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Purpose: Student learning achievement is the output of an educational institution. Achievement of learning achievement is determined by external and internal factors of students. Therefore, the learning achievement of each student varies. This phenomenon prompted this research to examine the influence of the use of social media as an external factor in learning achievement and learning motivation as an internal factor in learning achievement on learning achievement using empirical data. Design/methodology/approach: The research was conducted on 146 cadets of the Semarang Maritime Science Polytechnic (PIP) which was carried out through interviews using a questionnaire. The data obtained was then analyzed using the Structural Equation Modeling (SEM) approach. Findings: From the results of this research it can be proven that social media is statistically proven to have a significant positive effect on learning motivation and learning achievement and learning motivation is statistically proven to have a significant positive effect on learning achievement Research limitations/implications: This research has not categorized internal and external factors. Practical implications: Based on the results of this research, to improve student learning achievement, it can be done through two approaches. First, learning achievement can be improved by increasing students' learning motivation. The second approach to improving learning achievement is through the use or utilization of social media. Originality/value: This research focuses on vocational education. Paper type: Research Paper

Garis pantai pada umumnya mengalami perubahan posisi dari waktu ke waktu akibat adanya abrasi dan sedimentasi. Perubahan garis pantai dipengaruhi oleh beberapa faktor, salah satunya akibat adanya bangunan pantai. Penelitian ini bertujuan untuk melihat perubahan garis pantai akibat adanya bangunan pantai breakwater di Pulau Pramuka, Kepulauan Seribu. Metode pengolahan dan analisis data dilakukan menggunakan teknologi penginderaan jauh. Dari hasil pengolahan dan analisis data citra satelit Landsat 7 dan 8 dari tahun 2010 sampai tahun 2017 terdapat endapan sedimen atau akresi di pantai Pulau Pramuka akibat adanya bangunan breakwater. Luas endapan sedimen yang terjadi pada tahun 2010 sebesar 7.731 ha, pada tahun 2015 sebesar 7.974 ha, sedangkan pada tahun 2016 sebesar 5.285 ha dan pada tahun 2017 sebesar 5.387 ha. Timbulnya endapan sedimen di pinggiran pantai akibat breakwater ini mengakibatkan terjadinya perubahan garis pantai di sekitar Pulau Pramuka.

Abstract: The demands of the times are moving rapidly and dynamically forcing an organization to keep up with any changes that exist. Education is not free from change. This study aims to describe the application of Bridges transition model in Change Management in driving schools. This study uses survey research. This research method is descriptive qualitative. Source of research data are principals and teachers SDN Padaan 02 Pabelan, Kab. Semarang. Data collection techniques are by interviews and documentation studies. The results obtained from this study are the constraints and strategies of schools in the face of change, as well as the analysis of change management models. The obstacles faced are the absorption of new paradigm learning that is done online is not maximized, mastery of the Driving School Program is still not maximized, and the internet network that does not support. The strategy is to carry out joint activities collaboratively on weekends, academic supervision conducted by the principal at the beginning and at the end of the semester. The change management Model applied is the Bridges transition model. Keywords: change management, bridges model, sekolah penggerak Abstrak: Tuntutan zaman yang bergerak secara cepat dan dinamis memaksa sebuah organisasi untuk mengikuti setiap perubahan yang ada. Pendidikan tidak luput dari adanya perubahan. Penelitian ini bertujuan untuk mendeskripsikan penerapan model transisi Bridges dalam manajemen perubahan di sekolah penggerak. Penelitian ini menggunakan penelitian survey. Metode penelitian ini adalah deskriptif kualitatif. Sumber data penelitian adalah kepala sekolah dan guru SDN Padaan 02 Pabelan, Kab. Semarang. Teknik pengumpulan data adalah dengan wawancara dan studi dokumentasi. Hasil yang diperoleh dari penelitian ini adalah adanya kendala dan strategi sekolah dalam menghadapi perubahan, serta analisis model manajemen perubahan. Kendala yang dihadapi yaitu keterserapan pembelajaran paradigma baru yang dilakukan secara daring belum maksimal, penguasaan Program Sekolah Penggerak masih belum maksimal, serta jaringan internet yang tidak mendukung. Strategi yang dilakukan adalah melaksanakan kegiatan bersama secara kolaboratif di akhir pekan, adanya supervisi akademik yang dilakukan oleh kepala sekolah di awal dan di akhir semester. Model manajemen perubahan yang diterapkan adalah model transisi Bridges. Kata kunci: manajemen perubahan, model bridges, sekolah penggerak

The aim of this work is to study the influence of the number of membership functions (MF) of fuzzy logic controller (FLC) on the temporal performances of dynamical systems. A second contribution to this idea is the introduction of the disturbance signal as an additional input to the FLC and this makes it possible to deliver a command taking into account the values of this undesirable signal. In order to illustrate the influence of the number of membership functions of an FLC, the angular position in a linear model of an Autonomous Underwater Vehicle (AUV) will be controlled around a given reference. The simulation results show that it is sufficient to limit the number of membership functions to a maximum of 5 MF and this is interpreted by the boundary fuzzy decision surface of the fuzzy control because there is no influence, in the case of adding other supplementary MFs, on the performances of the system.

