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PubMed2025

Genome-Wide Identification of the TIFY Family in Cannabis sativa L. and Its Potential Functional Analysis in Response to Alkaline Stress and in Cannabinoid Metabolism.

TIFY transcription factors play crucial regulatory roles in secondary metabolism and stress response. However, the expression patterns of the Cannabis sativa L. TIFY gene family under alkali stress, their involvement in cannabinoid metabolism, and their underlying genetic evolutionary mechanisms remain largely unexplored. In this study, we used bioinformatics approaches to conduct genome-wide identification and functional characterization of the C. sativa TIFY gene family. Fourteen TIFY genes were identified and mapped onto seven chromosomes. These genes were classified into four subfamilies: TIFY, JAZ, ZML, and PPD, with the JAZ subfamily further subdivided into five distinct branches. Collinearity analysis suggested that gene duplication events contributed to the expansion of the TIFY gene family in C. sativa. Weighted gene coexpression network analysis (WGCNA) revealed that CsJAZ2, CsJAZ3, and CsJAZ6 participated in the cannabinoid regulatory network. Cis-element analysis indicated that the promoter regions of TIFY genes were enriched in hormone- and stress-responsive elements. Furthermore, transcriptome and RT-qPCR analyses were conducted to examine gene expression patterns under alkaline stress (the RNA employed in RT-qPCR was extracted from the apical leaves of samples subjected to short-duration alkaline stress treatment). The results showed that CsJAZ5 and CsJAZ6 were downregulated, whereas CsPPD1, CsTIFY1, and CsZML1 were upregulated in response to alkali stress. In summary, CsJAZ5, CsPPD1, and CsTIFY1 may serve as candidate genes for the development of alkali-tolerant cultivars, while CsJAZ2 and CsJAZ3 may be valuable targets for enhancing cannabinoid production. This study provides important molecular insights and a theoretical basis for future research on the evolutionary dynamics and functional roles of TIFY transcription factors, particularly in stress adaptation and cannabinoid metabolism.

Cannabis↗
PubMed2025

The Complete Chloroplast Genome and the Phylogenetic Analysis of Panicum bisulcatum (Thumb.) (Poaceae).

The chloroplast (cp) genome of Panicum bisulcatum (Thumb.), a significant agricultural weed, was sequenced and characterized to elucidate its genomic architecture, evolutionary dynamics, and phylogenetic relationships. The complete cp genome was assembled as a circular DNA molecule of 138,489 bp, exhibiting a typical quadripartite structure comprising a large single-copy (LSC, 82,260 bp), a small single-copy (SSC, 12,569 bp), and a pair of inverted repeats (IR, 21,830 bp each) regions. It encodes 135 genes, including 89 protein-coding genes, 49 tRNAs, and 8 rRNAs. Functional annotation revealed that most genes are involved in photosynthesis and genetic system. A total of 51 simple sequence repeats (SSRs) and 62 long repeats (LRs) were identified, providing potential molecular markers. Comparative analysis of IR boundaries highlighted both conserved features and species-specific expansion/contraction events among Panicum species. Phylogenomic analysis robustly placed P. bisulcatum within the genus Panicum, showing a closest relationship with P. incomtum and confirming the monophyly of the genus. Furthermore, single nucleotide polymorphism (SNP) analysis with its closest relative, P. incomtum, revealed 4659 SNPs, with a dominance of synonymous substitutions, indicating the action of purifying selection. This study provides the first comprehensive cp genomic resource for P. bisulcatum, which will facilitate future studies in species identification, phylogenetic reconstruction, population genetics, and the development of sustainable management strategies for this weed.

Phylogeny↗
PubMed2026

Exploring the Effect of Whole-Genome Duplication on Salmonid LincRNA Repertoire.

