25216421
Discontinuities in the DNA synthesized by an avian retrovirus.
The unintegrated linear DNA synthesized in cells infected by Rous sarcoma virus is a predominantly double-stranded structure in which most of the minus-strand DNA, complementary to the viral RNA genome, is genome sized, whereas the plus-strand DNA is present as subgenomic fragments. We previously reported the application of benzoylated naphthoylated DEAE-cellulose chromatography to demonstrate that of the linear viral DNA species synthesized in quail embryo fibroblasts infected with Rous sarcoma virus greater than 99.5% contain single-stranded regions and these regions are predominantly composed of plus-strand DNA sequences (T. W. Hsu and J. M. Taylor, J. Virol. 44:47-53, 1982). We now present the following additional findings. (i) There were on the average 3.5 single-stranded regions per linear viral DNA, and these single-stranded regions could occur at many locations. (ii) With a probe to the long terminal repeat, we detected, in addition to a heterogeneous size distribution of subgenomic plus-strand DNA species, at least three prominent discrete size classes. Each of these discrete species had its own specific initiation site, but all had the same termination site. Such species were analogous to those reported by Kung et al. (J. Virol. 37: 127-138, 1981). (iii) These discrete size classes of plus-strand DNA were present not only on the major size class of linear DNA but also on a heterogeneous of slower-sedimenting species, which we have called immature linears. Our interpretation is that we have thus detected several additional sites for the initiation of plus-strand DNA. (iv) The 340-base plus-strand strong-stop DNA was only found associated with the immature linears. (v) From a size and hybridization comparison of these discrete size classes of plus-strand DNA with minus-strand DNA species, as synthesized in the endogenous reaction of melittin-disrupted virions, it was found that the putative additional initiation sites for plus-strand DNA synthesis corresponded to many of the pause sites in the synthesis of minus-strand DNA.
12985098
A note on the incorporation of amino acids by hamster embryo cells in monolayer culture.
28296194
Retrovirus Genome Replication: Priming Specificities of Plus-Strand DNA Synthesis
SUMMARY The retroviral reverse transcriptase is a multifunctional protein. Not only does it contain both RNA- and DNA-directed DNA synthesis activities but also it contains an endonuclease activity necessary for the integration of viral RNA and a RNase H. This latter activity can reduce to oligoribonucleotides viral RNA that has been reverse transcribed into minus-strand DNA. However, during avian retrovirus genome replication it does this in a highly specific manner so as to generate a specific 12-base primer for plus-strand DNA synthesis. Even though many other oligoribonucleotides are also made there is an efficient selection of the specific primer followed by its efficient utilization in plus-strand DNA synthesis, and subsequent removal. We have used a reconstructed system to gain an understanding of the factors that contribute towards these observed specificities.
33501684
Tumor virus ribonucleic acid directed deoxyribonucleic acid synthesis: nucleotide sequence at the 5' terminus of nascent deoxyribonucleic acid.
27724235
Avian RNA tumor virus DNA before and after integration into the host genome.
11606238
Hepatitis delta virus.
Hepatitis delta virus (HDV) is a sub-viral agent that is dependent for its life cycle on hepatitis B virus (HBV). The help it obtains from HBV is limited to the sharing of envelope proteins. These proteins are needed to facilitate the assembly of the HDV genome into new virus particles, and in turn, to allow the attachment and entry of HDV into new host cells. In other respects, the replication of the small single-stranded circular RNA genome of HDV is independent of HBV. HDV genome replication produces two forms of a RNA-binding protein known as the long and small delta antigens (Ag). All other proteins needed for HDV genome replication, especially the RNA-directed RNA polymerase activity, are provided by the host cell. This mini-review article is a mixture of personal perspective and speculations about the future of HDV research. It starts with a brief overview of HDV and its replication, notes some of the major unresolved questions, and directs the interested reader to more detailed reviews.
12307738
Screening for disinhibited disorder cases in a college population: Performance of the SMAST, DAST, SCID-II-Q, and PDQ-4.
Psychiatric disorders characterized by disinhibition--substance use disorders, antisocial personality disorder (PD), and borderline PD--represent a serious risk to the safety and health of college students. The ability of researchers and clinicians to identify students most at risk for disinhibited disorders associated with campus crime, violence, and self-harm depends on measures with strong evidence of diagnostic efficiency, yet data on the diagnostic efficiency of screening measures in college populations are lacking. The authors addressed this need by examining the diagnostic efficiency of commonly used screening measures for disinhibited disorders in a sample of 2,085 students, 79 of whom also completed diagnostic interviews. Results suggest that the diagnostic efficiency (e.g., sensitivity, specificity) of screening measures for substance use disorders and antisocial PD in college samples can be increased by making simple adjustments in screening cutoff criteria. Similar adjustments did not increase the diagnostic efficiency of the screening measure for borderline PD, and this suggested that certain screeners may best be aimed at ruling out disorders. This type of information offers users flexibility with which to tailor the screening threshold to serve different objectives.
14002416
Strong and weak male mutation bias at different sites in the primate genomes: insights from the human-chimpanzee comparison.
Male mutation bias is a higher mutation rate in males than in females thought to result from the greater number of germ line cell divisions in males. If errors in DNA replication cause most mutations, then the magnitude of male mutation bias, measured as the male-to-female mutation rate ratio (alpha), should reflect the relative excess of male versus female germ line cell divisions. Evolutionary rates averaged among all sites in a sequence and compared between mammalian sex chromosomes were shown to be indeed higher in males than in females. However, it is presently unknown whether individual classes of substitutions exhibit such bias. To address this issue, we investigated male mutation bias separately at non-CpG and CpG sites using human-chimpanzee whole-genome alignments. We observed strong male mutation bias at non-CpG sites: alpha in the X-autosome comparison was approximately 6-7, which was similar to the male-to-female ratio in the number of germ line cell divisions. In contrast, mutations at CpG sites exhibited weak male mutation bias: alpha in the X-autosome comparison was only approximately 2-3. This is consistent with the methylation-induced and replication-independent mechanism of CpG transitions, which constitute the majority of mutations at CpG sites. Interestingly, our study also indicated weak male mutation bias for transversions at CpG sites, implying a spontaneous mechanism largely not associated with replication. Male mutation bias was equally strong at CpG and non-CpG sites located within unmethylated "CpG islands," suggesting the replication-dependent origin of these mutations. Thus, we found that the strength of male mutation bias is nonuniform in the primate genomes. Importantly, we discovered that male mutation bias depends on the proportion of CpG sites in the loci compared. This might explain the differences in the magnitude of primate male mutation bias observed among studies.
12400827
Peacock or Plum? Reflections on academic research career pathways.
UNLABELLED
PURPOSE OF THE PAPER: This paper critically deconstructs academic career pathways in research and explores possible future directions.


