Correction: High-resolution DNA size enrichment using a magnetic nano-platform and application in non-invasive prenatal testing

Correction for ‘High-resolution DNA size enrichment using a magnetic nano-platform and application in non-invasive prenatal testing’ by Bo Zhang et al., Analyst, 2020, 145, 5733–5739, DOI: 10.1039/D0AN00813C.

An algorithm and application to efficiently analyze DNA fiber data

The duplication of genetic information (DNA replication) is central to life. Numerous control mechanisms ensure the exact course of the process during each cell division. Disturbances of DNA replication have severe consequences for the affected cell, and current models link them to cancer development. One of the most accurate methods for studying DNA replication is labeling newly synthesized DNA molecules with halogenated nucleotides, followed by immunofluorescence and microscopy detection, known as DNA fiber labeling. The method allows the registration of the activity of single replication complexes by measuring the length of the "trace" left by each of them. The major difficulty of the method is the labor-intensive analysis, which requires measuring the lengths of a large number of labeled fragments. Recently, the interest in this kind of image analysis has grown rapidly. In this manuscript, we provide a detailed description of an algorithm and a lightweight Java application to automatically analyze single DNA molecule images we call "DNA size finder". DNA size finder significantly simplified the analysis of the experimental data while increasing reliability by the standardized measurement of a greater number of DNA molecules. It is freely available and does not require any paid platforms or services to be used. We hope that the application will facilitate both the study of DNA replication control and the effects of various compounds used in human activity on the process of DNA replication.

Insidensi dan Sebaran Tungau Hama pada Pepaya di Pulau Lombok (Incidence and Distribution of Mites on Papaya in Lombok Island)

<p>Tungau hama merupakan salah satu penyebab penurunan produksi pepaya di Pulau Lombok. Penelitian bertujuan menentukan insidensi, sebaran, dan identitas tungau hama pepaya di Pulau Lombok. Sebaran ditentukan berdasarkan insidensi tungau hama pada 50 lokasi pengambilan contoh dan tungau hama diidentifikasi secara morfologi dan molekuler berdasarkan runutan rDNA ITS2. Hasil penelitian menunjukkan terdapat 12 spesies tungau berdasarkan identifikasi morfologi, yaitu Aculops pelekassi, Calacarus carinatus, Brevipalpus californicus, B. obovatus, B. phoenicis, Tenuipalpus pasificus, Eutetranychus africanus, Panonychus citri, Tetranychus fijiensis, T. kanzawai, T. piercei, dan Tarsonemus bilobatus dengan insidensi berkisar antara 2–72%. Di antara spesies yang ditemukan, P. citri merupakan tungau hama dengan sebaran dan insidensi tertinggi (72%). Hasil analisis persebaran menunjukkan bahwa keanekaragaman spesies tungau hama pada tanaman pepaya di Pulau Lombok adalah tinggi dengan tingkat dominansi rendah dan tingkat kemerataan spesies yang tinggi. Uji PCR dan analisis runutan DNA berhasil mendeteksi dan mengidentifikasi enam spesies tungau hama, yaitu T. piercei, T. kanzawai, E. africanus, dan P. citri (Tetranychidae), pada 500–600 pb serta B. californicus dan B. phoenicis (Tenuipalpidae) pada 600–700 pb. Similaritas tertinggi ditemukan pada T. piercei dan T. kanzawai (100%). Ini merupakan laporan pertama keberadaan B. californicus sebagai hama pada tanaman pepaya di Pulau Lombok.</p><p><strong>Keywords</strong></p><p>Frekuensi kemunculan; PCR; Perunutan DNA; Sebaran</p><p><strong>Abstract</strong></p><p>Mites are one obstacle of papaya production in Lombok Island. Thus, the aim of research was to determine incidence, distribution and identity of mites on papaya plant in Lombok Island. Distribution is determined based on incidence of in 50 sampling area, while mites identified morphological and molecularly based on rDNA ITS2. This studies revealed that there were 12 species of mites based on morphological, namely Aculops pelekassi, Calacarus carinatus, Brevipalpus californicus, B. obovatus, B. phoenicis, Tenuipalpus pacificus Eutetranychus africanus, Panonychus citri, Tetranychus fijiensis, T. kanzawai, and T. pierce with an incidence ranging 2-72%. Among species found, P. citri has the highest distribution and incidence of 72%. The results of the distribution analysis showed that diversity of mite species was high, with low dominance and high evenness. PCR assay successfully amplified DNA of six species, namely T. piercei, T. kanzawai, E. africanus, P. citri with the DNA size of 500-600 bp and B. californicus, B. phoenicis with the DNA size of 600-700 bp. The highest similarity species was found on T .piercei and T. kanzawai (100%). This was the first report of B. californicus infestating on papaya in Lombok.</p>

The “Genomic Code”: DNA Pervasively Moulds Chromatin Structures Leaving no Room for “Junk”

