A New Method to Distinguish between Meiotic and Premeiotic Recombinational Events in DROSOPHILA MELANOGASTER

A new method is proposed to distinguish between meiotic and premeiotic exchange events in Drosophila melanogaster males associated with male recombination activities. The method was applied to data that have accumulated in this laboratory during the past five years, and it was concluded that a large fraction, perhaps the overwhelming majority, of the male recombinants were due to exchange events that took place before meiosis.     

Evolution of Orthologous Intronless and Intron-Bearing Globin Genes in Two Insect Species

While globin genes ctt-2β and ctt-9.1 in Chironomus thummi thummi each have a single intron, all of the other insect globin genes reported so far are intronless. We analyzed four globin genes linked to the two intron-bearing genes in C. th. thummi. Three have a single intron at the same position as ctt-2β and ctt-9.1; the fourth is intronless and lies between intron bearing genes. Finally, in addition to its intron, one gene (ctt-13RT) was recently interrupted by retrotransposition. Phylogenetic analyses show that the six genes in C. th. thummi share common ancestry with five globin genes in the distantly related species C. tentans, and that a 5-gene ancestral cluster predates the divergence of the two species. One gene in the ancestral cluster gave rise to ctn-ORFB in C. tentans, and duplicated in C. th. thummi to create ctt-11 and ctt-12. From parsimonious calculations of evolutionary distances since speciation, ctt-11, ctt-12, and ctn-ORFB evolved rapidly, while ctn-ORFE in C. tentans evolved slowly compared to other globin genes in the clusters. While these four globins are under selective pressure, we suggest that most chironomid globin genes were not selected for their unique function. Instead, we propose that high gene copy number itself was selected because conditions favored organisms that could synthesize more hemoglobin. High gene copy number selection to produce more of a useful product may be the basis of forming multigene families, all of whose members initially accumulate neutral substitutions while retaining essential function. Maintenance of a large family of globin genes not only ensured high levels of hemoglobin production, but may have facilitated the extensive divergence of chironomids into as many as 5000 species. Received: 31 December 1996 / Accepted: 16 May 1997     

通过一种新方法使T7基因I置换araBAD基因簇

目的:用T7 RNA聚合酶基因T17基因I置换大肠杆菌基因组中的araBAD基因簇.方法:通过分析大肠杆菌基因组中araBAD基因序列,设计两侧同源臂,构建高拷贝数的打靶质粒,并且在这个质粒上的打靶片段两侧各加上一个归巢内切酶位点;将辅助质粒和打靶质粒同时转化到宿主体内,在L-阿拉伯糖的诱导下表达归巢内切酶和Red重组酶,实现体内重组,使T7基因I置换araBAD基因簇.结果:在4株不同的大肠杆菌中用T7基因I置换了araBAD基因簇.结论:成功地将T7基因,整合到araBAD基因位置,为构建Para-PT7表达系统奠定了基础.     

Molecular Phylogenetic Analysis of Archaeal Intron-Containing Genes Coding for rRNA Obtained from a Deep-Subsurface Geothermal Water Pool

Molecular phylogenetic analysis of a naturally occurring microbial community in a deep-subsurface geothermal environment indicated that the phylogenetic diversity of the microbial population in the environment was extremely limited and that only hyperthermophilic archaeal members closely related to Pyrobaculum were present. All archaeal ribosomal DNA sequences contained intron-like sequences, some of which had open reading frames with repeated homing-endonuclease motifs. The sequence similarity analysis and the phylogenetic analysis of these homing endonucleases suggested the possible phylogenetic relationship among archaeal rRNA-encoded homing endonucleases.     

A New Approach to Distinguish Thixotropic and Viscoelastic Phenomena

A novel approach for distinguishing the viscoelastic and thixotropic phenomena of predisturbed and intact networks at short and long timescales of observation was proposed using stress relaxation, creep/recovery, single shear decay, and in-shear structural recovery experiments. The method was able to illustrate the connections patterns of the internal microstructure of hydrocolloids and its alteration over time. To test the universality of the new approach, we studied seven commercial and four emerging hydrocolloids. Moreover, to find out the correlation between the proposed parameters from this approach and the fundamental rheological parameters of the selected hydrocolloids, a principal component analysis (PCA) was employed, which showed an excellent correlation between the parameters of all hydrocolloids in predisturbed and intact states at short and long timescales. This work assumed that two different patterns of linkage connection exist, but the analysis can be extended to more than two connection patterns of linkages.

