Testing the "proto-splice sites" model of intron origin: evidence from analysis of intron phase correlations

A few nucleotide sites of nuclear exons that flank introns are often conserved. A hypothesis has suggested that these sites, called "proto-splice sites," are remnants of recognition signals for the insertion of introns in the early evolution of eukaryotic genes. This notion of proto-splice sites has been an important basis for the insertional theory of introns. This hypothesis predicts that the distribution of proto-splice sites would determine the distribution of intron phases, because the positions of introns are just a subset of the proto-splice sites. We previously tested this prediction by examining the proportions of the phases of proto-splice sites, revealing nothing in these proportion distributions similar to observed proportions of intron phases. Here, we provide a second independent test of the proto-splice site hypothesis, with regard to its prediction that the proto-splice sites would mimic intron phase correlations, using a CDS database we created from GenBank. We tested four hypothetical proto-splice sites G / G, AG / G, AG / GT, and C/AAG / R. Interestingly, while G / G and AG / GT site phase distributions are not consistent with actual introns, we observed that AG / G and C/AAG / R sites have a symmetric phase excess. However, the patterns of the excess are quite different from the actual intron phase distribution. In addition, particular amino acid repeats in proteins were found to partially contribute to the excess of symmetry at these two types of sites. The phase associations of all four sites are significantly different from those of intron phases. Furthermore, a general model of intron insertion into proto-splice sites was simulated by Monte Carlo simulation to investigate the probability that the random insertion of introns into AG / G and C/AAG / R sites could generate the observed intron phase distribution. The simulation showed that (1) no observed correlation of intron phases was statistically consistent with the phase distribution of proto-splice sites in the simulated virtual genes; (2) most conservatively, no simulation in 10,000 Monte Carlo experiments gave a pattern with an excess of symmetric (1, 1) exons larger than those of (0, 0) and (2, 2), a major statistical feature of intron phase distribution that is consistent with the directly observed cases of exon shuffling. Thus, these results reject the null hypothesis that introns are randomly inserted into preexisting proto-splice sites, as suggested by the insertional theory of introns.

Liquid chromatographic method for determination of patulin in clear and cloudy apple juices and apple puree: collaborative study

A collaborative trial was conducted to validate the effectiveness of a liquid chromatographic (LC) procedure for determination of patulin in both clear and cloudy apple juices and apple puree. The test portion of clear apple juice was directly extracted with ethyl acetate; cloudy apple juice and apple puree were treated with pectinase enzyme before extraction. After back-extraction into sodium carbonate to remove interfering acidic compounds, the extract was dried and concentrated, and patulin was determined by LC with UV detection. Clear and cloudy apple juices, apple puree test samples naturally contaminated with patulin, and blank test samples for spiking with patulin were sent to 14 collaborators in 12 different European countries. Test portions of each of the 3 test sample types were spiked with patulin at 75 ng/g. Recoveries of patulin ranged from 80 to 92%. Based on the results for spiked test samples (blind pairs) and naturally contaminated test samples (blind pairs at 3 levels), the relative standard deviations for repeatability (RSDr) and reproducibility (RSDR) ranged from 8 to 35% and 11 to 36%, respectively. Although HORRAT values of <1.4 were obtained for all 3 matrixes at patulin levels ranging from 26 to 121 ng/g, better performance values (RSDr values 6-10% and RSDR values 11-25%) were obtained for clear and cloudy apple juice spiked above 50 ng/g, which is either the statutory limit or the advisory level for patulin contamination in apple juices in many countries.

[Influence of solvents on IR spectrum of aromatic amines]

21 aromatic amines in different solution system are studied by FTIR. The IR spectra of these aromatic amines are greatly influenced by solvents. The IR stretching frequency of amino group in benzene has a larger bathochromic shift than that in tetrachloromethane (CCl4). It is also found that the frequency, the peak shape and relative strength of absorption for their amino group are not affected by the various concentrations.

