A review of recent advances in the spherical harmonics expansion method for semiconductor device simulation

The Boltzmann transport equation is commonly considered to be the best semi-classical description of carrier transport in semiconductors, providing precise information about the distribution of carriers with respect to time (one dimension), location (three dimensions), and momentum (three dimensions). However, numerical solutions for the seven-dimensional carrier distribution functions are very demanding. The most common solution approach is the stochastic Monte Carlo method, because the gigabytes of memory requirements of deterministic direct solution approaches has not been available until recently. As a remedy, the higher accuracy provided by solutions of the Boltzmann transport equation is often exchanged for lower computational expense by using simpler models based on macroscopic quantities such as carrier density and mean carrier velocity. Recent developments for the deterministic spherical harmonics expansion method have reduced the computational cost for solving the Boltzmann transport equation, enabling the computation of carrier distribution functions even for spatially three-dimensional device simulations within minutes to hours. We summarize recent progress for the spherical harmonics expansion method and show that small currents, reasonable execution times, and rare events such as low-frequency noise, which are all hard or even impossible to simulate with the established Monte Carlo method, can be handled in a straight-forward manner. The applicability of the method for important practical applications is demonstrated for noise simulation, small-signal analysis, hot-carrier degradation, and avalanche breakdown.

Dicke coupling by feasible local measurements at the superradiant quantum phase transition

We address characterization of many-body superradiant systems and establish a fundamental connection between quantum criticality and the possibility of locally estimating the coupling constant, i.e., extracting its value by probing only a portion of the whole system. In particular, we consider Dicke-like superradiant systems made of an ensemble of two-level atoms interacting with a single-mode radiation field at zero effective temperature, and address estimation of the coupling by measurements performed only on radiation. At first, we obtain analytically the quantum Fisher information (QFI) and show that optimal estimation of the coupling may be achieved by tuning the frequency of the radiation field to drive the system toward criticality. The scaling behavior of the QFI at the critical point is obtained explicitly upon exploiting the symplectic formalism for Gaussian states. We then analyze the performances of feasible detection schemes performed only on the radiation subsystem, namely homodyne detection and photon counting, and show that the corresponding Fisher informations (FIs) approach the global QFI in the critical region. We thus conclude that criticality is a twofold resource. On the one hand, global QFI diverges at the critical point, i.e., the coupling may be estimated with the arbitrary precision. On the other hand, the FIs of feasible local measurements (which are generally smaller than the QFI out of the critical region), show the same scaling of the global QFI; i.e., optimal estimation of coupling may be achieved by locally probing the system, despite its strongly interacting nature.

Anthropometric characteristics of primary school-aged children: accuracy of perception and differences by gender, age and BMI

BACKGROUND

Body perception has been mainly studied in adolescents and adults in relation to eating disorders and obesity because such conditions are usually associated with distortion in the perception of body size. The development of body perception in children was rather neglected despite the relevance of this issue in understanding the aetiology of health eating problems. The main aim of this study was to investigate body weight and body height perception in children by gender, age and body mass index (BMI), taking into account differences among underweight, healthy weight, overweight and obese children.

METHODS

A school-based sample of 572 Italian children (49% boys) aged 6-10 were involved in a cross-sectional survey. Current weight and height were measured by standard protocols, and BMI was calculated and converted in centile categories using the Italian growth curves for children. Perceived weight and height were assessed using visual methods (figures representing children of different weight and height).

RESULTS

About a third of the children do not show to have an accurate perception of their weight and height (weight: 36%; height: 32%): as for weight, an error of underestimation prevails and as for height, an error of overestimation prevails. In general, children who have different weight and height from the average tend to perceive their physical characteristics closer to average. However, overweight children underestimate their weight much more than obese children.

CONCLUSIONS

Distortions in the perception of their physical features, weight and height, appear to be related to the aesthetic models of Western culture. The tendency to underestimate weight, particularly in overweight children, has implications in interventions for health promotion and healthy lifestyle in school-aged children.

Genetic and epigenetic profiling of CLL disease progression reveals limited somatic evolution and suggests a relationship to memory-cell development

We examined genetic and epigenetic changes that occur during disease progression from indolent to aggressive forms of chronic lymphocytic leukemia (CLL) using serial samples from 27 patients. Analysis of DNA mutations grouped the leukemia cases into three categories: evolving (26%), expanding (26%) and static (47%). Thus, approximately three-quarters of the CLL cases had little to no genetic subclonal evolution. However, we identified significant recurrent DNA methylation changes during progression at 4752 CpGs enriched for regions near Polycomb 2 repressive complex (PRC2) targets. Progression-associated CpGs near the PRC2 targets undergo methylation changes in the same direction during disease progression as during normal development from naive to memory B cells. Our study shows that CLL progression does not typically occur via subclonal evolution, but that certain CpG sites undergo recurrent methylation changes. Our results suggest CLL progression may involve developmental processes shared in common with the generation of normal memory B cells.

Backscattering differential ghost imaging in turbid media

In this Letter we present experimental results concerning the retrieval of images of absorbing objects immersed in turbid media via differential ghost imaging (DGI) in a backscattering configuration. The method has been applied, for the first time to our knowledge, to the imaging of thin black objects located inside a turbid solution in proximity of its surface. We show that it recovers images with a contrast better than standard noncorrelated direct imaging, but equivalent to noncorrelated diffusive imaging. A simple theoretical model capable of describing the basic optics of DGI in turbid media is proposed.

