamic programming re-ranking for PPI interactor and pair extraction in full-text articles

Background  

Experimentally verified protein-protein interactions (PPIs) cannot be easily retrieved by researchers unless they are stored in PPI databases. The curation of such databases can be facilitated by employing text-mining systems to identify genes which play the interactor role in PPIs and to map these genes to unique database identifiers (interactor normalization task or INT) and then to return a list of interaction pairs for each article (interaction pair task or IPT). These two tasks are evaluated in terms of the area under curve of the interpolated precision/recall (AUC iP/R) score because the order of identifiers in the output list is important for ease of curation.     

Application of reactive extraction to recovery of carboxylic acids

Carboxylic acids are examples of compounds with wide industrial applications and high potential. This article presents the principles of reactive extraction along with the characteristics of tertiary amine extractants, while is given on considering the effect of the amine class and chain length. As such a brief overview the current research on reactive extraction, including the recovery of citric acid, selective amine-based extraction, and extractive fermentation is given. When discussing extractive fermentation, strategies for reducing solvent toxicity are also suggested based on specific examples. Finally, solvent regeneration and stripping of extracted acid are explained.     

The diagnostic yield of automatic EMG analysis in neuromuscular diseases

The aim of the study was to evaluate the diagnostic yield of automatic EMG analysis employed in differentiating normal from diseased muscle and myogenic, neural and spinal lesions. The material comprised 520 patients with neuromuscular diseases. Only diagnostically confirmed cases were included into the study. The control group comprised 51 healthy subjects. In all patients and healthy subjects routine EMG examination was performed by means of both the conventional technique and automatic method. On the basis of the statistical analysis of the material the authors concluded that the method of automated EMG using the Polish minicomputer Anops makes possible distinction of the main types of pathological processes affecting the muscles with higher than previously objectivity and reliability. They stress, however, the important role of the examiner and his experience.     

基于Bioperl实现远程自动获取抗逆基因序列

BioPerl对于现今大量的生物数据来说,具有很好的获取和处理能力,并且NCBI提供了可以直接访问它下属的Entrez数据库（包括PubMed）的编程接口,即E-Utilities。为了从NCBI中自动获取大量抗逆基因序列,使得生物抗逆基因二次数据库得以搭建,该文基于BioPerl设计了远程自动获取大量抗逆基因序列的程序。此程序灵巧、精悍,Perl语言强大的文本处理功能使程序能实现不同类型基因序列的远程获取。     

To pair or not to pair: chromosome pairing and evolution

Chromosome pairing in wild-type wheat closely resembles the process in both yeast and Drosophila. The recent characterisation of a mutant Ph1 wheat and the observation that chromosome pairing in the absence of Ph1 more closely resembles that of mammals and maize has shed light on the evolution of chromosome pairing in the cereals.     

Thermodynamics of RNA internal loops with a guanosine-guanosine pair adjacent to another noncanonical pair

Thermodynamic parameters measured by optical melting are reported for formation of RNA duplexes containing tandem noncanonical pairs with at least one guanosine-guanosine (GG) pair. For selected sequences, imino proton NMR provides evidence that the desired duplex forms and that the structure of a GG pair adjacent to a noncanonical pair depends on context. A GG pair next to a different noncanonical pair is more stable than expected from measurements of adjacent GG pairs. This is likely due to an unfavorable stacking interaction between adjacent GG pairs, where areas of high negative charge probably overlap. The results suggest a model where tandem noncanonical pairs closed by two GC pairs are assigned the following free energy increments at 37 degrees C: 0.8 kcal/mol for adjacent GG pairs, 1.0 kcal/mol for GG next to UU, and -0.3 kcal/mol for all others. These values are adjusted by 0.65 kcal/mol for each closing AU pair.     

The spread of infectious diseases in spatially structured populations: an invasory pair approximation

The invasion of new species and the spread of emergent infectious diseases in spatially structured populations has stimulated the study of explicit spatial models such as cellular automata, network models and lattice models. However, the analytic intractability of these models calls for the development of tractable mathematical approximations that can capture the dynamics of discrete, spatially-structured populations. Here we explore moment closure approximations for the invasion of an SIS epidemic on a regular lattice. We use moment closure methods to derive an expression for the basic reproductive number, R(0), in a lattice population. On lattices, R(0) should be bounded above by the number of neighbors per individual. However, we show that conventional pair approximations actually predict unbounded growth in R(0) with increasing transmission rates. To correct this problem, we propose an 'invasory' pair approximation which yields a relatively simple expression for R(0) that remains bounded above, and also predicts R(0) values from lattice model simulations more accurately than conventional pair and triple approximations. The invasory pair approximation is applicable to any spatial model, since it takes into account characteristics of invasions that are common to all spatially structured populations.     

