Direct DNA and PNA probe binding to telomeric regions without classical in situ hybridization

Nontraditional Method for Telomere Staining by PNA Probes

The standard FISH uses DNA probes to hybridize to the designated complementary strands. This is DNA-DNA interaction, and it usually takes much longer time to obtain detectable signals compared to other reactions such as immunochemical reactions and simple chemical reactions. Certain proteins bind to specific DNA sequences and regulate the biological function of DNA. These DNA-binding proteins have specific domains to interact with single- or double-stranded DNA. Some of telomere proteins apparently bind to telomere sequence and form nucleoprotein complex to protect chromosome ends. Using telomere PNA probes, probes can be accumulated at the telomere sites in a non-hybridization manner. This chapter introduces nontraditional PNA telomere staining protocol without DNA-DNA hybridization to visualize telomere locations on metaphase chromosomes.

The promise of graphene-based transistors for democratizing multiomics studies

As biological research has synthesized genomics, proteomics, metabolomics, and transcriptomics into systems biology, a new multiomics approach to biological research has emerged. Today, multiomics studies are challenging and expensive. An experimental platform that could unify the multiple omics approaches to measurement could increase access to multiomics data by enabling more individual labs to successfully attempt multiomics studies. Field effect biosensing based on graphene transistors have gained significant attention as a potential unifying technology for such multiomics studies. This review article highlights the outstanding performance characteristics that makes graphene field effect transistor an attractive sensing platform for a wide variety of analytes important to system biology. In addition to many studies demonstrating the biosensing capabilities of graphene field effect transistors, they are uniquely suited to address the challenges of multiomics studies by providing an integrative multiplex platform for large scale manufacturing using the well-established processes of semiconductor industry. Furthermore, the resulting digital data is readily analyzable by machine learning to derive actionable biological insight to address the challenge of data compatibility for multiomics studies. A critical stage of systems biology will be democratizing multiomics study, and the graphene field effect transistor is uniquely positioned to serve as an accessible multiomics platform.

An electrochemical biosensor based on a graphene oxide modified pencil graphite electrode for direct detection and discrimination of double-stranded DNA sequences

The ability to directly recognize double-stranded DNA (ds-DNA) is a major challenge in disease diagnosis and gene therapy because DNA is naturally double-stranded. Herein, a novel electrochemical biosensor for the sequence-specific recognition of ds-DNA using a peptide nucleic acid (PNA) probe and graphene oxide (GO) modified pencil graphite electrode is reported and applied for the direct detection of the desired sequence in plasmid samples. For this purpose, GO was assembled onto the pencil graphite electrode surface (GO/PGE) by a simple casting method and applied for PNA probe immobilization (PNA-GO/PGE). Upon addition of ds-DNA, the interaction of the PNA probe with ds-DNA induces probe detachment from the electrode surface which results in a guanine oxidation signal decrease. Under optimized conditions, the guanine oxidation signal decreased linearly with the ds-DNA concentration increasing in the range from 30 pM to 10 nM, with a detection limit of 1.3 pM. Moreover, the proposed biosensor was applied for the sensitive and selective detection of double-stranded target DNA in plasmid samples. This proposed method could be used as a platform for direct detection of various sequences in double-stranded genomic DNA.

Three-dimensional super-resolution fluorescence imaging of DNA

Recent advances in fluorescence super-resolution microscopy are providing important insights into details of cellular structures. To acquire three dimensional (3D) super-resolution images of DNA, we combined binding activated localization microscopy (BALM) using fluorescent double-stranded DNA intercalators and optical astigmatism. We quantitatively establish the advantage of bis- over mono-intercalators before demonstrating the approach by visualizing single DNA molecules stretched between microspheres at various heights. Finally, the approach is applied to the more complex environment of intact and damaged metaphase chromosomes, unravelling their structural features.

The Highest Chromosome Number and First Chromosome Fluorescent in situ Hybridization in the velvet worms of the family Peripatidae

The diversity of Onychophora is poorly studied, despite there being nearly 200 described species divided in two families: Peripatidae and Peripatopsidae. Peripatid velvet worms are found mainly in the Neotropical region. The low morphological diversity in Peripatidae is an obstacle to determining its taxonomy, and chromosomal analyses can help clarify this. The aim of this work was to chromosomally analyze one species of Epiperipatus from Mato Grosso do Sul, Brazil. Conventional staining and telomeric fluorescent in situ hybridization (FISH) were performed with the gonads of three males of Epiperipatus sp. The specimens showed 2n♂ = 73, the largest diploid number found in Onychophora to date, with the majority of chromosomes acro/telocentrics and the largest element submetacentric. The FISH marked the telomeric region of all elements and revealed one Interstitial Telomeric Site (ITS) on the proximal region of the long arm large submetacentric chromosome. The absence of male meiosis and female cell division in the analyzed specimens prevented us from determining whether the unpaired large submetacentric is a sex chromosome, which could lead to the description of a rare sex chromosome system (SCS) in Onychophora, or a case of fusion between autosomes. In either case, the presence of ITS is a clear indication of chromosomal fusion.

