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At least 19 recordsLinked to original sources
PubMed2025

The evolution of the plastid genomes in the holoparasitic Balanophoraceae.

The independent transition to a heterotrophic lifestyle in plants drove remarkably convergent evolutionary trajectories, characterized by morphological modifications and reductions in their plastomes. The characteristics of the minimum plastome required for survival, if they exist, remain a topic of debate. The holoparasitic family Balanophoraceae was initially presumed to have entirely lost their plastids, however, recent reports revealed the presence of reduced and aberrant plastids with odd genomes. Among the outstanding features of these genomes are the highest nucleotide composition bias across the tree of life and the only two genetic code changes ever recorded among plants. In this study, we assembled the plastomes from five genera, four of which had never been studied. Major common features include extremely high AT content, the lack of a typical quadripartite structure and extensive size reduction due to gene elimination and genome compaction. The family exhibits multiple gene and intron losses, and a broad range of scenarios regarding the evolution of the plastid trnE, a gene considered essential because of its dual function in tetrapyrrole biosynthesis and translation within the plastid. In addition, phylogenetic analyses suggest that the genus Scybalium is not monophyletic. An evolutionary model for the plastomes of the Balanophoraceae is proposed.

Genome, Plastid↗
PubMed2025

Comparative Phylogenetics Reveal Clade-specific Drivers of Recombination Rate Evolution Across Vertebrates.

Meiotic recombination is an integral cellular process, required for the production of viable gametes. Recombination rate is a fundamental genomic parameter, modulating genomic responses to selection. Our increasingly detailed understanding of its molecular underpinnings raises the prospect that we can gain insight into trait divergence by examining the molecular evolution of recombination genes from a pathway perspective, as in mammals, where protein-coding changes in later stages of the recombination pathway are connected to divergence in intra-clade recombination rate. Here, we leverage increased availability of avian and teleost genomes to reconstruct the evolution of the recombination pathway across two additional vertebrate clades: birds, which have higher and more variable rates of recombination and similar divergence times to mammals, and teleost fish, which have much deeper divergence times. Rates of molecular evolution of recombination genes are highly correlated between vertebrate clades and significantly elevated compared to control panels, suggesting that they experience similar selective pressures. Avian recombination genes are significantly more likely to exhibit signatures of positive selection than other clades, unrestricted to later stages of the pathway. Signatures of positive selection in genes linked to recombination rate variation in mammalian populations and those with signatures of positive selection across the avian phylogeny are highly correlated. In contrast, teleost fish recombination genes have significantly less evidence of positive selection despite high intra-clade recombination rate variability. Gaining clade-specific understanding of patterns of variation in recombination genes can elucidate drivers of recombination rate and thus, factors influencing genetic diversity, selection efficacy, and species divergence.

Animals↗
PubMed2025

Prioritization of causal genes from genome-wide association studies by Bayesian data integration across loci.

MOTIVATION: Genome-wide association studies (GWAS) have identified genetic variants, usually single-nucleotide polymorphisms (SNPs), associated with human traits, including disease and disease risk. These variants (or causal variants in linkage disequilibrium with them) usually affect the regulation or function of a nearby gene. A GWAS locus can span many genes, however, and prioritizing which gene or genes in a locus are most likely to be causal remains a challenge. Better prioritization and prediction of causal genes could reveal disease mechanisms and suggest interventions. RESULTS: We describe a new Bayesian method, termed SigNet for significance networks, that combines information both within and across loci to identify the most likely causal gene at each locus. The SigNet method builds on existing methods that focus on individual loci with evidence from gene distance and expression quantitative trait loci (eQTL) by sharing information across loci using protein-protein and gene regulatory interaction network data. In an application to cardiac electrophysiology with 226 GWAS loci, only 46 (20%) have within-locus evidence from Mendelian genes, protein-coding changes, or colocalization with eQTL signals. At the remaining 180 loci lacking functional information, SigNet selects 56 genes other than the minimum distance gene, equal to 31% of the information-poor loci and 25% of the GWAS loci overall. Assessment by pathway enrichment demonstrates improved performance by SigNet. Review of individual loci shows literature evidence for genes selected by SigNet, including PMP22 as a novel causal gene candidate.

Genome-Wide Association Study↗
PubMed2026

Codon bias variation in Staphylococcus aureus.

