Spatial distribution of GC- and AT-rich DNA sequences within human chromosome territories

Previous topological analyses of DNA sequence organization in the interphase chromosome mainly focused on the spatial distribution of individual gene copies within chromosome territories. In order to achieve a more comprehensive view into the subchromosomal arrangement of DNA, we isolated the GC-richest/gene-richest fraction (H3 isochores) as well as AT-richest/gene-poorest fraction of human genomic DNA (L1+L2 isochores) and visualized the respective DNA within individual chromosome territories by means of dual-color FISH. Application of confocal laser scanning microscopy and dedicated 3D image analysis software, which differentiated territory subvolumes by peeling shells one voxel in width, revealed a significant difference in the intraterritorial distribution of these two DNA sequence classes. While the H3 isochores were found localized in all subvolumes of the territories at similar frequency, simultaneously detected L1+L2 isochores were observed more to the interior of the same chromosome territories. Thus the GC-rich sequences display a much higher variability in their intraterritorial localization than AT-rich DNA fragments.     

Nuclear and territorial topography of chromosome telomeres in human lymphocytes

Nuclear and territorial positioning of p- and q-telomeres and centromeres of chromosomes 3, 8, 9, 13, and 19 were studied by repeated fluorescence in situ hybridization, high-resolution cytometry, and three-dimensional image analysis in human blood lymphocytes before and after stimulation. Telomeres were found on the opposite side of the territories as compared with the centromeres for all chromosome territories investigated. Mutual distances between telomeres of submetacentric chromosomes were very short, usually shorter than centromere-to-telomere distances, which means that the chromosome territory is nonrandomly folded. Telomeres are, on average, much nearer to the center of the cell nucleus than centromeres; q-telomeres were found, on average, more centrally localized as compared with p-telomeres. Consequently, we directly showed that chromosome territories in the cell nucleus are (1) polar and (2) partially oriented in cell nuclei. The distributions of genetic elements relative to chromosome territories (territorial distributions) can be either narrower or broader than their nuclear distributions, which reflects the degree of adhesion of an element to the territory or to the nucleus. We found no tethering of heterologous telomeres of chromosomes 8, 9, and 19. In contrast, both pairs of homologous telomeres of chromosome 19 (but not in other chromosomes) are tethered (associated) very frequently.     

The biology and polymer physics underlying large‐scale chromosome organization

Chromosome large‐scale organization is a beautiful example of the interplay between physics and biology. DNA molecules are polymers and thus belong to the class of molecules for which physicists have developed models and formulated testable hypotheses to understand their arrangement and dynamic properties in solution, based on the principles of polymer physics. Biologists documented and discovered the biochemical basis for the structure, function and dynamic spatial organization of chromosomes in cells. The underlying principles of chromosome organization have recently been revealed in unprecedented detail using high‐resolution chromosome capture technology that can simultaneously detect chromosome contact sites throughout the genome. These independent lines of investigation have now converged on a model in which DNA loops, generated by the loop extrusion mechanism, are the basic organizational and functional units of the chromosome.      

Acetylcholine-activated currents in quail myotubes expressing viral oncogenes

Acetylcholine-activated currents were recorded in cultured myotubes arising from embryonic quail myoblasts transformed by the v-src and v-ras oncogenes. In src-myotubes, the whole cell inward current decayed more slowly than in non-transformed controls. In ras-myotubes, the current had a faster decay and smaller amplitude than in the controls. The single-channel conductance and mean open times recorded from cell-attached patches were similar in transformed and control cells. However, in ras-myotubes the frequency of channel openings strongly decreased with time.

It is concluded that oncogenic tyrosine-specific protein kinase (v-src product) and G-like p21 protein (v-ras product) can induce differential changes in the function of nicotinic ACh receptor, perhaps related to specific biochemical events elicited in the establishment of the transformed state.     

