bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing the anti-fungal efficiency of filters coated with zinc oxide nanoparticles
Authors: Decelis Stephen , Sardella Davide , Triganza Thomas , Brincat Jean-Pierre , Gatt Ruben , Valdramidis Vasilis P.
Published: May 2017

Air filters support fungal growth, leading to generation of conidia and volatile organic compounds, causing allergies, infections and food spoilage. Filters that inhibit fungi are therefore necessary. Zinc oxide (ZnO) nanoparticles have anti-fungal properties and therefore are good candidates for inhibiting growth. Two concentrations (0.012 M and 0.12 M) were used to coat two types of filters (melt-blown and needle-punched) for three different periods (0.5, 5 and 50 min).
Rhizopus stolonifer
and
Penicillium expansum
isolated from spoiled pears were used as test organisms. Conidial suspensions of 10
5
to 10
3
spores ml
−1
were prepared in Sabouraud dextrose agar at 50°C, and a modified slide-culture technique was used to test the anti-fungal properties of the filters.
Penicillium expansum
was the more sensitive organism, with inhibition at 0.012 M at only 0.5 min coating time on the needle-punched filter. The longer the coating time, the more effective inhibition was for both organisms. Furthermore, it was also determined that the coating process had only a slight effect on the Young's Moduli of the needle-punched filters, while the Young's Moduli of the melt-blown filters is more susceptible to the coating method. This work contributes to the assessment of the efficacy of filter coating with ZnO nanopaticles aimed at inhibiting fungal growth.
Operating length and velocity of human M. vastus lateralis fascicles during vertical jumping
Authors: Nikolaidou Maria Elissavet , Marzilger Robert , Bohm Sebastian , Mersmann Falk , Arampatzis Adamantios
Published: May 2017

Humans achieve greater jump height during a counter-movement jump (CMJ) than in a squat jump (SJ). However, the crucial difference is the mean mechanical power output during the propulsion phase, which could be determined by intrinsic neuro-muscular mechanisms for power production. We measured M. vastus lateralis (VL) fascicle length changes and activation patterns and assessed the force–length, force–velocity and power–velocity potentials during the jumps. Compared with the SJ, the VL fascicles operated on a more favourable portion of the force–length curve (7% greater force potential, i.e. fraction of VL maximum force according to the force–length relationship) and more disadvantageous portion of the force–velocity curve (11% lower force potential, i.e. fraction of VL maximum force according to the force–velocity relationship) in the CMJ, indicating a reciprocal effect of force–length and force–velocity potentials for force generation. The higher muscle activation (15%) could therefore explain the moderately greater jump height (5%) in the CMJ. The mean fascicle-shortening velocity in the CMJ was closer to the plateau of the power–velocity curve, which resulted in a greater (15%) power–velocity potential (i.e. fraction of VL maximum power according to the power–velocity relationship). Our findings provide evidence for a cumulative effect of three different mechanisms—i.e. greater force–length potential, greater power–velocity potential and greater muscle activity—for an advantaged power production in the CMJ contributing to the marked difference in mean mechanical power (56%) compared with SJ.
Well-posed continuum equations for granular flow with compressibility and
μ
(
I
)-rheology
Authors: Barker T. , Schaeffer D. G. , Shearer M. , Gray J. M. N. T.
Published: May 2017

Continuum modelling of granular flow has been plagued with the issue of ill-posed dynamic equations for a long time. Equations for incompressible, two-dimensional flow based on the Coulomb friction law are ill-posed regardless of the deformation, whereas the rate-dependent
μ
(
I
)-rheology is ill-posed when the non-dimensional inertial number
I
is too high or too low. Here, incorporating ideas from critical-state soil mechanics, we derive conditions for well-posedness of partial differential equations that combine compressibility with
I
-dependent rheology. When the
I
-dependence comes from a specific friction coefficient
μ
(
I
), our results show that, with compressibility, the equations are well-posed for all deformation rates provided that
μ
(
I
) satisfies certain minimal, physically natural, inequalities.
Simulating tubulin-associated unit transport in an axon: using bootstrapping for estimating confidence intervals of best-fit parameter values obtained from indirect experimental data
Authors: Kuznetsov I. A. , Kuznetsov A. V.
Published: May 2017

In this paper, we first develop a model of axonal transport of tubulin-associated unit (tau) protein. We determine the minimum number of parameters necessary to reproduce published experimental results, reducing the number of parameters from 18 in the full model to eight in the simplified model. We then address the following questions: Is it possible to estimate parameter values for this model using the very limited amount of published experimental data? Furthermore, is it possible to estimate confidence intervals for the determined parameters? The idea that is explored in this paper is based on using bootstrapping. Model parameters were estimated by minimizing the objective function that simulates the discrepancy between the model predictions and experimental data. Residuals were then identified by calculating the differences between the experimental data and model predictions. New, surrogate ‘experimental’ data were generated by randomly resampling residuals. By finding sets of best-fit parameters for a large number of surrogate data the histograms for the model parameters were produced. These histograms were then used to estimate confidence intervals for the model parameters, by using the percentile bootstrap. Once the model was calibrated, we applied it to analysing some features of tau transport that are not accessible to current experimental techniques.
Innovative and collaborative industrial mathematics in Europe
Authors: Hjorth Poul G.
Published: May 2017

