Recent advances in rice genome and chromosome structure research by fluorescence in situ hybridization (FISH)

Fluorescence in situ hybridization (FISH) is an effective method for the physical mapping of genes and repetitive DNA sequences on chromosomes. Physical mapping of unique nucleotide sequences on specific rice chromosome regions was performed using a combination of chromosome identification and highly sensitive FISH. Increases in the detection sensitivity of smaller DNA sequences and improvements in spatial resolution have ushered in a new phase in FISH technology. Thus, it is now possible to perform in situ hybridization on somatic chromosomes, pachytene chromosomes, and even on extended DNA fibers (EDFs). Pachytene-FISH allows the integration of genetic linkage maps and quantitative chromosome maps. Visualization methods using FISH can reveal the spatial organization of the centromere, heterochromatin/euchromatin, and the terminal structures of rice chromosomes. Furthermore, EDF-FISH and the DNA combing technique can resolve a spatial distance of 1 kb between adjacent DNA sequences, and the detection of even a 300-bp target is now feasible. The copy numbers of various repetitive sequences and the sizes of various DNA molecules were quantitatively measured using the molecular combing technique. This review describes the significance of these advances in molecular cytology in rice and discusses future applications in plant studies using visualization techniques.     

A conserved karyotype of Sternopygus macrurus (Sternopygidae, Gymnotiformes) in the Amazon region: differences from other hydrographic basins suggest cryptic speciation

We studied the karyotypes of 35 Sternopygus macrurus fishes of four localities from rivers of the Eastern Amazon basin. In these four places the karyotypes have 2n = 46 chromosomes, NF = 92, where 30 are metacentric (M) and 16 submetacentric (SM). The constitutive heterochromatin (CH) is found in the centromeric region of most chromosomes and in the pericentromeric region of pairs 5, 17 and 19. Pair 1 has a large and not common heterochromatic block in the short arm, useful as a marker for this species if not found in other Sternopygus taxa. The NOR is located in the distal region of the short arm of pair 1, showing a size heteromorphism in some specimens. The CMA₃ and DAPI fluorochrome bandings and the fluorescent in situ hybridization (FISH), using pantelomeric human probes techniques are described for the first time for this species. DAPI has banding coincident with the C-banded regions, which suggests that the CH is AT base-pair-rich. CMA₃ banding is coincident with the NOR, meaning that this region is GC base-pair-rich. The FISH showed that the probes hybridized only with the telomeric regions, without any sign of interstitial telomeric regions. The karyotype of the samples from different places in the Amazon basin is quite conserved, probably because of the gene flow among the populations. The karyotype differences among the Sternopygus macrurus from the Amazon basin and the São Francisco and Paraná rivers suggest that these taxa may be different species.     

Cytogenetic analysis of two related Deltochilum (Coleoptera,Scarabaeidae) species: Diploid number reduction,extensive heterochromatin addition and differentiation

Male mitotic and meiotic chromosomes of two species of the genus Deltochilum (Scarabaeidae) were analyzed through conventional staining, C-banding, base-specific fluorochromes, silver nitrate staining (AgNO₃) and FISH (45S rDNA). The two species possessed karyotypes with 2n = 14, neo-XY and meta-submetacentric chromosomes. The analysis of constitutive heterochromatin (CH) revealed mainly diphasic chromosomes in the two species, showing heterochromatic long arms. Silver nitrate staining labeled the blocks corresponding to CH in D. (Deltohyboma) aff morbillosum while in D. (Deltohyboma) calcaratum, AgNO₃ staining revealed only the CH blocks of the diphasic autosomes. The fluorochrome staining revealed in D. (D.) calcaratum the diphasic autosomes and the sex chromosomes with CMA₃⁺ blocks, and in D. (D.) aff morbillosum, the GC-rich sequences were restricted to the terminal regions of the long arms of the pairs 1 and 2 and the X. The FISH revealed 45S rDNA sites in two autosomic pairs and in the X chromosome. The analyses performed allowed for the identification of cytogenetic markers and the discussion of possible chromosome rearrangements that have been involved in the karyotypic differentiation of these species mainly related to the repetitive genome.     

