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Adaptation by natural selection might improve the fitness of an organism and its probability to survive in unfavorable environmental conditions. Decoding the genetic basis of adaptive evolution is one of the great challenges to deal with. To this purpose, Saccharomyces cerevisiae has been largely investigated because of its short division time, excellent aneuploidy tolerance and the availability of the complete sequence of its genome with a thorough genome database. In the past, we developed a system, named bridge-induced translocation, to trigger specific, non-reciprocal translocations, exploiting the endogenous recombination system of budding yeast. This technique allows users to generate a heterogeneous population of cells with different aneuploidies and increased phenotypic variation. In this work, we demonstrate that ad hoc chromosomal translocations might induce adaptation, fostering selection of thermo-tolerant yeast strains with improved phenotypic fitness. This 'yeast eugenomics' correlates with a shift to enhanced expression of genes involved in stress response, heat shock as well as carbohydrate metabolism. We propose that the bridge-induced translocation is a suitable approach to generate adapted, physiologically boosted strains for biotechnological applications. [ABSTRACT FROM AUTHOR]

Homomorphic sex chromosomes and rapid turnover of sex-determining genes can complicate establishing the sex chromosome system operating in a given species. This difficulty exists in Xenopus tropicalis, an anuran quickly becoming a relevant model for genetic, genomic, biochemical, and ecotoxicological research. Despite the recent interest attracted by this species, little is known about its sex chromosome system. Direct evidence that females are the heterogametic sex, as in the related species Xenopus laevis, has yet to be presented. Furthermore, X. laevis' sex-determining gene, DM-W, does not exist in X. tropicalis, and the sex chromosomes in the two species are not homologous. Here we identify X. tropicalis' sex chromosome system by integrating data from (i) breeding sex-reversed individuals, (ii) gynogenesis, (iii) triploids, and (iv) crosses among several strains. Our results indicate that at least three different types of sex chromosomes exist: Y, W, and Z, observed in YZ, YW, and ZZ males and in ZW and WW females. Because some combinations of parental sex chromosomes produce unisex offspring and other distorted sex ratios, understanding the sex-determination systems in X. tropicalis is critical for developing this flexible animal model for genetics and ecotoxicology. [ABSTRACT FROM AUTHOR]

The 8;21 translocation is the most common chromosomal aberration occurring in acute myeloid leukemia (AML). This translocation causes expression of the RUNX1-ETO (AML1-ETO) fusion protein, which cooperates with additional mutations in leukemia development. We report here that interferons (IFNs) and IFN-stimulated genes are a group of genes consistently up-regulated by RUNX1-ETO in both human and murine models. RUNX1-ETO-induced up-regulation of IFN-stimulated genes occurs primarily via type I IFN signaling with a requirement for the IFNAR complex. Addition of exogenous IFN in vitro significantly reduces the increase in self-renewal potential induced by both RUNX1-ETO and its leukemogenic splicing isoform RUNX1-ETO9a. Finally, loss of type I IFN signaling via knockout of Ifnar1 significantly accelerates leukemogenesis in a t(8;21) murine model. This demonstrates the role of increased IFN signaling as an important factor inhibiting t(8;21) fusion protein function and leukemia development and supports the use of type I IFNs in the treatment of AML. [ABSTRACT FROM AUTHOR]

The article presents a case study of an 18-month-old propsitus with mosaic Down's syndrome (DS). The study included Robertsonian translocation (ROB), heteromorphism in chromosomes, and homology-mediated recombination between sister chromatids. He was diagnosed with broken pseudodicentric 'mirror-image' chromosome 21.

In large populations, multiple beneficial mutations may be simultaneously spreading. In asexual populations, these mutations must either arise on the same background or compete against each other. In sexual populations, recombination can bring together beneficial alleles from different backgrounds, but tightly linked alleles may still greatly interfere with each other. We show for well-mixed populations that when this interference is strong, the genome can be seen as consisting of many effectively asexual stretches linked together. The rate at which beneficial alleles fix is thus roughly proportional to the rate of recombination and depends only logarithmically on the mutation supply and the strength of selection. Our scaling arguments also allow us to predict, with reasonable accuracy, the fitness distribution of fixed mutations when the mutational effect sizes are broad. We focus on the regime in which crossovers occur more frequently than beneficial mutations, as is likely to be the case for many natural populations. [ABSTRACT FROM AUTHOR]

Understanding how increased genome size and diversity within polyploid genomes impacts plant evolution and breeding continues to be challenging. Although historical studies by McClintock suggested the importance of transposable elements mediated by polyploidisation on genomic changes, data from plant crosses remain scarce. Despite the absence of a conclusive proof regarding autonomous retrotransposon movement in synthetic allopolyploids, the transposition of retrotransposons and their ubiquitous dispersion in all plant species might explain the positive correlation between the genome size of plants and the prevalence of retrotransposons. Here, we address polyploidisation-mediated rearrangements of retrotransposon-associated sequences and discuss a tendency for a preferential restructuring of large ancestral genomes after polyploidisation. A comparative analysis of the frequency of modifications of retrotransposon-associated sequences in synthetic polyploids with marked differences in genome sizes is presented. Such analyses suggest the absence of a significant difference in the rates of rearrangements despite vast dissimilarities in the retrotransposon copy number between species, which emphasises the high plasticity of this genomic feature. See also the sister article focusing on animals by Arkhipova and Rodriguez in this themed issue. Copyright © 2013 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

The Neotropical fish Heptapterus mustelinus, collected in the Pindorama stream of the upper Paraná River basin (Brazil), was studied cytogenetically, verifying 54 chromosomes (26 m + 18 m + 4 st + 6 a). This diploid number has not been reported among the Heptapteridae that have been studied to date. Unlike most species of the family, there were multiple Ag-nucleolar organizer regions (NOR) and heterochromatin present in the centromeric region of most of the chromosomes of the complement, being Chromomycin A3 (CMA3+)/4′,6-diamidino-2-phenylindole (DAPI−) in nine chromosomal pairs, besides the one that coincides with the Ag-NORs. The data presented in this work reveal a different path in the karyotypic evolution of H. mustelinus when compared to the others Heptapteridae genera. [ABSTRACT FROM AUTHOR]

