bluuebunny/crossref_metadata_2025_split huggingface dataset:
Land-Use Change Scenarios of Chosen Small Water Body – Public Participation for a New Reality
Authors: Maślanko Weronika , Sender Joanna , Kułak Agnieszka 
Published: January 2017

Abstract
The object of this study was a small water body adjacent to the Zemborzycki Reservoir. The aim of the study was to find an optimal way of management of the small water body’s surroundings based on scenario building and public participation. The three following scenarios of the small water body’s surroundings’ management with a leading role were used: a) ecological and educational, b) representative and recreational, and c) left in its current form. As a result of the public participation conducted in 2011, it was shown that the ecological and educational scenario is the most optimal for the respondents; and in 2012, implementation had been undertaken. In the decision-making process, a public participation seems to play an important role because actions are accepted, thus fulfilling needs of most users and allowing for identification of the society within a given place.
Four New Species of the Genus Melanagromyza (Diptera, Agromyzidae) from Ukraine
Authors: Guglya Yu. A. 
Published: January 2017

Abstract
Melanagromyza trapezoidea sp. n., M. asymmetrica sp. n., M. cuprea sp. n. and M. pratensis sp. n. are described, and a key to Melanagromyza species known to occur in Ukraine is provided.
Regulatory Architecture of Gene Expression Variation in the Threespine Stickleback Gasterosteus aculeatus
Authors: Pritchard Victoria L , Viitaniemi Heidi M , McCairns R J Scott , Merilä Juha , Nikinmaa Mikko , Primmer Craig R , Leder Erica H 
Published: January 2017

Abstract
Much adaptive evolutionary change is underlain by mutational variation in regions of the genome that regulate gene expression rather than in the coding regions of the genes themselves. An understanding of the role of gene expression variation in facilitating local adaptation will be aided by an understanding of underlying regulatory networks. Here, we characterize the genetic architecture of gene expression variation in the threespine stickleback (Gasterosteus aculeatus), an important model in the study of adaptive evolution. We collected transcriptomic and genomic data from 60 half-sib families using an expression microarray and genotyping-by-sequencing, and located expression quantitative trait loci (eQTL) underlying the variation in gene expression in liver tissue using an interval mapping approach. We identified eQTL for several thousand expression traits. Expression was influenced by polymorphism in both cis- and trans-regulatory regions. Trans-eQTL clustered into hotspots. We did not identify master transcriptional regulators in hotspot locations: rather, the presence of hotspots may be driven by complex interactions between multiple transcription factors. One observed hotspot colocated with a QTL recently found to underlie salinity tolerance in the threespine stickleback. However, most other observed hotspots did not colocate with regions of the genome known to be involved in adaptive divergence between marine and freshwater habitats.
The CgHaa1-Regulon Mediates Response and Tolerance to Acetic Acid Stress in the Human Pathogen Candida glabrata
Authors: Bernardo Ruben T , Cunha Diana V , Wang Can , Pereira Leonel , Silva Sónia , Salazar Sara B , Schröder Markus S , Okamoto Michiyo , Takahashi-Nakaguchi Azusa , Chibana Hiroji , Aoyama Toshihiro , Sá-Correia Isabel , Azeredo Joana , Butler Geraldine , Mira Nuno Pereira 
Published: January 2017

Abstract
To thrive in the acidic vaginal tract, Candida glabrata has to cope with high concentrations of acetic acid. The mechanisms underlying C. glabrata tolerance to acetic acid at low pH remain largely uncharacterized. In this work, the essential role of the CgHaa1 transcription factor (encoded by ORF CAGL0L09339g) in the response and tolerance of C. glabrata to acetic acid is demonstrated. Transcriptomic analysis showed that CgHaa1 regulates, directly or indirectly, the expression of about 75% of the genes activated under acetic acid stress. CgHaa1-activated targets are involved in multiple physiological functions including membrane transport, metabolism of carbohydrates and amino acids, regulation of the activity of the plasma membrane H+-ATPase, and adhesion. Under acetic acid stress, CgHaa1 increased the activity and the expression of the CgPma1 proton pump and contributed to increased colonization of vaginal epithelial cells by C. glabrata. CgHAA1, and two identified CgHaa1-activated targets, CgTPO3 and CgHSP30, are herein demonstrated to be determinants of C. glabrata tolerance to acetic acid. The protective effect of CgTpo3 and of CgHaa1 was linked to a role of these proteins in reducing the accumulation of acetic acid inside C. glabrata cells. In response to acetic acid stress, marked differences were found in the regulons controlled by CgHaa1 and by its S. cerevisiae ScHaa1 ortholog, demonstrating a clear divergent evolution of the two regulatory networks. The results gathered in this study significantly advance the understanding of the molecular mechanisms underlying the success of C. glabrata as a vaginal colonizer.
The Physical Genome Mapping ofAnopheles albimanusCorrected Scaffold Misassemblies and Identified Interarm Rearrangements in GenusAnopheles
Authors: Artemov Gleb N , Peery Ashley N , Jiang Xiaofang , Tu Zhijian , Stegniy Vladimir N , Sharakhova Maria V , Sharakhov Igor V 
Published: January 2017

