Inferring the fitness effects of DNA mutations from polymorphism and divergence data: statistical power to detect directional selection under stationarity and free recombination

The fitness effects of classes of DNA mutations can be inferred from patterns of nucleotide variation. A number of studies have attributed differences in levels of polymorphism and divergence between silent and replacement mutations to the action of natural selection. Here, I investigate the statistical power to detect directional selection through contrasts of DNA variation among functional categories of mutations. A variety of statistical approaches are applied to DNA data simulated under Sawyer and Hartl's Poisson random field model. Under assumptions of free recombination and stationarity, comparisons that include both the frequency distributions of mutations segregating within populations and the numbers of mutations fixed between populations have substantial power to detect even very weak selection. Frequency distribution and divergence tests are applied to silent and replacement mutations among five alleles of each of eight Drosophila simulans genes. Putatively "preferred" silent mutations segregate at higher frequencies and are more often fixed between species than "unpreferred" silent changes, suggesting fitness differences among synonymous codons. Amino acid changes tend to be either rare polymorphisms or fixed differences, consistent with a combination of deleterious and adaptive protein evolution. In these data, a substantial fraction of both silent and replacement DNA mutations appear to affect fitness.

Immunohistochemical detection of MUC2 mucin core protein in ulcerative colitis

MUC2 mucin is predominantly expressed in the colon and is considered to play an important role in the protection of that organ. Recent findings suggested that MUC2 protein levels are significantly decreased in active ulcerative colitis (UC). We therefore performed an immunohistochemical study to reveal if the expression of MUC2 protein is altered in UC. Seventy-nine biopsy tissue specimens from 31 UC patients, along with normal colon tissues, were immunostained with anti-MUC2 mucin core protein monoclonal antibody (MoAb) CCP58 (IgG1). UC tissue specimens were divided into two groups based on the histological severity of inflammation, i.e., 64 with active inflammation (grades 2-5) and 15 without (grade 1). In the former group, 52 out of 64 (81.3%) tissue specimens contained sections of glands with a few cells positive for MoAb CCP58. These glands were small and consisted of MUC2 negative-short cells and a few positive cells without apparent mucus formation, considered to be immature regenerative glands. In contrast, the staining pattern was almost the same as that of the normal colon and no immature glands were seen in the group without active inflammation. The sections of immature regenerative glands with a few MUC2-positive cells were exclusively found in the UC tissues with active inflammation, but not in those without it, suggesting that the expression of MUC2 protein may be decreased in active UC.

Evaluation of equine infectious anemia virus core proteins produced in a baculovirus expression system in agar gel immunodiffusion test and enzyme-linked immunosorbent assay

Equine infectious anemia virus (EIAV) core proteins (Gag and p26) obtained from a baculovirus expression system were used in agar gel immunodiffusion (AGID) and enzyme-linked immunosorbent assay (ELISA) antigens to test seventy-six horse sera. Those sera showed false-positive reaction in AGID test using Nisseiken antigen. However, none of them showed false-positive reaction with both of the expressed antigens. The 76 horse sera were also tested by ELISA. The sera gave a high background in ELISA using Nisseiken antigen. Gag and p26 reacted strongly against positive sera from horses immunized with Nisseiken antigen.

[Surgical treatment of an aortic arch aneurysm: reports of 2 cases with lesion of the arch vessels]

<Case 1> A 48-year old woman underwent surgery for an aortic arch aneurysm with stenosis or dilatation of three arch vessels caused by aortitis syndrome. Total arch replacement and reconstruction of three arch vessels were performed with hypothermic selective cerebral perfusion (SCP). To avoid atheroembolism and malperfusion to the brain, the rt. common carotid artery was perfused via the rt. subclavian artery through the dacron vascular graft and the lt. subclavian artery was cannulated and perfused distally to stenosis. <Cases 2> A 65-year-old man who had an atherosclerotic aortic arch aneurysm with severe stenosis of the brachiocephalic artery underwent operation. In the operation, extracorporeal circulation was instituted with the arterial return through the lt. subclavian artery. Same as case 1, total arch replacement and reconstruction of three arch vessels were performed under hypthermic SCP. In this case, the left common carotid artery was transected and cannulated directly into the vessel, instead of cannulation through the aortic lumen because of atheromatous plaques in the orifice of the left common carotid artery. The patients recovered uneventfully and doing well now.