BACKGROUND AND CONTEXT
Development in NHS policy and practice has brought about something of a sea change in academic career pathways in nursing and midwifery. Whilst once there was a fairly prescribed route into nurse education and then research, contemporary factors no longer foster such traditional routes.


METHODS
In examining what a career pathway into academic nursing research may look like it may be useful first to delineate what are the basic assumptions that constitute 'achievement' within such a career. Once pinpointed it is possible to map out different pathways that illustrate the diversity with which this has occurred. This provides a useful mirror for examining what may or may not be useful for the future. This paper explores three areas of the nurse academic career pathway: introspectively to understand where we are at the moment, retrospectively by examining composite research careers in order to gain insight for the final prospective section, where we make recommendations for the future.


CONCLUSIONS
Nurses and midwives working in higher education require transparent and sustainable research strategies that facilitate clear research pathways in academia. The tensions between research and teaching are inevitable, but are manageable if workforce development uses individuals to their strengths and values diversity of contribution.
13468480
ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements.
Genomic sequence signals - such as base composition, presence of particular motifs, or evolutionary constraint - have been used effectively to identify functional elements. However, approaches based only on specific signals known to correlate with function can be quite limiting. When training data are available, application of computational learning algorithms to multispecies alignments has the potential to capture broader and more informative sequence and evolutionary patterns that better characterize a class of elements. However, effective exploitation of patterns in multispecies alignments is impeded by the vast number of possible alignment columns and by a limited understanding of which particular strings of columns may characterize a given class. We have developed a computational method, called ESPERR (evolutionary and sequence pattern extraction through reduced representations), which uses training examples to learn encodings of multispecies alignments into reduced forms tailored for the prediction of chosen classes of functional elements. ESPERR produces a greatly improved Regulatory Potential score, which can discriminate regulatory regions from neutral sites with excellent accuracy ( approximately 94%). This score captures strong signals (GC content and conservation), as well as subtler signals (with small contributions from many different alignment patterns) that characterize the regulatory elements in our training set. ESPERR is also effective for predicting other classes of functional elements, as we show for DNaseI hypersensitive sites and highly conserved regions with developmental enhancer activity. Our software, training data, and genome-wide predictions are available from our Web site (http://www.bx.psu.edu/projects/esperr).
45640355
A behavioral genetic analysis of the relationship between the socialization scale and self-reported delinquency.
This investigation examined the genetic (A), and shared (C) and nonshared (E) environmental variance contributions to the relationship of self-reported delinquency (as measured by the "Delinquent Behavior Inventory" [DBI; Gibson, 1967]) to the Socialization (So) scale of the California Psychological Inventory using univariate and bivariate structural equation models. The scales were administered to 222 male (145 monozygotic; 77 dizygotic) and 159 female (107 monozygotic; 52 dizygotic) 16- to 18-year-old same-sex twin pairs. Principal components analysis with varimax rotation revealed three interpretable So factors representing family/home environment, self-concept, and behavioral control. Univariate modeling suggested sex differences in etiological influences associated with individual differences in most scales. The bivariate ACE model fit the data, suggesting that the covariance between the So scale and self-reported delinquency owes in part to shared etiological factors.