This paper presents a brief review of how industrial mathematics, inspired by the Oxford Study Group activity, organized itself in Europe, gave rise to the European Consortium for Mathematics in Industry, the series of European Study Groups with Industry, and to new modes of productive contacts between industry and applied mathematicians in academia.
Genetic diversity is largely unpredictable but scales with museum occurrences in a species-rich clade of Australian lizards
Authors: Singhal Sonal , Huang Huateng , Title Pascal O. , Donnellan Stephen C. , Holmes Iris , Rabosky Daniel L.
Published: May 2017

Genetic diversity is a fundamental characteristic of species and is affected by many factors, including mutation rate, population size, life history and demography. To better understand the processes that influence levels of genetic diversity across taxa, we collected genome-wide restriction-associated DNA data from more than 500 individuals spanning 76 nominal species of Australian scincid lizards in the genus
Ctenotus
. To avoid potential biases associated with variation in taxonomic practice across the group, we used coalescent-based species delimitation to delineate 83 species-level lineages within the genus for downstream analyses. We then used these genetic data to infer levels of within-population genetic diversity. Using a phylogenetically informed approach, we tested whether variation in genetic diversity could be explained by population size, environmental heterogeneity or historical demography. We find that the strongest predictor of genetic diversity is a novel proxy for census population size: the number of vouchered occurrences in museum databases. However, museum occurrences only explain a limited proportion of the variance in genetic diversity, suggesting that genetic diversity might be difficult to predict at shallower phylogenetic scales.
General and species-specific impacts of a neonicotinoid insecticide on the ovary development and feeding of wild bumblebee queens
Authors: Baron Gemma L. , Raine Nigel E. , Brown Mark J. F.
Published: May 2017

Bumblebees are essential pollinators of crops and wild plants, but are in decline across the globe. Neonicotinoid pesticides have been implicated as a potential driver of these declines, but most of our evidence base comes from studies of a single species. There is an urgent need to understand whether such results can be generalized across a range of species. Here, we present results of a laboratory experiment testing the impacts of field-relevant doses (1.87–5.32 ppb) of the neonicotinoid thiamethoxam on spring-caught wild queens of four bumblebee species:
Bombus terrestris
,
B. lucorum
,
B. pratorum
and
B. pascuorum.
Two weeks of exposure to the higher concentration of thiamethoxam caused a reduction in feeding in two out of four species, suggesting species-specific anti-feedant, repellency or toxicity effects. The higher level of thiamethoxam exposure resulted in a reduction in the average length of terminal oocytes in queens of all four species. In addition to providing the first evidence for general effects of neonicotinoids on ovary development in multiple species of wild bumblebee queens, the discovery of species-specific effects on feeding has significant implications for current practices and policy for pesticide risk assessment and use.
Climate change alters the optimal wind-dependent flight routes of an avian migrant
Authors: Nourani Elham , Yamaguchi Noriyuki M. , Higuchi Hiroyoshi
Published: May 2017

Migratory birds can be adversely affected by climate change as they encounter its geographically uneven impacts in various stages of their life cycle. While a wealth of research is devoted to the impacts of climate change on distribution range and phenology of migratory birds, the indirect effects of climate change on optimal migratory routes and flyways, through changes in air movements, are poorly understood. Here, we predict the influence of climate change on the migratory route of a long-distant migrant using an ensemble of correlative modelling approaches, and present and future atmospheric data obtained from a regional climate model. We show that changes in wind conditions by mid-century will result in a slight shift and reduction in the suitable areas for migration of the study species, the Oriental honey-buzzard, over a critical section of its autumn journey, followed by a complete loss of this section of the traditional route by late century. Our results highlight the need for investigating the consequences of climate change-induced disturbance in wind support for long-distance migratory birds, particularly species that depend on the wind to cross ecological barriers, and those that will be exposed to longer journeys due to future range shifts.
How do seemingly non-vagile clades accomplish trans-marine dispersal? Trait and dispersal evolution in the landfowl (Aves: Galliformes)
Authors: Hosner Peter A. , Tobias Joseph A. , Braun Edward L. , Kimball Rebecca T.
Published: May 2017

Dispersal ability is a key factor in determining insular distributions and island community composition, yet non-vagile terrestrial organisms widely occur on oceanic islands. The landfowl (pheasants, partridges, grouse, turkeys, quails and relatives) are generally poor dispersers, but the Old World quail (Coturnix) are a notable exception. These birds evolved small body sizes and high-aspect-ratio wing shapes, and hence are capable of trans-continental migrations and trans-oceanic colonization. Two monotypic partridge genera,Margaroperdixof Madagascar andAnurophasisof alpine New Guinea, may represent additional examples of trans-marine dispersal in landfowl, but their body size and wing shape are typical of poorly dispersive continental species. Here, we estimate historical relationships of quail and their relatives using phylogenomics, and infer body size and wing shape evolution in relation to trans-marine dispersal events. Our results show thatMargaroperdixandAnurophasisare nested within theCoturnixquail, and are each ‘island giants’ that independently evolved from dispersive,Coturnix-like ancestral populations that colonized and were subsequently isolated on Madagascar and New Guinea. This evolutionary cycle of gain and loss of dispersal ability, coupled with extinction of dispersive taxa, can result in the false appearance that non-vagile taxa somehow underwent rare oceanic dispersal.
Manipulation of feeding regime alters sexual dimorphism for lifespan and reduces sexual conflict in
Drosophila melanogaster
Authors: Duxbury Elizabeth M. L. , Rostant Wayne G. , Chapman Tracey
Published: May 2017

