Using genomics to deliver natural products from symbiotic bacteria

The availability of some natural products with promising anticancer activity has been limited because they are synthesized by symbiotic bacteria associated with specific animals. Recent research has identified the clusters of bacterial genes responsible for their synthesis, so that the molecules can be synthesized in alternative, easily cultured bacteria.     

系统保护规划和不可代替性分析在区域规划中的应用

在区域规划中应该把保护和发展密切结合起来,才能为实施可持续发展战略奠定基础。遵循系统保护规划和不可代替性分析的观点,内蒙古克 什克腾旗应该建立10个不同类型的保护区,并与有关部门和社区实施共同管理,建设成为一个可持续发展的示范基地。     

Might makes right: Using force to align the mitotic spindle

Both symmetric and asymmetric divisions rely on alignment of the mitotic spindle with cues from the environment. A study now shows that mitotic spindles find their position by reading the map of forces that load-bearing retraction fibres exert on the cell body.     

BlastAlign: a program that uses blast to align problematic nucleotide sequences

BlastAlign uses NCBI blastn to build a multiple nucleotide alignment and is intended for use with sequences that have large indels or are otherwise difficult to align globally. The program builds a matrix representing regions of homology along the sequences, from which it selects the 'most representative' sequence and then extracts the blastn query-anchored multiple alignment for this sequence. The matrix is printed and allows subgroups to be identified visually and an option allows other sequences to be used as the 'most representative'. The program contains elements of both Perl and Python and will run on UNIX (including Mac OSX) and DOS. An additional Perl program BlastAlignP uses tblastn to align nucleotide sequences to a single amino acid sequence, thus allowing an open reading frame to be maintained in the resulting multiple alignment. AVAILABILITY: It is freely available at http://www.bio.ic.ac.uk/research/belshaw/BlastAlign.tar and at http://evolve.zoo.ox.ac.uk/software/blastalign.     

Using a priori knowledge to align sequencing reads to their exact genomic position

The use of a priori knowledge in the alignment of targeted sequencing data is investigated using computational experiments. Adapting a Needleman-Wunsch algorithm to incorporate the genomic position information from the targeted capture, we demonstrate that alignment can be done to just the target region of interest. When in addition use is made of direct string comparison, an improvement of up to a factor of 8 in alignment speed compared to the fastest conventional aligner (Bowtie) is obtained. This results in a total alignment time in targeted sequencing of around 7 min for aligning approximately 56 million captured reads. For conventional aligners such as Bowtie, BWA or MAQ, alignment to just the target region is not feasible as experiments show that this leads to an additional 88% SNP calls, the vast majority of which are false positives (～92%).     

Using clinicopathological analysis of general practitioner skin surgery to determine educational requirements and guidelines.

OBJECTIVE--To study the impact of skin surgery in general practice on the workload of a pathology laboratory and to identify what further training might be helpful. DESIGN--Analysis of skin biopsy specimens from general practitioners before and after their new contract to determine numbers of specimens, changes in diagnoses, adequacy of treatment of malignant tumours, and areas of low diagnostic accuracy. SETTING--District general hospital. SUBJECTS--All 1017 skin biopsy specimens from general practice for 15 months before and 12 months after the new general practitioner contract. RESULTS--The number of pathology specimens received increased from 16 to 65 per month (median = 6 submitted by each general practitioner in the post-contract year). The proportion of the more common pathological diagnoses was unchanged between the two periods, but the proportion of correctly diagnosed naevi, cysts, and seborrhoeic keratoses increased in the second. Although few diagnoses were overtly incorrect, accurate diagnosis of dermatofibromas and malignancies decreased after the contract, and the overall correct diagnosis rate for seborrhoeic keratoses, dermatofibromas, rashes, and malignancies was below 30%. Only nine out of 21 squamous cell carcinomas were adequately excised with tumour free margins, and follow up of malignant tumours may have been inadequate. CONCLUSIONS--Skin surgery in general practice has advantages but matters of concern are the increase in laboratory workload, the excision of some benign lesions, and the inappropriateness of biopsy of rashes. Squamous cell carcinoma and other malignant tumours submitted for pathological examination were often unsuspected and inadequately excised, and heightened suspicion is recommended. Pathology request forms may need redesigning to encourage provision of clinical details.     

Real time UAV path planning by parallel grey wolf optimization with align coefficient on CAN bus

Cluster Computing - Unmanned aerial vehicle (UAV) path planning is a complex optimization problem, which aims to achieve an optimal or nearly optimal flight path despite various threats and...     

