Nutrition Classics. Journal of the American Chemical Society 59:1052-4, 1937. Synthesis of vitamin B1. By Joseph K. Cline, Robert R. Williams, and Jacob Finkeltstein.
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Animals↗
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Geographic variation, speciation, and clines.
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Adaptation, Biological↗
The MexMAGIC population reveals the genetic architecture of traits exhibiting clinal variation in Mexican native maize.
Defining the genetic basis of local adaptation is a key goal of evolutionary biology and crop improvement. Theory predicts that when selective pressures follow differences in the environment, a cline will be established. Clines can be exploited to uncover adaptive variation by association of alleles with the environment. However, monotonic phenotypic change over a cline is not necessarily mirrored in the behavior of genetic variants and population structure can further complicate analysis. To study genetic and phenotypic variation across the environment, we developed a multi-parent advanced generation inter-cross (MAGIC) population using eight Mexican native maize (Zea mays L. ssp. mays) varieties sourced from distinct agroecological zones. We evaluated the population in a common garden in Mexico and mapped tassel branching and flowering time, two traits that exhibit clinal variation. Variation in tassel branching was dominated by a single QTL with allele effects aligning to a negative elevational cline. By contrast, allele effects associated with 11 identified flowering time QTL were not consistently correlated with any one source environmental factor. Our observations support the prediction that genotype-environment association will be strongest under simple genetic architecture, although, even then, analysis in native populations may be confounded by population structure.
MAGIC↗
Patterns of Genomic Divergence and Introgression in Two Primulina Hybrid Zones.
Hybrid zones have long been promoted as natural laboratories for understanding the mechanisms of speciation. Multiple or replicated hybrid zones are particularly informative, as they allow for assessing the consistency of genomic divergence and introgression across different environmental contexts and demographic histories, thereby improving our understanding of the factors that drive or hinder speciation on a broader scale. Here, using whole-genome resequencing data, we compare the patterns of genomic divergence and introgression in two Primulina hybrid zones. We found that genomic divergence in both hybrid zones is largely shaped by neutral processes, with only a few genomic regions showing signatures of balancing or lineage-specific selection. Genomic cline analyses identified numerous SNPs that showed significantly steeper clines and biased centres than the genome-wide expectation in both hybrid zones, consistent with the existence of reproductive barriers. Within regions of restricted gene flow, we identified 21 genes shared between the two hybrid zones. Annotation of gene function revealed that several genes are involved in reproductive processes. In addition, many zone-specific outlier loci were linked to genes associated with pollen and flower development, suggesting that these barriers may contribute to reproductive isolation under localised ecological conditions. Overall, these findings suggest that while certain reproductive barriers remain consistent across independent hybrid zones, others may be contingent on local environmental contexts. Our results demonstrate that both general and zone-specific mechanisms contribute to reproductive isolation in Primulina, providing empirical evidence that some genomic barriers recur across independent hybrid zones while others arise through localised adaptation.
Lamiales↗
Determination of the bacteriostatic capacity of neutrophils and monocytes in mixed cell populations.
Cline [1, 2] described a method of determining the phagocytic and bacteriostatic activity of individual types of leukocytes within mixed cell populations. We tried to improve the applicability of this method for the investigation of clinical problems.--Bacteria in the log-phase of growth were incubated in test tubes with leukocytes separated from venous blood. After a short period of phagocytosis 3H-thymidine was added to label DNA-synthesizing organisms. Smears were prepared and processed by autoradiography. The labeling indices of extracellular bacteria and of those phagocytized by neutrophils and monocytes were determined microscopically. The intracellular inhibition of DNA-synthesis was taken as indicative of the bacteriostatic activity of the leukocytes. The proposed modification of Cline's assay is suited to investigate clinical problems of phagocyte dysfunction.
Autoradiography↗
Heat-Induced Secondary Dormancy Contributes to Local Adaptation in Arabidopsis thaliana.
