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Summary: Chromosomal inversions occur in natural populations of many species, and may underlie reproductive isolation and local adaptation. Traditional methods of inversion discovery are labor‐intensive and lack sensitivity. Here, we report the use of three‐dimensional contact probabilities between genomic loci as assayed by chromosome‐conformation capture sequencing (Hi‐C) to detect multi‐megabase polymorphic inversions in four barley genotypes. Inversions are validated by fluorescence in situ hybridization and Bionano optical mapping. We propose Hi‐C as a generally applicable method for inversion discovery in natural populations. Significance Statement: This paper reports a method to detect megabase‐scale chromosomal inversions in plant species with large genomes through chromosome conformation capture sequencing. [ABSTRACT FROM AUTHOR]

The three dimensional folding of mammalian genomes is cell type specific and difficult to alter suggesting that it is an important component of gene regulation. However, given the multitude of chromatin-associating factors, the mechanisms driving the colocalization of active chromosomal domains and the role of this organization in regulating the transcription program in adipocytes are not clear. Analysis of genome-wide chromosomal associations revealed cell type-specific spatial clustering of adipogenic genes in 3T3-L1 cells. Time course analysis demonstrated that the adipogenic 'hub', sampled by PPARγ and Lpin1, undergoes orchestrated reorganization during adipogenesis. Coupling the dynamics of genome architecture with multiple chromatin datasets indicated that among all the transcription factors (TFs) tested, RXR is central to genome reorganization at the beginning of adipogenesis. Interestingly, at the end of differentiation, the adipogenic hub was shifted to an H3K27me3-repressive environment in conjunction with attenuation of gene transcription. We propose a stage-specific hierarchy for the activity of TFs contributing to the establishment of an adipogenic genome architecture that brings together the adipogenic genetic program. In addition, the repositioning of this network in a H3K27me3-rich environment at the end of differentiation may contribute to the stabilization of gene transcription levels and reduce the developmental plasticity of these specialized cells. Database All sequence data reported in this paper have been deposited at GEO () () [ABSTRACT FROM AUTHOR]

N6‐methyladenosine (m6A) is the most prevalent internal modification in mammalian messenger RNAs and is associated with numerous biological processes. However, its role in chromosomal instability remains to be established. Here, we report that an RNA m6A methyltransferase, METTL16, plays an indispensable role in the progression of chromosome segregation and is required to preserve chromosome stability in colorectal cancer (CRC) cells. Depletion or inhibition of the methyltransferase activity of METTL16 results in abnormal kinetochore‐microtubule attachment during mitosis, leading to delayed mitosis, lagging chromosomes, chromosome mis‐segregation and chromosomal instability. Mechanistically, METTL16 exerts its oncogenic effects by enhancing the expression of suppressor of glucose by autophagy 1 (Soga1) in an m6A‐dependent manner. CDK1 phosphorylates Soga1, thereby triggering its direct interaction with the polo box domain of PLK1. This interaction facilitates PLK1 activation and promotes mitotic progression. Therefore, targeting the METTL16‐Soga1 pathway may provide a potential treatment strategy against CRC because of its essential role in maintaining chromosomal stability. [ABSTRACT FROM AUTHOR]

The successful progression of meiosis prophase I requires integrating information from the structural and molecular levels. In this study, we show that ZFP541 and KCTD19 work in the same genetic pathway to regulate the progression of male meiosis and thus fertility. The Zfp541 and/or Kctd19 knockout male mice show various structural and recombination defects including detached chromosome ends, aberrant localization of chromosome axis components and recombination proteins, and globally altered histone modifications. Further analyses on RNA‐seq, ChIP‐seq, and ATAC‐seq data provide molecular evidence for the above defects and reveal that ZFP541/KCTD19 activates the expression of many genes by repressing several major transcription repressors. More importantly, we reveal an unexpected role of ZFP541/KCTD19 in directly modulating chromatin organization. These results suggest that ZFP541/KCTD19 simultaneously regulates the transcription cascade and chromatin organization to ensure the coordinated progression of multiple events at chromosome structural and biochemical levels during meiosis prophase I. [ABSTRACT FROM AUTHOR]

The use of genomic testing in pregnancy is increasing, giving rise to questions over how the information that is generated should be offered and returned in clinical practice. While these tests provide important information for prenatal decision‐making, they can also generate information of uncertain significance. This paper critically examines three models for approaching the disclosure of variants of uncertain significance (VUS), which can arise from forms of genomic testing such as prenatal chromosomal microarray analysis (CMA). Contrary to prevailing arguments, we argue that respect for reproductive autonomy does not justify adopting a model on which an offer to disclose VUS is a routine part of genetic counselling. Instead, we contend that a commitment both to solidarity between healthcare providers and pregnant women and to the acceptance of a novel principle of caution under normative uncertainty means that we should instead adopt a model of VUS disclosure that imposes a strong presumption against offering to disclose VUS. The upshot of this is that it should be standard practice to only offer to disclose VUS when this is requested by the woman undergoing CMA. We defend our position against claims that arise from an alleged right to such information and that a presumption against an offer will lead to inequity. [ABSTRACT FROM AUTHOR]

The physical map of 2C DNA (cf. following paper in this journal) was compared to the maps of SP0t, SP82 and Φe (three other Bacillus subtilis phages containing hydroxymethyluracil in place of thymine in their DNA). The overall organization of the four genomes was remarkably similar, as indicated by the topology of HaeIII and Sa/J cleavage segments. The proof was gathered for the presence in the four phage DNAs of large redundant ends carrying a single HaeIII recognition site. The location of the latter proved identical for 2C and SP01, but was shifted in the DNAs of SP 82 and Φe. Since the redundant end components of these hydroxymetbyluracil genomes are colinear, as shown by crossahybridization studies, the shifting of the HaeIII cleavage site is presumably due to two base substitutions, suppressing an endonuclease recognition site and establishing a new site elsewhere. Relatedness between the genomes of this family of viruses was evaluated from the fraction of conserved restriction fragments. According to these calculations. 6% base substitutions have occurred within the four viral DNAs, in the course of evolution. However, specific segments of 2 C DNA were not present in SP01 and Φe DNA, as shown by cross- hybridization with restriction fragments. These data indicate the occurrence of deletions, in addition to base substitutions, as evolutionary mechanisms prevailing in the genomes of this family of phages. [ABSTRACT FROM AUTHOR]