BACKGROUND: Staphylococcus aureus causes a multiplicity of human diseases acquired in community and healthcare settings alike around the globe. While most studies focus on coding changes to assess genome evolution and study genetic adaptation, interrogation of silent mutations in the form of synonymous codon usage bias is less well-studied. As such, understanding of patterns in codon bias at the gene and genome levels, and how codon bias impacts protein expression in S. aureus remains incomplete. METHODS: The codon bias of 2,565 protein encoding genes from NCTC 8325 was queried against all publicly available closed S. aureus genomes. Using public BioSample data, genomes were sorted by disease state, submitting institution, and collection site. Codon bias was assessed at the level of gene and genome using the codon adaptation index (CAI), calculated using 30S and 50S ribosomal genes. Gene set enrichment analysis was applied to determine associations between physiological functions, CAI gene scores, and interquartile ranges. CAI scores were also compared to an in vitro S. aureus proteomics database to correlate codon bias and protein expression. RESULTS: CAI scores varied within and between isolates at the gene and genome levels. Genes with ribosome-associated functions were most enriched among high CAI genes, and had low CAI interquartile ranges (IQR), suggesting selective pressure to maintain high expression of these genes across all S. aureus isolates. Genome sequences submitted by Aga Khan University Hospital, Nairobi, Kenya were most different from others. For the LAC USA 300 strain, CAI and protein expression were moderately positively correlated (cor&#x2009;=&#x2009;0.534, p&#x2009;<&#x2009;2.2e-16). CONCLUSIONS: Codon bias in S. aureus was shown to vary between gene, and to be a source of genetic variation between isolates; CAI and in vitro protein expression were positively correlated.

Staphylococcus aureus↗
PubMed1979

Some correlates of language deterioration in severely and profoundly retarded long-term institutionalized residents.

Progress or deterioration in language use was observed in two samples of retarded institutionalized residents. One sample was observed twice, and the other three times, at 5-year intervals. We coded change in language use as noncommunicating, regressed irregular, stable, or progressed. Change in language use was found to be related to two indicators of intellectual capacity. Central nervous system involvement may play a part in irregular or totally absent communication. Institutional policies regarding transfer of residents also affect the apparent language deficit in longer-term residents.

Age Factors↗
PubMed1979

Coding of incremental changes in skin temperature by single warm fibers in the monkey.

1. Experiments were designed to answer the question: how well does a single warm fiber innervating the glabrous skin of the monkey's hand resolve incremental changes in the intensity of near-rectangular warming pulses applied to the fiber's receptive field? 2. In these experiments the measure of the warm fiber's capacity to resolve incremental changes in the intensity of successive warming pulses was termed the discriminable stimulus increment (DSI). The DSI is defined as that incremental difference in the intensity of a pair of warming pulses that could be resolved correctly, with a probability of 0.75, by comparing the fiber's responses to these two stimuli. In the specified conditions of the experiment, DSI = 0.67 sigma delta tau/(dR/dI) where sigma delta tau is the standard deviation of the difference in responses of the fiber to pairs of stimuli, and dr/dI is the fiber's sensitivity to incremental stimulus change. (dr/dI) was experimentally determined as the mean rate of change of the fiber's responses to incremental changes in the intensity of the warming pulse. 3. The DSI, as defined above, assumes that the basis for differentiating the stimuli in each pair was that the larger response in the fiber was in each instance generated by the more intense stimulus. A more general form of the DSI was also developed and used to examine the effects on intensity resolution of different discrimination rules that the brain might use. 4. In the experimental analysis the response measure of each warm fiber was the cumulative impulse count over successively longer segments of the stimulus period. With short integration intervals the DSI was high (i.e., intensity resolution was poor), but typically the DSI fell to a plateau level within 2.0--2.5 s of the onset of the warming stimulus. 5. The DSI was measured on 23 warm fibers in Macaca nemestrina for warming pulses with intensities of 0, 2, 4, 6, and 8 degrees C, at T-base levels of 29, 34 (near normal temperature of palmar skin), and 39 degrees C. For most observations the intensity resolution possible from the responses of single warm fibers, measured over this wide variety of stimulus conditions, was less than is achieved by the human observer trained to differentiate comparable warming pulses applied to the skin of the thenar eminence.

Adaptation, Physiological↗
PubMed1979

Evolutionary nucleotide replacements in DNA.