The origin of the Jingwei gene and the complex modular structure of its parental gene, yellow emperor, in Drosophila melanogaster

Jingwei (jgw) is the first gene found to be of sufficiently recent origin in Drosophila to offer insights into the origin of a gene. While its chimerical gene structure was partially resolved as including a retrosequence of alcohol dehydrogenase (ADH:), the structure of its non-ADH: parental gene, the donor of the N-terminal domain of jgw, is unclear. We characterized this non-ADH: parental locus, yellow emperor (ymp), by cloning it, mapping it onto the polytene chromosomes, sequencing the entire locus, and examining its expression patterns in Drosophila melanogaster. We show that ymp is located in the 96-E region; the N-terminal domain of ymp has donated the non-ADH: portion of jgw via a duplication. The similar 5' portions of the gene and its regulatory sequences give rise to similar testis-specific expression patterns in ymp and jgw in Drosophila teissieri. Furthermore, between-species comparison of ymp revealed purifying selection in the protein sequence, suggesting a functional constraint in ymp. While the structure of ymp provides clear information for the molecular origin of the new gene jgw, it unexpectedly casts a new light on the concept of genes. We found, for the first time, that the single locus of the ymp gene encompasses three major molecular mechanisms determining structure of eukaryotic genes: (1) the 5' exons of ymp are involved in an exon-shuffling event that has created the portion recruited by jgw; (2) using alternative cleavage sites and alternative splicing sites, the 3' exon groups of ymp produce two proteins with nonhomologous C-terminal domains, both exclusively in the testis; and (3) in the opposite strand of the third intron of ymp is an essential gene, musashi (msi), which encodes an RNA-binding protein. The composite gene structure of ymp manifests the complexity of the gene concept, which should be considered in genomic research, e.g., gene finding.

Group II introns designed to insert into therapeutically relevant DNA target sites in human cells

Mobile group II intron RNAs insert directly into DNA target sites and are then reverse-transcribed into genomic DNA by the associated intron-encoded protein. Target site recognition involves modifiable base-pairing interactions between the intron RNA and a >14-nucleotide region of the DNA target site, as well as fixed interactions between the protein and flanking regions. Here, we developed a highly efficient Escherichia coli genetic assay to determine detailed target site recognition rules for the Lactococcus lactis group II intron Ll.LtrB and to select introns that insert into desired target sites. Using human immunodeficiency virus-type 1 (HIV-1) proviral DNA and the human CCR5 gene as examples, we show that group II introns can be retargeted to insert efficiently into virtually any target DNA and that the retargeted introns retain activity in human cells. This work provides the practical basis for potential applications of targeted group II introns in genetic engineering, functional genomics, and gene therapy.

Reactive hall response

The zero temperature Hall constant R(H), described by reactive (nondissipative) conductivities, is analyzed within linear response theory. It is found that in a certain limit R(H) is directly related to the density dependence of the Drude weight, implying a simple picture for the change of sign of charge carriers in the vicinity of a Mott-Hubbard transition. This novel formulation is applied to the calculation of R(H) in quasi-one-dimensional and ladder prototype interacting electron systems.

[Invasion behavior of hepatocellular carcinoma cells correlates with their rheological properties]

We investigated the viscoelasticity, mechanics of adhesion to collagen I coated surfaces and mechanics of adhesin to liver sinosoidal endothelial cells(LECs) among primary culture human hepatocytes, hepatocellular carcinoma(HCC) cells as well as HCC-Inv cells, namely HCC cells capable of invading the artificial basement membrane, Matrigel. The results showed that the above-mentioned rheological properties of HCC cells differed obviously from those of normal hepatocytes. HCC-Inv cells exhibited higher viscoelastic coefficients, higher adhesion forces to collagen I coated surfaces as well as higher adhesion forces to LECs than those of normal hepatocytes and HCC cells. Immunocytochemistry showed the differences in cell morphology and cytoskeleton structure between HCC cells and HCC-Inv cells. A brief discussion was presented in relation to the changes in cell rheological properties of hepatocellular carcinoma cells and their pathological significance.