     

Porcine E. coli: Virulence-Associated Genes,Resistance Genes and Adhesion and Probiotic Activity Tested by a New Screening Method

We established an automated screening method to characterize adhesion of Escherichia coli to intestinal porcine epithelial cells (IPEC-J2) and their probiotic activity against infection by enteropathogenic E. coli (EPEC). 104 intestinal E. coli isolates from domestic pigs were tested by PCR for the occurrence of virulence-associated genes, genes coding for resistances to antimicrobial agents and metals, and for phylogenetic origin by PCR. Adhesion rates and probiotic activity were examined for correlation with the presence of these genes. Finally, data were compared with those from 93 E. coli isolates from wild boars.Isolates from domestic pigs carried a broad variety of all tested genes and showed great diversity in gene patterns. Adhesions varied with a maximum of 18.3 or 24.2 mean bacteria adherence per epithelial cell after 2 or 6 hours respectively. Most isolates from domestic pigs and wild boars showed low adherence, with no correlation between adhesion/probiotic activity and E. coli genes or gene clusters. The gene sfa/foc, encoding for a subunit of F1C fimbriae did show a positive correlative association with adherence and probiotic activity; however E. coli isolates from wild boars with the sfa/foc gene showed less adhesion and probiotic activity than E. coli with the sfa/foc gene isolated from domestic pigs after 6 hour incubation.In conclusion, screening porcine E. coli for virulence associated genes genes, adhesion to intestinal epithelial cells, and probiotic activity revealed a single important adhesion factor, several probiotic candidates, and showed important differences between E. coli of domestic pigs and wild boars.     

In vivo Imaging Method to Distinguish Acute and Chronic Inflammation

Inflammation is a fundamental aspect of many human diseases. In this video report, we demonstrate non-invasive bioluminescence imaging techniques that distinguish acute and chronic inflammation in mouse models. With tissue damage or pathogen invasion, neutrophils are the first line of defense, playing a major role in mediating the acute inflammatory response. As the inflammatory reaction progresses, circulating monocytes gradually migrate into the site of injury and differentiate into mature macrophages, which mediate chronic inflammation and promote tissue repair by removing tissue debris and producing anti-inflammatory cytokines. Intraperitoneal injection of luminol (5-amino-2,3-dihydro-1,4-phthalazinedione, sodium salt) enables detection of acute inflammation largely mediated by tissue-infiltrating neutrophils. Luminol specifically reacts with the superoxide generated within the phagosomes of neutrophils since bioluminescence results from a myeloperoxidase (MPO) mediated reaction. Lucigenin (bis-N-methylacridinium nitrate) also reacts with superoxide in order to generate bioluminescence. However, lucigenin bioluminescence is independent of MPO and it solely relies on phagocyte NADPH oxidase (Phox) in macrophages during chronic inflammation. Together, luminol and lucigenin allow non-invasive visualization and longitudinal assessment of different phagocyte populations across both acute and chronic inflammatory phases. Given the important role of inflammation in a variety of human diseases, we believe this non-invasive imaging method can help investigate the differential roles of neutrophils and macrophages in a variety of pathological conditions.     

Population Density of Chimpanzees and Gorillas in the Petit Loango Reserve,Gabon: Employing a New Method to Distinguish Between Nests of the Two Species

We studied the vegetation and population density of chimpanzees (Pan troglodytes troglodytes) and gorillas (Gorilla gorilla gorilla) in the Petit Loango Reserve, Gabon. The study site consists mainly of primary and secondary forest, and it also includes patches of savanna, inundated forest, and coastal scrub. The density of herbaceous plants of Marantaceae and Zingiberaceae, which serve as important foods for great apes at other study sites, is extremely low. It was very difficult to distinguish between the nests of chimpanzees and gorillas because most gorilla nests were made in trees. We developed a new method to identify the builder of nests via a combination of field observation of nests and fecal samples, and examination of hair samples under a scanning electron microscope. Nests of chimpanzees were mainly in primary forest, and the estimated density (0.78 individual per km ² ) is higher than the average density in Gabon and comparable to the nest density in the Lopé Reserve, Gabon. Nests of gorillas were mainly in secondary forest, and their estimated density (0.21) is similar to the average next density in Gabon but lower than the gorilla nest density in the Lopé Reserve. The low density of herbaceous foods seemed to influence the density of gorillas but not the density of chimpanzees.     