Physical chromosome mapping of repetitive DNA sequences in Nile tilapia Oreochromis niloticus: evidences for a differential distribution of repetitive elements in the sex chromosomes

Repetitive DNAs have been extensively applied as physical chromosome markers on comparative studies, identification of chromosome rearrangements and sex chromosomes, chromosome evolution analysis, and applied genetics. Here we report the characterization of repetitive DNA sequences from the Nile tilapia (Oreochromis niloticus) genome by construction and screening of plasmid library enriched with repetitive DNAs, analysis of a BAC-based physical map, and hybridization to chromosomes. The physical mapping of BACs enriched with repetitive sequences and C(o)t-1 DNA (DNA enriched for highly and moderately repetitive DNA sequences) to chromosomes using FISH showed a predominant distribution of repetitive elements in the centromeric and telomeric regions and along the entire length of the largest chromosome pair (X and Y sex chromosomes) of the species. The distribution of repetitive DNAs differed significantly between the p arm of X and Y chromosomes. These findings suggest that repetitive DNAs have had an important role in the differentiation of sex chromosomes.     

Strategies of karyotype differentiation in Elateridae (Coleoptera, Polyphaga)

The chromosome study of five species of the family Elateridae, belonging to the subfamilies Agrypninae and Elaterinae, and the analysis of the cytogenetic data previously recorded for this family permitted the establishment of the main strategies of karyotypic differentiation that has occurred in the elaterids. In Agrypninae, the three species studied (Conoderus fuscofasciatus, Conoderus rufidens, and Conoderus sp.) showed the male karyotype 2n=16+X0. This karyotypic uniformity detected in these Conoderus species has also been shared with other species of the same genus, differing considerably from chromosomal heterogeneity verified in the subfamily Agrypninae. The use of the C-banding technique in C. fuscofasciatus and Conoderus sp. revealed constitutive heterochromatin in the pericentromeric region of the majority of the chromosomes. In C. fuscofasciatus, additional constitutive heterochromatin were also observed in the long arm terminal region of almost all chromosomes. Among the representatives of Elaterinae, the karyotype 2n=18+Xy(p) of Pomachilius sp.2 was similar to that verified in the majority of the Coleoptera species, contrasting with the chromosomal formula 2n=18+X0 detected in Cardiorhinus rufilateris, which is most common in the species of Elaterinae. In the majority of the elaterids, the chromosomal differentiation has frequently been driven by reduction of the diploid number; but, among the four cytogenetically examined subfamilies, there are some differences in relation to the trends of karyotypic evolution.     

Cytogenetics of four Omophoita species (Coleoptera,Chrysomelidae, Alticinae): A comparative analysis using mitotic and meiotic cells submitted to the standard staining and C-banding technique

Omophoita belongs to the tribe Oedionychini and is endemic from Neotropical region. The species of the tribe Oedionychini have revealed certain singular chromosomal features, such as sex chromosomes with extremely large size, asynapsis, and synthelic or amphithelic orientation during meiosis. Additionally, some species also showed post-reductional segregation of the gigantic sex chromosomes in meiotic division. The purpose of this work was to characterize cytogenetically four Omophoita species (O. magniguttis, O. octoguttata, O. personata, and O. sexnotata) in relation to their diploid number, chromosomal morphology, type of sex chromosome system, and constitutive heterochromatin pattern in mitotic and meiotic cells, and compare the obtained data with those of related species to establish the mechanism involved in the chromosomal differentiation of these species during the evolutionary process. The diploid number, 2n = 22 = 20 + X + y, and meiotic formulae, 10II + X + y, observed in these species were similar to those of the same genus and other species related. The autosomal morphology was acrocentric in O. magniguttis and O. octoguttata, metacentric in O. personata, and predominantly metacentric in O. sexnotata. In all these species, the sex chromosomes were metacentric. The secondary constriction occurred in pair 6 and X chromosome of O. personata, and in pair 6 and y chromosome of O. sexnotata. The constitutive heterochromatin was pericentromeric in O. magniguttis and centromeric in O. sexnotata, with the exception of the mitotic sex chromosomes of O. sexnotata, in which centromeric C band was lacking. Additional C bands in the sex chromosomes of O. magniguttis and certain autosomes and sex chromosomes of O. sexnotata were observed. Collochores were indirectly identified in the spermatocytes of O. octoguttata, O. personata, and O. sexnotata. The main mechanisms involved in the karyotype evolution of these species were discussed.     