The estimation of quinidine in human plasma by ion pair extraction and high-performance liquid chromatography

A rapid, sensitive, accurate method for determination of quinidine in plasma has been developed using ion-pair extraction and high-performance liquid chromatography. The method, which is capable of distinguishing between quinidine and dihydroquinidine, involves acidification of plasma with perchloric acid, extraction with methyl isobutyl ketone and chromatography of the carbonate-washed extract on a silica gel column with a mobile phase of methylene chloride—hexane—methanol—perchloric acid (60:35:5.5:0.1) followed by fluorometric detection. The procedure is sensitive to below 50 ng/ml (coefficient of variation 6.6%) and compares favourably with a standard spectrofluorometric method when tested with plasma from volunteer subjects.     

Application of modified supercritical carbon dioxide extraction to microbial quinone analysis

Supercritical carbon dioxide (scCO₂) was applied to extract microbial quinones from activated sludge. Identification and analysis was then performed using high-performance liquid chromatography (HPLC) equipped with ultraviolet–visible (UV–Vis) detector and photodiode array detector (PDA). Extracted microbial quinones were trapped and separated as menaquinones (MK) and ubiquinones (Q) species using two Sep-Pak Plus Silica cartridges joined in series. Four ubiquinones and 12 menaquinones species were identified in 0.1 g dried activated sludge based on retention time and spectrum analysis. Among the tested various polar solvents, methanol showed to be the best modifier, based on the highest total quinone content extracted and the lowest dissimilarity index. The diversity index of quinone and the number of quinone species using methanol-modified scCO₂ were similar to that of the conventional method (organic solvent extraction).     

Application of synthetic oligonucleotides to the diagnosis of human genetic diseases

Under appropriate conditions synthetic oligonucleotide hybridization probes display essentially absolute hybridization specificity. That is, every nucleotide must form a Watson-Crick base pair in order that the probe forms a stable duplex. All of the non-Watson-Crick base pairs, including G-T, have a destabilizing effect. Thus, it is possible to choose stringent conditions of hybridization such that, while a perfectly matched duplex between an oligonucleotide and complementary DNA will form, duplexes mismatched at one or more position will not. Mutations in a single base in the DNA sequence of a gene can and do result in genetic diseases. The hybridization of oligonucleotides to the region of DNA containing these base changes would be affected by the mutations and thus, oligonucleotide hybridization provides a means of detecting single base changes. In an attempt to develop a non-radioactive method for the detection of human genetic diseases, we have prepared biotinylated-oligonucleotides by an enzymatic method. An oligonucleotide probe (23-mer) containing a single biotinylated deoxyuridine residue at the 3'-terminus was prepared by a primer extention reaction using E. coli DNA polymerase I (Klenow fragment). The probe could be specifically and tightly bound with Avidin D in 1 M NaCl. It could be hybridized to a plasmid DNA containing a perfectly matched complementary sequence, but not to a DNA containing 5 non-consecutive non-complementary bases. The hybridized biotinylated probe could be visualized by Avidin D and biotinylated alkaline phosphatase, even when 1.8 ng of the plasmid DNA (0.5 fmol) was used. A general approach to the enzymatic synthesis of oligonucleotides containing a single biotinylated deoxyuridine at the 3' end is described.     

Application of automatic protease determination in a fermenter

A method is described for the automatic determination of proteolytic activity during fermentation, using an autolyser of the VEB Kombinat Medizin- und Labortechnik, Prüfgerätewerk Medingen, GDR, connected to a fermenter. After filtration, the culture filtrate is diluted and then incubated with casein solution (0.75%, pH 8.0, 55°C); low molecular cleavage products are separated from higher molecule ones by dialysis. The absorbance is measured at 600 nm after addition of alkaline copper tartrate and Folin solution. By use of different dilution rates, a range of 0–16 units ml^?1 may be measured.     

Method: automatic segmentation of mitochondria utilizing patch classification,contour pair classification,and automatically seeded level sets

Background  

While progress has been made to develop automatic segmentation techniques for mitochondria, there remains a need for more accurate and robust techniques to delineate mitochondria in serial blockface scanning electron microscopic data. Previously developed texture based methods are limited for solving this problem because texture alone is often not sufficient to identify mitochondria. This paper presents a new three-step method, the Cytoseg process, for automated segmentation of mitochondria contained in 3D electron microscopic volumes generated through serial block face scanning electron microscopic imaging. The method consists of three steps. The first is a random forest patch classification step operating directly on 2D image patches. The second step consists of contour-pair classification. At the final step, we introduce a method to automatically seed a level set operation with output from previous steps.