Targeted isolation of simple sequence repeat markers through the use of bacterial artificial chromosomes

 Simple sequence repeats (SSRs) are versatile DNA markers that are readily assayed and highly informative. Unfortunately, non-targeted approaches to SSR development often leave large genomic regions without SSR markers. In some cases these same genomic regions are already populated by other types of DNA markers, especially restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNAs (RAPDs), and amplified fragment length polymorphisms (AFLPs). To identify SSR markers in such regions, bacterial artificial chromosome (BAC) clones can be used as intermediaries. First, one or more BAC clones in a region of interest are identified through the use of an existing DNA marker. BAC clones uncovered in this initial step are then used to create a small insert DNA library that can be screened for the presence of SSR-containing clones. Because BAC inserts are often 100-kb pairs or more in size, most contain one or more SSRs. This strategy was applied to two regions of the soybean genome near genes that condition resistance to the soybean cyst nematode on molecular linkage groups G and A2. This targeted approach to identifying new DNA markers can readily be extended to other types of DNA markers, including single nucleotide polymorphisms. Received: 13 August 1998 / Accepted: 13 October 1998     

Clinical findings and cytogenetic analysis of small supernumerary ring chromosomes 7: report of two new cases

Two new patients, mosaic for a small supernumerary ring chromosome 7 are described. There are only seven published reported concerning supernumerary ring chromosome 7 and we reviewed the previously reported cases in an attempt to establish genotype-phenotype correlations, which are particularly important for genetic counselling and clinical genetics. Our first case was a 20 months old girl who was referred for a mild motor developmental delay, an asymmetric facial appearance, a plagiocephaly and a short nose with anteverted nostrils. Our second case was a 9 years old boy who was referred for a IQ at the lower end of the normal range (? 80), obesity, hyperactivity and some dysmorphic features including hypertelorism and down slanting palpebral fissures. In both cases, chromosome analysis after G and R banding and FISH showed a small ring chromosome 7 in respectively 76% and 50% of consecutively scored metaphases. Both ring chromosomes were labelled by FISH using the Williams Syndrome locus probe (Elastin Gene D7S486). Comparison between these two cases and previously published cases allowed to delineate frequent clinical findings. A mild mental retardation was found in the majority of patients. which is an important data for genetic counselling.     

DNA amplifications and deletions in Streptomyces lividans 66 and the loss of one end of the linear chromosome

Thirty-two 2-deoxygalactose-resistant mutants with DNA amplifications were isolated from Streptomyces lividans 66 strains carrying plasmid pMT664, which carries an agarase gene (dagA) and IS466. Thirty-one of the mutants carried amplified DNA sequences from a 70 kb region about 300 kb from one end of the linear chromosome in this species. In 28 of the mutants, all the wild-type sequences between the amplified region and the start of the 30 kb inverted repeat that forms the chromosome end were deleted. Thus, there appeared to be loss of one chromosome end and its replacement by the DNA amplification. In some mutants there amplification of a previously characterised 5.7 kb sequence that lies about 600 kb from the other chromosome end was also noted.     

Preventing broken Borrelia telomeres: ResT couples dual hairpin telomere formation with product release

Spirochetes of the genus Borrelia include the tick-transmitted causative agents of Lyme disease and relapsing fever. They possess unusual genomes composed mainly of linear replicons terminated by closed DNA hairpins. Hairpin telomeres are formed from inverted repeat replicated telomere junctions (rTels) by the telomere resolvase ResT. ResT uses a reaction mechanism similar to that of the type IB topoisomerases and tyrosine recombinases. ResT can catalyze three distinct reactions: telomere resolution, telomere fusion, and Holliday junction (HJ) formation. HJ formation is known to occur only in the context of a synapsed pair of rTels. To test whether telomere resolution was synapsis-dependent, we performed experiments with rTel substrates immobilized on streptavidin-coated beads. We report that telomere resolution by ResT is synapsis-independent, indicating that alternative complexes are formed for telomere resolution and HJ formation. We also present evidence that dual hairpin telomere formation precedes product release. This mechanism of telomere resolution prevents the appearance of broken telomeres. We compare and contrast this mechanism with that proposed for TelK, the telomere resolvase of φKO2.     

