bluuebunny/crossref_metadata_2025_split huggingface dataset:
Third Chromosome Balancer Inversions Disrupt Protein-Coding Genes and Influence Distal Recombination Events inDrosophila melanogaster
Authors: Miller Danny E , Cook Kevin R , Arvanitakis Alexandra V , Hawley R Scott 
Published: August 2016

AbstractBalancer chromosomes are multiply inverted chromosomes that suppress meiotic crossing over and prevent the recovery of crossover products. Balancers are commonly used in Drosophila melanogaster to maintain deleterious alleles and in stock construction. They exist for all three major chromosomes, yet the molecular location of the breakpoints and the exact nature of many of the mutations carried by the second and third chromosome balancers has not been available. Here, we precisely locate eight of 10 of the breakpoints on the third chromosome balancer TM3, six of eight on TM6, and nine of 11 breakpoints on TM6B. We find that one of the inversion breakpoints on TM3 bisects the highly conserved tumor suppressor gene p53—a finding that may have important consequences for a wide range of studies in Drosophila. We also identify evidence of single and double crossovers between several TM3 and TM6B balancers and their normal-sequence homologs that have created genetic diversity among these chromosomes. Overall, this work demonstrates the practical importance of precisely identifying the position of inversion breakpoints of balancer chromosomes and characterizing the mutant alleles carried by them.
Fitness Effects of Spontaneous Mutations in Picoeukaryotic Marine Green Algae
Authors: Krasovec Marc , Eyre-Walker Adam , Grimsley Nigel , Salmeron Christophe , Pecqueur David , Piganeau Gwenael , Sanchez-Ferandin Sophie 
Published: August 2016

AbstractEstimates of the fitness effects of spontaneous mutations are important for understanding the adaptive potential of species. Here, we present the results of mutation accumulation experiments over 265–512 sequential generations in four species of marine unicellular green algae, Ostreococcus tauri RCC4221, Ostreococcus mediterraneus RCC2590, Micromonas pusilla RCC299, and Bathycoccus prasinos RCC1105. Cell division rates, taken as a proxy for fitness, systematically decline over the course of the experiment in O. tauri, but not in the three other species where the MA experiments were carried out over a smaller number of generations. However, evidence of mutation accumulation in 24 MA lines arises when they are exposed to stressful conditions, such as changes in osmolarity or exposure to herbicides. The selection coefficients, estimated from the number of cell divisions/day, varies significantly between the different environmental conditions tested in MA lines, providing evidence for advantageous and deleterious effects of spontaneous mutations. This suggests a common environmental dependence of the fitness effects of mutations and allows the minimum mutation/genome/generation rates to be inferred at 0.0037 in these species.
An Improved Genome Assembly of Azadirachta indica A. Juss.
Authors: Krishnan Neeraja M , Jain Prachi , Gupta Saurabh , Hariharan Arun K , Panda Binay 
Published: August 2016

Abstract
Neem (Azadirachta indica A. Juss.), an evergreen tree of the Meliaceae family, is known for its medicinal, cosmetic, pesticidal and insecticidal properties. We had previously sequenced and published the draft genome of a neem plant, using mainly short read sequencing data. In this report, we present an improved genome assembly generated using additional short reads from Illumina and long reads from Pacific Biosciences SMRT sequencer. We assembled short reads and error-corrected long reads using Platanus, an assembler designed to perform well for heterozygous genomes. The updated genome assembly (v2.0) yielded 3- and 3.5-fold increase in N50 and N75, respectively; 2.6-fold decrease in the total number of scaffolds; 1.25-fold increase in the number of valid transcriptome alignments; 13.4-fold less misassembly and 1.85-fold increase in the percentage repeat, over the earlier assembly (v1.0). The current assembly also maps better to the genes known to be involved in the terpenoid biosynthesis pathway. Together, the data represent an improved assembly of the A. indica genome.
Improved Placement of Multi-mapping Small RNAs
Authors: Johnson Nathan R , Yeoh Jonathan M , Coruh Ceyda , Axtell Michael J 
Published: August 2016