Sexual dimorphism for lifespan (SDL) is widespread, but poorly understood. A leading hypothesis, which we test here, is that strong SDL can reduce sexual conflict by allowing each sex to maximize its sex-specific fitness. We used replicated experimental evolution lines of the fruit fly,
Drosophila melanogaster
, which had been maintained for over 360 generations on either unpredictable ‘Random’ or predictable ‘Regular’ feeding regimes. This evolutionary manipulation of feeding regime led to robust, enhanced SDL in Random over control, Regular lines. Enhanced SDL was associated with a significant increase in the fitness of focal males, tested with wild-type (WT) females. This was due to sex-specific changes to male life history, manifested as increased early reproductive output and reduced survival. In contrast, focal female fitness, tested with WT males, did not differ across regimes. Hence increased SDL was associated with a reduction in sexual conflict, which increased male fitness and maintained fitness in females. Differences in SDL were not associated with developmental time or developmental survival. Overall, the results showed that the expression of enhanced SDL, resulting from experimental evolution of feeding regimes, was associated with male-specific changes in life history, leading to increased fitness and reduced sexual conflict.
Coal-Miner: a coalescent-based method for GWA studies of quantitative traits with complex evolutionary origins
Authors: Hejase Hussein A. , Pol Natalie Vande , Bonito Gregory M. , Edger Patrick P. , Liu Kevin J.
Published: May 2017

Association mapping (AM) methods are used in genome-wide association (GWA) studies to test for statistically significant associations between genotypic and phenotypic data. The genotypic and phenotypic data share common evolutionary origins – namely, the evolutionary history of sampled organisms – introducing covariance which must be distinguished from the covariance due to biological function that is of primary interest in GWA studies. A variety of methods have been introduced to perform AM while accounting for sample relatedness. However, the state of the art predominantly utilizes the simplifying assumption that sample relatedness is effectively fixed across the genome. In contrast, population genetic theory and empirical studies have shown that sample relatedness can vary greatly across different loci within a genome; this phenomena – referred to as local genealogical variation – is commonly encountered in many genomic datasets. New AM methods are needed to better account for local variation in sample relatedness within genomes.

We address this gap by introducing Coal-Miner, a new statistical AM method. The Coal-Miner algorithm takes the form of a methodological pipeline. The initial stages of Coal-Miner seek to detect candidate loci, or loci which contain putatively causal markers. Subsequent stages of Coal-Miner perform test for association using a linear mixed model with multiple effects which account for sample relatedness locally within candidate loci and globally across the entire genome.

Using synthetic and empirical datasets, we compare the statistical power and type I error control of Coal-Miner against state-of-theart AM methods. The simulation conditions reflect a variety of genomic architectures for complex traits and incorporate a range of evolutionary scenarios, each with different evolutionary processes that can generate local genealogical variation. The empirical benchmarks include a large-scale dataset that appeared in a recent high-profile publication. Across the datasets in our study, we find that Coal-Miner consistently offers comparable or typically better statistical power and type I error control compared to the state-of-art methods.

CCS CONCEPTS

Applied computing →Computational genomics; Computational biology; Molecular sequence analysis; Molecular evolution; Computational genomics; Systems biology; Bioinformatics; Population genetics;

ACM Reference format

Hussein A. Hejase, Natalie Vande Pol, Gregory M. Bonito, Patrick P. Edger, and Kevin J. Liu. 2017. Coal-Miner: a coalescent-based method for GWA studies of quantitative traits with complex evolutionary origins. InProceedings of ACM BCB, Boston, MA, 2017 (BCB),10 pages. DOI: 10.475/123 4
Perceived closeness and autistic traits modulate interpersonal vocal communication
Authors: Spinola Olivia , Sumathi T.A. , Singh Nandini Chatterjee , Chakrabarti Bhismadev
Published: May 2017

Vocal modulation is a critical component of interpersonal communication. It not only serves as a dynamic and flexible tool for self-expression and linguistic information but also plays a key role in social behaviour. Variation in vocal modulation can be driven by individual traits of the individual interlocutors, as well as by factors relating to the dyad, such as the perceived closeness between interlocutors. Accordingly, the current study examines the role of a) individual differences in autism-related traits, and b) perceived closeness between interlocutors on vocal modulation. Since lack of appropriate vocal modulation is often associated with Autism Spectrum Disorders we also focus on autism-related individual traits. The role of these individual and dyad-level factors on vocal modulation is tested for cultural generalizability by conducting this study in three separate samples from India, Italy, and the UK. Articulatory features were extracted from recorded conversations between a total of 85 same-sex pairs of participants and correlated with their self-reported perceived closeness (CR) to the other member of the pair and with the individual Autism Spectrum Quotient (AQ). Results indicated a significant positive correlation between interpersonal closeness and articulation area in all three samples. A significant negative correlation between AQ and articulation area was observed only in the UK sample. This study thus provides novel insights into determinants of interpersonal vocal communication and a test of their cultural generalizability.
Gene annotation bias impedes biomedical research
Authors: Haynes Winston A. , Tomczak Aurelie , Khatri Purvesh
Published: May 2017