Long intergenic non-coding RNAs (lincRNAs) are key epigenetic regulators of genome function, yet their evolutionary dynamics following whole-genome duplication (WGD) events remain poorly understood. Salmonids, which underwent a lineage-specific autotetraploidization (salmonid-specific WGD, ~88-100 million years ago), provide an excellent model to investigate the retention, divergence, and functional potential of recently duplicated non-coding elements. LincRNA repertoires were compared across five genome-annotated salmonids (Oncorhynchus tshawytscha, O. kisutch, O. mykiss, Salmo salar, and S. trutta) and their closest non-duplicated relative, northern pike (Esox lucius). LincRNAs represented ~5-7% of annotated genes in all salmonids except S. salar (18%). Sequence conservation was low relative to coding genes, with only 11-68 highly similar (e-value < 1 &#xd7; 10-30; similarity > 70% and alignments > 100 nucleotides) putative orthologues shared between salmonids and northern pike, and 161-338 among salmonids alone. Synteny conservation was modest in lincRNAs, with lower conservation in putative orthologues (8-16%) compared to putative ohnologues (8-33%). Secondary structure conservation was associated with sequence similarity (&#x3c1; = -0.45; p = 2.2 &#xd7; 10-16), and the association was stronger among WGD ohnologues than orthologues. In S. salar and O. mykiss, lincRNA putative ohnologues showed weaker expression correlations than coding genes, suggesting widespread regulatory divergence, possibly through neo- and subfunctionalisation. Conserved salmonid lincRNAs showed enriched predicted interactions with miRNAs involved in tumour suppression, brain, bone, and muscle development (e.g., miR-455, miR-365, miR124, miR-133a, miR-140, and miR-9), a finding supported by limited transcriptomic data. Although salmonid WGD expanded lincRNA repertoires, lincRNAs have undergone rapid sequence and transcriptional divergence, with limited conservation across species based on sequence similarity, chromosomal position, synteny, and secondary structure. A subset of conserved lincRNAs retains structural features and regulatory signatures consistent with roles as miRNA sponges in brain, skeletal, and muscle development and tumour suppression, potentially acting within conserved regulatory networks. These findings provide new insights into lincRNA evolution following genome duplication and highlight the need for experimental validation of their regulatory functions.

Animals↗
PubMed2025

Molecular Characterization and Epidemiology of Human Noroviruses in the Sverdlovsk Region, Russian Federation.

Human noroviruses (HuNoVs) stand as the primary cause of acute viral gastroenteritis outbreaks worldwide, particularly impacting children under the age of five. In Russia, reports of norovirus gastroenteritis have surged, especially in the post-COVID-19 era starting in 2022, with elevated infection rates reported into 2024. These viruses exhibit significant mutational variability, leading to the emergence of recombinant strains that can evade immune responses. A comprehensive examination of the complete genome is crucial for understanding the evolution of norovirus genes and for predicting potential outbreaks. This research focuses on analyzing the genotypic composition of HuNoVs circulating in the Sverdlovsk region during 2024, using Sanger sequencing and next-generation sequencing (NGS). Biological samples were collected (n = 384) from patients diagnosed with norovirus infection within the region. Bioinformatics analysis targeted the nucleotide sequences of the ORF1/ORF2 fragment and the assembly of complete genomes for the GII.4 and GII.7 genotypes. In total, 220 HuNoVs were characterized, representing 57.3% of the collected samples. The main capsid variants forming the predominant genotypic profile included GII.4 (n = 88, 40%), GII.7 (n = 86, 39%), and GII.17 (n = 14, 6%). Using NGS, we successfully assembled 8 out of 10 complete genomes for noroviruses GII.4[P16] and GII.7[P7]. Non-synonymous substitutions appeared at amino acid sites corresponding to the subdomains of VP1 in these strains. This molecular-genetic analysis provides contemporary insights into the genotypic composition, circulation patterns, and evolutionary dynamics associated with the dominant genovariants GII.4[P16] and GII.7[P7].

Norovirus↗
PubMed2026

Long-term small effective population size, inbreeding, and a recessive lethal haplotype drive premature death in the endangered Devils Hole pupfish (Cyprinodon diabolis).