A New Criterion by Which to Distinguish Aspergillus sojae,a Koji-mold,from Related Taxa Producing Echinulate Conidia

Milk powders (commercial skim milk and modified milk powders) were stored at 30°C and 40°C for one month under various water activities (Aw), 0.23~0.82. After storage under Aw 0.57 and 0.80, they turned a dark brown color, and the contents of methionine and lysine had significantly decreased: methionine had been oxidized to methionine sulfoxide and lysine had changed to an unavailable form. The contents of arginine, tyrosine and tryptophan had also decreased, as had the contents of leucine and histidine in the skim milk powder. The tryptic digestibility of the milk powders had markedly decreased, and both the chymotryptic and peptic digestibilities of the skim milk powder had also decreased. The samples lost the property of being clotted by chymosin treatment.

No significant change was observed with casein under these conditions, nor with milk powders under dry conditions and Aw 0.23.     

The Human Intron-Containing Gene for Glycogenin Maps to Chromosome 3, Band q24

Glycogenin is the autocatalytic, self-glucosylating primer for glycogen synthesis, providing the anchor on which the macromolecule is constructed. We have sequenced the cDNA coding for human muscle glycogenin and have deduced the corresponding amino acid sequence. By means of the polymerase chain reaction and fluorescencein situhybridization, we have found the chromosomal location of the gene coding for glycogenin. This is localized to human chromosome 3, band q24.     

New Genes on Human Chromosome 7: Bioinformation Analysis of a Cluster of Genes from the POLR2J Family

Four independent genes encoding various variants of the hRPB11 subunit of Homo sapiens RNA polymerase II were revealed in human chromosome 7. Three genes (POLR2J1, POLR2J2, and POLR2J3) form a cluster of total length of 214 530 bp in the genetic locus 7q22.1 on the long arm of chromosome 7 (contig NT_007933). The fourth gene (POLR2J4, 31 040 bp) was localized in the cytogenetic locus 7p13 of the short arm of chromosome 7 (contig NT_007819). An analysis enabled us to refine dissimilar experimental data on the mapping of the hRPB11 subunit gene on chromosome 7. In particular, the presence of three sites of its localization according to data on hybridization with fluorescent-labeled probes (the FISH method) was explained. It was established that, upon the expression of the four human POLR2J genes, at least 14 types of mature mRNAs encoding somewhat differing hRPB11 isoforms can be synthesized. Eleven of these mRNAs were revealed (as full-length copies or clearly identifiable fragments) in the available databases of expressed sequence tags and cDNAs. The most probable scheme of origination of the multiple genes of the POLR2J family as a result of three consecutive segmented duplications increasing in size was proposed and substantiated. On the basis of the scheme, some assumptions on the pathways of evolution of separate human genes and the mechanisms of generation of protein diversity in higher eukaryotes were made.     

Helping Students Distinguish between Mixtures and Chemical Compounds

For most middle school-level students, summarizing main ideas can prove to be difficult, especially for those with low vocabulary and language acquisition skills. Working specifically with students who are English Language Learners (ELLs) and in a special education program, we discovered that teaching summarization as a reading strategy increased students' abilities to (a) acquire and use information and (b) better comprehend science concepts. In combination with other vocabulary attainment activities, summary frames enhanced the students' ability to apply information to discussions, laboratory reports, and projects. In this article, we demonstrate how to use the summary frame strategy in the context of a lesson on cells. This lesson allows for (a) knowledge of terminology through vocabulary card activities, (b) comprehension of concepts presented through summary frame activities, and (c) application of concepts through cell models and organelle classroom responsibilities.     

A PCR-based Genotyping Method to Distinguish Between Wild-type and Ornamental Varieties of Imperata cylindrica