Chromosomal rearrangements, including reciprocal translocations, may prevent recombinational transfer of genes from a donor genotype to a recipient, especially when the gene is located in an interstitial segment. The effect of trisomy of chromosome arm 1RS on recombination was studied in translocation heterozygote T248W of rye (Secale cereale), involving chromosome arms 1RS and 6RS. (Pro)metaphase I configuration frequencies were analyzed. Crossing over, estimated as chiasma parameters, in five genetically different euploid heterozygotes was compared with those of 10 different single arm trisomics. The addition of 1RS greatly altered the crossing over pattern around the translocation break point, with a special increase in the interstitial segment of 6RS and adjoining regions, normally hardly accessible to recombination. Furthermore, there was considerable variation between plants of closely related genotypes. Heterogeneity widens the distribution of crossing overs, including segments normally not accessible to recombination, but decreases average recombination in other segments. The extra chromosome and abnormal segregants are eliminated by using the trisomic as the pollen parent. [ABSTRACT FROM AUTHOR]

Background: It is now nearly a century since it was first discovered that crossovers between homologous parental chromosomes, originating at the Prophase stage of Meiosis I, are not randomly placed. In fact, the number and distribution of crossovers are strictly regulated with crossovers/chiasmata formed in optimal positions along the length of individual chromosomes, facilitating regular chromosome segregation at the first meiotic division. In spite of much research addressing this question, the underlying mechanism(s) for the phenomenon called crossover/ chiasma interference is/are still unknown; and this constitutes an outstanding biological enigma. Results: The Chromosome Oscillatory Movement (COM) model for crossover/chiasma interference implies that, during Prophase of Meiosis I, oscillatory movements of the telomeres (attached to the nuclear membrane) and the kinetochores (within the centromeres) create waves along the length of chromosome pairs (bivalents) so that crossing-over and chiasma formation is facilitated by the proximity of parental homologs induced at the nodal regions of the waves thus created. This model adequately explains the salient features of crossover/chiasma interference, where (1) there is normally at least one crossover/chiasma per bivalent, (2) the number is correlated to bivalent length, (3) the positions are dependent on the number per bivalent, (4) interference distances are on average longer over the centromere than along chromosome arms, and (5) there are significant changes in carriers of structural chromosome rearrangements. Conclusions: The crossover/chiasma frequency distribution in humans and mice with normal karyotypes as well as in carriers of structural chromosome rearrangements are those expected on the COM model. Further studies are underway to analyze mechanical/mathematical aspects of this model for the origin of crossover/chiasma interference, using string replicas of the homologous chromosomes at the Prophase stage of Meiosis I. The parameters to vary in this type of experiment will include: (1) the mitotic karyotype, i.e. ranked length and centromere index of the chromosomes involved, (2) the specific bivalent/multivalent length and flexibility, dependent on the way this structure is positioned within the nucleus and the size of the respective meiocyte nuclei, (3) the frequency characteristics of the oscillatory movements at respectively the telomeres and the kinetochores. [ABSTRACT FROM AUTHOR]

Retrotranspostion of I factors in the female germline of Drosophila melanogaster is responsible for the so called I-R hybrid dysgenesis, a phenomenon that produces a broad spectrum of genetic abnormalities including reduced fertility, increased frequency of mutations and chromosome loss. Transposition of I factor depends on cellular conditions that are established in the oocytes of the reactive females and transmitted to their daughters. The so-called reactivity is a cellular state that may exhibit variable levels of expression and represents a permissive condition for I transposition at high levels. Defective I elements have been proposed to be the genetic determinants of reactivity and, through their differential expression, to modulate transposition of active copies in somatic and/or germ line cells. Recently, control of transposable element activity in the germ line has been found to depend on pi-RNAs, small repressive RNAs interacting with Piwi-family proteins and derived from larger transposable elements (TE)-derived primary transcripts. In particular, maternally transmitted I-element piRNAs originating from the 42AB region of polytene chromosomes were found to be involved in control of I element mobility. In the present work, we use a combination of cytological and molecular approaches to study the activity of I elements in three sublines of the inducer y; cn bw; sp isogenic strain and in dysgenic and non-dysgenic genetic backgrounds. Overall, the results of FISH and Southern blotting experiments clearly show that I elements are highly unstable in the Montpellier subline in the absence of classical dysgenic conditions. Such instability appears to be correlated to the amount of 5′ and 3′ I element transcripts detected by quantitative and real-time RT-PCR. The results of this study indicate that I elements can be highly active in the absence of a dysgenic crosses. Moreover, in the light of our results caution should be taken to assimilate the genomic annotation data on transposable elements to all y; cn bw sp sublines. [ABSTRACT FROM AUTHOR]

For most secretory pathway proteins, crossing the endoplasmic reticulum (ER) membrane is an irreversible process. However, in some cases this flow can be reversed. For instance, misfolded proteins retained in the ER are retrotranslocated to the cytosol to be degraded by the proteasome. This mechanism, known as ER associated degradation (ERAD), is exploited by several bacterial toxins to gain access to the cytosol. Interestingly, some ER resident proteins can also be detected in the cytosol or nucleus, calreticulin (CRT) being the most studied. Here we show that in Trypanosoma cruzi a minor fraction of CRT localized to the cytosol. ER calcium depletion, but not increasing cytosolic calcium, triggered the retrotranslocation of CRT in a relatively short period of time. Cytosolic CRT was subsequently degraded by the proteasome. Interestingly, the single disulfide bridge of CRT is reduced when the protein is located in the cytosol. The effect exerted by ER calcium was strictly dependent on the C-terminal domain (CRT-C), since a CRT lacking it was totally retained in the ER, whereas the localization of an unrelated protein fused to CRT-C mirrored that of endogenous CRT. This finding expands the regulatory mechanisms of protein sorting and may represent a new crossroad between diverse physiological processes. [ABSTRACT FROM AUTHOR]