Genomic organization of human TCF12 gene and spliced mRNA variants producing isoforms of transcription factor HTF4

The human TCF12 gene, mapping to 15q21, encodes the helix-loop-helix transcription factor 4 (HTF4). A detailed analysis of this genomic region established the organization of the TCF12 gene. The gene includes 21 exons and is significantly larger than an average human gene. Preceding the second exon, two alternative acceptor sites for mRNA splicing yield two distinguishable transcripts (HTF4a and HTF4b) which differ in their 5' untranslated region but share identical coding sequences. Differential utilization of exon 15 in the TCF12 gene may reflect a mechanism producing a cell-type-specific protein (HTF4c). In addition, intron 5 in the TCF12 gene corresponds to the region involved in a translocation, t(9;15)(q22;q21), that results in a form of extraskeletal myxoid chondrosarcoma.

Sequence patterns defining the 5' boundary of human genes

In studies of both short and relatively long human genomic DNA, we found a clustering of the consensus site for the transcription factor GCF at the 5' boundary of a subset of human genes. In studies of promoter regions with known transcription initiation site, the cluster of consensus GCF site appeared near the transcription initiation site and in some sequences it extended into the transcribed region defining the leader mRNA. We also found a detectable correlation between the 5' boundary of human genes and recognition motifs for other transcription factors that bind to GC-rich sequences. But in these cases, the correlation was not as general as the correlation observed for the consensus GCF site.

Mental health in the Islamic Republic of Iran: achievements and areas of need

The development of mental health in the Islamic Republic of Iran is described with particular reference to the integration mental health into the primary health care system. The achievements made so far are outlined and the areas of need discussed.

Proteomics of glycoproteins based on affinity selection of glycopeptides from tryptic digests

Identification of glycoproteins in complex mixtures derived from either human blood serum or a cancer cell line was achieved in a process involving the steps of (1) reduction and alkylation, (2) proteolysis of all proteins in the mixture with trypsin, (3) affinity chromatographic selection of the glycopeptides with an immobilized lectin, (4) direct transfer of the glycopeptide fraction to a reversed-phase liquid chromatography (RPLC) column and further fractionation by gradient elution, (5) matrix-assisted laser desorption ionization mass spectrometry of individual fractions collected from the RPLC column, and (6) peptide identification based on a database search. The types of glycoproteins analyzed were; (1) N-type glycoproteins of known primary structure, (2) N-type glycoproteins of unknown structure, and (3) O-type glycoproteins glycosylated with a single N-acetylglucosamine. Identification of peptides from complex mixtures was greatly facilitated by either C-terminal sequencing with a carboxypeptidase mixture or by comparing chromatographic behavior and mass to standards, as in the case of a known protein. In addition, deglycosylation of peptides with N glycosidase F was necessary to identify N-type glycoproteins of unknown structure. The strength of this approach is that it is fast and targets specific molecular species or classes of glycoproteins for identification. The weakness is that it does not discriminate between glycoforms.

Neural network schemes for detecting rare events in human genomic DNA

MOTIVATION

Many problems in molecular biology as well as other areas involve detection of rare events in unbalanced data. We develop two sample stratification schemes in conjunction with neural networks for rare event detection in such databases. Sample stratification is a technique for making each class in a sample have equal influence on decision making. The first scheme proposed stratifies a sample by adding up the weighted sum of the derivatives during the backward pass of training. The second scheme proposed uses a technique of modified bootstrap aggregating. After training neural networks with multiple sets of bootstrapped examples of the rare event classes and subsampled examples of common event classes, multiple voting for classification is performed.

RESULTS

These two schemes make rare event classes have a better chance of being included in the sample used for training neural networks and thus improve the classification accuracy for rare event detection. The experimental performance of the two schemes using two sets of human DNA sequences as well as another set of Gaussian data indicates that proposed schemes have the potential of significantly improving accuracy of neural networks to recognize rare events.

Strategy for qualitative and quantitative analysis in proteomics based on signature peptides

This paper describes a new analytical strategy for identifying proteins in concentration flux based on isotopic labeling peptides in tryptic digests. Primary amino groups in peptides from control and experimental samples were derivatized with acetate and trideuteroacetate, respectively. After mixing samples thus labeled from these two sources, the relative concentration of peptides was determined by isotope ratio analysis with MALDI and ESI mass spectrometry. More than a 100-fold difference in relative concentration could be detected. Simplification of complex tryptic digests prior to mass spectral analysis was achieved by selection of histidine-containing peptides with immobilized metal affinity sorbents or of glycopeptides by lectin columns. Because most of these peptides have sequences that are unique to a single protein, they are a signature of the protein from which they were derived; providing a facile route to protein analysis.

Syndromes associated with Homo sapiens pol II regulatory genes

The molecular basis of human characteristics is an intriguing but an unresolved problem. Human characteristics cover a broad spectrum, from the obvious to the abstract. Obvious characteristics may include morphological features such as height, shape, and facial form. Abstract characteristics may be hidden in processes that are controlled by hormones and the human brain. In this review we examine exaggerated characteristics presented as syndromes. Specifically, we focus on human genes that encode transcription factors to examine morphological, immunological, and hormonal anomalies that result from deletion, insertion, or mutation of genes that regulate transcription by RNA polymerase II (the Pol II genes). A close analysis of abnormal phenotypes can give clues into how sequence variations in regulatory genes and changes in transcriptional control may give rise to characteristics defined as complex traits.