The chromatin of the human genome was analyzed at three DNA size levels. At the first, compartment level, two “gene spaces” were found many years ago: A GC-rich, gene-rich “genome core” and a GC-poor, gene-poor “genome desert”, the former corresponding to open chromatin centrally located in the interphase nucleus, the latter to closed chromatin located peripherally. This bimodality was later confirmed and extended by the discoveries (1) of LADs, the Lamina-Associated Domains, and InterLADs; (2) of two “spatial compartments”, A and B, identified on the basis of chromatin interactions; and (3) of “forests and prairies” characterized by high and low CpG islands densities. Chromatin compartments were shown to be associated with the compositionally different, flat and single- or multi-peak DNA structures of the two, GC-poor and GC-rich, “super-families” of isochores. At the second, sub-compartment, level, chromatin corresponds to flat isochores and to isochore loops (due to compositional DNA gradients) that are susceptible to extrusion. Finally, at the short-sequence level, two sets of sequences, GC-poor and GC-rich, define two different nucleosome spacings, a short one and a long one. In conclusion, chromatin structures are moulded according to a “genomic code” by DNA sequences that pervade the genome and leave no room for “junk”.

Effect of Plasmid DNA Size on Chitosan or Polyethyleneimine Polyplexes Formulation

Gene therapy could be simply defined as a strategy for the introduction of a functional copy of desired genes in patients, to correct some specific mutation and potentially treat the respective disorder. However, this straightforward definition hides very complex processes related to the design and preparation of the therapeutic genes, as well as the development of suitable gene delivery systems. Within non-viral vectors, polymeric nanocarriers have offered an ideal platform to be applied as gene delivery systems. Concerning this, the main goal of the study was to do a systematic evaluation on the formulation of pDNA delivery systems based on the complexation of different sized plasmids with chitosan (CH) or polyethyleneimine (PEI) polymers to search for the best option regarding encapsulation efficiency, surface charge, size, and delivery ability. The cytotoxicity and the transfection efficiency of these systems were accessed and, for the best p53 encoding pDNA nanosystems, the ability to promote protein expression was also evaluated. Overall, it was showed that CH polyplexes are more efficient on transfection when compared with the PEI polyplexes, resulting in higher P53 protein expression. Cells transfected with CH/p53-pDNA polyplexes presented an increase of around 54.2% on P53 expression, while the transfection with the PEI/p53-pDNA polyplexes resulted in a 32% increase.

Microchip Electrophoresis

Microchip electrophoresis (MCE) is a miniaturized form of capillary electrophoresis. Electrophoresis is a common technique to separate macromolecules such as nucleic acids (DNA, RNA) and proteins. This technique has become a routine method for DNA size fragmenting and separating protein mixtures in most laboratories around the world. The application of higher voltages in MCE achieves faster and efficient electrophoretic separations.

Near-atomic resolution structures of interdigitated nucleosome fibres

Chromosome structure at the multi-nucleosomal level has remained ambiguous in spite of its central role in epigenetic regulation and genome dynamics. Recent investigations of chromatin architecture portray diverse modes of interaction within and between nucleosome chains, but how this is realized at the atomic level is unclear. Here we present near-atomic resolution crystal structures of nucleosome fibres that assemble from cohesive-ended dinucleosomes with and without linker histone. As opposed to adopting folded helical ‘30 nm’ structures, the fibres instead assume open zigzag conformations that are interdigitated with one another. Zigzag conformations obviate extreme bending of the linker DNA, while linker DNA size (nucleosome repeat length) dictates fibre configuration and thus fibre–fibre packing, which is supported by variable linker histone binding. This suggests that nucleosome chains have a predisposition to interdigitate with specific characteristics under condensing conditions, which rationalizes observations of local chromosome architecture and the general heterogeneity of chromatin structure.

