Isolation of mutant promoters in the Escherichia coli galactose operon using local mutagenesis on cloned DNA fragments

We have worked out a system to obtain mutations that map in the promoter region of the Escherichia coli galactose operon. In order to easily detect small changes in gal promoter activity, we constructed a plasmid containing an operon fusion in which the lactose operon structural genes were controlled by the galactose operon promoter region. In cells harbouring this plasmid, even modest variations in the expression of the lac genes could be detected on MacConkey lactose indicator plates.Enrichment for mutations that map in the promoter segment of the galactose operon was achieved by mutagenesis in vitro of a small fragment of DNA covering the promoter region. After insertion of the mutagenized gal promoter fragment into the gal-lac fusion plasmid, lac^?1 cells were transformed and screened for an altered Lac⁺ phenotype on indicator plates. Several mutants were isolated due to lesions mapping in the small fragment covering the galactose promoter. In these mutants, the level of β-galactosidase was between 15 and 50% of the wild-type level.The mutant promoters were subsequently reinserted into a plasmid containing the intact galactose operon. Cells harbouring such plasmids, reconstituted with mutant galactose promoters, contained decreased levels of galactokinase that paralleled the decreases in β-galactosidase. The biochemical properties of these mutants are reported in the accompanying paper (Busby et al., 1982).     

Identification of donor splice sites using support vector machine: a computational approach based on positional,compositional and dependency features

Background

Identification of splice sites is essential for annotation of genes. Though existing approaches have achieved an acceptable level of accuracy, still there is a need for further improvement. Besides, most of the approaches are species-specific and hence it is required to develop approaches compatible across species.

Results

Each splice site sequence was transformed into a numeric vector of length 49, out of which four were positional, four were dependency and 41 were compositional features. Using the transformed vectors as input, prediction was made through support vector machine. Using balanced training set, the proposed approach achieved area under ROC curve (AUC-ROC) of 96.05, 96.96, 96.95, 96.24 % and area under PR curve (AUC-PR) of 97.64, 97.89, 97.91, 97.90 %, while tested on human, cattle, fish and worm datasets respectively. On the other hand, AUC-ROC of 97.21, 97.45, 97.41, 98.06 % and AUC-PR of 93.24, 93.34, 93.38, 92.29 % were obtained, while imbalanced training datasets were used. The proposed approach was found comparable with state-of-art splice site prediction approaches, while compared using the bench mark NN269 dataset and other datasets.

Conclusions

The proposed approach achieved consistent accuracy across different species as well as found comparable with the existing approaches. Thus, we believe that the proposed approach can be used as a complementary method to the existing methods for the prediction of splice sites. A web server named as ‘HSplice’ has also been developed based on the proposed approach for easy prediction of 5′ splice sites by the users and is freely available at http://cabgrid.res.in:8080/HSplice.

     

Effect of rapamycin on bone mass and strength in the α2(I)‐G610C mouse model of osteogenesis imperfecta

Osteogenesis imperfecta (OI) is commonly caused by heterozygous type I collagen structural mutations that disturb triple helix folding and integrity. This mutant‐containing misfolded collagen accumulates in the endoplasmic reticulum (ER) and induces a form of ER stress associated with negative effects on osteoblast differentiation and maturation. Therapeutic induction of autophagy to degrade the mutant collagens could therefore be useful in ameliorating the ER stress and deleterious downstream consequences. To test this, we treated a mouse model of mild to moderate OI (α2(I) G610C) with dietary rapamycin from 3 to 8 weeks of age and effects on bone mass and mechanical properties were determined. OI bone mass and mechanics were, as previously reported, compromised compared to WT. While rapamycin treatment improved the trabecular parameters of WT and OI bones, the biomechanical deficits of OI bones were not rescued. Importantly, we show that rapamycin treatment suppressed the longitudinal and transverse growth of OI, but not WT, long bones. Our work demonstrates that dietary rapamycin offers no clinical benefit in this OI model and furthermore, the impact of rapamycin on OI bone growth could exacerbate the clinical consequences during periods of active bone growth in patients with OI caused by collagen misfolding mutations.     

Sperm ultrastructure in the nudibranch genus Halgerda with reference to other Discodorididae and to Chromodorididae (Mollusca: Opisthobranchia)