Seeds should not germinate in conditions unsuitable for seedling growth. Dormancy, which allows seeds to remain inactive in an environment that would otherwise enable germination, helps optimise the timing of germination. Primary dormancy, developed during seed maturation on the parent plant, prevents immediate germination post-dispersal, regardless of external conditions. Secondary dormancy, however, is triggered post-dispersal when seeds face unfavourable conditions, enabling them to re-enter dormancy even if initially non-dormant. This mechanism allows seeds to fine-tune germination according to environmental conditions. In this study, we examined the role of heat-induced secondary dormancy in local adaptation by analysing natural variations within 361 Arabidopsis thaliana accessions from across Europe. We discovered that secondary dormancy acquisition varies with primary dormancy levels and after-ripening. Both primary and heat-induced secondary dormancy exhibited adaptive clines along temperature and precipitation gradients, with secondary dormancy showing a steeper cline, indicating its significant role in local adaptation. Using species distribution models, we predicted that genotypes with high secondary dormancy would show greater resilience to future climate changes. Additionally, we identified specific genomic regions controlling secondary dormancy levels including a novel candidate gene for secondary dormancy variation. Our findings show that secondary dormancy is a complex adaptive mechanism and a predominant contributor to the dormancy trait syndrome that favours plant survival in habitats exposed to harsh summers.
Arabidopsis↗
The detection of virus DNA sequences in a herpes type 2 transformed hamster cell line (333-8-9).
Herpes simplex virus type 2 DNA labelled in vitro with 125I has been used as a probe to search for virus DNA sequences in the 333-8-9 line of transformed primary hamster cells and in clines derived from the line. Virus DNA sequences were present when the cells were examined initially but these sequences were lost on subsequent handling. No virus sequences were detected in clones derived from the line. It is suggested that the presence of virus DNA is an unstable characteristic of the cell line and that these sequences may be lost at cell division. The possibility that a small fragment of the genome remains cannot be excluded.
Base Sequence↗
Gm and Km(Inv) frequencies in two Roumanian populations.
Serum samples from 170 unrelated individuals from the Suceava District of Roumania and from 199 unrelated individuals from Bucharest, Roumania were tested fro Gm(1,2,3,5,6,13,14,17,21) and Km(1)[Inv(1)]. Selected samples were also tested for Gm(15) and Gm(16). The frequencies of the three common Caucasoid haplotypes, Gm3,5,13,14, Gm1,17,21, and Gm1,2,17,21 in these two populations were found to be similar to those in neighboring Slavic states and Hungary. Racial admixture was evidenced by the presence of the Gm1,13,15,16,17 and Gm1,3,5,13,14 haplotypes, which are primarily Mongoloid, and the Gm1,5,13,14,17 haplotype which is primarily Negroid. Comparisons of these data with those from earlier studies of populations from Central Europe indicate that the frequency of the Gm3,5,13,14 haplotype within this region is high and essentially uniform. Published data for several blood group systems also indicate essentially uniform distributions of frequencies in this region. It is suggested that this region may be the center of a cline that radiates from it.
Asian People↗
Polymorphism at the alpha-glycerophosphate dehydrogenase locus in Drosophila melanogaster. I. Properties of adult allozymes.
A biochemical comparison was made between alpha-glycerophosphate dehydrogenase allozymes from Drosophila melanogaster. Enzymes extracted from the three major genotypes were indistinguishable in terms of their pH optima and thermal stabilities. Distinctive differences were observed for three parameters; temperature dependence of specific activity, temperature dependence of K-m, and reaction rate constancy over a physiological temperature range. These results are discussed in terms of a model of balancing selection and the existence of spatial and temporal allele frequency clines in natural populations.
Alleles↗
From sporulation to village differentiation: The shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia.
Despite established roles in human health and profound global diversity, microbiome datasets remain biased toward Western urban cohorts, with especial under-representation of Southeast Asia. Here, we present a gut microbiome dataset from 116 Indonesians spanning transitional hunter-gatherer, rural agricultural, and urban lifestyles. We identify 1,304 species and 3,258 subspecies by assembling 11,070 metagenome-assembled genomes, revealing substantial species- (15%) and subspecies- (50%) level novelty. Novel taxa are rare, often village specific, and depleted for sporulation genes, revealing a link between bacterial physiology, transmission, prevalence, and discovery. We identify rural-to-urban clines across multiple levels of biological organization, from species abundance to microbiome composition and diversity. Furthermore, between-community, but not within-community, diet variation is strongly predictive of microbiome composition, suggesting that microbiome divergence is driven by community-level differences. Our work highlights the interplay of host lifestyle, population structure, and bacterial physiology in shaping microbiome diversity and biogeography, at the key scale of human communities.
Humans↗
The Jumonji C domain-containing proteins GmJMJ19 and GmJMJ20 link florigen signaling with epigenetic regulation of photoperiodic flowering and post-flowering plant height in soybean.
