Unexpected Linkage Research Articles

Stem cells "aclymatise" to regenerate the blood system.

How blood stem cells balance fate decisions between quiescence maintenance and differentiation during recovery from cancer treatment remains poorly understood. A recent study by Umemoto etal (2022) uncovers an unexpected linkage between metabolic and epigenetic regulation of haematopoiesis, suggesting new targets in haematopoietic regeneration, with possible implications in leukaemogenesis and therapy resistance.

Identification of a dihydropyridine scaffold that blocks ryanodine receptors

SummaryRyanodine receptors (RyRs) are large, intracellular ion channels that control Ca2+ release from the sarco/endoplasmic reticulum. Dysregulation of RyRs in skeletal muscle, heart, and brain has been implicated in various muscle pathologies, arrhythmia, heart failure, and Alzheimer's disease. Therefore, there is considerable interest in therapeutically targeting RyRs to normalize Ca2+ homeostasis in scenarios involving RyR dysfunction. Here, a simple invertebrate screening platform was used to discover new chemotypes targeting RyRs. The approach measured Ca2+ signals evoked by cyclic adenosine 5′-diphosphate ribose, a second messenger that sensitizes RyRs. From a 1,534-compound screen, FLI-06 (currently described as a Notch “inhibitor”) was identified as a potent blocker of RyR activity. Two closely related tyrosine kinase inhibitors that stimulate and inhibit Ca2+ release through RyRs were also resolved. Therefore, this simple screen yielded RyR scaffolds tractable for development and revealed an unexpected linkage between RyRs and trafficking events in the early secretory pathway.

Transcriptome analysis of activated sludge microbiomes reveals an unexpected role of minority nitrifiers in carbon metabolism

Although metagenomics researches have illuminated microbial diversity in numerous biospheres, understanding individual microbial functions is yet difficult due to the complexity of ecosystems. To address this issue, we applied a metagenome-independent, de novo assembly–based metatranscriptomics to a complex microbiome, activated sludge, which has been used for wastewater treatment for over a century. Even though two bioreactors were operated under the same conditions, their performances differed from each other with unknown causes. Metatranscriptome profiles in high- and low-performance reactors demonstrated that denitrifiers contributed to the anaerobic degradation of heavy oil; however, no marked difference in the gene expression was found. Instead, gene expression-based nitrification activities that fueled the denitrifiers by providing the respiratory substrate were notably high in the high-performance reactor only. Nitrifiers—small minorities with relative abundances of <0.25%—governed the heavy-oil degradation performances of the reactors, unveiling an unexpected linkage of carbon- and nitrogen-metabolisms of the complex microbiome.

Genome-wide association multi-locus and multi-variate linear mixed models reveal two linked loci with major effects on partial resistance of apricot to bacterial canker

BackgroundDiseases caused by Pseudomonas syringae (Ps) are recognized as the most damaging factors in fruit trees with a significant economic and sanitary impact on crops. Among them, bacterial canker of apricot is exceedingly difficult to control due to a lack of efficient prophylactic measures. Several sources of partial resistance have been identified among genetic resources but the underlying genetic pattern has not been elucidated thus far. In this study, we phenotyped bacterial canker susceptibility in an apricot core-collection of 73 accessions over 4 years by measuring canker and superficial browning lengths issued from artificial inoculations in the orchard.In order to investigate the genetic architecture of partial resistance, we performed a genome-wide association study using best linear unbiased predictors on genetic (G) and genetic x year (G × Y) interaction effects extracted from linear mixed models.Using a set of 63,236 single-nucleotide polymorphism markers genotyped in the germplasm over the whole genome, multi-locus and multi-variate mixed models aimed at mapping the resistance while controlling for relatedness between individuals.ResultsWe detected 11 significant associations over 7 candidate loci linked to disease resistance under the two most severe years. Colocalizations between G and G × Y terms indicated a modulation on allelic effect depending on environmental conditions. Among the candidate loci, two loci on chromosomes 5 and 6 had a high impact on both canker length and superficial browning, explaining 41 and 26% of the total phenotypic variance, respectively. We found unexpected long-range linkage disequilibrium (LD) between these two markers revealing an inter-chromosomal LD block linking the two underlying genes. This result supports the hypothesis of a co-adaptation effect due to selection through population demography. Candidate genes annotations suggest a functional pathway involving abscisic acid, a hormone mainly known for mediating abiotic stress responses but also reported as a potential factor in plant-pathogen interactions.ConclusionsOur study contributed to the first detailed characterization of the genetic determinants of partial resistance to bacterial canker in a Rosaceae species. It provided tools for fruit tree breeding by identifying progenitors with favorable haplotypes and by providing major-effect markers for a marker-assisted selection strategy.

