A new rapid fluorogenic method for measuring bacteriocin activity

We describe a novel bacteriocin screening assay based on fluorescence emitted by berberine following its influx into compromised cells. This technique showed agreement with the conventional well-diffusion method, and results can be obtained within one hour. This assay could facilitate the rapid identification of bacteriocinogenic bacterial isolates.     

A new method for the rapid separation of cell organelles

A rapid procedure is described for the separation of plant cell organelles from castor bean endosperm (Ricinus communis). This method is based on the reorientation of sucrose density gradients during centrifugation in a vertical rotor, thus resulting in a shorter path length and drastically reduced run times. Comparison to a separation by a standard procedure shows that, by using this method, equal resolution is possible in less than 10% spin time.     

A new method for rapid identification of influenza virus isolates.

With the use of bacteria sensitized by influenza virus strain-specific antisera, virus isolates can be identified rapidly. One drop of virus suspension is mixed with one drop of sensitized bacteria on a slide that is then agitated; reaction occurs within 10 minutes. The test is subtype-specific. The mehod is based on the fact that the cell wall of the Cowan type 1 strain of Staphylococcus aureus contains abundant quantities of an antigen, known as protein A, that reacts with the IgG molecule by binding it in such a manner that the antibody-combining sites remain free. If an antigen homologous to the antibody coated on the surface of the bacteria is added to the suspension of sensitized staphylococci, agglutination occurs.     

A new method for rapid assignment of S-S bridges in proteins

A new method for complementing existing protein chemical techniques for the assignment of S-S bridge positions in amino-acid sequences is described. The principle of the method is the direct examination of the masses of protein fragments, obtained by chemical or enzymatic degradation. Proteins are digested under conditions known to minimise disulphide reduction and reshuffling, and the unfractionated digest is examined directly by high field magnet (or other high mass) fast atom bombardment or Californium mass spectrometry. Disulphide linked peptides are identified from their unique masses, and by comparison with the spectrum of digested and reduced samples in which the signal corresponding to the S-S linked peptide(s) is replaced by two signals corresponding to the respective thiol peptide components, if INTER-bridged, or shifted by two mass units (dithiol) if INTRA-bridged. This rapid procedure has considerable potential in assisting with studies on the primary structure of proteins, in crystallographic studies and the monitoring of denaturation/renaturation of recombinant proteins.     

一种快速鉴定转基因植物纯合体的新方法

植物转化中鉴定转基因植物的整合性是一个很重要的步骤,常规方法是对独立分离的转基因T1代植株产生的T2代进行转基因分离比率研究,以检测T1代的转基因整合状态,不仅费时费力,而且浪费了T1代资源。本介绍一种应用双重定量实时PCR技术鉴定转基因植物纯合子的新方法：以T1代植物DNA为模板,根据转基因后代的Ct表型值鉴定其转基因整合状态,Ct值接近2的为转基因纯合型,Ct值接近1的为转基因杂合型。用这种方法,可以同时对数十个T1代转基因幼苗的整合状态进行快速鉴定,准确率为100％。     

The pipette method: A new rapid technique for chromosome analysis in prenatal diagnosis

Summary A new method has been developed to abridge the time between amniocentesis and chromosome analysis in prenatal diagnosis. With this method cells in metaphase are separated from the clones by a micropipette with the help of a micromanipulator and then prepared.     

A new method for the analysis of age trends in CPK levels with application to Duchenne muscular dystrophy.

Measurement of serum creatine phosphokinase (CPK) is the most commonly applied test for carrier detection in Duchenne muscular dystrophy. About two thirds of all carriers have markedly elevated CPK levels. Age correction of CPK measurements would be straightforward if carriers of all ages could be unambiguously identified. Since such identification is impossible, we elaborate an indirect statistical method which is based on Haldane's theory of the balance between selection and mutation for X-linked lethals. We also apply this method to a large body of data gathered on female relatives of Duchenne muscular dystrophy patients and on controls. The results are compared with earlier partial findings.     

A new method for the rapid diagnosis of acute streptococcal infection]

The work deals with the development of the rapid method of the identification of acute streptococcal infection on the basis of the coagglutination test. The rapid method of the extraction of group-specific polysaccharide antigen from the cell walls of group A streptococci is proposed. The data on the use of native sera and their fractions in the development of coagglutination diagnostica have been described and analyzed. The advantages of the new method of the diagnosis of acute streptococcal infection in comparison with the traditional microbiological method are shown.     