AbstractThe genome of the Neotropical malaria vector Anopheles albimanus was sequenced as part of the 16 Anopheles Genomes Project published in 2015. The draft assembly of this species consisted of 204 scaffolds with an N50 scaffold size of 18.1 Mb and a total assembly size of 170.5 Mb. It was among the smallest genomes with the longest scaffolds in the 16 Anopheles species cluster, making An. albimanus the logical choice for anchoring the genome assembly to chromosomes. In this study, we developed a high-resolution cytogenetic photomap with completely straightened polytene chromosomes from the salivary glands of the mosquito larvae. Based on this photomap, we constructed a chromosome-based genome assembly using fluorescent in situ hybridization of PCR-amplified DNA probes. Our physical mapping, assisted by an ortholog-based bioinformatics approach, identified and corrected nine misassemblies in five large genomic scaffolds. Misassemblies mostly occurred in junctions between contigs. Our comparative analysis of scaffolds with the An. gambiae genome detected multiple genetic exchanges between pericentromeric regions of chromosomal arms caused by partial-arm translocations. The final map consists of 40 ordered genomic scaffolds and corrected fragments of misassembled scaffolds. The An. albimanus physical map comprises 98.2% of the total genome assembly and represents the most complete genome map among mosquito species. This study demonstrates that physical mapping is a powerful tool for correcting errors in draft genome assemblies and for creating chromosome-anchored reference genomes.
CRISPR/Cas9-Induced Double-Strand Break Repair in Arabidopsis Nonhomologous End-Joining Mutants
Authors: Shen Hexi , Strunks Gary D , Klemann Bart J P M , Hooykaas Paul J J , de Pater Sylvia 
Published: January 2017

Abstract
Double-strand breaks (DSBs) are one of the most harmful DNA lesions. Cells utilize two main pathways for DSB repair: homologous recombination (HR) and nonhomologous end-joining (NHEJ). NHEJ can be subdivided into the KU-dependent classical NHEJ (c-NHEJ) and the more error-prone KU-independent backup-NHEJ (b-NHEJ) pathways, involving the poly (ADP-ribose) polymerases (PARPs). However, in the absence of these factors, cells still seem able to adequately maintain genome integrity, suggesting the presence of other b-NHEJ repair factors or pathways independent from KU and PARPs. The outcome of DSB repair by NHEJ pathways can be investigated by using artificial sequence-specific nucleases such as CRISPR/Cas9 to induce DSBs at a target of interest. Here, we used CRISPR/Cas9 for DSB induction at the Arabidopsis cruciferin 3 (CRU3) and protoporphyrinogen oxidase (PPO) genes. DSB repair outcomes via NHEJ were analyzed using footprint analysis in wild-type plants and plants deficient in key factors of c-NHEJ (ku80), b-NHEJ (parp1 parp2), or both (ku80 parp1 parp2). We found that larger deletions of &gt;20 bp predominated after DSB repair in ku80 and ku80 parp1 parp2 mutants, corroborating with a role of KU in preventing DSB end resection. Deletion lengths did not significantly differ between ku80 and ku80 parp1 parp2 mutants, suggesting that a KU- and PARP-independent b-NHEJ mechanism becomes active in these mutants. Furthermore, microhomologies and templated insertions were observed at the repair junctions in the wild type and all mutants. Since these characteristics are hallmarks of polymerase θ-mediated DSB repair, we suggest a possible role for this recently discovered polymerase in DSB repair in plants.
First in Vivo Batrachochytrium dendrobatidis Transcriptomes Reveal Mechanisms of Host Exploitation, Host-Specific Gene Expression, and Expressed Genotype Shifts
Authors: Ellison Amy R , DiRenzo Graziella V , McDonald Caitlin A , Lips Karen R , Zamudio Kelly R 
Published: January 2017