On cultivating an attitude of precision with language: An uncommon prescription for conditioning creative excellence in scientific discovery and education

Investing years of intensive training, scientists ready themselves to make sense of the world. But are they prepared to make sense of a world of words? The aim of this paper is to explore the pivotal role that cultivating an attitude of precision with language could play in conditioning creative excellence in scientific discovery and education. First, the unexpected linkage between the processes of language precision and successful failure is explored. Next, an attempt is made to situate language precision within the creative process. Then, another potential dividend from developing exactitude with language is explored—the power of neologism. Finally, an attempt is made to construct a useful synthesis—one favoring a new educational prescription in which creative excellence in the sciences is informed and catalyzed by the humanities.

ROS in Nature 2016: Part I

Nature (along with its several sister journals) is among the most highly influential journals that publish cutting edge scientific findings in diverse fields, including biomedical sciences. The purpose of the “ROS in Nature” series is to provide a platform to introduce the high profile research discoveries related to the molecular and cell biology of reactive oxygen species (ROS) published in Nature as well as some of its sister journals, including Nature Medicine, Nature Genetics, and Nature Communications. This “ROS in Nature 2016: Part I” paper highlights the major findings relevant to ROS bioscience, and these findings are reported in four articles in Nature over the past three months (January 1, 2016–March 31, 2016). The major findings from these articles include: (1) a novel role for mitochondrial ROS in regulating thermogenesis and energy expenditure in brown and beige fat; (2) an unexpected linkage between lipid dysfunction and impaired anticancer immunosurveillance, and an essential role for mitochondria-derived ROS in this linkage; (3) autophagy as a decisive stem–cell–fate regulator and an important role for cellular (likely mitochondria-derived) ROS in this process; and finally (4) the involvement of cellular (likely mitochondria-derived) ROS in GCN2-regulated gut inflammation. The elegant studies reported in the four Nature articles attest to the continued excitement about deciphering the detailed biochemistry and cell biology of ROS, species that result from the utilization of molecular oxygen in aerobic organisms. It is hoped that introducing such high profile research discoveries on ROS would help point to the new directions for innovative research in this rapidly evolving area of bioscience.

Crumbs and Xpd in mitosis.

Crumbs and Xpd in mitosis.

A new piece in the kinetochore jigsaw puzzle.

In eukaryotic cell division, the kinetochore mediates chromosome attachment to spindle microtubules and acts as a scaffold for signaling pathways, ensuring the accuracy of chromosome segregation. The architecture of the kinetochore underlies its function in mitosis. In this issue, Hornung et al. (2014. J. Cell Biol. http://dx.doi.org/201403081) identify an unexpected linkage between the inner and outer regions of the kinetochore in budding yeast that suggests a new model for the construction of this interface.

Interleukin-1 Receptor-Associated Kinase-2 (IRAK2) Is a Critical Mediator of Endoplasmic Reticulum (ER) Stress Signaling

