The utility of PacBio circular consensus sequencing for characterizing complex gene families in non-model organisms

BACKGROUND: Molecular characterization of highly diverse gene families can be time consuming, expensive, and difficult, especially when considering the potential for relatively large numbers of paralogs and/or pseudogenes. Here we investigate the utility of Pacific Biosciences single molecule real-time (SMRT) circular consensus sequencing (CCS) as an alternative to traditional cloning and Sanger sequencing PCR amplicons for gene family characterization. We target vomeronasal gene receptors, one of the most diverse gene families in mammals, with the goal of better understanding intra-specific V1R diversity of the gray mouse lemur (Microcebus murinus). Our study compares intragenomic variation for two V1R subfamilies found in the mouse lemur. Specifically, we compare gene copy variation within and between two individuals of M. murinus as characterized by different methods for nucleotide sequencing. By including the same individual animal from which the M. murinus draft genome was derived, we are able to cross-validate gene copy estimates from Sanger sequencing versus CCS methods. RESULTS: We generated 34,088 high quality circular consensus sequences of two diverse V1R subfamilies (here referred to as V1RI and V1RIX) from two individuals of Microcebus murinus. Using a minimum threshold of 7× coverage, we recovered approximately 90% of V1RI sequences previously identified in the draft M. murinus genome (59% being identical at all nucleotide positions). When low coverage sequences were considered (i.e. < 7× coverage) 100% of V1RI sequences identified in the draft genome were recovered. At least 13 putatively novel V1R loci were also identified using CCS technology. CONCLUSIONS: Recent upgrades to the Pacific Biosciences RS instrument have improved the CCS technology and offer an alternative to traditional sequencing approaches. Our results suggest that the Microcebus murinus V1R repertoire has been underestimated in the draft genome. In addition to providing an improved understanding of V1R diversity in the mouse lemur, this study demonstrates the utility of CCS technology for characterizing complex regions of the genome. We anticipate that long-read sequencing technologies such as PacBio SMRT will allow for the assembly of multigene family clusters and serve to more accurately characterize patterns of gene copy variation in large gene families, thus revealing novel micro-evolutionary patterns within non-model organisms. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-720) contains supplementary material, which is available to authorized users

Favouritism: exploring the 'uncontrolled' spaces of the leadership experience

In this paper, we argue that a focus on favouritism magnifies a central ethical ambiguity in leadership, both conceptually and in practice. The social process of favouritism can even go unnoticed, or misrecognised if it does not manifest in a form in which it can be either included or excluded from what is (collectively interpreted as) leadership. The leadership literature presents a tension between what is an embodied and relational account of the ethical, on the one hand, and a more dispassionate organisational ‘justice’ emphasis, on the other hand. We conducted 23 semi-structured interviews in eight consultancy companies, four multinationals and four internationals. There were ethical issues at play in the way interviewees thought about favouritism in leadership episodes. This emerged in the fact that they were concerned with visibility and conduct before engaging in favouritism. Our findings illustrate a bricolage of ethical justifications for favouritism, namely utilitarian, justice, and relational. Such findings suggest the ethical ambiguity that lies at the heart of leadership as a concept and a practice

Latitude drives diversification in M adagascar's endemic dry forest rodent E liurus myoxinus (subfamily N esomyinae)

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/100288/1/bij12143.pd

Measurement of associated Z plus charm production in proton-proton collisions at root s=8TeV

A study of the associated production of a Z boson and a charm quark jet (Z + c), and a comparison to production with a b quark jet (Z + b), in pp collisions at a centre-of-mass energy of 8 TeV are presented. The analysis uses a data sample corresponding to an integrated luminosity of 19.7 fb(-1), collected with the CMS detector at the CERN LHC. The Z boson candidates are identified through their decays into pairs of electrons or muons. Jets originating from heavy flavour quarks are identified using semileptonic decays of c or b flavoured hadrons and hadronic decays of charm hadrons. The measurements are performed in the kinematic region with two leptons with pT(l) > 20 GeV, vertical bar eta(l)vertical bar 25 GeV and vertical bar eta(jet)vertical bar Z + c + X) B(Z -> l(+)l(-)) = 8.8 +/- 0.5 (stat)+/- 0.6 (syst) pb. The ratio of the Z+c and Z+b production cross sections is measured to be sigma(pp -> Z+c+X)/sigma (pp -> Z+b+X) = 2.0 +/- 0.2 (stat)+/- 0.2 (syst). The Z+c production cross section and the cross section ratio are also measured as a function of the transverse momentum of theZ boson and of the heavy flavour jet. The measurements are compared with theoretical predictions.Peer reviewe

Measurement of the underlying event activity in inclusive Z boson production in proton-proton collisions at root s=13 TeV

This paper presents a measurement of the underlying event activity in proton-proton collisions at a center-of-mass energy of 13TeV, performed using inclusive Z boson production events collected with the CMS experiment at the LHC. The analyzed data correspond to an integrated luminosity of 2.1 fb(-1). The underlying event activity is quantified in terms of the charged particle multiplicity, as well as of the scalar sum of the charged particles' transverse momenta in different topological regions defined with respect to the Z boson direction. The distributions are unfolded to the stable particle level and compared with predictions from various Monte Carlo event generators, as well as with similar CDF and CMS measurements at center-of-mass energies of 1.96 and 7TeV respectively.Peer reviewe

Effects of gesture+verbal treatment for noun and verb retrieval in aphasia

Links between verbs and gesture knowledge suggest that verb retrieval may be particularly amenable to gesture+verbal training (GVT) in aphasia compared to noun retrieval. This study examines effects of GVT for noun and verb retrieval in nine individuals with aphasia subsequent to left hemisphere stroke. Participants presented an array of noun and verb retrieval deficits, including impairments of semantic and/or phonologic processing. In a single-participant experimental design, we investigated effects of GVT for noun and verb retrieval in two counterbalanced treatment phases. Effects were evaluated in spoken naming and gesture production to pictured objects and actions. Spoken naming improvements associated with large effect sizes were noted for trained nouns (5/9) and verbs (5/9); no improvements were evident for untrained words. Gesture production improved for trained nouns (8/9) and verbs (6/9), and for untrained nouns (2/9) and verbs (2/9). No significant differences were evident between nouns and verbs in spoken naming or gesture production. Improvements were evident across individuals with varied sources of word retrieval impairments. GVT has the potential to improve communication by increasing spoken word retrieval of trained nouns and verbs and by promoting use of gesture as a means to communicate when word retrieval fails. (JINS, 2006, 12, 867-882.) © 2006 The International Neuropsychological Society

Treatment of limb apraxia - Moving forward to improved action

Limb apraxia is a common disorder of skilled, purposive movement that is frequently associated with stroke and degenerative diseases such as Alzheimer disease. Despite evidence that several types of limb apraxia significantly impact functional abilities, surprisingly few studies have focused on development of treatment paradigms. Additionally, although the most disabling types of apraxia reflect damage to gesture and/or object memory systems, existing treatments have not fully taken advantage of principles of experience known to affect learning and neural plasticity. We review the current state of the art in the rehabilitation of limb apraxia, indicate possible points of contact with the learning literature, and generate suggestions for how translational principles might be applied to the development of future research on treatment of this disabling disorder

Cytochrome-b alignment

Cytochrome-b DNA sequence alignment for all individuals included

Specimen numbers

Field collection numbers and associated museum collection specimen numbers for a subset of individuals that are referred to by both numbers