A signal encoded in vertebrate DNA that influences nucleosome positioning and alignment

Evidence is provided that the nucleotide triplet con-sensus non-T(A/T)G (abbreviated to VWG) influences nucleosome positioning and nucleosome alignment into regular arrays. This triplet consensus has been recently found to exhibit a fairly strong 10 bp periodicity in human DNA, implicating it in anisotropic DNA bendability. It is demonstrated that the experimentally determined preferences for nucleosome positioning in native SV40 chromatin can, to a large extent, be pre-dicted simply by counting the occurrences of the period-10 VWG consensus. Nucleosomes tend to form in regions of the SV40 genome that contain high counts of period-10 VWG and/or avoid regions with low counts. In contrast, periodic occurrences of the dinucleotides AA/TT, implicated in the rotational positioning of DNA in nucleosomes, did not correlate with the preferred nucleosome locations in SV40 chromatin. Periodic occurrences of AA did correlate with preferred nucleosome locations in a region of SV40 DNA where VWG occurrences are low. Regular oscillations in period-10 VWG counts with a dinucleosome period were found in vertebrate DNA regions that aligned nucleosomes into regular arrays in vitro in the presence of linker histone. Escherichia coli and plasmid DNA, which fail to align nucleosomes in vitro, lacked these regular VWG oscillations.

Simple miniaturized gel system for DNA sequence analysis

A simple miniaturized gel system suitable for DNA sequencing is described. Small ultrathin polyacrylamide gels are cast, eight or more at a time, using standard microscope slides. Gels, ready to use, can be stored for approximately 2 weeks. Gels are run horizontally in a standard mini-agarose gel apparatus. Typical run times are 6-8 min. A novel sample loading system permits volumes of standard sequencing reactions as small as 0.1 microl to be analyzed. Sequencing ladders were visualized using 35S-labeled DNA by autoradiography and by colorimetric detection. Band resolution compares favorably with that of large gels. The methods introduced here serve as a step toward the miniaturization of DNA sequencing and are amenable to automated sample loading and detection.

A statistical model for locating regulatory regions in genomic DNA

In addition to genes, chromosomal DNA contains sequences that serve as signals for turning on and off gene expression. These signals are thought to be distributed as clusters in the regulatory regions of genes. We develop a Bayesian model that views locating regulatory regions in genomic DNA as a change-point problem, with the beginning of regulatory and non-regulatory regions corresponding to the change points. The model is based on a hidden Markov chain. The data consist of nucleotide positions of protein-binding elements in a genomic DNA sequence. These positions are identified using a reference catalogue containing elements that interact with transcription factors implicated in controlling the expression of protein-encoding genes. Among the protein-binding elements in a genomic DNA sequence, the statistical model automatically selects those that tend to predict regulatory regions. We test the model using viral sequences that include known regulatory regions and provide the results obtained for human genomic DNA corresponding to the beta globin locus on chromosome 11.

Regulation of HIV-1 gene expression by NF-IL6

Previous studies have shown that in human T-cells (Jurkat) and hepatoma cells (HepG2), exogenous NF-IL6 can activate HIV-1 gene expression even in the absence of its consensus binding elements in the viral long terminal repeat (LTR). To identify the LTR elements that mediate this response, we have analysed constructs containing mutated and deleted LTR sequences. We have also examined heterologous plasmids to evaluate a potential requirement for the natural LTR sequences in producing HIV-1 gene activation by NF-IL6. As observed for Jurkat and HepG2 cells, we find that in the absence of NF-IL6 binding elements, NF-IL6 can elicit LTR-mediated gene expression in cotransient expression assays performed in monocytic (U937) cells. However, we detect distinct modes of regulation depending on cell type. In U937 cells, the basal LTR sequences retain a significant fraction (42%) of NF-IL6 responsiveness in the absence of upstream regulatory elements in the LTR while these elements are required for maximal response. In HepG2 cells, NF-IL6 elicits a relatively low level of gene activation from the basal LTR elements; response to NF-IL6 is restored with either the Sp1 binding sequences or the other upstream regulatory elements in the LTR. In addition, even though NF-IL6 induces a relatively low gene activity from the basal LTR sequences analysed in HepG2 cells, study of a heterologous construct indicates that these sequences are required for the responsiveness of Sp1 elements to NF-IL6 in this cellular background.

Localization of the human HTF4 transcription factors 4 gene (TCF12) to chromosome 15q21

Identification and localization of genes that encode regulators of transcription could provide landmarks for functional analysis of the human genome. Toward this goal, we examined a panel of somatic cell hybrids and assigned the gene (TCF12) encoding the helix-loop-helix transcription factors 4 (HTF4) to chromosome 15. Fluorescence in situ hybridization further localized TCF12 to chromosome 15q21. Northern analysis revealed that the relative abundance of HTF4 gene transcripts is not constant but varies depending on the human cell-line or tissue examined.

