Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequ

Molecular phylogeny and taxonomy of wood mice (genus Apodemus Kaup, 1829) based on complete mtDNA cytochrome b sequences, with emphasis on Chinese species

Phylogenetic relationships among 15 species of wood mice (genus Apodemus) were reconstructed to explore some long-standing taxonomic problems. The results provided support for the monophyly of the genus Apodemus, but could not reject the hypothesis of paraphyly for this genus. Our data divided the 15 species into four major groups: (1) the Sylvaemus group (A. sylvaticus, A. flavicollis, A. alpicola, and A. uralensis), (2) the Apodemus group (A. peninsulae, A. chevreri, A. agrarius, A. speciosus, A. draco, A. ilex, A. semotus, A. latronum, and A. mystacinus), (3) A. argenteus, and (4) A. gurkha. Our results also suggested that orestes should be a valid subspecies of A. draco rather than an independent species; in contrast, A. ilex from Yunnan may be regarded as a separate species rather than a synonym of orestes or draco. The species level status of A. latronum, tscherga as synonyms of A. uralensis, and A. chevrieri as a valid species and the closest sibling species of A. agrarius were further corroborated by our data. Applying a molecular clock with the divergences of Mus and Rattus set at 12 million years ago (Mya) as a calibration point, it was estimated that five old lineages (A. mystacinus and four major groups above) diverged in the late Miocene (7.82-12.74 Mya). Then the Apodemus group (excluding A. mystacinus) split into two subgroups: agrarius and draco, at about 7.17-9.95 Mya. Four species of the Sylvaemus group were estimated to diverge at about 2.92-5.21 Mya. The Hengduan Mountains Region was hypothesized to have played important roles in Apodemus evolutionary histories since the Pleistocene. (C) 2004 Elsevier Inc. All rights reserved.

THE PHYLOGENETIC-RELATIONSHIPS AND CLASSIFICATION OF THE DOUCS AND SNUB-NOSED LANGURS OF CHINA AND VIETNAM

The taxonomy of the douc and snub-nosed langurs has changed several times during the 20th century. The controversy over the systematic position of these animals has been due in part to difficulties in studying them: both the doucs and the snub-nosed langurs are rare in the wild and are generally poorly represented in institutional collections. This review is based on a detailed examination of relatively large numbers of specimens of most of the species of langurs concerned. An attempt was made to draw upon as many types of information as were available in order to make an assessment of the phyletic relationships between the langur species under discussion. Toward this end, quantitative and qualitative features of the skeleton, specific features of visceral anatomy and characteristics of the pelage were utilized. The final data matrix comprised 178 characters. The matrix was analyzed using the program Hennig86. The results of the analysis support the following conclusions: (1) that the douc and snub-nosed langurs are generically distinct and should be referred to as species of Pygathrix and Rhinopithecus, respectively; (2) that the Tonkin snub-nosed langur be placed in its own subgenus as Rhinopithecus (Presbytiscus) avunculus and that the Chinese snub-nosed langur thus be placed in the subgenus Rhinopithecus (Rhinopithecus); (3) that four extant species of Rhinopithecus be recognized: R. (Rhinopithecus) roxellana Milne Edwards, 1870; R. (Rhinopithecus) bieti Milne Edwards, 1897; R. (Rhinopithecus) brelichi Thomas, 1903, and R. (Presbytiscus) avunculus Dollman, 1912; (4) that the Chinese snub-nosed langurs fall into northern and southern subgroups divided by the Yangtze river; (5) that R. lantianensis Hu and Qi, 1978, is a valid fossil species, and (6) the precise affinities and taxonomic status of the fossil species R. tingianus Matthew and Granger, 1923, are unclear because the type specimen is a subadult.

Buyer-supplier relationships in a servitized environment: An examination with Cannon and Perreault's framework

Purpose: The purpose of this study is to examine a buyer's adoption of servitization and the associated implications for the relationships with its suppliers. Design/methodology/approach: The authors use the case study approach to examine the tripartite relationship between a manufacturing company and two of its two suppliers. The paper explores the perspectives of employees on multiple organisational levels, and collects evidence on both sides of a relationship. The authors use template analysis utilising Cannon and Perreault's relationship connectors framework to analyse the data. Findings: There are overarching implications of servitization adoption for buyer-supplier relationships. The implications are notable in all five relationship connectors. Parties expected more open exchange of information, operational linkages were strengthened and changes in the structural arrangements of relationships were witnessed. Legal contracts are complemented by relational norms. The authors also observed a departure away from a win-lose mentality and increased levels of supplier adaptation to support the buyer's provision of integrated solutions. Research limitations/implications: The findings are confined to this tripartite relationship and to an extent are context specific. Practical implications: The study unveils buyer-supplier relationships in a servitized context and provides managers with a better understanding of some of the potential implications that the adoption of a servitization strategy may have for managing buyer-supplier relationships. Originality/value: This is the first empirical study that explores the implications of servitization on buyer-supplier relationships. It advances the understanding of the implications that the adoption of servitization has on the manner in which two parties interrelate and conduct commercial exchange. © Emerald Group Publishing Limited.

