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PubMed1991

A microcomputer program to analyze the CD spectrum of proteins and nucleic acids--use of LOTUS 1-2-3 spread sheet.

A user friendly interactive computer program, CIRDIC, is developed which calculates the molar ellipticity and molar circular dichroic absorption coefficients from the CD spectrum. This, in combination with LOTUS 1-2-3 spread sheet, will give the spectra of above parameters vs wavelength. The code is implemented in MicroSoft FORTRAN 77 which runs on any IBM compatible PC under MSDOS environment.

Algorithms↗
PubMed2026

Exploring the Mitochondrial Genomes of Phoebe Species (Lauraceae): Structural Dynamics and Functional Conservation.

Plant mitochondrial genomes (mitogenomes) vary markedly in size and architecture despite generally slow rates of sequence evolution. Phoebe is an ecologically and economically valuable genus of Lauraceae, yet its mitogenome diversity remains poorly characterized. In this study, we newly sequenced, assembled, and annotated the mitogenomes of three nationally protected Class II wild plants (P. bournei, P. chekiangensis, P. zhennan) from China and compared their mitogenomic characteristics. The three assemblies were resolved into representative circular configurations ranging from 808 to 864 kb, with similar GC contents and conserved protein-coding capacity. Each mitogenome contained distinct 41 protein-coding genes, 27-28 transfer RNAs, and three ribosomal RNAs. Synteny analysis revealed extensive changes in homologous-block order and orientation despite substantial sequence homology among the three species. Abundant repeats occurred predominantly in noncoding regions, while plastid-derived fragments documented historical intracellular DNA transfer. The three species exhibited similar codon usage and predicted RNA-editing patterns, whereas low synonymous divergence limited inference from pairwise ratios. Phylogenetic analysis based on mitochondrial protein-coding genes recovered Phoebe as a well-supported monophyletic lineage. These results reveal substantial structural divergence accompanied by conserved nucleotide composition and coding capacity, providing valuable data for further understanding the evolutionary variation of plant mitogenomes of Phoebe and the Lauraceae.

Phoebe↗
PubMed1975

Incidence and nature of cytoplasmic hepatitis B antigen in hepatocytes.

Hepatitis B antigen (HB Ag) in the hepatocytic cytoplasm is detected by immunofluorescence after reaction with fluoresceinated antiserum to HB Ag or by electron microscopy as numerous 20- to 30-nm. tubular and circular structures in dilated cisternae of excess endoplasmic reticulum. On light microscopy, these hepatocytes can be recognized because their cytoplasm has a ground-glass appearance and stains with Gomori's aldehyde fuchsin. Aldehyde fuchsin-positive ground-glass hepatocytes were detected in all 14 asymptomatic carriers of HB Ag and in 16 of 60 HB Ag-seropositive patients with chronic hepatitis, but not in HB Ag-seropositive acute viral hepatitis or in various other HB Ag-seronegative liver diseases. These cells are helpful in identifying on light microscopy HB Ag carriers and a portion of patients with HB Ag-positive chronic hepatitis. Nuclear HB Ag did not stain with aldehyde fuchsin. Nucleic acids were not detected in the ground-glass cytoplasm by special stains at the light or electron microscopic level. We suggest that the tubular and circular structures in the hepatocytic cytoplasm are coat material of the hepatitis B virus or virally coded host cell reaction product rather than the complete hepatitis B virus.

Acute Disease↗
PubMed1975

Size, conformation and purity of chloroplast DNA of some higher plants.

