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Heterochromatic features of an 11-megabase transgene in brain cells.

Transgenic mice provide a remarkable experimental setting for the study of nuclear architecture. The three-dimensional localization and fine structure of a foreign DNA within the mouse genome can be conveniently followed by using high-resolution in situ hybridization. Foreign DNAs designed with specific characteristics, such as base bias, sequence motif(s), and size can stably integrate into finite positions on host chromosomes. Thus the relative importance of each of these characteristics in determining the three-dimensional nuclear position and the detailed morphology of the transgene can be evaluated in different cell types. The aim of this study was to evaluate a transgene with sequence characteristics that might contribute to the de novo formation of heterochromatin in interphase nuclei. The structure of a phenotypically silent 11-megabase transgene, containing tandem repeats of beta-globin-pBR sequences integrated into the peritelomeric region of both mouse chromosome 3 homologs, was determined in adult brain cells. Neurons that are largely euchromatic were especially informative in three-dimensional studies of transgene position. The two transgenic loci behaved much like centromeric or paracentromeric A + T-rich satellite DNAs of comparable length from a single chromosome; one or both transgene domains localized together with centromeric satellite DNA on the nucleolus. This is an unusual nuclear position for a telomeric or chromosome arm region that does not contain a substantial amount of constitutively heterochromatic satellite DNA. G + C richness did not prevent these regions from assembling as dense heterochromatic bodies of approximately 1 micron3 in volume. Ultrastructurally, transgenic domains were often intimately connected with constitutive heterochromatin and were highly condensed. Labeled supercoils, formed by a discrete approximately 250-nm-wide fiber, were observed in oblique thin sections through the center of the domain. The structural data were consistent with negligible transcriptional activity detected for this locus, as well as the predicted conformation of constitutive heterochromatin. Interestingly, in transgenic but not control mice, a substantial number of large neurons, including approximately 30% of cerebellar Purkinje cells, showed excessive invaginations of the nuclear membrane.

Animals↗

Intron positions correlate with module boundaries in ancient proteins.

We analyze the three-dimensional structure of proteins by a computer program that finds regions of sequence that contain module boundaries, defining a module as a segment of polypeptide chain bounded in space by a specific given distance. The program defines a set of "linker regions" that have the property that if an intron were to be placed into each linker region, the protein would be dissected into a set of modules all less than the specified diameter. We test a set of 32 proteins, all of ancient origin, and a corresponding set of 570 intron positions, to ask if there is a statistically significant excess of intron positions within the linker regions. For 28-A modules, a standard size used historically, we find such an excess, with P < 0.003. This correlation is neither due to a compositional or sequence bias in the linker regions nor to a surface bias in intron positions. Furthermore, a subset of 20 introns, which can be putatively identified as old, lies even more explicitly within the linker regions, with P < 0.0003. Thus, there is a strong correlation between intron positions and three-dimensional structural elements of ancient proteins as expected by the introns-early approach. We then study a range of module diameters and show that, as the diameter varies, significant peaks of correlation appear for module diameters centered at 21.7, 27.6, and 32.9 A. These preferred module diameters roughly correspond to predicted exon sizes of 15, 22, and 30 residues. Thus, there are significant correlations between introns, modules, and a quantized pattern of the lengths of polypeptide chains, which is the prediction of the "Exon Theory of Genes."

Algorithms↗

Loss of a primordial identity element for a mammalian mitochondrial aminoacylation system.

In mammalian mitochondria the translational machinery is of dual origin with tRNAs encoded by a simplified and rapidly evolving mitochondrial (mt) genome and aminoacyl-tRNA synthetases (aaRS) coded by the nuclear genome, and imported. Mt-tRNAs are atypical with biased sequences, size variations in loops and stems, and absence of residues forming classical tertiary interactions, whereas synthetases appear typical. This raises questions about identity elements in mt-tRNAs and adaptation of their cognate mt-aaRSs. We have explored here the human mt-aspartate system in which a prokaryotic-type AspRS, highly similar to the Escherichia coli enzyme, recognizes a bizarre tRNA(Asp). Analysis of human mt-tRNA(Asp) transcripts confirms the identity role of the GUC anticodon as in other aspartylation systems but reveals the non-involvement of position 73. This position is otherwise known as the site of a universally conserved major aspartate identity element, G73, also known as a primordial identity signal. In mt-tRNA(Asp), position 73 can be occupied by any of the four nucleotides without affecting aspartylation. Sequence alignments of various AspRSs allowed placing Gly-269 at a position occupied by Asp-220, the residue contacting G73 in the crystallographic structure of E. coli AspRS-tRNA(Asp) complex. Replacing this glycine by an aspartate renders human mt-AspRS more discriminative to G73. Restriction in the aspartylation identity set, driven by a rapid mutagenic rate of the mt-genome, suggests a reverse evolution of the mt-tRNA(Asp) identity elements in regard to its bacterial ancestor.