A new rapid and simple method for large-scale purification of mycobacterial lipoarabinomannan

Lipoarabinomannan (LAM) is a major and structurally important outer cell wall component of all mycobacteria. LAM is also generally regarded as an important immunomodulating substance affecting several immunologic networks and hence important in the pathogenesis of mycobacterial infections. We here describe a new method for large-scale purification of mycobacterial LAM. A crude cell wall preparation was prepared from batch-grown Mycobacterium tuberculosis H37Rv. From this cell wall preparation LAM was purified by sequential extractions and chromatographic steps. From 20 g dry weight cell wall preparation 313 mg of highly purified (> 98%) LAM was obtained in only 3 days. The LAM content of the final purification step was quantified by ELISA using reference LAM as standard. The identity and purity of the LAM preparation was further confirmed by comparison with reference LAM preparation from M. tuberculosis strain Erdman in polyacrylamide gel electrophoresis and Western blots, using reference anti-LAM monoclonals CS-35 and CS-40.     

A new method for identifying rapid decline dynamics in wild vertebrate populations

Tracking trends in the abundance of wildlife populations is a sensitive method for assessing biodiversity change due to the short time‐lag between human pressures and corresponding shifts in population trends. This study tests for proposed associations between different types of human pressures and wildlife population abundance decline‐curves and introduces a method to distinguish decline trajectories from natural fluctuations in population time‐series. First, we simulated typical mammalian population time‐series under different human pressure types and intensities and identified significant distinctions in population dynamics. Based on the concavity of the smoothed population trend and the algebraic function which was the closest fit to the data, we determined those differences in decline dynamics that were consistently attributable to each pressure type. We examined the robustness of the attribution of pressure type to population decline dynamics under more realistic conditions by simulating populations under different levels of environmental stochasticity and time‐series data quality. Finally, we applied our newly developed method to 124 wildlife population time‐series and investigated how those threat types diagnosed by our method compare to the specific threatening processes reported for those populations. We show how wildlife population decline curves can be used to discern between broad categories of pressure or threat types, but do not work for detailed threat attributions. More usefully, we find that differences in population decline curves can reliably identify populations where pressure is increasing over time, even when data quality is poor, and propose this method as a cost‐effective technique for prioritizing conservation actions between populations.     

A transgene-free method for rapid and efficient generation of precisely edited pigs without monoclonal selection

Gene-edited pigs for agricultural and biomedical applications are typically generated using somatic cell nuclear transfer (SCNT). However, SCNT requires the use of monoclonal cells as donors, and the time-consuming and laborious monoclonal selection process limits the production of large populations of gene-edited animals. Here, we developed a rapid and efficient method named RE-DSRNP (reporter RNA enriched dual-sgRNA/CRISPR-Cas9 ribonucleoproteins) for generating gene-edited donor cells. RE-DSRNP takes advantage of the precise and efficient editing features of dual-sgRNA and the high editing efficiency, low off-target effects, transgene-free nature, and low cytotoxic characteristics of reporter RNA enriched RNPs (CRISPR-Cas9 ribonucleoproteins), thus eliminating the need for the selection of monoclonal cells and thereby greatly reducing the generation time of donor cells from 3–4 weeks to 1 week, while also reducing the extent of apoptosis and chromosomal aneuploidy of donor cells. We applied RE-DSRNP to produce cloned pigs bearing a deletion edit of the wild-type p53-induced phosphatase 1 (WIP1) gene: among 32 weaned cloned pigs, 31 (97%) carried WIP1 edits, and 15 (47%) were homozygous for the designed fragment deletion, and no off-target event was detected. The WIP1 knockout (KO) pigs exhibited male reproductive disorders, illustrating the utility of RE-DSRNP for rapidly generating precisely edited animals for functional genomics and disease research. RE-DSRNP’s strong editing performance in a large animal and its marked reduction in the required time for producing SCNT donor cells support its application prospects for rapidly generating populations of transgene-free cloned animals.

     

A new PCR based method for the generation of nested deletions.

We have developed a simple, PCR-based protocol, random primed/anchored-PCR (RPA-PCR), that allows the selective amplification and efficient cloning of segments that are adjacent to any known sequence. We demonstrate that RPA-PCR can be used to prepare a nested set of evenly spaced deletions suitable for DNA sequencing. However, it should also be possible to use this technique for a number of other purposes: generating deletions for the analysis of eukaryotic promoters, extending cDNA clones in the 5' direction, cloning the insertion sites of retroviral proviruses and transposons, and analyzing intron/exon boundaries.     