Distinguishable patterns of protein-DNA interactions involving complexes of basic helix-loop-helix proteins

Myogenic factors and TAL1 possess distinguishable DNA binding characteristics when they form a complex with basic helix-loop-helix (bHLH) proteins of class A. These characteristics were evident in electrophoretic mobility shift assays showing that complexes of myogenic factors and HTF4 displayed a relatively high affinity for the enhancer in the muscle creatine kinase gene, whereas TAL1 appeared to greatly attenuate the interaction of HTF4 with this enhancer. In addition, by forming a complex with HTF4 in solution, TAL1 could exert a negative effect on the interactions of HTF4 with elements that include E box motifs of microE2 (CAGCTG) and kappa E2/microE5 (CACCTG) type. Similarly, heterodimers containing TAL1 and the DNA binding domain of E47 exhibited a relatively weak affinity for microE2 and kappa E2/microE5 core motifs. The results of both studies invoked the hypothesis that in vivo TAL1 might act as a negative regulator of microE2 and kappa E2/microE5 sequence motifs by forming a complex with the products of the E2A and HTF4 genes. Support for this hypothesis was obtained by transient expression analyses where TAL1 was found to inhibit the activation effects produced by E2-5 and HTF4a on a reporter gene construct containing repeated microE2 and microE5 motifs, derived from the immunoglobulin gene enhancer.

Periodicity of dinucleotides in nucleosomes derived from simian virus 40 chromatin

It is thought that statistical analysis of dinucleotide periodicities can provide insight into the general features of nucleosome forming sequences. The chromatin of simian virus 40 (SV40) provides a model for a unique DNA sequence that is found in association with histones in vivo. I have therefore analyzed the periodicity of dinucleotides in a collection of cloned nucleosomal DNA fragments prepared from SV40 chromatin isolated under relatively mild conditions, in order to learn about the generality of results obtained from the statistical approach and to examine the SV40 data set in the context of models that have been proposed to explain the molecular basis of nucleosome formation. In one study, I assumed a symmetry in the distribution of dinucleotides with respect to the nucleosome dyad position and considered complementary dinucleotides to be equivalent, i.e. AA = TT and GG = CC. The results showed a periodic signal for GG/CC but not for AA/TT, purine-purine, and pyrimidine-pyrimidine dinucleotides. In a second study, the SV40 nucleosomal DNA fragments were aligned and examined with respect to the late strand of the viral genome to determine the distribution of dinucleotides in one direction. Fourier analysis revealed periodic signals for AA/TT (10.26 bp) and GG/CC (10.0 bp) and indicated that AA dominates the occurrences of AA/TT and GG dominates the occurrences of GG/CC. The results of both studies implied that there might be an asymmetry and a directionality in the distribution of certain dinucleotides in nucleosomes.

NF-IL6-mediated transcriptional activation of the long terminal repeat of the human immunodeficiency virus type 1

An upstream control region in the long terminal repeat (LTR) of human immunodeficiency virus type 1 (HIV-1) includes a potential negative regulatory element (NRE1). Cotransfecting multimers of a sequence spanning this element with an LTR-CAT construct produced an increase in chloramphenicol acetyltransferase (CAT) activity in Jurkat and HepG2 cells, providing further evidence and support for the existence of an NRE. In screening experiments aimed at identifying those factors that regulate HIV-1 transcription through interactions with the NRE1 region, we isolated a cDNA for NF-IL6. Previous studies have shown that NF-IL6 is a key nuclear factor that activates gene expression in response to interleukin 6. By methylation interference analysis, we have localized the NF-IL6 binding site within the NRE1 region and found that it overlaps an E box that has previously been implicated as the binding element for a negative regulator of HIV-1 expression. Through a database search, we identified an additional consensus binding sequence for NF-IL6 in the LTR of many HIV-1 variants and found that over this sequence, purified NF-IL6 can produce an extended footprint that overlaps one of the binding sites for NF-kappa B. A product of the nf-il6 gene activated transcription from several LTR-CAT constructs in transient transfection assays. Thus, NF-IL6 could play a central role in the control of HIV-1 gene expression and this protein might be a key mediator in signaling pathways where HIV-1 is activated by interleukin 6.

Interactions of HTF4 with E-box motifs in the long terminal repeat of human immunodeficiency virus type 1

We have identified three consensus E-box motifs in the long terminal repeat of human immunodeficiency virus type 1. One of these E boxes interacts selectively with representative members of the class A group of basic helix-loop-helix proteins, including HTF4, E47, and their heterodimers. Our analyses implicate the helix-loop-helix proteins in regulation of human immunodeficiency virus type 1 gene expression.

The nucleotide sequence of the human transcription factor HTF4a cDNA

A partial cDNA has previously been isolated that encodes HTF4, a new member of the basic helix-loop-helix family of DNA binding proteins. We have reconstructed a full cDNA, designated HTF4a cDNA, which spans the entire HTF4 coding region. The 5' end of the reconstructed cDNA includes an open reading frame encoding a 117-residue polypeptide. Three closely spaced ATG codons in the major open reading frame may potentially serve as sites of initiation for HTF4a synthesis, to yield proteins that contain 682, 675, and 657 amino acid residues, respectively. Pairwise dot matrix analysis indicates that there are at least three distinct human genes which encode proteins related to the Drosophila daughterless.

