Regulation, replication, and integration functions of the Vibrio cholerae CTXφ are encoded by region RS2

CTXφ is a filamentous phage that encodes cholera toxin, one of the principal virulence factors of Vibrio cholerae . CTXφ is unusual among filamentous phages because it can either replicate as a plasmid or integrate into the V. cholerae chromosome at a specific site. The CTXφ genome has two regions, the 'core' and RS2. Integrated CTXφ is frequently flanked by an element known as RS1 which is related to RS2. The nucleotide sequences of RS2 and RS1 were determined. These related elements contain three nearly identical open reading frames (ORFs), which in RS2 were designated rstR , rstA2 and rstB2 . RS1 contains an additional ORF designated rstC . Functional analyses indicate that rstA2 is required for CTXφ replication and rstB2 is required for CTXφ integration. The amino terminus of RstR is similar to the amino termini of other phage-encoded repressors, and RstR represses the expression of rstA2 . Although genes with related functions are clustered in the genome of CTXφ in a way similar to those for other filamentous phages, the CTXφ RS2-encoded gene products mediating replication, integration and repression appear to be novel.     

Fossil Homo femur from Berg Aukas,northern Namibia

The proximal half of a hominid femur was recovered from deep within a paleokarst feature at the Berg Aukas mine, northern Namibia. The femur is fully mineralized, but it is not possible to place it in geochrono logical context. It has a very large head, an exceptionally thick diaphyseal cortex, and a very low collodiaphyseal angle, which serve to differentiate it from Holocene homologues. The femur is not attributable to Australopithecus, Paranthropus, or early Homo (i.e., H. habilis sensu lato). Homo erectus femora have a relatively longer and AP flatter neck, and a shaft that exhibits less pilaster than the Berg Aukas specimen. Berg Aukas also differs from early modern femora in several features, including diaphyseal cortical thickness and the degree of subtrochanteric AP flattening. The massive diaphyseal cortex of Berg Aukas finds its closest similarity within archaic H. sapiens (e.g., Castel di Guido) and H. erectus (e.g., KNM-ER 736) samples. It has more cortical bone at midshaft than any other specimen, although relative cortical thickness and the asymmetry of its cross-sectional disposition at this level are comparable with those of other Pleistocene fem ora. The closest morphological comparisons with Berg Aukas are in archaic (i.e., Middle Pleistocene) H. sapiens and Neandertal samples. © 1995 Wiley-Liss, Inc.     

Development of a Robust Flow Cytometric Assay for Determining Numbers of Viable Bacteria

Several fluorescent probes were evaluated as indicators of bacterial viability by flow cytometry. The probes monitor a number of biological factors that are altered during loss of viability. The factors include alterations in membrane permeability, monitored by using fluorogenic substrates and fluorescent intercalating dyes such as propidium iodide, and changes in membrane potential, monitored by using fluorescent cationic and anionic potential-sensitive probes. Of the fluorescent reagents examined, the fluorescent anionic membrane potential probe bis-(1,3-dibutylbarbituric acid)trimethine oxonol [DiBAC(inf4)(3)] proved the best candidate for use as a general robust viability marker and is a promising choice for use in high-throughput assays. With this probe, live and dead cells within a population can be identified and counted 10 min after sampling. There was a close correlation between viable counts determined by flow cytometry and by standard CFU assays for samples of untreated cells. The results indicate that flow cytometry is a sensitive analytical technique that can rapidly monitor physiological changes of individual microorganisms as a result of external perturbations. The membrane potential probe DiBAC(inf4)(3) provided a robust flow cytometric indicator for bacterial cell viability.     

Comparison of methods for searching protein sequence databases.

We have compared commonly used sequence comparison algorithms, scoring matrices, and gap penalties using a method that identifies statistically significant differences in performance. Search sensitivity with either the Smith-Waterman algorithm or FASTA is significantly improved by using modern scoring matrices, such as BLOSUM45-55, and optimized gap penalties instead of the conventional PAM250 matrix. More dramatic improvement can be obtained by scaling similarity scores by the logarithm of the length of the library sequence (In()-scaling). With the best modern scoring matrix (BLOSUM55 or JO93) and optimal gap penalties (-12 for the first residue in the gap and -2 for additional residues), Smith-Waterman and FASTA performed significantly better than BLASTP. With In()-scaling and optimal scoring matrices (BLOSUM45 or Gonnet92) and gap penalties (-12, -1), the rigorous Smith-Waterman algorithm performs better than either BLASTP and FASTA, although with the Gonnet92 matrix the difference with FASTA was not significant. Ln()-scaling performed better than normalization based on other simple functions of library sequence length. Ln()-scaling also performed better than scores based on normalized variance, but the differences were not statistically significant for the BLOSUM50 and Gonnet92 matrices. Optimal scoring matrices and gap penalties are reported for Smith-Waterman and FASTA, using conventional or In()-scaled similarity scores. Searches with no penalty for gap extension, or no penalty for gap opening, or an infinite penalty for gaps performed significantly worse than the best methods. Differences in performance between FASTA and Smith-Waterman were not significant when partial query sequences were used. However, the best performance with complete query sequences was obtained with the Smith-Waterman algorithm and In()-scaling.     

Toward a complete linkage map of the human X chromosome: regional assignment of 16 cloned single-copy DNA sequences employing a panel of somatic cell hybrids.