Abstract
High-throughput sequencing of small RNAs (sRNA-seq) is a popular method used to discover and annotate microRNAs (miRNAs), endogenous short interfering RNAs (siRNAs), and Piwi-associated RNAs (piRNAs). One of the key steps in sRNA-seq data analysis is alignment to a reference genome. sRNA-seq libraries often have a high proportion of reads that align to multiple genomic locations, which makes determining their true origins difficult. Commonly used sRNA-seq alignment methods result in either very low precision (choosing an alignment at random), or sensitivity (ignoring multi-mapping reads). Here, we describe and test an sRNA-seq alignment strategy that uses local genomic context to guide decisions on proper placements of multi-mapped sRNA-seq reads. Tests using simulated sRNA-seq data demonstrated that this local-weighting method outperforms other alignment strategies using three different plant genomes. Experimental analyses with real sRNA-seq data also indicate superior performance of local-weighting methods for both plant miRNAs and heterochromatic siRNAs. The local-weighting methods we have developed are implemented as part of the sRNA-seq analysis program ShortStack, which is freely available under a general public license. Improved genome alignments of sRNA-seq data should increase the quality of downstream analyses and genome annotation efforts.
CRISPR/Cas9-Mediated Insertion of loxP Sites in the Mouse Dock7 Gene Provides an Effective Alternative to Use of Targeted Embryonic Stem Cells
Authors: Bishop Kathleen A , Harrington Anne , Kouranova Evguenia , Weinstein Edward J , Rosen Clifford J , Cui Xiaoxia , Liaw Lucy 
Published: August 2016

Abstract
Targeted gene mutation in the mouse is a primary strategy to understand gene function and relation to phenotype. The Knockout Mouse Project (KOMP) had an initial goal to develop a public resource of mouse embryonic stem (ES) cell clones that carry null mutations in all genes. Indeed, many useful novel mouse models have been generated from publically accessible targeted mouse ES cell lines. However, there are limitations, including incorrect targeting or cassette structure, and difficulties with germline transmission of the allele from chimeric mice. In our experience, using a small sample of targeted ES cell clones, we were successful ∼50% of the time in generating germline transmission of a correctly targeted allele. With the advent of CRISPR/Cas9 as a mouse genome modification tool, we assessed the efficiency of creating a conditional targeted allele in one gene, dedicator of cytokinesis 7 (Dock7), for which we were unsuccessful in generating a null allele using a KOMP targeted ES cell clone. The strategy was to insert loxP sites to flank either exons 3 and 4, or exons 3 through 7. By coinjecting Cas9 mRNA, validated sgRNAs, and oligonucleotide donors into fertilized eggs from C57BL/6J mice, we obtained a variety of alleles, including mice homozygous for the null alleles mediated by nonhomologous end joining, alleles with one of the two desired loxP sites, and correctly targeted alleles with both loxP sites. We also found frequent mutations in the inserted loxP sequence, which is partly attributable to the heterogeneity in the original oligonucleotide preparation.
Fruiting Body Formation in Volvariella volvacea Can Occur Independently of Its MAT-A-Controlled Bipolar Mating System, Enabling Homothallic and Heterothallic Life Cycles
Authors: Chen Bingzhi , van Peer Arend F , Yan Junjie , Li Xiao , Xie Bin , Miao Juan , Huang Qianhui , Zhang Lei , Wang Wei , Fu Junsheng , Zhang Xiang , Zhang Xiaoyin , Hu Fengli , Kong Qingfang , Sun Xianyun , Zou Feng , Zhang Hanxing , Li Shaojie , Xie Baogui 
Published: August 2016

