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PubMed1990

Protein structure and function at low temperatures.

Proteins represent the major components in the living cell that provide the whole repertoire of constituents of cellular organization and metabolism. In the process of evolution, adaptation to extreme conditions mainly referred to temperature, pH and low water activity. With respect to life at low temperatures, effects on protein structure, protein stability and protein folding need consideration. The sequences and topologies of proteins from psychrophilic, mesophilic and thermophilic organisms are found to be highly homologous. Commonly, adaptive changes refer to multiple alterations of the amino acid sequence, which presently cannot be correlated with specific changes of structure and stability; so far it has not been possible to attribute specific increments in the free energy of stabilization to well-defined amino-acid exchanges in an unambiguous way. The stability of proteins is limited at high and low temperatures. Their expression and self-organization may be accomplished under conditions strongly deviating from optimum growth conditions. Molecular adaptation to extremes of temperature seems to be accompanied by a flattening of the temperature profile of the free energy of stabilization. In principle, the free energy of stabilization of proteins is small compared to the total molecular energy. As a consequence, molecular adaptation to extremes of physical conditions only requires marginal alterations of the intermolecular interactions and packing density. Careful statistical and structural analyses indicate that altering the number of ion pairs and hydrophobic interactions allows the flexibility of proteins to be adjusted so that full catalytic function is maintained at varying temperatures.

Drug Stability↗
PubMed2026

Patterns of Drug Resistance, Drug Resistance Conferring Mutations and Genomic DNA Methylation Revealed in Mycobacterium tuberculosis From South Africa.

Tuberculosis remains a major public health threat globally, with drug-resistant strains undermining treatment efficacy. We analyzed 126 Mycobacterium tuberculosis (M. tuberculosis) isolates with diverse drug resistance spectra and selected 35 for whole genome sequencing (WGS) using Illumina NextSeq, SMRT PacBio Onso and SMRT PacBio Revio sequencing platforms. The study aimed to characterize drug resistance profiles, compare short- and long-read sequencing performance, identify lineages among South African isolates, detect known drug resistance mutations and their lineage-specific patterns, and utilize long-read SMRT platforms for epigenetic profiling. Multiple drug resistance mutations were identified, some lineage-specific, and notably, East-African-Indian (EAI) Lineage 1 isolates often considered less pathogenic, showed significant potential for multidrug-resistance development, including higher fluoroquinolone resistance as compared to other lineages. Three DNA motifs with methylated adenines, namely CACGCaG, CtCCaG and GaTNNNNRtAC, were detected, with methylation patterns varying by lineage and strain due to mutations in the corresponding methyltransferases (MTases). A particularly notable finding was the stable maintenance of a genetic heterogeneity in the mamB MTase, performing methylation at CACGCaG motifs. These results highlight the combined role of genetic and epigenetic variation in M. tuberculosis adaptive evolution and underscore the value of integrating long-read sequencing into TB surveillance and research.

Mycobacterium tuberculosis↗
PubMed1992

Sexually antagonistic genes: experimental evidence.

When selection differs between the sexes, a mutation beneficial to one sex may be harmful to the other (sexually antagonistic). Because the sexes share a common gene pool, selection in one sex can interfere with the other's adaptive evolution. Theory predicts that sexually antagonistic mutations should accumulate in tight linkage with a new sex-determining gene, even when the harm to benefit ratio is high. Genetic markers and artificial selection were used to make a pair of autosomal genes segregate like a new pair of sex-determining genes in a Drosophila melanogaster model system. A 29-generation study provides experimental evidence that sexually antagonistic genes may be common in nature and will accumulate in response to a new sex-determining gene.

Animals↗
PubMed1994

Phylogenetic analysis of sequences from diverse bacteria with homology to the Escherichia coli rho gene.

Genes from Pseudomonas fluorescens, Chromatium vinosum, Micrococcus luteus, Deinococcus radiodurans, and Thermotoga maritima with homology to the Escherichia coli rho gene were cloned and sequenced, and their sequences were compared with other available sequences. The species for all of the compared sequences are members of five bacterial phyla, including Thermotogales, the most deeply diverged phylum. This suggests that a rho-like gene is ubiquitous in the Bacteria and was present in their common ancestor. The comparative analysis revealed that the Rho homologs are highly conserved, exhibiting a minimum identity of 50% of their amino acid residues in pairwise comparisons. The ATP-binding domain had a particularly high degree of conservation, consisting of some blocks with sequences of residues that are very similar to segments of the alpha and beta subunits of F1-ATPase and of other blocks with sequences that are unique to Rho. The RNA-binding domain is more diverged than the ATP-binding domain. However, one of its most highly conserved segments includes a RNP1-like sequence, which is known to be involved in RNA binding. Overall, the degree of similarity is lowest in the first 50 residues (the first half of the RNA-binding domain), in the putative connector region between the RNA-binding and the ATP-binding domains, and in the last 50 residues of the polypeptide. Since functionally defective mutants for E. coli Rho exist in all three of these segments, they represent important parts of Rho that have undergone adaptive evolution.

