<Emphasis Type="Bold">A user guide to the</Emphasis><Emphasis Type="BoldItalic">Brassica</Emphasis><Emphasis Type="Bold">60K Illumina Infinium</Emphasis>™ <Emphasis Type="Bold">SNP genotyping array</Emphasis>

The Brassica napus 60K Illumina Infinium? SNP array has had huge international uptake in the rapeseed community due to the revolutionary speed of acquisition and ease of analysis of this high-throughput genotyping data, particularly when coupled with the newly available reference genome sequence. However, further utilization of this valuable resource can be optimized by better understanding the promises and pitfalls of SNP arrays. We outline how best to analyze Brassica SNP marker array data for diverse applications, including linkage and association mapping, genetic diversity and genomic introgression studies. We present data on which SNPs are locus-specific in winter, semi-winter and spring B. napus germplasm pools, rather than amplifying both an A-genome and a C-genome locus or multiple loci. Common issues that arise when analyzing array data will be discussed, particularly those unique to SNP markers and how to deal with these for practical applications in Brassica breeding applications.     

<Emphasis Type="BoldItalic">The President’s Physician: An African Play</Emphasis>

This review examines issues relating to biomedical ethics and literature in the African drama The President’s Physician by Emmanuel Babatunde Omobowale. The play investigates the psychological dilemma of Doctor Bituki Warunga, a personal physician to General Kalunga Ntibantunganyah who brutally and inhumanely rules Wavaria, a fictional African country. The doctor is faced with deciding to uphold the ethics of his profession versus terminating the tyrant’s life to set the nation free. The play aims to help budding medical doctors rightly inculcate the principles of medical ethics—autonomy, beneficence, competence, and power—by providing a fictional platform to investigate difficult issues that can arise in clinical practice. The play highlights Warunga’s complex dilemma as he struggles to uphold the Hippocratic Oath and at the same time satisfy his conscience towards his contribution to his country’s freedom. This review explores the difficulties in decision-making when professional duties not only clash with personal preferences but also with the well-being of an entire nation. This discussion is done alongside the ethical concept of utilitarianism and also highlights significant literary concepts such as satire, symbolism, intertextuality, utopian aesthetics, and authorial vision as conveyed in the text.     

Butterfly diversity in Mediterranean islands and in Pentadaktylos <Emphasis Type="Italic">Pinus</Emphasis><Emphasis Type="BoldItalic"> </Emphasis><Emphasis Type="Italic">brutia</Emphasis> forests of Cyprus

We analysed the influence of contemporary geography on butterfly diversity for islands in the Mediterranean Basin. We found that island size and distance from the mainland has a significant effect on the number of species. We also used butterflies as an indicator group to identify the importance of forest habitats for biodiversity conservation in the island of Cyprus. To understand the relative importance of local vegetation characteristics of butterflies in the Pentadaktylos mountains transect counts were used to assess the abundance and butterfly diversity in two different forest types. A total of 1,602 butterflies and 23 species were recorded during this research. We observed highly significant effects of forest type on abundance and species richness of butterflies. For example, number of butterflies was significantly higher in old forest than young pine forest. Also, the abundance of endemic butterflies was highest in old forest habitats. Therefore, the survival of the majority of endemic butterflies in Cyprus may depend on conservation of old forests and their understorey plants.     

<Emphasis Type="BoldItalic">Regeneration</Emphasis>: Thomas Hunt Morgan’s Window into Development

Early in his career Thomas Hunt Morgan was interested in embryology and dedicated his research to studying organisms that could regenerate. Widely regarded as a regeneration expert, Morgan was invited to deliver a series of lectures on the topic that he developed into a book, Regeneration (1901). In addition to presenting experimental work that he had conducted and supervised, Morgan also synthesized and critiqued a great deal of work by his peers and predecessors. This essay probes into the history of regeneration studies by looking in depth at Regeneration and evaluating Morgan’s contribution. Although famous for his work with fruit fly genetics, studying Regeneration illuminates Morgan’s earlier scientific approach which emphasized the importance of studying a diversity of organisms. Surveying a broad range of regenerative phenomena allowed Morgan to institute a standard scientific terminology that continues to inform regeneration studies today. Most importantly, Morgan argued that regeneration was a fundamental aspect of the growth process and therefore should be accounted for within developmental theory. Establishing important similarities between regeneration and development allowed Morgan to make the case that regeneration could act as a model of development. The nature of the relationship between embryogenesis and regeneration remains an active area of research.     

