Automated Sanger DNA sequencing with one label in less than four lanes on gel

Novel Sanger dideoxy sequencing with only one fluorescent dye label for the four bases of one clone and sequence determination in two lanes on polyacrylamide gel is presented, loading A greater than G in one lane and T greater than C in the other. Sequencing reactions for the two bases in each lane are carried out in one tube. At present the ratio of ddATP:ddGTP and ddTTP:ddCPT is set to 5:1 in the two tubes. Distinction between the two bases in one lane is done by comparing the different magnitudes of the peaks. This method increases the capacity since more clones may be run simultaneously on one gel, while keeping the reliability and simplicity that comes with the use of only one fluorescent dye for the four bases of one clone. At present about 200 bases are determined with the one-dye two-lane method on the EMBL's automated fluorescent DNA sequencer, using T7 DNA polymerase. The error rate in the deduced sequence is about 1%. The technique is used for the determination of overlaps in mapping projects. In principle, it is possible to determine the sequence with one dye in only one lane on the gel by choosing the proper ddNTP ratios for all four bases, carrying out reactions in one tube and applying the product in one lane, but the error rate for this one-lane method seems too high at present and further improvements in the uniformity of peaks obtainable with the T7 DNA polymerase or other enzymes are required.     

Length–weight relationships for 20 species collected in the Jurumirim reservoir (Paranapanema Basin, Brazil)

Length–weight relationships were estimated for 20 species of the Jurumirim reservoir (southern Brazil): one Pimelodidae, one Callichthyidae, six Characidae, one Prochilodontidae, six Anastomidae, one Erythrinidae, two Curimatidae, one Paradontidae and one Cichlidae. The fishes were collected during 2001–2002 using three different types of fishing gear that allowed collection of both adult and juvenile specimens. The first reference of length–weight relationships for 12 species is provided.     

Genetic Structure of Races of Heterodera glycines and Inheritance of Ability to Reproduce on Resistant Soybeans

Four field populations of Heterodera glycines tested for ability to reproduce on three host differentials were each classified into one of the recognized races. A fifth population represented a new race. Genetic analysis indicated that the designated races are actually field populations that differ from each other primarily in the frequencies of three groups of genes (genes for parasitism) that act quantitatively and control the ability of the nematode to reproduce on resistant P.I. 88788, Pickett, and P.I. 90763 soybeans. Populations of race-3 have none of these genes for parasitism, or they have some in low frequency that results in an index of parasitism of less than 10 on any one of the resistant soybeans. Race-1 has a high frequency of one group of genes that enable it to reproduce on P.I. 88788. Race-2 has two groups of genes for parasitism in high frequency; one for P.I. 88788, and one for Pickett. Based on these findings, it was assumed that race-4 has three groups of genes for parasitism; one for P.I. 88788, one for Pickett, and one for P.I. 90763. Additional races may be recognized when new genes are identified, or when new gene combinations are discovered. The ability to reproduce on P. I. 88788 is inherited independently from the ability to reproduce on Pickett. Although the genetic structure of field populations does not provide a solid foundation for race designation, recognizing races under the present system may be useful when it clearly characterizes the behavior of field populations. Race designations, however, should be regarded as provisional since gene frequencies change with time in response to selection forces and, therefore, the race status of a population may change accordingly.     

Centric fission consequences in man

The authors summarise the consequences of centric fission in man as follows: classical (monocentric) isochromosomes; usually either for p or q, exceptionally for both arms; stable telocentrics for either one or both arms; isochromosome for one arm, stable telocentric for the other; isochromosome for one arm concurring with translocation of the telocentric for the other; telocentric/isochromosome mosaicism for the same arm; stable telocentric for a part of one arm, the remaining of the chromosome forming a smaller element (obviously this rearrangement requires an additional break outside the centromere), and whole-arm translocations. These events are discussed in the light of current notions about centromere structure and function.     

Threshold model for clustered firing of neurons

Two probabilistic threshold models for burst activity of cortical neurons are proposed. In model I every input impulse increases the summed effect of previous input impulses by one unit. The decay of the summed effect takes place in discrete steps of one unit. A response occurs on arrival of an input impulse, when a threshold value is attained.Although after a response the summed effect is not reset to zero, it cannot exceed the threshold either. The distribution of intervals can be resolved in two components, one for long and one for short intervals. In model II intervals of the short component are terminated by a multiple response instead of one response.     