As anthropogenic habitat fragmentation and population decline accelerate globally, growing numbers of species face compounding demographic and genetic threats to long-term survival. Many populations are already forced to persist at chronically small sizes, yet the genomic and fitness consequences of this fate remain poorly understood. Here we leverage the demographic history of the Devils Hole pupfish to investigate how long-term small population size and recent bottlenecks have shaped genetic diversity, genetic load, inbreeding, and fitness through comparative population genomics, historical sequencing, and sampling embryos that died prematurely during development. We find that genetic diversity in Devils Hole pupfish is among the lowest recorded in the wild and that fixed load is high, consistent with thousands of generations of isolation at small population size. Even in the face of this low diversity and high fixed load, we show that inbreeding is still strongly associated with premature embryonic death, which affects up to 25% of offspring in the captive refuge and can be identified in advance based on a characteristic elongated heart tube and reduced heart rate. We discovered a recessive lethal haplotype segregating at ~20% frequency that accounts for 50% of embryonic deaths and contains mutations in MIB1 and MMP16, genes associated with cardiomyopathy and atrial fibrillation. Our findings link genotype, phenotype, and fitness in an iconic endangered species to provide a rare comprehensive view into the evolutionary dynamics and consequences of long-term small effective population size, demonstrating that endangered species remain vulnerable to inbreeding depression despite extremely low genetic diversity.

Journal Article↗
PubMed1993

Six honest serving men.

The practice of medical-surgical nursing is "a dynamic, evolutionary process" and the proliferation of health care technology has been instrumental in its evolution. This proliferation and the goal of quality patient care in medical-surgical nursing practice are unlikely to change. However, the provision of quality care depends on the use of appropriate technology. Nurses and materiel managers working collaboratively can identify and promote the use of appropriate health care technology by applying the framework of technology assessment. This framework is analogous to Kipling's six honest serving men (They taught me all I knew); Their names are What and Why and When And How and Where and Who. The Elephant's Child What, Why, and When advise selective and judicious use of appropriate health care technology. How, Where, and Who reaffirm knowledgeable and proficient use with registered nurses, the patients' "link with the personal, human world within an impersonal, electronic world." Together, the six honest serving men emphasize that the primary purpose of health care technology is the improvement of human health "from the individual level through and including national health policy."

Cost-Benefit Analysis↗
PubMed1999

Population structure, speciation, and introgression in the Anopheles gambiae complex.

We review here what is known about the population structure and evolutionary dynamics of members of the Anopheles gambiae complex with emphasis on the situation in West Africa. First, the importance of the 2nd chromosome inversion polymorphism is demonstrated especially in adaptation to levels of aridity, a major environmental variable in Africa. This affects the distribution of karyotypes on both a macro- and micro-geographic scale as well as temporally. Such differentiation leads to karyotypes being differentially effective transmitters of malaria and differentially susceptible to indoor residual spraying of insecticides. Second, we review the evidence that cryptic taxa, especially in An. gambiae s.s., exist. This observation stems from both karyotype studies and molecular studies. It is abundantly clear that West African populations of An. gambiae s.s. are often not panmictic units, with premating factors evidently acting to maintain distinct genetic forms. Third, we review phylogenetic studies that have revealed the presence of introgression between the two most important vectors, An. gambiae and An. arabiensis. This is most evident for the 2nd chromosome inversions. This interpretation of phylogenetic data is consistent with a direct laboratory study indicating inversions in this chromosome are stably maintained in back-crossed populations. All of this information has led to the view that members of the An. gambiae complex are highly variable with an abundance of adaptive genetic variation. This presents a significant challenge to vector control programs designed to reduce malaria in sub-Saharan Africa.

Africa, Western↗
PubMed2001

Role of viral isolate in the etiopathogenetic determinism of HCV infection: diagnostic and epidemiological evaluation.

HCV genotyping by nucleic acid sequencing emphasizes the difficulties involved in carrying out a more precise determination of the infectant viral population, probably due in part to the finding of still unknown isolates. Signs of heterogeneity in the genotype composition of the viral quasi-species and its evolutionary dynamism over time, together with the role played by some, more potentially aggressive, isolates in causing hepatic damage, encourage a more in-depth study of such topics.

Alanine Transaminase↗
PubMed2004

Parasitism increases and decreases the costs of insecticide resistance in mosquitoes.