Life‐history theory predicts that reproductive investments are traded‐off against self‐maintenance. Telomeres, the protective caps on the ends of chromosomes, offer a promising avenue for assessing life‐history trade‐offs, as they shorten in response to stressors and are predictive of the remaining lifespan. In males, testosterone frequently mediates life‐history trade‐offs, in part, through its effects on sexual ornamentation, which is an important aspect of reproductive investment. However, studies of within‐individual associations between telomere dynamics and sexual ornamentation are limited in number and have produced mixed results. Furthermore, most such studies have been observational, making it difficult to discern the nature of any causal relationship. To address this, we used short‐acting testosterone implants in free‐living male superb fairy‐wrens (Malurus cyaneus) to stimulate the production of a sexual ornament: early moult into a costly blue breeding plumage. We found no evidence that elevated testosterone, and the consequent earlier moult into breeding plumage, accelerated telomere shortening. We therefore followed up with a systematic review and two meta‐analyses (28 studies, 54 effect sizes) exploring the associations between telomeres and (1) testosterone and (2) sexual ornamentation. In line with our experimental findings, neither meta‐analysis showed an overall correlation of testosterone or sexual ornamentation with telomere length or telomere dynamics. However, meta‐regression showed that experimental, compared to observational, studies reported greater evidence of trade‐offs. Our meta‐analyses highlight the need for further experimental studies to better understand potential responses of telomere length or telomere dynamics to testosterone or sexual ornamentation. [ABSTRACT FROM AUTHOR]

The article offers information on the International Organization of Plant Biosystematists (IOPB), that was established in 1960 to promote global cooperation in the study of biosystematics. IOPB, an interest group of International Association for Plant Taxonomy (IAPT), focuses on publishing chromosome number reports. IOPB has been organizing conferences since 1983 to bring various biosystematic research in light.

In the age of noninvasive prenatal testing, there is still an important role for invasive prenatal diagnosis, even for chromosomes 13, 18, and 21. [ABSTRACT FROM AUTHOR]

Background: Beckwith‐Wiedemann syndrome and Silver‐Russel syndrome are two imprinting disorders caused by opposite molecular alterations in 11p15.5. With the current diagnostic tests, their molecular diagnosis is challenging due to molecular heterogeneity and mosaic occurrence of the most frequent alterations. As the determination of precise (epi)genotype of patients is relevant as the basis for a personalized treatment, different approaches are needed to increase the sensitivity of diagnostic testing of imprinting disorders. Methods: We established methylation‐specific droplet digital PCR approaches (MS‐ddPCR) for the two imprinting centers in 11p15.5, and analyzed patients with paternal uniparental disomy of chromosome 11p15.5 (upd(11)pat) and other imprinting defects in the region. The results were compared to those from MS‐MLPA (multiplex ligation‐dependent probe amplification) and MS‐pyrosequencing. Results: MS‐ddPCR confirmed the molecular alterations in all patients and the results matched well with MS‐MLPA. The results of MS‐pyrosequencing varied between different runs, whereas MS‐ddPCR results were reproducible. Conclusion: We show for the first time that MS‐ddPCR is a reliable and easy applicable method for determination of MS‐associated changes in imprinting disorders. It is therefore an additional tool for multimethod diagnostics of imprinting disorders suitable to improve the diagnostic yield. [ABSTRACT FROM AUTHOR]

Summary: Asparagus bean (Vigna unguiculata ssp. sesquipedialis), a subspecies of V. unguiculata, is a vital legume crop widely cultivated in Asia for its tender pods consumed as vegetables. However, the existing asparagus bean assemblies still contain numerous gaps and unanchored sequences, which presents challenges to functional genomics research. Here, we present an improved reference genome sequence of an elite asparagus bean variety, Fengchan 6, achieved through the integration of nanopore ultra‐long reads, PacBio high‐fidelity reads, and Hi‐C technology. The improved assembly is 521.3 Mb in length and demonstrates several enhancements, including a higher N50 length (46.4 Mb), an anchor ratio of 99.8%, and the presence of only one gap. Furthermore, we successfully assembled 14 telomeres and all 11 centromeres, including four telomere‐to‐telomere chromosomes. Remarkably, the centromeric regions cover a total length of 38.1 Mb, providing valuable insights into the complex architecture of centromeres. Among the 30 594 predicted protein‐coding genes, we identified 2356 genes that are tandemly duplicated in segmental duplication regions. These findings have implications for defence responses and may contribute to evolutionary processes. By utilizing the reference genome, we were able to effectively identify the presence of the gene VuMYB114, which regulates the accumulation of anthocyanins, thereby controlling the purple coloration of the pods. This discovery holds significant implications for understanding the underlying mechanisms of color determination and the breeding process. Overall, the highly improved reference genome serves as crucial resource and lays a solid foundation for asparagus bean genomic studies and genetic improvement efforts. [ABSTRACT FROM AUTHOR]

This paper describes a method for the identification of single copy genes in Drosophila melanogaster polytene chromosomes, using fluorescence in situ hybridization (FISH). We demonstrate the detection of white (w), a gene previously mapped to 1-1.5 region of the linkage map, and to 3C2 region of the cytogenetic map of X chromosome. Squash preparations of polytene chromosomes from salivary glands dissected out from third instar larvae of Drosophila melanogaster were denatured and subjected to hybridization with a digoxigenin labeled probe, corresponding to mini-white gene. The preparations were then washed and incubated with anti-digoxigenin-fluorescein antibodies. After removal of the nonspecifically bound antibodies, the polytene chromosomes were counterstained with propidium iodide. Fluorescence microscopy revealed white locus in the X chromosome in a subterminal location, in agreement with the above mentioned maps. The protocol is efficient and adaptable for simultaneously multiple signal detection.