Climate change is one of the biggest threats that human society currently needs to face. Heat waves associated with global warming negatively affect plant growth and development and will increase in intensity and frequency in the coming years. Tomato is one of the most produced and consumed fruit in the world but remarkable yield losses occur every year due to the sensitivity of many cultivars to heat stress (HS). New insights into how tomato plants are responding to HS will contribute to the development of cultivars with high yields under harsh temperature conditions. In this study, the analysis of microsporogenesis and pollen germination rate of eleven tomato cultivars after exposure to a chronic HS revealed differences between genotypes. Pollen development was either delayed and/or desynchronized by HS depending on the cultivar considered. In addition, except for two, pollen germination was abolished by HS in all cultivars. The transcriptome of floral buds at two developmental stages (tetrad and pollen floral buds) of five cultivars revealed common and specific molecular responses implemented by tomato cultivars to cope with chronic HS. These data provide valuable insights into the diversity of the genetic response of floral buds from different cultivars to HS and may contribute to the development of future climate resilient tomato varieties.

This research aims to analyze the use of Google Classroom as a learning tool at Satya Wacana Christian Elementary School, those are; (1) whether the existence of ICT helps in teaching, (2) how effective and interactive the use of Google Classroom is as a learning tool, (3) what features are often used, (4) explain the advantages of Google Classroom, and (5) the obstacles faced when using Google Classroom as a learning tool at Satya Wacana Christian Elementary School. This research used a qualitative descriptive method by conducting interviews and distributing questionnaires. The research subjects are 12 teachers at Satya Wacana Christian Elementary School. Based on the results of observations, interviews, and questionnaires, it was found that 100% of teachers felt that ICT was very helpful in teaching, 83.3% of teachers stated that the use, interaction, and assessment in Google Classroom were considered effective in their implementation, 100% of teachers often used Google Forms, the rest were Google Docs. , Slides, and Spreadsheets, 83.3% of respondents stated that GC is easy to use, 66.6% said GC’ features are complete, and 50% of respondents stated that GC is more effective and flexible. The obstacles that are often faced when using GC are the lack of stability of the internet network, there are still students who do not have their own gadget/computer/laptop facilities, charging grades that are still not appropriate, and limited video transmission capacity.

The all-flesh type of tomato fruits is caused by mutation of the MBP3 gene, however, knocking down MBP3 in certain genotypes also affect plant and fruit development. Here, the authors show that a natural mutation of AGL11, a close homolog of MBP3, is responsible for the phenotypic divergence.

As a result of the exhaustion of fossil energy sources and the corresponding increase of their negative environmental impact, recent research has intensively focused on regions of alternative energy resources and, especially, on solar energy. Slow tracking of the maximum power point (MPP) and fluctuations around the MPP reduce the efficiency of photovoltaic power generation systems (PV). This study offers a novel design for the MPPT controller, which we refer to as the “hybrid IC-LQI approach”, which combines the incremental conductance (IC) technique and the linear quadratic integral (LQI) controller based on the boost converter’s small signal model. We conduct a comparative study of the proposed hybrid IC-LQI, and the classical one-stage IC technique in order to show the effectiveness of our proposal under three different scenarios of weather conditions and load. According to simulation findings, the proposed hybrid IC-LQI approach has a high tracking efficiency of up to 98.92%, owing to faster tracking of MPP with very large reduction of oscillations. On the other hand, the IC technique provides less efficiency, up to 96.1%, showing very slow tracking and high oscillations. The presented analysis of the results confirms the superior performance of the developed hybrid IC-LQI technique to the classical IC technique.

The cryptocurrency market is a market that attracts researchers and investors because it is open every day. This can be seen by the anomalies that occur in the cryptocurrency market. This research uses cryptocurrencies with the largest market cap in 2020, namely Bitcoin, Ethereum, Tether, XRP, and Bitcoin cash as research objects. The data in this study uses daily returns for testing the day of the week effect and daily volatility on the cryptocurrencies under study. This study uses GARCH (1,1) to determine the day of the week effect and daily volatility in the cryptocurrency under study. The results of this study indicate that there is a day of the week effect and daily volatility in the cryptocurrency under study, and it does not move freely. This causes the cryptocurrency market to become an inefficient market. The patterns that occur can be exploited by investors as well as other research on the cryptocurrency under study. Investors can avoid days that have high volatility for example in Bitcoin which experiences high volatility on Fridays and Saturdays because it has a high risk as well. Investors are advised to be able to trade on Thursday for high returns and less risk. DOI: https://doi.org/10.26905/afr.v4i1.5713

Summary: Leydig cells (LCs) are the major androgen-producing cells in the testis. They arise from steroidogenic progenitors (SPs), whose origins, maintenance, and differentiation dynamics remain largely unknown. Single-cell transcriptomics reveal that the mouse steroidogenic lineage is specified as early as embryonic day 12.5 (E12.5) and has a dual mesonephric and coelomic origin. SPs specifically express the Wnt5a gene and evolve rapidly. At E12.5 and E13.5, they give rise first to an intermediate population of pre-LCs, and finally to fetal LCs. At E16.5, SPs possess the characteristics of the dormant progenitors at the origin of adult LCs and are also transcriptionally closely related to peritubular myoid cells (PMCs). In agreement with our in silico analysis, in vivo lineage tracing indicates that Wnt5a-expressing cells are bona fide progenitors of PMCs as well as fetal and adult LCs, contributing to most of the LCs present in the fetal and adult testis.