The chromosomes of two Drosophila races: Drosophila nasuta nasuta and Drosophila nasuta albomicana V. Introgression and the evolution of new karyotypes

Reciprocal crosses were made between an Indian strain of D. n. nasuta (2n=8) and the Thailand strain of D. n. albomicana (2n=6). Hybrids were fertile. They were inbred for over four years. Later, the karyotypes of the hybrid populations were analysed. In the hybrid progeny of the cross between D. n. nasuta females and D. n. albomicana males, there were six types of kaotypes. Of these, only two types had a diploid content of chromosomes. They were males with 2n=7 and females with 2n= 8 , while others were aneuploids. This hybrid population is designated as Cytorace III. On the other hand, hybrid progeny of the reciprocal cross had 2n-8 in both males and females; and there was no karyotypic variation. This hybrid population is named as Cytorace IV. The composition of these new karyotypes of Cytorace III and IV have been presented and compared with those of Cytorace I and II reported by Ramachandra and Ranganath (1986).     

Decoding the genome beyond sequencing: the new phase of genomic research

While our understanding of gene-based biology has greatly improved, it is clear that the function of the genome and most diseases cannot be fully explained by genes and other regulatory elements. Genes and the genome represent distinct levels of genetic organization with their own coding systems; Genes code parts like protein and RNA, but the genome codes the structure of genetic networks, which are defined by the whole set of genes, chromosomes and their topological interactions within a cell. Accordingly, the genetic code of DNA offers limited understanding of genome functions. In this perspective, we introduce the genome theory which calls for the departure of gene-centric genomic research. To make this transition for the next phase of genomic research, it is essential to acknowledge the importance of new genome-based biological concepts and to establish new technology platforms to decode the genome beyond sequencing.     

FramePlot: a new implementation of the Frame analysis for predicting protein-coding regions in bacterial DNA with a high G+C content

FramePlot is a web-based tool for predicting protein-coding regions in bacterial DNA with a high G + C content, such as Streptomyces. The graphical output provides for easy distinction of protein-coding regions from non-coding regions. The plot is a clickable map. Clicking on an ORF provides not only the nucleotide sequence but also its deduced amino acid sequence. These sequences can then be compared to the NCBI sequence database over the Internet. The program is freely available for academic purposes at http://www.nih.go.jp/jun/cgi-bin/frameplot.pl.     

Cheats as first propagules: A new hypothesis for the evolution of individuality during the transition from single cells to multicellularity

The emergence of individuality during the evolutionary transition from single cells to multicellularity poses a range of problems. A key issue is how variation in lower‐level individuals generates a corporate (collective) entity with Darwinian characteristics. Of central importance to this process is the evolution of a means of collective reproduction, however, the evolution of a means of collective reproduction is not a trivial issue, requiring careful consideration of mechanistic details. Calling upon observations from experiments, we draw attention to proto‐life cycles that emerge via unconventional routes and that transition, in single steps, individuality to higher levels. One such life cycle arises from conflicts among levels of selection and invokes cheats as a primitive germ line: it lays the foundation for collective reproduction, the basis of a self‐policing system, the selective environment for the emergence of development, and hints at a plausible origin for a soma/germ line distinction.     