Many common diseases are known to have genetic components, but since they are non-Mendelian, i.e. a large number of genetic factors affect the phenotype, these components are difficult to localize. These traits are often called complex and analysis of siblings is a valuable tool for mapping them. It has been shown that the power of the affected relative pairs method to detect linkage of a disease susceptibility locus depends on the locus contribution to increased risk of relatives compared with population prevalence ( Risch, 1990a,b ). In this paper we generalize calculation of relative risk to arbitrary phenotypes and genetic models, but also show that the relative risk can be split into the relative risk at the main locus and the relative risk due to interaction between the main locus and loci at other chromosomes. We demonstrate how the main locus contribution to the relative risk is related to probabilities of allele sharing identical by descent at the main locus, as well as power to detect linkage. To this end we use the effective number of meioses, introduced by Hössjer (2005a) as a convenient tool. Relative risks and effective number of meioses are computed for several genetic models with binary or quantitative phenotypes, with or without polygenic effects. [ABSTRACT FROM AUTHOR]

The correct formation of stable but dynamic links between chromosomes and spindle microtubules (MTs) is essential for accurate chromosome segregation. However, the molecular mechanisms by which kinetochores bind MTs and checkpoints monitor this binding remain poorly understood. In this paper, we analyze the functions of six kinetochore-bound MT-associated proteins (kMAPs) using RNAi, live-cell microscopy and quantitative image analysis. We find that RNAi-mediated depletion of two kMAPs, the adenomatous polyposis coli protein (APC) and its binding partner, EB1, are unusual in affecting the movement and orientation of paired sister chromatids at the metaphase plate without perturbing kinetochore–MT attachment per se. Quantitative analysis shows that misorientation phenotypes in metaphase are uniform across chromatid pairs even though chromosomal loss (CIN) during anaphase is sporadic. However, errors in kinetochore function generated by APC or EB1 depletion are detected poorly if at all by the spindle checkpoint, even though they cause chromosome missegregation. We propose that impaired EB1 or APC function generates lesions invisible to the spindle checkpoint and thereby promotes low levels of CIN expected to fuel aneuploidy and possibly tumorigenesis. [ABSTRACT FROM AUTHOR]

Normal human somatic cells have a limited division potential when they grow in vitro. It is believed that shortening of telomeres, specialized structures at the ends of chromosomes, controls cell growth. When one telomere achieves a critical minimal length, the cell cycle control mechanism recognizes it as DNA damage and causes the cell's exit from the cycle in G1-phase. Because it is not possible to extend telomeres in normal cells, this non-dividing state is prolonged indefinitely, and is known as cellular senescence. The immortal cell line MDA-MB-231 has active telomerase, which prevents telomere shortening and allows cells’ permanent divisions. However, there is a fraction of cells that do not divide over several days in culture as documented for some other tumour cell lines. Combination of methods has made it possible to isolate these non-growing cells and compare them with the fraction of fast-growing cells from the same culture. Although the non-growing fraction contains a significant percentage of typical senescent cells, both fractions have equal telomerase activity and telomere length. In this paper we discuss possible mechanisms that cause the appearance of this non-growing fraction of cells in cultures of MDA-MB-231, which indicate stress and genome instability rather than variation in telomerase activity or telomere shortening to affect individual cells. [ABSTRACT FROM AUTHOR]

Presents abstracts of papers presented at the 33rd European Mathematical Genetics Meeting, EMGM 2005, held in Le Kremlin-Bicêtre, France, in April 2005. "A method for homozygosity mapping which allows for missing genealogical information," by Y. S. Aulchenko and C. M. van Duijn; "Appropriate Treatment of the Correlation Structure in Chromosome-Wide Haplotype-Based Association Analysis," by Tim Becker and Michael Knapp.

Eukaryotic genomes are composed of isochores, i.e. long sequences relatively homogeneous in GC content. In this paper, the isochore structure of Arabidopsis thaliana genome has been studied using a windowless technique based on the Z curve method and intuitive curves are drawn for all the five chromosomes. Using these curves, we can calculate the GC content at any resolution, even at the base level. It is observed that all the five chromosomes are composed of several GC-rich and AT-rich regions alternatively. Usually, these regions, named ‘isochore-like regions’, have large fluctuations in the GC content. Five isochores with little fluctuations are also observed. Detailed analyses have been performed for these isochores. A GC-rich ‘isochore-like region’ and a GC-isochore in chromosome II and IV, respectively, are the nucleolar organizer regions (NORs), and genes located in the two regions prefer to use GC-ending codons. Another GC-isochore located in chromosome II is a mitochondrial DNA insertion region, the position and size of this region is precisely predicted by the current method. The amino acid usage and codon preference of genes in this organellar-to-nuclear transfer region show significant difference from other regions. Moreover, the centromeres are located in GC-rich ‘isochore-like regions’ in all the five chromosomes. The current method can provide a useful tool for analyzing whole genomic sequences of eukaryotes. [ABSTRACT FROM AUTHOR]

Haplotype based linkage disequilibrium (LD) mapping exhibits higher power than the single locus approach because it makes use of the LD information contained in the flanking markers. New statistical methods have been proposed to help to infer haplotype effects on human diseases using multi-locus genotype data collected from unrelated individuals. In this paper, we introduce a statistical procedure for measuring haplotype effects on human survival using the popular logistic regression model with haplotype based parameterizations. By modeling haplotype frequency as a function of age, our model infers haplotype effects by estimating and testing the slope parameters under different genetic mechanisms (multiplicative, dominant, or recessive). In addition, by estimating the sex-specific slope parameters, our model allows the detection of sex-specific haplotype effects or haplotype-sex interactions. As an example, we apply our model to an empirical dataset on a stress related gene,interleukin-6, to look for haplotypes that affect individual survival and for haplotype-sex interactions. We show that our logistic regression based haplotype model can be a helpful tool for researchers interested in the genetics of human aging and longevity. [ABSTRACT FROM AUTHOR]

Late-onset Alzheimer's disease (AD) is a complex and multifactorial disease with the possible involvement of several genes. Apolipoprotein E ( APOE), especially the APOE* 4 allele, has been established as a strong susceptibility marker that accounts for nearly 30% of the risk in late-onset AD. However, as the APOE* 4 allele is neither necessary nor sufficient for the development of AD, it emphasizes the involvement of other genetic and/or environmental factors which, alone or in conjunction with APOE* 4, can modify the risk of AD. Recently, genome-wide linkage or linkage disequilibrium studies on late-onset AD have provided informative data for the existence of multiple putative genes for AD on several chromosomes, with the strongest evidence on chromosomes 12, 10, 9 and 6. This paper attempts to review the current progress on the identification of additional genetic loci for late-onset AD. [ABSTRACT FROM AUTHOR]