Different chromatin fractions of tomato (Solanum lycopersicum L.) and related species

Conventional chromosome staining has suggested that more than 75% of the tomato chromosomes are constituted by heterochromatin. In order to determine whether more deeply stained proximal regions are classic heterochromatin, the distributions of C-bands and chromomycin A₃ (CMA) bands, and the prophase condensation patterns, were analysed in tomato. In this and most other species of the tomato clade, the 5S and 45S rDNA sites were also localised. In tomato, CMA banding was similar to C-banding. After conventional staining, all species displayed large condensed heteropycnotic regions that did not correspond to C-bands or CMA bands. Analyses of the CMA banded karyotypes revealed a low heterochromatin content. Around 12–17% of the chromatin of tomato was CMA⁺ and 1/4 to 1/5 of this heterochromatin corresponded to 45S rDNA. In other species, the CMA⁺ heterochromatin showed extensive variation (8–35%), but was never near the values found in the literature for tomato. These data suggest the existence of three principal fractions of chromatin in tomato and related species: the late condensed euchromatin corresponding to the terminal regions of the chromosomes, the precocious condensed euchromatin that occupies the major part of the chromosomes and the constitutive heterochromatin that represents those regions revealed by C-bands.     

Suiformes orthologous satellite DNAs as a hallmark of Pecari tajacu and Tayassu pecari (Tayassuidae) evolutionary rearrangements

In a broad general way, eukaryotic satellite DNA sequences are characterized by a highly dynamic molecular behavior due to concerted evolution that leads to rapid change between repeat sequences of different species, achieved by amplification of new variants during speciation or by gradual sequence evolution due to the accumulation of nucleotide substitutions. There are, although exceptions for this almost universal rule. We isolated variants from both the Mc1 and Ac2 pig (Sus scrofa, Suidae) satellite DNA families from the genomes of two Tayassuidae members: Pecari tajacu and Tayassu pecari, which have highly derived karyotypes. The presence of these sequences in both families’ genomes (Suidae and Tayassuidae) implies their existence in a common ancestor, what confers to the variants the status of orthology and the approximate age of, at least 40 million years.While at the molecular composition level these orthologous sequences are highly homologous, cross-species physical mapping revealed a completely different chromosomal location in Suidae versus Tayassuidae families, most probably, reflecting the high level of divergence and chromosomes evolution pathways after radiation of each family. Detailed comparative analysis of the satellites assignment on the peccary's chromosomes revealed its co-localization with homologous evolutionary breakpoints in both species, suggesting their involvement in the rearrangement events. The complex behavior of the repeats evolution in the pig/peccaries genomes is here clearly illustrated. These sequences are molecularly preserved for a considerable period of time and display slow rates of sequence change, but show a dynamic motion behavior throughout the peccary's genomes that accompanied the great architectonic reorganization of Tayassuidae chromosomes during evolution.     

Chromosomal differentiation of populations of Lysapsus limellus limellus, L. l. bolivianus, and of Lysapsus caraya (Hylinae, Hylidae)

Cytogenetic analysis were done on specimens from two populations of Lysapsus limellus limellus, three of L. l. bolivianus and of one of Lysapsus caraya. All animals showed a diploid chromosomal number of 2n=24. The karyotypes of the two L. limellus subspecies were very similar, differing only by the larger amount of telomeric heterochromatin and a small pericentromeric C-band on the short arms of pair 2 in L. l. limellus specimens. The karyotype of L. caraya differed from those of the two L. limellus subspecies in terms of chromosomal morphology, C-banding pattern and location of the main NOR on chromosomes 7 and 6, respectively. The karyotype of the L. l. bolivianus population from Guajará-Mirim/RO differed from those of the other populations of the same subspecies in morphology and heterochromatin pattern of chromosomes 7 and 8. Additional NORs were detected by silver staining and confirmed by FISH in one of the homologues of pairs 1 and 8 in L. l. bolivianus and in pair 7 in L. caraya. These results suggest that a reassessment of the taxonomic status of L. limellus subspecies, especially of the L. l. bolivianus populations, may be necessary.     