Abstract
Volvariella volvacea is an important crop in Southeast Asia, but erratic fruiting presents a serious challenge for its production and breeding. Efforts to explain inconsistent fruiting have been complicated by the multinucleate nature, typical lack of clamp connections, and an incompletely identified sexual reproductive system. In this study, we addressed the life cycle of V. volvacea using whole genome sequencing, cloning of MAT loci, karyotyping of spores, and fruiting assays. Microscopy analysis of spores had previously indicated the possible coexistence of heterothallic and homothallic life cycles. Our analysis of the MAT loci showed that only MAT-A, and not MAT-B, controlled heterokaryotization. Thus, the heterothallic life cycle was bipolar. Karyotyping of single spore isolates (SSIs) using molecular markers supported the existence of heterokaryotic spores. However, most SSIs were clearly not heterokaryotic, yet contained structural variation (SV) markers relating to both alleles of both parents. Heterokaryons from crossed, self-sterile homokaryons could produce fruiting bodies, agreeing with bipolar heterothallism. Meanwhile, some SSIs with two different MAT-A loci also produced fruiting bodies, which supported secondary homothallism. Next, SSIs that clearly contained only one MAT-A locus (homothallism) were also able to fruit, demonstrating that self-fertile SSIs were not, per definition, secondary homothallic, and that a third life cycle or genetic mechanism must exist. Finally, recombination between SV markers was normal, yet 10 out of 24 SV markers showed 1:2 or 1:3 distributions in the spores, and large numbers of SSIs contained doubled SV markers. This indicated selfish genes, and possibly partial aneuploidy.
Inter-genomic DNA Exchanges and Homeologous Gene Silencing Shaped the Nascent Allopolyploid Coffee Genome (Coffea arabicaL.)
Authors: Lashermes Philippe , Hueber Yann , Combes Marie-Christine , Severac Dany , Dereeper Alexis 
Published: August 2016

AbstractAllopolyploidization is a biological process that has played a major role in plant speciation and evolution. Genomic changes are common consequences of polyploidization, but their dynamics over time are still poorly understood. Coffea arabica, a recently formed allotetraploid, was chosen to study genetic changes that accompany allopolyploid formation. Both RNA-seq and DNA-seq data were generated from two genetically distant C. arabica accessions. Genomic structural variation was investigated using C. canephora, one of its diploid progenitors, as reference genome. The fate of 9047 duplicate homeologous genes was inferred and compared between the accessions. The pattern of SNP density along the reference genome was consistent with the allopolyploid structure. Large genomic duplications or deletions were not detected. Two homeologous copies were retained and expressed in 96% of the genes analyzed. Nevertheless, duplicated genes were found to be affected by various genomic changes leading to homeolog loss or silencing. Genetic and epigenetic changes were evidenced that could have played a major role in the stabilization of the unique ancestral allotetraploid and its subsequent diversification. While the early evolution of C. arabica mainly involved homeologous crossover exchanges, the later stage appears to have relied on more gradual evolution involving gene conversion and homeolog silencing.
An Intronic MBTPS2 Variant Results in a Splicing Defect in Horses with Brindle Coat Texture
Authors: Murgiano Leonardo , Waluk Dominik P , Towers Rachel , Wiedemar Natalie , Dietrich Joëlle , Jagannathan Vidhya , Drögemüller Michaela , Balmer Pierre , Druet Tom , Galichet Arnaud , Penedo M Cecilia , Müller Eliane J , Roosje Petra , Welle Monika M , Leeb Tosso 
Published: August 2016

Abstract
We investigated a family of horses exhibiting irregular vertical stripes in their hair coat texture along the neck, back, hindquarters, and upper legs. This phenotype is termed “brindle” by horse breeders. We propose the term “brindle 1 (BR1)” for this specific form of brindle. In some BR1 horses, the stripes were also differentially pigmented. Pedigree analyses were suggestive of a monogenic X-chromosomal semidominant mode of inheritance. Haplotype analyses identified a 5 Mb candidate region on chromosome X. Whole genome sequencing of four BR1 and 60 nonbrindle horses identified 61 private variants in the critical interval, none of them located in an exon of an annotated gene. However, one of the private variants was close to an exon/intron boundary in intron 10 of the MBTPS2 gene encoding the membrane bound transcription factor peptidase, site 2 (c.1437+4T&gt;C). Different coding variants in this gene lead to three related genodermatoses in human patients. We therefore analyzed MBTPS2 transcripts in skin, and identified an aberrant transcript in a BR1 horse, which lacked the entire exon 10 and parts of exon 11. The MBTPS2:c1437+4T&gt;C variant showed perfect cosegregation with the brindle phenotype in the investigated family, and was absent from 457 control horses of diverse breeds. Altogether, our genetic data, and previous knowledge on MBTPS2 function in the skin, suggest that the identified MBTPS2 intronic variant leads to partial exon skipping, and causes the BR1 phenotype in horses.
Whole Genome Comparison of Thermus sp. NMX2.A1 Reveals Principal Carbon Metabolism Differences with Closest Relation Thermus scotoductus SA-01
Authors: Müller Walter J , Tlalajoe Nokuthula , Cason Errol D , Litthauer Derek , Reva Oleg , Brzuszkiewicz Elzbieta , van Heerden Esta 
Published: August 2016