Zinc environment in sheep liver sorbitol dehydrogenase

The extended X-ray absorption fine structure (EXAFS) associated with the zinc K-absorption edge has been recorded for sorbitol dehydrogenase. It is interpreted in terms of one cysteine sulfur among the ligands to the active site zinc atom. Simulations of the EXAFS based on the presence of two such sulfurs are less satisfactory, and comparison with the EXAFS of such systems points to the presence of only one sulfur ligand in sorbitol dehydrogenase. These results provide evidence that sorbitol dehydrogenase does not have the characteristic one water, one His, two Cys arrangement of ligands to the active site zinc found in the homologous alcohol dehydrogenases and are consistent with the one water, one His, one Cys, one Glu ligand arrangement of the proposed model of sorbitol dehydrogenase [Eklund, H., Horjales, E., J?rnvall, H., Br?ndén, C.-I., & Jeffery J. (1985) Biochemistry 24, 8005-8012]. Evidence for the correctness of the model is also evidence for validity of predictive techniques used in constructing the model, i.e., computer graphics fitting of the amino acid sequence to the crystallographically derived structure of a different but homologous protein.     

Chemical constituents from the aerial parts of Juncus setchuensis

Juncus setchuensis is a perennial herbaceous plant found in marshes, swamps, and other poorly drained sites. Despite being so abundant in the southwest of China, only one literature reference has reported about its chemical components. The present phytochemical investigation on this plant led to isolations of 13 compounds (including four 9,10-dihydrophenanthrenes, one phenanthrene, one flavonone, two mono-aromatics, one steroid, one anthraquinone and three diterpenoid tanshinones), five of them were isolated form this plant for the first time, four of them, one anthraquinone and three diterpenoid tanshinones, were reported for the first time in this genus. The presence of phenanthrenes, 9,10-dihydrophenanthrenes in the Juncus genus could be of taxonomic importance.     

Length–weight relationships of six freshwater fish species from the semiarid region of Brazil

Evaluated were the length–weight relationships of six freshwater fish species caught in the Santa Cruz Reservoir in the semiarid region of Brazil: one Characidae, one Prochilodontidae, one Anostomidae, two Loricariidae and one Cichlidae, providing the first references of length–weight relationships and new maximum lengths for these species.     

Heavy metal tolerance and metal homeostasis in Pseudomonas putida as revealed by complete genome analysis

The genome of Pseudomonas putida KT2440 encodes an unexpected capacity to tolerate heavy metals and metalloids. The availability of the complete chromosomal sequence allowed the categorization of 61 open reading frames likely to be involved in metal tolerance or homeostasis, plus seven more possibly involved in metal resistance mechanisms. Some systems appeared to be duplicated. These might perform redundant functions or be involved in tolerance to different metals. In total, P. putida was found to bear two systems for arsenic (arsRBCH), one for chromate (chrA), four to six systems for divalent cations (two cadA and two to four czc chemiosmotic antiporters), two systems for monovalent cations: pacS, cusCBA (plus one cryptic silP gene containing a frameshift mutation), two operons for Cu chelation (copAB), one metallothionein for metal(loid) binding, one system for Te/Se methylation (tpmT) and four ABC transporters for the uptake of essential Zn, Mn, Mo and Ni (one nikABCDE, two znuACB and one mobABC). Some of the metal-related clusters are located in gene islands with atypical genome signatures. The predicted capacity of P. putida to endure exposure to heavy metals is discussed from an evolutionary perspective.     

VisGenome: visualization of single and comparative genome representations

VisGenome visualizes single and comparative representations for the rat, the mouse and the human chromosomes at different levels of detail. The tool offers smooth zooming and panning which is more flexible than seen in other browsers. It presents information available in Ensembl for single chromosomes, as well as homologies (orthologue predictions including ortholog one2one, apparent ortholog one2one, ortholog many2many) for any two chromosomes from different species. The application can query supporting data from Ensembl by invoking a link in a browser.     