Endoplasmic reticulum (ER) stress occurs when unfolded proteins accumulate in the lumen of the organelle, triggering signal transduction events that contribute either to cellular adaptation and recovery or alternatively to cellular dysfunction and death. ER stress has been implicated in numerous diseases. To identify novel modulators of ER stress, we undertook a siRNA library screen of the kinome, revealing Interleukin-1 Receptor-Associated Kinase-2 (IRAK2) as a contributor to unfolded protein response (UPR) signaling and ER stress-induced cell death. Knocking down expression of IRAK2 (but not IRAK1) in cultured mammalian cells suppresses ER stress-induced expression of the pro-apoptotic transcription factor CHOP and activation of stress kinases. Similarly, RNAi-mediated silencing of the IRAK family member Tube (but not Pelle) suppresses activation of stress kinase signaling induced by ER stress in Drosophila cells. The action of IRAK2 maps to the IRE1 pathway, rather than the PERK or ATF6 components of the UPR. Interestingly, ER stress also induces IRAK2 gene expression in an IRE1/XBP1-dependent manner, suggesting a mutually supporting amplification loop involving IRAK2 and IRE1. In vivo, ER stress induces Irak2 expression in mice. Moreover, Irak2 gene knockout mice display defects in ER stress-induced CHOP expression and IRE1 pathway signaling. These findings demonstrate an unexpected linkage of the innate immunity machinery to UPR signaling, revealing IRAK2 as a novel amplifier of the IRE1 pathway.

Abstract 2928: Interleukin-1 receptor-associated kinase-2 (IRAK2) is a critical mediator of endoplasmic reticulum (ER) stress.

Abstract Endoplasmic reticulum (ER) stress occurs when unfolded proteins accumulate in the lumen of the organelle, triggering signal transduction events that contribute either to cellular adaptation and recovery or alternatively to cellular dysfunction and death. ER stress has been implicated in numerous diseases, including cancer where harsh tumor microenvironments induce ER stress and create pressure for evolution of malignant clones that have acquired mechanisms for successful adaptation to stressful environments. To identify novel modulators of ER stress, we undertook a siRNA library screen of the kinome, revealing Interleukin-1 Receptor-Associated Kinase-2 (IRAK2) as a contributor to unfolded protein response (UPR) signaling and ER stress-induced cell death. Knocking down expression of IRAK2 (but not IRAK1) in cultured mammalian cells suppresses ER stress-induced expression of the pro-apoptotic transcription factor CHOP and activation of stress kinases. Similarly, RNAi-mediated silencing of the IRAK family member Tube (but not Pelle) suppresses activation of stress kinase signaling induced by ER stress in Drosophila cells. The action of IRAK2 maps to the IRE1 pathway, rather than the PERK or ATF6 components of the UPR. Interestingly, ER stress also induces IRAK2 gene expression in an IRE1/XBP1-dependent manner, suggesting a mutually supporting amplification loop involving IRAK2 and IRE1. In vivo, ER stress induces Irak2 expression in mice. Moreover, Irak2 gene knockout mice display defects in ER stress-induced CHOP expression and IRE1 pathway signaling. These findings demonstrate an unexpected linkage of the innate immunity machinery to UPR signaling, revealing IRAK2 as a novel amplifier of the IRE1 pathway involved in ER stress signaling. Future analysis of the role of IRAK2 in animal models of cancer will aid in assessing whether IRAK2 provides a novel targets for potential cancer therapeutics development. (Supported by NIH grant AG-15393). Citation Format: Ravanan Palaniyandi, Samir Benosman, Ying-Chen Hou, Ricardo G. Correa, Minjia Yu, Muhammet Fatih Gulen, Xiaoxia Li, James Thomas, Yasuko Matsuzawa, Shu-Ichi Matsuzawa, John C. Reed. Interleukin-1 receptor-associated kinase-2 (IRAK2) is a critical mediator of endoplasmic reticulum (ER) stress. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2928. doi:10.1158/1538-7445.AM2013-2928 Note: This abstract was not presented at the AACR Annual Meeting 2013 because the presenter was unable to attend.