Making use of a numerical self-consistent field method and polymer brush concepts, we model the solvated corona of neurofilaments (NF) composed of projection domains (unstructured tails) of constituent proteins. Projections are modeled with amino acid resolution. We focus on the importance of the two shortest ones (α-internexin and NF-L) in regulating the conformations of the two longer ones (NF-M and NF-H) in an isolated NF. We take the wild-type NF with no α-internexin as the reference, for which the phosphorylation-induced translocation of M- and H-tails has been examined previously. We demonstrate that a subbrush of L-tails creates an electrostatic potential profile with an approximately parabolic shape. An experimentally relevant (2:1) ratio of L- to α-projections reduces the charge density of the L subbrush and shifts the translocation transition of the H-tails to slightly higher degrees of phosphorylation. Replacing all L-tails by α-projections destroys the substructure of the NF corona and this alters the NF response to the phosphorylation of long tails. [ABSTRACT FROM AUTHOR]

Robertsonian translocations are one of the most frequent reorganizations in humans. Their segregational behavior and their implication in the occurrence of interchromosomal effects (ICEs) has been an important topic of research for the past 10 years. Most of the cases analyzed correspond to rearrangements with chromosomes from the D-group (chromosomes 13, 14 and 15), whereas some rare Robertsonian translocations are scarcely found in the literature, mainly those with both chromosomes from the G-group (chromosomes 21 and 22) and those involving chromosomes from both groups (D;G translocations). Results supporting/rejecting the existence of the ICE phenomenon have been reported, showing the need for more studies to characterize its distribution. In this study, sperm fluorescent in situ hybridization studies have been performed in three D;G Robertsonian translocation carriers: two men with the translocation t(14;21) and a third individual with the rare t(13;22) reorganization. Segregation and ICE results have been considered in relation to their cytogenetic features and all previously published data. The compiled information discards a particular segregation behavior related to the chromosomes involved. In contrast with this segregational homogeneity, heterogeneous ICE results were observed, indicating a significant but random distribution of such phenomenon. [ABSTRACT FROM AUTHOR]

The analysis of structural variants associated with specific phenotypic features is promising for the elucidation of the function of involved genes. There is, however, at present no approach allowing the rapid mapping of chromosomal translocation breakpoints to the basepair level from a single chromosome. Here we demonstrate that we have advanced both the microdissection and the subsequent unbiased amplification to an extent that breakpoint mapping to the basepair level has become possible. As a case in point we analysed the two breakpoints of a t(7;13) translocation observed in a patient with split hand/foot malformation (SHFM1). The amplification products of the der(7) and of the der(13) were hybridized to custom-made arrays, enabling us to define primers at flanking breakpoint regions and thus to fine-map the breakpoints to the basepair level. Consequently, our results will also contribute to a further delineation of causative mechanisms underlying SHFM1 which are currently unknown. [ABSTRACT FROM AUTHOR]

A genetic algorithm is a time consuming technique, especially for the big complex problems. Therefore, any run-time optimization regarding applying the genetic operators is very useful, taking into account that these operators apply many times in every generation. In this paper we propose run-time efficient implementations for three well-known mutation operators, specific to the permutation encoding needed in the vast area of scheduling problems. These operators are: frame-shift, translocation and inversion. [ABSTRACT FROM AUTHOR]

AbstractWe study the problem of transforming a multichromosomal genome into another using Double Cut-and-Join (DCJ) operations, which simulates several types of rearrangements, as reversals, translocations, and block-interchanges. We introduce the notion of a DCJ scenario that does not break families of common intervals (groups of genes co-localized in both genomes). Such scenarios are called perfect, and their properties are well known when the only considered rearrangements are reversals. We show that computing the minimum perfect DCJ rearrangement scenario is NP-hard, and describe an exact algorithm which exponential running time is bounded in terms of a specific pattern used in the NP-completeness proof. The study of perfect DCJ rearrangement leads to some surprising properties. The DCJ model has often yielded algorithmic problems which complexities are comparable to the reversal-only model. In the perfect rearrangement framework, however, while perfect sorting by reversals is NP-hard if the family of common intervals to be preserved is nested, we show that finding a shortest perfect DCJ scenario can be answered in polynomial time in this case. Conversely, while perfect sorting by reversals is tractable when the family of common intervals is weakly separable, we show that the corresponding problem is still NP-hard in the DCJ case. This shows that despite the similarity of the two operations, easy patterns for revervals are hard ones for DCJ, and vice versa. [ABSTRACT FROM AUTHOR]

Translocations are becoming increasingly popular as appropriate management strategies for the genetic restoration of endangered species and populations. Although a few studies have shown that the introduction of novel alleles has reversed the detrimental effects of inbreeding over the short-term (i.e., genetic rescue), it is not clear how effective such translocations are for both maintaining neutral variation that may be adaptive in the future (i.e., genetic restoration) and increasing population viability over the long-term. In addition, scientists have expressed concerns regarding the potential genetic swamping of locally adapted populations, which may eliminate significant components of genetic diversity through the replacement of the target population by the source individuals used for translocations. Here we show that bird translocations into a wild population of greater prairie-chickens (Tympanuchus cupido pinnatus) in southeastern Illinois were effective in both removing detrimental variation associated with inbreeding depression as well as restoring neutral genetic variation to historical levels. Furthermore, we found that although translocations resulted in immediate increases in fitness, the demographic recovery and long-term viability of the population appears to be limited by the availability of suitable habitat. Our results demonstrate that although translocations can be effective management tools for the genetic restoration of wild populations on the verge of extinction, their long-term viability may not be guaranteed unless the initial conditions that led to most species declines (e.g., habitat loss) are reversed. [ABSTRACT FROM AUTHOR]