With the increasing availability of analytical information on mRNA molecules, it is now possible to compare homologous nucleotide sequences from different organisms and to draw conclusions about their evolution. Such comparisons have shown that silent changes in codons occur more frequently than nucleotide replacements that produce changes in amino acid sequences (code-altering changes). Furthermore, there is an important difference between amino acid sequence comparisons and nucleotide sequence comparisons. The former show only differences in amino acid residues, but the latter show several types of differences when corresponding codons are compared. Single-base replacements may be degenerate (silent) or expressed as amino acid replacements. Two-base codon changes may be degenerate, single-base changes, or be visible as such. Three-base codon changes may be degenerate (involving serine), simulate either single-base or two-base changes or be visible as such. All nine types of change are found in comparisons of genes from the viruses phi X174 and G4. The relative numbers of these nine types as based on all possible interchanges between all 61 amino acid codons were listed by Holmquist et al. and are shown in Table 1. We discuss these results in the light of the significance of nucleotide changes in molecular evolution.

Base Sequence↗
PubMed2025

Single-Cell Splicing Isoform Atlas of the Adult Human Heart and Heart Failure.

BACKGROUND: Alternative splicing plays crucial roles in normal heart development and cardiac disease by influencing protein-coding sequences, functional domains, and molecular networks. However, a detailed characterization of the human heart isoform landscape remains incomplete. METHODS: Leveraging long-read single-nucleus RNA sequencing and computational analysis, we dissected full-length isoform heterogeneities, expression patterns, and usage shifts across cell types, cell states, and cardiac conditions of the adult left ventricle. We applied in silico approaches to assess the functional relevance of identified isoforms; validated isoform compositions of representative cardiac genes using reverse transcription quantitative polymerase chain reaction and targeted amplicon sequencing; and developed a web server for interactive navigation of our results. RESULTS: The data revealed that isoform heterogeneity is widespread in the cardiac cellular system, serving as a posttranscriptional buffer mechanism that calibrates the molecule reservoirs in human hearts. In healthy left ventricles, &#x2248;30% of cell type-specific genes were polyform, using multiple isoforms tailored to cell type-specific programs. Among ubiquitously expressed genes, >300 showed differential isoform usage with cell type specificity in normal hearts. Comparisons of cardiomyocytes across conditions uncovered 379 genes with marked isoform usage shifts, most of which are predicted to change protein coding outcomes through direct changes in protein coding sequences and switches between intron retention and non-protein-coding biotypes. In contrast, cell state-specific programs tend to operate on monoform genes associated with changes among cell states. In addition, our data revealed heart failure-associated differential isoform usage events in stromal and immune cell types in the cardiac microenvironment. CONCLUSIONS: We present a comprehensive atlas of splicing isoforms in the normal adult heart and heart failure through long-read single-nucleus RNA sequencing and computational analyses. The results suggest crucial roles of isoforms in buffering core cellular programs and contributing to disease-associated cell states. The full-length details of these cell-specific isoforms serve as an important reference for downstream translational and mechanistic studies and are available on our online data portal at https://github.com/gaolabtools/heart-isoform-atlas.

Humans↗
PubMed1977

Vertical eye movement related unit activity in the rostral mesencephalic reticular formation of the alert monkey.

Eye movement related unit activity was recorded in the rostral mesencephalic reticular formation (MRF) of the alert monkey. Most units (78 out of 117) were activated with a short activity burst starting before the eye movement and were otherwise silent. The activity was the same whether movements occurred spontaneously in the light or dark, or were fast phases of vestibular or optokinetic nystagmus, and could be related to parameters of a vector representing the eye movement such as amplitude, position changes along certain planes or direction of movements. Units coding position changes or direction of movement had their preferred direction always close to the vertical. Other units (18 out of 117) showed some tonic activity, which was also only related to vertical eye position. It is suggested that this region of the rostral MRF acts an an immediate supranuclear structure, mediating eye movements in the vertical plane.

Action Potentials↗
PubMed1978

Legalized abortion: effect on national trends of maternal and abortion-related mortality (1940 through 1976).

Both non-abortion-related maternal and abortion-related mortality declined prior to the Supreme Court decisions of 1973. In order to determine the effect of legalized abortion on maternal mortality, we have analyzed the secular trends in national abortion mortality ratios for 1940 through 1976, compared the trends to those maternal mortality ratios, and hypothesized reasons for differences between these trends. Between 1940 and 1950 and after 1965, deaths from abortion declined more rapidly than deaths from other causes associated with childbirth. However, between 1951 and 1965, maternal mortality related to pregnancy of childbirth declined more rapidly than abortion-related mortality. Five possible explanations exist for the more rapid decline in abortion deaths since 1965--selected underreporting, changes in coding practices, improved safety of illegal abortion, introduction of more effective contraception, and increased availability of legal abortion. We consider the last two explanations as the most likely reasons for the accelerated decline in abortion-related deaths.

Abortion, Legal↗