Lessons to be learned: a case study approach: ascites and elevated serum CA 125 due to a pancreatic carcinoma. A diagnostic dilemma

A 72 year-old lady with unrecognised cancer of the body of the pancreas presented with a 4-month history of progressive loss of weight and ascites. The results of laboratory investigations were either negative or within normal limits--apart from a raised serum CA 125 level; no tumour mass was detected on diagnostic imaging. She underwent exploratory laparotomy for a suspected ovarian tumour, but this proved not to be the correct diagnosis. A serum CA 19-9 level was subsequently requested and found to be significantly raised; a second contrast CT scan then showed the presence of ill-defined peri-aortic tissue. A further exploratory laparotomy was carried out in order to establish the true nature of the problem; a large pancreatic carcinoma was revealed.

ExInt: an Exon/Intron database

The Exon/Intron (ExInt) database incorporates information on the exon/intron structure of eukaryotic genes. Features in the database include: intron nucleotide sequence, amino acid sequence of the corresponding protein, position of the introns at the amino acid level and intron phase. From ExInt, we have also generated four additional databases each with ExInt entries containing predicted introns, introns experimentally defined, organelle introns or nuclear introns. ExInt is accessible through a retrieval system with pointers to GenBank. The database can be searched by keywords, locus name, NID, accession number or length of the protein. ExInt is freely accessible at http://intron.bic.nus.edu.sg/exint/exint.html

Effects of oxidative damage of membrane protein thiol groups on erythrocyte membrane viscoelasticities

In three oxidative damaging systems: the diamide-mercaptoethanol redox modification system (DM), the pyrogallol oxygen free radicals system (PG) and the hypoxanthine-xanthine oxidase oxygen free radical system (HXO), the effect of erythrocyte membrane oxidative damage on membrane viscoelasticities was investigated with micropipette aspiration method. The experimental results indicated that erythrocyte membrane oxidative damage has a great influence upon the membrane mechanical properties. The oxidative damage led to decrease of contents of membrane protein thiol radical. The scanning of SDS-PAGE presented that membrane proteins form the higher molecular weight component (HMP) by the cross-linking of membrane protein thiol radicals that might hinder the conformational change of membrane protein. This might be the reason for the increased membrane elastic modulus and viscous coefficient upon treating erythrocytes with the oxidative damaging systems. A significant negative logarithm regression relation was found between the membrane elastic modulus, mu, or viscoefficient, eta, and the contents of membrane protein thiol radicals. These experimental results suggested that thiol radicals oxidative damage reaction due to the superoxides anions (*O2-) may be an important molecular mechanism inducing changes of membrane viscoelasticities or whole cell deformability of erythrocyte under physiological and pathological oxidative stress.

Association of intron phases with conservation at splice site sequences and evolution of spliceosomal introns

How exon-intron structures of eukaryotic genes evolved under various evolutionary forces remains unknown. The phases of spliceosomal introns (the placement of introns with respect to reading frame) provide an opportunity to approach this question. When a large number of nuclear introns in protein-coding genes were analyzed, it was found that most introns were of phase 0, which keeps codons intact. We found that the phase distribution of spliceosomal introns is strongly correlated with the sequence conservation of splice signals in exons; the relatively underrepresented phase 2 introns are associated with the lowest conservation, the relatively overrepresented phase 0 introns display the highest conservation, and phase 1 introns are intermediate. Given the detrimental effect of mutations in exon sequences near splice sites as found in molecular experiments, the underrepresentation of phase 2 introns may be the result of deleterious-mutation-driven intron loss, suggesting a possible genetic mechanism for the evolution of intron-exon structures.