Abstract
For generalist pathogens, host species represent distinct selective environments, providing unique challenges for resource acquisition and defense from host immunity, potentially resulting in host-dependent differences in pathogen fitness. Gene expression modulation should be advantageous, responding optimally to a given host and mitigating the costs of generalism. Batrachochytrium dendrobatidis (Bd), a fungal pathogen of amphibians, shows variability in pathogenicity among isolates, and within-strain virulence changes rapidly during serial passages through artificial culture. For the first time, we characterize the transcriptomic profile of Bd in vivo, using laser-capture microdissection. Comparison of Bd transcriptomes (strain JEL423) in culture and in two hosts (Atelopus zeteki and Hylomantis lemur), reveals &gt;2000 differentially expressed genes that likely include key Bd defense and host exploitation mechanisms. Variation in Bd transcriptomes from different amphibian hosts demonstrates shifts in pathogen resource allocation. Furthermore, expressed genotype variant frequencies of Bd populations differ between culture and amphibian skin, and among host species, revealing potential mechanisms underlying rapid changes in virulence and the possibility that amphibian community composition shapes Bd evolutionary trajectories. Our results provide new insights into how changes in gene expression and infecting population genotypes can be key to the success of a generalist fungal pathogen.
Imputation-Based Fine-Mapping Suggests That Most QTL in an Outbred Chicken Advanced Intercross Body Weight Line Are Due to Multiple, Linked Loci
Authors: Brandt Monika , Ahsan Muhammad , Honaker Christa F , Siegel Paul B , Carlborg Örjan 
Published: January 2017

AbstractThe Virginia chicken lines have been divergently selected for juvenile body weight for more than 50 generations. Today, the high- and low-weight lines show a &gt;12-fold difference for the selected trait, 56-d body weight. These lines provide unique opportunities to study the genetic architecture of long-term, single-trait selection. Previously, several quantitative trait loci (QTL) contributing to weight differences between the lines were mapped in an F2-cross between them, and these were later replicated and fine-mapped in a nine-generation advanced intercross of them. Here, we explore the possibility to further increase the fine-mapping resolution of these QTL via a pedigree-based imputation strategy that aims to better capture the genetic diversity in the divergently selected, but outbred, founder lines. The founders of the intercross were high-density genotyped, and then pedigree-based imputation was used to assign genotypes throughout the pedigree. Imputation increased the marker density 20-fold in the selected QTL, providing 6911 markers for the subsequent analysis. Both single-marker association and multi-marker backward-elimination analyses were used to explore regions associated with 56-d body weight. The approach revealed several statistically and population structure independent associations and increased the mapping resolution. Further, most QTL were also found to contain multiple independent associations to markers that were not fixed in the founder populations, implying a complex underlying architecture due to the combined effects of multiple, linked loci perhaps located on independent haplotypes that still segregate in the selected lines.
Efficient Screening of CRISPR/Cas9-Induced Events in Drosophila Using a Co-CRISPR Strategy
Authors: Kane Nanci S , Vora Mehul , Varre Krishna J , Padgett Richard W 
Published: January 2017