Translational selection and molecular evolution

An interplay among experimental studies of protein synthesis, evolutionary theory, and comparisons of DNA sequence data has shed light on the roles of natural selection and genetic drift in 'silent' DNA evolution.

A new reduction technique for a patellar fracture

We report 4 cases of patellar fracture with skin injury over the patella which were treated operatively immediately after onset with a new reduction technique using Ilizarov pins. This technique made it possible to perform early operative treatment even in the cases with skin injury over the patella which prevents conventional surgical approach.

Mutation pressure, natural selection, and the evolution of base composition in Drosophila

Genome sequencing in a number of taxa has revealed variation in nucleotide composition both among regions of the genome and among functional classes of sites in DNA. Mutational biases, biased gene conversion, and natural selection have been proposed as causes of this variation. Here, we review patterns of base composition in Drosophila DNA. Nucleotide composition in Drosophila melanogaster varys regionally, and base composition is correlated between introns and exons. Drosophila species also show striking patterns of non-random codon usage. Patterns of synonymous codon usage and the biochemistry of translation suggest that natural selection may act at 'silent' sites. A relationship between recombination rates and codon usage and comparisons of the evolutionary dynamics of silent mutations within and between species support natural selection discriminating among synonymous codons. The causes of regional base composition variation are less clear. Progress in functional studies of non-coding DNA, further investigations of genome patterns, and statistical tests based on evolutionary theory will lead to a greater understanding of the contributions of mutational processes and natural selection in patterning genome-wide nucleotide composition.

MRI monitoring of tarsal navicular stress fracture healing--a case report

Stress fractures of the tarsal navicular bone are rare injury and assessing its healing is difficult. Tenderness over the tarsal navicular on physical examination is the most reliable sign for assessing fracture healing. However, it is desirable to assess fracture healing with some imaging method. We used serial magnetic resonance imaging (MRI) to assess healing in a patient with a tarsal navicular stress fracture. MRI was useful for the assessment of fracture healing of tarsal navicular stress fracture in our case.

Effect of heparin on hemagglutination by equine arteritis virus

Heparin inhibited hemagglutination (HA) by equine arteritis virus (EAV) as well as did HA by Aujeszky's disease virus (ADV), but failed to inhibit HA by parainfluenza virus type 3 (PIV-3). The minimal concentration of heparin required to inhibit 8 HA U of EAV was 0.1 U/ml. In addition, most EAV hemagglutinin was retained by heparin acrylic beads, as was ADV hemagglutinin, but was not PIV-3 hemagglutinin. Mouse erythrocytes failed to combine with the HA inhibitory factor of heparin. However, mouse erythrocytes treated with heparinase had greatly reduced agglutinability by EAV. All these findings suggest that a heparin-like molecule on the surface of mouse erythrocytes serves as the virus-cell receptor.

Application of equine infectious anemia virus core proteins produced in a baculovirus expression system to serological diagnosis

Equine infectious anemia virus (EIAV) core proteins were obtained from a baculovirus expression system. Recombinant baculoviruses (rBVs) highly expressed the Gag precursor and p26 antigens in an rBV-infected Sf21 cell culture supernatant. Enzyme-linked immunosorbent assay (ELISA) and agar gel immunodiffusion (AGID) were conducted using the expressed proteins to detect antibodies from experimentally infected horses. The expressed antigens showed low background levels, high specificity and sensitivity in ELISA and AGID. The results of the serological tests using the expressed antigens were identical to those using a manufactured trial antigen. rBVs containing gag and p26 genes were found to express high quality and large quantities of Gag and p26 antigens, respectively. The antigens were quite useful for detecting anti-EIAV antibodies from virus-infected horses.

Nucleotide sequence homology to bovine viral diarrhea virus 2 (BVDV 2) in the 5' untranslated region of BVDVs from cattle with mucosal disease or persistent infection in Japan

Cytopathogenic and non-cytopathogenic bovine viral diarrhea viruses (BVDVs) were isolated from cattle with mucosal disease or persistent infection in Japan. These isolates were compared for antigenic properties by cross-neutralization tests with Japanese reference strains of BVDV belonging to classical type 1. Significantly low cross-reactivity to reference strains was noted, indicating the viruses to possibly represent a new serotype in Japan. Thus, to determine the genotype of the isolates, nucleotide sequences of the 5' untranslated region were determined and compared with those of previously reported BVDV 1 and 2. The isolates were clearly shown to belong to BVDV 2, not to BVDV 1.

