From Sanger to genome sequencing - an overview of DNA sequencing technologies / Od Sangera do sekwencjonowania genomów ­ przeglad technologii sekwencjonowania DNA.

There is no technique that would make a greater contribution to the development of genetics, molecular biology and medicine than DNA sequencing. For many years, the method based on enzymatic DNA synthesis developed by Frederic Sanger was the gold standard in this area. At the end of the 20th century, there was a dynamic development of next-generation sequencing (NGS) technologies, which ended the era of single gene analysis and initiated the era of genome sequencing. Despite fierce competition, one NGS technology has practically completely dominated the global market. In the article, we present our own review of DNA sequencing methods, starting from the Sanger method to high-throughput second- and third-generation sequencing technologies, with particular emphasis on those that have achieved commercial success. We present their short history, principles of operation, technical possibilities, applications and limitations. In the summary, we reveal how much human genome sequencing costs at the current stage of the genomic revolution and outline the prospects for further development of genomics.

Differences in the intraspecies copy number variation of Arabidopsis thaliana conserved and nonconserved miRNA genes.

MicroRNAs (miRNAs) regulate gene expression by RNA interference mechanism. In plants, miRNA genes (MIRs) which are grouped into conserved families, i.e. they are present among the different plant taxa, are involved in the regulation of many developmental and physiological processes. The roles of the nonconserved MIRs-which are MIRs restricted to one plant family, genus, or even species-are less recognized; however, many of them participate in the responses to biotic and abiotic stresses. Both over- and underproduction of miRNAs may influence various biological processes. Consequently, maintaining intracellular miRNA homeostasis seems to be crucial for the organism. Deletions and duplications in the genomic sequence may alter gene dosage and/or activity. We evaluated the extent of copy number variations (CNVs) among Arabidopsis thaliana (Arabidopsis) MIRs in over 1000 natural accessions, using population-based analysis of the short-read sequencing data. We showed that the conserved MIRs were unlikely to display CNVs and their deletions were extremely rare, whereas nonconserved MIRs presented moderate variation. Transposon-derived MIRs displayed exceptionally high diversity. Conversely, MIRs involved in the epigenetic control of transposons reactivated during development were mostly invariable. MIR overlap with the protein-coding genes also limited their variability. At the expression level, a higher rate of nonvariable, nonconserved miRNAs was detectable in Col-0 leaves, inflorescence, and siliques compared to nonconserved variable miRNAs, although the expression of both groups was much lower than that of the conserved MIRs. Our data indicate that CNV rate of Arabidopsis MIRs is related with their age, function, and genomic localization.

AthCNV: A Map of DNA Copy Number Variations in the Arabidopsis Genome.

Copy number variations (CNVs) greatly contribute to intraspecies genetic polymorphism and phenotypic diversity. Recent analyses of sequencing data for >1000 Arabidopsis (Arabidopsis thaliana) accessions focused on small variations and did not include CNVs. Here, we performed genome-wide analysis and identified large indels (50 to 499 bp) and CNVs (500 bp and larger) in these accessions. The CNVs fully overlap with 18.3% of protein-coding genes, with enrichment for evolutionarily young genes and genes involved in stress and defense. By combining analysis of both genes and transposable elements (TEs) affected by CNVs, we revealed that the variation statuses of genes and TEs are tightly linked and jointly contribute to the unequal distribution of these elements in the genome. We also determined the gene copy numbers in a set of 1060 accessions and experimentally validated the accuracy of our predictions by multiplex ligation-dependent probe amplification assays. We then successfully used the CNVs as markers to analyze population structure and migration patterns. Finally, we examined the impact of gene dosage variation triggered by a CNV spanning the SEC10 gene on SEC10 expression at both the transcript and protein levels. The catalog of CNVs, CNV-overlapping genes, and their genotypes in a top model dicot will stimulate the exploration of the genetic basis of phenotypic variation.

Genome-scale de novo assembly using ALGA.

MOTIVATION: There are very few methods for de novo genome assembly based on the overlap graph approach. It is considered as giving more exact results than the so-called de Bruijn graph approach but in much greater time and of much higher memory usage. It is not uncommon that assembly methods involving the overlap graph model are not able to successfully compute greater datasets, mainly due to memory limitation of a computer. This was the reason for developing in last decades mainly de Bruijn-based assembly methods, fast and fairly accurate. However, the latter methods can fail for longer or more repetitive genomes, as they decompose reads to shorter fragments and lose a part of information. An efficient assembler for processing big datasets and using the overlap graph model is still looked out. RESULTS: We propose a new genome-scale de novo assembler based on the overlap graph approach, designed for short-read sequencing data. The method, ALGA, incorporates several new ideas resulting in more exact contigs produced in short time. Among these ideas, we have creation of a sparse but quite informative graph, reduction of the graph including a procedure referring to the problem of minimum spanning tree of a local subgraph, and graph traversal connected with simultaneous analysis of contigs stored so far. What is rare in genome assembly, the algorithm is almost parameter-free, with only one optional parameter to be set by a user. ALGA was compared with nine state-of-the-art assemblers in tests on genome-scale sequencing data obtained from real experiments on six organisms, differing in size, coverage, GC content and repetition rate. ALGA produced best results in the sense of overall quality of genome reconstruction, understood as a good balance between genome coverage, accuracy and length of resulting sequences. The algorithm is one of tools involved in processing data in currently realized national project Genomic Map of Poland. AVAILABILITY AND IMPLEMENTATION: ALGA is available at http://alga.put.poznan.pl. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Morphological characterization and electronic properties of pristine and oxygen-exposed graphene nanoribbons on Ag(110).