XMIPP: a new generation of an open-source image processing package for electron microscopy

X-windows based microscopy image processing package (Xmipp) is a specialized suit of image processing programs, primarily aimed at obtaining the 3D reconstruction of biological specimens from large sets of projection images acquired by transmission electron microscopy. This public-domain software package was introduced to the electron microscopy field eight years ago, and since then it has changed drastically. New methodologies for the analysis of single-particle projection images have been added to classification, contrast transfer function correction, angular assignment, 3D reconstruction, reconstruction of crystals, etc. In addition, the package has been extended with functionalities for 2D crystal and electron tomography data. Furthermore, its current implementation in C++, with a highly modular design of well-documented data structures and functions, offers a convenient environment for the development of novel algorithms. In this paper, we present a general overview of a new generation of Xmipp that has been re-engineered to maximize flexibility and modularity, potentially facilitating its integration in future standardization efforts in the field. Moreover, by focusing on those developments that distinguish Xmipp from other packages available, we illustrate its added value to the electron microscopy community.     

A new deep learning method for image deblurring in optical microscopic systems

Deconvolution is the most commonly used image processing method in optical imaging systems to remove the blur caused by the point‐spread function (PSF). While this method has been successful in deblurring, it suffers from several disadvantages, such as slow processing time due to multiple iterations required to deblur and suboptimal in cases where the experimental operator chosen to represent PSF is not optimal. In this paper, we present a deep‐learning‐based deblurring method that is fast and applicable to optical microscopic imaging systems. We tested the robustness of proposed deblurring method on the publicly available data, simulated data and experimental data (including 2D optical microscopic data and 3D photoacoustic microscopic data), which all showed much improved deblurred results compared to deconvolution. We compared our results against several existing deconvolution methods. Our results are better than conventional techniques and do not require multiple iterations or pre‐determined experimental operator. Our method has several advantages including simple operation, short time to compute, good deblur results and wide application in all types of optical microscopic imaging systems. The deep learning approach opens up a new path for deblurring and can be applied in various biomedical imaging fields.     

A rapid method for counting nucleated erythrocytes on stained blood smears by digital image analysis

Measures of parasitemia by intraerythrocytic hematozoan parasites are normally expressed as the number of infected erythrocytes per n erythrocytes and are notoriously tedious and time consuming to measure. We describe a protocol for generating rapid counts of nucleated erythrocytes from digital micrographs of thin blood smears that can be used to estimate intensity of hematozoan infections in nonmammalian vertebrate hosts. This method takes advantage of the bold contrast and relatively uniform size and morphology of erythrocyte nuclei on Giemsa-stained blood smears and uses ImageJ, a java-based image analysis program developed at the U.S. National Institutes of Health and available on the internet, to recognize and count these nuclei. This technique makes feasible rapid and accurate counts of total erythrocytes in large numbers of microscope fields, which can be used in the calculation of peripheral parasitemias in low-intensity infections.     

The H-2KbtsA58 transgenic mouse: A new tool for the rapid generation of novel cell lines

The ability to generate expanded populations of individual cell types able to undergo normal differentiationin vitro andin vivo is of critical importance in the investigation of the mechanisms that underly differentiation and in studies on the use of cell transplantation to repair damaged tissues. This review discusses the development of a strain of transgenic mice that allows the direct derivation of conditionally immortal cell lines from a variety of tissues, simply by dissociation of the tissue of interest and growth of cells in appropriate conditions. In these mice the tsA58 mutant of SV40 large T antigen is controlled by the interferon-inducible Class I antigen promoter. Cells can be grown for extended periodsin vitro simply by growing them at 33°C in the presence of interferon, while still retaining the capacity to undergo normal differentiationin vivo andin vitro. In addition, it appears that cell lines expressing mutant phenotypes can readily be generated by preparing cultures from appropriate offspring of matings between H-2K^btsA58 transgenic mice and mutant mice of interest.     

Hot water percolation (HWP): A new rapid soil extraction method

A new, easily applicable soil extraction method has been developed using the coffee percolator principle. The hot water percolation method (HWP) was examined on 36 soils with different properties. During hot water percolation the available, desorbable, easily soluble elements are extracted by hot water (102–105°C) at 120–150 kPa pressure. The average time for one extraction is 2.6 mm. It is possible to carry out kinetic measurements too. Nearly every nutrient is extracted by this method in measurable quantities, and the macroelements in appreciable quantities. The variation coefficient (CV%) of the method is in average 11%. The results are in close correlation with those of conventional soil testing methods and with the nutrient uptake of the sunflower and ryegrass used as test plants.