Haplotype-resolved genome assemblies were produced for Chasselas and Ugni Blanc, two heterozygous Vitis vinifera cultivars by combining high-fidelity long-read sequencing and high-throughput chromosome conformation capture (Hi-C). The telomere-to-telomere full coverage of the chromosomes allowed us to assemble separately the two haplo-genomes of both cultivars and revealed structural variations between the two haplotypes of a given cultivar. The deletions/insertions, inversions, translocations, and duplications provide insight into the evolutionary history and parental relationship among grape varieties. Integration of de novo single long-read sequencing of full-length transcript isoforms (Iso-Seq) yielded a highly improved genome annotation. Given its higher contiguity, and the robustness of the IsoSeq-based annotation, the Chasselas assembly meets the standard to become the annotated reference genome for V. vinifera. Building on these resources, we developed VitExpress, an open interactive transcriptomic platform, that provides a genome browser and integrated web tools for expression profiling, and a set of statistical tools (StatTools) for the identification of highly correlated genes. Implementation of the correlation finder tool for MybA1, a major regulator of the anthocyanin pathway, identified candidate genes associated with anthocyanin metabolism, whose expression patterns were experimentally validated as discriminating between black and white grapes. These resources and innovative tools for mining genome-related data are anticipated to foster advances in several areas of grapevine research. [ABSTRACT FROM AUTHOR]

Summary: Cucumis melo displays a large diversity of horticultural groups with cantaloupe melon the most cultivated type. Using a combination of single-molecule sequencing, 10X Genomics link-reads, high-density optical and genetic maps, and chromosome conformation capture (Hi-C), we assembled a chromosome scale C. melo var. cantalupensis Charentais mono genome. Integration of RNA-seq, MeDip-seq, ChIP-seq, and Hi-C data revealed a widespread compartmentalization of the melon genome, segregating constitutive heterochromatin and euchromatin. Genome-wide comparative and evolutionary analysis between melon botanical groups identified Charentais mono genome increasingly more divergent from Harukei-3 (reticulatus), Payzawat (inodorus), and HS (ssp. agrestis) genomes. To assess the paleohistory of the Cucurbitaceae, we reconstructed the ancestral Cucurbitaceae karyotype and compared it to sequenced cucurbit genomes. In contrast to other species that experienced massive chromosome shuffling, melon has retained the ancestral genome structure. We provide comprehensive genomic resources and new insights in the diversity of melon horticultural groups and evolution of cucurbits.

SUMMARY: Endoreduplication, during which cells increase their DNA content through successive rounds of full genome replication without cell division, is the major source of endopolyploidy in higher plants. Endoreduplication plays pivotal roles in plant growth and development and is associated with the activation of specific transcriptional programmes that are characteristic of each cell type, thereby defining their identity. In plants, endoreduplication is found in numerous organs and cell types, especially in agronomically valuable ones, such as the fleshy fruit (pericarp) of tomato presenting high ploidy levels. We used the tomato pericarp tissue as a model system to explore the transcriptomes associated with endoreduplication progression during fruit growth. We confirmed that expression globally scales with ploidy level and identified sets of differentially expressed genes presenting only developmental‐specific, only ploidy‐specific expression patterns or profiles resulting from an additive effect of ploidy and development. When comparing ploidy levels at a specific developmental stage, we found that non‐endoreduplicated cells are defined by cell division state and cuticle synthesis while endoreduplicated cells are mainly defined by their metabolic activity changing rapidly over time. By combining this dataset with publicly available spatiotemporal pericarp expression data, we proposed a map describing the distribution of ploidy levels within the pericarp. These transcriptome‐based predictions were validated by quantifying ploidy levels within the pericarp tissue. This in situ ploidy quantification revealed the dynamic progression of endoreduplication and its cell layer specificity during early fruit development. In summary, the study sheds light on the complex relationship between endoreduplication, cell differentiation and gene expression patterns in the tomato pericarp. [ABSTRACT FROM AUTHOR]

هدف هذه الورقة البحثية لتبيان مستوى التنويع الإقتصادي في الجزائر في ظل أزمة إنهيار أسعار البترول، حيث سيتم حساب التنويع الإقتصادي على مستوى الناتج المحلي الإجمالي وفق مؤشر هرفندال- هرشمان، وتبين من النتائج أن نسب التنويع الإقتصادي السائد في الجزائر وللفترة 2010-2019 هو مرهون بالتغيرات الحاصلة في أسعار البترول، حيث يأخذ مؤشر هرفندال-هرشمان نسب عالية بالموازاة مع إرتفاع أسعار البترول وهذا قبل أزمة منتصف 2014 أما بعدها وعلى إمتداد فترة التحليل شهد هذا المؤشر نسب لم تقل عن 0.20 وهذا راجع لسببين أولهما هو تراجع مساهمة قطاع المحروقات وثانيهما إلى ضعف مساهمة القطاعات الأخرى خاصة قطاعي الصناعة والفلاحة. This paper aims to show the level of economic diversification in Algeria in the light of the oil price collapse, where economic diversification will be calculated at the level of GDP according to the Hervendal-Hirschmann index, and the results of this study show that the ratios of economic diversification prevailing in Algeria and for the period 2010-2 019 is subject to changes in oil prices, where the Hervendal-Hirschmann index takes high proportions in parallel with the rise in oil prices and this is before the crisis of mid-2014, after that and then throughout the period of analysis saw ratios not less than 0.20 and this The first is due to the decline in the contribution of the hydrocarbon sector and the second to the weak contribution of other sectors, particularly industry and agriculture.