Contra-rotating open rotor operation for improved aerodynamics and noise at takeoff

The contra-rotating open rotor is, once again, being considered as an alternative to the advanced turbofan to address the growing pressure to cut aviation fuel consumption and carbon dioxide emissions. One of the key challenges is meeting community noise targets at takeoff. Previous open rotor designs are subject to poor efficiency at takeoff due to the presence of large regions of separated flow on the blades as a result of the high incidence needed to achieve the required thrust. This is a consequence of the fixed rotor rotational speed constraint typical of variable pitch propellers. Within the study described in this paper, an improved operation is proposed to improve performance and reduce rotorrotor interaction noise at takeoff. Three-dimensional computational fluid dynamics (CFD) calculations have been performed on an open rotor rig at a range of takeoff operating conditions. These have been complemented by analytical tone noise predictions to quantify the noise benefits of the approach. The results presented show that for a given thrust, a combination of reduced rotor pitch and increased rotor rotational speed can be used to reduce the incidence onto the front rotor blades. This is shown to eliminate regions of flow separation, reduce the front rotor tip loss and reduce the downstream stream tube contraction. The wakes from the front rotor are also made wider with lower velocity defect, which is found to lead to reduced interaction tone noise. Unfortunately, the necessary increase in blade speed leads to higher relative Mach numbers, which can increase rotor alone noise. In summary, the combined CFD and aero-acoustic analysis in this paper shows how careful operation of an open rotor at takeoff, with moderate levels of re-pitch and speed increase, can lead to improved front rotor efficiency as well as appreciably lower overall noise across all directivities. Copyright © 2011 by ASME.

Change impact on a product and its redesign process: A tool for knowledge capture and reuse

Change propagates, potentially affecting many aspects of a design and requiring much rework to implement. This article introduces a cross-domain approach to decompose a design and identify possible change propagation linkages, complemented by an interactive tool that generates dynamic checklists to assess change impact. The approach considers the information domains of requirements, functions, components, and the detail design process. Laboratory experiments using a vacuum cleaner suggest that cross-domain modelling helps analyse a design to create and capture the information required for change prediction. Further experiments using an electronic product show that this information, coupled with the interactive tool, helps to quickly and consistently assess the impact of a proposed change. © 2012 Springer-Verlag London Limited.

Methods of monitoring of metro lining in Prague

There are several reasons for monitoring of underground structures and they have already been discussed many times, e.g. from the view of ageing or state after accidental event like flooding of Prague metro in 2002. Monitoring of Prague metro is realized in the framework of international research project sponsored by ESF-S3T. The monitoring methods used in Prague are either classical one or new or developing one. The reason for different monitoring methods is the different precision of each method and also for cross-checking between them and their evaluation. Namely we use convergence, tiltmetres, crackmetres, geophysical methods, laser scanning, computer vision and finally installation of MEMS monitoring devices. In the paper more details of each method and obtained results will be presented. The monitoring methods are complemented by wireless data collection and transfer for real-time monitoring. © 2012 Taylor & Francis Group.

Slowness and sparseness lead to place, head-direction, and spatial-view cells.

We present a model for the self-organized formation of place cells, head-direction cells, and spatial-view cells in the hippocampal formation based on unsupervised learning on quasi-natural visual stimuli. The model comprises a hierarchy of Slow Feature Analysis (SFA) nodes, which were recently shown to reproduce many properties of complex cells in the early visual system []. The system extracts a distributed grid-like representation of position and orientation, which is transcoded into a localized place-field, head-direction, or view representation, by sparse coding. The type of cells that develops depends solely on the relevant input statistics, i.e., the movement pattern of the simulated animal. The numerical simulations are complemented by a mathematical analysis that allows us to accurately predict the output of the top SFA layer.

Assessment of dry weight by monitoring changes in blood volume during hemodialysis using Crit-Line.