INDUCING GENETIC VARIABILITY OF BLACK PEPPER (Piper nigrum L.) by IRRADIATION

<p>Genetic variability of black pepper germplasm in Indonesia is low. To broaden genetic variability, newly growth shoot tips from in vitro culture of black pepper var. LDL were y irradiated with doses 0, 0.3 0.6, 0.9, 1.2 and 1.5 krad. The treatments were designed in a complete block with five replications. The irradiaed plantlets were grown on MS medium. Response of the variety is described by recording an increase in leaves, shoots and node, numbers, plantlet height, and morphological abnormality in the irst vegetative mutation generation (MVI) and the second vegetative mutation generation (MV2). Ater 6 weeks, the plantlets were sub cultured and the leaves of MV2 were used for RAPD analysis. Six random primers were used for the study, i.e. OPC-01 (TTCGAGC- CAG), OPC-02 (GTGAGGCGTC), OPC-04 (CCGCATCTAC), OPC-05 (GATGACCGCC), OPC-06 (GAACGGACTC) and Abi 117.17 (GCTC- GTCAAC). The results showed that the lowest averages value on the increase of leaves, shoots, nodes and plantlets height al MVI are resulted at dose 1.5 krad, whereas dose 0.3 krad increases averages value on shoots and plantlet height. The highest percentage of abnormal leaves is resulted at dose 1.2 krad. Ater subculture, the MV2 plantlets showed higher averages value for almost all parameters observed than the untreated plantlets. The number of score able bands varied from 2-5 bands with molecular weight 0.4-12 kb. Thirty three bands were detected from the six primers, with OPC-01, OPC-04 and OPC-06 showed polymorphisms with 8 (24%) polymorphic bands. In OPC-01 one band with DNA size 1 -1.5 kb was absence rom the treated plants at dose 0.9-1.5 krad, while with OPC- 04, one band size 1 5 kb present only at 1.2 krad and with OPC-06 one band size 12 kb absence from 0.6 and 0.9 krad, and 3-5 bands size 1.5, 1.8 and bands with size 3-12 kb disappeared at dose 1.2 and 1.5 krad. The appearance and disappearance of bands may be related to the genetic changes due to y irradiation, and further exploration may be needed to ind how much genetic variation induced by irradiation in ield and the relationships with the changes in plant characters.</p><p>Key words: Piper nigrum L., mutation, irradiation, RAPD, genetic variation</p><p> </p><p><strong>ABSTRAK </strong></p><p><strong>Peningkatan keragaman genetik tanaman lada (Piper nigrum L.) dengan iradiasi sinar gamma</strong></p><p>Keragaman genetik plasma nutfah lada sempit, untuk meningkatkan keragaman genetik, mata tunas yang tumbuh dari biakan lada varietas LDL diradiasi dengan sinar y dengan dosis 0, 0.3 0.6, 0.9, 1.2, dan 1.5 krad. Perlakuan menggunakan rancangan acak lengkap dengan lima ulangan. Tunas hasil radiasi ditanam pada media MS. Respon tanaman terhadap perlakuan iradiasi dilakukan dengan mengamati peningkatan jumlah daun, tunas, buku, tinggi tanaman dan morfologi pada planlet hasil perbanyakan vegetatif generasi pertama (MVI) dan kedua setelah iradiasi (MV2). Tunas hasil perbanyakan sub-kultur setelah iradiasi (MV2) dianaltsa keragaman genetiknya dengan RAPD (Randomly Ampliied Polymorphic DNA) menggunakan enam primer acak, yaitu OPC-01 (TTCGAGCCAG), OPC-02 (GTGAGGCGTC), OPC-04 (CCGCATCTAC), OPC-05 (GATGACCGCC), OPC-06 (GAACGGACTC) dan Abi 117.17 (GCTCGTCAAC). Hasil penelitian menunjukkan bahwa iradiasi menyebabkan perubahan yang nyata pada planlet generasi pertama setelah perbanyakan vegetatif (MVI) terutama pada jumlah buku dan tinggi tanaman. tetapi tidak berbeda nyata untuk penambahan jumlah daun dan<br /><br />166 <br /><br />tunas. Nilai rata-rata penambahan jumlah daun, tunas, buku dan tinggi planlet terendah ditunjukkan oleh perlakuan iradiasi pada dosis 1.5 krad, sedangkan pada iradiasi 0.3 krad meningkatkan nilai rata-rata jumlah tunas dan tinggi planlet. Persentase daun abnormal diperoleh pada perlakuan 1.2 krad. Setelah sub-kultur, planlet generasi kedua setelah perbanyakan vegetatif (MV2) yang tumbuh menunjukkan nilai rata-rata yang lebih tinggi dari normal pada semua parameter. Persentase daun variegata pada MVI diperoleh dari perlakuan 1.2 krad tetapi pada MV2 diperoleh dari perlakuan 0.6 krad. Jumlah pita DNA yang terampliikasi berkisar antara 2-5 dengan berat molekul 0.4-12 kb. Tiga puluh tiga pita tcrdetcksi, 8 (24 %) pita diantaranya polimorfik, yang berasal dari primer OPC-01, OPC-04 dan OPC-06. Pada OPC-01 satu pita dengan ukuran 1-1.5 kb hilang dari perlakuan 0.9-1.5 krad, sementara pada OPC-04, satu pita dengan ukuran 1.5 kb muncul hanya pada perlakuan 1.2 krad dan pada OPC-06 satu pita 12 kb hilang dari perlakuan 0-6 dan 0.9 krad, 3-5 pita dengan ukuran 1.5 kb, 1.8 kb dan antara 3-12 kb hilang dari perlakuan 1.2 dan 1.5 krad. Hilang dan munculnya pita kemungkinan berhubungan dengan perubahan genetik akibat radiasi sinar y dan penelitian lanjut perlu dilakukan untuk menge¬ tahui tingkat keragaman yang ditimbulkan akibat iradiasi di lapang dan hubungannya dengan perubahan sifat terutama sifat yang mengunlungkan<br /><br />Kara kunci: Piper nigrum L„ Lada, mutasi, radiasi, RAPD, variasi genetik</p>