Safety management of a patient undergoing thoracic aortic surgery by spinal evoked potential monitoring

We have presented a patient (48 year-old male) in whom the evoked spinal potential monitor detected impending spinal ischemia after aortic cross-clamping, which allowed surgical intervention to be modified so as to restore the decaying evoked spinal potential. The patient received replacement of the dissecting aneurysm in the thoracic descending aorta with clamping of the aorta at the sites immediately proximal and distal to the aneurysm and initiation of femoro-femoral venoarterial bypass under normothermia. The evoked spinal potential was recorded via the T12/L1 epidural electrode in response to transdural electric stimulation of the spinal cord at the C7/T1 level. As the evoked spinal potential gradually decreased in amplitude without latency prolongation after aortic cross-clamping, the distal clamp was moved from the T6 vertebral level to the T4. The reduced spinal potential then returned to the baseline amplitude. This episode was repeated twice from surgical necessity. The patient was free from any neurological disorders postoperatively.

A novel gastric-cancer-associated mucin antigen defined by a monoclonal antibody A3D4

De-glycosylation of mucins may expose new tumor-associated core protein epitopes. In this study, to attempt to develop useful markers for gastric cancers, we have purified and de-glycosylated gastric mucin and tried to establish monoclonal antibodies (MAbs). A MAb designated A3D4 among established MAbs was shown to react with gastric cancer with high frequency, but not with normal gastric epithelium. Among normal digestive organs, only the colon and gall bladder were positive for MAb A3D4. The incidence of positivity in gastric cancer was 75% for intestinal-type adenocarcinoma (n = 28), 40% for solid-type adenocarcinoma (n = 5) and 33% for signet/scirrhous-type adenocarcinoma (n = 15). Interestingly, adenoma and intestinal metaplasia (IM) with chronic gastritis or peptic ulcer were negative for MAb A3D4, whereas 8 out of 13 cases (62%) of IM with gastric cancer was positive. Western-blot analysis using the lysate from normal colon tissues revealed a high-molecular-weight (> 300-kDa) smear-like band. Immunohistochemical analysis indicated that the reactivity of MAb A3D4 was clearly increased when tissue sections were pre-treated with periodic acid or O-glycanase, while it was decreased by pre-treatment with trypsin or protease V8. There was no reactivity with the synthetic peptide encompassing the tandem-repeat sequence of MUC2 or MUC3. These data suggest that MAb A3D4 detects a novel gastric-cancer-associated mucin antigen whose epitope may be peptide in nature.

Aortic root replacement for Takayasu arteritis associated with ulcerative colitis and ankylosing spondylitis--report of a case

A 26-year-old man was admitted for treatment of congestive heart failure resulting from aortic regurgitation. The patient had been on medical treatment for ulcerative colitis (UC) since he was 14 years old and for ankylosing spondylitis (AS) since he was 20 years old. On admission, gradients of blood pressure among the extremities were observed. Echocardiography revealed marked dilation of the left ventricle (LV), hypokinetic wall motion of the LV, slightly prolapsed aortic cusps with annular dilatation, and severe aortic regurgitation. Computed tomographic scans demonstrated an aneurysmal dilation of the ascending aorta and thickening of the descending and abdominal aortic wall. Digital subtraction angiography demonstrated an aneurysmal dilation of the ascending aorta; however, there was no clear evidence of steno-occlusive lesions in the brachiocephalic vessels. Blood studies showed positive inflammatory signs and negative rheumatoid factor. HLA typing showed A2, 24(9), B27, 67, Cw1, 7, and DR1, 2. Based on these data, the diagnosis of Takayasu arteritis associated with UC and AS was made. Aortic root replacement was performed. Steroid therapy was restarted immediately after surgery. Histologic studies of the aortic wall showed findings compatible with Takayasu arteritis. The combination of these rare diseases suggests that they have a common pathophysiologic background.