Origin of new genes and source for N-terminal domain of the chimerical gene, jingwei, in Drosophila

This paper deals with a general question posed by the origin of new processed chimerical genes: when a new retrosequence inserts into a new genome position, how does it become activated and acquire novel protein function by recruiting new functional domains and regulatory elements? Jingwei (jgw), a newly evolved functional gene with a chimerical structure in Drosophila, provides an opportunity to examine such questions. The source of its exon encoding C-terminal peptide has been identified as an Adh retrosequence, which extends the concept of exon shuffling from recombination to retroposition as a general molecular mechanism for the origin of a new gene. However, the origin of 5' exons remains unclear. We examined two hypotheses concerning the origin of these non-Adh-derived jgw exons: (i) these exons might originate from a unique genomic sequence that fortuitously evolved a standard intron-exon structure and regulatory sequence for jgw; (ii) these exons might be a duplicate of an unrelated previously existing gene. Genomic Southern analysis, in conjunction with construction and screening of a genomic bookshelf (sub-library), was conducted in a group of Drosophila species. The results demonstrated that there are duplicate genes containing the same structure as the recruited portion of jgw. We name this duplicate gene in Drosophila teissieri and Drosophila yakuba and its orthologous gene in Drosophila melanogaster as yellow-emperor (ymp). Thus, the 5' exons/introns originated from a previously existing gene that provided new modules with specific sub-function to create jgw.

[Investigation on the adhesive properties of different cycle hepatoma cells]

OBJECTIVE

To study the adhesive forces of HTC cells on different concentration of artificial basement membrane (collagen IV coated)and synchronous G1&S phase HTC cells on a certain concentration of artificial basement membrane.

METHODS

The adhesive forces of HTC cells were investigated by micropipette aspiration technique. The synchronous G1 and S phase cells were achieved through thymine-2-desoryriboside and cochicine sequential blockage method and double thymine-2-desoryriboside blockage method respectively.

RESULTS

HTC cells with 72.10% of G1 phase and 98.94% of S phase were achieved through thymine-2-desoryriboside and cochicine sequential blockage method and double thymine-2-desoryriboside blockage method respectively. The adhesive force of HTC cells on artificial basement membrane was in direct proportion to the concentration of collagen IV. G1 phase HTC cells had higher adhesive forces than S phase cells.

CONCLUSION

These studies suggested that the increase of basement membrane might be conducive to the chemotactic motion and adhesion of tumor cells; G1 phase cells were more capable of adhering to and getting through basement membrane than S phase cells, and reflected the differences of receptors between G1 phase cells and S phase cells.

Intron-exon structures of eukaryotic model organisms

To investigate the distribution of intron-exon structures of eukaryotic genes, we have constructed a general exon database comprising all available intron-containing genes and exon databases from 10 eukaryotic model organisms: Homo sapiens, Mus musculus, Gallus gallus, Rattus norvegicus, Arabidopsis thaliana, Zea mays, Schizosaccharomyces pombe, Aspergillus, Caenorhabditis elegans and Drosophila. We purged redundant genes to avoid the possible bias brought about by redundancy in the databases. After discarding those questionable introns that do not contain correct splice sites, the final database contained 17 102 introns, 21 019 exons and 2903 independent or quasi-independent genes. On average, a eukaryotic gene contains 3.7 introns per kb protein coding region. The exon distribution peaks around 30-40 residues and most introns are 40-125 nt long. The variable intron-exon structures of the 10 model organisms reveal two interesting statistical phenomena, which cast light on some previous speculations. (i) Genome size seems to be correlated with total intron length per gene. For example, invertebrate introns are smaller than those of human genes, while yeast introns are shorter than invertebrate introns. However, this correlation is weak, suggesting that other factors besides genome size may also affect intron size. (ii) Introns smaller than 50 nt are significantly less frequent than longer introns, possibly resulting from a minimum intron size requirement for intron splicing.

Generation of a widespread Drosophila inversion by a transposable element

Although polymorphic inversions in Drosophila are very common, the origin of these chromosomal rearrangements is unclear. The breakpoints of the cosmopolitan inversion 2j of D. buzzatii were cloned and sequenced. Both breakpoints contain large insertions corresponding to a transposable element. It appears that the two pairs of target site duplications generated upon insertion were exchanged during the inversion event, and that the inversion arose by ectopic recombination between two copies of the transposon that were in opposite orientations. This is apparently the mechanism by which transposable elements generate natural inversions in Drosophila.