Abstract: The bacterial transposon Tn7 maintains two distinct lifestyles, one in horizontally transferred DNA and the other in bacterial chromosomes. Access to these two DNA pools is mediated by two separate target selection pathways. The proteins involved in these pathways have evolved to specifically activate transposition into their cognate target-sites using entirely different recognition mechanisms, but the same core transposition machinery. In this review we discuss how the molecular mechanisms of Tn7-like elements contribute to their diversification and how they affect the evolution of their host genomes. The analysis of over 50 Tn7-like elements provides insight into the evolution of Tn7 and Tn7 relatives. In addition to the genes required for transposition, Tn7-like elements transport a wide variety of genes that contribute to the success of diverse organisms. We propose that by decisively moving between mobile and stationary DNA pools, Tn7-like elements accumulate a broad range of genetic material, providing a selective advantage for diverse host bacteria. [Copyright &y& Elsevier]

In many bacteria, the twin arginine translocation (Tat) system transports folded proteins across the cytoplasmic membrane, and these proteins can play a role in symbiotic or pathogenic infections. A role for the Vibrio fischeri Tat system was identified during symbiotic colonization of its host Euprymna scolopes, demonstrating a function for the Tat system in host colonization by a member of the Vibrionaceae. Using bioinformatics, mutant analyses, and green fluorescent protein fusions, a set of Tat-targeted proteins in V. fischeri was identified. [ABSTRACT FROM AUTHOR]

Translocation of undersize rock lobsters Jasus edwardsii from low-growth to high-growth areas has been proposed as a method to improve yield and marketability. The economic feasibility of these operations was examined for translocations by either charter vessels or by fishers retaining their sub-legal catch and releasing these on their return trip to port. Benefit was quantified by the increase in revenue relative to leaving lobsters at their original site, less cost for translocating lobsters. Scenarios were considered feasible when costs per kg gain in yield were below that for quota leased through the market. Lower cost fisher translocations appeared feasible except for short distance translocations from deep to shallow water in the same region. Greatest net benefit occurred from long distance translocations between regions with extreme differences in growth (from SW to NW Tasmania). These operations required vessel charter and led to a net state benefit of Australian169,000 per 5-tonne trip, with internal rates of return approaching 400%. Cost per kg gain in catch for these operations was estimated at less than A3/kg and thus substantially less than the current lease price of around A16/kg. The apparent economic feasibility of translocation provides support for pilot-scale trials. [ABSTRACT FROM AUTHOR]

During Bacillus subtilis sporulation, the SpoIIIE DNA translocase moves a trapped chromosome across the sporulation septum into the forespore. The preferential assembly of SpoIIIE complexes in the mother cell provided the idea that SpoIIIE functioned as a DNA exporter, which ensured translocation orientation. In this issue of Molecular Microbiology, Becker and Pogliano reinvestigate the molecular mechanisms that orient the activity of SpoIIIE. Their findings indicate that SpoIIIE reads the polarity of DNA like its Escherichia coli homologue, FtsK. [ABSTRACT FROM AUTHOR]

SpoIIIE and FtsK are related proteins that translocate chromosomes across septa. Previous results suggested that SpoIIIE exports DNA and that translocation polarity is governed by the cell-specific regulation of its assembly, but that FtsK is a reversible motor for which translocation polarity is governed by its DNA substrate. Seeking to reconcile these conclusions, we used cell-specific GFP tagging to demonstrate that SpoIIIE assembles a complex only in the mother cell, from which DNA is exported, but that DNA translocation-defective SpoIIIE proteins assemble in both cells. Altering chromosome architecture by soj-spo0J and racA soj-spo0J mutations allowed wild-type SpoIIIE to assemble in the forespore and export the forespore chromosome. Combining LacI-CFP tagging of oriC with time-lapse microscopy, we demonstrate that the chromosome is exported from the forespore when oriC fails to be trapped in the forespore. Thus, the position of oriC after septation determines which cell will receive the chromosome and which will assemble SpoIIIE. [ABSTRACT FROM AUTHOR]

The twin-arginine translocation (Tat) system is a protein translocation system that is adapted to the translocation of folded proteins across biological membranes. An understanding of the folding requirements for Tat substrates is of fundamental importance for the elucidation of the transport mechanism. We now demonstrate for the first time Tat transport for fully unstructured proteins, using signal sequence fusions to naturally unfolded FG repeats from the yeast Nsp1p nuclear pore protein. The transport of unfolded proteins becomes less efficient with increasing size, consistent with only a single interaction between the system and the substrate. Strikingly, the introduction of six residues from the hydrophobic core of a globular protein completely blocked translocation. Physiological data suggest that hydrophobic surface patches abort transport at a late stage, most likely by membrane interactions during transport. This study thus explains the observed restriction of the Tat system to folded globular proteins on a molecular level. [ABSTRACT FROM AUTHOR]

Bacterial translocation (BT) is a phenomenon in which live bacteria or its products cross the intestinal barrier. Gut translocation of bacteria has been shown in both animal and human studies. BT and its complications have been shown clearly to occur in animal models, but its existence and importance in humans has been difficult to ascertain. We review the mechanisms of BT and its clinical impact based on the current literature. [ABSTRACT FROM AUTHOR]

The karyotype of the giant beetle Dynastes hercules hercules is composed of only 16 autosomes and large sex chromosomes. Meiotic studies in the males showed that a large part of the sex chromosomes undergo synapsis at pachynema similarly to autosomes, demonstrating that both derived from an autosome-gonosome translocation. Therefore, karyotype formula is 18,neoXY. The heterochromatisation of the neoX short arm at pachynema indicates that it corresponds to the ancestral X. It carries the nucleolar organizer region (NOR) in its proximal part, which is undercondensed, especially in male mitotic and meiotic cells. In female mitotic cells, both NOR staining and undercondensation were more difficult to observe in the neoX short arms. In somatic interphase nuclei, NOR expression strongly varies with the sex. Two separated compact groups of silver dots were observed in female nuclei, while a single dispersed and large group of silver deposit exists in the males. Both the lower condensation and the higher NOR expression of the single neoX of the males, compared to each of the two neoXs of the females, is interpreted to be a consequence of dosage compensation, a mechanism not yet described in Coleoptera. In mammals as well as in Coleoptera, the carriers of gonosome-autosome translocations not exhibiting deleterious phenotypes show constitutive heterochromatin at the autosome-gonosome junction. Thus, heterochromatin may play an important universal role by clearly separating chromosome segments with different regulations of gene expression, such as inactivation or dosage compensation of the X chromosome on the one side and a conventional autosomal structure on the other side. Copyright © 2007 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