Acylation↗

Effect of variation in seat tube angle at different seat heights on submaximal cycling performance in man.

The effect of seat tube angle at selected seat heights (96, 100 and 104% trochanteric height) on heart rate, VO2 and lower limb kinematics was evaluated in 14 competitive male road racing cyclists during discontinuous submaximal exercise (200 W) on an air-resistance ergometer at seat tube angles of 68, 74 and 80 degrees. The tests were randomized to complete the nine combinations (three seat heights, three tube angles) in opposite directions from a starting tube angle of 74 degrees and 100% trochanteric height to avoid any time or sequence bias. Power efficiency was calculated for each combination from work done and VO2. All results were analysed using ANOVA for repeated measures. At a seat tube angle of 80 degrees, mean VO2 was significantly lower and power efficiency significantly higher compared with an angle of 74 degrees at all three seat heights, while heart rate was significantly lower only at a seat height equal to trochanteric height. At a seat tube angle of 74 degrees, mean VO2 and heart rate were significantly lower and power efficiency significantly higher compared with an angle of 68 degrees at all three seat heights. Hip range of movement and maximum and minimum hip angle were significantly less at an angle of 80 degrees compared with 68 degrees. Further biomechanical analysis suggested that the improvement in cycling efficiency observed at steeper seat tube angles was produced in part by the resultant altered ankling pattern of the cyclist.

Adult↗

Kinetic parameter estimation from SPECT cone-beam projection measurements.

Kinetic parameters are commonly estimated from dynamically acquired nuclear medicine data by first reconstructing a dynamic sequence of images and subsequently fitting the parameters to time-activity curves generated from regions of interest overlaid upon the image sequence. Biased estimates can result from images reconstructed using inconsistent projections of a time-varying distribution of radiopharmaceutical acquired by a rotating SPECT system. If the SPECT data are acquired using cone-beam collimators wherein the gantry rotates so that the focal point of the collimators always remains in a plane, additional biases can arise from images reconstructed using insufficient, as well as truncated, projection samples. To overcome these problems we have investigated the estimation of kinetic parameters directly from SPECT cone-beam projection data by modelling the data acquisition process. To accomplish this it was necessary to parametrize the spatial and temporal distribution of the radiopharmaceutical within the SPECT field of view. In a simulated chest image volume, kinetic parameters were estimated for simple one-compartment models for four myocardial regions of interest. Myocardial uptake and washout parameters estimated by conventional analysis of noiseless simulated cone-beam data had biases ranging between 3-26% and 0-28%, respectively. Parameters estimated directly from the noiseless projection data were unbiased as expected, since the model used for fitting was faithful to the simulation. Statistical uncertainties of parameter estimates for 10,000,000 events ranged between 0.2-9% for the uptake parameters and between 0.3-6% for the washout parameters.

Heart↗

Phylogenomic Analyses Reveal that Panguiarchaeum Is a Clade of Genome-Reduced Asgard Archaea Within the Njordarchaeia.

The Asgard archaea are a diverse archaeal phylum important for our understanding of cellular evolution because they include the lineage that gave rise to eukaryotes. Recent phylogenomic work has focused on characterizing the diversity of Asgard archaea in an effort to identify the closest extant relatives of eukaryotes. However, resolving archaeal phylogeny is challenging, and the positions of 2 recently described lineages-Njordarchaeales and Panguiarchaeales-are uncertain, in ways that directly bear on hypotheses of early evolution. In initial phylogenetic analyses, these lineages branched either with Asgards or with the distantly related Korarchaeota, and it has been suggested that their genomes may be affected by metagenomic contamination. Resolving this debate is important because these clades include genome-reduced lineages that may help inform our understanding of the evolution of symbiosis within Asgard archaea. Here, we performed phylogenetic analyses revealing that the Njordarchaeales and Panguiarchaeales constitute the new class Njordarchaeia within Asgard archaea. We found no evidence of metagenomic contamination affecting phylogenetic analyses. Njordarchaeia exhibit hallmarks of adaptations to (hyper-)thermophilic lifestyles, including biased sequence compositions that can induce phylogenetic artifacts unless adequately modeled. Panguiarchaeum is metabolically distinct from its relatives, with reduced metabolic potential and various auxotrophies. Phylogenetic reconciliation recovers a complex common ancestor of Asgard archaea that encoded the Wood-Ljungdahl pathway. The subsequent loss of this pathway during the reductive evolution of Panguiarchaeum may have been associated with the switch to a symbiotic lifestyle, potentially based on H2-syntrophy. Thus, Panguiarchaeum may contain the first obligate symbionts within Asgard archaea besides the lineage leading to eukaryotes.