Cellular and genomic approaches for exploring structural chromosomal rearrangements

Human chromosomes are arranged in a linear and conserved sequence order that undergoes further spatial folding within the three-dimensional space of the nucleus. Although structural variations in this organization are an important source of natural genetic diversity, cytogenetic aberrations can also underlie a number of human diseases and disorders. Approaches for studying chromosome structure began half a century ago with karyotyping of Giemsa-banded chromosomes and has now evolved to encompass high-resolution fluorescence microscopy, reporter-based assays, and next-generation DNA sequencing technologies. Here, we provide a general overview of experimental methods at different resolution and sensitivity scales and discuss how they can be complemented to provide synergistic insight into the study of human chromosome structural rearrangements. These approaches range from kilobase-level resolution DNA fluorescence in situ hybridization (FISH)-based imaging approaches of individual cells to genome-wide sequencing strategies that can capture nucleotide-level information from diverse sample types. Technological advances coupled to the combinatorial use of multiple methods have resulted in the discovery of new rearrangement classes along with mechanistic insights into the processes that drive structural alterations in the human genome.

RABiT-II-DCA: A Fully-automated Dicentric Chromosome Assay in Multiwell Plates

We developed a fully-automated dicentric chromosome assay (DCA) in multiwell plates. All operations, from sample loading to chromosome scoring, are performed, without human intervention, by the second-generation Rapid Automated Biodosimetry Tool II (RABiT-II) robotic system, a plate imager and custom software, FluorQuantDic. The system requires small volumes of blood (30 µl per individual) to determine radiation dose received as a result of a radiation accident or terrorist attack. To visualize dicentrics in multiwell plates, we implemented a non-classical protocol for centromere FISH staining at 37°C. The RABiT-II performs rapid analysis of chromosomes after extracting them from metaphase cells. With the use of multiwell plates, many samples can be screened at the same time. Thus, the RABiT-II DCA provides an advantage during triage when risk-based stratification and medical management are required for a large population exposed to unknown levels of ionizing radiation.

Karyotypes of three species of Hyperophora Brunner von Wattenwyl, 1878 (Tettigoniidae, Phaneropterinae) enable morphologically similar species to be distinguished

Phaneropterinae is the largest subfamily of Tettigoniidae, distributed across the globe. There are few cytogenetic studies regarding this group, as in the case of the genus group Aniarae, which represents only two karyotyped species. The current study aims to analyze cytogenetically three species of Hyperophora Brunner von Wattenwyl, 1878 from Brazil. The male diploid number of Hyperophoraminor Brunner von Wattenwyl, 1891 and Hyperophoramajor Brunner von Wattenwyl, 1878 is 2n♂= 31, whereas Hyperophorabrasiliensis Brunner von Wattenwyl, 1878 has shown 2n♂= 29. These three species possess an X0 sex chromosome system and telo/acrocentric chromosome morphology. The only species found in the Pantanal biome, H.brasiliensis, can be chromosomally distinguished from the Cerrado biome species H.major and H.minor, due to the difference in chromosome number (2n♂= 29 and 2n♂= 31, respectively).

Developing novel methods to image and visualize 3D genomes

To investigate three-dimensional (3D) genome organization in prokaryotic and eukaryotic cells, three main strategies are employed, namely nuclear proximity ligation-based methods, imaging tools (such as fluorescence in situ hybridization (FISH) and its derivatives), and computational/visualization methods. Proximity ligation-based methods are based on digestion and re-ligation of physically proximal cross-linked chromatin fragments accompanied by massively parallel DNA sequencing to measure the relative spatial proximity between genomic loci. Imaging tools enable direct visualization and quantification of spatial distances between genomic loci, and advanced implementation of (super-resolution) microscopy helps to significantly improve the resolution of images. Computational methods are used to map global 3D genome structures at various scales driven by experimental data, and visualization methods are used to visualize genome 3D structures in virtual 3D space-based on algorithms. In this review, we focus on the introduction of novel imaging and visualization methods to study 3D genomes. First, we introduce the progress made recently in 3D genome imaging in both fixed cell and live cells based on long-probe labeling, short-probe labeling, RNA FISH, and the CRISPR system. As the fluorescence-capturing capability of a particular microscope is very important for the sensitivity of bioimaging experiments, we also introduce two novel super-resolution microscopy methods, SDOM and low-power super-resolution STED, which have potential for time-lapse super-resolution live-cell imaging of chromatin. Finally, we review some software tools developed recently to visualize proximity ligation-based data. The imaging and visualization methods are complementary to each other, and all three strategies are not mutually exclusive. These methods provide powerful tools to explore the mechanisms of gene regulation and transcription in cell nuclei.

Bucrates lanista Rehn 1918 (Tettigoniidae: Conocephalinae): The First Record from the Brazilian Pantanal, the First Description of the Male, the First Karyotypic Report for the Genus, and the First Telomeric Hybridization of the Subfamily

Bucrates lanista, the most southerly distributed species in the genus Bucrates Burmeister, was originally described from Brazil based on a female collected in the state of Rio Grande do Sul, but the species has not been recorded since 1918. In this work, we report that B. lanista inhabits the Pantanal Wetland in the state of Mato Grosso do Sul and, for the first time, describe the male. Individuals of B. lanista are gregarious and present a brown/green color dimorphism; this behavior and color variation are also observed in species of closely related genera. Individuals from the Pantanal vary slightly from those of Rio Grande do Sul. The karyotype was determined to be 2n♂ = 21 = 20 + X0 and 2n♀ = 22 = 20 + XX. The X chromosome is metacentric and the largest of the complement, and all of the autosomes are submetacentrics. All chromosomes solely present telomeric (TTAGG)n repeats at their ends, and some chromosomes present positive and negative DAPI bands.