In vitro assembly of a positioned nucleosome near the hypersensitive region in simian virus 40 chromatin

Previous studies have identified a nucleosome near a potential late boundary for the nuclease-hypersensitive region in simian virus 40 chromatin. We have performed in vitro reconstitution analysis to determine whether the underlying DNA sequence encodes for the assembly of this nucleosome and applied hydroxyl radical and DNase I footprinting techniques to examine the structure of the reconstituted nucleosome. Both methods revealed the formation of a precisely positioned nucleosome in vitro, on a fragment spanning the strong in vivo nucleosome location site determined previously in the viral chromatin. The center of the positioned nucleosome maps between nucleotide 384 and 387 on simian virus 40 DNA. The corresponding nucleosome core includes the major-late transcription site (12 base-pairs within the core), the MspI site, and a segment shown previously to adopt a bent structure in the absence of proteins. The hydroxyl radical produces a strikingly well-defined cleavage pattern over the bent DNA incorporated in nucleosomes. The dominant periodicity of DNA in this nucleosome is 10.26 base-pairs per turn. The distribution of the .OH cut sites in the positioned nucleosome provides strong support for models in which the minor grooves of the A/T-rich tracts are oriented toward the histone core while the minor grooves of the G/C-rich sequences are facing outward.

Sequence of a HeLa cDNA provides the DNA binding domain and carboxy terminus of HE47: a human helix-loop-helix protein related to the enhancer binding factor E47

In order to identify cDNA encoding regulators of gene expression, a HeLa lambda gt11 expression library was screened with a DNA segment containing multiple copies of a sequence spanning the AP4 site in the simian virus 40 control region. We identified a partial cDNA encoding HE47, a sequence-specific DNA binding protein. The HeLa clone overlaps with a previously reported human B-cell partial cDNA encoding E47. The HeLa cDNA includes the HE47 DNA binding domain, its carboxy terminus, and the 3' untranslated region of its mRNA.

An alternative and convenient strategy for generation of substantial quantities of singly 5'-32P-end-labeled double-stranded DNA for binding studies: development of a protocol for examination of functional features of (+)-CC-1065 and the duocarmycins that contribute to their sequence-selective DNA alkylation properties

Development of an alternative strategy for securing substantial quantities of singly 5'-32P-end-labeled double-stranded DNA suitable for binding studies is described based on M13 cloning techniques and offers advantages of production of replenishable quantities of singly 5'-32P-end-labeled double-stranded DNA of homogenous length without need for DNA isolation (restriction fragment), dephosphorylation, and lengthy preparative gel electrophoresis procedures. The 32P label is introduced onto the free 5'-hydroxyl group of a chemically synthesized universal primer [5'-32P-d(GTAAAACGACGGCCAGT)-3'] which is used to initiate DNA synthesis on M13-derived single-stranded DNA templates. Following DNA synthesis, a restriction enzyme cleavage reaction produces a uniform length duplex suitable for agent binding studies. The strategy further permits the use of the Sanger dideoxynucleotide sequencing technique for direct and unambiguous identification of cleavage sites introduced by an agent on the end-labeled DNA. The use of the procedure in the examination of the DNA alkylation properties of (+)-CC-1065 (1) and a series of synthetic analogs is reviewed. From these studies a refined definition of the alkylation selectivity of (+)-CC-1065 is detailed. Employing agents possessing the parent 1,2,7,7a-tetrahydrocycloprop[1,2-c]indol-4-one (CI) alkylation subunit constituting the minimum pharmacophore of the CC-1065 alkylation subunit (CPI), comparative DNA alkylation studies illustrate that the activated cyclopropane is not obligatory for observation of the CI/CPI characteristic alkylation, highlight the relative nonselectivity of the alkylation event in the absence of noncovalent binding selectivity, illustrate a prominent role for agent binding selectivity for agents that possess such capabilities, and demonstrate that a sequence dependent autocatalytic phosphate activation of the alkylation event may not be uniquely responsible for the nonselective or selective alkylations. The ease with which the procedure may be extended to the rapid and convenient examination of additional agents is illustrated with the demonstration of the strikingly similar DNA alkylation properties of the duocarmycins (3-8) and (+)-CC-1065 (1) which suggest that the agents may be acting by a common mechanism.

Strategy for statistical-mapping of potential regulatory regions in the human genome

We have explored the feasibility of using crude nuclear extracts and band-shift experiments, to select and clone short human DNA fragments that contain binding sites for sequence-specific nuclear proteins. We show that this strategy is feasible. It provides a means to systematically identify the recognition sequences of proteins found in nuclear extracts prepared from various tissues, in order to compile a protein-binding-sequence catalogue. A complete catalogue would provide the data needed for searching the "raw" human DNA sequences for occurrence of protein-binding sites and thus, to construct a statistical map of potential regulatory regions in the human genome.

Temperature-mediated regulation and downstream inducible selection for controlling gene expression from the bacteriophage lambda pL promoter

We have examined in detail the effects of various induction temperatures on the expression of a heterologous fusion gene controlled by the bacteriophage lambda PL promoter in a heat-inducible Escherichia coli expression system which utilizes the CIts857 repressor. Experiments performed over a temperature range spanning 29-42 degrees C indicate that, under our conditions, temperatures as low as 29 degrees C may be required to fully repress the CI857-controlled transcription from PL, and that the highest protein yields are obtained after induction at 36 degrees C for 6 h. We cloned the cat reporter gene downstream from a heterologous gene controlled by PL and found that cat expression at a low induction temperature permits the monitoring of productive transcription through the heterologous gene and thus aids in selecting transformants that are capable of producing the heterologous protein in E. coli.