小盗龙亚科(兽脚亚目:驰龙科)——新标本及简评复合骨在兽脚亚目中的演化（英文）

小盗龙亚科是驰龙科兽脚类恐龙中新近发现的一个亚群,多数属种产自中国辽宁西部下白垩统热河群。本文描记一件产自辽宁省朝阳县大平房地区九佛堂组(热河群上段)的小盗龙亚科的新标本,该标本具有一些未曾报道过的有趣形态特征。尤其值得关注的是,一些特征呈现出介于中国鸟龙和小盗龙之间的过渡状态,其中部分来自牙齿和坐骨。这些特征突出显示了在更接近典型驰龙类的中国鸟龙和具有许多伤齿龙科特征的小盗龙之间存在着一系列的形态变异。然而,这些变异特征在分类上的意义尚未得到充分评估。特别值得一提的是该标本中相互愈合的耻骨和肠骨,这一特征有助于阐明复合骨在兽脚类恐龙中的演化模式。初步分析显示许多鸟类的复合骨都是通过在过型形成过程中各组分的顺序愈合形成的。     

Genetic diversity of the harmful family Kareniaceae (Gymnodiniales,Dinophyceae) in France,with the description of Karlodinium gentienii sp. nov.: A new potentially toxic dinoflagellate

The family Kareniaceae is mostly known in France for recurrent blooms of Karenia mikimotoi in the Atlantic, English Channel, and Mediterranean Sea and for the unusual green discoloration in the saltwater lagoon of Diana (Corsica) caused by Karlodinium corsicum in April 1994. In terms of diversity, this taxonomic group was long overlooked owing to the difficult identification of these small unarmored dinoflagellates. In this study, thanks to the molecular characterization performed on single cells from field samples and cultures, twelve taxonomic units were assigned to the known genera Karenia, Karlodinium and Takayama, whereas one could not be affiliated to any described genus. The molecular phylogeny inferred from the D1–D2 region of the LSU rDNA showed that five of them formed a sister taxon of a known species, and could not be identified at species-level, on the basis of molecular analysis only. Among these latter taxa, one Karlodinium which was successfully cultured was investigated by studying the external morphological features (using two procedures for cells fixation), ultrastructure, pigment composition, and haemolytic activity. The results of our analyses corroborate the genetic results in favour of the erection of Karlodinium gentienii sp. nov., which possesses an internal complex system of trichocysts connected to external micro-processes particularly abundant in the epicone, and a peculiar pigment composition. In addition, preliminary assays showed a haemolytic activity.     

Flood mapping with remote sensing and hydrochemistry: A new method to distinguish the origin of flood water during floods

River flooding is important for the ecological functioning of river floodplains. It is implicitly assumed that in many river floodplains during floods, river water is spreading all over the floodplain. We hypothesize that during flood events a spatial distribution of water types exists, which is correlated to different water sources (river water, atmospheric water and groundwater) and to the spatial distribution of vegetation types. The objective of this paper is to assess a new methodology to determine the extent of flooding and the spatial distribution of different water sources during the flood, using GPS, multispectral remote sensing and hydrochemical analyses. This methodology is applied to the Biebrza River Lower Basin, which has little human impact. Remote sensing resulted in a map distinguishing inundated areas from dry areas, which showed 85% agreement with GPS field measurements. Principal Component Analyses and Cluster Analyses on the measured water chemistry identified different water sources during the flood (river water, groundwater, rainwater) and showed the effects of human impact on water quality. River flood water dominated the entire inundation zone in the northern Lower Basin, which is narrower and steeper than the southern Lower Basin where groundwater and rainwater were significant contributors to the major part of the inundated area. Vegetation in the river flood zone is distinctly different from the rest of the floodplain. Due to mixing of ground- and rainwater, correlation analyses between vegetation and water type were not possible outside the river flood zone. The new methodology is effective in distinguishing inundated areas from dry regions and in separating river flood water from other water sources during a flood.     

