Long-read sequence assembly: a technical evaluation in barley

Sequence assembly of large and repeat-rich plant genomes has been challenging, requiring substantial computational resources and often several complementary sequence assembly and genome mapping approaches. The recent development of fast and accurate long-read sequencing by circular consensus sequencing (CCS) on the PacBio platform may greatly increase the scope of plant pan-genome projects. Here, we compare current long-read sequencing platforms regarding their ability to rapidly generate contiguous sequence assemblies in pan-genome studies of barley (Hordeum vulgare). Most long-read assemblies are clearly superior to the current barley reference sequence based on short-reads. Assemblies derived from accurate long reads excel in most metrics, but the CCS approach was the most cost-effective strategy for assembling tens of barley genomes. A downsampling analysis indicated that 20-fold CCS coverage can yield very good sequence assemblies, while even 5-fold CCS data may capture the complete sequence of most genes. We present an updated reference genome assembly for barley with near-complete representation of the repeat-rich intergenic space. Long-read assembly can underpin the construction of accurate and complete sequences of multiple genomes of a species to build pan-genome infrastructures in Triticeae crops and their wild relatives.

Phylogenetic of Four Bamboo Genera Based on NdhH Sequences, Chloroplast DNA

Bamboos are versatile plants with many usages. Indonesia has a high diversity of Bamboos species and has been using them for a long time. As multipurpose plants, they are vulnerable to over exploration. Much of the bamboo land has been converted into housing or agricultural land. Development and conservation need to be balanced, to protect the genetic diversity, bamboo in particular. We studied the relationship among four genera of bamboo that mostly found in Indonesia using gene that presents in chloroplast DNA, ndhH. DNA from twenty-four samples from Bambusa, Dendrocalamus, Gigantochloa and Schizostachyum were extracted and amplified using specific ndhH primer. Sequencing results were analysed with BioEdit 7.2 software. Phylogenetic tree was build using raxmlGUI 2.0 software. The result showed that ndhH gene generated good sequence quality. It has small variation among samples. The result suggested that ndhH was able to differentiate some species within Schizostachyum, however; it was not a success for others.

THE EFFECT OF WORD BOX GAME ON THE EIGHTH GRADE STUDENTS’ VOCABULARY MASTERY

Vocabulary is first thing to do and one micro skill that must be raise to help the students mastering four language skills. If the students have a lack of vocabulary, they will find some difficulties in expressing ideas in oral or written. In addition, if the students have less vocabulary, they also cannot access the information or knowledge. Moreover, without the words the students cannot really understand facts or ideas that the students have met. Therefore, the students should have to obtain vocabulary mastery to communicate effectively or express his ideas in both oral and written form and also used as basic foundation to construct a word into a good sequence of sentence. Due to the statement, this study is aimed to find out the effect of word box game on the eighth grade students’ vocabulary mastery at Mts Mathla’ul Anwar. The research method is using quasi experimental design and analyze the data by using statitistical hypothesis. Based on the data analysis, it was found that the data was normally distributed and homogeneous. Then, the researchers used t-test formula to analyze the hypotheses. From hypothesis test using t-test, obtained tcount was smaller than ttable or 1.54 < 1.67 on pre-test and on post-test that tcount was higher than ttable or 8.92 > 1.67 with the degree of significant α = 0.05 and df = 35 + 35 - 2 = 68. Thus, it can be concluded that there is difference of students’ vocabulary mastery between using word box game and without word box game in experiment and control class.

A colorimetric method for the sequence-specific recognition of double-stranded DNA on the surface of a silver-coated glass slide

In this study, a colorimetric method for sequence-specific recognition of double-stranded DNA (dsDNA) was established on the surface of a silver-coated glass slide. Oligo-1 was assembled on the surface of a silver-coated glass slide through an Ag–S bond, and Oligo-2 as reporter was used to bind with streptavidin-horseradish peroxidase (SA–HRP). They could bind with target dsDNA that was composed of Oligo-3 and Oligo-4 on the surface of a silver-coated glass slide through triplex formation. The bound HRP could be moved into the solution by DNase I and catalyze the oxidation of 3,3′,5,5′-tetramethylbenzidine (TMB). Therefore, the concentration of target dsDNA could be determined with the colour change of TMB. Under the optimum conditions, the absorbance was proportional to the concentration of target dsDNA over the range of 100 pmol/L to 2.0 nmol/L, with a detection limit of 13 pmol/L. In addition, this method showed good sequence selectivity, enabling it to be further developed for the detection of other polymerase chain reaction (PCR) products.