Large-cell calcifying Sertoli cell tumors (LCCSCTs) are among the most frequent lesions occurring in male Carney complex (CNC) patients. Although they constitute a key diagnostic criterion for this rare multiple neoplasia syndrome resulting from inactivating mutations of the tumor suppressor PRKAR1A, leading to unrepressed PKA activity, LCCSCT pathogenesis and origin remain elusive. Mouse models targeting Prkar1a inactivation in all somatic populations or separately in each cell type were generated to decipher the molecular and paracrine networks involved in the induction of CNC testis lesions. We demonstrate that the Prkar1a mutation was required in both stromal and Sertoli cells for the occurrence of LCCSCTs. Integrative analyses comparing transcriptomic, immunohistological data and phenotype of mutant mouse combinations led to the understanding of human LCCSCT pathogenesis and demonstrated PKA-induced paracrine molecular circuits in which the aberrant WNT4 signal production is a limiting step in shaping intratubular lesions and tumor expansion both in a mouse model and in human CNC testes., Introduction Carney complex (CNC) is a rare multiple neoplasia syndrome mainly associated with inactivating mutations of the PRKAR1A gene encoding the R1[alpha] subunit of the PKA, which results in overactive [...]

Climate change is one of the biggest threats that human society currently needs to face. Heat waves associated with global warming negatively affect plant growth and development and will increase in intensity and frequency in the coming years. Tomato is one of the most produced and consumed fruit in the world but remarkable yield losses occur every year due to the sensitivity of many cultivars to heat stress (HS). New insights into how tomato plants are responding to HS will contribute to the development of cultivars with high yields under harsh temperature conditions. In this study, the analysis of microsporogenesis and pollen germination rate of eleven tomato cultivars after exposure to a chronic HS revealed differences between genotypes. Pollen development was either delayed and/or desynchronized by HS depending on the cultivar considered. In addition, except for two, pollen germination was abolished by HS in all cultivars. The transcriptome of floral buds at two developmental stages (tetrad and pollen floral buds) of five cultivars revealed common and specific molecular responses implemented by tomato cultivars to cope with chronic HS. These data provide valuable insights into the diversity of the genetic response of floral buds from different cultivars to HS and may contribute to the development of future climate resilient tomato varieties. [ABSTRACT FROM AUTHOR]

RNA editing is a posttranscriptional process leading to differences between genomic DNA and transcript sequences, potentially enhancing transcriptome diversity. With recent advances in high-throughput sequencing, many efforts have been made to describe mRNA editing at the transcriptome scale, especially in mammals, yielding contradictory conclusions regarding the extent of this phenomenon. We show, by detailed description of the 25 studies focusing so far on mRNA editing at the whole-transcriptome scale, that systematic sequencing artifacts are considered in most studies whereas biological replication is often neglected and multi-alignment not properly evaluated, which ultimately impairs the legitimacy of results. We recently developed a rigorous strategy to identify mRNA editing using mRNA and genomic DNA sequencing, taking into account sequencing and mapping artifacts, and biological replicates. We applied this method to screen for mRNA editing in liver and white adipose tissue from eight chickens and confirm the small extent of mRNA recoding in this species. Among the 25 unique edited sites identified, three events were previously described in mammals, attesting that this phenomenon is conserved throughout evolution. Deeper investigations on five sites revealed the impact of tissular context, genotype, age, feeding conditions, and sex on mRNA editing levels. More specifically, this analysis highlighted that the editing level at the site located on COG3 was strongly regulated by four of these factors. By comprehensively characterizing the mRNA editing landscape in chickens, our results highlight how this phenomenon is limited and suggest regulation of editing levels by various genetic and environmental factors.

The voltage stability is an important factor needing to be taken into consideration in planning and operation of electric power systems. There are several methods and techniques available to determine the voltage stability and identify the power system weak buses, such as the P-V and Q-V curves, singular value decomposition, modal analysis, V-Q sensitivity and reduced determinant. The paper compares three load flow analysis methods: the modal analysis, V-Q sensitivity analysis and Continuation Power Flow. The modal analysis method uses the power system Jacobian matrix to determine the eigenvalues necessary to evaluate voltage stability. The V-Q sensitivity method uses the diagonal elements of the inverse of the reduced Jacobian matrix. In the paper, the V-Q sensitivity and modal analysis method are applied to analyze the effect of a weak coupling between the reactive power (Q) and voltage angle (δ). The results of using the three methods to analyse the western Algerian power system are compared in terms of detecting the weak buses. [ABSTRACT FROM AUTHOR]