Karyotype differentiation patterns in species of the subfamily Scarabaeinae (Scarabaeidae, Coleoptera)

The aim of this study was to describe the karyotype of species belonging to the subfamily Scarabaeinae (Coleoptera, Scarabaeidae) and to compile the conventional cytogenetic data available in the literature for this group. The karyotypes of ten species belonging to the tribes Canthonini, Coprini, Onthophagini and Phanaeini were analyzed by conventional staining. Eight of these species were described for the first time (Canthon aff carbonarius, Canthon chalybaeus, Coprophanaeus dardanus, Deltochilum aff amazonicum, Dichotomius geminatus, Oxysternon silenus, Phanaeus chalcomelas and Malagoniella aff astyanax) and two were redescribed (Diabroctis mimas and Digitonthophagus gazella) since their karyotypes differed from those previously published in the literature. Four species studied showed a diploid number of 2n = 20 and a parachute type sex determining system and the karyotype was 2n = 20,Xy in two species and 2n = 18,Xy_p, 2n = 19,X0, 2n = 12,XY and 2n = 14,neoXY in one each. The chromosome morphology of the different species varied, with the observation of metacentric, submetacentric, subacrocentric and acrocentric chromosomes. The X chromosome was predominantly meta or submetacentric in the species analyzed, whereas the y chromosome presented two arms or was punctiform. In conclusion, the subfamily Scarabaeinae comprises 120 species analyzed cytogenetically, and are observed the occurrence of five chromosome rearrangements (autosome–autosome and X-autosome fusions, pericentric inversions, fissions and loss of the y chromosome) that are related to the chromosome variability and evolution in the group.     

Chaos game representation walk model for the protein sequences

A new chaos game representation of protein sequences based on the detailed hydrophobic--hydrophilic (HP) model has been proposed by Yu et al (Physica A 337 (2004) 171). A CGR-walk model is proposed based on the new CGR coordinates for the protein sequences from complete genomes in the present paper. The new CGR coordinates based on the detailed HP model are converted into a time series, and a long-memory ARFIMA(p, d, q) model is introduced into the protein sequence analysis. This model is applied to simulating real CGR-walk sequence data of twelve protein sequences. Remarkably long-range correlations are uncovered in the data and the results obtained from these models are reasonably consistent with those available from the ARFIMA(p, d, q) model.     

Modified C-band technique for the analysis of chromosome abnormalities in irradiated human lymphocytes

A modified C-band technique was developed in order to analyze more accurately dicentric, tricentric, and ring chromosomes in irradiated human peripheral lymphocytes. Instead of the original method relying on treatment with barium hydroxide Ba(OH)₂, C-bands were obtained using a modified form of heat treatment in formamide followed with DAPI staining. This method was tentatively applied to the analysis of dicentric chromosomes in irradiated human lymphocytes to examine its availability. The frequency of dicentric chromosome was almost the same with conventional Giemsa staining and the modified C-band technique. In the analysis using Giemsa staining, it is relatively difficult to identify the centromere on the elongated chromosomes, over-condensed chromosomes, fragment, and acentric ring. However, the modified C-band method used in this study makes it easier to identify the centromere on such chromosomes than with the use of Giemsa staining alone. Thus, the modified C-band method may give more information about the location of the centromere. Therefore, this method may be available and more useful for biological dose estimation due to the analysis of the dicentric chromosome in human lymphocytes exposed to the radiation. Furthermore, this method is simpler and faster than the original C-band protocol and fluorescence in situ hybridization (FISH) method with the centromeric DNA probe.     