Adenosine Triphosphate↗
PubMed1992

Heterogeneity of the mutation rates of influenza A viruses: isolation of mutator mutants.

The rates of mutation to the mar (monoclonal antibody-resistant) genotype of individual influenza virus plaque isolates, obtained from a stock generated after two successive cloning steps, have been determined by the fluctuation test. When a random sample of 60 clones was analyzed, 7 contained a proportion of mar mutants significantly higher than the average, and among them, 2 showed a mutation rate two to three times higher than the average value obtained for the virus population when the hemagglutinin-specific monoclonal antibody 2G10 was used. In order to look for mutants with higher mutation rates, a systematic search was carried out with a nonmutagenized virus stock, and several clones with increased mutation rates were isolated. One of them (mut43) was characterized further and was shown to have a mutation rate three to four times higher than that of the virus population at the sites defined by two nonoverlapping, hemagglutinin-specific monoclonal antibodies as well as at the site defined by a neuraminidase-specific monoclonal antibody. These results indicate that the mutation rate of an influenza virus is a weighted average of the contributions of a heterogeneous population. The consequences of this fact for the adaptive evolution of influenza viruses are discussed.

Antibodies, Monoclonal↗
PubMed2026

Chloroplast genome comparative analysis and phylogenetic relationships of 15 Syringa species (Oleaceae).

Syringa is a crucial shrub genus in the family Oleaceae, which has significant ornamental, economic, and medicinal value. However, research on the chloroplast genome (CPG) phylogeny and lineage diversification of this genus remains limited. In this study, all 15 Syringa CPGs exhibited a characteristic quadripartite structure, with genome lengths ranging from 154,019-158,020 bp. These CPGs were highly conserved and moderately differentiated, each containing 130-132 genes. Analysis of inverted repeat (IR) boundaries indicated structural conservation, with six genes: rps19, rpl2, ycf1, trnN, ndhF, and trnH present at the IR/single-copy (SC) junctions. The small single copy (SSC) region displayed greater sequence variability than the IR regions. ycf1, ndhH, trnL-rpl32, ndhF-ycf1, and rbcL-accD were identified as potential molecular markers and rps11, ycf2, and ycf4 may have contributed to the adaptive evolution of Syringa. Phylogenetic reconstruction based on whole CPG data supported the monophyly of the 15 species, which were divided into three distinct subclades. Molecular dating estimated that Syringa diverged from its sister genus approximately 58 million years ago, with most Syringa species diversifying further approximately 47.49 million years ago during the Eocene. Our findings will hopefully stimulate further studies on this genus that may enhance biodiversity knowledge.

Journal Article↗
PubMed2026

Chromosome-Level Genome Assembly of Solanum carolinense.

Horsenettle (Solanum carolinense L.) is a noxious weed widely distributed across North America and increasingly invasive in other regions. Its strong environmental adaptability, complex defense strategies, and distinctive reproductive traits make it an important model for studying plant-herbivore coevolution. However, the absence of high-quality genomic resources has limited deeper investigation into its adaptive evolutionary mechanisms. In this study, we generated a chromosome-level reference genome assembly for S. carolinense using an integrated approach combining PacBio HiFi long-read sequencing, Illumina second-generation sequencing, and Hi-C chromatin interaction scaffolding. The final genome assembly had a total length of 915.40 Mb, with a contig N50 of 51.06 Mb and a scaffold N50 of 73.17 Mb; 96.05% of the sequences were successfully anchored onto 12 pseudochromosomes. The genome was characterized by a high proportion of repetitive sequences (73.64%) and substantial heterozygosity (1.13%), consistent with a highly repetitive and moderately high heterozygous genome. BUSCO analysis indicated that the chromosome-level genome assembly of S. carolinense reached a completeness score of 94.8%. A total of 32,206 protein-coding genes were annotated, of which 97.95% received functional annotations. The evaluation of the annotated protein-coding gene set returned a completeness value of 94.9%. This reference genome provides a valuable resource for advancing research on the adaptive evolution of weedy Solanaceae species, supports the development of more effective management strategies for this troublesome species, and offers a technical reference for assembling other highly heterozygous weed genomes.