Comparative analysis of the G- and C-banding patterns in six morphologically similar species of the genus Gerbilliscus(G. gambianus, G. guineae, G. kempi, Gerbilliscus sp., G. robustus and G. leucogaster) and one belonging to the genus Gerbillurus (G. tytonis) from 27 West, East and South African localities was carried out. Our study revealed that 17 rearrangements comprising seven fissions, five translocations and five inversions occurred in the evolution of this group, with 1–13 rearrangements differentiating the various species. In addition the unusually large sex chromosomes appear to be species-specific as judged by size and morphology reflecting structural rearrangements as well as the variable presence of a large amount of C-heterochromatin found in each species at a particular chromosomal location. These karyotypic features allow us to recognize five distinct species in West Africa (compared to the two recognized in recent taxonomic lists) and to roughly delimit their geographical distributions. The pattern of phylogenetic relationships inferred from a cladistic analysis of the chromosomal data is in good agreement with recent molecular phylogenetic studies that recognize a West African species group within the genus Gerbilliscus, and the monophyly of both Gerbilliscus and Gerbillurus. Copyright © 2007 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

Unmethylated CpG oligodeoxynucleotides (ODNs) activate immune responses in a TLR9-dependent manner. In this study, stimulation of mouse macrophages with CpG-B ODN increased cellular Hsp70 expression and prevented apoptosis induced by serum starvation or staurosporine treatment. CpG-B ODN-induced Hsp70 expression depended on TLR9, MyD88, and phosphatidylinositol 3-kinase. Inhibition of Hsp70 synthesis by an inhibitor (quercetin) or antisense hsp70 attenuated not only Hsp70 expression but also the anti-apoptotic capacity of CpG-B ODN. Ectopic expression of Hsp70 rescued the inhibitory effect of quercetin on CpG-B ODN-induced anti-apoptosis. Additional experiments demonstrated that quercetin and anti-sense hsp70 modulated CpG-B ODN-induced anti-apoptosis via a caspase-3-independent pathway by down-regulating the survival gene bcl-xL and by increasing translocation of apoptosis-inducing factor. These findings suggest that CpG-B ODN may up-regulate Hsp70 via a TLR9/MyD88/phosphatidylinositol 3-kinase pathway to increase Bcl-xL and to decrease apoptosis-inducing factor nuclear translocation, resulting in anti-apoptosis. [ABSTRACT FROM AUTHOR]

Abstract: The diagnosis of hibernoma has historically been made by histopathologic examination and finding of characteristic brown fat cells with granular multivacuolated cytoplasm. The diagnosis of hibernoma may be complicated, however, because seemingly diagnostic cells could be mistakenly identified as lipoblasts, leading to the erroneous diagnosis of well-differentiated liposarcoma. Cytogenetic alterations in lipomatous tumors are well established and could be used for diagnostic purposes. Previous cytogenetic abnormalities reported in hibernomas have included alteration of 11q13 region. Here, we present a case of a hibernoma with a novel cytogenetic alteration involving a reciprocal translocation between 9q and 11q that was useful in establishing the final diagnosis. [Copyright &y& Elsevier]

Even proteins that fold well in bacteria are frequently displayed poorly on filamentous phages. Low protein presentation on phage might be caused by premature cytoplasmic folding, leading to inefficient translocation into the periplasm. As translocation is an intermediate step in phage assembly, we tested the display levels of a range of proteins using different translocation pathways by employing different signal sequences. Directing proteins to the cotranslational signal recognition particle (SRP) translocation pathway resulted in much higher display levels than directing them to the conventional post-translational Sec translocation pathway. For example, the display levels of designed ankyrin-repeat proteins (DARPins) were improved up to 700-fold by simply exchanging Sec- for SRP-dependent signal sequences. In model experiments this exchange of signal sequences improved phage display from tenfold enrichment to >1,000-fold enrichment per phage display selection round. We named this method 'SRP phage display' and envision broad applicability, especially when displaying cDNA libraries or very stable and fast-folding proteins from libraries of alternative scaffolds. [ABSTRACT FROM AUTHOR]

The identification of genes that affect quantitative traits has been of great interest to geneticists for many decades, and many statistical methods have been developed to map quantitative trait loci (QTL). Most QTL mapping studies in experimental organisms use purely inbred lines, where the two homologous chromosomes in each individual are identical. As a result, many existing QTL mapping methods developed for experimental organisms are applicable only to genetic crosses between inbred lines. However, it may be difficult to obtain inbred lines for certain organisms, e.g., mosquitoes. Although statistical methods for QTL mapping in outbred populations, e.g., humans, can be applied for such crosses, these methods may not fully take advantage of the uniqueness of these crosses. For example, we can generally assume that the two grandparental lines are homozygous at the QTL of interest, but such information is not be utilized through methods developed for outbred populations. In addition, mating types and phases can be relatively easy to establish through the analysis of adjacent markers due to the large number of offspring that can be collected, substantially simplifying tile computational need. In this article, motivated by a mosquito intercross experiment involving two selected lines that are not genetically homozygous across the genome, we develop statistical methods for QTL mapping for genetic crosses involving noninbred lines. In our procedure, we first infer parental mating types and use likelihood-based methods to infer phases in each parent on the basis of genotypes of offspring and one parent. A hidden Markov model is then employed to estimate the number of high-risk alleles at marker positions and putative QTL positions between markers in each offspring, and QTL mapping is finally conducted through the inferred QTL configuration across all offspring in all crosses. The performance of the proposed methods is assessed through simulation studies, and the usefulness of this method is demonstrated through its application to a mosquito data set. [ABSTRACT FROM AUTHOR]