Phylogeny↗

The unusual gene organization of Leishmania major chromosome 1 may reflect novel transcription processes.

The complete chromosomal sequence for chromosome 1 from Leishmania major Friedlin predicts that this chromosome has 79 protein-coding genes. Surprisingly, the first 29 of these genes are encoded in tandem on one strand of DNA, and the remaining 50 genes are encoded in tandem on the other. No RNA polymerase promoters, centromeric sequences or origins of DNA replication have been identified in the DNA sequence. Statistical analyses of the nucleotide content reveal striking, non-random, sequence-biases that are correlated with genome organization. Analysis of coding regions suggests that novel transcription processes in Leishmania may be responsible for the nucleotide bias, which in turn affects gene organization in the chromosome. These results also suggest that the region between the two units of in-tandem genes is a candidate for an origin of DNA replication.

Algorithms↗

Adaptive sex differences in growth of pre-ovulation oocytes in a passerine bird.

Maternal modification of offspring sex in birds has strong fitness consequences, however the mechanisms by which female birds can bias sex of their progeny in close concordance with the environment of breeding are not known. In recently established populations of house finches (Carpodacus mexicanus), breeding females lay a sex-biased sequence of eggs when ambient temperature causes early onset of incubation. We studied the mechanisms behind close association of incubation and sex-determination strategies in this species and discovered that pre-ovulation oocytes that produce males and females differed strongly in the temporal patterns of proliferation and growth. In turn, sex-specific exposure of oocytes to maternal secretion of prolactin and androgens produced distinct accumulation of maternal steroids in oocyte yolks in relation to oocyte proliferation order. These findings suggest that sex difference in oocyte growth and egg-laying sequence is an adaptive outcome of hormonal constraints imposed by the overlap of early incubation and oogenesis in this population, and that the close integration of maternal incubation, oocytes' sex-determination and growth might be under control of the same hormonal mechanism. We further document that population establishment and the evolution of these maternal strategies is facilitated by their strong effects on female and offspring fitness in a recently established part of the species range.

Adaptation, Physiological↗

Gas exchange and lung mechanics during percutaneous transtracheal ventilation in an unparalyzed canine model.

OBJECTIVE: To compare the efficacy of percutaneous transtracheal ventilation (PTV) in the unparalyzed state with that in the paralyzed state using a sedated nonobstructed canine model. METHODS: Eight mongrel dogs (16.8-32 kg) were anesthetized, instrumented, and placed in a volume plethysmograph. Anesthesia was achieved with pentobarbital sodium (up to 30 mg/kg). The spontaneous respiratory drive was kept intact. PTV was performed using a 13-ga transtracheal catheter and compressed air at 45 psi at an I:E ratio of 1:3 (15 breaths/min). Each dog was sequentially ventilated in both the paralyzed and unparalyzed states. The paralyzed/unparalyzed sequence was alternated among the animals to avoid sequence bias. Paralysis was achieved with succinylcholine (0.1 mg/kg bolus and 0.01 mg/kg/min drip). Reversal of paralysis was achieved by discontinuing the succinylcholine infusion. Key variables, including arterial blood gas, tidal volume, and pulmonary mechanics, were measured and compared for the paralyzed and unparalyzed states. RESULTS: Gas exchanges and lung mechanics were similar between the unparalyzed and paralyzed states. There was no significant difference in mean pH, pCO2, pO2, tidal volume, or peak inspiratory transpulmonary pressure. There was also no significant difference in pulmonary resistance or pulmonary compliance. CONCLUSION: In a sedated nonobstructed canine model, PTV is as efficacious in the unparalyzed state as it is in the paralyzed state. The lung mechanics are also similar in the 2 states. These data suggest that it may be unnecessary to induce paralysis when using PTV for emergency ventilation in the heavily sedated state.

Animals↗

[Assessment of research methodology on diagnostic laboratory test in Revista Clínica Española and Medicina Clínica].