1

We found tremendous inequality across gene and protein annotation resources. We observe that this bias leads biomedical researchers to focus on richly annotated genes instead of those with the strongest molecular data. We advocate for researchers to reduce these biases by pursuing data-driven hypotheses.
A universal metric for evaluating, optimising and benchmarking the performance of a Research Technology Platform (RTP)
Authors: Petrunkina A.M. , Filby A.
Published: May 2017

Research Technology Platforms (RTPs) exist to facilitate the application and utilisation of specific analytical technologies to the highest possible standard thus delivering reputable data across a broad spectrum of research themes. Specifically, RTPs centralise expertise in a given technology and provide an unparalleled level of continuity and practical knowledge retention that simply cannot be achieved by more organic, ad hoc means of support. As small non profit businesses often tasked with recovering all or a percentage of their running costs, RTPs are under significant pressure to keep pace with rapidly advancing technology and new methodologies against a back drop of dwindling funding for scientific research. At present there are a number of non-trivial issues that make assessing the operational performance of a RTP difficult to determine on a standalone basis let alone attempting to benchmark against other RTPs within the same or different technology fields. Firstly, depending on the technological speciality the RTP may work to one of essentially three operational models. RTPs such as Bio-Imaging or Cytometry provide access to well-maintained analytical systems that can be utilised by trained individuals for a timed access charge. In some cases there will be a requirement for assisted operation of certain instruments by core staff (e.g. cell sorters). Genomics and Proteomics RTPs tend to function on a project basis whereby users will not access the technology themselves rather pay for a full analytical service often with a milestone-based approach for tracking progress. Other RTPs work to a hybrid approach were technical staff provide certain elements of sample preparation for specific projects prior to analysis on core supported, user accessible instrumentation. Secondly the specific operational costs that each RTP is tasked to recover varies significantly on a local, national and international level due to institutional subsidies. These operational costs can include staff salaries, instrument maintenance, associated running consumables, and in some cases instrument depreciation but there is standardised rule as to what each RTP is tasked to recover and to what percentage.

Here we present a generalised mathematical approach to describe the customisable metrics of any given RTP serviceThe general strategy how to increase performance within the framework of this approach has been identified through breaking down these customisable metrics into components and maximising them according to specific requirements. These strategies could be potentially adopted for different operational or local procedures, integrating the specifics related to the institutional or national policies. The approach laid down here should be considered as a trigger for opening a discussion around how to address optimising RTP performance and allow for benchmarking across the full breadth of RTPs.
The landscape of human mutually exclusive splicing
Authors: Hatje Klas , Vidal Ramon O. , Rahman Raza-Ur , Simm Dominic , Hammesfahr Björn , Shomroni Orr , Bonn Stefan , Kollmar Martin
Published: May 2017

Mutually exclusive splicing of exons is a mechanism of functional gene and protein diversification with pivotal roles in organismal development and diseases such as Timothy syndrome, cardiomyopathy and cancer in humans. In order to obtain a first genome-wide estimate of the extent and biological role of mutually exclusive splicing in humans we predicted and subsequently validated mutually exclusive exons (MXEs) using 515 publically available RNA-seq datasets. Here, we provide evidence for the expression of over 855 MXEs, 42% of which represent novel exons, increasing the annotated human mutually exclusive exome more than five-fold. The data provides strong evidence for the existence of large and multi-cluster MXEs in higher vertebrates and offers new insights into MXE splicing mechanics and evolution. Finally, MXEs are significantly enriched in pathogenic mutations and their spatio-temporal expression predicts human disease pathology.
Focal versus distributed temporal cortex activity for speech sound category assignment
Authors: Bouton Sophie , Chambon Valérian , Tyrand Rémi , Guggisberg Adrian G. , Seeck Margitta , Karkar Sami , van de Ville Dimitri , Giraud Anne-Lise
Published: May 2017

Percepts and words can be decoded from largely distributed neural activity measures. The existence of widespread representations might, however, conflict with the fundamental notions of hierarchical processing and efficient coding. Using fMRI and MEG during syllable identification, we first show that sensory and decisional activity co-localize to a restricted part of the posterior superior temporal cortex. Next, using intracortical recordings we demonstrate that early and focal neural activity in this region distinguishes correct from incorrect decisions and can be machine-decoded to classify syllables. Crucially, significant machine-decoding was possible from neuronal activity sampled across widespread regions, despite weak or absent sensory or decision-related responses. These findings show that a complex behavior like speech sound categorization relies on an efficient readout of focal neural activity, while distributed activity, although decodable by machine-learning, reflects collateral processes of sensory perception and decision.
Stable membrane topologies of small dual-topology membrane proteins
Authors: Fluman Nir , Tobiasson Victor , von Heijne Gunnar
Published: May 2017