Abstract
Genome editing using the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and associated nuclease (Cas9) enables specific genetic modifications, including deletions, insertions, and substitutions in numerous organisms, such as the fruit fly Drosophila melanogaster. One challenge of the CRISPR/Cas9 system can be the laborious and time-consuming screening required to find CRISPR-induced modifications due to a lack of an obvious phenotype and low frequency after editing. Here we apply the successful co-CRISPR technique in Drosophila to simultaneously target a gene of interest and a marker gene, ebony, which is a recessive gene that produces dark body color and has the further advantage of not being a commonly used transgenic marker. We found that Drosophila broods containing higher numbers of CRISPR-induced ebony mutations (“jackpot” lines) are significantly enriched for indel events in a separate gene of interest, while broods with few or no ebony offspring showed few mutations in the gene of interest. Using two different PAM sites in our gene of interest, we report that ∼61% (52–70%) of flies from the ebony-enriched broods had an indel in DNA near either PAM site. Furthermore, this marker mutation system may be useful in detecting the less frequent homology-directed repair events, all of which occurred in the ebony-enriched broods. By focusing on the broods with a significant number of ebony flies, successful identification of CRISPR-induced events is much faster and more efficient. The co-CRISPR technique we present significantly improves the screening efficiency in identification of genome-editing events in Drosophila.
One-Cell Doubling Evaluation by Living Arrays of Yeast, ODELAY!
Authors: Herricks Thurston , Dilworth David J , Mast Fred D , Li Song , Smith Jennifer J , Ratushny Alexander V , Aitchison John D 
Published: January 2017

Abstract
Cell growth is a complex phenotype widely used in systems biology to gauge the impact of genetic and environmental perturbations. Due to the magnitude of genome-wide studies, resolution is often sacrificed in favor of throughput, creating a demand for scalable, time-resolved, quantitative methods of growth assessment. We present ODELAY (One-cell Doubling Evaluation by Living Arrays of Yeast), an automated and scalable growth analysis platform. High measurement density and single-cell resolution provide a powerful tool for large-scale multiparameter growth analysis based on the modeling of microcolony expansion on solid media. Pioneered in yeast but applicable to other colony forming organisms, ODELAY extracts the three key growth parameters (lag time, doubling time, and carrying capacity) that define microcolony expansion from single cells, simultaneously permitting the assessment of population heterogeneity. The utility of ODELAY is illustrated using yeast mutants, revealing a spectrum of phenotypes arising from single and combinatorial growth parameter perturbations.
Caenorhabditis elegansDAF-2 as a Model for Human Insulin Receptoropathies
Authors: Bulger David A , Fukushige Tetsunari , Yun Sijung , Semple Robert K , Hanover John A , Krause Michael W 
Published: January 2017

AbstractHuman exome sequencing has dramatically increased the rate of identification of disease-associated polymorphisms. However, examining the functional consequences of those variants has created an analytic bottleneck. Insulin-like signaling in Caenorhabditis elegans has long provided a model to assess consequences of human insulin signaling mutations, but this has not been evaluated in the context of current genetic tools. We have exploited strains derived from the Million Mutation Project (MMP) and gene editing to explore further the evolutionary relationships and conservation between the human and C. elegans insulin receptors. Of 40 MMP alleles analyzed in the C. elegans insulin-like receptor gene DAF-2, 35 exhibited insulin-like signaling indistinguishable from wild-type animals, indicating tolerated mutations. Five MMP alleles proved to be novel dauer-enhancing mutations, including one new allele in the previously uncharacterized C-terminus of DAF-2. CRISPR-Cas9 genome editing was used to confirm the phenotypic consequence of six of these DAF-2 mutations and to replicate an allelic series of known human disease mutations in a highly conserved tyrosine kinase active site residue, demonstrating the utility of C. elegans for directly modeling human disease. Our results illustrate the challenges associated with prediction of the phenotypic consequences of amino acid substitutions, the value of assaying mutant isoform function in vivo, and how recently developed tools and resources afford the opportunity to expand our understanding even of highly conserved regulatory modules such as insulin signaling. This approach may prove generally useful for modeling phenotypic consequences of candidate human pathogenic mutations in conserved signaling and developmental pathways.
Preliminary characterization of the enzyme polyphenol oxidase and rheological behavior from Averrhoa carambola juice
Authors: Murillo Elizabeth , Aristizábal Juan Guillermo , Murillo Walter , Ibarz Ribas Albert , Méndez Jonh Jairo , Solanilla José Fernando 
Published: January 2017