BASIS: The identification of the methodological limitations of diagnostic research on laboratory tests is the basis in order to guide its enhancement and facilitate the application of the results to the clinical decisions. METHODS: Seventeen articles published in Revista Clínica Española and Medicina Clínica from 1997 to 2000 were analyzed, in which the sensitivity and specificity of a diagnostic laboratory test were determined. Some standardized criteria of methodological quality were independently applied by three investigators. RESULTS: A high frequency in the fulfillment of some key methodological aspects was observed: adequate description of the standard of reference (88%), of the test investigated (88%), of the clinical sample evaluated (71%), and of the prevention of the sequence bias (82%). The assessment of indeterminate results (12%), the test reproducibility (12%), or the description of the origin of the evaluated population (6%) were infrequent. CONCLUSION: The methodological defects of diagnostic laboratory research could be prevented through the collaboration with clinical services and with simple modifications of the trial's designs.

Clinical Laboratory Techniques↗

Mariner mutagenesis of Brucella melitensis reveals genes with previously uncharacterized roles in virulence and survival.

BACKGROUND: Random gene inactivation used to identify cellular functions associated with virulence and survival of Brucella spp has relied heavily upon the use of the transposon Tn5 that integrates at G/C base pairs. Transposons of the mariner family do not require species-specific host factors for efficient transposition, integrate nonspecifically at T/A base pairs, and, at a minimum, provide an alternative approach for gene discovery. In this study, plasmid vector pSC189, containing both the hyperactive transposase C9 and transposon terminal inverted repeats flanking a kanamycin resistance gene, were used to deliver Himar1 transposable element into the B. melitensis genome. Conjugation was performed efficiently and rapidly in less than one generation in order to minimize the formation of siblings while assuring the highest level of genome coverage. RESULTS: Although previously identified groups or classes of genes required for virulence and survival were represented in the screen, additional novel identifications were revealed and may be attributable to the difference in insertion sequence biases of the two transposons. Mutants identified using a fluorescence-based macrophage screen were further evaluated using gentamicin-based protection assay in macrophages, survival in the mouse splenic clearance model and growth in vitro to identify mutants with reduced growth rates. CONCLUSION: The identification of novel genes within previously described groups was expected, and nearly two-thirds of the 95 genes had not been previously reported as contributing to survival and virulence using random Tn5-based mutagenesis. The results of this work provide added insight with regard to the regulatory elements, nutritional demands and mechanisms required for efficient intracellular growth and survival of the organism.

Animals↗

A method to assess compositional bias in biological sequences and its application to prion-like glutamine/asparagine-rich domains in eukaryotic proteomes.

We have derived a novel method to assess compositional biases in biological sequences, which is based on finding the lowest-probability subsequences for a given residue-type set. As a case study, the distribution of prion-like glutamine/asparagine-rich ((Q+N)-rich) domains (which are linked to amyloidogenesis) was assessed for budding and fission yeasts and four other eukaryotes. We find more than 170 prion-like (Q+N)-rich regions in budding yeast, and, strikingly, many fewer in fission yeast. Also, some residues, such as tryptophan or isoleucine, are unlikely to form biased regions in any eukaryotic proteome.

Amino Acid Motifs↗

A new method for RAPD primers selection based on primer bias in nucleotide sequence data.

Sequence analysis has proved that decamer nucleotides, used as primers of RAPD (random amplified polymorphic DNA), differ with each other greatly in number of annealing sites in the Arabidopsis thaliana genome. It is called the 'primer bias' by the authors. The biased primers produce a highly variable number of amplicons by polymerase chain reaction (PCR). The number of amplicons is proved to correlate with the number of annealing sites. Therefore, a statistical method is proposed for selecting efficient primers based on the primer bias in the genomic sequence. The method was tested by experiment in A. thaliana genome, and the results demonstrate that the method outperforms routine methods and can substantially increase the efficiency of RAPD methodologies. We also proved that the expressed sequence tags (ESTs) show a highly coincident bias pattern with that of the whole genomic sequence, and can therefore be used to assess efficiencies of primers for species whose genomic sequence data are currently unknown.

Arabidopsis↗

DNA variation in the metallothionein genes in wild rice Oryza rufipogon: relationship between DNA sequence polymorphism, codon bias and gene expression.