Bacterial plasmids introduced into the human malaria parasite Plasmodium falciparum replicate well but are poorly segregated during mitosis. In this paper, we screened a random P.falciparum genomic library in order to identify sequences that overcome this segregation defect. Using this approach, we selected for parasites that harbor a unique 21 bp repeat sequence known as Rep20. Rep20 is one of six different repeats found in the subtelomeric regions of all P.falciparum chromosomes but which is not found in other eukaryotes or in other plasmodia. Using a number of approaches, we demonstrate that Rep20 sequences lead to dramatically improved episomal maintenance by promoting plasmid segregation between daughter merozoites. We show that Rep204, but not Rep20, plasmids colocalize with terminal chromosomal clusters, indicating that Rep20 mediates plasmid tethering to chromosomes, a mechanism that explains the improved segregation phenotype. This study implicates a direct role for Rep20 in the physical association of chromosome ends, which is a process that facilitates the generation of diversity in the terminally located P.falciparum virulence genes. [ABSTRACT FROM AUTHOR]

Introduction: In the era of precision preventive medicine, susceptible genetic markers for oro‐/hypopharyngeal squamous cell carcinoma (OPSCC) have been investigated for genome‐wide associations. Materials and Methods: A case–control study including 659 male head and neck squamous cell carcinoma (HNSCC) patients, including 331 oropharyngeal cancer, treated between March 1996 and December 2016 and 2400 normal controls was performed. A single‐nucleotide polymorphism (SNP) array was used to determine genetic loci that increase susceptibility to OPSCC. Results: We analyzed the allele frequencies of 664,994 autosomal SNPs in 659 HNSCC cases; 7 SNPs scattered in loci of chromosomes 5, 7, 9, 11, and 19 were significant in genome‐wide association analysis (Pc < 1.0669 × 10−7). In OPSCCs (n = 331), two clustered regions in chromosomes 4 and 6 were significantly different from the controls. We successfully identified a missense alteration of the SNP region in alcohol dehydrogenase 1B (ADH1B) (https://genome.ucsc.edu; hg38); the top correlated locus was rs1229984 (p = 1 × 10−11). Adjusted for environmental exposure, including smoking, alcohol, and areca quid, a region in chromosome 12, related to alcohol metabolism, was found to independently increase the susceptibility to OPSCC. The ADH1B rs1229984 AA genotype had better overall survival compared to the AG and GG genotypes (p = 0.042) in OPSCC. The GG genotype in rs1229984 was significantly associated with a younger age of onset than other genotypes (p = 0.001 and <0.001, respectively) in OPSCC patients who consumed alcohol. Conclusion: ADH1B was an important genetic locus that significantly correlated with the development of OPSCCs and patient survival. [ABSTRACT FROM AUTHOR]

Deciphering variations in chromosome conformations based on bulk three‐dimensional (3D) genomic data from heterogenous tissues is a key to understanding cell‐type specific genome architecture and dynamics. Surprisingly, computational deconvolution methods for high‐throughput chromosome conformation capture (Hi‐C) data remain very rare in the literature. Here, a deep convolutional neural network (CNN), deconvolve bulk Hi‐C data (deCOOC) that remarkably outperformed all the state‐of‐the‐art tools in the deconvolution task is developed. Interestingly, it is noticed that the chromatin accessibility or the Hi‐C contact frequency alone is insufficient to explain the power of deCOOC, suggesting the existence of a latent embedded layer of information pertaining to the cell type specific 3D genome architecture. By applying deCOOC to in‐house‐generated bulk Hi‐C data from visceral and subcutaneous adipose tissues, it is found that the characteristic chromatin features of M2 cells in the two anatomical loci are distinctively bound to different physiological functionalities. Taken together, deCOOC is both a reliable Hi‐C data deconvolution method and a powerful tool for functional extraction of 3D genome architecture. [ABSTRACT FROM AUTHOR]

SUMMARY: Mitosis and cytokinesis are fundamental processes through which somatic cells increase their numbers and allow plant growth and development. Here, we analyzed the organization and dynamics of mitotic chromosomes, nucleoli, and microtubules in living cells of barley root primary meristems using a series of newly developed stable fluorescent protein translational fusion lines and time‐lapse confocal microscopy. The median duration of mitosis from prophase until the end of telophase was 65.2 and 78.2 min until the end of cytokinesis. We showed that barley chromosomes frequently start condensation before mitotic pre‐prophase as defined by the organization of microtubules and maintain it even after entering into the new interphase. Furthermore, we found that the process of chromosome condensation does not finish at metaphase, but gradually continues until the end of mitosis. In summary, our study features resources for in vivo analysis of barley nuclei and chromosomes and their dynamics during mitotic cell cycle. Significance Statement: We studied 3D chromosome organization and nuclear and microtubule dynamics in the live root apical meristems using a newly developed series of barley (Hordeum vulgare) translational fusion fluorescent marker lines. We measured the duration of the mitotic stages and analyzed the arrangement of specific cellular components such as chromosomes, nucleoli, and mitotic microtubules. We bring new insights into the dynamics of chromosome (de)condensation and microtubule organization during mitosis. [ABSTRACT FROM AUTHOR]

The Escherichia coli chromosome contains about 300 bacterial interspersed mosaic elements (BIMEs). These elements, located at the 3' end of genes, are composed of three types of alternating repetitive extragenic palindromes (REPs). Based on the type of REP they contain and on their ability to interact with the integration host factor (IHF), BIMEs are subdivided into two families: BIME-1 elements contain an IHF binding site flanked by converging Y and Z1 REPs, whereas BIME-2 elements contain a variable number of alternating Y and Z2 REPs without an IHF site. Although some BIMEs have been implicated in the protection of mRNA against 3' exonucleolytic degradation, the main role of elements belonging to both families remains to be elucidated. In this paper, we used oxolinic acid, a drug that reveals potential sites of DNA gyrase action, to demonstrate that DNA gyrase interacts in vivo with BIME-2 elements. The frequency of cleavage varied from one element to another, and the cleavage pattern observed in elements containing several REPs indicated that DNA gyrase cut DNA every two REPs. A single cleavage site has been identified in the Y REP in six out of seven instances, and the nucleotide sequence of a 44 bp fragment containing the scission point displayed conserved residues at six positions. The lack of one of the conserved residues accounted for the absence of cleavage in most of the Z2 REPs. Our results also showed that cleaved REPs were always associated with another REP, suggesting that a pair of diverging REPs constitutes the target of DNA gyrase. DNA gyrase cleavage at repetitive BIME-2 elements may have consequences for DNA topology and genomic rearrangements. [ABSTRACT FROM AUTHOR]