The deterrent effect of bird song in territory defense

Using the responses of territory owners to playback to inferthe territorial function of acoustic signals is common practice.However, difficulties with interpreting the results of suchexperiments have obscured our understanding of territorial signalling.For instance, a stronger response to playback is often interpretedas more aggressive, but there is no consensus as to whetherthis should be in response to the least or most threateningsimulated intruder. Rather than following a gradual increaseor decrease, the relationship between signal intensity and responsestrength may instead describe a peaked curve. We manipulatedbanded wren (Thryophilus pleurostictus) songs to simulate low-,median-, and high-performance singers and used these songs asstimuli in playback experiments. Banded wrens were less likelyto approach the high-performance stimulus compared with thelow- and median-performance stimuli. However, the birds thatdid approach the high-performance stimulus sang more than thosethat approached the low-performance stimulus. In addition, birdswere more likely to match the songs when exposed to the median-and high-performance stimuli compared with the low-performancestimuli, and song matching predicted approach behavior. Theseresults are in accordance with theoretical models of aggressiveencounters in which low-performance opponents are challengedwithout further assessment. Median- and high-performance opponents,however, may require further assessment, and the latter maybe perceived as too intimidating for approach.     

Simulation study of territory size distributions in subterranean termites

In this study, on the basis of empirical data, we have simulated the foraging tunnel patterns of two subterranean termites, Coptotermes formosanus Shiraki and Reticulitermes flavipes (Kollar), using a two-dimensional model. We have defined a territory as a convex polygon containing a tunnel pattern and explored the effects of competition among termite territory colonies on the territory size distribution in the steady state that was attained after a sufficient simulation time. In the model, territorial competition was characterized by a blocking probability P_block that quantitatively describes the ease with which a tunnel stops its advancement when it meets another tunnel; higher P_block values imply easier termination. In the beginning of the simulation run, N=10, 20,…,100 territory seeds, representing the founding pair, were randomly distributed on a square area. When the territory density was less (N=20), the differences in the territory size distributions for different P_block values were small because the territories had sufficient space to grow without strong competitions. Further, when the territory density was higher (N>20), the territory sizes increased in accordance with the combinational effect of P_block and N. In order to understand these effects better, we introduced an interference coefficient γ. We mathematically derived γ as a function of P_block and N: γ(N,P_block)=a(N)P_block/(P_block+b(N)). a(N) and b(N) are functions of N/(N+c) and d/(N+c), respectively, and c and d are constants characterizing territorial competition. The γ function is applicable to characterize the territoriality of various species and increases with both the P_block values and N; higher γ values imply higher limitations of the network growth. We used the γ function, fitted the simulation results, and determined the c and d values. In addition, we have briefly discussed the predictability of the present model by comparing it with our previous lattice model that had been used to explain the territory size distributions of mangrove termites on the Atlantic coast of Panama.     

Mapping four genes from human chromosome 4 to porcine chromosome 8 further develops the comparative map for an economically important chromosome of the swine genome

Because porcine chromosome (SSC) 8 has become the focal point of many efforts aimed at identifying quantitative trait loci affecting ovulation rate, genes distributed across human chromosome (HSA) 4 were physically mapped in the pig. A more refined comparative map of this region for these two species was produced. In this study, four genes were selected based on their location in the human genome, the availability of nucleotide sequence and their genomic organization. The genes selected were fibroblast growth factor basic (FGF2; HSA 4q25-27), gonadotropin releasing hormone receptor (GNRHR; HSA 4q13), phosphodiesterase 6 B (PDE6B; HSA 4p16.3) and aminopeptidase S (PEPS; HSA 4p11-q12). Genomic libraries were screened via PCR and clones were physically assigned using fluorescence in situ hybridization (FISH). These four genes from HSA 4 were physically mapped to SSC 8p2.3 (PDE6B), 8p1.1 (PEPS), 8q1.1-1.2 (GNRHR) and 8q2.2-2.4 (FGF2). These assignments provide additional benchmarks for the comparative map and help define the level of gene order conserved between HSA 4 and SSC 8.     

A radiation hybrid map of bovine chromosome 24 and comparative mapping with human chromosome 18

We present herein a bovine chromosome 24 (BTA24) radiation hybrid (RH) map using 40 markers scored on a panel of 90 RHs. Of these markers, 29 loci were ordered with odds of at least 1000:1 in a framework map. An average retention frequency of 17.4% was observed, with relatively higher frequencies near the centromere. The length of the comprehensive map was 640 centiray5000 (cR5000) with an average marker interval of approximately 17.3 cR5000. The observed locus order is generally consistent with currently published bovine linkage and physical maps. Nineteen markers were either Type I loci or closely associated with expressed sequences and thus could be used to compare the BTA24 RH map with human mapping information. All genes located on BTA24 were located on human chromosome 18, and previously reported regions of conserved synteny were extended. The comparative data revealed the presence of at least six conserved regions between these chromosomes.     