A new species of Carpolestes (Mammalia,Plesiadapoidea) from the late Paleocene of southern Wyoming: assessing changes in size and shape during the evolution of a key anatomical feature

A new and phylogenetically basal species of Carpolestes, the youngest and most derived genus of the plesiadapoid family Carpolestidae in North America, is described from a late Tiffanian (Ti-5) site in Sweetwater County, Wyoming, USA. Carpolestids differ from closely related plesiadapoid clades in having an enlarged, multicuspidate, blade-like P₄ that is partly convergent on that of multituberculates and other mammals showing plagiaulacoid dental adaptations. With some notable exceptions, the evolutionary history of North American carpolestids is characterized by the progressive development of larger and more elaborate P₄ blades through time. In particular, species of the monophyletic genus Carpolestes differ from species assigned to the earlier and apparently paraphyletic genus Carpodaptes in terms of both the size and shape of their P₄. A geometric morphometric analysis reveals that, with respect to P₄ shape, the closest approximation to the highly derived morphology of Carpolestes is made by Carpodaptes hobackensis, which is one of the smallest known species of Carpodaptes. In contrast, the largest known species of Carpodaptes, Carpodaptes jepseni, has a P₄ that falls within the metric range of variation for species of Carpolestes, yet Carpodaptes jepseni shows a uniquely derived P₄ shape that seems to exclude it from any special phylogenetic relationship with Carpolestes. A phylogenetic analysis based on dental characters reconstructs Carpodaptes hobackensis as the sister group of the Carpolestes clade. Shape seems to have been a more important factor than size during the final transformation of the blade-like P₄ of North American carpolestids.

http://zoobank.org/urn:lsid:zoobank.org:pub:212F9ECC-DA9A-44F8-BE7E-43F3EBAD636A     

A new hypothesis for the evolution of overproduction of ovules: an advantage of selective abortion for females not associated with variation in genetic quality of the resulting seeds

A new hypothesis for the evolution of overproduction of ovules within flowers is proposed: overproduction is a counter-strategy of female seed production in the conflict with males and/or offspring. It is advantageous for females to produce a uniform size of seeds, whereas it is advantageous for fertilized ovules to absorb more resources than this size. If there is a variance in resource absorption ability among fertilized ovules, nonuniform seeds are produced. Then, by overproducing ovules, females should select fertilized ovules with similar resource absorption rates, resulting in seeds of uniform size. A model analysis confirmed that this hypothesis works. In the model, the fertilized ovules of a plant consist of two genotypes that differ in resource absorption rate. I found that overproduction of ovules and selective abortion is advantageous if the difference in the resource absorption rates of the genotypes is large. The new hypothesis is different from the selective abortion hypothesis in that selecting ovules is advantageous even if there are no differences in the genetic quality of resulting seeds.     

Activation of apoptosis, but not necrosis, during Mycobacterium tuberculosis infection correlated with decreased bacterial growth: role of TNF-alpha, IL-10, caspases and phospholipase A2

Monocyte/macrophage cell death is an important event during mycobacterial infection. To get insights about the influence of mononuclear phagocyte maturation in this event we compared the response to Mycobacterium tuberculosis (Mtb) infection of fresh isolated monocytes and monocyte-derived macrophages (MDM) from healthy tuberculin positive individuals. Both monocytes and MDM underwent apoptosis, however, there was a higher numbers of apoptotic macrophages with active Caspases 8 and 9. We also compared Mtb-induced cell death in U937 pro-monocytes and PMA-differentiated cells (U937D). In response to Mtb infection, U937D cells underwent apoptosis and promonocytes both apoptosis and necrosis. There were high number of U937D cells producing TNF-α and high number of IL-10⁺ promonocytes. These evidences suggest that U937 could be a valid model to study the mechanisms that rule Mtb-induced cell death. Experiments with the cell line and fresh isolated mononuclear cells with pharmacological inhibitors showed that induction of necrosis involved calcium and cAMP signals resulting in IL-10 production. Necrosis also correlated with Caspase 3, PLA2 activity and bacterial growth. In U937D cells and monocytes from healthy donors there was activation of calcium, TNF-α and Caspase 8 activation and decreased bacterial load. Understanding the mechanisms that control the dichotomy events between apoptosis and necrosis/oncosis associated with cell maturity might open new strategies to better control the course of mycobacterial infections.