Members of two genera of Gram-negative bacteria, Serratia and Erwinia, produce a β-lactam antibiotic, 1-carbapen-2-em-3-carboxylic acid. We have reported previously the cloning and sequencing of the genes responsible for production of this carbapenem in Erwinia carotovora. These genes are organized as an operon, carA-H, and are controlled by a LuxR-type transcriptional activator, encoded by the linked carR gene. We report in this paper the genetic dissection of this putative operon to determine the function of each of the genes. We demonstrate by mutational analysis that the products of the first five genes of the operon are involved in the synthesis of the carbapenem molecule. Three of these, carABC, are absolutely required. In addition, we provide evidence for the existence of a novel carbapenem resistance mechanism, encoded by the carF and carG genes. Both products of these overlapping and potentially traznslationally coupled genes have functional, N-terminal signal peptides. Removal of these genes from the Erwinia chromosome results in a carbapenem-sensitive phenotype. We assume that these novel β-lactam resistance genes have evolved in concert with the biosynthetic genes to ensure 'self-resistance' in the Erwinia carbapenem producer. [ABSTRACT FROM AUTHOR]

The uropathogenic Escherichia coli strain 536 (O6:K15:H31) carries two unstable DNA regions on its chromosome which were termed pathogenicity islands (Pais). Both pathogenicity islands, Pai I and Pai II, are incorporated into tRNA specific loci: Pai I is located in the tRNA gene for selenocysteine (selC), and Pai II is integrated in the leucine-specific tRNA locus leuX. Mutant strain 536-21 has lost the two pathogenicity islands together with the intact tRNA genes. While 536 is a virulent strain, 536-21 has lost a number of properties, including in vivo virulence. In previous publications we reported that the genes coding for two haemolysins (hly I, hly II) and P-related fimbria (prf) are located on the Pais. In this paper, we demonstrate that the expression of other gene products influencing metabolic properties in addition to in vivo virulence are strongly dependent on the intact tRNA loci selC and leuX. In order to determine the influence of the two tRNAs on the expression of these properties, the genes selC and leuX were cloned from the genome of strain 536 and then introduced into the mutant 536-21. Our results clearly show that the seleno-cysteine-specific tRNA (tRNASec) directly influences the ability of the bacteria to grow under anaerobic conditions, because selenocysteine is part of the enzyme formate dehydrogenase (FDH) which is involved in mixed acid fermentation. The rare leucine-specific tRNA5Leu, encoded by leuX, influences a number of properties including type 1 fimbria production, flagellation and motility, production of enterobactin and serum resistance, and is also necessary for full in vivo virulence. While the tRNASec is directly involved in the production of FDHs, the leuX specific tRNAs5Leu appears to influence the expression of various factors through specific transcriptional or translational control mechanisms. [ABSTRACT FROM AUTHOR]

Mitosis is a highly coordinated process that assures the fidelity of chromosome segregation. Errors in this process result in aneuploidy which can lead to cell death or oncogenesis. In this paper we describe a putative mammalian protein kinase, AIM-1 (Aurora and Ipl1-like midbody­associated protein), related to Drosophila Aurora and Saccharomyces cerevisiae Ipl1, both of which are required for chromosome segregation. AIM-1 message and protein accumulate at G2/M phase. The protein localizes at the equator of central spindles during late anaphase and at the midbody during telophase and cytokinesis. Overexpression of kinase­inactive AIM-1 disrupts cleavage furrow formation without affecting nuclear division. Furthermore, cytokinesis frequently fails, resulting in cell polyploidy and subsequent cell death. These results strongly suggest that AIM-1 is required for proper progression of cytokinesis in mammalian cells. [ABSTRACT FROM AUTHOR]

As shown in a previous paper[i. i. Lawrence et al. (1980) Eur. J. Biochem. 107, 263 -269], covalent spin labeling of basis residues in histone H I allows the study of the interaction of this protein with DNA. Using a step gradient dialysis procedure to reconstitute chromatin from labeled HI and stripped chromatin, it is shown that the process of interaction of the lysine residues and DNA is the same whether histone HI is bound to linear purified DNA or to HI- depleted chromatin. In contrast, spin labeling of the unique tyrosine of histone H 1 located in the globular part of the molecule shows that this part is more involved in the interaction with chromatin than it is with linear DNA (as judged from the lengthening of the rotational correlation time). These data are interpreted as reflecting different roles for the N and C termini of the molecule of H 1 and the central globular part. A model, based on these observations together with examination of the primary structures of histones HI, is proposed which accounts for the HI involvement in the chromatosome structure. [ABSTRACT FROM AUTHOR]

[14C]Thymidine-labeled simian virus 40 nucleoprotein complexes were prepared from nuclei of lytically infected African green monkey kidney cells. The nucleoprotein complexes were further purified by sucrose gradient centrifugation and then incubated in the presence of [3H]acetyl coenzyme A. We observed a transfer of pH]acetyl groups to the endogenous histones H2B, H3 and H4. The enzyme was solubilized in the presence of 0.5 M NaCl and showed properties described for the DNA-binding acetyltransferase (J. Böhm, E. J. Schlaeger and R, Knippers, preceding paper in this journal). [ABSTRACT FROM AUTHOR]

The simian virus 40 (SV40) enhancer contains three 8-bp purine-pyrimidine alternating sequences which are known to adopt the left-handed Z-DNA conformation in vitro. In this paper, we have undertaken the determination of the DNA conformation adopted by these Z-motifs in the SV40 minichromosome. We have analyzed the presence of Z-DNA through the change in linkage which should accompany formation of this left-handed conformation. Our results indicate that, regardless of the precise moment of the viral lytic cycle at which minichromosomes are harvested and the condition of the transfected DNA, either relaxed or negatively supercoiled, none of the three Z motifs of the SV40 enhancer exist to a significant extent as Z-DNA in SV40 minichromosomes. The SV40 enhancer adopts predominantly a right-handed B-DNA conformation in vivo. [ABSTRACT FROM AUTHOR]