Comparative sperm ultrastructure within the molluscan nudibranch genus Halgerda (Discodorididae) was examined for the first time using transmission electron microscopy (TEM), based on 17 of the 35 known species. In addition, observations on two other discodorids are made to facilitate outgroup comparison with Halgerda, including one species of Discodoris (D. boholiensis) and Asteronotus cespitosus (currently accepted as the closest sister taxon to Halgerda). Comparison was also made with some genera of the Chromodorididae in view of sperm similarities. Spermatozoa of all species examined were of the complex, helical, elongate ( approximately 300-400 micro m) type characteristic of most heterobranch gastropods. These cells exhibit the following discrete regions (in anteroposterior sequence) : an acrosomal complex (composed of a rounded, membrane-bound vesicle and a column-like pedestal); a solid, helical nucleus; an elongate, helical midpiece (composed of an axoneme and associated nine coarse fibers, an enveloping mitochondrial derivative of matrix, and paracrystalline materials and glycogen helix); an annular complex; and a short glycogen piece. Of these regions, the midpiece is by far the longest, occupying over 90% of the total sperm length. Comparison with other members of the radula-bearing cryptobranch dorids reveals several sperm similarities to other genera in the clade, particularly those of other Discodorididae and also with the Chromodorididae. Comparison with previously studied genera reveals noteworthy sperm differences within the Discodorididae. The most notable differences are the internal structure of the acrosomal pedestal (long and homogeneous in Halgerda, Discodoris; short and homogeneous in Asteronotus; long and finely striated in Rostanga; oblong with angular electron-lucent striations in Jorunna) and the internal structure of the glycogen piece. The pronounced helical keels of most Halgerda and Discodoris nuclei contrast with the weakly helical nucleus of Asteronotus. Sperm features alone do not provide a means of defining the genus Halgerda or the family Discodorididae nor do they support the monophyletic status of the caryophyllidia-bearing dorids. Important sperm characters such as the acrosome, nucleus, and midpiece can often still be determined from specimens that have been initially fixed in formalin, then stored in ethanol for extended periods of time (i.e., museum material). Of all sperm features, the mitochondrial derivative of the midpiece is the most resistant to long-term fixation : the survival of acrosomal, nuclear, and axonemal components is variable, presumably a factor of prefixation autolysis, varied primary fixation times and temperatures, formalin quality, and duration of alcohol storage.     

Mycobacterium leprae binds to a major human peripheral nerve glycoprotein myelin P zero (P0)

We have previously shown that a major phosphorylated 25-kDa glycoprotein of the human peripheral nerve binds to Mycobacterium leprae. In the present study, we confirm that the 25-kDa glycoprotein of the human peripheral nerve is myelin P zero (P₀) by immunoprecipitation and Western blot experiments using monoclonal antibodies to myelin P₀. Immunohistochemical studies on human nerve using these antibodies to myelin P₀ exhibited a strong immunoreactivity to the myelin and Schwann cells. Myelin P₀ is a peripheral nerve specific protein; therefore it could likely be one of the key target molecules for M. leprae binding/internalization or even contact-dependent demyelination. This finding of M. leprae binding to myelin P₀ adds to the present understanding on neural predilection of M. leprae.     

Regeneration and transformation of Egyptian maize inbred lines via immature embryo culture and a biolistic particle delivery system

Summary A regeneration system was developed for elite Egyptain maize inbred lines using immature embryos as explants. This system proved to be highly genotype-dependent. Line Gz 643 was identified as the best line, revealing the highest regeneration frequency (42.2%). Addition of l-proline and silver nitrate to culture media greatly enhanced the formation of embryogenic type II callus and the regenerability of some of the tested lines. Transformation of the scutellar tissue of immature embryos from inbred line Gz643 was performed with the particle delivery system using a single plasmid carrying both the GUS and Bar genes (pAB-6) or by co-transformation with two plasmids, pAct1-F (GUS) and pTW-a(Bar). Different transformation parameters were evaluated, i.e. ostomic treatment, acceleration pressure, and number of shots. Osmotic treatment (0.25 M sorbitol + 0.25 M mannitol) along with the use of either acceleration pressure 1300 psi and one shot per plate (for co-transformation with pAB-6) or 1100 psi and two shots per plate (for transformation with pAct1-F and pTW-a) gave the best results, as expressed by the number of blue spots in the β-glucuronidase (GUS) assay. Stable transformation was confirmed in Ro transformed plants by means of histochemical GUS assay and herbicide application. PCR and Southern blot analysis proved the integration of the full-length genes in some of the transgenics.     

Probing the Mechanism of pH-Induced Large-Scale Conformational Changes in Dengue Virus Envelope Protein Using Atomistic Simulations

One of the key steps in the infection of the cell by dengue virus is a pH-induced conformational change of the viral envelope proteins. These envelope proteins undergo a rearrangement from a dimer to a trimer, with large conformational changes in the monomeric unit. In this article, metadynamics simulations were used to enable us to understand the mechanism of these large-scale changes in the monomer. By using all-atom, explicit solvent simulations of the monomers, the stability of the protein structure is studied under low and high pH conditions. Free energy profiles obtained along appropriate collective coordinates demonstrate that pH affects the domain interface in both the conformations of E monomer, stabilizing one and destabilizing the other. These simulations suggest a mechanism with an intermediate detached state between the two monomeric structures. Using further analysis, we comment on the key residue interactions responsible for the instability and the pH-sensing role of a histidine that could not otherwise be studied experimentally. The insights gained from this study and methodology can be extended for studying similar mechanisms in the E proteins of the other members of class II flavivirus family.