A field study investigating effects of landmarks on territory size and shape

Few studies have examined how landmarks affect territories'' fundamental characteristics. In this field study, we investigated effects of landmarks on territory size, shape and location in a cichlid fish (Amatitlania siquia). We provided cans as breeding sites and used plastic plants as landmarks. During 10 min trials, we recorded locations where residents chased intruders and used those locations to outline and measure the territory. In two experiments, we observed pairs without landmarks and with either a point landmark (one plant) or linear landmark (four plants) placed near the nest can. We alternated which trial occurred first and performed the second trial 24 h after the first. Territories were approximately round without landmarks or with a point landmark but were significantly more elongated when we added a linear landmark. Without landmarks, nests were centrally located; however, with any landmark, pairs set territory boundaries closer to the landmark and thus the nest. Territory size was significantly reduced in the presence of any landmark. This reduction suggests that a smaller territory with well-defined boundaries has greater benefits than a larger territory with less well-defined borders.     

The potential function of post-fledging dispersal behavior in first breeding territory selection for males of a migratory bird

One possible hypothesis for the function of post-fledging dispersal is to locate a suitable future breeding area. This post-fledging period may be particularly important in migratory species because they have a limited period to gather information prior to autumn migration, and in protandrous species, males must quickly acquire a territory after returning from spring migration to maximize their fitness. Here we use color-ring resightings to investigate how the post-fledging dispersal movements of the Cyprus wheatear Oenanthe cypriaca, a small migratory passerine, relate to their first breeding territory the following year when they return from migration. We found that males established first breeding territories that were significantly closer to their post-fledging location than to their natal sites or to post-fledging locations of other conspecifics, but these patterns were not apparent in females. Our findings suggest that familiarity with potential breeding sites may be important for juveniles of migratory species, particularly for the sex that acquires and advertises breeding territories. Exploratory dispersal prior to a migrant’s first autumn migration may contribute toward its breeding success the following year, further highlighting the importance of early seasonal breeding on fitness and population dynamics more generally.     

Meiosis and chromosome painting of sex chromosome systems in Ceboidea

The identity of the chromosomes involved in the multiple sex system of Alouatta caraya (Aca) and the possible distribution of this system among other Ceboidea were investigated by chromosome painting of mitotic cells from five species and by analysis of meiosis at pachytene in two species. The identity of the autosome #7 (X2) involved in the multiple system of Aca and its breakage points were demonstrated by both meiosis and chromosome painting. These features are identical to those described by Consigliere et al. [1996] in Alouatta seniculus sara (Assa) and Alouatta seniculus arctoidea (Asar). This multiple system was absent in the other four Ceboidea species studied here. However, data from the literature strongly suggest the presence of this multiple in other members of this genus. The presence of this multiple system among several species and subspecies that show high levels of chromosome rearrangements may suggest a special selective value of this multiple. The meiotic features of the sex systems of Aca and Cebus apella paraguayanus (Cap) are strikingly different at pachytene, as the latter system is similar to the sex pair of man and other primates. The relatively large genetic distances between species presently showing this multiple system suggest that its origin is not recent. Other members of the same genus should be investigated at meiosis and by chromosome painting in order to know the extent and distribution of this complex sex-chromosome system.     

The oxidative costs of territory quality and offspring provisioning

The costs of reproduction are an important constraint that shapes the evolution of life histories, yet our understanding of the proximate mechanism(s) leading to such life‐history trade‐offs is not well understood. Oxidative stress is a strong candidate measure thought to mediate the costs of reproduction, yet empirical evidence supporting that increased reproductive investment leads to oxidative stress is equivocal. We investigated whether territory quality and offspring provisioning increase oxidative stress in male snow buntings (Plectrophenax nivalis) using a repeated sampling design. We show that arrival oxidative stress is not a constraint on territory quality or the number of offspring fledged. Nevertheless, owners of higher‐quality territories experienced an oxidative cost, with this cost increasing more rapidly in younger males. Males that provisioned offspring at a high rate also experienced increased oxidative stress. Together, these findings support the potential role of oxidative stress in mediating life‐history trade‐offs. Future work should consider that reproductive workload is not limited to offspring care, and other activities – including territory defence – may contribute significantly to the costs of reproduction.     