Abstract
Genome sequencing of the yellow-pigmented, thermophilic bacterium Thermus sp. NMX2.A1 resulted in a 2.29 Mb draft genome that encodes for 2312 proteins. The genetic relationship between various strains from the genus Thermus was assessed based on phylogenomic analyses using a concatenated set of conserved proteins. The resulting phylogenetic tree illustrated that Thermus sp. NMX2 A.1 clusters together with Thermus scotoductus SA-01, despite being isolated from vastly different geographical locations. The close evolutionary relationship and metabolic parallels between the two strains has previously been recognized; however, neither strain’s genome data were available at that point in time. Genomic comparison of the Thermus sp. NMX2.A1 and T. scotoductus SA-01, as well as other closely related Thermus strains, revealed a high degree of synteny at both the genomic and proteomic level, with processes such as denitrification and natural cell competence appearing to be conserved. However, despite this high level of similarity, analysis revealed a complete, putative Calvin–Benson–Bassham (CBB) cycle in NMX2.A1 that is absent in SA-01. Analysis of horizontally transferred gene islands provide evidence that NMX2 selected these genes due to pressure from its HCO3- rich environment, which is in stark contrast to that of the deep subsurface isolated SA-01.
Characterization of a Novel MMS-Sensitive Allele ofSchizosaccharomyces pombe mcm4+
Authors: Ranatunga Nimna S , Forsburg Susan L 
Published: August 2016

AbstractThe minichromosome maintenance (MCM) complex is the conserved helicase motor of the eukaryotic replication fork. Mutations in the Mcm4 subunit are associated with replication stress and double strand breaks in multiple systems. In this work, we characterize a new temperature-sensitive allele of Schizosaccharomyces pombe mcm4+. Uniquely among known mcm4 alleles, this mutation causes sensitivity to the alkylation damaging agent methyl methanesulfonate (MMS). Even in the absence of treatment or temperature shift, mcm4-c106 cells show increased repair foci of RPA and Rad52, and require the damage checkpoint for viability, indicating genome stress. The mcm4-c106 mutant is synthetically lethal with mutations disrupting fork protection complex (FPC) proteins Swi1 and Swi3. Surprisingly, we found that the deletion of rif1+ suppressed the MMS-sensitive phenotype without affecting temperature sensitivity. Together, these data suggest that mcm4-c106 destabilizes replisome structure.
Developing the Capacity for Rapid-Cycle Improvement at a Large Freestanding Children’s Hospital
Authors: Fieldston Evan S. , Jonas Jennifer A. , Lederman Virginia A. , Zahm Ashley J. , Xiao Rui , DiMichele Christina M. , Tracy Ellen , Kurbjun Katherine , Tenney-Soeiro Rebecca , Geiger Debra L. , Hogan Annique , Apkon Michael 
Published: August 2016

BACKGROUND:
To develop the capacity for rapid-cycle improvement at the unit level, a large freestanding children’s hospital designated 2 inpatient units with normal patient loads and workforce as pilot “Innovation Units” where frontline staff was trained to lead rigorous improvement portfolios.

METHODS:
Frontline staff received improvement training, and interdisciplinary teams brainstormed ideas for tests of change. Ideas were prioritized using an impact-effort evaluation and an assessment of how they aligned with high-level goals. A template for each test summarized the following: the opportunity for improvement, the test being conducted, dates for the tests, driver diagrams, metrics to measure effects, baseline data, results, findings, and next steps. Successful interventions were implemented and disseminated to other units.

RESULTS:
Multidisciplinary staff generated 150 improvement ideas and Innovation Units collectively ran &gt;40 plan-do-study-act cycles. Of the 10 distinct improvement projects, elements of all 10 were deemed “successful” and fully implemented on the unit, and elements from 8 were spread to other units. More than 3 years later, elements of all of the successful improvements are still in practice in some form on the units, and each unit has tested &gt;20 additional improvement ideas, using multiple plan-do-study-act cycles to refine them.