Sensitive Fluorescent Sensor for Recognition of HIV-1 dsDNA by Using Glucose Oxidase and Triplex DNA

A sensitive fluorescent sensor for sequence-specific recognition of double-stranded DNA (dsDNA) was developed on the surface of silver-coated glass slide (SCGS). Oligonucleotide-1 (Oligo-1) was designed to assemble on the surface of SCGS and act as capture DNA, and oligonucleotide-2 (Oligo-2) was designed as signal DNA. Upon addition of target HIV-1 dsDNA (Oligo-3•Oligo-4), signal DNA could bind on the surface of silver-coated glass because of the formation of C•GoC in parallel triplex DNA structure. Biotin-labeled glucose oxidase (biotin-GOx) could bind to signal DNA through the specific interaction of biotin-streptavidin, thereby GOx was attached to the surface of SCGS, which was dependent on the concentration of target HIV-1 dsDNA. GOx could catalyze the oxidation of glucose and yield H2O2, and the HPPA can be oxidized into a fluorescent product in the presence of HRP. Therefore, the concentration of target HIV-1 dsDNA could be estimated with fluorescence intensity. Under the optimum conditions, the fluorescence intensity was proportional to the concentration of target HIV-1 dsDNA over the range of 10 pM to 1000 pM, the detection limit was 3 pM. Moreover, the sensor had good sequence selectivity and practicability and might be applied for the diagnosis of HIV disease in the future.

Analisis senam angguk di Kabupaten Kulonprogo, Daerah Istimewa Yogyakarta

Penelitian bertujuan mendeskripsikan, menganalisis, dan menginterpretasikan Senam Angguk di Kabupaten Kulonprogo Daerah Istimewa Yogyakarta. Metode atau jenis penelitian yang digunakan menggunakan pendekatan kualitatif yaitu dengan mengobservasi langsung ke lapangan kemudian melakukan wawancara ringan tentang Senam Angguk dan mengambil film sebagai dokumentasi. Kemudian menganalisis Senam Angguk yang ada di Kabupaten Kulonprogo dengan melibatkan pakar senam sebagai Expert Jusment. Setelah dianalisis apakah Senam Angguk termasuk dalam karakteristik senam, maka diperoleh hasil sebagai berikut: Senam Angguk cenderung masuk dalam senam aerobik ringan, dengan intensitas waktu yang relatif pendek (15 menit), dengan tujuan untuk rekreatif, dan dapat untuk menjaga kebugaran lansia muda kurang lebih usia 50 tahun. Namun secara sistematika, gerakan masih banyak yang tidak berurutan. Analyzing the Angguk Exercise in the Regency of Kulonprogo AbstractThe study aims at describing, analysing and interpreting Angguk Exercise in the Regency of Kulonprogo, the Province of Yogyakarta Special Region. The study is a qualitative research using direct observation, small interview and film documentation with regards to the exercise. While the study was conducted, the analysis toward the exercise involved the experts of Gymnastics as part of Expert Judgment. After Angguk exercise has been analysed, the following characteristics are found: (1) Angguk exercise is inclined to be part of light aerobic exercise with relative short time intensity (15 minutes); (2) the objective of performing Angguk exercise is recreational; and (3) the exercise is suitable for the people who has just entered the beginning of their elderhood. Despite these characteristics most of the movements in Angguk exercise are not in a good sequence.

Protein Structure Prediction Using Homology Modeling

Sequence-structure deficit marks one of the critical problems in today's scenario where high-throughput sequencing has resulted in large datasets of protein sequences but their corresponding 3D structures still needs to be determined. Homology modeling, also termed as Comparative modeling refers to modeling of 3D structure of a protein by exploiting structural information from other known protein structures with good sequence similarity. Homology models contain sufficient information about the spatial arrangement of important residues in the protein and are often used in drug design for screening of large libraries by molecular docking techniques. This chapter provides a brief description about protein tertiary structure prediction and Homology modeling. The authors provide a description of the steps involved in homology modeling protocols and provide information on the various resources available for the same.