Location of nucleosomes in simian virus 40 chromatin

Over the past decade, the results of numerous indirect mappings analyses have not clarified whether or not nucleosomes occupy preferred positions in simian virus 40 (SV40) chromatin. To address this question more directly, we followed a shotgun cloning approach and determined the nucleotide sequences of over 400 cloned nucleosomal DNA fragments obtained from digestion of SV40 chromatin with micrococcal nuclease. Our results demonstrate and establish that nucleosomes do not occupy unique positions in SV40 minichromosomes and thus indicate the existence of at least several types of chromatin molecules having different nucleosome organization patterns. We developed two types of statistical analysis in order to examine the cloning data in greater detail. One type, overlap analysis, revealed the distribution of the cloned fragments with respect to SV40 DNA. The distribution exhibits an oscillating pattern, dividing the genome into regions of weak or strong nucleosome density. The other analysis determined the distribution of the midpoints of the cloned fragments and revealed potential strong and weak nucleosome location sites, and an early versus late distinction in organization of nucleosomes in SV40 chromatin. The late region appears to contain more strong nucleosome location sites (8) than the early region (4). The strongest nucleosome abuts the late side of the nuclease-hypersensitive region and includes the major transcription initiation site of the late genes. Another strong site precedes this nucleosome and includes sequences implicated in controlling the expression of the SV40 early and late genes. A strong or weak nucleosome location site is not apparent near the early side of the nucleosome-hypersensitive region. Only weak and overlapping nucleosome location sites are found in the region where replication terminates in the SV40 minichromosomes.

Correlation between dinucleotide periodicities and nucleosome positioning on mouse satellite DNA

Previous studies demonstrated 16 well-defined nucleosome locations (A-P) on a tandemly repeated prototype 234 base pair (bp) mouse satellite repeat unit. We have aligned the A-P fragments to search for DNA sequence elements that might contribute to nucleosome placement at these positions. Our results demonstrate a strikingly regular, uninterrupted, periodic pattern for the AA dinucleotide occurrences along the entire length of the aligned fragments. The periodicity of the AA occurrences is about 9.7 bp. The pattern exhibits a local minimum at position 74, near the nucleosome dyad axis of symmetry. Other dinucleotides--including AC: GT, CA: TG, and CC: GG--are also placed periodically, but their patterns of occurrence are less regular and less frequent than AA. The calculated spacings between consecutive preferred nucleosome locations on mouse satellite DNA are nearly identical, corresponding to multiples of 9.7 bp. The correlation between the periodicity of dinucleotide occurrences and the average spacing of nucleosome positions suggests that the preferred nucleosome locations recur at intervals that may correspond to the DNA helical repeat in the mouse satellite nucleosomes, and that the histone octamers sample (or slip along) the duplex in steps of 9.7 bp during nucleosome formation on mouse satellite DNA.

Locations of nucleosomes on the regulatory region of simian virus 40 chromatin

We have asked where the nucleosomes are located with respect to the replication origin and regulatory region of simian virus 40 DNA, what would be the possible functional consequences of the identified locations, and to what extent these locations correlate with the current views on mechanisms involved in establishing nucleosome-free regions in chromatin. To identify the precise location of nucleosomes, we have shot-gun cloned and sequenced nucleosomal DNA obtained from micrococcal nuclease digestion of wt776 chromatin prepared late in infection. Our results indicate that nucleosomes do not occupy unique positions over the replication origin or the elements involved in transcriptional control. However, it appears that the nucleosome distribution is not random, since several nucleosomes are represented by two or more independently generated clones. Two nearly identical cloned fragments map over the replication origin; five include 1.5 copies of the 72 base-pair enhancer sequences; and eight map to a region that spans a DNA bending locus and the major transcription initiation site of the late genes. The complex nucleosome distribution pattern observed in our direct analysis suggests that disparate nucleosome-free regions may be involved in controlling replication, and selective expression of the viral early or late genes.

Evaluation and optimization of variables in immunofixation electrophoresis for the detection of IgG paraproteins

We examined different antisera and varying serum dilutions for their effects on the sensitivity of immunofixation electrophoresis (IFE) for detecting and characterizing serum IgG paraproteins. Different antisera reacted unequally with a single paraprotein and conversely, a single antiserum reacted unequally with several different paraproteins. The dilution of serum was extremely important; the adoption of a single dilution for all sera could result in failure to detect low-concentration or poorly immunoreactive paraproteins. While the application of a standardized amount of paraprotein is recommended, it must be emphasized that no single antiserum can be relied on to provide unequivocal detection of all paraproteins of that particular isotype.

Photochemically induced binding of Rh(phen)2Cl2+ to DNA

The photoinduced covalent binding of the title compound to native and heat denatured DNA is described. The level of binding has been measured by UV (for DNA) and atomic absorption (for Rh) analysis. Quantum efficiencies of 6.4 x 10(-4) mol Rh per mol photons and 1.6 x 10(-3) mol Rh per mol photons have been determined for binding to native and denatured calf thymus DNA, respectively. Levels of bound rhodium as high as 1 molecule per five bases have been achieved. There is no binding of the complex in the absence of light, and there is evidence that at least a portion of the binding may be due to the photolytic conversion of the complex into one or more stable intermediates. Studies with polyribonucleotides indicate a strong preference for binding to the purine bases.