Soybean (Glycine max) is a photoperiod-sensitive legume whose latitudinal adaptation depends on the precise control of flowering time and plant height. Histone demethylases of the JmjC domain-containing (JMJ) protein family have been implicated in these processes across plant species, but their specific roles in soybean remain largely unexplored. Here, we identify soybean GmJMJ19 and GmJMJ20, two closely related JMJD5/KDM8 orthologs, as master epigenetic regulators that coordinately control both photoperiodic flowering and post-flowering plant height. Both genes exhibit intrinsic, rhythmic expression peaking at ZT12, and their encoded proteins physically interact with the florigen proteins FT2a and FT5a. Loss-of-function mutants display delayed flowering under long days (LDs) and increased plant height under both LDs and short days (SDs), whereas overexpression phenocopies the mutant flowering phenotype, indicating revealing a critical dosage requirement for proper function. Mechanistically, GmJMJ19 and GmJMJ20 are recruited by the FT/FD transcriptional complex to directly activate AP1a and AP1c expression through chromatin modulation. Population genomic analyses reveal distinct selection signatures: GmJMJ19 underwent sustained directional selection during cultivation, whereas GmJMJ20 experienced an early domestication sweep with limited subsequent change. Haplotype analysis identifies coordinated latitudinal clines, with the JMJ19H1/JMJ20H1 combination predominating at high latitudes to promote early flowering and limit height, while JMJ19H2/JMJ20H2 and wild JMJ19H3/JMJ20H3 alleles prevail at low latitudes, conferring later flowering and increased height. Collectively, our findings establish GmJMJ19 and GmJMJ20 as central chromatin regulators linking florigen signaling to downstream target expression and provide valuable allelic resources for breeding regionally adapted soybean varieties across a wide range of latitudinal environments.
Histone modulation↗
Dissecting contributions of directional and balancing selection to trajectories of mitochondrial haplotype evolution in Drosophila melanogaster.
Emerging evidence suggests mtDNA haplotypes contribute to fitness variation and local adaptation, with directional thermal selection and negative frequency-dependent selection shaping haplotype diversity. However, their interplay remains unexplored. We conducted experimental evolution using Drosophila melanogaster populations from opposite ends of an Australian latitudinal cline (Melbourne and Townsville), exposing them to contrasting temperatures (17°C versus 27°C) and varying starting frequencies of two mtDNA haplotypes (A1 and B1) that occur at appreciable frequencies in these populations. We paired this with population genetic simulations to estimate selection and its influence on haplotype trajectories. Haplotype frequencies were influenced by interactions involving temperature, starting frequency, and nuclear genomic background (Melbourne, Townsville, or admixed). Although prior work predicted A1 should be favoured at the warmer temperature and B1 at the cooler temperature, A1 was generally favoured across both temperatures. Simulations supported directional selection in populations evolving at 17°C in the Melbourne background; otherwise dynamics were best explained by balancing selection shaped by negative frequency-dependent fitness effects. Patterns also varied across nuclear backgrounds, suggestive of mito-nuclear epistasis. These findings challenge a simple thermal adaptation model of mtDNA dynamics, suggesting that mtDNA evolution is shaped by interacting effects of temperature, frequency-dependence, nuclear background and experimental environment.
adaptation↗
Immunogenetic studies on wild pigs in Japan.
The variations of blood groups in the two subspecies of wild pigs in Japan (Sus scrofa leucomystax and S.s. riukiuanus) were investigated by serological techniques. S.s. leucomystax showed polymorphism in the A and F systems. S.s. riukiuanus showed a little polymorphism in the F system only. As a whole, there was a great similarity in erythrocyte antigen structures of both S.s. leucomystax and S.s. riukiuanus. In comparison with the erythrocyte antigen frequenties of wild pigs in the Eurasian Continent reported by other workers. East-West geographical clines in the frequencies of Ea, Fa, Ga, Ka, Kb and Lh antigens were clearly observed. From the results of investigation on genetic similarities among seven wild pig populations, it was made clear that the two Japanese strains were very close and were closer to Far Eastern TS.s. ussuricus) than Middle Asian (S.s. nigripes), Transcausian (S.s. attila) and European pigs (S.s. ferus).
Animals↗
Experimental Validation of Genome-Environment Associations in Arabidopsis.