Solanum carolinense↗
PubMedDate not supplied

Putting the wrong fuel in the tank.

Three recent observations when considered together indicate means whereby the health of Western countries could be improved and certain diseases still rare in developing countries avoided. The first is the recognition that many of the commonest chronic disorders in more economically developed countries are characteristic of modern Western lifestyles; the second is that these disorders can be considered to be manifestations of maladaptation to a new environment; and the third is the knowledge now available of the types of environment to which man has, through evolution, adapted.

Diet↗
PubMed2026

Contrasting signals of selection at the EDAR gene in global and Latin American populations.

The EDAR gene is a classic target of positive selection in humans, mainly through the nonsynonymous variant rs3827760 (EDARV370A) associated with ectodermal traits. Using high-resolution data from the 1000 Genomes Project, we combined sliding-window F_ST, BayeScan, and extended haplotype homozygosity (EHH) analyses to examine global and Latin American patterns of differentiation. Globally, a strong signal of positive selection was confirmed at EDAR, dominated by the rs3827760 haplotype background and its extended linkage disequilibrium structure. In contrast, within Latin America, differentiation reflected admixture-driven haplotype persistence rather than contemporary selection. A genome-wide FST scan comparing individuals from the upper and lower quartiles of Native American ancestry showed that EDAR lies among the most highly differentiated regions in this contrast, consistent with ancestry-driven haplotype structure rather than post-admixture adaptive evolution. These results indicate that EDAR retains its evolutionary signature globally but not within recently admixed populations, where demographic history rather than selection shapes its genetic landscape.

Humans↗
PubMed1983

[Quantitative histoenzymological and biochemical studies of the stages of atherogenesis in human coronary arteries (based on the data of early autopsies].

Histochemical methods were used to study the dynamics of activity of energetic metabolism enzymes (EME) in cell elements of the human coronary artery (CA) wall in comparison with biochemical values of lipid metabolism in the plasma. The development of CA atherosclerosis was shown to be determined to a large extent by reciprocal relations of antiatherogenic alpha-lipoproteins and atherogenic beta-lipoproteins in their influence on EME activity. An increased EME activity at early stages of atherogenesis (lipid plaque) is an adaptation to changed homeostasis. The lipid plaque is a turning point in the process of metabolic adaptation. Evolution of atherosclerotic changes is accompanied by disjunction and transformation of correlative connections between EME activity in CA wall cells.

Adenosine Triphosphatases↗
PubMed1978

Experiences with U.C.I. total knee.

In 200 low friction knee arthroplasties with a minimum follow-up of 2 years the primary goal of relief from pain was accomplished in most patients. However, the evaluation of the result of a knee arthroplasty is difficult. Many of the patients who rated good or better had, to some extent, patellofemoral complaints. Cold flow deformation and prosthetic loosening is a definite concern about the tibial component. A longer follow-up study is needed to better evaluate the significance of the one to 2 mm radiolucent line at the bone cement interface of the tibial component. Collateral and cruciate ligament deterioration with time is also of concern and warrants careful follow-up. Although most patients patients in this series were greatly relieved of pain, even better results might have been obtained if the arthroplasty included the patellofemoral joint and a more substantial tibial component with better fixation. By our rating criteria, rheumatoid patients, in general, were benefited the most. Patients, surgeons and engineers realize that the natural human knee joint is a remarkable product of adaptive evolution, and that it may be imitated with increasing success though it can never be duplicated.

Adult↗
PubMed1995

[Water homeostasis in amphibia: vasotocin and hydrins].