The topologies of α-helical membrane proteins are generally thought to be determined during their cotranslational insertion into the membrane. It is typically assumed that membrane topologies remain static after this process has ended. Recent findings, however, question this static view by suggesting that some parts of, or even the whole protein, can reorient in the membrane on a biologically relevant time scale. Here, we focus on anti-parallel homo-or hetero-dimeric Small Multidrug Resistance proteins, and examine whether the individual monomers can undergo reversible topological inversion (flip-flop) in the membrane until they are trapped in a fixed orientation by dimerization. By perturbing dimerization using various means, we show that the membrane topology of a monomer is unaffected by the presence or absence of its dimerization partner. Thus, membrane-inserted monomers attain their final topologies independently of dimerization, suggesting that wholesale topological inversion is an unlikely eventin vivo.
Carrion fly-derived DNA metabarcoding is an effective tool for mammal surveys: evidence from a known tropical mammal community
Authors: Rodgers Torrey W. , Xu Charles C. Y. , Giacalone Jacalyn , Kapheim Karen M. , Saltonstall Kristin , Vargas Marta , Yu Douglas W. , Somervuo Panu , Owen McMillan W. , Jansen Patrick A.
Published: May 2017

Metabarcoding of vertebrate DNA derived from carrion flies has been proposed as a promising tool for biodiversity monitoring. To evaluate its efficacy, we conducted metabarcoding surveys of carrion flies on Barro Colorado Island (BCI), Panama, which has a well-known mammal community, and compared our results against diurnal transect counts and camera-trapping. We collected 1084 flies in 29 sampling days, which were pooled into 102 DNA extractions. We then conducted metabarcoding with mammal-specific (16S) and vertebrate-specific (12S) primers targeting mtDNA, and sequenced these amplicons on Illumina MiSeq. For taxonomic assignment, we compared BLAST with the new program PROTAX, and we found PROTAX significantly improved species identifications. We detected 20 mammal, four bird, and one lizard species from carrion fly metabarcoding, all but one of which were previously known from BCI. Fly metabarcoding detected more mammal species than concurrent transect counts (29 sampling days, 13 species) and concurrent camera-trapping (84 sampling days, 17 species), and detected 67% of the number of mammal species documented by 8 years of transect counts and camera-trapping combined, although fly metabarcoding missed several abundant species. This study demonstrates that carrion fly metabarcoding is a powerful tool for mammal biodiversity surveys, and has the potential to detect a broader range of species than more commonly used methods.
BugBase predicts organism-level microbiome phenotypes
Authors: Ward Tonya , Larson Jake , Meulemans Jeremy , Hillmann Ben , Lynch Joshua , Sidiropoulos Dimitri , Spear John R. , Caporaso Greg , Blekhman Ran , Knight Rob , Fink Ryan , Knights Dan
Published: May 2017

Shotgun metagenomics and marker gene amplicon sequencing can be used to directly measure or predict the functional repertoire of the microbiotaen masse, but current methods do not readily estimate the functional capability of individual microorganisms. Here we present BugBase, an algorithm that predicts organism-level coverage of functional pathways as well as biologically interpretable phenotypes such as oxygen tolerance, Gram staining and pathogenic potential, within complex microbiomes using either whole-genome shotgun or marker gene sequencing data. We find BugBase’s organism-level pathway coverage predictions to be statistically higher powered than current ‘bag-of-genes’ approaches for discerning functional changes in both host-associated and environmental microbiomes.
Exon-based phylogenomics strengthens the phylogeny of Neotropical cichlids and identifies remaining conflicting clades (Cichliformes: Cichlidae: Cichlinae)
Authors: Ilves Katriina L. , Torti Dax , Lépez-Fernández Hernán
Published: May 2017

The phenotypic, geographic, and species diversity of cichlid fishes have made them a group of great interest for studying evolutionary processes. Here we present a targeted-exon next-generation sequencing approach for investigating the evolutionary relationships of cichlid fishes (Cichlidae), with focus on the Neotropical subfamily Cichlinae using a set of 923 primarily single-copy exons designed through mining of the Nile tilapia (Oreochromis niloticus) genome. Sequence capture and assembly were robust, leading to a complete dataset of 415 exons for 139 species (147 terminals) that consisted of 128 Neotropical species, six African taxa, and five Indo-Malagasy cichlids. Gene and species trees were calculated using alternative partitioning schemes and reconstruction methods. In general, all methods yielded similar topologies to previously hypothesized relationships within the Cichlinae and clarified several relationships that were previously poorly supported or in conflict. Additional work will be needed to fully resolve all aspects of Cichlinae phylogeny. Overall, this approach yielded a well-resolved phylogeny of Neotropical cichlids that will be of utility for future assessments of the evolutionary and ecological processes within this diverse group of fishes. Furthermore, the general methodology employed here of exon targeting and capture should be applicable to any group of organisms with the availability of a reference genome.
Identification of Three Additional Genes Contiguous to the Glucocerebrosidase Locus on Chromosome 1q21: Implications for Gaucher Disease
Authors: Winfield Suzanne L. , Tayebi Nahid , Martin Brian M. , Ginns Edward I. , Sidransky Ellen
Published: May 2017