As a result of the exhaustion of fossil energy sources and the corresponding increase of their negative environmental impact, recent research has intensively focused on regions of alternative energy resources and, especially, on solar energy. Slow tracking of the maximum power point (MPP) and fluctuations around the MPP reduce the efficiency of photovoltaic power generation systems (PV). This study offers a novel design for the MPPT controller, which we refer to as the "hybrid IC-LQI approach", which combines the incremental conductance (IC) technique and the linear quadratic integral (LQI) controller based on the boost converter's small signal model. We conduct a comparative study of the proposed hybrid IC-LQI, and the classical one-stage IC technique in order to show the effectiveness of our proposal under three different scenarios of weather conditions and load. According to simulation findings, the proposed hybrid IC-LQI approach has a high tracking efficiency of up to 98.92%, owing to faster tracking of MPP with very large reduction of oscillations. On the other hand, the IC technique provides less efficiency, up to 96.1%, showing very slow tracking and high oscillations. The presented analysis of the results confirms the superior performance of the developed hybrid IC-LQI technique to the classical IC technique. [ABSTRACT FROM AUTHOR]

Background De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved. Results We built a de novo RNA-Seq Assembly Pipeline (DRAP) which wraps these two assemblers (Trinity and Oases) in order to improve their results regarding the above-mentioned criteria. DRAP reduces from 1.3 to 15 fold the number of resulting contigs of the assemblies depending on the read set and the assembler used. This article presents seven assembly comparisons showing in some cases drastic improvements when using DRAP. DRAP does not significantly impair assembly quality metrics such are read realignment rate or protein reconstruction counts. Conclusion Transcriptome assembly is a challenging computational task even if good solutions are already available to end-users, these solutions can still be improved while conserving the overall representation and quality of the assembly. The de novo RNA-Seq Assembly Pipeline (DRAP) is an easy to use software package to produce compact and corrected transcript set. DRAP is free, open-source and available under GPL V3 license at http://www.sigenae.org/drap.

The purpose of this thesis is to advance knowledge about Organizational Culture on Organizational Performance Through Total Quality Management in Culinary MSMEs in Ambon City measured using a Likert scale. A total of 50 respondents were involved in this study using a purposive sampling technique. Respondents were selected based on the criteria, namely, the owners of culinary SMEs in the city of Ambon. To test the hypothesis proposed empirically, a hierarchical regression analysis was conducted as a method for analyzing data using XLSTAT PLS PM 2014 software. The results showed that organizational culture had a positive relationship with organizational performance, organizational culture had a positive relationship with total quality management. [ABSTRACT FROM AUTHOR]

High-throughput sequencing technologies have offered in recent years new opportunities to study genome variations. These studies have mostly focused on single nucleotide polymorphisms, small insertions or deletions and on copy number variants. Other structural variants, such as large insertions or deletions, tandem duplications, translocations, and inversions are less well-studied, despite that some have an important impact on phenotypes. In the present study, we performed a large-scale survey of structural variants in cattle. We report the identification of 6,426 putative structural variants in cattle extracted from whole-genome sequence data of 62 bulls representing the three major French dairy breeds. These genomic variants affect DNA segments greater than 50 base pairs and correspond to deletions, inversions and tandem duplications. Out of these, we identified a total of 547 deletions and 410 tandem duplications which could potentially code for CNVs. Experimental validation was carried out on 331 structural variants using a novel high-throughput genotyping method. Out of these, 255 structural variants (77%) generated good quality genotypes and 191 (75%) of them were validated. Gene content analyses in structural variant regions revealed 941 large deletions removing completely one or several genes, including 10 single-copy genes. In addition, some of the structural variants are located within quantitative trait loci for dairy traits. This study is a pan-genome assessment of genomic variations in cattle and may provide a new glimpse into the bovine genome architecture. Our results may also help to study the effects of structural variants on gene expression and consequently their effect on certain phenotypes of interest.

RNA editing results in a post-transcriptional nucleotide change in the RNA sequence that creates an alternative nucleotide not present in the DNA sequence. This leads to a diversification of transcription products with potential functional consequences. Two nucleotide substitutions are mainly described in animals, from adenosine to inosine (A-to-I) and from cytidine to uridine (C-to-U). This phenomenon is described in more details in mammals, notably since the availability of next generation sequencing technologies allowing whole genome screening of RNA-DNA differences. The number of studies recording RNA editing in other vertebrates like chicken is still limited. We chose to use high throughput sequencing technologies to search for RNA editing in chicken, and to extend the knowledge of its conservation among vertebrates. We performed sequencing of RNA and DNA from 8 embryos. Being aware of common pitfalls inherent to sequence analyses that lead to false positive discovery, we stringently filtered our datasets and found fewer than 40 reliable candidates. Conservation of particular sites of RNA editing was attested by the presence of 3 edited sites previously detected in mammals. We then characterized editing levels for selected candidates in several tissues and at different time points, from 4.5 days of embryonic development to adults, and observed a clear tissue-specificity and a gradual increase of editing level with time. By characterizing the RNA editing landscape in chicken, our results highlight the extent of evolutionary conservation of this phenomenon within vertebrates, attest to its tissue and stage specificity and provide support of the absence of non A-to-I events from the chicken transcriptome.