The karyotype and sex chromosomes of Praomys tullbergi (Muridae, Rodentia): a detailed characterization

Here we present the first detailed characterization of Praomys tullbergi karyotype, enlightening several chromosome features such as constitutive heterochromatin, telomeric and LINE-1 sequences. The combination of these approaches provided some interesting insights about the genome organization of this African species, which is one of the tullbergi complex elements, a group of species belonging to Murinae (Rodentia, Muridae). Evolutionary considerations on Praomys chromosomes were also achieved, namely, the autosomal complement and the X chromosome from P. tullbergi seem to be derivative chromosomes, most probably resulting from extensive reshufflings during the course of evolution. This conclusion came from the fact that the majority of the chromosomes telomeric sequences are located interstitially, seeming footprints of evolutionary chromosome rearrangements. The detailed analysis of Praomys tullbergi X chromosome suggests that chromosome rearrangements and/or centromere transpositions and addition/elimination of heterochromatin must have been the main evolutionary events that shaped this chromosome.     

Cytochemical characterization of Triatoma infestans and Panstrongylus megistus salivary gland cells (Hemiptera, Reduviidae, Triatominae)

The Triatominae subfamily has medical sanitary importance, since these insects are vectors of Trypanosoma cruzi, etiologic agent of Chagas Disease, and Trypanosoma rangeli, which develops in the salivary glands and it is frequently found in mixed infections with T. cruzi. Triatomines of Triatoma and Panstrongylus genera possess a salivary gland complex composed of a pair with three well differentiated units: the anterior (D1), median (D2) and posterior (D3). Saliva is secreted during blood meal and antagonizes hemostatic, inflammatory and immunological systems imposed by the host, which facilitate the hematophagy. In order to identify nuclear structures, we studied interphase nuclei of salivary gland cells of adult insects, males and females, of Triatoma infestans and Panstrongylus megistus. The glands were removed from insects, fixed in acetic acid (45%) and lactic acid (50%), squashed and submitted to different cytochemical methods: lacto-acetic orcein, silver ion impregnation, Feulgen reaction, Toluidine Blue, Variant method of critical electrolyte concentration and C-banding. The preparations were examined with a Zeiss Jenaval photomicroscope and photographed. The results evidenced predominance of binucleated cells in D1 and D2 glands and mononucleated ones in D3. In all salivary glands were observed bulky and polyploid nucleus, a clear association between nucleolar and heterochromatic corpuscles, cytoplasmatic metachromasy and many pre-secretion vesicles in cytoplasm. Such characteristics were associated with intense synthesis activity to produce the saliva. Species were mainly differentiated by a larger heterochromatic corpuscle observed only in T. infestans (called as chromocenter), while P. megistus showed a predominance of euchromatin, with some heterochromatic corpuscles just in males. Females of both species showed a smaller quantity of heterochromatin, which could be related to the high metabolism because of the oviposition.     

Scanning transmission X‐ray microscopy probe for in situ mechanism study of graphene‐oxide‐based resistive random access memory

Here, an in situ probe for scanning transmission X‐ray microscopy (STXM) has been developed and applied to the study of the bipolar resistive switching (BRS) mechanism in an Al/graphene oxide (GO)/Al resistive random access memory (RRAM) device. To perform in situ STXM studies at the C K‐ and O K‐edges, both the RRAM junctions and the I₀ junction were fabricated on a single Si₃N₄ membrane to obtain local XANES spectra at these absorption edges with more delicate I₀ normalization. Using this probe combined with the synchrotron‐based STXM technique, it was possible to observe unique chemical changes involved in the BRS process of the Al/GO/Al RRAM device. Reversible oxidation and reduction of GO induced by the externally applied bias voltages were observed at the O K‐edge XANES feature located at 538.2 eV, which strongly supported the oxygen ion drift model that was recently proposed from ex situ transmission electron microscope studies.     

In situ multi‐axial loading frame to probe elastomers using X‐ray scattering

An in situ tensile–shear loading device has been designed to study elastomer crystallization using synchrotron X‐ray scattering at the Synchrotron Soleil on the DiffAbs beamline. Elastomer tape specimens of thickness 2 mm can be elongated by up to 500% in the longitudinal direction and sheared by up to 200% in the transverse direction. The device is fully automated and plugged into the TANGO control system of the beamline allowing synchronization between acquisition and loading sequences. Experimental results revealing the evolution of crystallization peaks under load are presented for several tension/shear loading sequences.     