Identifying the genetic basis of local adaptation is a key goal in evolutionary biology. Allele frequency clines along environmental gradients, known as genotype-environment associations (GEA), are often used to detect potential loci causing local adaptation but are rarely followed by experimental validation. Here, we tested loci identified in three moisture-related GEA studies on Arabidopsis. We studied 42 GEA-identified genes using t-DNA knockout lines under drought and tested effects on flowering time, an adaptive trait, and genotype-by-environment (GxE) interactions for performance and fitness. In total, 16/42 genes had significant effects on traits involved in local adaptation or performance responses to the environment. We found that wrky38 mutants had significant GxE effects for fitness; lsd1 plants had a significant GxE effect for flowering time, and 11 genes showed flowering time effects with no drought interaction. However, most GEA candidates did not exhibit GxE. In the follow-up experiments, wrky38 caused decreased stomatal conductance and specific leaf area under drought, indicating potentially adaptive drought avoidance. Additionally, GEA identified natural putative LoF variants of WRKY38 associated with dry environments, as well as alleles associated with variation in LSD1 expression. While only a few GEA-identified genes were validated for GxE interactions for fitness, we likely overlooked some genes because experiments might not well represent natural environments and t-DNA insertions might not well represent natural alleles. Nevertheless, GEAs apparently identified some genes contributing to local adaptation. GEA and follow-up experiments are straightforward to implement in model systems and demonstrate prospects for GEA discovery of new local adaptations.
Arabidopsis↗
Synthetic maps of human gene frequencies in Europeans.
Multivarate techniques can be used to condense the information for a large number of loci and alleles into one or a few synthetic variables. The geographic distribution of synthetic variables can be plotted by the same technique used in mapping the gene frequency of a single allele. Synthetic maps were constructed for Europe and the Near East, with the use of principal components to condense the information of 38 independent alleles from ten loci. The first principal component summarizes close to 30% of the total information and shows gradients. Maps thus constructed show clines in remarkable agreement with those expected on the basis of the spread of early farming in Europe, thus supporting the hypothesis that this spread was a demic spread rather than a cultural diffusion of farming technology.
Agriculture↗
[Qualitative study of a mathematical model of the open futile cycle fructose-6-P--fructose-1,6-P2].
A simple mathematical model of the open futile cycle fructose-6-P in equilibrium fructose-1,6-P2 in which the fructose bisphosphatase reaction is inhibited by excess of its substrate has been analysed. A detailed qualitative investigation of the model shows that it possesses all properties characteristic of any other dynamical system of the second order which has a hysteretic major null-cline, 1 to 3 steady states and is capable of generating self-oscillations.
Chemical Phenomena↗
[Geographical pathology and genetic markers: detection of associations (author's transl)].
The study of potential associations between genetic markers and various diseases is an important approach in epidemiology. With such studies it is possible to reveal an hereditary component for multifactorial diseases. There are three kinds of analyses: --comparisons of the frequency of the marker in patients and in a control group; --investigations of genetic markers in families with high incidence of disease; --studies of geographical clines between the incidence of the disease and the marker frequency. The interpretation of such geographical associations is difficult. These associations can be the reflect of the migration of susceptibility genes with genetic markers. The HLA system is the better for this kind of approach.
Breast Neoplasms↗
Recent advances in the aetiology of viral gastroenteritis.
Studies with the human reovirus-like (HRVL) agnet, also designated rotavirus and duovirus, have revealed that it is a major aetiological agent of diarrhoea of infants and young children in many parts of the world. In a study of patients admitted with a diarrhoeal illness to the Children's Hospital of the District of Columbia in the United States from January 1974 to June 1975, it was found that half of the patients studied by both virus shedding (by electron microscopy) and serological (complement-fixation) techniques demonstrated evidence of infection with the HRVL agent. The temporal distribution of infections with the HRVL agent followed a seasonal pattern with this agent being shed exclusively by patients admitted during the cooler months of the year. Electron microscopic examination of stools was as efficient as serological methods for detecting infection with the HRVL agent. We also initiated studies to determine the possible mode of transmission of the HRVL agent by studying contacts of hospitalized patients. We found that 35% parents of patients with HRVL infections were also infected with the HRVL agent. Serological studies revealed that the HRVL agent was antigenically related to the Nebraska Calf Diarrhoea Virus, the epizootic diarrhoea of infant mice virus, the SA-11 virus, and the "O" agent.
Animals↗