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.
27724235
Avian RNA tumor virus DNA before and after integration into the host genome.
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.
33909578
The polypeptides of influenza virus. 1. Cytoplasmic synthesis and nuclear accumulation.
24802359
Structure and replication of hepatitis delta virus RNA.
While this volume covers many different aspects of hepatitis delta virus (HDV) replication, the focus in this chapter is on studies of the structure and replication of the HDV RNA genome. An evaluation of such studies is not only an integral part of our understanding of HDV infections but it also sheds new light on some important aspects of cell biology, such as the fidelity of RNA transcription by a host RNA polymerase and on various forms of post-transcriptional RNA processing. Representations of the replication of the RNA genome are frequently simplified to a form of rolling-circle model, analogous to what have been described for plant viroids. One theme of this review is that such models, even after some revision, deceptively simplify the complexity of HDV replication and can fail to make clear major questions yet to be solved.
33501684
Tumor virus ribonucleic acid directed deoxyribonucleic acid synthesis: nucleotide sequence at the 5' terminus of nascent deoxyribonucleic acid.
32584830
Genetic and Environmental Influences on Psychopathy Trait Dimensions in a Community Sample of Male Twins
Psychopathy appears to be comprised of two broad dimensions: impulsivity/antisocial behavior and interpersonal detachment/callousness. This study examined the extent to which variance in these 2 psychopathy trait dimensions was associated with common or unique genetic, shared, and nonshared environmental factors in two independent samples of reared together 16–18-year-old male twins. One sample included 142 monozygotic (MZ) and 70 dizygotic (DZ) pairs; the other sample included 128 MZ and 58 DZ pairs. Boys completed the Minnesota Temperament Inventory (MTI), a 19-item measure that contains separate subscales: Antisocial and Detachment. Variance in the Antisocial and Detachment scales was associated with additive genetic factors and neither scale was associated with shared environmental factors. As expected, the bivariate biometric analysis suggested genetic influence on the covariance of the scales. The results are consistent with theoretical models of psychopathy that posit some independence in the etiology of the two major trait dimensions of psychopathy.
205158145
Using galaxy to perform large-scale interactive data analyses.
While most experimental biologists know where to download genomic data, few have a concrete plan on how to analyze it. This situation can be corrected by: (1) providing unified portals serving genomic data and (2) building Web applications to allow flexible retrieval and on-the-fly analyses of the data. Powerful resources, such as the UCSC Genome Browser already address the first issue. The second issue, however, remains open. For example, how to find human protein-coding exons with the highest density of single nucleotide polymorphisms (SNPs) and extract orthologous sequences from all sequenced mammals? Indeed, one can access all relevant data from the UCSC Genome Browser. But once the data is downloaded how would one deal with millions of SNPs and gigabytes of alignments? Galaxy (http://g2.bx.psu.edu) is designed specifically for that purpose. It amplifies the strengths of existing resources (such as UCSC Genome Browser) by allowing the user to access and, most importantly, analyze data within a single interface in an unprecedented number of ways.
20214634
Preparation of free-standing films from kafirin protein microparticles: mechanism of formation and functional properties.
A method of preparing free-standing films using kafirin microparticles made by phase separation from acetic acid is described. Film preparation involved the suspension of the microparticles in acetic acid solution containing plasticizer. On evaporation of the acetic acid, a complete, smooth, flexible, transparent film was formed. A minimum concentration of acid was required to form a cohesive film relative to the concentration of kafirin. This was approximately 10.8:1, percent acetic acid to percent kafirin. Film formation appears to be by controlled aggregation of kafirin microparticles, followed by dissolution of the microparticles in acetic acid and drying into a cohesive film. The functional properties of microparticle films were generally superior to films cast directly from a solution of kafirin, at the same protein content. Kafirin microparticle films were very thin (<15 microm), relatively strong but not very extensible, with better water barrier properties and lower protein digestibility than conventionally cast kafirin films.
30655670
Development of a short form of the Test Anxiety Inventory (TAI).
The Test Anxiety Inventory (TAI) is widely used in research and practical settings and has particular application to the assessment and treatment of test anxiety in student populations. However, there are a number of instances in which a short version of the TAI would be more appropriate, especially when time constraints preclude the use of the full form. Similar short forms have been developed for other measures such as the State scale of the State-Trait Anxiety Inventory (STAI; T. M. Marteau & H. Bekker, 1992). The authors of the present study aimed to develop a short form of the TAI. The TAI was completed by 333 undergraduate psychology students. Item-remainder correlations were used to compare short forms with varying numbers of items. Internal consistency and concurrent and construct validity were assessed in hypothetical and actual examination conditions. A 5-item short form produced optimal reliability and validity, and a balance of items from the Worry and Emotionality subscales of the TAI. Further research is needed to replicate these results, but the 5-item short form of the TAI shows promise, particularly for contexts in which time demands preclude the use of longer versions.
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).