The aim of this work is to study the influence of the number of membership functions (MF) of fuzzy logic controller (FLC) on the temporal performances of dynamical systems. A second contribution to this idea is the introduction of the disturbance signal as an additional input to the FLC and this makes it possible to deliver a command taking into account the values of this undesirable signal. In order to illustrate the influence of the number of membership functions of an FLC, the angular position in a linear model of an Autonomous Underwater Vehicle (AUV) will be controlled around a given reference. The simulation results show that it is sufficient to limit the number of membership functions to a maximum of 5 MF and this is interpreted by the boundary fuzzy decision surface of the fuzzy control because there is no influence, in the case of adding other supplementary MFs, on the performances of the system. [ABSTRACT FROM AUTHOR]

Transcriptome analysis based on a de novo assembly of next generation RNA sequences is now performed routinely in many laboratories. The generated results, including contig sequences, quantification figures, functional annotations and variation discovery outputs are usually bulky and quite diverse. This article presents a user oriented storage and visualisation environment permitting to explore the data in a top-down manner, going from general graphical views to all possible details. The software package is based on biomart, easy to install and populate with local data. The software package is available under the GNU General Public License (GPL) at http://bioinfo.genotoul.fr/RNAbrowse.

In this study, we propose an approach aiming at fine-mapping adiposity QTL in chicken, integrating whole genome re-sequencing data. First, two QTL regions for adiposity were identified by performing a classical linkage analysis on 1362 offspring in 11 sire families obtained by crossing two meat-type chicken lines divergently selected for abdominal fat weight. Those regions, located on chromosome 7 and 19, contained a total of 77 and 84 genes, respectively. Then, SNPs and indels in these regions were identified by re-sequencing sires. Considering issues related to polymorphism annotations for regulatory regions, we focused on the 120 and 104 polymorphisms having an impact on protein sequence, and located in coding regions of 35 and 42 genes situated in the two QTL regions. Subsequently, a filter was applied on SNPs considering their potential impact on the protein function based on conservation criteria. For the two regions, we identified 42 and 34 functional polymorphisms carried by 18 and 24 genes, and likely to deeply impact protein, including 3 coding indels and 4 nonsense SNPs. Finally, using gene functional annotation, a short list of 17 and 4 polymorphisms in 6 and 4 functional genes has been defined. Even if we cannot exclude that the causal polymorphisms may be located in regulatory regions, this strategy gives a complete overview of the candidate polymorphisms in coding regions and prioritize them on conservation- and functional-based arguments.

Despite massive research efforts, the molecular etiology of bovine polledness and the developmental pathways involved in horn ontogenesis are still poorly understood. In a recent article, we provided evidence for the existence of at least two different alleles at the Polled locus and identified candidate mutations for each of them. None of these mutations was located in known coding or regulatory regions, thus adding to the complexity of understanding the molecular basis of polledness. We confirm previous results here and exhaustively identify the causative mutation for the Celtic allele (PC) and four candidate mutations for the Friesian allele (PF). We describe a previously unreported eyelash-and-eyelid phenotype associated with regular polledness, and present unique histological and gene expression data on bovine horn bud differentiation in fetuses affected by three different horn defect syndromes, as well as in wild-type controls. We propose the ectopic expression of a lincRNA in PC/p horn buds as a probable cause of horn bud agenesis. In addition, we provide evidence for an involvement of OLIG2, FOXL2 and RXFP2 in horn bud differentiation, and draw a first link between bovine, ovine and caprine Polled loci. Our results represent a first and important step in understanding the genetic pathways and key process involved in horn bud differentiation in Bovidae.

The regular decrease of female fertility over time is a major concern in modern dairy cattle industry. Only half of this decrease is explained by indirect response to selection on milk production, suggesting the existence of other factors such as embryonic lethal genetic defects. Genomic regions harboring recessive deleterious mutations were detected in three dairy cattle breeds by identifying frequent haplotypes (>1%) showing a deficit in homozygotes among Illumina Bovine 50k Beadchip haplotyping data from the French genomic selection database (47,878 Holstein, 16,833 Montbéliarde, and 11,466 Normande animals). Thirty-four candidate haplotypes (p

SUMMARY: Tomato is a widely cultivated crop, which can grow in many environments. However, temperature above 30°C impairs its reproduction, subsequently impacting fruit yield. We assessed the impact of high‐temperature stress (HS) in two tomato experimental populations, a multi‐parental advanced generation intercross (MAGIC) population and a core‐collection (CC) of small‐fruited tomato accessions. Both populations were evaluated for 11 traits related to yield components, phenology and fruit quality in optimal and HS conditions. HS significantly impacted all traits in both populations, but a few genotypes with stable yield under HS were identified. A plasticity index was computed for each individual to measure the extent of the heat impact for each trait. Quantitative trait loci (QTL) were detected in control and HS conditions as well as for plasticity index. Linkage and genome‐wide association analyses in the MAGIC and CC populations identified a total of 98 and 166 QTLs, respectively. Taking the two populations together, 69 plasticity QTLs (pQTLs) were involved in tomato heat response for 11 traits. The transcriptome changes in the ovary of six genotypes with contrasted responses to HS were studied, and 837 genes differentially expressed according to the conditions were detected. Combined with previous transcriptome studies, these results were used to propose candidate genes for HS response QTLs. Significance Statement: Tomato genotypes tolerant to heat stress were identified in two experimental populations covering a large range of variation grown in control and heat stress conditions. Heat‐response QTLs were mapped for agronomic, fruit set and fruit quality traits. Genes differentially expressed in the ovary under heat and control conditions were identified in three susceptible and three tolerant genotypes. Candidate genes for plasticity QTLs were then proposed. [ABSTRACT FROM AUTHOR]