<Emphasis Type="BoldItalic">Yartsa Gunbu</Emphasis> (<Emphasis Type="Italic">Cordyceps sinensis</Emphasis>) and the Fungal Commodification of Tibet’s Rural Economy

Yartsa Gunbu (Cordyceps sinensis) and the Fungal Commodification of Tibet’s Rural Economy. Cordyceps sinensis is a mushroom that parasitizes larvae of Thitarodes (Hepialus) moths, which inhabit the alpine grasslands of the Tibetan Plateau. Tibetans have used the mushroom, which they call yartsa gunbu (“summer-grass, winter-worm”) for many centuries, if not millennia. A 350% increase in the price paid to pickers between 1997 and 2004 has turned this tiny mushroom into the single most important source of cash for rural households in contemporary Tibet. On average, 40% of the rural cash income in the Tibet Autonomous Region is derived from its collection, which government statistics figured at 50,000 kg in 2004, contributing at least CNY (Chinese yuan) 1.8 billion (USD 225 million) to the Tibet Autonomous Region’s GDP. A dramatic fungal commodification of the rural Tibetan economy is occurring, as the income from sale of Cordyceps often accounts for 70%–90% of a family’s annual cash income in areas where it grows. The ever-increasing harvesting pressure raises the question of sustainability. The fact that Cordyceps has been collected for centuries and is still common argues for its resilience, but the lack of harvest studies for C. sinensis precludes a definite answer as to whether the harvest can be sustained at its current level.     

Genetic causes of Parkinson’s disease: <Emphasis Type="Italic">UCHL-1</Emphasis>

The ubiquitin proteasome system is an important cellular pathway that ubiquitinates damaged proteins and degrades them via the 26S proteasome. Abnormalities of this pathway can result in molecular protein aggregation and have been associated with Parkinsons disease (PD). UCHL-1, an enzyme central to the system, possesses catalytic hydrolase activity that can hydrolyze peptide-ubiquitin bonds and recycle ubiquitin monomers for re-use in the same process. Recently, UCHL-1 has been shown to possess a second dimerisation-dependent ligase activity and, at least in vitro, this ligase activity promotes alpha synuclein aggregation. UCHL-1 was first implicated in PD by the discovery of an I93M mutation identified in a German sib-pair with probable autosomal dominant PD. Although no further UCHL-1 mutations have been identified, a common non-synonymous S18Y polymorphism has been suggested to reduce disease susceptibility in non-mendelian forms of PD. In vitro functional data support this protective effect, with evidence that S18Y possesses reduced ligase activity compared with wild type UCHL-1. One study has found increased hydrolase activity associated with S18Y, although another study has not. Important issues regarding UCHL-1 and its role in PD remain inconclusive, especially regarding the pathogenicity of the mendelian I93M mutation. This review tries to address some of these uncertainties.D.G.H. is a clinical research fellow at the Institute of Neurology, Queen Square and is supported by a grant from the UK Parkinsons Disease Society (grant no. 4073). P.A.S. is supported by a grant from the Brain Research Trust (grant no. 6AAC). N.W.W. is supported by the UK Parkinsons Disease Society (grant no. 4029)     

Cookie-cutter shark <Emphasis Type="Italic">Isistius brasiliensis</Emphasis> eats Bryde’s whale <Emphasis Type="Italic">Balaenoptera brydei</Emphasis>

We examined the stomach contents of cookie-cutter sharks, Isistius brasiliensis, collected by drift-net surveys in the western North Pacific in the early summer. The stomachs contained fresh flesh plugs and cephalopod beaks. Approximately half of the flesh plugs were identified as Bryde’s whale, Balaenoptera brydei, based on genetic analysis, and several of the lower beaks were identified as boreal clubhook squid, Onychoteuthis borealijaponica. The range of estimated dorsal mantle lengths for the squids was 60–172 mm. These results are evidence of predation by of cookie-cutter sharks on cetaceans and of an overlap in the vertical distribution of both species.     