Disease risk analysis: a tool for primate conservation planning and decision making

Concern about emerging and re-emerging diseases plays an increasing role in conservation and management of both captive and free-ranging nonhuman primates (NHPs). Managers and policy makers must formulate conservation plans in an arena plagued by uncertainty, complexity, emotion, and politics. The risk analysis paradigm provides a framework that brings together scientists and policy experts to make better decisions for both people and animals. Risk analysis is a multidisciplinary, science-based process that provides an organized and logical approach for incorporating scientific information into policy development in the real world. By blending four specific goal-oriented stages-hazard identification, risk assessment, risk management, and risk communication-one can logically assess the probability that an adverse event, such as the introduction of an emerging disease into a na?ve population, will occur. The following is a review of this process as it pertains to NHP conservation and risks associated with infectious diseases.     

Applying QTL analysis to conservation genetics

Both analytical and molecular tools currently exist that can be used to prolifically apply quantitative trait loci (QTL) analysis to the study of natural populations. In this communication, we review and exemplify the use of QTL mapping tools and genetic modeling for conservation geneticists. We simulate populations inspired by relevant cases that can be encountered in the field and analyze them using the recently developed flexible intercross analysis (FIA) method. We then reanalyze these results with the also recently developed natural and orthogonal interactions (NOIA) model of genetic effects. Next, we further exemplify the potential of genetic modeling for the interpretation of the output of QTL analyses by reviewing studies on hybrids between wild individuals and their domesticated relatives. Based on the results here presented we emphasize several points that are pertinent in conservation genetics including (i) the advantages of FIA as a powerful tool to be applied to line crosses in which the parental lines are not inbred, (ii) the importance of obtaining estimates of genetic effects that are adequate to address the research issue under consideration, (iii) the versatility of genetic modeling, particularly NOIA, to dissect complex genetic architectures and (iv) the possibility of using currently available methods to address non-equilibrium multiallelic systems.     

Using BEES to select cost-effective green products

The BEES (Building for Environmental and Economic Sustainability) software brings to your fingertips a powerful technique for balancing the environmental and economic performance of building products. The tool is based on consensus standards and designed to be practical, flexible, and transparent. Version 2.0 of the Windows™-based decision support software, aimed at designers, builders, and product manufacturers, includes actual environmental and economic performance data for 65 building products. The purpose is to support purchasing decisions by providing key science-based information often lacking in ‘green’ product selection. The intended result is a cost-effective reduction in building-related contributions to environmental problems. Contribution of the National Institute of Standards and Technology (NIST) and not subject to copyright in the United States. NIST does not endorse any particular brand, product, or service.     

Using phenotypic manipulations to study multivariate selection of floral trait associations

Background

A basic theme in the study of plant–pollinator interactions is that pollinators select not just for single floral traits, but for associations of traits. Responses of pollinators to sets of traits are inherent in the idea of pollinator syndromes. In its most extreme form, selection on a suite of traits can take the form of correlational selection, in which a response to one trait depends on the value of another, thereby favouring floral integration. Despite the importance of selection for combinations of traits in the evolution of flowers, evidence is relatively sparse and relies mostly on observational approaches.

Scope

Here, methods for measuring selection on multivariate suites of floral traits are presented, and the studies to date are reviewed. It is argued that phenotypic manipulations present a powerful, but rarely used, approach to teasing apart the separate and combined effects of particular traits. The approach is illustrated with data from studies of alpine plants in Colorado and New Zealand, and recommendations are made about several features of the design of such experiments.

Conclusions

Phenotypic manipulations of two or more traits in combination provide a direct way of testing for selection of floral trait associations. Such experiments will be particularly valuable if rooted in hypotheses about differences between types of pollinators and tied to a proposed evolutionary history.Key words: Colour, correlational selection, experiment, floral integration, multivariate selection, phenotypic manipulation, pollination syndrome, pollinator visitation     

Spatial conservation planning under climate change: Using species distribution modeling to assess priority for adaptive management of Fagus crenata in Japan

Protected areas are the basis of modern conservation systems, but current climate change causes gaps between protected areas and the species distribution ranges. To mitigate the impact of climate change on species distribution ranges, revision of protected areas are necessary. Alternatively, active management such as excluding competitive species or transplanting target species would be effective. In this study, we assessed optimal actions (revision of protected areas or active management) in each geographical region to establish an effective spatial conservation plan in Japan. Gaps between the protected areas and future potential habitats were assessed using species distribution models and 20 future climate simulations. Fagus crenata, an endemic and dominant species in Japan, was used as a target species. Potential habitats within the protected areas were predicted to decrease from 22,122 km² at present to 12,309 km² under future climate conditions. Sustainable potential habitats (consistent potential habitats both at present and in future) without the protected areas extended to 13,208 km², and were mainly found in northeast Japan. These results suggest that, in northeast Japan, revisions to protected areas would be effective in preserving sustainable potential habitats under future climate change. However, the potential habitats of southwestern Japan, in which populations were genetically different from northeastern populations, were predicted to virtually disappear both within and outside of protected areas. Active management is thus necessary in southwestern Japan to ensure intraspecific genetic diversity under future climate change.