BACKGROUND: Routine assessment of dry weight in chronic hemodialysis patients relies primarily on clinical evaluation of patient fluid status. We evaluated whether measurement of postdialytic vascular refill could assist in the assessment of dry weight. METHODS: Twenty-eight chronic, stable hemodialysis patients were studied during routine treatment sessions using constant dialysate temperature and dialysate sodium concentration, and relative changes in blood volume were monitored using Crit-Line III monitors throughout this study. The study was divided into three phases. Phase 1 studies evaluated the time-dependence of vascular compartment refill after completion of hemodialysis. Phase 2 studies evaluated the relationships in patient subgroups between intradialytic changes in blood volume and the presence of postdialytic vascular compartment refill during that last 10 minutes of hemodialysis after stopping ultrafiltration. Phase 3 studies evaluated the extent of dry weight changes following the application of a protocol for blood volume reduction, postdialytic vascular compartment refill, and correlation with clinical evidence of intradialytic hypovolemia and/or postdialytic fatigue. Phase 3 included anywhere from three to five treatments. RESULTS: Phase 1 studies demonstrated that despite interpatient variability in the magnitude of postdialytic vascular compartment refill, when significant refill was evident, it always continued for at least 30 minutes. However, the majority of refill took place within 10 minutes postdialysis. Phase 2 studies identified 3 groups of patients: those who exhibited intradialytic reductions in blood volume but not postdialytic vascular compartment refill (group 1), those who exhibited intradialytic reductions in blood volume and postdialytic vascular compartment refill (group 2), and those whose blood volume did not change substantially during hemodialysis treatment (group 3). In phase 3 studies, use of an ultrafiltration protocol for blood volume reduction and monitoring of postdialytic vascular compartment refill combined with clinical assessment of hypovolemia and postdialytic fatigue demonstrated that patients often had a clinical dry weight assessment which was too low or too high. In all 28 patients studied, dry weight was either increased or decreased following use of this protocol. CONCLUSION: Determination of the extent of both intradialytic decreases in blood volume and postdialytic vascular compartment refill, combined with clinical assessment of intradialytic hypovolemia and postdialytic fatigue, can help assess patient dry weight and optimize volume status while reducing dialysis associated morbidity. The number of hospital admissions due to fluid overload may be reduced.

Identification of an additional two-cysteine containing type I interferon in rainbow trout Oncorhynchus mykiss provides evidence of a major gene duplication event within this gene family in teleosts

Multiple type I interferons (IFNs) have recently been identified in salmonids, containing two or four conserved cysteines. In this work, a novel two-cysteine containing (2C) IFN gene was identified in rainbow trout. This novel trout IFN gene (termed IFN5) formed a phylogenetic group that is distinct from the other three salmonid IFN groups sequenced to date and had a close evolutionary relationship with IFNs from advanced fish species. Our data demonstrate that two subgroups are apparent within each of the 2C and 4C type I IFNs, an evolutionary outcome possibly due to two rounds of genome duplication events that have occurred within teleosts. We have examined gene expression of the trout 2C type I IFN in cultured cells following stimulation with lipopolysaccharide, phytohaemagglutinin, polyI:C or recombinant IFN, or after transfection with polyI:C. The kinetics of gene expression was also studied after viral infection. Analysis of the regulatory elements in the IFN promoter region predicted several binding sites for key transcription factors that potentially play an important role in mediating IFN5 gene expression.

Estimation of the detection probability for Yangtze finless porpoises (Neophocaena phocaenoides asiaeorientalis) with a passive acoustic method

Yangtze finless porpoises were surveyed by using simultaneous visual and acoustical methods from 6 November to 13 December 2006. Two research vessels towed stereo acoustic data loggers, which were used to store the intensity and sound source direction of the high frequency sonar signals produced by finless porpoises at detection ranges up to 300 m on each side of the vessel. Simple stereo beam forming allowed the separation of distinct biosonar sound source, which enabled us to count the number of vocalizing porpoises. Acoustically, 204 porpoises were detected from one vessel and 199 from the other vessel in the same section of the Yangtze River. Visually, 163 and 162 porpoises were detected from two vessels within 300 m of the vessel track. The calculated detection probability using acoustic method was approximately twice that for visual detection for each vessel. The difference in detection probabilities between the two methods was caused by the large number of single individuals that were missed by visual observers. However, the sizes of large groups were underestimated by using the acoustic methods. Acoustic and visual observations complemented each other in the accurate detection of porpoises. The use of simple, relatively inexpensive acoustic monitoring systems should enhance population surveys of free-ranging, echolocating odontocetes. (C) 2008 Acoustical Society of America.

alpha-tocopherol is essential for acquired chill-light tolerance in the cyanobacterium Synechocystis sp strain PCC 6803

Unlike Escherichia coli, the cyanobacterium Synechocystis sp. strain PCC 6803 is insensitive to chill (5 degrees C) in the dark but rapidly losses viability when exposed to chill in the light (100 mu mol photons m(-2) s(-1)). Preconditioning at a low temperature (15 degrees C) greatly enhances the chill-light tolerance of Synechocystis sp. strain PCC 6803. This phenomenon is called acquired chill-light tolerance (ACLT). Preconditioned wild-type cells maintained a substantially higher level of alpha-tocopherol after exposure to chill-light stress. Mutants unable to synthesize alpha-tocopherol, such as slr1736, slr1737, slr0089, and slr0090 mutants, almost completely lost ACLT. When exposed to chill without light, these mutants showed no or a slight difference from the wild type. When complemented, the slr0089 mutant regained its ACLT. Copper-regulated expression of slr0090 from P-petE controlled the level of et-tocopherol and ACLT. We conclude that alpha-tocopherol is essential for ACLT of Synechocystis sp. strain PCC 6803. The role of a-tocopherol in ACLT may be based largely on a nonantioxidant activity that is not possessed by other tocopherols or pathway intermediates.