Cytological diagnosis of soft tissue tumours

Cytological diagnosis of soft tissue tumours The aims of this study were to determine the patterns of soft tissue tumours and also to try to assess the utility of fine needle aspiration cytology (FNAC) in diagnosing soft tissue tumours. Of 15 361 patients who visited the cytology diagnostic service of the Pathology Department, Medical Faculty, Addis Ababa University, 623 (4.1%) cases with a diagnosis of soft tissue tumours were retrieved from the department's records for the years 1991-96. Fifty-three soft tissue tumours (25 benign and 28 malignant tumours) with combined FNAC and surgical biopsy results were traced for cyto-histological correlations. Twenty-two out of 25 benign soft tissue tumours were correctly diagnosed, with three false cytologic diagnoses where one mesenchmal neoplasm, one haemangioma, and one haemorragic lesion were identified; and out of 28 malignant soft tissue, 23 were correctly diagnosed however, the five false cytological diagnoses were one soft tissue sarcoma, one dermatofibrosarcoma, one malignant mesenchymal neoplasm, one spindle cell neoplasm and one menechymal neoplasm. Thus, in this study a sensitivity and specificity of 88.5% and 81.5% respectively for the diagnosis of soft tissue tumours were reported. In conclusion, FNAC of soft tissue tumours is a fast, effective and reliable diagnostic tool that may help in categorizing soft tissue tumours into benign and malignant groups for clinical management.     

A Note on Contingency Tables with one Structural Zero

Based on a definition of Quasi-Independence, which is equivalent to the usual one but easier to interpret, rules for the calculation of ML-estimates in Contingency Tables with one structural zero are given. These rules are much simpler than the usual ones; even explicit solutions exist up to five dimensions. Possible extensions for other hypotheses and for more than one structural zero are suggested.     

Interaction of saposins, acidic lipids, and glucosylceramidase

Activity of lysosomal glucosylceramidase is stimulated by two small glycoproteins, saposin A and C, which are, together with two other similar glycoproteins, derived from a single precursor protein. This enzyme is also stimulated by naturally occurring acidic lipids, such as phosphatidylserine and gangliosides. Using highly purified glucosylceramidase, saposins, and acidic lipids, the mechanism of enzyme stimulation was studied by investigating complex formation between the three components and by examining effects on activity caused by changing amounts of saposins and acidic lipids, individually or in combination. The results indicated that acidic lipids form a water-soluble complex with glucosylceramidase but not with saposins and that saposins and acidic lipids each bind to the enzyme at two different sites for the activation. Based on these observations, the previously proposed three-binding sites model of glucosylceramidase, activator, and substrate was modified to one composed of four binding sites: one for carbohydrate of the substrate, one for aglycon, one for acidic lipids, and one for saposins.     

Reliability of aneuploidy estimates in human sperm: Results of fluorescence in situ hybridization studies using two different scoring criteria

Aneuploidy estimates for chromosomes 1, 12, X, and Y were obtained in human sperm from five donors using multicolor fluorescence in situ hybridization (FISH) analysis. Disomy frequencies were obtained by scoring a minimum of 10,000 sperm for each chromosome probe per donor. This analysis was replicated for two scoring criteria: one used one half of a signal domain as the minimum distance between two signals to be counted as two and thus disomic; the other set one signal domain as the minimum distance between two signals. A total of 120,870 sperm were assessed using one half of a domain as the criterion, and 113,478 were scored using one domain as the criterion. The percentage of disomy for chromosomes 1, 12, X, Y, and XY was 0.18, 0.16, 0.15, 0.19, and 0.25, respectively, using the one-half-domain criterion, and 0.08, 0.17, 0.07, 0.12, and 0.16, respectively, using the one-domain criterion. The percentage of disomy decreased significantly with use of one domain as the minimum distance for signal separation for all chromosomes except for chromosome number 12. These lower disomy frequencies correlated well with frequencies derived from human sperm karyotypes analyzed in our laboratory. This suggests that the fluorescent signals for chromosomes 1, X, and Y split into more than one domain in decondensed interphase sperm, and that the use of the one-half-domain criterion would lead to an overestimate of aneuploidy frequencies. The factors known to affect aneuploidy estimates derived from FISH studies are discussed, and recommendations for stringent scoring criteria are proposed. © 1995 wiley-Liss, Inc.     

Improving genomic prediction for two Yorkshire populations with a limited size using the single‐step method

In this study, we conducted genomic prediction for two Yorkshire purebred populations (Yichun and Chifeng) from two different provinces of China that both had a limited population size. Two growth traits (age adjusted to 100 kg weight, AGE; back‐fat thickness adjusted to 100 kg weight, BF) and one reproduction trait (total number of piglets born, TNB) were analyzed with four prediction strategies: one‐population BLUP, joint two‐population BLUP, one‐population single‐step BLUP (SSBLUP) and joint two‐population SSBLUP. Our results illustrate that accuracies of genomic estimated breeding values were improved for BF and TNB for the Yichun population and for BF for the Chifeng population by genomic prediction (one‐population SSBLUP and joint two‐population SSBLUP). The accuracy of TNB for the Yichun population was increased two fold when comparing the one‐population SSBLUP to the one‐population BLUP prediction. Meanwhile, prediction biases were dramatically reduced for AGE for the Yichun population and for TNB for the Chifeng population. The conclusions of this study are as follows: first, genomic prediction is useful for improving prediction accuracy for purebred pig breeding farms with a limited population size; second, joint genomic prediction for different populations of the same breed with certain genetic links has the trend to further improve prediction accuracy.     