Gaucher disease results from the deficiency of the lysosomal enzyme glucocerebrosidase (EC 3.2.1.45). Although the functional gene for glucocerebrosidase (GBA) and its pseudogene (psGBA), located in close proximity on chromosome 1q21, have been studied extensively, the flanking sequence has not been well characterized. The recent identification of human metaxin (MTX) immediately downstream of psGBA prompted a closer analysis of the sequence of the entire region surrounding theGBA gene. We now report the genomic DNA sequence and organization of a 75-kb region around GBA, including the duplicated region containing GBA and MTX. The origin and endpoints of the duplication leading to the pseudogenes forGBA and MTX are now clearly established. We also have identified three new genes within the 32 kb of sequence upstream toGBA, all of which are transcribed in the same direction asGBA. Of these three genes, the gene most distal toGBA is a protein kinase (clk2). The second gene,propin1, has a 1.5-kb cDNA and shares homology to a rat secretory carrier membrane protein 37 (SCAMP37). Finally,cote1, a gene of unknown function lies most proximal toGBA. The possible contributions of these closely arrayed genes to the more atypical presentations of Gaucher disease is now under investigation.

[The sequence data described in this paper have been submitted to the GenBank data library under accession no.AF023268.]
Steady-State Transcript Levels of the Porphobilinogen Deaminase Gene in Patients with Acute Intermittent Porphyria
Authors: Mustajoki Sami , Kauppinen Raili , Mustajoki Pertti , Suomalainen Anu , Peltonen Leena
Published: May 2017

PCR-based solid-phase minisequencing method was used to analyze the steady-state mRNA levels of the porphobilinogen deaminase gene in eight patients with acute intermittent porphyria. The patients had the earlier characterized mutations 517C → T (R173W), 518G → A (R173Q), 673C → G (R225G), 673C → T (R225X), 713T → G (L278P), and 1073delA (frame shift). All mutations, except the missense mutation 517C → T in exon 10, affected the steady-state transcript levels of the mutant allele. The mutant mRNA levels in lymphocytes varied from 5% to 95% of the corresponding wild-type allele levels. In contrast to the CRIM-negative mutation 517C → T, the CRIM-positive mutation in the same codon 518G → A resulted in reduction of the steady-state transcript level of the mutant allele to 65% of that of the normal allele. The two mutations, 673C → G or T, affecting the same nucleotide in exon 12 also differed considerably in their effect on mRNA levels: The transcript level of the allele with a missense mutation was decreased to 80% of that of the normal allele, whereas a nonsense mutation at the same position resulted in a dramatic decrease (fivefold) in the levels of the mutant transcript. Our data showed large variations between the levels of mutant transcript in AIP patients and these variations did not correlate either to CRIM class, to the location of the disease causing mutation in the PBGD gene, or to the clinical phenotype of AIP.

[The sequence data described in this paper have been submitted to EMBL under accession nos. AJ002126–AJ002137.]
AluInsertion Polymorphisms and Human Evolution: Evidence for a Larger Population Size in Africa
Authors: Stoneking Mark , Fontius Jennifer J. , Clifford Stephanie L. , Soodyall Himla , Arcot Santosh S. , Saha Nilmani , Jenkins Trefor , Tahir Mohammad A. , Deininger Prescott L. , Batzer Mark A.
Published: May 2017

Alu insertion polymorphisms (polymorphisms consisting of the presence/absence of an Alu element at a particular chromosomal location) offer several advantages over other nuclear DNA polymorphisms for human evolution studies. First, they are typed by rapid, simple, PCR-based assays; second, they are stable polymorphisms—newly inserted Alu elements rarely undergo deletion; third, the presence of an Alu element represents identity by descent—the probability that different Aluelements would independently insert into the exact same chromosomal location is negligible; and fourth, the ancestral state is known with certainty to be the absence of an Alu element. We report here a study of 8 loci in 1500 individuals from 34 worldwide populations. African populations exhibit the most between-population differentiation, and the population tree is rooted in Africa; moreover, the estimated effective time of separation of African versus non-African populations is 137,000 ± 15,000 years ago, in accordance with other genetic data. However, a principal coordinates analysis indicates that populations from Sahul (Australia and New Guinea) are nearly as close to the hypothetical ancestor as are African populations, suggesting that there was an early expansion of tropical populations of our species. An analysis of heterozygosity versus genetic distance suggests that African populations have had a larger effective population size than non-African populations. Overall, these results support the African origin of modern humans in that an earlier expansion of the ancestors of African populations is indicated.
A Streamlined Mutation Detection System: Multicolor Post-PCR Fluorescence Labeling and Single-Strand Conformational Polymorphism Analysis by Capillary Electrophoresis
Authors: Inazuka Masakazu , Wenz Hans-Michael , Sakabe Munechika , Tahira Tomoko , Hayashi Kenshi
Published: May 2017