Abstract 2535: Regulation of Chk1 by the mTOR pathway is essential for cancer cells to complete DNA replication in response to replication stress

Abstract Oncogenic signaling leads to DNA replication stress, DNA damage and consequently DNA damage response (DDR), a barrier for tumorigenesis. For survival and proliferation, cancer cells must overcome this oncogene-induced DDR, but the molecular mechanism by which this is achieved is largely unknown. Here we report that the mTOR pathway prevents either spontaneous or drug induced DNA damage by sustaining ATR-Chk1 checkpoint in pediatric rhabdomyosarcoma (RMS) both in vivo and in vitro. Pharmacological inhibition of mTOR signaling by the selective TOR kinase inhibitor AZD8055 lead to spontaneous DNA damage and apoptosis as demonstrated by the induction of H2AX phosphorylation and PARP1 cleavage both in cell culture and tumor xenografts of RMS. Treatment RMS Rh30 cells with AZD8055 enhanced hydroxyurea induced H2AX phosphorylation and attenuated ATR-Chk1 checkpoint activation, as shown by decreased levels of phospho-Chk1(S345). We further found that mTOR signaling controls CHK1 expression at the transcriptional level via enhancing the activity of cyclin dependent kinases (CDKs). Consistent with its essential role for cells to survive DNA replication stress, siRNA-mediated knockdown of Chk1, or inhibition of Chk1 function by a Chk1 kinase inhibitor resulted in H2AX phosphorylation, while ectopic increase of Chk1 attenuated the DNA damage induced by mTOR kinase inhibition. Most importantly, the mTOR kinase inhibitor prevented the slow S-phase progression following DNA replication stress, which was accompanied with a decrease of Chk1 protein levels and phospho-Chk1(S345). Our data suggest that the TORC1/TORC2 pathway promotes RMS tumorigenesis by enhancing the cell survival functions of the ATR-Chk1 checkpoint in response to DNA replication stress. Our findings discovered an important unexpected functional linkage between TOR signaling and the ATR-Chk1 checkpoint signaling cascade and may impact targeting these two prominent cancer cell signaling pathways. Supported by CA77776. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2535. doi:1538-7445.AM2012-2535

Diverse functions of nuclear non-coding RNAs in eukaryotic gene expression

Recent genome-wide analyses revealed that eukaryotic genomes are almost entirely transcribed, generating a large number of short or long non-protein coding RNAs (non-coding RNAs; ncRNAs). Rapidly accumulating experimental evidence suggests that ncRNAs are not just transcriptional noise, but have biological roles in gene expression. In this review, we focus on the functions of nuclear-localized ncRNAs including the spliceosomal small nuclear RNAs. These nuclear ncRNAs play diverse regulatory roles in a wide-range of nuclear reactions, such as transcription, precursor-mRNA (pre-mRNA) splicing, nuclear structure formation, nuclear trafficking, and chromatin remodeling. The regulatory functions of ncRNAs in these reactions are reinforced by target-site recognition through base-pairing or formation of an RNA/DNA triple helix. Recent studies revealed an unexpected linkage between the machineries for RNA interference (RNAi)-mediated gene silencing and pre-mRNA splicing. In addition, the biogenesis of some ncRNAs was found to overlap with the pathway of pre-mRNA splicing. Our understanding of the mechanisms of coordinated gene regulation in the nucleus has increased dramatically through studies on nuclear ncRNAs. A new paradigm of "ncRNA regulation" is now emerging.

Abstract 4774: Epimorphin inhibits mammary epithelial cell apoptosis through induction of IKBKE

Abstract Epimorphin is a stromally produced factor that plays a role in normal mammary branching morphogenesis, but deregulated expression of epimorphin can have oncogenic consequences, although the oncogenic processes activated by epimorphin have not been elucidated. We had previously found that treatment of cultured mammary epithelial cells with epimorphin blocked activation of cell death pathways by a variety of apoptotic stimuli. These results implicated a potential role for epimorphin for inhibition of cellular apoptosis, a critical stage of tumor development. To identify potential mediators by which epimorphin could be affecting cell death pathways, we used a transcriptional profiling approach comparing mammary epithelial cells treated with epimorphin versus untreated cells. We found that epimorphin treatment led to significantly increased expression of IKBKE, which inhibits apoptosis through activation of NF-kappaB and which has recently been characterized as a key breast cancer oncogene. We found that epimorphin specifically blocks induction of apoptosis and activation of caspase-3 in cells treated with tumor necrosis factor-alpha, and that this activity was linked to epimorphin-mediated activation of IKBKE. We also found that knockdown of IKBKE blocked epimorphin-mediated induction of branching morphogenesis, implicating activation of IKBKE by epimorphin as a critical function for its normal morphogenic activities as well. These studies provide insight into an additional and unexpected linkage between mammary gland developmental processes and breast cancer progression. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4774. doi:10.1158/1538-7445.AM2011-4774