The capsid of small papova viruses contains 72 pentameric capsomeres: direct evidence from cryo-electron-microscopy of simian virus 40

The three-dimensional structure of the simian virus 40 capsid is remarkably similar to the structure of the polyoma empty capsid. This similarity is apparent despite striking differences in the methods used to determine the two structures: image analysis of electron micrographs of frozen-hydrated samples (SV40 virions) and an unconventional x-ray crystallographic analysis (polyoma empty capsids). Both methods have clearly resolved the 72 prominent capsomere units which comprise the T = 7d icosahedral capsid surface lattice. The 12 pentavalent and 60 hexavalent capsomeres consist of pentameric substructures. A pentameric morphology for hexavalent capsomeres clearly shows that the conserved bonding specificity expected from the quasi-equivalence theory is not present in either SV40 or polyoma capsids. Determination of the SV40 structure from cryo-electron microscopy supports the correctness of the polyoma structure solved crystallographically and establishes a strong complementarity of the two techniques. Similarity between the SV40 virion and the empty polyoma capsid indicates that the capsid is not detectably altered by the loss of the nucleohistone core. The unexpected pentameric substructure of the hexavalent capsomeres and the arrangement of the 72 pentamers in the SV40 and polyoma capsid lattices may be characteristic features of all members of the papova virus family, including the papilloma viruses such as human wart and rabbit papilloma.

Analysis of temperature-sensitive mutations in the simian virus 40 gene encoding virion protein 1

Temperature-sensitive (ts) assembly mutants of the tumorigenic virus simian virus 40 (SV40) fail to follow the normal pathway of virion morphogenesis at 40 degrees C. The mutations were previously mapped to the gene coding for the major virion protein VP1 and fall into three groups: tsB, tsBC, and tsC. We have determined the tsB/C mutations by DNA sequence analysis and deduced the corresponding amino acid substitutions. We find that the mutations are global and span 68% of the VP1 gene. They result predominantly in single amino acid substitutions. The B mutations are localized between nucleotides 1667 and 2091, spanning the VP1 amino acid residues 54-195. With the exception of one mutation in tsC260, the C group mutations occur between the nucleotides 2141 and 2262, spanning VP1 residues 212-252. The tsBC substitutions are not localized within a distinct region. We present a model for the VP1 structure. The model correlates the distribution of ts assembly mutations in the SV40 VP1 gene with the VP1 functional domains, deduced form the phenotypes exhibited by the assembly mutants, and the VP1 structural domains, deduced recently from the cryoelectron microscopic studies of the SV40 virions. We summarize the behavior of the SV40 ts mutants and discuss the possible relationship between the ts phenotype and amino acid substitutions.

High-level expression of the simian virus 40 genes LP1, VP1 and VP2 as fusion proteins in Escherichia coli

The complete sequences of the SV40 agnogene (LP1) and the genes coding for the capsid proteins VP1 and VP2 have been cloned into Escherichia coli expression plasmids. High levels of expression were obtained when the SV40 genes were inserted into the coding sequence of the influenza virus NS1 gene, which has previously been expressed in E. coli. The NS1A-LP1 and NS1A-VP2 chimeric proteins consist of the 81 N-terminal residues of NS1 (designated as peptide NS1A) fused to the complete sequence of the corresponding SV40 protein. The NS1A-VP1 chimera consists of NS1A followed by a linker of nine arbitrary residues and the complete sequence of the SV40 major capsid protein. The observed levels of expression vary considerably among the three chimeric proteins, ranging from approx. 70 micrograms/ml in the case of NS1A-LP1 to approx. 5 micrograms/ml in the case of NS1A-VP2. Cyanogen bromide cleavage of the NS1A-LP1 fusion protein produces fragments with Mrs expected for isolated NS1A and LP1 peptides. A plasmid has also been constructed which expresses the NS1A peptide in high yield.

Sensitivity of immunofixation electrophoresis for detecting IgM paraproteins in serum

Detection and characterization of small IgM paraproteins by immunoelectrophoresis are often difficult because of (a) slow diffusion of the macromolecular immunoglobulin, and (b) the obscuring of the light chain, especially kappa, by the light chains of background polyclonal immunoglobulin (the "umbrella effect"). Various methods of sample pretreatment have been tried in an attempt to overcome this problem. Using immunofixation electrophoresis (IFE), we were able to detect and characterize IgM paraproteins in serum at concentrations as low as 0.25 g/L, even when the polyclonal immunoglobulin background was increased. With routine IFE, our laboratory identified 58 patients with IgM paraproteinemia in a four-year period. In 36, the paraproteins were present at less than 5 g/L; 10 of these were detectable only by IFE.

Sensitivity of immunofixation electrophoresis for detecting IgM paraproteins in serum

Detection and characterization of small IgM paraproteins by immunoelectrophoresis are often difficult because of (a) slow diffusion of the macromolecular immunoglobulin, and (b) the obscuring of the light chain, especially kappa, by the light chains of background polyclonal immunoglobulin (the "umbrella effect"). Various methods of sample pretreatment have been tried in an attempt to overcome this problem. Using immunofixation electrophoresis (IFE), we were able to detect and characterize IgM paraproteins in serum at concentrations as low as 0.25 g/L, even when the polyclonal immunoglobulin background was increased. With routine IFE, our laboratory identified 58 patients with IgM paraproteinemia in a four-year period. In 36, the paraproteins were present at less than 5 g/L; 10 of these were detectable only by IFE.