Effective use of knowledge of human genome sequences in studies of hereditary diseases or cancer heavily depends on efficient methods for detection of mutations in individual samples. We describe here a simple and efficient mutation scanning system in which PCR products arepost-labeled with two different fluorescent dyes in one tube, and analyzed by an automatedcapillary electrophoresis system using single-strand conformation polymorphism (SSCP) conditions (PLACE–SSCP). With the appropriate use of an internal control DNA, differences in electrophoretic mobilities between a reference and samples are precisely evaluated, then the presence of mutations is statistically judged. Thirty-three of 34 known mutations in fragments of three unrelated sequence contexts up to 741 bp were detected using one electrophoresis condition at the confidence level of <0.3% false positive. All the mutations were detected by analyzing at two temperatures. The described system has the advantage of little human intervention, short analysis time, high sensitivity, and objectivity of data interpretation.
Zooming in on the Human–Mouse Comparative Map: Genome Conservation Re-examined on a High-Resolution Scale
Authors: Carver Ethan A. , Stubbs Lisa
Published: May 2017

Over the past decade, conservation of genetic linkage groups has been shown in mammals and used to great advantage, fueling significant exchanges of gene mapping and functional information especially between the genomes of humans and mice. As human physical maps increase in resolution from chromosome bands to nucleotide sequence, comparative alignments of mouse and human regions have revealed striking similarities and surprising differences between the genomes of these two best-mapped mammalian species. Whereas, at present, very few mouse and human regions have been compared on the physical level, existing studies provide intriguing insights to genome evolution, including the observation of recent duplications and deletions of genes that may play significant roles in defining some of the biological differences between the two species. Although high-resolution conserved marker-based maps are currently available only for human and mouse, a variety of new methods and resources are speeding the development of comparative maps of additional organisms. These advances mark the first step toward establishment of the human genome as a reference map for vertebrate species, providing evolutionary and functional annotation to human sequence and vast new resources for genetic analysis of a variety of commercially, medically, and ecologically important animal models.
The Comparative Genomic Structure and Sequence of the Surfeit Gene Homologs in the Puffer Fish Fugu rubripes and their Association with CpG-Rich Islands
Authors: Armes Niall , Gilley Jonathan , Fried Mike
Published: May 2017

The puffer fish Fugu rubripes (Fugu) has a compact genome approximately one-seventh the size of man, mainly owing to small intron size and the presence of few dispersed repetitive DNA elements, which greatly facilitates the study of its genes at the genomic level. It has been shown previously that, whereas the Surfeit genes are tightly clustered at a single locus in mammals and birds, the genes are found at three separate loci in the Fugu genome. Here, Fugu gene homologs of all six Surfeit genes (Surf-1 to Surf-6) have been cloned and sequenced, and their gene structure has been compared with that of their mammalian and avian homologs. The predicted protein products of each gene are well conserved between vertebrate species, and in most cases their gene structures are identical to their mammalian and avian homologs except for the Fugu Surf-6 gene, which was found to lack an intron present in the mouse gene. In addition, we have identified conserved regulatory elements at the 5′ and 3′ ends of theSurf-3/rpL7a gene by comparison with the mammalian and chickenSurf-3/rpL7a gene homologs, including the presence of a polypyrimidine tract at the extreme 5′ end of this ribosomal protein gene. The Fugu Surfeit gene homologs appear to be associated with CpG-rich islands, like the Surfeit genes in higher vertebrates, but these Fugu CpG islands are similar to the nonclassical islands characteristic of other fish species. Our observations support the use of the Fugu genome to study vertebrate gene structure, to predict the structure of mammalian genes, and to identify vertebrate regulatory elements.

[The sequence data described in this paper have been submitted to the data library under accession nos. Y15170 (Surf-2, Surf-4), Y15171(Surf-3, Surf-1, Surf-6), and Y15172(Surf-5.)]
A First-Generation Whole Genome–Radiation Hybrid Map Spanning the Mouse Genome
Authors: McCarthy Linda C. , Terrett Jonathan , Davis Maria E. , Knights Catherine J. , Smith Angela L. , Critcher Ricky , Schmitt Karin , Hudson Jim , Spurr Nigel K. , Goodfellow Peter N.
Published: May 2017

We have assembled a first-generation anchor map of the mouse genome using a panel of 94 whole-genome–radiation hybrids (WG–RHs) and 271 sequence-tagged sites (STSs). This is the first genome-wide RH anchor map of a model organism. All of the STSs have been previously localized on the genetic map and are located 8.8 Mb apart on average. This mouse WG–RH panel, known as T31, has an average retention frequency of 27.6% and an estimated potential resolution of 145 kb, making it a powerful resource for efficient large-scale expressed sequence tag mapping.

[All of the mapping data for the maps presented here have been deposited at the Research Genetics, Inc., web site and can be freely accessed and downloaded athttp://www.resgen.com/.]
Cloning-Free PCR-Based Allele Replacement Methods
Authors: Erdeniz Naz , Mortensen Uffe H. , Rothstein Rodney
Published: May 2017