Protein Structure Prediction using Homology Modeling

Sequence-structure deficit marks one of the critical problems in today's scenario where high-throughput sequencing has resulted in large datasets of protein sequences but their corresponding 3D structures still needs to be determined. Homology modeling, also termed as Comparative modeling refers to modeling of 3D structure of a protein by exploiting structural information from other known protein structures with good sequence similarity. Homology models contain sufficient information about the spatial arrangement of important residues in the protein and are often used in drug design for screening of large libraries by molecular docking techniques. This chapter provides a brief description about protein tertiary structure prediction and Homology modeling. The authors provide a description of the steps involved in homology modeling protocols and provide information on the various resources available for the same.

The genome ofHyperthermus butylicus: a sulfur-reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108 °C

Hyperthermus butylicus, a hyperthermophilic neutrophile and anaerobe, is a member of the archaeal kingdom Crenarchaeota. Its genome consists of a single circular chromosome of 1,667,163 bp with a 53.7% G+C content. A total of 1672 genes were annotated, of which 1602 are protein-coding, and up to a third are specific toH. butylicus. In contrast to some other crenarchaeal genomes, a high level of GUG and UUG start codons are predicted. Twocdc6genes are present, but neither could be linked unambiguously to an origin of replication. Many of the predicted metabolic gene products are associated with the fermentation of peptide mixtures including several peptidases with diverse specificities, and there are many encoded transporters. Most of the sulfur-reducing enzymes, hydrogenases and electron-transfer proteins were identified which are associated with energy production by reducing sulfur to H2S. Two large clusters of regularly interspaced repeats (CRISPRs) are present, one of which is associated with a crenarchaeal-typecasgene superoperon; none of the spacer sequences yielded good sequence matches with known archaeal chromosomal elements. The genome carries no detectable transposable or integrated elements, no inteins, and introns are exclusive to tRNA genes. This suggests that the genome structure is quite stable, possibly reflecting a constant, and relatively uncompetitive, natural environment.

First Line Treatment with the R-VAD+C Regimen Followed by ASCT for Patients under 65 with a Mantle Cell Lymphoma (MCL). From the GOELAMS Group.

This protocol followed the first GOELAMS protocol (also presented at ASH 2006) for MCL pts testing the addition of Rituximab with the VAD+C regimen followed by ASCT. Thirty nine pts were included in this phase II prospective study opened between January 2003 and December 2005. Inclusion criteria: MCL by the WHO (common or blastoïd variants), under 65 years with PS under 3, who never received chemotherapy. Treatment: the first step consist of 4 courses of R-VAD+C regimen (J1, Rituximab 375 mg/sqm; J1 to J4, Vincristin 0,4 mg/D, Adriblastin 9 mg/D and Dexamethasone 40 mg/D; J20 to J29 Chlorambucil 12 mg/D) every 35 days. Evaluation after 4 cycles with the Cheson criterias. Responders (at least 50%) have been collected after a 4 g/sqm cyclophosphamide stimulation and an in vivo purge with rituximab (375). Then, the second step consisted on one R-VAD+C and one VAD+C regimens followed by the transplantation prepared by the myeloablative regimen including Alkeran 140 mg/sqm and 8 grays/4 fr TBI. Results: 38/39 pts are evaluable. 34 biopsies were reviewed and consisted of 26 common forms and 8 blastoïd variants. 4 other diagnosis were possible only on blood (n=3) or bone marrow (n=1) analysis. Treatment: 28/38 (74%) have had a response to the first 4 R-VAD+C, 6 progressed (16%) and 4 (10%) have had only a minor response under 50%. 17/38pts (44,5%) were in CR or CRu after 4 R-VAD+C courses and 11 (29%) in PR&gt;50%. Among the 23 pts evaluated after the transplantation, 20 were in CR, two progressed and one have a PR&gt;50%. Survival: With a median follow-up of 19 months, OS and PFS at 2 years are 80% and 50 % respectively. The PFS is significantly affected by the Goelams Index for MCL described recently from a cohort of patients studied in our previous protocol (see abstract ASH 2006). Conclusion The R-VAD+C regimen followed by PBSCT is a good sequence for the treatment in first line of MCL patients, especially for those with a good prognosis profile defined by the new Goelams prognostic index which would worth being tested on a larger cohort.