Previously we described highly unstable mutations in the yellow locus, induced by the chimeric element and consisting of sequences from a distally located 1A unique genomic region, flanked by identical copies of an internally deleted 1.2-kb Pelement. Here we show that a sequence, which is part of the yellow 1A region, can be transmitted to the AS-C by successive inversion and reinversion generated by yellow- and AS-C-located Pelements. The chimeric element contains a regulatory element from the 1A region that specifically blocks yellow wing and body enhancers and simultaneously stimulates yellow expression in bristles. These results suggest that P-element-generated chimeric elements may play a certain role in rapid changes of regulatory regions of genes during evolution. [ABSTRACT FROM AUTHOR]

Recurrent and non-recurrent chromosomal rearrangements seem to reflect susceptibility to DNA rearrangements due to the presence of recombinogenic motifs in at least one partner chromosomal region. While specific genomic motifs such as AT-rich repeats, fragile sites and Alu repeats are often found in recurrent translocations, the molecular mechanisms underlying non-recurrent chromosomal rearrangements remain largely unknown. Here, we map the breakpoint region of a non-recurrent translocation, t(7;9)(q11.23;p24.3), present in a healthy woman who inherited the apparently balanced translocation from her mother and transmitted the same rearrangement to two sons—respectively healthy and aborted. Characterisation by a two-step FISH analysis, first with BAC clones and then with small locus-specific probes, restricted the breakpoint intervals to 8–10 kb. Both regions contained specific Alu sequences, which, together with the flanking low copy repeat block Ac in 7q11.23, might stimulate the translocation. We noted that, although the translocation is non-recurrent, 7q11.23 is recurrently involved in different chromosomal rearrangements, supporting the hypothesis that the 7q11.23 genomic structure is prone to recombination events. [ABSTRACT FROM AUTHOR]

There is reported a large family with four healthy persons possessing Robertsonian t(13q14q) translocation. After karyotype investigation in 106 relatives, three additional individuals with sex chromosome aneuploidies were established: one carrier of translocation has a son with chromosome mosaics 45,X/46,XY/47,XYY, and in a collateral branch of the family by the woman 45,X the karyotype of her grandmother was 46,XX/45,X. The possible genetic control of aneuploidy is discussed (the role of centromere, heterochromatin, centrosome, proteolytic enzymes). In some cases the factors predetermining aneuploidy show the Mendelian inheritance. However, the familial concentration of chromosome anomalies should be evaluated as multifactorially influenced. [ABSTRACT FROM AUTHOR]

Positioning of a radial array of microtubules (MTs) in the cell centre is crucial for cytoplasmic organization, but the mechanisms of such centering are difficult to study in intact cells that have pre-formed radial arrays. Here, we use cytoplasmic fragments of melanophores, and cytoplasts of BS-C-1 cells to study MT centering mechanisms. Using live imaging and computer modelling, we show that the MT aster finds a central location in the cytoplasm by moving along spontaneously nucleated non-astral MTs towards a point at which MT nucleation events occur equally on all sides. We hypothesize that similar mechanisms, in the presence of the centrosome, contribute to this centering mechanism and ensure the robustness of cytoplasmic organization. [ABSTRACT FROM AUTHOR]

Robertsonian translocations are the most frequent structural chromosomal abnormalities in humans and can affect fertility, with various degrees of sperm alterations in men; or the pregnancy outcome of the carriers. The studies on meiotic segregation of chromosomes in sperm of Robertsonian translocation males find a majority of normal or balanced spermatozoa for the chromosomes related to the translocation (mean 85.42%; range 60–96.60%). Furthermore, recent studies suggest an interchromosomal effect. Studies on spermatozoa from translocation carriers, and in mouse models help the comprehension of the meiotic segregation mechanisms. Results of meiotic segregation analysis in man could be integrated in genetic counselling especially when assisted reproductive technology is required. Copyright © 2005 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

Individuals carrying translocations suffer from reduced fertility or spontaneous abortions and seek help in form of assisted reproductive technology (ART) and preimplantation genetic diagnosis (PGD). While most translocations are relatively easy to detect in metaphase cells, the majority of embryonic cells biopsied in the course of in vitro fertilization (IVF) procedures are in interphase. These nuclei are thus unsuitable for analysis by chromosome banding or painting using fluorescence in situ hybridization (FISH). Thus several methods have been devised to detect translocation imbalance through FISH in single cells for purpose of PGD, among them polar body chromosome painting, interphase FISH with combination of subtelomeric and centromeric probes, breakpoint spanning probes, and cell conversion. Results with PGD indicate a significant decrease in spontaneous abortions, from 81% before PGD to 13% after PGD. They also indicate very high rates of chromosome abnormalities in embryos from translocation carriers, 72% for Robertsonian translocations and 82% for reciprocal translocations. Sperm analysis was found to be a good predictor of IVF and PGD outcome, with samples with more than 60% abnormal forms indicating poor prognosis. Similarly, the predictability from first PGD cycle results for future cycles was 90%. In summary, PGD can help translocation carriers to achieve viable pregnancies, but the success of the process is conversely related to the baseline of unbalanced gametes. Copyright © 2005 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