Wild-type I. cylindrica (cogongrass) is one of the top ten worst invasive plants in the world, negatively impacting agricultural and natural resources in 73 different countries throughout Africa, Asia, Europe, New Zealand, Oceania and the Americas^1-2. Cogongrass forms rapidly-spreading, monodominant stands that displace a large variety of native plant species and in turn threaten the native animals that depend on the displaced native plant species for forage and shelter. To add to the problem, an ornamental variety [I. cylindrica var. koenigii (Retzius)] is widely marketed under the names of Imperata cylindrica ''Rubra'', Red Baron, and Japanese blood grass (JBG). This variety is putatively sterile and noninvasive and is considered a desirable ornamental for its red-colored leaves. However, under the correct conditions, JBG can produce viable seed (Carol Holko, 2009 personal communication) and can revert to a green invasive form that is often indistinguishable from cogongrass as it takes on the distinguishing characteristics of the wild-type invasive variety⁴ (Figure 1). This makes identification using morphology a difficult task even for well-trained plant taxonomists. Reversion of JBG to an aggressive green phenotype is also not a rare occurrence. Using sequence comparisons of coding and variable regions in both nuclear and chloroplast DNA, we have confirmed that JBG has reverted to the green invasive within the states of Maryland, South Carolina, and Missouri. JBG has been sold and planted in just about every state in the continental U.S. where there is not an active cogongrass infestation. The extent of the revert problem in not well understood because reverted plants are undocumented and often destroyed.Application of this molecular protocol provides a method to identify JBG reverts and can help keep these varieties from co-occurring and possibly hybridizing. Cogongrass is an obligate outcrosser and, when crossed with a different genotype, can produce viable wind-dispersed seeds that spread cogongrass over wide distances^5-7. JBG has a slightly different genotype than cogongrass and may be able to form viable hybrids with cogongrass. To add to the problem, JBG is more cold and shade tolerant than cogongrass^8-10, and gene flow between these two varieties is likely to generate hybrids that are more aggressive, shade tolerant, and cold hardy than wild-type cogongrass. While wild-type cogongrass currently infests over 490 million hectares worldwide, in the Southeast U.S. it infests over 500,000 hectares and is capable of occupying most of the U.S. as it rapidly spreads northward due to its broad niche and geographic potential^3,7,11. The potential of a genetic crossing is a serious concern for the USDA-APHIS Federal Noxious Week Program. Currently, the USDA-APHIS prohibits JBG in states where there are major cogongrass infestations (e.g., Florida, Alabama, Mississippi). However, preventing the two varieties from combining can prove more difficult as cogongrass and JBG expand their distributions. Furthermore, the distribution of the JBG revert is currently unknown and without the ability to identify these varieties through morphology, some cogongrass infestations may be the result of JBG reverts. Unfortunately, current molecular methods of identification typically rely on AFLP (Amplified Fragment Length Polymorphisms) and DNA sequencing, both of which are time consuming and costly. Here, we present the first cost-effective and reliable PCR-based molecular genotyping method to accurately distinguish between cogongrass and JBG revert.     

Novel Method to Load Multiple Genes onto a Mammalian Artificial Chromosome

Mammalian artificial chromosomes are natural chromosome-based vectors that may carry a vast amount of genetic material in terms of both size and number. They are reasonably stable and segregate well in both mitosis and meiosis. A platform artificial chromosome expression system (ACEs) was earlier described with multiple loading sites for a modified lambda-integrase enzyme. It has been shown that this ACEs is suitable for high-level industrial protein production and the treatment of a mouse model for a devastating human disorder, Krabbe’s disease. ACEs-treated mutant mice carrying a therapeutic gene lived more than four times longer than untreated counterparts. This novel gene therapy method is called combined mammalian artificial chromosome-stem cell therapy. At present, this method suffers from the limitation that a new selection marker gene should be present for each therapeutic gene loaded onto the ACEs. Complex diseases require the cooperative action of several genes for treatment, but only a limited number of selection marker genes are available and there is also a risk of serious side-effects caused by the unwanted expression of these marker genes in mammalian cells, organs and organisms. We describe here a novel method to load multiple genes onto the ACEs by using only two selectable marker genes. These markers may be removed from the ACEs before therapeutic application. This novel technology could revolutionize gene therapeutic applications targeting the treatment of complex disorders and cancers. It could also speed up cell therapy by allowing researchers to engineer a chromosome with a predetermined set of genetic factors to differentiate adult stem cells, embryonic stem cells and induced pluripotent stem (iPS) cells into cell types of therapeutic value. It is also a suitable tool for the investigation of complex biochemical pathways in basic science by producing an ACEs with several genes from a signal transduction pathway of interest.     