Generation of a widespread Drosophila inversion by a transposable element

Although polymorphic inversions in Drosophila are very common, the origin of these chromosomal rearrangements is unclear. The breakpoints of the cosmopolitan inversion 2j of D. buzzatii were cloned and sequenced. Both breakpoints contain large insertions corresponding to a transposable element. It appears that the two pairs of target site duplications generated upon insertion were exchanged during the inversion event, and that the inversion arose by ectopic recombination between two copies of the transposon that were in opposite orientations. This is apparently the mechanism by which transposable elements generate natural inversions in Drosophila.

Probabilistic modeling of shear-induced formation and breakage of doublets cross-linked by receptor-ligand bonds

A model was constructed to describe previously published experiments of shear-induced formation and breakage of doublets of red cells and of latexes cross-linked by receptor-ligand bonds (. Biophys. J. 65:1318-1334; Tees and Goldsmith. 1996. Biophys. J. 71:1102-1114;. Biophys. J. 71:1115-1122). The model, based on McQuarrie's master equations (1963. J. Phys. Chem. 38:433-436), provides unifying treatments for three distinctive time periods in the experiments of particles in a Couette flow in which a doublet undergoes 1) formation upon two-body collision between singlets; 2) evolution of bonds at low shear rate; and 3) break-up at high shear rate. Neglecting the applied force at low shear rate, the probability of forming a doublet per collision as well as the evolution of probability distribution of bonds in a preformed doublet were solved analytically and found to be in quite good agreement with measurements. At high shear rate with significant force acting to accelerate bond dissociation, the predictions for break-up of doublets were obtained numerically and compared well with data in both individual and population studies. These comparisons enabled bond kinetic parameters for three types of particles cross-linked by two receptor-ligand systems to be calculated, which agreed well with those computed from Monte Carlo simulations. This work can be extended to analyze kinetics of receptor-ligand binding in cell aggregates, such as those of neutrophils and platelets in the circulation.

Titanium alloys in total joint replacement--a materials science perspective

Increased use of titanium alloys as biomaterials is occurring due to their lower modulus, superior biocompatibility and enhanced corrosion resistance when compared to more conventional stainless steels and cobalt-based alloys. These attractive properties were a driving force for the early introduction of alpha (cpTi) and alpha + beta (Ti-6A1-4V) alloys as well as for the more recent development of new Ti-alloy compositions and orthopaedic metastable beta titanium alloys. The later possess enhanced biocompatibility, reduced elastic modulus, and superior strain-controlled and notch fatigue resistance. However, the poor shear strength and wear resistance of titanium alloys have nevertheless limited their biomedical use. Although the wear resistance of beta-Ti alloys has shown some improvement when compared to alpha + beta alloys, the ultimate utility of orthopaedic titanium alloys as wear components will require a more complete fundamental understanding of the wear mechanisms involved. This review examines current information on the physical and mechanical characteristics of titanium alloys used in artifical joint replacement prostheses, with a special focus on those issues associated with the long-term prosthetic requirements, e.g., fatigue and wear.

Toward a resolution of the introns early/late debate: only phase zero introns are correlated with the structure of ancient proteins

We present evidence that a well defined subset of intron positions shows a non-random distribution in ancient genes. We analyze a database of ancient conserved regions drawn from GenBank 101 to retest two predictions of the theory that the first genes were constructed by exon shuffling. These predictions are that there should be an excess of symmetric exons (and sets of exons) flanked by introns of the same phase (positions within the codon) and that intron positions in ancient proteins should correlate with the boundaries of compact protein modules. Both these predictions are supported by the data, with considerable statistical force (P values < 0.0001). Intron positions correlate to modules of diameters around 21, 27, and 33 A, and this correlation is due to phase zero introns. We suggest that 30-40% of present day intron positions in ancient genes correspond to phase zero introns originally present in the progenote, while almost all of the remaining intron positions correspond to introns added, or moved, appearing equally in all three intron phases. This proposal provides a resolution for many of the arguments of the introns-early/introns-late debate.