A critical test of bivelocity hydrodynamics for mixtures

The present paper provides direct noncircumstantial evidence in support of the existence of a diffuse flux of volume j(v) in mixtures. As such, it supersedes an earlier paper [H. Brenner, J. Chem. Phys. 132, 054106 (2010)], which offered only indirect circumstantial evidence in this regard. Given the relationship of the diffuse volume flux to the fluid's volume velocity, this finding adds additional credibility to the theory of bivelocity hydrodynamics for both gaseous and liquid continua, wherein the term bivelocity refers to the independence of the fluid's respective mass and volume velocities. Explicitly, the present work provides a new and unexpected linkage between a pair of diffuse fluxes entering into bivelocity mixture theory, fluxes that were previously regarded as constitutively independent, except possibly for their coupling arising as a consequence of Onsager reciprocity. In particular, for the case of a binary mixture undergoing an isobaric, isothermal, external force-free, molecular diffusion process we establish by purely macroscopic arguments-while subsequently confirming by purely molecular arguments-the validity of the ansatz j(v)=(v(1)-v(2))j(1) relating the diffuse volume flux j(v) to the diffuse mass fluxes j(1)(=-j(2)) of the two species and, jointly, their partial specific volumes v(1),v(2). Confirmation of that relation is based upon the use of linear irreversible thermodynamic principles to embed this ansatz in a broader context, and to subsequently establish the accord thereof with Shchavaliev's solution of the multicomponent Boltzmann equation for dilute gases [M. Sh. Shchavaliev, Fluid Dyn. 9, 96 (1974)]. Moreover, because the terms v(1), v(2), and j(1) appearing on the right-hand side of the ansatz are all conventional continuum fluid-mechanical terms (with j(1) given, for example, by Fick's law for thermodynamically ideal solutions), parity requires that j(v) appearing on the left-hand side of that relation also be a continuum term. Previously, diffuse volume fluxes, whether in mixtures or single-component fluids, were widely believed to be noncontinuum in nature, and hence of interest only to those primarily concerned with transport phenomena in rarefied gases. This demonstration of the continuum nature of bivelocity hydrodynamics suggests that the latter subject should be of general interest to all fluid mechanicians, even those with no special interest in mixtures.

The Medicago truncatula reference accession A17 has an aberrant chromosomal configuration

Medicago truncatula (barrel medic) has emerged as a model legume and accession A17 is the reference genotype selected for the sequencing of the genome. In the present study we compare the A17 chromosomal configuration with that of other accessions by examining pollen viability and genetic maps of intraspecific hybrids. Hybrids derived from crosses between M. truncatula accessions, representative of the large genetic variation within the germplasm collection, were evaluated for pollen viability using Alexander's stain. Genetic maps were generated for the following crosses: SA27063 x SA3054 (n = 94), SA27063 x A17 (n = 92), A17 x Borung (n = 99) and A17 x A20 (n = 69). All F(1) individuals derived from crosses involving A17 showed 50% pollen viability or less. Examination of the recombination frequencies between markers of chromosomes 4 and 8 revealed an apparent genetic linkage between the lower arms of these chromosomes in genetic maps derived from A17. Semisterility and unexpected linkage relationship are both good indicators of a reciprocal translocation. The implications of the A17 distinctive chromosomal rearrangement on studies of genetic mapping, genome sequencing and synteny between species are discussed.