CONCLUSIONS:
The Innovation Unit model successfully engaged frontline staff in improvement work and established a sustainable system and framework for managing rigorous improvement portfolios at the unit level. Other hospitals and health care delivery settings may find our quality improvement approach helpful, especially because it is rooted in the microsystem of care delivery.
Telemedicine: A Reliable Tool to Assess the Severity of Respiratory Distress in Children
Authors: Gattu Rajender , Scollan Joey , DeSouza Amita , Devereaux Danielle , Weaver Holli , Agthe Alexander G. 
Published: August 2016

BACKGROUND AND OBJECTIVES:
Remote assessment of respiratory distress using telemedicine enabled audio-video conferencing (TM) is of value for medical decision-making. Our goal was to evaluate the interobserver reliability (IOR) of TM compared with face-to-face (FTF) assessment of respiratory distress in children.

METHODS:
A prospective, cohort study was performed in pediatric emergency department from July 2012 to February 2013. Children (aged 0–18 years) who presented with signs of respiratory distress were included in the study. The respiratory score is a 4-item, 12-point scale (respiratory rate [1–3], retractions [0–3], dyspnea [0–3], and wheezing [0–3]) that assesses the severity of a child’s respiratory distress. Each child was evaluated by a pair of observers from a pool of 25 observers. The first observer evaluated the patient FTF, and the second observer simultaneously and independently evaluated remotely via TM. The overall respiratory distress severity is based on the respiratory scale and reported as nonsevere (≤8) and severe (≥9) respiratory distress. The IOR reliability between FTF and TM assessment was measured using a 2-way mixed model, absolute agreement and average measure intraclass correlation coefficient (ICC).

RESULTS:
Forty-eight patients and 135 paired observations were recorded. IOR between the FTF and TM groups for total respiratory score had an ICC of 0.95 (confidence interval 0.93–0.96) and for subscores, the ICC range was as follows: respiratory rate = 0.92, retractions = 0.85, dyspnea = 0.94, and wheezing = 0.77.

CONCLUSIONS:
TM is a reliable tool to assess the severity of respiratory distress in children.
Kajian teknologi High Altitude Platform (HAP) [Study of High Altitude Platform (HAP) technology]
Authors: Gultom Amry Daulat , Yuniarti Diah 
Published: August 2016

High Altitude Platform (HAP) merupakan solusi alternatif untuk mengatasi keterbatasan infrastruktur terestrial maupun satelit. HAP merupakan pesawat ataupun balon udara yang ditempatkan pada ketinggian 20-50 km di atas permukaan bumi. Kelebihan yang utama dari HAP adalah kemudahan dalam penempatan, fleksibilitas, biaya operasionalnya rendah, delay propagasi rendah, sudut elevasi lebar, cakupan yang luas. Penelitian ini dilakukan untuk mengetahui potensi HAP untuk komunikasi pita lebar dan perkembangannya di Indonesia. Analisis dilakukan secara deskriptif dengan mengolah data literatur yang didapat. Hasil penelitian menunjukkan bahwa di Indonesia terdapat potensi teknologi HAP untuk komunikasi pita lebar dengan lebar pita 2x300 MHz di band 27,9-28,2 GHz dan 31-31,3 GHz. Namun, belum ada peraturan yang mengatur alokasi frekuensi untuk HAP secara khusus di Indonesia.*****High Altitude Platform (HAP) has been developed as an alternative solution in order to overcome limitation of terrestrial and satellite communication system. HAP is an aircraft or balloon situated on 20-50 km above the earth. Main advantages of HAP are flexibility in deployment, low propagation delay, wide elevation angle and broad coverage. The research is conducted to gather HAP potential for broadband communication and its development in Indonesia. Analysis is conducted by descriptive analysis from literature study gather. The research result shows that in Indonesia, there is potential of HAP technology for broadband communication with 2x300 MHz bandwidth within 27,9-28,2 GHz and 31-31,3 GHz. Yet, there are no specific regulations managing frequency allocation for HAP in Indonesia.