Adaptations conferring resistance to xenobiotics (antibiotics, insecticides, herbicides, etc.) are often costly to the organism's fitness in the absence of the selecting agent. In such conditions, and unless other mutations compensate for the costs of resistance, sensitive individuals are expected to out-reproduce resistant individuals and drive resistance alleles to a low frequency, with the rate and magnitude of this decline being proportional to the costs of resistance. However, this evolutionary dynamic is open to modification by other sources of selection acting on the relative fitness of susceptible and resistant individuals. Here we show parasitism not only as a source of selection capable of modifying the costs of organophosphate insecticide resistance in mosquitoes, but also that qualitatively different interactions (increasing or decreasing the relative fitness of resistant individuals) occurred depending on the particular form of resistance involved. As estimates of the parasite's fitness also varied according to its host's form of resistance, our data illustrate the potential for epidemiological feedbacks to influence the strength and direction of selection acting on resistance mutations in untreated environments.

Adaptation, Physiological↗
PubMed2005

Environmental origins of sexually selected variation and a critique of the fluctuating asymmetry-sexual selection hypothesis.

Identifying sources of phenotypic variability in secondary sexual traits is critical for understanding their signaling properties, role in sexual selection, and for predicting their evolutionary dynamics. The present study tests for the effects of genotype, developmental temperature, and their interaction, on size and fluctuating asymmetry of the male sex comb, a secondary sexual character, in Drosophila bipectinata Duda. Both the size and symmetry of elements of the sex comb have been shown previously to be under sexual selection in a natural population in northeastern Australia. Two independent reciprocal crosses were conducted at 25 degrees and 29 degrees C between genetic lines extracted from this population that differed in the size of the first (TC1) and third (TC3) comb segments. These temperatures are within the documented range experienced by the species in nature. Additive and dominance genetic effects were detected for TC1, whereas additive genetic, and Y-chromosomal effects were detected for TC3. TC2 and TC3 decreased sharply with increasing temperature, by 10% and 22%, respectively. In contrast, positional fluctuating asymmetry (PFA) significantly increased with temperature, by up to 38%. The results (1) document an important source of environmental variance in a sexual ornament expected to reduce trait heritability in field populations, and thus act to attenuate response to sexual selection, (2) suggest that variation in ornament size reflects differences in male condition; and (3) support the general hypothesis that asymmetry in a sexual ornament is indicative of developmental instability arising from environmental stress. The "environmental heterogeneity" (EH) hypothesis is proposed, and supportive evidence for it presented, to explain negative size-FA correlations in natural populations. Data and theory challenge the use of negative size-FA correlations observed in nature to support the FA-sexual selection hypothesis, which posits that such correlations are driven by differences in genetic quality among individuals.

Analysis of Variance↗
PubMedDate not supplied

Playing God? Moral agency in an emerging world.

Arguments against intervening in nature's ways have been used against many new technologies in the last century. Many of these arguments have employed the metaphor of "playing God." In this essay I briefly review the use of the term "playing God" in recent decades. I then examine the cosmology that lies implicit in this language. My thesis is that the language of "playing God" (or not) overlooks the dynamic, evolutionary nature of world process--the role played by the interdeterminacy of statistical probabilities. I review the notion of "emergent probability" (Lonergan) in order, in the end, to advocate an ethic of risk that both recognizes the dangers of hubris and includes an open and emergent view of creation.

Biotechnology↗
PubMed2005

The genetic basis for fruit odor discrimination in Rhagoletis flies and its significance for sympatric host shifts.

Rhagoletis pomonella (Diptera: Tephritidae) use volatile compounds emitted from the surface of ripening fruit as important chemosensory cues for recognizing and distinguishing among alternative host plants. Host choice is of evolutionary significance in Rhagoletis because these flies mate on or near the fruit of their respective host plants. Differences in host choice based on fruit odor discrimination therefore result in differential mate choice and prezygotic reproductive isolation, facilitating sympatric speciation in the absence of geographic isolation. We test for a genetic basis for host fruit odor discrimination through an analysis of F2 and backcross hybrids constructed between apple-, hawthorn-, and flowering dogwood-infesting Rhagoletis flies. We recovered a significant proportion (30-65%) of parental apple, hawthorn, and dogwood fly response phenotypes in F2 hybrids, despite the general failure of F1 hybrids to reach odor source spheres. Segregation patterns in F2 and backcross hybrids suggest that only a modest number of allelic differences at a few loci may underlie host fruit odor discrimination. In addition, a strong bias was observed for F2 and backcross flies to orient to the natal fruit blend of their maternal grandmother, implying the existence of cytonuclear gene interactions. We explore the implications of our findings for the evolutionary dynamics of sympatric host race formation and speciation.