For a healthier community

Understanding the concept of community is crucial to improving the health status of our citizens. This author used her knowledge of community, understanding of nursing principles, and strong commitment to volunteerism to create the first outreach clinic in Atlanta. Her career story unfolds as she tells of moving from a single community to a role of advocate for a national community population.

[Changes in trace elements contents of renal cells in cadmium poisoning]

OBJECTIVE

To understand the possible role of trace elements in renal damage caused by cadmium poisoning and its mechanism.

METHODS

An experimental animal model with renal damage caused by cadmium poisoning was prepared, and trace elements contents in subcellular components in renal cells, lipid peroxidation reaction, renal function and its ultrastructural changes were determined.

RESULTS

Uptake of cadmium could cause transfer of copper, zinc and manganese mainly distributed in the mitochondrion to cell nuclei and cytoplasm, and content of selenium and activity of glutathione-peroxidase (GSH-px) in cytosol declined and content of propandiolal increased.

CONCLUSION

It suggests that changes in trace elements contents, especially in selenium content, during renal damage caused by cadmium poisoning, could correlate with the increase of lipid peroxidation, and abnormal subcellular distribution of trace elements was one of the important roles in renal damage caused by cadmium poisoning.

Relationship between "proto-splice sites" and intron phases: evidence from dicodon analysis

The coding sequence at the boundaries of exons flanking nuclear introns shows some degree of conservation. To the extent that such sequences might be recognized by the splicing machinery, this conservation may be a derived result of evolution for efficient splicing. Alternatively, such conserved sequences might be remnants of proto-splice sites, which might have existed early in eukaryotic genes and served as the targets for the insertion of introns, as has been proposed by the introns-late theory. The distribution of intron phases, the position of the intron within a codon, is biased with an over-representation of phase 0 introns. Could any distribution of proto-splice sites account for today's intron phase distribution? Here, we examine the dicodon usage in six model organisms, based on current sequences in the GenBank database, and predict the phase distribution that would be expected if introns had been inserted into proto-splice sites. However, these predictions differ between the various model organisms and disagree with the observed intron phase distributions. Thus, we reject the hypothesis that introns are inserted into hypothetical proto-splice sites. Finally, we analyze the sequences around the splice sites of introns in all six of the species to show that the actual conservation of sequence in exon regions near introns is very small and differs considerably between these species, which is inconsistent with a general proto-splice sites model.

Cadmium Accumulation and Toxicity in The Bottlenose Dolphin Tursiops truncatus, The Common Dolphin Delphinus delphis, and Some Dolphin Prey Species in South Australia

Twenty Tursiops truncatus and 20 Delphinus delphis from South Australia were analysed for cadmium levels, as were some fish and squid species which form part of their diet. In the dolphins, cadmium was accumulated mainly in the kidneys (range 0-38 μg/g), with levels in many individuals exceeding 20 μg/g (wet weight). On average, levels in kidney were three-fold higher than in liver and 26-fold higher than in muscle. Cadmium concentrations related to dolphin body length, but the relationship with tooth development class was less clear. 80% of the prey fish species analysed from Spencer Gulf exceeded NH & MRC health recommendations of 0.2 μg/g (wet weight) for human consumption. Sepioteuthis australis from upper Spencer Gulf contained significantly higher cadmium levels than Ceduna samples (0.21 ± 0.01 μg/g versus 0.13 ± 0.01 μg/g, p&lt;0.001) (wet weight). On histological examination, 32% of adult dolphin kidneys showed pathological changes, proteinuria being the most common abnormality. High levels of cadmium were found in dolphins from widely spaced locations in South Australia.