<Emphasis Type="Italic">TNF</Emphasis><Emphasis Type="Italic">α</Emphasis> and <Emphasis Type="Italic">LT</Emphasis><Emphasis Type="Italic">α</Emphasis> gene polymorphisms as additional markers of celiac disease susceptibility in a DQ2-positive population

TNFalpha and TNFbeta, or linfotoxin (LTalpha), are two molecules playing an important role in inflammation. Their genes map on Chromosome 6, between the HLA class II and class I loci. Polymorphisms in, or near, TNF genes have been associated with susceptibility to several autoimmune diseases. Studies of TNF genes in celiac disease (CD) have presented contradictory results. We have assessed the role of TNFalpha and linfotoxin alpha (TNFbeta) in CD and their relative value as CD markers in addition to the presence of DQ2. The TNFA -308 polymorphism and the polymorphism at the first intron of the LTA gene were typed in CD patients and healthy controls and the results were correlated with the presence of DQ2. Significant differences were found in genotype and allele frequencies for the TNFA and LTA genes between CD patients and controls, with an increase in the presence of the TNFA*2 and LTA*1 alleles in CD patients. These differences increase when DQ2-positive CD patients and DQ2-positive controls are compared. In DQ2-positive individuals, allele 2 (A) in position -308 of the promoter of TNFA and allele 1 (G) of the NcoI RFLP in the first intron of LTA are additional risk markers for CD.     

<Emphasis Type="Italic">Bacillus anthracis</Emphasis>, <Emphasis Type="Italic">Francisella tularensis</Emphasis> and <Emphasis Type="Italic">Yersinia pestis</Emphasis>. The most important bacterial warfare agents — <Emphasis Type="Italic">review</Emphasis>

There are three most important bacterial causative agents of serious infections that could be misused for warfare purposes: Bacillus anthracis (the causative agent of anthrax) is the most frequently mentioned one; however, Fracisella tularensis (causing tularemia) and Yersinia pestis (the causative agent of plague) are further bacterial agents enlisted by Centers for Disease Control and Prevention into the category A of potential biological weapons. This review intends to summarize basic information about these bacterial agents. Military aspects of their pathogenesis and the detection techniques suitable for field use are discussed.     

Brood cell size of <Emphasis Type="Italic">Apis</Emphasis> <Emphasis Type="Italic">mellifera</Emphasis> modifies the reproductive behavior of <Emphasis Type="Italic">Varroa</Emphasis> <Emphasis Type="Italic">destructor</Emphasis>

We undertook a field study to determine whether comb cell size affects the reproductive behavior of Varroa destructor under natural conditions. We examined the effect of brood cell width on the reproductive behavior of V. destructor in honey bee colonies, under natural conditions. Drone and worker brood combs were sampled from 11 colonies of Apis mellifera. A Pearson correlation test and a Tukey test were used to determine whether mite reproduction rate varied with brood cell width. Generalized additive model analysis showed that infestation rate increased positively and linearly with the width of worker and drone cells. The reproduction rate for viable mother mites was 0.96 viable female descendants per original invading female. No significant correlation was observed between brood cell width and number of offspring of V. destructor. Infertile mother mites were more frequent in narrower brood cells.     

Functional expression of the lipase gene Lip2 of <Emphasis Type="Italic">Pleurotus</Emphasis> <Emphasis Type="Italic">sapidus</Emphasis> in <Emphasis Type="Italic">Escherichia</Emphasis> <Emphasis Type="Italic">coli</Emphasis>

The lipase Lip2 of the edible basidiomycete, Pleurotus sapidus, is an extracellular enzyme capable of hydrolysing xanthophyll esters with high efficiency. The gene encoding Lip2 was expressed in Escherichia coli TOP10 using the gene III signal sequence to accumulate proteins in the periplasmatic space. The heterologous expression under control of the araBAD promoter led to the high level production of recombinant protein, mainly as inclusion bodies, but partially in a soluble and active form. A fusion with a C-terminal His tag was used for purification and immunochemical detection of the target protein. This is the first example of a heterologous expression and periplasmatic accumulation of a catalytically active lipase from a basidiomycete fungus.     