1. Chloroplast DNA of Antirrhinum majus, Oenothera hookeri, Beta vulgaris and Spinacia oleracea band at the same buoyant density of 1.697 g-cm-3 in neutral CsCl equilibrium gradients. The corresponding nuclear DNAs band at 1.691, 1.703, 1.695 and 1.695 g-cm-3, respectively. The purity of chloroplast and nuclear DNA can be assessed objectively only in the cases of Antirrhinum and Oenothera. 2. Electron microscopic analysis of chloroplast DNA, purified in CsCl or CsCl/ethidium bromide gradients, revealed up to 80% circular molecules. Of these about 15% were of supertwisted conformation. Best yields of circular molecules were recovered when populations of unbroken chloroplasts were subjected to DNAase and phosphodiesterase treatment, and when the DNA was purified from viscous lysates by centrifugation into a CsCl cushion. Treatment of plastids with DNAase alone did not guarantee complete degradation of nuclear DNA. 3. The average contour length of the open circular chloroplast DNA molecules was basically similar for all four plants. They were 45.9 plus or minus 2.1 mum for Antirrhinum, 45.7 plus or minus 1.9 mum for Spinacia, 44.9 plus or minus 1.7 mum for Beta and 45.2 mum for Oenothera. This is comparable to the size derived for the coding capacity of chloroplast DNA from reassociation experiments. As much as 15% of the total population of circles in chloroplast DNA of Spinacia were circular dimers.

Centrifugation, Density Gradient↗
PubMed1985

The perception of a dotted line in noise: a model of good continuation and some experimental results.

A formal model is proposed, describing how the perceptual interpretation of dot figures is guided by the Gestalt rule of good continuation. The algorithm will be restricted to figures with a collinear dot array (line) embedded in a background of randomly placed dots. The model, CODE-2, is an elaboration of the model, CODE-1, of grouping dots on the basis of the Gestalt rule of (relative) proximity, and consists of the introduction of non-circular symmetric gaussian distribution functions for the representation of the orientation dependent strength of interaction between collinear dots. Supra-threshold contours of the function, resulting from a superposition on each dot of the gaussian functions, are assumed to predict the perceptual grouping of the dots. A quantitative measure for the perceptual salience of dotted lines was defined as the contrast between the internal coherence of the line dots, and their interference with the noise dots. For 20 stimuli the CODE-2 grouping of the dots is reported, together with the results of a line-in-noise latency experiment. There was a significant correlation between the predicted saliences and the experimental results. The results support the usefulness of representing good continuation between collinear dots by non-circular symmetric gaussian distribution functions.

Adult↗
PubMed1987

The nucleotide sequence of a geminivirus from Digitaria sanguinalis.

The encapsidated single-stranded circular DNA of a geminivirus isolated from Digitaria sanguinalis has been sequenced. The data obtained are consistent with there being one DNA circle of 2701 nucleotides. Comparison of the nucleotide sequence with those of maize streak virus (MSV) and wheat dwarf virus showed 64 and 47% DNA homology, respectively. The sequence has four potential coding regions for proteins of greater than 10 kDa, two in the viral (+) sense and two in the complementary (-) sense. Each of these potential coding regions has a highly homologous counterpart among the seven open reading frames previously described for MSV. Virion DNA contained, in addition to the circular single-stranded DNA, a population of small DNA molecules similar to those associated with MSV particles. A comparison with MSV DNA of the region complementary to these small DNA molecules revealed conserved sequences, which may have a role in defining the limits of these primer-like molecules.

Base Sequence↗
PubMed1990

The quantitative study of the orientation of collagen in compact bone slices.

We describe and validate a simple method for the study of the proportion of collagen fibers (and apatite crystals) in a bone slice parallel with the plane of section. Viewed between crossed circular polarizers, all bone areas with collagen lying more nearly in the plane of section (i.e., transverse [TS] collagen) appear bright whatever its direction in this plane; longitudinal [LS] collagen appears dark, but not as dark as the background. The degree of brightness increases with section thickness, which must therefore be standardized--we chose 100 microns plane parallel sections. We transferred the circularly polarized light [CPL] image via a CCD TV camera to an image analyzing computer. Color-coded maps of the CPL image were used to compare regions within and between sections. The new analytical procedure makes more detailed studies of the fine-structural orientation in compact bone possible, but does this have any significance? To answer this question, a bone in which the in vivo strain pattern had been clearly documented was chosen for particular study. Transverse mid-diaphyseal sections of the equine radius showed a distribution of CPL bright areas which correlated closely with previously reported strain patterns.