The nucleotide sequence of a 5.1 kb region in the Haemophilus influenzae type b capsulation locus has been determined and found to contain four open reading frames: bexD, bexC, bexB, and bexA. Comparison of the deduced products of bexC, bexB, and bexA to known proteins, and TnphoA mutagenesis, suggests that they form components of an ATP-driven polysaccharide export apparatus. Furthermore, close sequence similarity between BexA and BexB and products of the kpsTand kpsM genes at the Escherichia coli K5 capsulation locus (Smith et at., 1990 -- accompanying paper) suggests that capsulation genes in these organisms may have a common ancestry. [ABSTRACT FROM AUTHOR]

This paper describes software (written in Pascal and running on Macintosh computers) allowing localization of unknown DNA fragments from the Escherichia coli chromosome on the restriction map established by Kohara et al. (1987). The program identifies the segment's map position using a restriction pattern analysis obtained with all, or some, of the eight enzymes used by Kohara et al. (1987), Therefore, the sequenced genes available in the EMBL library may be localized on the E. coli chromosome restriction map. This allowed correction of the map (mainly by introducing missing sites in the published maps) at the corresponding positions. Analysis of the data indicates that there is only a very low level of polymorphism, at the nucleotide level, between the E. coli K12 strains used by the various laboratories involved in DNA sequencing. The program is versatile enough to be used with other genomes. [ABSTRACT FROM AUTHOR]

This paper describes the isolation and purification of two RNA polymerases (CI and CII) and several protein fractions (A, B and C) from the chromosomal acidic proteins of coconut endosperm nuclei. The method involves disruption of isolated nuclei in dilute salt medium, centrifugation to sediment the crude chromatin, solubilization of chromatin in concentrated salt, dialysis of soluble chromatin to dilute salt to precipitate DNA-histone complex and centrifugation to get the acidic proteins in the supernatant. Further purification involves ammonium sulphate fractionation and chromatography on DEAE-cellulose and QAE-Sephadex. RNA polymerase CI purified through the QAE-Sephadex step gives a single band on polyacrylamide gel electrophoresis. In gels containing dodecylsulfate, this enzyme shows multiple bands indicating its subunit nature. The pH optima for both RNA polymerases is 8.0. RNA polymerase CI is maximally activated by Mn2+; while CII, by Mg2+. The activities of both the enzymes are stimulated by fraction B. All the fractions except A are substantially free from nucleases. Both RNA polymerases require the addition of DNA for activity. Fraction B is ineffective either with denatured coconut, DNA or native γ DNA. [ABSTRACT FROM AUTHOR]

SUMMARY: Fusarium head blight (FHB), mainly caused by Fusarium graminearum, is one of the most destructive diseases of wheat (Triticum aestivum) around the world. FHB causes significant yield losses and reduces grain quality. The lack of resistance resources is a major bottleneck for wheat FHB resistance breeding. As a wheat relative, Thinopyrum elongatum contains many genes that can be used for wheat improvement. Although the novel gene Fhb‐7EL was mapped on chromosome 7EL of Th. elongatum, successful transfer of the FHB resistance gene into commercial wheat varieties has not been reported. In this study, we developed 836 wheat–Th. elongatum translocation lines of various types by irradiating the pollen of the wheat–Th. elongatum addition line CS‐7EL at the flowering stage, among which 81 were identified as resistant to FHB. By backcrossing the FHB‐resistant lines with the main cultivar Jimai 22, three wheat–Th. elongatum translocation lines, Zhongke 1878, Zhongke 166, and Zhongke 545, were successfully applied in wheat breeding without yield penalty. Combining karyotype and phenotype analyses, we mapped the Fhb‐7EL gene to the distal end of chromosome 7EL. Five molecular markers linked with the FHB resistance interval were developed, which facilitates molecular marker‐assisted breeding. Altogether, we successfully applied alien chromatin with FHB resistance from Th. elongatum in wheat breeding without yield penalty. These newly developed FHB‐resistant wheat–Th. elongatum translocation lines, Zhongke 1878, Zhongke 166, and Zhongke 545, can be used as novel resistance resources for wheat breeding. Significance Statement: Fusarium head blight (FHB) seriously threatens wheat (Triticum aestivum) production around the world. Deploying wheat cultivars with FHB resistance is considered as the most effective and environment‐friendly measure. Eighty‐one wheat–Th. elongatum translocation lines with FHB resistance were systemically developed in this study. Among them, three Zhongke lines were successfully applied in wheat breeding without yield penalty. These lines can be used as novel resistance sources for wheat FHB resistance breeding. [ABSTRACT FROM AUTHOR]

Forcing budding yeast to chromatinize their DNA with human histones manifests an abrupt fitness cost. We previously proposed chromosomal aneuploidy and missense mutations as two potential modes of adaptation to histone humanization. Here, we show that aneuploidy in histone‐humanized yeasts is specific to a subset of chromosomes that are defined by their centromeric evolutionary origins but that these aneuploidies are not adaptive. Instead, we find that a set of missense mutations in outer kinetochore proteins drives adaptation to human histones. Furthermore, we characterize the molecular mechanism underlying adaptation in two mutants of the outer kinetochore DASH/Dam1 complex, which reduce aneuploidy by suppression of chromosome instability. Molecular modeling and biochemical experiments show that these two mutants likely disrupt a conserved oligomerization interface thereby weakening microtubule attachments. We propose a model through which weakened microtubule attachments promote increased kinetochore‐microtubule turnover and thus suppress chromosome instability. In sum, our data show how a set of point mutations evolved in histone‐humanized yeasts to counterbalance human histone‐induced chromosomal instability through weakening microtubule interactions, eventually promoting a return to euploidy. Synopsis: Chromosome segregation relies on proper centromere‐kinetochore attachments to microtubules. This study shows that centromere/kinetochore dysfunction in yeast, caused by chromatinization with human histones, is rescued by DASH/Dam1c mutants that reduce the strength of kinetochore‐microtubule attachments. Histone humanization in yeast leads to centromere dysfunction, kinetochore declustering, and persistent aneuploidy.Alteration‐of‐function DASH/Dam1c mutants are adaptive to yeast with human chromatin.DASH/Dam1c mutants stabilize ploidy levels in histone‐humanized yeast.Ploidy stabilization is achieved by disrupting DASH/Dam1c oligomerization thereby weakening microtubule attachments. [ABSTRACT FROM AUTHOR]