Advanced intercross lines (AIL) and interval–specific congenic strains (ISCS) were used to fine map previously coarsely defined quantitative trait loci (QTL) on Chromosomes 1,10, and 19, influencing behaviors in the open Field (OF) and light–dark (LD) paradigms in mice. F12(A × B) AIL mice ( N = 1130) were phenotyped, genotyped, and mapped. The ISCS were studied only in the telomeric Chromosome 10 region of interest, containing the exploratory and excitability QTL1 ( Exq1). The Chromosome 10 Exq1 and Chromosome 19 Exq4 loci mapped robustly in the AIL. The most significant QTL findings (2.0 LOD score intervals; peak; LOD score) came from the TD15 and LD transitions traits, yielding estimated intervals of 2.2 cM for Exq1 (71.3–73.5 cM; peak 72.3 cM; LOD 11.9) and 9.0 cM for Exq4 (29.0–38.2 cM; peak 34 cM; LOD 4.2). The replicated QTLs on Chromosome 1 failed to map in this AIL population. The ISCS data confirmed Exq1 loci in general. However, the ISCS data were complex and less definitive for localizing the Exq1 loci. These exploratory and fear-like behaviors result from inheriting “many small things,” namely, QTL explaining 2%–7% of the phenotypic variance. These results highlight the challenges of positionally cloning loci of small effect for complex traits. In particular, fine-mapping success may depend on the genetic architecture underlying complex traits. [ABSTRACT FROM AUTHOR]

Heterozygous tandem duplications that appear inEscherichia coliconjugation matings segregate different types of haploid and diploid recombinants formed by unequal crossing over between sister chromosomes. As shown previously, the frequency of segregants in the extended duplication D104 (~150 kb or more than 3 min of the genetic map) heterozygous forE. coli deo-operon genes (deoA deoB::Tn5/deoC deoD) is not decreased in strains with defective RecBCD and RecF recombination pathways. Analysis of a shorter duplication of this type (~46 kb) showed that the frequency of segregants in the strainrecBC sbcBC recFwas similar to that in a strain with undamaged system of recombination. Thus, genetic exchange between direct DNA repeats in tandem duplications may follow a special pathway of homologous recombination, which is independent of therecBCandrecFgenes. [ABSTRACT FROM AUTHOR]

Condensins are heteropentameric complexes that were first identified as structural components of mitotic chromosomes. They are composed of two SMC (structural maintenance of chromosomes) and three non-SMC subunits. Condensins play a role in the resolution and segregation of sister chromatids during mitosis, as well as in some aspects of mitotic chromosome assembly. Two distinct condensin complexes, condensin I and condensin II, which differ only in their non-SMC subunits, exist. Here, we used an RNA interference approach to deplete hCAP-D2, a non-SMC subunit of condensin I, in HeLa cells. We found that the association of hCAP-H, another non-SMC subunit of condensin I, with mitotic chromosomes depends on the presence of hCAP-D2. Moreover, chromatid axes, as defined by topoisomerase II and hCAP-E localization, are disorganized in the absence of hCAP-D2, and the resolution and segregation of sister chromatids are impaired. In addition, hCAP-D2 depletion affects chromosome alignment in metaphase and delays entry into anaphase. This suggests that condensin I is involved in the correct attachment between chromosome kinetochores and microtubules of the mitotic spindle. These results are discussed relative to the effects of depleting both condensin complexes. [ABSTRACT FROM AUTHOR]

We demonstrate biochemically that the genes identi- fied by sequence similarity as orthologs of the mitochondrial import machinery are functionally conserved in Caenorhabditis elegans. Specifically, tin-9.1 and tin-10 RNA interference (RNAi) treatment of nematodes impairs import of the ADP/ATP carrier into isolated mitochondria. Developmental phenotypes are associated with gene knock-down of the mitochondrial import com- ponents. RNAi of tomm-7 and ddp-1 resulted in mito- chondria with an interconnected morphology in vivo, presumably due to defects in the assembly of outer membrane fission/fusion components. RNAi of the small Tim proteins TIN-9.1, TIN-9.2, and TIN-10 resulted in a small body size, reduced number of progeny produced, and partial embryonic lethality. An additional phenotype of the tin-9.2(RNAi) animals is defective formation of the somatic gonad. The biochemical demonstration that the protein import activity is reduced, under the same conditions that yield the defects in specific tissues and lethality in a later generation, suggests that the developmental abnormalities observed are a consequence of defects in mitochondrial inner membrane biogenesis. [ABSTRACT FROM AUTHOR]

A comparative analysis of the phenotypic values of the proximal and distal fragments of the radial wing vein was carried out in heterogeneous lines of Drosophila melanogaster and in isogenic lines derived from them with the help of a balancer line. The mean values of the traits in the isogenic lines were shown to significantly differ from the corresponding values in the “parental” heterogeneous lines. Apparently, the change in the trait values was caused by a double recombination exchange between the inverted and the “normal” chromosomes, which suggests partial crossing over suppression in the balancer lines. [ABSTRACT FROM AUTHOR]

Chromosomal rearrangements involving 3q26 either due to inversion or translocation with various partner chromosomes are a recurrent finding in malignant myeloid disorders. Typically, these chromosome aberrations contribute to ectopic expression of or to the formation of fusion genes involving the EVI1 proto-oncogene. Chromosomal translocations involving the short arm of chromosome 2 (p15-p23) and the distal part of the long arm of chromosome 3 (q26-q27) are a rare but recurrent finding in patients with myeloid malignancies, and are assumed to be part of this spectrum of disorders. Thus far, however, these translocations have been poorly studied. Here, we present 21 new cases with myelodysplasia, acute myeloid leukemia or CML in blast crisis, which upon karyotyping showed the presence of a t(2;3). Furthermore, an extensive literature review disclosed 29 additional cases. Morphological, clinical and cytogenetic assessment revealed the typical hallmarks of 3q26/EVI1 rearrangements, that is, trilineage dysplasia and dysmegakaryopoiesis, poor prognosis and additional monosomy 7. Molecular cytogenetic analysis and PCR in selected samples indicated that in most cases the translocation indeed targets the EVI1 locus. Mapping of the chromosome 2 breakpoints confirmed the initially suspected cytogenetic breakpoint heterogeneity at the 2p arm.Leukemia (2004) 18, 1108-1114. doi:10.1038/sj.leu.2403346 Published online 15 April 2004 [ABSTRACT FROM AUTHOR]