Animals↗
PubMed2005

Loci affecting long-term hybrid survivorship in Louisiana irises: implications for reproductive isolation and introgression.

Iris fulva and I. brevicaulis are long-lived plant species known to hybridize where they coexist in nature. Year-to-year survival contributes significantly to overall fitness for both species and their hybrid derivatives, and differences in hybrid survivability may have important consequences to interspecific gene flow in nature. We examined the genetic architecture of long-term survivorship of reciprocal backcross I. fulva x I. brevicaulis hybrids in a common-garden, greenhouse environment. Differences in mortality were found between the two backcross (BC1) hybrid classes, with hybrids crossed toward I. fulva (BCIF) revealing twice the mortality of those hybrids backcrossed toward I. brevicaulis (BCIB). Using genomic scans on two separate genetic linkage maps derived from the reciprocal hybrid populations, we found that hybrid survivorship is influenced by several genetic regions. Multiple interval mapping (MIM) revealed four quantitative trait loci (QTLs) in BCIF hybrids that were significantly associated with survivorship. Introgressed I. brevicaulis DNA increased survivorship at three of the four QTLs. For the fourth QTL, introgressed I. brevicaulis DNA was associated with decreased survivorship. No QTLs were detected in BCIB hybrids; however, single-marker analysis revealed five unlinked loci that were significantly associated with survivorship. At all five markers, survivorship was positively associated with introgressed I. fulva DNA. The present findings have important implications for the evolutionary dynamics of naturally occurring hybrid zones. Regions of the genome that increase survivorship when in a heterozygous (i.e., hybrid) state should have an increased likelihood of passing across species boundaries, whereas those that decrease survivorship will be less likely to introgress.

Chimera↗
PubMed2006

Extensive introgression of mitochondrial DNA relative to nuclear genes in the Drosophila yakuba species group.

Studies of gene flow between recently diverged species can illuminate the role of natural selection in the formation of new species. Drosophila santomea and D. yakuba are recently diverged, partially reproductively isolated species that continue to hybridize in the wild, and appear to be reproductively isolated from the more distantly related species D. teissieri. We examine patterns of nucleotide polymorphism and divergence in these three species at multiple X-linked, Y-linked, and mitochondrial markers. All three species harbor drastically reduced variability on the Y chromosome relative to the X, as expected for a nonrecombining chromosome subject to variation-reducing selection. The three species are generally well differentiated at the nuclear markers, with little evidence for recent introgression for either the X- or Y-linked genes. Based on the nuclear genes, we estimate that D. santomea and D. yakuba diverged about one-half million years ago and split from D. teissieri about one million years ago. In contrast to the pattern at nuclear loci, all three species share a very similar mtDNA haplotype. We show that the mtDNA must have recently introgressed across species boundaries in the D. yakuba subgroup and that its fixation was driven by either selection on the mitochondria itself or other cytoplasmic factors. These results demonstrate that different regions of the genome can have distinct evolutionary dynamics in the context of species formation. Although natural selection is usually thought of as accentuating divergence between species, our results imply that it can also act as a homogenizing force.

Animals↗
PubMed2006

Self-imposed silence: parental antagonism and the evolution of X-chromosome inactivation.

A model is proposed for the evolution of X-chromosome inactivation (XCI) in which natural selection initially favors the silencing of paternally derived alleles of X-linked demand inhibitors. The compensatory upregulation of maternally derived alleles establishes a requirement for monoallelic expression in females. For this reason, XCI is self-reinforcing once established. However, inactivation of a particular X chromosome is not. Random XCI (rXCI) is favored over paternal XCI because rXCI reduces the costs of functional hemizygosity in females. Once present, rXCI favors the evolution of locus-by-locus imprinting of X-linked loci, which creates an evolutionary dynamic in which different chromosomes compete to remain active.

Animals↗
PubMed1990

Methylprednisolone interventions in myocardial infarction: a controversial subject.