Closely linked restriction fragment length polymorphisms (RFLPs) are potentially useful as diagnostic markers of genetic defects, and, in principle, RFLPs can be employed to construct a complete linkage map of the human genome. On the X chromosome, linkage studies are particularly rewarding because in man more than 120 X-linked genes are known. Thus, it is probable that each X-specific RFLP will be of use as a genetic marker of one or several X-linked disorders. To facilitate the search for closely linked RFLPs, we have regionally assigned 16 cloned DNA sequences to various portions of the human X chromosome, employing a large panel of somatic cell hybrids. These probes have been used to correlate genetic and physical distances on Xp, and it can be extrapolated from these data that the number and distribution of available Xq sequences will also suffice to span the long arm of the X chromosome.     

Activation of ADP-ribosyltransferase in polyamine-depleted mammalian cells.

Mammalian fibroblasts were cultured in the presence of alpha-methylornithine and/or methylglyoxal bis(guanylhydrazone), which inhibit the synthesis of polyamines. This led to a decrease in the cellular content of the polyamines spermine and spermidine by up to 60% when the cells were grown in the presence of both drugs together. The activity of the chromatin-associated enzyme ADP-ribosyltransferase was enhanced 2-3-fold in the drug-treated cells when measured in cells subsequently rendered permeable to exogenous NAD+, the substrate for the transferase. This is a novel and surprising observation, since the transferase is invariably activated by the addition of polyamines to a suitable incubation system such as permeabilized cells, isolated nuclei or the purified enzyme. We found no evidence that the activation was due to the appearance of DNA strand breaks, by using a variety of procedures including both neutral [the 'nucleoid' technique of Cook & Brazell [(1975) J. Cell Sci. 19, 261-279; (1976) J. Cell Sci. 22, 287-302]] and alkaline sucrose-gradient centrifugation and gel electrophoresis, suggesting that this therefore may not be the only means of regulating the activity of ADP-ribosyltransferase and that polyamines may have a role to play in this regard in vivo.     

Pelvic infection: a comparison of the Dalkon shield and three other intrauterine devices.

A detailed analysis was undertaken of reports of possible pelvic infection in relation to the use of four commonly fitted intrauterine contraceptive devices during 1971 to 1978 in the United Kingdom. The four devices were the Dalkon shield, Lippes loops 3C and 2D, and the Gravigard (copper 7), and data used were those collected systematically through the UK intrauterine device research network. Prospective reports that the Dalkon shield was uniquely related to high levels of infection when compared with other intrauterine devices were not substantiated in this prospective study among 13 349 users. Though some factors such as social class and previous experience of abortion appeared to influence the rate of infection, the type of intrauterine device being worn did not appear to be a significant factor. Various methods of analysis were used including life table, regression, and discriminant analysis, using information relating to the type of intrauterine device worn, the characteristics of the user, the fitting centre, and the pattern of diagnosis and treatment of reported or suspected pelvic infection. The results of this study suggest that fears that the Dalkon shield may be associated with a higher incidence of pelvic infection than other intrauterine devices may have been unjustified.     

Pigmentation and skin reaction to sun as risk factors for cutaneous melanoma: Western Canada Melanoma Study.

Between 1 April 1979 and 31 March 1981, 904 residents of the four western provinces of Canada (population 6.5 million), were diagnosed as suffering from primary cutaneous malignant melanoma. Of 801 patients aged 20-79 years, 665 (83%) were interviewed along with control subjects chosen at random from the general population and matched for age, sex, and province. After exclusion of 70 subjects with lentigo maligna or acral lentiginous melanoma, comparisons of the 595 case-control pairs showed that light hair, skin, and eye colour, a history of heavy freckling in adolescence, and a tendency to burn readily and tan poorly in the sun were significant risk factors for melanoma. The strongest primary associations were with blond hair (relative risk 7.1 compared with black hair), light colour of unexposed skin (relative risk 2.4), and severe freckling (relative risk 2.1). These associations were independent of ethnic origin and of recorded amount of exposure to the sun and were somewhat stronger for superficial spreading than for nodular melanoma. This study is the largest and most detailed of an incident series of melanomas to be published to date. The results were consistent with other studies reporting associations between melanoma and poor tanning ability, a tendency to burn easily, and a history of sunburn and showed that light hair colour was the strongest risk factor for the disease.     

Therapeutic application of various immunostimulators on the L2C guinea-pig leukemia

Summary Immunostimulators such as Corynebacterium parvum (C. parvum), Bacillus Calmette-Guerin (BCG), pyran copolymer, and glucan were examined in the guinea pig L ₂ C lymphoblastic leukemia model to determine their capacity for therapeutic modulation of the immune response of the host toward controlling leukemic cell proliferation. The dose, route, and frequency of administration of the stimulators were also evaluated as a function of time in order to obtain an optimal antileukemic effect. Results indicated that only C. parvum and BCG were capable of significantly increasing host survival when given 1 day after an inoculation of 1.5×10 ⁴ viable leukemic cells. Administration of BCG or C. parvum, alone or in combination with irradiated blast cells on either days 4 or 7, was totally ineffective in prolonging survival. In the majority of cases, enhanced leukemic growth was observed on these days. The combination of BCG and/or C. parvum with irradiated syngeneic blast cells given 24 h after leukemia inoculation promoted a synergistic response with a significant increase in median survival time and a number of long-term survivors.This work was supported by contract N01-CP-53566 within the Virus Cancer Program of the National Cancer Institute     

Food habits of channel catfish in a reservoir receiving heated waters

The diet of channel catfish captured near the mouth of a channel carrying heated waters was not significantly different from the diet of catfish captured elsewhere in the same reservoir during the cool months of the year. In summer months, however, the diet of catfish captured near the effluent was significantly different from the diet of catfish from other locations and seemed to indicate that catfish were foraging in cool, deeper waters beneath the thermal plume.Department of Biological Sciences, North Texas State UniversityFinancial support for the study was provided by a Faculty Research Grant at North Texas State University.