Averrhoa carambola fruit represents a potential as an agro-industrial production line. A restriction on the use of this exotic fruit is the susceptibility to enzymatic browning, affecting nutritional and visual acceptance. The aim of this study was to determine the physical and chemical composition of A. carambola at three stages of maturity. The polyphenol oxidase enzyme has also been characterized on the fruits and juices. Also, the enzymatic effect on the ripening stages and the fruit juices flow behavior were equally determined using different rheological models. The increasing in degrees Brix (unripe (UR) 6.63 ± 0.25, intermediate (IN) 6.8 ± 0.10 and ripe (R) 8.26 ± 0.37) and the decreasing of the pectinic content (UR 4.35% ± 0.98, IN 3.6% ± 1.26 and R 2.25% ± 0.76) could be considered as indicators of fruit ripening. The protein content and levels of organic acids decreased during the ripening of fruit was observed, indicate a high metabolic rate during this process. For all stages, the polyphenol oxidase exhibited a maximum activity at pH 8 and 40 °C. In the fruit aqueous fraction, the enzyme would be an appropriate indicator in industrial handling (temperatures below 20 °C and pH less than 7), which would control enzymatic browning. According to the rheological study, the viscosity variation (η: UR (13.4 to 1.1), IN (15.4 to 1.4), R (69.6 to 2.9)) with temperature changes (10 to 50 °C) is adjusted to the Arrhenius equation, whereas the effect of soluble solids content on the samples viscosity was accurately described by an exponential equation. This appears to be the first work to study the rheological properties and polyphenol oxidase enzyme of A. carambola fruit in our country, the information provided from this study could be helpful to the successful development of new food functional products.
KEPADATAN STOK IKAN DEMERSAL DAN UDANG DI SAMUDERA HINDIA BARAT SUMATERA PADA MUSIM PERALIHAN II
Authors: Nurulludin Nurulludin , Hidayat Thomas , Mamun Asep 
Published: January 2017

Kepadatan stok ikan merupakan indikasi dari potensi perikanan di suatu wilayah yang sangat penting diketahui. Tujuan tulisan ini membahas tentang laju tangkap, kepadatan stok dan perkiraan biomassa ikan demersal serta udang. Penelitian sumber daya ikan demersal dan udang di Samudera Hindia Barat Sumatera dilakukan dengan menggunakan Kapal Riset Baruna Jaya IV (1.200 GT) pada bulan Oktober dan November 2015 (Musim peralihan II). Penghitungan kepadatan stok menggunakan metode sweept area dengan panjang tali ris atas dari jaring trawl 36 m, kecepatan kapal saat menarik jaring berkisar 2,5 – 3 knot, lama penarikan jaring maksimal 1 jam. Perairan Samudera Hindia Barat Sumatera terdiri dari 151 spesies yang tergolong dalam 59 famili. Famili ikan demersal yang dominan tertangkap (5 besar), yaitu Leiognathidae sebesar 23,6 %, Trichiuridae 9,8%, Haemulidae 8,0%, Engraulididae 6,6%, dan Polynemidae 6,05%. Famili udang yaitu Penaeidae (79,08%), Scyllaridae 19,49%, dan Solenoceridae 1,43%. Rata-rata laju tangkap ikan demersal 205,80 kg/jam, dengan kepadatan stok 6,66 ton/km2 dan udang 2,30 kg/jam dengan kepadatan stok 0,053 ton/km2. Biomassa ikan demersal diperkirakan sebesar 470.122 ton dan udang 3.706 ton. Fish stock density is an index of stock abundance indicating the fish resources potential in a region. This paper discusses the catch rate, stock density and biomass estimates of the demersal fish and shrimp resources. Research on the demersal fish and shrimp resources in the Indian Ocean-Western Sumatera conducted using the Research Vessel Baruna Jaya IV (1200 GT) carried out during October and November 2015 (2nd intermonsoon season). Stock density was estimated through the swept area method. The trawl used has 36 m headrope, trawling speed of 2.5 - 3 knots, and maximum towing time was 1 hour. It was found that the fish resources in the waters of the Indian Ocean-Western Sumatera consisted of 151 species belonging to 59 families. The top five dominant fish families caught were Leiognathidae of 23.6%, Trichiuridae 9.8%, Haemulidae 8.0%, Engraulididae 6.6%, and Polynemidae 6.05%, while the shrimp families were Penaeidae of 79.08%, Scyllaridae 19.49%, and Solenoceridae 1.43%. The average catch rate of demersal fish was 205.80 kg/hour, with a stock density of 6.66 tons/km2 and shrimp of 2.30 kg/hour with a stock density of 5.3 kgs/km2. The estimated biomass of demersal fish was 470,122 tons and shrimp was 3,706 tons.