Hunter Movement and its Role in National Game Bird Surveys

Analysis of sample survey data on the species composition of waterfowl kill for resident and nonresident hunters for provinces of Canada during 1974 and 1975 showed that a successful game bird hunter who hunted in more than one area (degree block) had both a higher average season kill and more successful days of hunting in which one or more birds were bagged, than one who hunted in the same area during the season. Adjustment for days hunted resulted in a higher daily hunting for those who hunted in more than one degree block. However, the higher kill of the successful hunter is attributable more to a larger number of days hunted than to a larger kill per successful day. Also, hunters hunting in more than one degree block had their successful hunting days more evenly spread across the season. The estimates of kill per successful hunter and days hunted for stratified sampling by areas of hunting were considerably more efficient than simple random sampling.     

Codon usage and genome composition

Summary The GC levels of codon third positions from 49 genomes coveering a wide phylogenetic range are linearly correlated with the GC levels of the corresponding genomes. Three different relationships have been found: one for prokaryotes and viruses, one for lower eukaryotes, and one for vertebrates. All points not fitting the first relationship can be brought into quasi coincidence with it when plotted against GC levels of coding sequences.     

Differential organellar inheritance in Passiflora’s (Passifloraceae) subgenera

Four chloroplast (cp), one mitochondrial (mt), and one ribosomal nuclear (ITS) DNA regions were studied in four artificial and one natural interspecific Passiflora hybrids. The ITS results confirmed their hybrid origin and all mtDNAs were maternally inherited. The same, however, was not true for cpDNA. The four hybrids (three artificial and one natural) derived from species of the Passiflora subgenus showed a cpDNA paternal inheritance, while the one involving taxa of the Decaloba subgenus gave evidence of maternal transmission. These results are of significance for the ongoing studies which are being performed on the molecular evolution of this genus and furnish important background for investigations aimed at clarifying the factors which determine cpDNA inheritance.     

Many‐to‐one form‐to‐function mapping weakens parallel morphological evolution

Evolutionary ecologists aim to explain and predict evolutionary change under different selective regimes. Theory suggests that such evolutionary prediction should be more difficult for biomechanical systems in which different trait combinations generate the same functional output: “many‐to‐one mapping.” Many‐to‐one mapping of phenotype to function enables multiple morphological solutions to meet the same adaptive challenges. Therefore, many‐to‐one mapping should undermine parallel morphological evolution, and hence evolutionary predictability, even when selection pressures are shared among populations. Studying 16 replicate pairs of lake‐ and stream‐adapted threespine stickleback (Gasterosteus aculeatus), we quantified three parts of the teleost feeding apparatus and used biomechanical models to calculate their expected functional outputs. The three feeding structures differed in their form‐to‐function relationship from one‐to‐one (lower jaw lever ratio) to increasingly many‐to‐one (buccal suction index, opercular 4‐bar linkage). We tested for (1) weaker linear correlations between phenotype and calculated function, and (2) less parallel evolution across lake‐stream pairs, in the many‐to‐one systems relative to the one‐to‐one system. We confirm both predictions, thus supporting the theoretical expectation that increasing many‐to‐one mapping undermines parallel evolution. Therefore, sole consideration of morphological variation within and among populations might not serve as a proxy for functional variation when multiple adaptive trait combinations exist.     

Regional assignment of catalase (CAT) gene to band 11p13. Association with the aniridia-Wilms' tumor-Gonadoblastoma (WAGR) complex

A gene dosage effect for catalase (CAT) was investigated in three individuals : one with 11p13 deletion, aniridia, ambiguous genitalla, and gonadoblastoma ; one trisomic for 11p with the exception of 11p13; and one trisomic for 11p13. Results were compatible with the assignment of CAT to 11p13 and its linkage with the aniridia-gonadoblastoma or Wilms' tumor complex (WAGR).