Unstable mutations caused by regional tandem multiplications in the gene for ribosomal protein S4 show thermosensitivity in Escherichia coli

Summary The nucleotide sequence of the gene rpsD for the ribosomal protein S4 of three thermosensitive mutants of Escherichia coli K 12 was determined. It was found that two of them contained regional multiplications of a nucleotide sequence within the gene rpsD. In one case, it is a duplication of a 31 nucleotide stretch and in another it is a triplication of a 41 nucleotide stretch. The thermosensitive phenotype of the two mutants is unstable and reverts at the frequency of approximately 10^-4. The revertants regain the wild-type nucleotide sequence. We postulate that the two mutant genes that contain regional multiplications possibly take an intra-strands secondary structure, which is cleaved to regenerate the wild-type sequence, probably during DNA replication.Dedicated to Professor Georg Melchers to celebrate his 50-year association with the journal     

A framework for considering prior information in network-based approaches to omics data analysis

For decades, molecular biologists have been uncovering the mechanics of biological systems. Efforts to bring their findings together have led to the development of multiple databases and information systems that capture and present pathway information in a computable network format. Concurrently, the advent of modern omics technologies has empowered researchers to systematically profile cellular processes across different modalities. Numerous algorithms, methodologies, and tools have been developed to use prior knowledge networks (PKNs) in the analysis of omics datasets. Interestingly, it has been repeatedly demonstrated that the source of prior knowledge can greatly impact the results of a given analysis. For these methods to be successful it is paramount that their selection of PKNs is amenable to the data type and the computational task they aim to accomplish. Here we present a five-level framework that broadly describes network models in terms of their scope, level of detail, and ability to inform causal predictions. To contextualize this framework, we review a handful of network-based omics analysis methods at each level, while also describing the computational tasks they aim to accomplish.     

Two sympatric spotted gum species are molecularly homogeneous

Large fruited spotted gum eucalypt Corymbia henryi occurs sympatrically with small fruited spotted gum Corymbia citriodora subspecies variegata over a large portion of its range on the east coast of Australia. The two taxa are interfertile, have overlapping flowering times and share a common set of insect and vertebrate pollinators. Previous genetic analysis of both taxa from two geographically remote sites suggested that the two were morphotypes rather than genetically distinct species. In this study we further explore this hypothesis of genic species by expanding sampling broadly through their sympatric locations and examine local-scale spatial genetic structure in stands that differ in species and age composition. Delineation of populations at five microsatellite loci, using an individual-based approach and Bayesian modelling, as well as clustering of individuals based on allele frequencies showed the two species to be molecularly homogeneous. Genetic structure aligned largely with geographic areas of origin, and followed an isolation-by-distance model, where proximal populations were generally less differentiated than more distant ones. At the stand level, spotted gums also generally showed little structure consistent with the high levels of gene flow inferred across the species range. Disturbances in the uniformity of structuring were detected, however, and attributed to localised events giving rise to even aged stands, probably due to regeneration from a few individuals following fire.     

Isolation and characterization of a granulosis virus from the tomato moth,Lacanobia oleracea,and its potential as a control agent

A disease causing death in Lacanobia oleracea (Lepidoptera: Noctuidae) occurring in glasshouses in Scotland was shown to be caused by a granulosis virus (GV). Structural properties of the virus were examined by electron microscopy, immunodiffusion, polyacrylamide gel electrophoresis, and restriction endonuclease analysis and compared with an isolate of GV from L. oleracea obtained from France. The two isolates were structurally very similar but could be distinguished by analysis of EcoRI digests of their DNAs. Bioassays of the virus gave LD₅₀ values from 10^4.3 capsules for second-instar larvae to 10^6.6 capsules for fifth-instar larvae. The French isolate was bioassayed in third-instar larvae and was not found to differ significantlyfrom the Scottish isolate. Two small glasshouse trials using the virus to control artificial infestations of L. oleracea indicated that high-volume sprays of virus at 10⁸ to 10⁹ capsules/ml achieved good control. An alternative strategy using much smaller amounts of virus to control the insect is discussed.     

The relationship between the classification of Scottish ground beetle assemblages (Coleoptera, Carabidae) and the National Vegetation Classification of British plant communities

A sufficiently large body of knowledge on British ground beetle (Carabidae) communities now exists to allow investigation of whether habitats may be classified or described on the basis of their ground beetle communities, in the same way that the National Vegetation Classification (NVC) describes British plant communities. A data set of ground beetle abundances from pitfall traps at 481 sites in a range of natural, semi-natural and agricultural habitats throughout Scotland was available for analysis. Multivariate analysis (detrended correspondence analysis and fuzzy cluster analysis) was carried out on proportional catch data of 156 species of ground beetle from 444 of these sites and the results related to the NVC of the sites.
Initial analysis classified the sites into five broad categories: 1) peatlands, 2) calcifugous, 3) mesotrophic, 4) dry river sediments and 5) damp river sediments. Further analysis identified 15 ground beetle assemblages, each corresponding to a relatively well defined vegetation type within one of these broad categories. The major environmental factors appearing to determine the distribution of ground beetle assemblages were substratum type, disturbance and soil moisture, all of which are also important determinants of the distribution of plant communities. The presence and absence of relatively stenotopic species were important discriminants of certain habitats such as wetlands and river sediments but the relative abundances within assemblages of more eurytopic species provided good indications of a relationship between ground beetle assemblages and NVC categories.     

Preliminary observations on the collection of baboon oviducal fluid

Five sexually mature and regularly ovulating baboons (Papio cyanocephalus) were subjected to bilateral oviducal cannulation. Prior to failure of the primary cannulation, peri-ovulatory fluids were collected during three menstrual cycles from one animal, during two cycles from a second animal, and during a single cycle from each of two additional animals. These four animals were subsequently recannulated and oviducal fluids obtained during six additional cycles, but tubal fluid collection after the second procedure was generally less satisfactory than following the initial manipulation. Two attempted cannulations in the fifth animal did not result in oviducal fluid collection. Of the 13 menstrual cycles during which tubal fluid was collected, four were apparently anovulatory. Collections from two of these as well as from three ovulatory cycles were characterized by erratic flow and mucous-blood contamination. Tubal fluids were collected without apparent technical interference or serum contamination from six ovulatory and two anovulatory cycles. Maximum volumes (1.77±.34 ml/oviduct/24 hours) of tubal fluids were collected during the 48 hours following the midcycle LH peak. Thereafter, the rate of oviducal fluid collection declined rapidly.     

Cell surface changes in the proteins of rabbit spermatozoa during epididymal passage

Differences in the exposure of spermatozoa surface components during epididymal passage have been examined using lactoperoxidase-catalyzed ¹²⁵I-iodination or labeling with ¹²⁵I-diazodiiodosulfanilic acid. Labeled surface proteins obtained from caput and cauda epididymides were solubilized in detergent, separated by sodium dodecylsulfate polyacrylamide slab gel electrophoresis, and identified by radiography. Densitometer scans of autoradiograms revealed increased amounts or exposures of surface proteins of ～35,000, ～39,000, ～50,000, and ～78,000 molecular weight on the cauda epididymal spermatozoa.