De novo LINE-1 (long interspersed element­1, or L1) retrotransposition events are responsible for ∼1/1,000 disease-causing mutations in humans. Previously, L1.2 was identified as the likely progenitor of a mutagenic insertion in the factor VIII gene in a patient with hemophilia A. It subsequently was shown to be one of a small number of active L1s in the human genome. Here, we demonstrate that L1.2 is present at an intermediate insertion allele frequency in worldwide human populations and that common alleles (L1.2A and L1.2B) exhibit an ∼16-fold difference in their ability to retrotranspose in cultured human HeLa cells. Chimera analysis revealed that two amino acid substitutions (S1259L and I1220M) downstream of the conserved cysteine-rich motif in L1 open reading frame 2 are largely responsible for the observed reduction in L1.2A retrotransposition efficiency. Thus, common L1 alleles can vary widely in their retrotransposition potential. We propose that such allelic heterogeneity can influence the potential L1 mutational load present in an individual genome. [ABSTRACT FROM AUTHOR]

L1 elements are the only active autonomous retrotransposons in the human genome. The nonautonomous Alu elements, as well as processed pseudogenes, are retrotransposed by the L1 retrotransposition proteins working in trans. Here, we describe another repetitive sequence in the human genome, the SVA element. Our analysis reveals that SVA elements are currently active in the human genome. SVA elements, like Alus and L1s, occasionally insert into genes and cause disease. Furthermore, SVA elements are probably mobilized in trans by active L1 elements. [ABSTRACT FROM AUTHOR]

A population derived from a doubled-haploid backcrossed to its parent has a unique genetic structure, which affects the mapping and genetic analysis of molecular-marker data. In such a cross: (1) repulsion linkages are reduced dramatically and can be detected only in restricted chromosome sections; each repulsion-linkage group represents a section of a chromosome carrying a crossover that occurred in the meiosis that produced the gamete from which the doubled-haploid was derived; (2) the number of coupling-linkage groups observed depends on how many crossovers occurred during the meiosis; the observed size of a linkage group will be only a fraction of a total chromosome if the chromosome carried in the doubled-haploid resulted from crossover exchanges; (3) the size covered by all the observed linkages is only equivalent to the haploid genome; and (4) the ratio of single-dose to multi-dose markers is inflated. These features have not been recognized in previous reports, resulting in misinterpretations in genetic mapping and analysis of the molecular-marker data. The ratio of single- to multi-dose markers has been used inappropriately to distinguish polyploid type. [ABSTRACT FROM AUTHOR]

An Italian family in which Waardenburg syndrome type II (WS2) segregates together with a der(8) chromosome from a (4p;8p) balanced translocation was studied. Cytogenetic analysis by painting and subtelomeric probe hybridization positioned the chromosome 8 breakpoint at p22-pter. Fluorescence in situ hybridization analysis with yeast artificial chromosomes from a contig spanning the 8p21-pter region refined the breakpoint in an interval of less than 170 kb between markers WI-3823 and D8S1819. The only cloned gene for WS2 is that for microphtalmia (MITF) on chromosome 3p. In this family, MITF mutations were excluded by sequencing the whole coding region. The 8p23 region may represent a third locus for WS2 (WS2C). [ABSTRACT FROM AUTHOR]

The t(11;22)(q23;q11) translocation is the most common recurrent balanced translocation described in humans. Carriers are phenotypically normal and often go undetected until diagnosis as a result of infertility investigations or following the birth of chromosomally unbalanced offspring. Efficient diagnostics of t(11;22) is important for children born to carriers of the translocation and for prenatal and pre-implantation diagnosis. The translocation breakpoint on chromosome 22 is located within a region containing low copy repeats, and this site is one of the last unfilled gaps in the sequence of this chromosome. This autosome harbors multiple other low copy repeats, which have been entirely sequenced. We report a combined sequencing and fiber FISH breakpoint characterization in five translocation carriers. From one carrier a cosmid library was constructed, and two chimeric cosmids (cos4_der11 and cos6_der22) were sequenced, which showed that strong palindromes (or inverted repeats) occur on both chromosomes. The translocation breakpoints occur at the tip of both inverted repeats. The palindrome on chromosomes 22 and 11 is composed of 852 and 166 bases, respectively. Four additional carriers were studied using fiber FISH with a resolution limit of 2 kb. Analysis of breakpoints on the DNA sequence level, or at the level of fiber FISH, indicate that they occur at the same position on both chromosomes in all five carriers. Using cos6_der22, PAC 158L19 and BAC 3009A19, we demonstrate that FISH is an attractive alternative in molecular diagnostics of t(11;22), as PCR assays are not reliable, due to the presence of numerous copies of low copy repeats. [ABSTRACT FROM AUTHOR]

The Central European and the Mediterranean Vicia faba gene poois carry different traits favourable for selecting cultivars with a high and stable yield performance. Interpool crosses, therefore, should provide interesting new basic material, although lack of adaptation of each "exotic" parent and linkage of genes may act against the introgression of favourable genes. In a first approach, five German and five Syrian parents (bred by ICARDA) of an interpool-crossing programme were tested in two years in both regions of origin. The Syrian cultivars proved to be fairly well adapted in the German trials, while the German cultivars were highly unadapted to the Syrian conditions. The advantage of interpool-crosses for both gene pools is discussed and recommendations on the further breeding strategy for adaptation of interpool-cross-progenies are given. [ABSTRACT FROM AUTHOR]

The article presents the case report of a mentally handicapped female with unbalanced form of translocation deletion between chromosomes 6 and 22. Her general appearance is rather masculine. She is microcephalic, with a sloping short forehead, some bossing of frontal bones and flattened occiput with a low hairline. Orbital ridges are prominent with bushy eyebrows meeting at the mid-line. The clinical manifestations in this patient appear to be the result of partial deletion of the long arm of chromosome 6.

The article discusses research which was conducted to investigate gene translocations in testicular lymphomas. Researchers conducted fluorescence in situ hybridization analysis on 16 B cell testicular lymphoma patients. They found that there was at least one gene translocation in 10 of the 16 patients and that there were multiple translocations in three of the patients.