Summary: The endonuclease methyl methanesulfonate and UV‐sensitive protein 81 (MUS81) has been reported to participate in DNA repair during mitosis and meiosis. However, the exact meiotic function of MUS81 in rice remains unclear.Here, we use a combination of physiological, cytological, and genetic approaches to provide evidence that MUS81 functions in atypical recombination intermediate resolution rather than crossover designation in rice.Cytological and genetic analysis revealed that the total chiasma numbers in mus81 mutants were indistinguishable from wild‐type. The numbers of HEI10 foci (the sites of interference‐sensitive crossovers) in mus81 were also similar to that of wild‐type. Moreover, disruption of MUS81 in msh5 or msh4 msh5 background did not further decrease chiasmata frequency, suggesting that rice MUS81 did not function in crossover designation. Mutation of FANCM and ZEP1 could enhance recombination frequency. Unexpectedly, chromosome fragments and bridges were frequently observed in mus81 zep1 and mus81 fancm, illustrating that MUS81 may resolve atypical recombination intermediates.Taken together, our data suggest that MUS81 contributes little to crossover designation but plays a crucial role in the resolution of atypical meiotic intermediates by working together with other anti‐crossover factors. [ABSTRACT FROM AUTHOR]

Premise: Previously published evidence suggests that Draba maguirei, a mustard endemic to a few localities in the Bear River, Wellsville, and Wasatch Mountains of northern Utah, may represent a cryptic species complex rather than a single species. Conservation concerns prompted an in‐depth systematic study of this taxon and its putative relatives. Methods: Sampling most known populations of D. maguirei s.l. (D. maguirei var. maguirei and D. maguirei var. burkei), we integrate data from geography, ecology, morphology, cytogenetics and pollen, enzyme electrophoresis, and the phylogenetic analysis of nuclear internal transcribed spacer sequences to explore potential taxonomic diversity in the species complex. Results: Draba maguirei var. burkei is shown here to be a distinct species (D. burkei) most closely related to D. globosa, rather than to D. maguirei. Within D. maguirei s.s., the northern (high elevation) and southern (low elevation) population clusters are genetically isolated and morphologically distinguishable, leading to the recognition here of the southern taxon as D. maguirei subsp. stonei. Conclusions: Our study reveals that plants traditionally assigned to D. maguirei comprise three genetically divergent lineages (D. burkei and two newly recognized subspecies of D. maguirei), each exhibiting a different chromosome number and occupying a discrete portion of the geographic range. Although previously overlooked and underappreciated taxonomically, the three taxa are morphologically recognizable based on the distribution and types of trichomes present on the leaves, stems, and fruit. Our clarification of the diversity and distribution of these taxa provides an improved framework for conservation efforts. [ABSTRACT FROM AUTHOR]

SUMMARY: Polyploidy is a common mode of evolution in flowering plants. Both the natural tetraploid Thinopyrum elongatum and the diploid one from the same population show a diploid‐like pairing in meiosis. However, debate on the chromosome composition and origin of the tetraploid Th. elongatum is ongoing. In the present study, we obtained the induced tetraploid Th. elongatum and found that the induced and natural tetraploids are morphologically close, except for slower development and lower seed setting. Using probes developed from single chromosome microdissection and a Fosmid library, obvious differentiations were discovered between two chromosome sets (E1 and E2) of the natural tetraploid Th. elongatum but not the induced one. Interestingly, hybrid F1 derived from the two different wheat‐tetraploid Th. elongatum amphiploids 8802 and 8803 produced seeds well. More importantly, analysis of meiosis in F2 individuals revealed that chromosomes from E1 and E2 could pair well on the durum wheat background with the presence of Ph1. No chromosome set differentiation on the FISH level was discovered from the S1 to S4 generations in the induced one. In metaphase of the meiosis first division in the natural tetraploid, more pairings were bivalents and fewer quadrivalents with ratio of 13.94 II + 0.03 IV (n = 31). Chromosome pairing configuration in the induced tetraploid is 13.05 II + 0.47 IV (n = 19), with the quadrivalent ratio being only slightly higher than the ratio in the natural tetraploid. Therefore, the natural tetraploid Th. elongatum is of autoploid origin and the induced tetraploid Th. elongatum evolutionarily underwent rapid diploidization in the low generation. Significance Statement: Chromosomes of the natural tetraploid Thinopyrum elongatum could be classified into two groups (E1 and E2) evenly using probes developed from single chromosome microdissection and a Fosmid library, and were different from the induced tetraploid with uniform chromosome pattern. However, the E1 and E2 chromosome sets could pair well in the presence of Ph1. These results suggest that the natural tetraploid Th. elongatum is of autoploid origin and underwent rapid diploidization. [ABSTRACT FROM AUTHOR]

Background: Although the understanding of resistance to oxaliplatin (OXA) chemotherapy in colorectal cancer (CRC) has been sought for many years, drug tolerance remains a major challenge for cancer therapy. Revealing the molecular mechanism of OXA resistance could help to explain the poor prognosis of patients. Methods: Gene expression omnibus (GEO) database was searched, GSE83129, which contains RNA profiling in metastatic CRC patients treated first‐line with OXA, was chosen for the following analysis. Differential expressed genes (DEGs) between the adenocarcinoma and adjacent_normal team, respectively, in the OXA responders and no‐responders were analyzed. The Gene Ontology (GO) and hub genes in the protein–protein interaction (PPI) network were used for the molecular mechanism of OXA resistance. Tumor‐related databases were used for the clinical relevance of the structural maintenance of chromosomes 5 (SMC5) in CRC. The in vitro assays were used to detect the molecular function of SMC5 in CRC cells. Quantitative real‐time PCR (qRT‐PCR) and western blot were used to detect the expression of the structural maintenance of chromosomes 5/6 (SMC5/6) complex components upon OXA and raltitrexed (RTX) treatment. CCK‐8 was used to detect the cell viability of cells with different treatment. Results: SMC5 was downregulated in CRC tissues of OXA no‐response patients. Lower expression of SMC5 was correlated with a poor prognosis in CRC patients, improved this gene expression, inhibited the CRC cell growth and invasion in vitro. Furthermore, SMC5 was downregulated upon OXA treatment in CRC cells, while RTX would reverse its expression, and the combination of these two drugs restored the SMC5 level to the normal situation. Finally, RTX treatment enhanced the OXA cytotoxicity. Conclusion: SMC5 is a tumor suppressor, that low expression of this gene is benefit for the development of CRC. Combination treatment with RTX and OXA may be more suitable for those OXA no‐responders with lower SMC5. [ABSTRACT FROM AUTHOR]