Origin of human chromosome 2 revisited

Similarities in chromosome banding patterns and hornologies in DNA sequence between chromosomes of the great apes and humans have suggested that human chromosome 2 originated through the fusion of two ancestral ape chromosomes. A lot of work has been directed at understanding the nature and mechanism of this fusion. The recent availability of the human chrornosome-2-specific alpha satellite DNA probe D2Z and the human chromosome-2p-specific subtelomeric DNA probe D2S445 prompted us to attempt cross-hybridization with chromosomes of the chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla) and orangutan (Pongo pygmaeus) to search for equivalent locations in the great apes and to comment on the origin of human chromosome 2. The probes gave different results. No hybridization to the chromosome-2-specific alpha satellite DNA probe was observed on the presumed homologous great ape chromosomes using both high-stringency and low-stringency post-hybridization washes, whereas the subtelomeric-DNA probe specific for chromosome 2p hybridized to telomeric sites of the short arm of chromosome 12 of all three great apes. These observations suggest an evolutionary difference in the number of alpha satellite DNA repeat units in the equivalent ape chromosomes presumably involved in the chromosome fusion. Nevertheless, complete conservation of DNA sequence of the subtelomeric repeat sequence D2S445 in the ape chromosomes is demonstrated.     

Human influence on the vascular flora of the Veggiano territory (Padova - Italy)

Abstract

This paper is the result of 10 years of floristic research carried out in the Veggiano area (Padova). A floristic list of 612 taxa was drawn from bibliography (BEGUINOT, 1909–1914). According to our data (1990) 386 taxa are still present, with a loss of approximately 40%. The main cause of this loss is the disappearance of certain habitats (i.e. wood) and the alteration of others due to human influence.     

Tumorigenesis in transgenic mice: identification and characterization of synergizing oncogenes.

Transgenic mice carrying oncogenes present a useful model with which to assess the tissue-specific action of oncogenes. These mice are usually predisposed to a specific type of neoplastic growth. The tumors that arise are usually monoclonal in origin and become only apparent after a variable latency period, suggesting that additional events are required for tumor formation. Identification of these additional events is highly relevant: it might give access to the genes that can synergize with a preselected oncogene in tumorigenesis and could facilitate the identification of the biochemical pathways in which these genes act. Retroviruses can be instrumental in identifying cooperating oncogenes. Proto-oncogene activation or tumor suppressor gene inactivation by insertional mutagenesis is an important mechanism by which the non-acute transforming retroviruses can induce tumors in several species. Owing to the sequence tag provided by the provirus, the relevant proto-oncogene can be directly identified by cloning of the DNA flanking the proviral insertion site. We have exploited this potential of retroviruses by infecting E mu-pim-1 and E mu-myc transgenic mice, which are predisposed to lymphomagenesis, with Moloney murine leukemia virus (MuLV). A strong acceleration of tumor induction ensued upon infection of these mice with MuLV. More importantly, it allowed us to identify a number of additional common insertion sites marking both previously known as well as new (putative) oncogenes. In a significant portion of the tumors more than one oncogene was found to be activated, indicating that within this system the synergistic effect of at least three genes can be established.(ABSTRACT TRUNCATED AT 250 WORDS)     

Construction of a novel human artificial chromosome vector for gene delivery

Potential problems of conventional transgenes include insertional disruption of the host genome and unpredictable, irreproducible expression of the transgene by random integration. Alternatively, human artificial chromosomes (HACs) can circumvent some of the problems. Although several HACs were generated and their mitotic stability was assessed, a practical way for introducing exogenous genes by the HACs has yet to be explored. In this study, we developed a novel HAC from sequence-ready human chromosome 21 by telomere-directed chromosome truncation and added a loxP sequence for site-specific insertion of circular DNA by the Cre/loxP system. This 21HAC vector, delivered to a human cell line HT1080 by microcell fusion, bound centromere proteins A, B, and C and was mitotically stable during long-term culture without selection. The EGFP gene inserted in the HAC vector expressed persistently. These results suggest that the HAC vector provides useful system for functional studies of genes in isogenic cell lines.