Animals↗
PubMed2025

Comprehensive circRNA expression profile and hub genes screening during human liver development.

BACKGROUND: Understanding the expression of non-coding RNA in the liver during embryonic development provides important insights into liver diseases. Therefore, we investigated circular RNA (circRNA) roles in human liver development, an unexplored research domain. METHODS: Using high-throughput sequencing and bioinformatics, we analysed foetal liver samples across developmental stages (7-20 weeks post-conception). Differentially expressed (DE) genes were identified and subjected to enrichment analysis using Gene Ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG), and Disease Ontology (DO). Modular analysis was performed using the Search Tool for Retrieval of Interacting Genes (STRING), followed by construction of a protein-protein interaction (PPI) network using Cytoscape software. The key genes were screened using Molecular Complex Detection (MCODE). The mRNA levels of hub genes were validated using quantitative reverse transcription polymerase chain reaction (qRT-PCR). RESULTS: There were 645 DE circRNAs and 5,145 DE mRNAs between human livers at the three growth stages (HB, EH, and LH). It was found that the activity of circRNAs was boosted remarkably in the hepatoblastic stage. Enrichment analysis found they mainly involved in nervous system regulation of liver function, embryonic organ development and digestive system development. In addition, DE circRNAs were primarily involved in the PI3K-AKT, MAPK and calcium pathways, potentially contributing to adult liver diseases. Notably, only hsa_circ_001471 and novel_circ_017382 were simultaneously identified at all stages and were persistently downregulated. A co-expression regulatory network involving these circRNAs was established. Three hub genes (LGR5, FOXL1 and RSPO3) were identified from the PPI network of 167 genes and may play key roles in human liver development. The RT-qPCR validation results were in agreement with the sequencing data. CONCLUSIONS: Our findings provide the first insights into the roles and regulatory networks of circRNAs in human liver development, laying the groundwork for further investigations of molecular and signalling networks.

Humans↗
PubMed1982

Analysis of the expression of cloned genes using an Escherichia coli cell-free system.

An Escherichia coli coupled transcription-translation cell-free system, which is efficient in the synthesis of proteins directed by exogenously added DNA, is described. These cell-free extracts direct protein synthesis against a low background of endogenous protein synthesis providing a means for analyzing the expression of isolated genes. This is especially important when using restriction enzyme-linearized DNAs which are less efficient templates than circular DNAs. This cell-free system has been used to study the expression of the proteins coded by plasmids pBR322 and pBL101.

Bacterial Proteins↗
PubMed1991

Depth-coded motion signals in plaid perception and optokinetic nystagmus.

When two sine-wave gratings drift in different directions at the same speed behind a circular window, a single coherent plaid is seen rather than one grating sliding over the other. We find that as the stereo depth separation of the two component gratings increases, the probability of seeing a plaid declines. The gain of the slow phase of vertical optokinetic nystagmus (OKN) also falls as the separation of the components increases. When the two grating components are in the same depth plane, the vertical eye velocity is greater than that of either component. This shows that the OKN is being driven by the plaid, whose vertical speed is roughly twice as fast as the components. We conclude that both perception and OKN are fed by the same motion signal, which arises after binocular combination and after plaid synthesis.

Depth Perception↗
PubMed1977

Isolation of transcriptionally active chromatin from mammalian nucleoli.

Nucleoli isolated from HeLa cells are functionally active but contain large amounts of RNA and proteins (RNA/DNA ratio 1:1; protein/DNA ratio 7:1). We have isolated from the nucleolus a DNA-protein complex that has the characteristics of nucleolar chromatin (RNA/DNA ratio less than 0.05:1; protein/DNA ratio 1.7:1). This nucleolar chromatin has most of the transcriptional activity of the intact nucleolus and, as assayed by circular dichroism and dye binding, has largely preserved its structure. The isolation of a transcriptionally active, fragment of chromatin, which constitutes only a small part of the total genome and codes for only one recognizable product, offers several advantages for the study of chromatin structure and function.