Water homeostasis is ensured in vertebrates through neuroendocrine reflexes involving hormones and specialized exchange organs depending whether the habitat is freshwater, sea or land. Amphibians have a development recapitulating two adaptive programs, first a freshwater fish program as a tadpole, then a land vertebrate program as an adult. The second, however, is imperfect because of the great evaporative water loss through the skin when the animal is in the open air. This loss must be compensated by water reabsorption through the nephron, the urinary bladder and mainly by water uptake through the skin. Water reabsorption by the nephron is not as efficient as in higher vertebrates but water uptake through the skin is crucial because adult amphibians, like tadpoles, do not drink. Adaptation occurred at the level of three organs, nephron, urinary bladder and skin whose permeability is under control of specific hormones. Aside from vasotocin, active on these three organs, differential maturation of provasotocin led to processing-arrested intermediates, namely vasotocinyl-Gly in virtually all anuran amphibians and vasotocinyl-Gly-Lys-Arg in Xenopus laevis. These intermediates result from a down regulation of the alpha-amidating enzyme or carboxypeptidase E, respectively. They have been termed hydrin 2 and hydrin 1 because they are endowed with hydroosmotic properties equal or superior to those of vasotocin on the skin and the bladder. However, in contrast to vasotocin, they are devoid of antidiuretic activity. Adaptive evolution has created, aside from the osmoregulatory vasotocin-nephron system that was preserved in strictly terrestrial nonmammalian tetrapods, additional functions such as the hydrin-skin and the hydrin-bladder rehydrations with specific messengers and organs. The adjuvant systems disappeared in true land vertebrates because the vasotocin-nephron system became more efficient.

Amphibians↗
PubMed1996

[Protozoa as reservoirs for human bacterial pathogens].

The ability of bacterial pathogens to survive within the human host cells results from their evolutional adaptation of which the most important stage could be the development of parasitic relations between bacteria and free-living protozoa. This paper shows the bacterial species, pathogenic for man, surviving in protozoans cells.

Adaptation, Physiological↗
PubMedDate not supplied

[Kinetics of xylanase and cellulase production by Ascobolus gamundii (Fungi, Ascomycotina)].

Growth and cellulase-xylanase enzyme systems production by Ascobolus gamundii were evaluated in synthetic media with or without natural inducers. The basal level of enzyme complexes was determined using glucose as carbon source. With crystalline cellulose, the amount of endoglucanase and beta-glucosidase was 2-4 times the basal, and the level of endoxylanase and beta-xylosidase was 3 times higher than that observed with glucose. When using xylan as carbon source, endoxylanase and endoglucanase were induced. The higher production of the enzyme systems was observed during the log-phase growth of A. gamundii with a mixture of cellulose and xylan as carbon source. The generalized induction of both enzyme complexes could be due to evolutive adaptation to the substrate (herbivore dung) in which cellulose and hemicellulose are associated to conform the plants cell-walls.

Ascomycota↗
PubMed1997

Molecular domestication of mobile elements.

Transposable elements are ubiquitous in all organisms and represent a dynamic component of their genomes, causing mutations and thereby genetic variation. Because of their independent and expansive replication strategy, these elements are called selfish and were thought to have no impact on the adaptive evolution of their host organisms. Although most TE-induced mutations seem to exert only negative effects on the fitness of their carrier, recent evidence indicates that in the course of evolution at least some TE-mediated changes have become established features of the host genome. For example, the insertion of TEs may provide novel cis-regulatory regions to preexisting host genes or TE-derived trans-acting factors may undergo a molecular transition into novel host genes through a process described as molecular domestication. The stationary P element related gene clusters of D. guanche, D. madeirensis and D. subobscura provide an excellent model system to study the evolutionary impact of TEs on genome evolution. Each cluster unit consists of a cis-regulating section composed of different insertion sequences followed by the first three exons of a P element that are coding for a 66 kDa 'repressor-like' protein.

Animals↗
PubMed1992

Vertical clinging, small body size, and the evolution of feeding adaptations in the Callitrichinae.

Primates of the subfamily Callitrichinae (Callimico, Callithrix, Leontopithecus, and Saguinus) are small-bodied New World monkeys (105-700 g) possessing clawlike nails on all manual and pedal digits excluding the hallux. Specialized nails in these genera serve a critical function in feeding by enabling tamarins and marmosets to cling to trunks and other large vertical supports while exploiting food resources. Within the subfamily, there is evidence of at least four distinct large-branch feeding patterns. These include (1) seasonal exudate feeding and occasional trunk foraging (many Saguinus spp.); (2) exploitation of bark surface insects and the use of trunks as a platform to locate terrestrial prey (Saguinus fuscicollis, S. nigricollis, and Callimico); (3) manipulative foraging and bark stripping to locate concealed insects and small vertebrates (Leontopithecus); and (4) tree gouging and year-round exudate feeding (many Callithrix). Large-branch feeding and the use of vertical clinging postures appear to be a primary adaptation among virtually all callitrichines, distinguishing them ecologically from other platyrrhine taxa. Given the anatomy and behavior of extant callitrichines, Saguinus appears to be the most ecologically generalized member of this subfamily, and species of this genus may provide useful models for reconstructing the feeding and foraging adaptations of early callitrichines.

Adaptation, Physiological↗