Interrelationships between strains of Salmonella enteritidis belonging to phage types 4, 7, 7a, 8, 13, 13a, 23, 24 and 30

Salmonella enteritidis strain P278849 expressed long-chain lipopolysaccharide (LPS, termed 'smooth'), carried plasmids of 38, 34 (pDEP 44, incompatibility group N, R-type AS), 2.0 and 1 MDa, and belonged to phage type (PT) 23. Introduction of pDEP 44 into a smooth strain of Salm. enteritidis PT 4 produced a smooth strain of Salm. enteritidis of PT 24. Transfer of this plasmid into a strain of PT 8 also resulted in formation of a smooth strain of Salm. enteritidis of PT 24. Moving pDEP 44 into strains of Salm. enteritidis of PTs 7 or 7a which did not express LPS (termed 'rough') resulted in rough strains of PT 23. In contrast, transfer of this plasmid into a smooth strain of Salm. enteritidis PT 7a resulted in a smooth strain of PT 23. Introduction of pDEP 44 into strains of Salm. enteritidis of PT 13 or PT 13a did not change the phage type, whereas transferring the plasmid into strains of PT 30 caused strains to become resistant to lysis by the typing phages and therefore untypable. The possibility of strains of Salm. enteritidis of PT 8 being the progenitors of strains of Salm. enteritidis of PT 24 must now be considered when investigating the epidemiology of Salm. enteritidis of PT 24 infections in areas where Salm. enteritidis PT 8 is common.     

三点测交基因连锁作图计算的新方法

提出了三点测交基因连锁作图的一种新的计算方法,弥补了经典经典计算方法的不足之处,使基因连锁作图更准确。     

Characterization of a New Bacteriocin Operon in Sakacin P-Producing Lactobacillus sakei, Showing Strong Translational Coupling between the Bacteriocin and Immunity Genes

Previous studies of genes involved in the production of sakacin P by Lactobacillus sakei Lb674 revealed the presence of an inducible promoter downstream of the known spp gene clusters. We show here that this promoter drives the expression of an operon consisting of a bacteriocin gene (sppQ), a cognate immunity gene (spiQ), another gene with an unknown function (orf4), and a pseudoimmunity gene containing a frameshift mutation (orf5). The leader peptide of the new one-peptide bacteriocin sakacin Q contains consensus elements that are typical for so-called “double-glycine” leader peptides. The mature bacteriocin shows weak similarity to the BrcA peptide of the two-peptide bacteriocin brochocin C. Sakacin Q has an antimicrobial spectrum that differs from that of sakacin P, thus expanding the antimicrobial properties of the producer strain. The genes encoding sakacin Q and its cognate immunity protein showed strong translational coupling, which was investigated in detail by analyzing the properties of a series of β-glucuronidase fusions. Our results provide experimental evidence that production of the bacteriocin and production of the cognate immunity protein are tightly coregulated at the translational level.     

Use of Two-Dimensional Electrophoresis to Identify and Map New Mouse Genes

Cytosol polypeptides from mouse liver have been examined using two-dimensional electrophoresis. About 250 spots were readily discernible. When cytosols from strains BALB/cBy and C57BL/6By were compared eight genetically determined differences were observed. Other strain pairs show comparable numbers of differences. These eight phenotypes were scored in seven recombinant inbred lines derived from the two parental strains, and their strain distribution patterns were compared with previously determined patterns for other genetic markers that differ between the two progenitor strains. Using this information, tentative chromosomes assignments for the genes controlling five of the variant phenotypes have been made, and two of the assignments have been confirmed using congenic resistant strains. These eight genes will be useful reference markers in future crosses designed to map new genes.     

Integration of New Genes into Cellular Networks,and Their Structural Maturation

It has been recently discovered that new genes can originate de novo from noncoding DNA, and several biological traits including expression or sequence composition form a continuum from noncoding sequences to conserved genes. In this article, using yeast genes I test whether the integration of new genes into cellular networks and their structural maturation shows such a continuum by analyzing their changes with gene age. I show that 1) The number of regulatory, protein–protein, and genetic interactions increases continuously with gene age, although with very different rates. New regulatory interactions emerge rapidly within a few million years, while the number of protein–protein and genetic interactions increases slowly, with a rate of 2–2.25 × 10⁻⁸/year and 4.8 × 10⁻⁸/year, respectively. 2) Gene essentiality evolves relatively quickly: the youngest essential genes appear in proto-genes ∼14 MY old. 3) In contrast to interactions, the secondary structure of proteins and their robustness to mutations indicate that new genes face a bottleneck in their evolution: proto-genes are characterized by high β-strand content, high aggregation propensity, and low robustness against mutations, while conserved genes are characterized by lower strand content and higher stability, most likely due to the higher probability of gene loss among young genes and accumulation of neutral mutations.