Efficient homologous recombination permits the directed introduction of specific mutations into the yeast genome. Here we describe a cloning-free, PCR-based allele replacement method that simplifies allele transfer between yeast strains. The desired allele from one strain is amplified by PCR, along with a selectable/counterselectable marker. After transformation, the resident allele in the target strain is replaced by creating a duplication of the new allele. Selection for direct repeat recombinants results in a single copy of the new allele in the target strain. Specifically, the desired allele is amplified by PCR with a pair of adaptamers, which are chimeric oligonucleotides that are used to amplify the allele and differentially tag its 5′ and 3′ ends. These tags allow the directed fusion to two different, but overlapping, regions of an appropriately tagged selectable/counterselectable marker after a second round of PCR amplification. Following cotransformation of the two fusion fragments into yeast, homologous recombination efficiently generates a duplication of the amplified allele flanking the intact selectable marker in the genome. After counterselection, only the desired allele is retained as a result of direct repeat recombination. A simple modification of this method allows the creation of de novo mutations in the genome.
Large-Scale Comparative Sequence Analysis of the Human and Murine Bruton’s Tyrosine Kinase Loci Reveals Conserved Regulatory Domains
Authors: Oeltjen John C. , Malley Tracy M. , Muzny Donna M. , Miller Webb , Gibbs Richard A. , Belmont John W.
Published: May 2017

Large-scale genomic DNA sequencing of orthologous and paralogous loci in different species should contribute to a basic understanding of the evolution of both the protein-coding regions and noncoding regulatory elements. We compared 93 kb of human sequence to 89 kb of mouse sequence in the Bruton’s tyrosine kinase (BTK) region. In addition to showing the conservation of both position and orientation of the five functionally unrelated genes in the region (BTK, α-d-galactosidase A, L44L, FTP-3, and FCI-12), the comparison revealed conservation of clusters of noncoding sequence flanking the first exon of each gene. Furthermore, in the sequence comparison at the BTK locus, the conservation of clusters of noncoding sequence extends throughout the locus; the noncoding sequence is more highly conserved in the BTK locus in comparison to the flanking loci. This suggests a correlation with the complex developmental regulation of expression of btk. To determine whether a highly conserved 3.5-kb segment flanking the first exon of BTK contains transcriptional regulatory signals, we tested various portions of the segment for promoter and expression activity in several appropriate cell lines. The results demonstrate the contribution of the conserved region flanking the first exon to the cell lineage-specific expression pattern of btk. These data show the usefulness of large scale sequence comparisons to focus investigation on regions of noncoding sequence that play essential roles in complex gene regulation.

[The sequence data described in this paper have been submitted to GenBank under accession nos.U78027andU58105.]
Analysis of the 1.1-Mb Human α/δ T-Cell Receptor Locus with Bacterial Artificial Chromosome Clones
Authors: Boysen Cecilie , Simon Melvin I. , Hood Leroy
Published: May 2017

Bacterial artificial chromosome (BAC) clones are effective mapping and sequencing reagents. The 1.1-Mb α/δ T-cell receptor locus of humans was mapped and partially sequenced with BAC clones. Seventeen BAC clones covered the 1.1-Mb α/δ locus, with the exception of one small gap that was expected from the coverage that a 3.7-fold BAC library is likely to provide. The end sequences of the BAC inserts could be obtained directly from the BAC DNA by sequencing with the chain terminator chemistry. Five complete BAC inserts were sequenced directly by the shotgun approach. The ends of the 17 BAC inserts were distributed evenly across the locus. By several independent criteria, the BAC clones faithfully represented the genomic DNA, with the exception of a single clone with a 68-kb deletion. These BAC features led to the proposal of a new approach to sequence the human genome.

[The sequenced BAC clones, BAC956, BAC810, BAC480, BAC378, and BAC129, have been submitted to GenBank under accession nos.U85199, U85198, U85197, U85196, and U85195, respectively.]
Cloning, Characterization, and Copy Number of the Murine Survival Motor Neuron Gene: Homolog of the Spinal Muscular Atrophy-Determining Gene
Authors: DiDonato Christine J. , Chen Xiao-Ning , Noya David , Korenberg Julie R. , Nadeau Joseph H. , Simard Louise R.
Published: May 2017

Because of a 500-kb inverted duplication, there are two copies of the survival motor neuron (SMN) gene in humans, cenSMN and telSMN. Both genes produce identical ubiquitously expressed transcripts; however, only mutations in telSMN are responsible for spinal muscular atrophy (SMA), the second most common autosomal recessive childhood disease. We have cloned the murine homolog Smn and mapped the gene to Chromosome 13 within the conserved syntenic region of human chromosome 5q13. We show that the Smn transcript (1.4 kb) is expressed as early as embryonic day 7. In contrast to humans, we found no evidence of alternative splicing. The predicted amino acid sequence between mouse and human SMN is 82% identical, and a putative nuclear localization signal is conserved. FISH data indicate that the duplication of the SMA region observed in humans is not present in the mouse. We also found no evidence of multiple Smn genes using Southern blot hybridization and single-strand conformation analysis. Using these methods, we detected at least four copies of Naipexon 5 clustering distal to Smn. Finally, three biallelic markers were identified within the Smn coding region; two are silent polymorphisms, whereas the third changes a cysteine residue to a tyrosine residue in exon 7. Overall, our results indicate thatSmn is single copy within the mouse genome, which should facilitate gene disruption experiments to create an animal model of SMA.

[The murine Smn cDNA sequence has been submitted to GenBank under accession no. U77714. The Mouse Genome Database accession no. for FISH mapping of Smn andNaip is MGD-INEX-31 and for the genetic mapping of theSmn exon 2b microsatellite marker is MGD-CREX-705.]