Summary: Zanthoxylum armatum and Zanthoxylum bungeanum, known as 'Chinese pepper', are distinguished by their extraordinary complex genomes, phenotypic innovation of adaptive evolution and species‐special metabolites. Here, we report reference‐grade genomes of Z. armatum and Z. bungeanum. Using high coverage sequence data and comprehensive assembly strategies, we derived 66 pseudochromosomes comprising 33 homologous phased groups of two subgenomes, including autotetraploid Z. armatum. The genomic rearrangements and two whole‐genome duplications created large (~4.5 Gb) complex genomes with a high ratio of repetitive sequences (>82%) and high chromosome number (2n = 4x = 132). Further analysis of the high‐quality genomes shed lights on the genomic basis of involutional reproduction, allomones biosynthesis and adaptive evolution in Chinese pepper, revealing a high consistent relationship between genomic evolution, environmental factors and phenotypic innovation. Our study provides genomic resources and new insights for investigating diversification and phenotypic innovation in Chinese pepper, with broader implications for the protection of plants under severe environmental changes. [ABSTRACT FROM AUTHOR]

The above article, published online on 15 October 2015 in Wiley Online Library (), has been retracted by agreement between the authors, the journal Editor in Chief, Allen Moore, and John Wiley & Sons Ltd. The authors have requested the retraction of their paper because they mistakenly analyzed the wrong backcross lines. This mistake was only recently discovered and they are now in the process of repeating the experiment using the correct Backcross Introgression Lines. The authors apologize for this mistake. Reference Nie, Y. Y., L. Zhang, Y. H. Wu, H. J. Liu, W. W. Mao, J. Du, et al. 2015. Screening of candidate genes and fine mapping of drought tolerance quantitative trait loci on chromosome 4 in rice ( Oryza sativa L.) under drought stress. Ecology and Evolution 5(21):5007-5015. doi: . [ABSTRACT FROM AUTHOR]

SUMMARY: Structural chromosome variations (SCVs) are large‐scale genomic variations that can be detected by fluorescence in situ hybridization (FISH). SCVs have played important roles in the genome evolution of wheat (Triticum aestivum L.), but little is known about their genetic effects. In this study, a total of 543 wheat accessions from the Chinese wheat mini‐core collection and the Shanxi Province wheat collection were used for chromosome analysis using oligonucleotide probe multiplex FISH. A total of 139 SCVs including translocations, pericentric inversions, presence/absence variations (PAVs), and copy number variations (CNVs) in heterochromatin were identified at 230 loci. The distribution frequency of SCVs varied between ecological regions and between landraces and modern cultivars. Structural analysis using SCVs as markers clearly divided the landraces and modern cultivars into different groups. There are very clear instances illustrating alien introgression and wide application of foreign germplasms improved the chromosome diversity of Chinese modern wheat cultivars. A genome‐wide association study (GWAS) identified 29 SCVs associated with 12 phenotypic traits, and five (RT4AS•4AL‐1DS/1DL•1DS‐4AL, Mg2A‐3, Mr3B‐10, Mr7B‐13, and Mr4A‐7) of them were further validated using a doubled haploid population and advanced sib‐lines, implying the potential value of these SCVs. Importantly, the number of favored SCVs that were associated with agronomic trait improvement was significantly higher in modern cultivars compared to landraces, indicating positive selection in wheat breeding. This study demonstrates the significant effects of SCVs during wheat breeding and provides an efficient method of mining favored SCVs in wheat and other crops. Significance Statement: A total of 139 structural chromosome variations (SCVs) were identified in 543 wheat accessions via high‐resolution karyotypes. A genome‐wide association study of SCVs identified 29 favored SCVs associated with important agronomic traits. Modern cultivars showed higher chromosome polymorphic information content than landraces, and the distribution of favored SCVs highlighted significant breeding selection during Chinese wheat breeding. In summary, SCVs play critical roles in wheat domestication and cultivar evolution. [ABSTRACT FROM AUTHOR]

SUMMARY: Simple telomeric repeats composed of six to seven iterating nucleotide units are important sequences typically found at the ends of chromosomes. Here we analyzed their abundance and homogeneity in 42 gymnosperm (29 newly sequenced), 29 angiosperm (one newly sequenced), and eight bryophytes using bioinformatics, conventional cytogenetic and molecular biology approaches to explore their diversity across land plants. We found more than 10 000‐fold variation in the amounts of telomeric repeats among the investigated taxa. Repeat abundance was positively correlated with increasing intragenomic sequence heterogeneity and occurrence at non‐telomeric positions, but there was no correlation with genome size. The highest abundance/heterogeneity was found in the gymnosperm genus Cycas (Cycadaceae), in which megabase‐sized blocks of telomeric repeats (i.e., billions of copies) were identified. Fluorescent in situ hybridization experiments using variant‐specific probes revealed canonical Arabidopsis‐type telomeric TTTAGGG repeats at chromosome ends, while pericentromeric blocks comprised at least four major telomeric variants with decreasing abundance: TTTAGGG>TTCAGGG >TTTAAGG>TTCAAGG. Such a diversity of repeats was not found in the sister cycad family Zamiaceae or in any other species analyzed. Using immunocytochemistry, we showed that the pericentromeric blocks of telomeric repeats overlapped with histone H3 serine 10 phosphorylation signals. We show that species of Cycas have amplified their telomeric repeats in centromeric and telomeric positions on telocentric chromosomes to extraordinary high levels. The ancestral chromosome number reconstruction suggests their occurrence is unlikely to be the product of ancient Robertsonian chromosome fusions. We speculate as to how the observed chromosome dynamics may be associated with the diversification of cycads. [ABSTRACT FROM AUTHOR]