Codon bias evolution in Drosophila. Population genetics of mutation-selection drift

Although non-random patterns of synonymous codon usage are a prominent feature in the genomes of many organisms, the relatives roles of mutational biases and natural selection in maintaining codon bias remain a contentious issue. In some species, patterns of codon bias and empirical findings on the biology of translation suggest 'major codon preference', a balance among mutation pressure, genetic drift, and weak selection in favor of translationally superior codons. Population genetics theory makes testable predictions to distinguish such a model from a strictly mutational model of codon bias. Major codon preference predicts two fitness classes of synonymous DNA changes: 'preferred' mutations from non-major to major codons and 'unpreferred' changes in the opposite direction. An extension of current statistical methods is employed to reveal differences in the within and between species dynamics of preferred and unpreferred silent mutations in Drosophila simulans. In this lineage, codon bias appears to be maintained under roughly equal magnitudes of natural selection and genetic drift. In the sibling species, D. melanogaster, however, a reduction in N(e)s, the product of effective population size and selection coefficient, appears to have allowed a genome-wide reduction in codon bias.

A novel gastric-cancer-associated mucin antigen defined by a monoclonal antibody A3D4

De-glycosylation of mucins may expose new tumor-associated core protein epitopes. In this study, to attempt to develop useful markers for gastric cancers, we have purified and de-glycosylated gastric mucin and tried to establish monoclonal antibodies (MAbs). A MAb designated A3D4 among established MAbs was shown to react with gastric cancer with high frequency, but not with normal gastric epithelium. Among normal digestive organs, only the colon and gall bladder were positive for MAb A3D4. The incidence of positivity in gastric cancer was 75% for intestinal-type adenocarcinoma (n = 28), 40% for solid-type adenocarcinoma (n = 5) and 33% for signet/scirrhous-type adenocarcinoma (n = 15). Interestingly, adenoma and intestinal metaplasia (IM) with chronic gastritis or peptic ulcer were negative for MAb A3D4, whereas 8 out of 13 cases (62%) of IM with gastric cancer was positive. Western-blot analysis using the lysate from normal colon tissues revealed a high-molecular-weight (> 300-kDa) smear-like band. Immunohistochemical analysis indicated that the reactivity of MAb A3D4 was clearly increased when tissue sections were pre-treated with periodic acid or O-glycanase, while it was decreased by pre-treatment with trypsin or protease V8. There was no reactivity with the synthetic peptide encompassing the tandem-repeat sequence of MUC2 or MUC3. These data suggest that MAb A3D4 detects a novel gastric-cancer-associated mucin antigen whose epitope may be peptide in nature.

Genetic variation of envelope gp90 gene of equine infectious anemia virus isolated from an experimentally infected horse

Six strains of equine infectious anemia virus (EIAV) were recovered from febrile and non-febrile stages of a horse experimentally infected with the P337-V70 strain given once to a horse. The env gp90 genes of the isolates, the P337-V70 and P337-V26, avirulent virus derived from the P337-V70 strain, were sequenced. A comparison of the gp90 gene sequences revealed that amino acid variations among the viruses tested showed as high as 8.2 to 11.5%. In addition, the comparison also indicated that the isolates that recovered from the non-febrile stage were contained in nucleotide insertions in the principal neutralizing domain (PND) region. The insertions were arranged regularly with smaller segments. The nucleotide sequence of the P337-V26 gp90 gene was found to contain a six-nucleotides insertion and seven nucleotide substitutions outside the PND region, when compared with that of the P337-V70 strain.

Sequence determination and phylogenetic analysis of the Akabane bunyavirus S RNA genome segment

The nucleotide sequence of the small (S) RNA segment of Akabane (AKA) bunyavirus was determined. The segment is 858 nucleotides long and contains two overlapping open reading frames (ORFs), which encode the nucleocapsid (N) and nonstructural (NSs) proteins, consistent with other bunyaviruses. Comparisons with the Aino virus S RNA sequence indicated that there is 73.5% identity in nucleotide sequence. However, the sequence identity of the 5' non-coding region of the genomic RNA between these two viruses is only 55%. The N ORFs from 20 Japanese and 2 Australian isolates of AKA virus were sequenced and subjected to phylogenetic analysis. This suggested that AKA virus has evolved in multiple lineages. Twenty-three isolates were grouped into three major clusters, and the cluster which includes recent isolates was subdivided into two branches. Thus, phylogenetic analysis of the AKA virus N protein gene gives a greater insight into bunyavirus evolution.