Myocardial infarction is a dynamic evolutionary process which can progress over a relatively prolonged interval after its onset. The ultimate extent of damage depends on coronary artery anatomy, the balance between myocardial oxygen supply and demand, and metabolic modulators of myocardial injury. The possibility that methylprednisolone, a synthetic anti-inflammatory corticosteroid, may exert a beneficial effect on ischemic myocardium has been studied in both animal models and patients. However, the results of these experimental and clinical investigations have been controversial, in that some have demonstrated efficacy of the drug to limit extension of evolving myocardial infarction, while others have not. The effects of dose regimen and duration of methylprednisolone administration on preservation of myocardium and infarct size remain unclear, especially in clinical studies. The problem resides in the large interindividual variations among patients in degree and distribution of coronary disease, concomitant drugs, the accuracy of techniques for measuring and monitoring changes in myocardial infarct size, and the small numbers of patients involved in the majority of these studies. The absence of clarity will continue to cast doubts over the use of methylprednisolone until its marked beneficial effects can be significantly demonstrated.

Animals↗
PubMed1988

Clonal dominance of primary tumours by metastatic cells: genetic analysis and biological implications.

A new method is described for analysing the clonal evolutionary dynamics of tumour growth and the lineage relationship of primary tumours to their metastases. It exploits random integrations of transfected plasmid or retroviral infected (proviral) DNA as a means of generating very large numbers of uniquely marked cell clones in a single-step selection whose fates can then be tracked during progressive tumour growth. Using a mouse breast adenocarcinoma we undertook experiments in which syngeneic mice were injected with a mixture of very large numbers of uniquely marked cell clones, only one or a few of which were metastatic, or with reconstituted mixtures containing a genetically tagged metastatic clone with an excess of non-marked non-metastatic tumour cells. Among the results we summarize is the finding that spontaneous metastases developed in a non-random fashion from genotypically distinct cell clones. They were clonal or biclonal at the time of analysis. We also found that the progeny of a single metastatic clone could eventually overgrow the primary tumour. Thus malignant (metastatic) cells may manifest a striking growth advantage within the primary tumour site as well as for dissemination and growth at distant, secondary sites. As a result, late-stage advanced primary tumours, if left intact, may evolve to become biologically similar or equivalent to distant metastases. This 'clonal dominance' phenomenon can reconcile many of the discrepant experimental findings with respect to the putative selective nature of metastatic phenotype. Furthermore, it has important consequences for understanding one source of biological variability in experiments in which different primary tumours are compared to each other or to metastases; it also has implications for theories regarding the clonal origin of neoplasms, and for the physiological and biochemical changes that cause malignant disease.

Animals↗
PubMed1983

Two-dimensional gel comparisons of murine H-2D region-associated antigens of different H-2 haplotypes.

The heterogeneity of histocompatibility antigens encoded within the H-2D region of murine chromosome 17 was investigated in several mouse strains using monoclonal antibodies. Sequential immunoprecipitation and two dimensional gel electrophoresis (2D) were used to determine the number and structural relatedness of antigenically distinct products of the same H-2D region. Strikingly different, haplotype-specific patterns were observed. The three antigenically distinct molecules, Dd, Ld and Rd, all encoded within the Dd region, each showed a unique constellation of spots by 2D analysis, although the Ld and Rd molecules showed more structural similarity to each other than either molecule showed to the Dd molecule. Comparisons of the Ld and Rd molecules using sequential precipitations and a cloned Ld gene suggested that they are not conformation or glycosylation variants of the same polypeptide, implying they have different primary amino acid sequences. Using an anti-Ld antibody, the Ldml molecule was isolated from cells of the Dd region mutant mouse strain B10.D2-H-2dml and was found to have a 2D gel profile clearly distinguishable from the profile of either Ld or Dd molecules isolated from the wild-type strain B10.D2. Of the three antigenically-distinct molecules determined by the Dq region, the 2D gel profile of the Rq molecule was different from that of the Dq and Lq, the latter two molecules being indistinguishable. In contrast to these findings, analysis of the gene products of the Db region failed to resolve either antigenic or molecular heterogeneity and the multiple, antigenically distinct gene products of the Dw16 region were indistinguishable by 2D comparisons. These haplotype specific variations in the structural relatedness and number of antigenically distinct molecules determined by D region genes support the hypothesis that class I MHC genes are in a dynamic evolutionary state of gene expansion and contraction.

Animals↗