Gill cell toxicity of northern boreal scyphomedusae <Emphasis Type="Italic">Cyanea</Emphasis> <Emphasis Type="Italic">capillata</Emphasis> and <Emphasis Type="Italic">Aurelia</Emphasis> <Emphasis Type="Italic">aurita</Emphasis> measured by an in vitro cell assay

Scyphozoan medusae are very successful foragers which occasionally occur in high abundances in boreal waters and may impact many different groups in the marine ecosystem by means of a variety of toxins. A rainbow trout gill cell line, RTgill-W1, was tested for its suitability as quantitative indicator of the cytotoxicity of Cyanea capillata and Aurelia aurita; the major scyphozoan species in the North and Baltic seas. Cultures of rainbow trout gill cells were exposed to whole venoms extracted from fishing tentacles and oral arms at increasing protein concentrations. The venom caused detachment, clumping and lysis of cells, as well as a drop in vitality, in a dose-dependent manner. Morphological changes in the cells were evident within 1 h after venom addition. The damage to gill cells was quantified by measuring the metabolic activity of the cells by means of the fluorescence of resorufin derived from the nonfluorescent substrate, resazurin. In general, a decrease in the metabolic activity of the cells was detected at a venom (protein) concentration above 2.0 μg ml⁻¹ (corresponding to 0.2 μg 10⁴ cells⁻¹), and a total loss of activity was observed above 40.0 μg ml⁻¹ (corresponding to 4.0 μg 10⁴ cells⁻¹). C. capillata venoms had increased cytotoxic activity as compared to A. aurita venoms at the same concentration. Cnidocyst extracts from oral arms of A. aurita induced an 85% loss of gill cell viability at concentrations of 0.2 μg 10⁴ cells⁻¹, whereas crude venoms from fishing tentacles reduced cell viability by 18% at the same concentration. Gel electrophoresis of the venoms indicated that these consist of a large number of proteins in a fairly wide size range, from 6 to 200 kDa, including some that are the same size as those found in cubomedusae. It also appears that larger (i.e., older) medusae have more complex venoms and, in some cases, more potent venoms than smaller animals.     

Contribution of <Emphasis Type="Italic">rs11465788</Emphasis> in <Emphasis Type="Italic">IL23R</Emphasis> gene to Crohn’s disease susceptibility and phenotype in Chinese population

Multiple studies have shown that IL23 cytokine plays an essential role in the development of autoimmune diseases by activating IL17-producing helper T (Th17) cells. Given that the susceptibility loci in IL23R for Crohn’s disease (CD) is present in Western population and not in Asian population; we screened the IL23R gene by DNA sequencing to identify susceptibility loci in a selected CD cohort and confirmed it in all our subjects (134 CD and 131 controls). A novel nonsynonymous SNP (p.Gly149Arg, c.445G>A) and 35 single nucleotide polymorphisms (SNPs) were identified. Among them, only rs11465788 was implicated in CD susceptibility (P = 4.9 × 10⁻⁴, OR = 0.30). Genotype-phenotypic interaction analysis showed that rs11465788 is associated with nonstricturing and nonpenetrating disease behaviour in CD patients (P = 0.015). Our results provide the evidence that rs11465788 may influence the susceptibility and clinical features of CD in Chinese population.     