How to Say Things with Guns: Military Technology and the Politics of Robinson Crusoe

How to Say Things with Guns:Military Technology and the Politics of Robinson Crusoe Christopher F. Loar (bio) As for the gun it self, he would not so much as touch it for several days after; but would speak to it, and talk to it, as if it had answer'd him, when he was by himself; which, as I afterwards learn'd of him, was to desire it not to kill him.1 Friday may understand Robinson Crusoe's gun better than Crusoe does. In the scene noted in the epigraph above, although Friday is innocent of the gun's inner workings, he sees something that Crusoe has missed: Crusoe's power to dispense violence, rather than cultural authority or friendship, has started Friday down the path towards civility and virtue. Conversely, Crusoe's disavowal of his own violence reverberates throughout the novel, from his escape from the Barbary captivity to his trip across the Pyrenees at the novel's end. But his disavowal is particularly pronounced in the novel's precolonial settings: Africa and Crusoe's Caribbean island. In the scenes of colonial encounter and technological power, Daniel Defoe uses Crusoe and his gun to explore the operations of violence in politics, as well as the ways in which the ideology of British liberty veils that violence. Crusoe's weapons serve as a figure for the violence and warfare that lurk at the foundational moment of sovereignty as well as of the ideology of liberty that makes sovereignty's violence tolerable. [End Page 1] Though many scholars have noted the prominence of violence in Defoe's Life and Strange Surprising Adventures of Robinson Crusoe (1719), identifying the particular significance of that violence has proved elusive. Once considered an exemplification of Lockean theory, the novel has more recently been understood in relation to postcolonial theory or critical race studies.2 This shift in focus is propelled in part by the increasingly visible connections between seventeenth-century political theory and imperial practices. John Locke's Second Treatise, with its defence of labour and enclosure as that which confers ownership of land and property, is highlighted in Britain's defence of its management of colonies and plantations. The connection between contemporary political theory and imperial practice is nowhere clearer than in the novel's setting—the late seventeenth-century Caribbean, where French and British settlers sought to cultivate land that appeared, to their eyes, essentially unused by the inhabitants, the Caribs.3 Thus previous criticism that sought to locate Robinson Crusoe in the tradition of Locke and Hobbes has been confronted by a newer criticism that locates the novel's central problems in the birth of a violent British empire. But few scholars have pointed out the specific ways in which Defoe's first novel connects the violence of its colonial setting with the political controversies in the imperial centre. Among those who have examined the novel's connection of colonial violence and [End Page 2] British politics, Manuel Schonhorn and Carol Kay offer the most provocative accounts. Schonhorn links the novel to a shift in Defoe's political orientation towards sympathy with royalism and sovereignty, seeing the island as an experimental setting for those ideas.4 Kay, on the other hand, sees Defoe's novel as an engagement with the fraught nature of contractual relationships, and downplays the importance of absolute sovereignty on Crusoe's island as simply a brief and transitional phase of political development.5 These approaches both have merit, but neither entirely accounts for the novel's unexpected linkage of violence and technology with scenes of contract and consent in a text that strongly emphasizes the island as a space of cultural and political contact. I will argue that Robinson Crusoe offers a meditation on the scene of colonial encounter and its disturbance of British political thought, and that Crusoe's colonialism stands in a synecdochal relationship to politics more generally. I will examine Defoe's first novel in light of a question posed by Michel Foucault: Are "military institutions, and the practices that surround them—and in more general terms all the techniques that are used to fight a war— ... the nucleus of political institutions?"6...

Late blight resistance linkages in a novel cross of the wild potato species Solanum paucissectum (series Piurana)

The cultivated potato, Solanum tuberosum, is affected by a variety of diseases with late blight, caused by Phytophthora infestans, being the most severe. Wild potato species have proven to be a continuing source of resistance, sometimes of an extreme type, to this disease. The present study constructs the first late blight linkage map of a member of series Piurana, S. paucissectum, a tuber-bearing relative of potato, using probes for conserved sequences from potato and tomato. Eight probes mapped to unexpected linkage groups, but syntenic differences with prior maps of potato were not supported by any blocks of rearranged chromosome segments. All 12 linkage groups were resolved and significant associations with late blight resistance were found on chromosomes 10, 11 and 12. A major quantitative trait locus (QTL) on chromosome 11 accounts for more than 25% of the phenotypic variance measured in a field trial. Crossing of S. paucissectum with cultivated potato resulted in very few seeds indicating partial reproductive barriers. Differential reactions of accessions of this potential donor species with simple and complex isolates of P. infestans suggest that it carries major resistance genes that are not those previously described from the Mexican species, S. demissum. However, the additivity of the QTL effects argues for the quantitative nature of resistance in this cross.