Reconstruction of the three-dimensional structure of simian virus 40 and visualization of the chromatin core

The three-dimensional structure of the capsid and the nucleohistone core of simian virus 40 (SV40) has been reconstructed by image analysis of electron micrographs of frozen hydrated samples. The 72 prominent capsomere units that comprise the T = 7d icosahedral surface lattice of the capsid are clearly resolved. Both the pentavalent and hexavalent capsomeres appear with pentameric substructure, indicating that bonding specificity in the shell is not quasi-equivalent. There is a remarkable similarity between the structure of the SV40 virion capsid and the structure reported for the polyoma empty capsid. This result establishes that (i) the unexpected pentameric substructure of the hexavalent capsomeres is also present in virions and (ii) the arrangement of the 72 pentamers in the capsid lattice may be a characteristic feature of the entire papova family of viruses. The center of the SV40 reconstruction reveals electron density corresponding to the nucleohistone core. This density is smeared, suggesting that the minichromosome is not organized with icosahedral symmetry matching the capsid symmetry. The visualization of the virion chromatin provides a basis for invoking new models for the higher order structure of the encapsidated minichromosome.

The flexibility and topology of simian virus 40 DNA in minichromosomes

The linking number of DNA in minichromosomes increases by 2 turns during SV40 assembly. Changes in temperature also influence the average linking number of the total intracellular forms of SV40 DNA. When the isolated minichromosomes assembled in vivo are incubated with topoisomerase I at 33 degrees C in vitro, the linking number of SV40 DNA decreases. This decrease is about: -1.1 turns for minichromosomes with an average nucleosome spacing of 198 base pairs (bp), wt776; and -0.6 turns for minichromosomes containing a shorter average nucleosome repeat (177 bp), tsC219. The difference between the average linking number of naked SV40 DNA relaxed with topoI at 33 degrees C and minichromosomes relaxed with the enzyme at the same temperature indicates that SV40 chromatin contains on the average 26 nucleosomes. However, the results of studies obtained both on DNA flexibility in chromatin and in naked DNA, and on the shape of the topoisomer distribution curves, indicate that all of the minichromosomes, regardless of their overall structure, do not contain the same number of nucleosomes; this heterogeneity may be as large as 8 nucleosomes. We find no apparent correlation between the amount of minichromosomes containing unconstrained torsional stress and the abundance of the molecules with a structure characteristic of transcriptionally active chromatin.

Simian virus 40 protein VP1 is involved in spacing nucleosomes in minichromosomes

We have investigated the average nucleosome spacing in the chromatin from several simian virus 40 virion assembly mutants temperature-sensitive in the major capsid protein VP1. Viral assembly intermediates that accumulate in cells infected with mutants that block virion assembly at the propagation step (tsB) have an average nucleosome repeat length similar to that of wild-type SV40 chromatin, approximately 198(+/- 4) base-pairs. This repeat length is longer than that of the host (BSC-40) cellular chromatin, which has a value of 187(+/- 4) base-pairs. In contrast, SV40 chromatin from cells infected with virus containing a mutation that blocks virion assembly at the initiation step (tsC) has a significantly shorter average repeat length of 177(+/- 4) base-pairs. At the permissive temperature (33 degrees C), tsC chromatin has a nucleosome spacing periodicity essentially the same as that of wild-type SV40 chromatin. In addition to possessing a chromatin structure with nucleosomes that are, on the average, closer together, tsC chromatin contains a nuclease-hypersensitive or open region in nearly all molecules, but apparently the same number of nucleosomes. These findings suggest that nucleosomes are deposited initially on newly replicated SV40 chromatin in such a way as to leave the DNA region containing the origin of replication and transcription enhancers uncovered. Subsequent interaction with capsid proteins appears to increase the average nucleosome spacing and consequently to cover the open region for encapsidation.

A block in initiation of simian virus 40 assembly results in the accumulation of minichromosomes containing an exposed regulatory region

The initiation of simian virus 40 assembly is blocked at the nonpermissive temperature in cells infected with the viral capsid protein VP1 mutant tsC219. Greater than 95% of the minichromosomes isolated from these cells are accessible to cleavage by Bgl I and Sph I, which recognize the sequences near the viral replication origin and in the transcription enhancer elements, respectively. The accessibility of the Ori region to Bgl I is considerably reduced when virion assembly is allowed to proceed in tsC219-infected cells at the permissive temperature. A reduced accessibility to Bgl I is also observed for chromatin isolated from cells infected with wt776, the wild-type parental strain of tsC219. For wt776 chromatin, variability to Bgl I sensitivity is observed and this can be correlated to the relative virion-to-chromatin yield. A similar correlation is not apparent for restriction endonucleases that recognize sequences within the coding region of simian virus 40 chromatin. These results, considered together, indicate that, when virion assembly initiation is blocked, nucleosomes are nonrandomly arranged with respect to the viral regulatory sequences. It appears that the open regulatory region in minichromosomes is established during replication and that a protected regulatory region is generated with the onset of virion assembly.

Salt-stable association of simian virus 40 capsid with simian virus 40 DNA

In 8 M CsCl, a fraction of the wild-type previrions and tsB228 nucleoprotein complexes lose their core histones but retain their capsid. These histone-depleted complexes appear in the electron microscope as a protein shell attached to supercoiled DNA. Consistent with this result, we find that in 1 M NaCl, the wild-type previrions dissociate into two populations of nucleoprotein complexes. One population sediments between 50 and 140 S and morphologically resembles the shell-DNA complexes isolated in CsCl gradients. The other population is comprised primarily of nucleoproteins which sediment at 40 S.