SUMMARY: Ethylene modulates plant developmental processes including flower development. Previous studies have suggested ethylene participates in pollen tube (PT) elongation, and both ethylene production and perception seem critical at the time of fertilization. The full gene set regulated by ethylene during PT growth is unknown. To study this, we used various EThylene Receptor (ETR) tomato (Solanum lycopersicum) mutants: etr3‐ko, a loss‐of‐function (LOF) mutant; and NR (NEVER RIPE), a gain‐of‐function (GOF) mutant. The etr3‐ko PTs grew faster than wild‐type (WT) PTs. Oppositely, NR PT elongation was slower than in WT, and PTs displayed larger diameters. ETR mutations result in feedback control of ethylene production. Furthermore, ethylene treatment of germinating pollen grains increased PT length in etr‐ko mutants and WT, but not in NR. Treatment with the ethylene perception inhibitor 1‐methylcyclopropene decreased PT length in etr‐ko mutants and WT, but had no effect on NR. This confirmed that ethylene regulates PT growth. The comparison of PT transcriptomes in LOF and GOF mutants, etr3‐ko and NR, both harboring mutations of the ETR3 gene, revealed that ethylene perception has major impacts on cell wall‐ and calcium‐related genes as confirmed by microscopic observations showing a modified distribution of the methylesterified homogalacturonan pectic motif and of calcium load. Our results establish links between PT growth, ethylene, calcium, and cell wall metabolism, and also constitute a transcriptomic resource. [ABSTRACT FROM AUTHOR]

Summary: Fruit formation comprises a series of developmental transitions among which the fruit set process is essential in determining crop yield. Yet, our understanding of the epigenetic landscape remodelling associated with the flower‐to‐fruit transition remains poor.We investigated the epigenetic and transcriptomic reprogramming underlying pollination‐dependent and auxin‐induced flower‐to‐fruit transitions in the tomato (Solanum lycopersicum) using combined genomewide transcriptomic profiling, global ChIP‐sequencing and whole genomic DNA bisulfite sequencing (WGBS).Variation in the expression of the overwhelming majority of genes was associated with change in histone mark distribution, whereas changes in DNA methylation concerned a minor fraction of differentially expressed genes. Reprogramming of genes involved in processes instrumental to fruit set correlated with their H3K9ac or H3K4me3 marking status but not with changes in cytosine methylation, indicating that histone posttranslational modifications rather than DNA methylation are associated with the remodelling of the epigenetic landscape underpinning the flower‐to‐fruit transition.Given the prominent role previously assigned to DNA methylation in reprogramming key genes of the transition to ripening, the outcome of the present study supports the idea that the two main developmental transitions in fleshy fruit and the underlying transcriptomic reprogramming are associated with different modes of epigenetic regulations. [ABSTRACT FROM AUTHOR]

Fuel consumption is an energy conversion that converts the chemical energy of a fuel into another energy at a certain time. Fuel consumption must always be monitored because it will affect the company’s profit. Since fuel is a significant expense, the company must be efficient in its usage to allow the company to grow. The author summarizes the problem and tries to solve the problem using quantitative research methods. The research is conducted at the branch office by interviewing the company’s staff. PT. Transcoal Pacific is a company that focused on its service at preparing ships to carry cargo in coal. The company monitors the fuel consumption using a fuel lock system, so the target can be reached in using fuel as few as possible and get maximum profit. Based on the result of this research, it is clear that the company lacks the aspect of fuel monitoring. This causes the target cannot be reached. The old fuel lock cannot be applied by the tugboat and dragging where the vessel swept away by sea current that may increase fuel consumption. The company has to increase the monitoring aspect and implement the obligation to solve the problem to improve fuel consumption efficiency. [ABSTRACT FROM AUTHOR]

As part of normal development most eukaryotic organisms, ranging from insects and mammals to plants, display variations in nuclear ploidy levels resulting from somatic endopolyploidy. Endoreduplication is the major source of endopolyploidy in higher plants. Endoreduplication is a remarkable characteristic of the fleshy pericarp tissue of developing tomato fruits, where it establishes a highly integrated cellular system that acts as a morphogenetic factor supporting cell growth. However, the functional significance of endoreduplication is not fully understood. Although endoreduplication is thought to increase metabolic activity due to a global increase in transcription, the issue of gene-specific ploidy-regulated transcription remains open. To investigate the influence of endoreduplication on transcription in tomato fruit, we tested the feasibility of a RNA sequencing ( RNA-Seq) approach using total nuclear RNA extracted from purified populations of flow cytometry-sorted nuclei based on their DNA content. Here we show that cell-based approaches to the study of RNA-Seq profiles need to take into account the putative global shift in expression between samples for correct analysis and interpretation of the data. From ploidy-specific expression profiles we found that the activity of cells inside the pericarp is related both to the ploidy level and their tissue location. [ABSTRACT FROM AUTHOR]