Close Physical Linkage of Human Troponin Genes: Organization, Sequence, and Expression of the Locus Encoding Cardiac Troponin I and Slow Skeletal Troponin T

Based on chromosomal mapping data, we recently revealed an unexpected linkage of troponin genes in the human genome: the six genes encoding striated muscle troponin I and troponin T isoforms are located at three chromosomal sites, each of which carries a troponin I–troponin T gene pair. Here we have investigated the organization of these genes at the DNA level in isolated P1 and PAC genomic clones and demonstrate close physical linkage in two cases through the isolation of individual clones containing a complete troponin I–troponin T gene pair. As an initial step toward fully characterizing this pattern of linkage, we have determined the organization and complete sequence of the locus encoding cardiac troponin I and slow skeletal troponin T and thereby also provide the first determination of the structure and sequence of a slow skeletal troponin T gene. Our data show that the genes are organized head to tail and are separated by only 2.6 kb of intervening sequence. In contrast to other troponin genes, and despite their close proximity, the cardiac troponin I and slow skeletal troponin T genes show independent tissue-specific expression. Such close physical linkage has implications for the evolution of the troponin gene families, for their regulation, and for the analysis of mutations implicated in cardiomyopathy.

A novel isoform of platelet glycoprotein Ib alpha is prevalent in African Americans.

The heavy chain of platelet glycoprotein Ib (GPIb) contains two prevalent sequence polymorphisms. The first, Thr/Met145 is responsible for the human platelet alloantigen system, human platelet antigen (HPA)-2. The second is a tandem repeat polymorphism that consists of four variants, A, B, C, and D. Previous linkage studies in Caucasian and Eastern Asian populations have demonstrated that HPA-2a (Thr145) is associated with variants C and D, while HPA-2b (Met145) is associated with variants A and B. We have determined HPA-2 and variable number of tandem repeats (VNTR) genotypes in three different North American ethnic groups. The gene frequency of HPA-2b in the North American Indians was intermediate between African Americans and Caucasians, and similar to the frequency previously reported in Japanese. Furthermore, the VNTR-A allele, which previously has been reported only in Eastern Asian populations, was present in two of 101 North American Indian individuals. These data are consistent with the hypothesis that the first Native Americans migrated to North America from Eastern Asia. Analysis of HPA-2 and VNTR haplotypes demonstrated an unexpected linkage pattern in the African American population. A rare GPIb alpha isoform, HPA-2b/VNTR-C, was present in 2.2% of African American haplotypes. Furthermore, a novel GPIb alpha isoform, HPA-2a/VNTR-B, was present in 6.5% of African American haplotypes. These data suggest a more complex evolutionary pattern of GPIb alpha isoforms than previously proposed.

New alleles of the platelet glycoprotein Ibalpha gene.

Platelet membrane glycoprotein Ibalpha (GP Ibalpha) bears two molecular polymorphisms which are in linkage disequilibrium: the C/T dimorphism at codon 145 (HPA-2) and the variable number of tandem repeats (VNTR) polymorphism in the macroglycopeptide region. The frequencies of these two polymorphisms, and of another three recently described silent polymorphisms, were investigated by genotypic identification in 729 Caucasian individuals from the south of Spain. Eight different alleles of this gene, including the longest VNTR A allele of the GP Ibalpha gene, were found in this population. Moreover, we detected an unexpected linkage between the B and A variants of the VNTR polymorphism and the HPA-2a allele in 5.9% of this population. These results suggest a new evolutionary model of GP Ibalpha, in which homologous recombination could account for the genetic diversity of the GP Ibalpha.