Cytogenetics of four species of Spirostreptidae (Diplopoda, Spirostreptida)

Considering an estimated number of millipedes of approximately 80,000, cytogenetic studies on these animals are rare, as only a total of 70 species have their karyotypes described. The present study reports on the chromosomal number of four Brazilian diplopods of the family Spirostreptidae: Urostreptus atrobrunneus with 2n = 24, XY; Gymnostreptus olivaceus 2n = 12, XY and Alloporus araraquarensis and A. principes, 2n = 18, XY. The C-banding pattern and NOR staining of U. atrobrunneus, G. olivaceus and A. araraquarensis are described.     

In situ 57Fe Mössbauer Investigation of Solid-State Redox Reactions of Lithium Insertion Electrodes for Advanced Batteries

A novel in situ electrochemical cell for ⁵⁷Fe Mössbauer measurements was developed in order to clarify the mechanisms of solid-state redox reactions in lithium insertion materials containing iron. Our in situ Mössbauer technique was successfully applied to the determination as to which transition metal ion was a redox center in the insertion electrodes, such as LiFe_0.5Mn_1.5O₄, LiFeTiO₄, or LiFe_0.25Ni_0.75O₂, for the lithium-ion batteries.     

A comparative study of two marine catfish (Siluriformes,Ariidae): Cytogenetic tools for determining cytotaxonomy and karyotype evolution

The family Ariidae comprises approximately 130 catfish species on both warm-temperate and tropical continental shelves around the world. The systematics of the group is problematic, with several misidentification problems. In order to better understand the evolutionary relationships in the family, the present study used a cytogenetic approach to characterize two populations of Genidens genidens and two populations of Aspistor luniscutis from the southern coast of Brazil using conventional techniques and fluorescent in situ hybridization with 18S rDNA probes. The two species had the same diploid number (2n = 56), high fundamental numbers and similar banding patterns, thereby corroborating the karyotypic homogeneity proposed for the group. Single nucleolus organizer regions (NORs) were found in the genus Genidens and multiple NORs were found in Aspistor, which are considered an important cytotaxonomic marker for this genus. Karyotypic evolution trends were hypothesized, providing a better understanding of the karyotype diversity and chromosome evolution processes.     

Mechanism for enhancing dispersion of Co3O4 nanoparticles in Co/SiO2 Fischer–Tropsch synthesis catalyst by adding glycol to impregnating solution: a quick‐XAFS study

In situ Co K‐edge quick‐EXAFS (QEXAFS) coupled with temperature‐programmed oxidation as well as ex situ XAFS was applied to investigating the mechanism for enhancing the dispersion of Co₃O₄ nanoparticles in a calcined Co/SiO₂ Fischer–Tropsch synthesis catalyst prepared by adding triethylene glycol (TEG) to a Co(NO₃)₂.6H₂O impregnating solution. Ex situ Co K‐edge XAFS indicated that, regardless of whether the catalysts were prepared with or without using TEG, the hexaaqua Co (II) complex was formed in impregnated samples which then underwent the dehydration process to some extent during the subsequent drying step at 393 K. In situ QEXAFS and ex situ EXAFS results also indicated that small oxide clusters were formed in the TEG‐modified catalyst calcined at ～400–470 K which interacted with polymer species derived from TEG. Since the Fischer–Tropsch synthesis activity of the TEG‐modified catalyst increased with an increase in the calcination temperature in a similar temperature range [Koizumi et al. (2011), Appl. Catal. A, 395 , 138–145], it was suggested that such an interaction enables the clusters to be distributed over the support surface uniformly, resulting in enhancing their dispersion. After combustion of polymer species, Co₃O₄‐like species were formed, and agglomeration of the Co₃O₄‐like species at high calcination temperatures was suppressed by the addition of TEG to the impregnating solution. It was speculated that the addition of TEG induced the formation of some surface silicate which worked as an anchoring site for Co₃O₄ and Co⁰ nanoparticles during calcination and H₂ reduction, respectively.