This study examines the relationship between DNA sequence variation and level of gene expression in four metallothionein genes from wild rice Oryza rufipogon. The nucleotide diversity was 0.0028 to 0.0117 over the entire coding and non-coding region, and it was negatively correlated with gene expression for three type 2 metallothionein genes. In contrast, codon bias and percent of preferred codons correlated positively with gene expression. These results indicate that the intensity of natural selection depends on the level of gene expression, which in turn shapes the level of nucleotide polymorphism. In addition, significant linkage disequilibria were frequent between the metallothionein genes, although significance was not confirmed after multiple test correction. This result suggests that metallothionein genes expressed at different levels are epistatic with respect to fitness, and that gene expression is an important factor determining level of DNA polymorphism.

Amino Acid Sequence↗

The orientation bias of Chi sequences is a general tendency of G-rich oligomers.

The Chi sequences are specific oligomers that stimulate DNA repair by homologous recombination, and are different sequences in each organism. Approximately 75% of the copies of the Chi sequence (5'-GCTGGTGG-3') of Escherichia coli reside on the leading strand, and this orientation bias is often believed to be a consequence of the biological role of Chi sequences as the signal sequence of RecBCD pathway in DNA replication. However, our computer analysis found that many G-rich oligomers also show this asymmetric orientation pattern. The shift in the Chi orientation bias appears around the replication origin and terminus, but these locations are also coincident with the shift points in GC content or GC skew. We conducted the same analysis with the genome of Bacillus subtilis, and found that in addition to Chi, other G-rich oligomers show similar asymmetric orientation patterns, whose shift points were coincident with those of the GC skew. However, the genome of Haemophilus influenzae Rd, whose GC skew is not so pronounced, does not clearly show asymmetric orientation patterns of Chi or other G-rich oligomers. These results lead us to suggest that the uneven distribution of the Chi orientation between the two strands of the double helix is mostly due to the uneven distribution of G content (GC skew) and that the replication-related function of Chi sequences is not the primary factor responsible for the evolutionary pressure causing the orientation bias.

Bacillus subtilis↗

[High-level expression of phenylalanine ammonia-lyase in Lactococcus Lactis via synthesized sequence based on bias codons].

To construct a safer and more efficient gene engineering Lactococcus Lactis for expressing phenylalaine ammonia lyase (PAL) which will be benefit for PKU therapy, pal cDNA of Parsly and synthesized sequence based on Lactococcus Lactis bias codons were recombined into two Lactococcus Lactis NICE systems. The activities of the expressed PAL were detected, and the effect of Lactococcus Lactis bias codons on the expression of exterior protein was analyzed. The results showed that the expression level of PAL was increased by using Lactococcus Lactis bias codons in both Lactococcus Lactis NICE systems. Through which several safer andmore efficient strains of the gene engineering Lactococcus Lactis were obtained.

Cloning, Molecular↗

Structural features of multiple nifH-like sequences and very biased codon usage in nitrogenase genes of Clostridium pasteurianum.

The structural gene (nifH1) encoding the nitrogenase iron protein of Clostridium pasteurianum has been cloned and sequenced. It is located on a 4-kilobase EcoRI fragment (cloned into pBR325) that also contains a portion of nifD and another nifH-like sequence (nifH2). C. pasteurianum nifH1 encodes a polypeptide (273 amino acids) identical to that of the isolated iron protein, indicating that the smaller size of the C. pasteurianum iron protein does not result from posttranslational processing. The 5' flanking region of nifH1 or nifH2 does not contain the nif promoter sequences found in several gram-negative bacteria. Instead, a sequence resembling the Escherichia coli consensus promoter (TTGACA-N17-TATAAT) is present before C. pasteurianum nifH2, and a TATAAT sequence is present before C pasteurianum nifH1. Codon usage in nifH1, nifH2, and nifD (partial) is very biased. A preference for A or U in the third position of the codons is seen. nifH2 could encode a protein of 272 amino acid residues, which differs from the iron protein (nifH1 product) in 23 amino acid residues (8%). Another nifH-like sequence (nifH3) is located on a nonadjacent EcoRI fragment and has been partially sequenced. C. pasteurianum nifH2 and nifH3 may encode proteins having several amino acids that are conserved in other proteins but not in C. pasteurianum iron protein, suggesting a possible role for the multiple nifH-like sequences of C. pasteurianum in the evolution of nifH. Among the nine sequenced iron proteins, only the C. pasteurianum protein lacks a conserved lysine residue which is near the extended C terminus of the other iron proteins. The absence of this positive charge in the C. pasteurianum iron protein might affect the cross-reactivity of the protein in heterologous systems.

Amino Acid Sequence↗