Bidirectional promoters are regulatory regions co-regulating the expression of two neighbouring genes organized in a head-to-head orientation. In recent years, these regulatory regions have been studied in many organisms; however, no investigation to date has been done to analyse the genetic variation of the activity of this type of promoter regions. In our study, we conducted an investigation to first identify bidirectional promoters sharing genes expressed in bovine Longissimus thoracis and then to find genetic variants affecting the activity of some of these bidirectional promoters. Combining bovine gene information and expression data obtained using RNA-Seq, we identified 120 putative bidirectional promoters active in bovine muscle. We experimentally validated in vitro 16 of these bidirectional promoters. Finally, using gene expression and whole-genome genotyping data, we explored the variability of the activity in muscle of the identified bidirectional promoters and discovered genetic variants affecting their activity. We found that the expression level of 77 genes is correlated with the activity of 12 bidirectional promoters. We also identified 57 single nucleotide polymorphisms associated with the activity of 5 bidirectional promoters. To our knowledge, our study is the first analysis in any species of the genetic variability of the activity of bidirectional promoters. [ABSTRACT FROM AUTHOR]

High-throughput sequencing technologies have offered in recent years new opportunities to study genome variations. These studies have mostly focused on single nucleotide polymorphisms, small insertions or deletions and on copy number variants. Other structural variants, such as large insertions or deletions, tandem duplications, translocations, and inversions are less well-studied, despite that some have an important impact on phenotypes. In the present study, we performed a large-scale survey of structural variants in cattle. We report the identification of 6,426 putative structural variants in cattle extracted from whole-genome sequence data of 62 bulls representing the three major French dairy breeds. These genomic variants affect DNA segments greater than 50 base pairs and correspond to deletions, inversions and tandem duplications. Out of these, we identified a total of 547 deletions and 410 tandem duplications which could potentially code for CNVs. Experimental validation was carried out on 331 structural variants using a novel high-throughput genotyping method. Out of these, 255 structural variants (77%) generated good quality genotypes and 191 (75%) of them were validated. Gene content analyses in structural variant regions revealed 941 large deletions removing completely one or several genes, including 10 single-copy genes. In addition, some of the structural variants are located within quantitative trait loci for dairy traits. This study is a pan-genome assessment of genomic variations in cattle and may provide a new glimpse into the bovine genome architecture. Our results may also help to study the effects of structural variants on gene expression and consequently their effect on certain phenotypes of interest. [ABSTRACT FROM AUTHOR]

RNA editing results in a post-transcriptional nucleotide change in the RNA sequence that creates an alternative nucleotide not present in the DNA sequence. This leads to a diversification of transcription products with potential functional consequences. Two nucleotide substitutions are mainly described in animals, from adenosine to inosine (A-to-I) and from cytidine to uridine (C-to-U). This phenomenon is described in more details in mammals, notably since the availability of next generation sequencing technologies allowing whole genome screening of RNA-DNA differences. The number of studies recording RNA editing in other vertebrates like chicken is still limited. We chose to use high throughput sequencing technologies to search for RNA editing in chicken, and to extend the knowledge of its conservation among vertebrates. We performed sequencing of RNA and DNA from 8 embryos. Being aware of common pitfalls inherent to sequence analyses that lead to false positive discovery, we stringently filtered our datasets and found fewer than 40 reliable candidates. Conservation of particular sites of RNA editing was attested by the presence of 3 edited sites previously detected in mammals. We then characterized editing levels for selected candidates in several tissues and at different time points, from 4.5 days of embryonic development to adults, and observed a clear tissue-specificity and a gradual increase of editing level with time. By characterizing the RNA editing landscape in chicken, our results highlight the extent of evolutionary conservation of this phenomenon within vertebrates, attest to its tissue and stage specificity and provide support of the absence of non A-to-I events from the chicken transcriptome. [ABSTRACT FROM AUTHOR]

Free fatty acid receptors (FFAR) belong to a family of five G-protein coupled receptors that are involved in the regulation of lipid metabolism, so that their loss of function increases the risk of obesity. The aim of this study was to determine the expansion of genes encoding paralogs of FFAR2 in the chicken, considered as amodel organism for developmental biology and biomedical research. By estimating the gene copy number using quantitative polymerase chain reaction, genomic DNA resequencing, and RNA sequencing data, we showed the existence of 23 ±1.5 genes encoding FFAR2 paralogs in the chicken genome. The FFAR2 paralogs shared an identity from 87.2%up to 99%. Extensive gene conversion was responsible for this high degree of sequence similarities between these genes, and this concerned especially the four amino acids known to be critical for ligand binding. Moreover, elevated nonsynonymous/ synonymous substitutionratios onsomeamino acids withinor inclose-vicinity of the ligand-bindinggroove suggest that positive selectionmay have reduced the effective rate of gene conversion in this region, thus contributing to diversify the function of some FFAR2 paralogs. All the FFAR2 paralogs were located on a microchromosome in a same linkage group. FFAR2 genes were expressed in different tissues and cells such as spleen, peripheral blood mononuclear cells, abdominal adipose tissue, intestine, and lung, with the highest rate of expression in testis. Further investigations are needed to determine whether these chicken-specific events along evolution are the consequence of domestication and may play a role in regulating lipid metabolism in this species. [ABSTRACT FROM AUTHOR]