Heterologous expression of a gene for thermostable xylanase from <Emphasis Type="Italic">Chaetomium</Emphasis> <Emphasis Type="Italic">thermophilum</Emphasis> in <Emphasis Type="Italic">Pichia</Emphasis> <Emphasis Type="Italic">pastoris</Emphasis> GS115

We studied heterologous expression of xylanase 11A gene of Chaetomium thermophilum in Pichia pastoris and characterized the thermostable nature of the purified gene product. For this purpose, the xylanase 11A gene of C. thermophilum was cloned in P. pastoris GS115 under the control of AOX1 promoter. The maximum extracellular activity of recombinant xylanase (xyn698: gene with intron) was 15.6 U ml⁻¹ while that of recombinant without intron (xyn669) was 1.26 U ml⁻¹ after 96 h growth. The gene product was purified apparently to homogeneity level. The optimum temperature of pure recombinant xylanase activity was 70°C and the enzyme retained its 40.57% activity after incubation at 80°C for 10 min. It exhibited quite lower demand of activation energy, enthalpy, Gibbs free energy, entropy, and xylan binding energy during substrate hydrolysis than that required by that of the donor, thus indicating its thermostable nature. pH-dependent catalysis showed that it was quite stable in a pH range of 5.5–8.5. This revealed that gene was successfully processed in P. pastoris and remained heat stable and may qualify for its potential use in paper and pulp and animal feed applications.     

Rapid induction of <Emphasis Type="Italic">Agrobacterium</Emphasis> <Emphasis Type="Italic">tumefaciens</Emphasis>-mediated transgenic roots directly from adventitious roots in <Emphasis Type="Italic">Panax</Emphasis> <Emphasis Type="Italic">ginseng</Emphasis>

Root segments from seedlings of Panax ginseng produced adventitious roots directly when cultured on 1/2 MS solid medium lacking NH₄NO₃ and containing 3.0 mg l⁻¹ IBA. Using this adventitious root formation, we developed rapid and efficient transgenic root formation directly from adventitious root segments in P. ginseng. Root segments were co-cultivated with Agrobacterium tumefaciens (GV3101) caring β-glucuronidase (GUS) gene. Putative transgenic adventitious roots were formed directly from root segments on medium with 400 mg l⁻¹ cefotaxime and 50 mg l⁻¹ kanamycin. Kanamycin resistant adventitious roots were selected and proliferated as individual lines by subculturing on medium with 300 mg l⁻¹ cefotaxime and 50 mg l⁻¹ kanamycin at two weeks subculture interval. Frequency of transient and stable expression of GUS gene was enhanced by acetosyringon (50 mg l⁻¹) treatment. Integration of transgene into the plants was confirmed by the X-gluc reaction, PCR and Southern analysis. Production of transgenic plants was achieved via somatic embryogenesis from the embryogenic callus derived from independent lines of adventitious roots. The protocol for rapid induction of transgenic adventitious roots directly from adventitious roots can be applied for a new Agrobacterium tumefaciens-mediated genetic transformation protocol in P. ginseng.     

Whole Mitochondrial Genome of Blakiston’s Fish Owl <Emphasis Type="Italic">Bubo</Emphasis> (<Emphasis Type="Italic">Ketupa</Emphasis>) <Emphasis Type="Italic">blakistoni</Emphasis> Suggests Its Redescription in the Genus <Emphasis Type="Italic">Ketupa</Emphasis>

The paper reports the whole mitochondrial genome (approximately 13 kb) sequencing in three individual representatives of the continental population of Blakiston’s fish owl Bubo blakistoni (Seebohm 1884), the IUCN Red List species in the family Strigidae. The analysis revealed extremely low mtDNA genetic diversity, which may be indicative of the critical state of the studied population. The phylogenetic analysis performed on the basis of the whole mitochondrial genome sequencing data showed that Blakiston’s fish owl is more closely related to the Strix genus than to the Bubo genus with the genetic divergence between blakistoni and either of the two genera being statistically significant and close to intergeneric level (p-distance of 0.135 in the case of the Strix genus and p-distance of 0.151 in the case of the Bubo genus). The results obtained in this work do not match the published data on the mitochondrial cytochrome b gene and the nuclear RAG-1 gene, which laid the basis for the assignment of Blackiston’s fish owl to the Bubo genus in the recent taxonomic bulletins, but rather support the earlier taxonomic classification according to which all four Asian forms, blakistoni, flavipes, zeylonensis, and ketupu, constituted a separate Ketupa genus.