Cell Nucleolus↗
PubMed2026

Genomic analysis of an Arctic marine Tenacibaculum sp. SM2510 reveals its genetic potential for glutathione utilization.

Glutathione is a key intracellular antioxidant, playing a crucial role in resisting oxidative stress and maintaining cellular redox homeostasis. However, the glutathione metabolic capacity of Tenacibaculum remains poorly characterized. In this study, a Gram-stain-negative bacterium, Tenacibaculum sp. SM2510, was isolated from seawater collected from Kongsfjorden, Svalbard, Norway. Genome sequencing revealed that the strain possesses a single circular chromosome of 2,904,982 bp with a G + C content of 31.44%, encoding 2564 protein-coding genes. Genomic analysis indicates that Tenacibaculum sp. SM2510 may directly take up extracellular oxidized glutathione (GSSG) and reduce it to reduced glutathione (GSH) through a reductive pathway, which potentially allows the strain to alleviate the accumulation of reactive oxygen species (ROS) caused by strong ultraviolet radiation and low temperature in polar environments. Furthermore, genomic analysis predicts that the strain degrades GSH to produce essential life-sustaining substances. In conclusion, these results suggest that Tenacibaculum sp. SM2510 may potentially utilize exogenous glutathione for both antioxidant defense and nutrient acquisition through direct GSH degradation, providing new insights into the environmental adaptive evolution of polar marine bacteria.

Tenacibaculum↗
PubMed1980

Association of Mu-containing plasmids with the Escherichia coli chromosome upon prophage induction.

To determine the structure of a prophage-containing plasmid during Mu transposition, we have monitored the physical state of pSC101[unk]Mucts after thermoinduction. We have also examined the fate of a mini Mu plasmid constructed in vitro by deleting 27 kilobases from the center of the Mu prophage in pSC101[unk]Mucts. At various times after prophage induction, DNA was extracted from Mu or mini Mu plasmid-containing strains and subjected to electrophoresis in low concentration agarose gels followed by transfer of the DNA to nitrocellulose paper. Separate hybridization with (32)P-labeled pSC101 and Mu DNA revealed the position of the plasmids and the replication of Mu DNA. At times after induction when Mu replication was clearly visible, Mu and mini Mu plasmids were found to migrate with Escherchia coli DNA. This Mu-specific association requires the phage coded A and B proteins. Electron microscopy has shown that some of the associated DNA is comprised of circular plasmid molecules which appear to be in contact with the chromosomal DNA. These structures may represent intermediates or end products of the replication-integration process. The finding that Mu and mini Mu plasmids do not give rise to any detectable excision products and apparently remain intact during Mu transposition supports our proposal that the predominant event after Mu induction is the replication of Mu DNA in situ to generate integrative intermediates.

Bacteriophage mu↗
PubMed1990

[Human hepatitis B virus and hepatocellular carcinoma].

Hepatitis B virus (HBV) is the causative agent of hepatocellular carcinoma (HCC) in man. The HBV genome is a circular partially double-stranded DNA molecule of about 3.2 kb. The HBV genome contains four structural genes coding for the HBV envelope (HBsAg) and core (HBcAg/HBeAg) proteins, endogenous DNA-polymerase with the additional enzymatic activity of a reverse transcriptase and polypeptide X functioning as a trans-activator of cellular and viral genes. HBV DNA integration in the genomes of HCCs and hepatocytes of HBV carriers is an important evidence establishing a relationship between the HBV infection and the development of HCC. The mechanism of HBV DNA integration into the cellular genome and the possible role of integrated HBV DNA sequences in the malignant transformation of hepatocytes are discussed.

Carcinoma, Hepatocellular↗