Investigations into the perplexing interrelationship of the Genus Takifugu Abe, 1949 (Tetraodontiformes, Tetraodontidae)

The phylogenetic relationships within the genus Takifugu Abe, 1949 (Tetraodontiformes, Tetraodontidae) remain unresolved. Because of the use of Takifugu as model organisms, the resolution of these relationships is crucial for the interpretation of evolutionary trends in biology. Pufferfishes of this genus are comprised of a comparatively small number of species and are mainly distributed along the coastal region of the western part of the Sea of Japan and the coastline of China. Mitochondrial gene sequences were employed to test the phylogenetic hypotheses within the genus. Seventeen species of the genus were examined. Molecular phylogenetic trees were constructed using the maximum parsimony, neighbor-joining, maximum likelihood and Bayesian methods. Our hypothesis of internal relationships within the genus differs from previous hypotheses. Our results indicate that (1) the genus Takifugu is a monophyletic assemblage; (2) the genus is divided into 6 subgroups based on the molecular data; and (3) there is low genetic diversity among the species within this genus. In addition, speciation within Takifugu appears to be driven by hybridization and isolation by distribution. Our results also suggested that the taxonomy in the genus should be clarified based on both molecular and morphological data.

Population genetic structure of Carchesium polypinum (Ciliophora : Peritrichia) in four chinese lakes inferred from ISSR fingerprinting: High diversity but low differentiation

Although the peritrichous ciliate Carchesium polypinum is common in freshwater, its population genetic structure is largely unknown. We used inter-simple sequence repeat (ISSR) fingerprinting to analyze the genetic structure of 48 different isolates of the species from four lakes in Wuhan, central China. Using eight polymorphic primers, 81 discernible DNA fragments were detected, among which 76 (93.83%) were polymorphic, indicating high genetic diversity at the isolate level. Further, Nei's gene diversity (h) and Shannon's Information index (I) between the different isolates both revealed a remarkable genetic diversity, higher than previously indicated by their morphology. At the same time, substantial gene flow was found. So the main factors responsible for the high level of diversity within populations are probably due to conjugation (sexual reproduction) and wide distribution of swarmers. Analysis of molecular variance (AMOVA) showed that there was low genetic differentiation among the four populations probably due to common ancestry and flooding events. The cluster analysis and principal component analysis (PCA) suggested that genotypes isolated from the same lake displayed a higher genetic similarity than those from different lakes. Both analyses separated C. polypinum isolates into subgroups according to the geographical locations. However, there is only a weak positive correlation between the genetic distance and geographical distance, suggesting a minor effect of geographical distance on the distribution of genetic diversity between populations of C. polypinum at the local level. In conclusion, our studies clearly demonstrated that a single morphospecies may harbor high levels of genetic diversity, and that the degree of resolution offered by morphology as a marker for measuring distribution patterns of genetically distinct entities is too low.

Identification of one intron loss and phylogenetic evolution of Dfak gene in the Drosophila melanogaster species group

Intron loss and its evolutionary significance have been noted in Drosophila. The current study provides another example of intron loss within a single-copy Dfak gene in Drosophila. By using polymerase chain reaction (PCR), we amplified about 1.3 kb fragment spanning intron 5-10, located in the position of Tyr kinase (TyK) domain of Dfak gene from Drosophila melanogaster species group, and observed size difference among the amplified DNA fragments from different species. Further sequencing analysis revealed that D. melanogaster and D. simulans deleted an about 60 bp of DNA fragment relative to other 7 Drosophila species, such as D. elegans, D. ficusphila, D. biarmipes, D. takahashii, D. jambulina, D. prostipennis and D. pseudoobscura, and the deleted fragment located precisely in the position of one intron. The data suggested that intron loss might have occurred in the Dfak gene evolutionary process of D. melanogaster and D. simulans of Drosophila melanogaster species group. In addition, the constructed phylogenetic tree based on the Dfak TyK domains clearly revealed the evolutionary relationships between subgroups of Drosophila melanogaster species group, and the intron loss identified from D. melanogaster and D. simulans provides a unique diagnostic tool for taxonomic classification of the melanogaster subgroup from other group of genus Drosophila.