Hemagglutination with equine arteritis virus

Equine arteritis virus (EAV) grown on RK13 cell cultures was tested for hemagglutination (HA) with erythrocytes from a variety of species at 4 degrees C, room temperature and 37 degrees C. HA was observed at all temperatures with erythrocytes from mouse and chicken but not with those of cattle, horse, rabbit, guinea pig, mongolian gerbil, goose or chick embryo. Chickens showed an individual variation in agglutinability of their erythrocytes, requiring selection of birds to obtain erythrocytes for HA. The HA activity was enhanced by treatment of virus materials with Tween 80 followed by treatment with ether. The HA reaction was inhibited by specific antiserum. Higher HA-inhibiting (HI) antibody titers were obtained by the incubation of serum-HA antigen mixture at 4 degrees C for 24 hr. HI antibody titers of individual horse sera showed a significant positive correlation with their neutralizing antibody titers.

Restriction fragment length polymorphism analysis of Akabane virus nucleoprotein gene

The nucleoprotein genes of Akabane virus S RNA segment from 21 Japanese and two Australian isolates were amplified by the reverse transcriptase-polymerase chain reaction (RT-PCR) using a primer set containing the initiation and termination codon of the gene. The RT-PCR products were sufficiently produced from the purified virion RNAs of all the isolates, and then analyzed by enzymatic digestion with 11 restriction endonucleases. Digestion with the eight restriction enzymes revealed sequence variation of the isolates. Restriction fragment length polymorphism (RFLP) profiles obtained by digestion revealed the existence of four major groups (genogroups) among the isolates. The two Australian isolates had extremely different RFLP profiles than the Japanese isolates. The data demonstrate the usefulness of analyzing the RFLP patterns to understand the genetic variability of AKA virus isolated in Japan and Australia.

Antigenic and genetic comparisons of Japanese and Australian Simbu serogroup viruses: evidence for the recovery of natural virus reassortants

The antigenicity and RNA genome structures of five Simbu serogroup bunyaviruses isolated in Japan and Australia were analyzed using monoclonal antibodies (Mabs) raised to Akabane (AKA) virus and oligonucleotide fingerprinting. The virion surface glycoprotein (G1) and the nucleocapsid (N) protein of heterologous viruses showed no reactivity to the Mabs, while the AKA-derived anti-G1 Mab (2F1) reacted with Peaton virus and all three AKA anti-N Mabs reacted with Tinaroo (TIN) virus at almost the same antibody titers as the homologous virus. Oligonucleotide fingerprinting analyses indicated that the three RNA species of all the viruses were unique and distinguishable. However, AKA and TIN viruses exhibited very similar S RNA oligonucleotide fingerprints, while the L and M RNA fingerprints were quite different. The S RNA sequence of TIN virus has been determined and compared with that of AKA and Aino viruses. The results revealed 95.1% S sequence homology between the AKA and TIN viruses. The antigenic and genetic comparisons of AKA and TIN viruses suggest that the two viruses may represent naturally occurring reassortant viruses.

[Aortic arch surgery in the elderly]

A consecutive series of 16 patients over 75 years old who underwent aortic arch operations with hypothermic selective cerebral perfusion from 1994 to 1997 was analyzed. These patients (group O) was compared with 18 patients aged from 70 to 74-year-old (group M) and 38 patients under the age of 69 (group Y) who underwent aortic arch operation during the same period. There were 5 males and 11 females with a mean age of 77.8 years (range 75 to 86) in group O. Twelve patients were in aortic dissection and 4 patients were in atherosclerotic aneurysms. There were 5 hospital deaths (31.2%) in group O, 2 (11.1%) in group M and 2 (5.3%) in group Y. There was significant difference in hospital mortality rate between group O and group Y. Cerebral complication occurred in 2 patients (12.5%) and postoperative respiratory failure occurred in 7 (47%) in group O. Aortic arch operations for the elderly patients can be performed with increased but operative mortality in the elderly patients remains high. In this study, we discussed that influence of risk factors on the operative result and operative indication in the elderly patients.