Graphene nanoribbons (GNRs) are at the frontier of research on graphene materials since the 1D quantum confinement of electrons allows for the opening of an energy gap. GNRs of uniform and well-defined size and shape can be grown using the bottom-up approach, i.e. by surface assisted polymerization of aromatic hydrocarbons. Since the electronic properties of the nanostructures depend on their width and on their edge states, by careful choice of the precursor molecule it is possible to design GNRs with tailored properties. A key issue for their application in nanoelectronics is their stability under operative conditions. Here, we characterize pristine and oxygen-exposed 1.0 nm wide GNRs with a well-defined mixed edge-site sequence (two zig-zag and one armchair) synthesized on Ag(110) from 1,6-dibromo-pyrene precursors. The energy gap and the presence of quantum confined states are investigated by scanning tunneling spectroscopy. The effect of oxygen exposure under ultra-high vacuum conditions is inferred from scanning tunneling microscopy images and photoemission spectra. Our results demonstrate that oxygen exposure deeply affects the overall system by interacting both with the nanoribbons and with the substrate; this factor must be considered for supported GNRs under operative conditions.

NPM1 alternative transcripts are upregulated in acute myeloid and lymphoblastic leukemia and their expression level affects patient outcome.

BACKGROUND: Expression of the NPM1 gene, encoding nucleophosmin, is upregulated in cancers. Although more than ten NPM1 transcripts are known, the reports were usually limited to one predominant transcript. In leukemia, the NPM1 expression has not been widely studied so far. In acute myeloid leukemia (AML), the mutational status of the gene seems to play a pivotal role in carcinogenesis. Therefore, the aim of the study was to quantify alternative NPM1 transcripts in two types of acute leukemia, AML and ALL (acute lymphoblastic leukemia). METHODS: Using droplet digital PCR, we analyzed the levels of three protein-coding NPM1 transcripts in 66 samples collected from AML and ALL patients and 16 control samples. Using RNA-seq, we detected 8 additional NPM1 transcripts, including non-coding splice variants with retained introns. For data analysis, Welch two sample t-test, Pearson's correlation and Kaplan-Meier analysis were applied. RESULTS: The levels of the particular NPM1 transcripts were significantly different but highly correlated with each other in both leukemia and control samples. Transcript NPM1.1, encoding the longest protein (294 aa), had the highest level of accumulation and was one of the most abundant transcripts in the cell. Comparing to NPM1.1, the levels of the NPM1.2 and NPM1.3 transcripts, encoding a 265-aa and 259-aa proteins, were 30 and 3 times lower, respectively. All three NPM1 transcripts were proportionally upregulated in both types of leukemia compared to control samples. In AML, the levels of NPM1 transcripts decreased in complete remission and increased again with relapse of the disease. Low levels of NPM1.1 and NPM1.3 were associated with better prognosis. The contribution of non-coding transcripts to the total level of NPM1 gene seemed to be marginal, except for one short 5-end transcript accumulated at high levels in AML and control cells. Aberrant proportions of particular NPM1 splice variants could be linked to abnormal expression of genes encoding alternative splicing factors. CONCLUSIONS: The levels of the studied NPM1 transcripts were different but highly correlated with each other. Their upregulation in AML and ALL, decrease after therapy and association with patient outcome suggests the involvement of elevated NPM1 expression in the acute leukemia pathogenesis.

Directional growth of iron oxide nanowires on a vicinal copper surface.

Single-crystal magnetic nanostructures with well-defined shapes attract lots of interest due to their potential applications in magnetic and spintronic devices. However, development of methods allowing controlling their mutual crystallographic and geometric orientation constitutes a significant scientific challenge. One of the routes for obtaining such structures is to grow the materials epitaxially on naturally-structured supports, such as vicinal surfaces of single-crystal substrates. Iron oxides are among the most well-known magnetic materials which, depending on the phase, may exhibit ferro/ferri- or antiferromagnetic ordering. We have grown iron oxide nanowires on a Cu(410) single-crystal substrate faceted with molecular oxygen. Scanning tunneling microscopy and low energy electron diffraction revealed that the oxide grows in the [111] direction, along the step edges of the substrate and rotated by ±15° with respect to the [010] direction of copper atomic terraces (so that the the growing elongated structures are orientated parallel to each other). Notably, x-ray photoelectron spectroscopy confirmed that the nanowires represent the ferrimagneticγ-Fe2O3(maghemite) iron oxide phase, while micromagnetic simulations indicated that the wires are single-domain, with the easy magnetization axis orientated in-plane and along the long axis of the wire.

Augmentation Therapies as Treatments for Coexisting Somatic Problems in Schizophrenia-A Systematic Review.

The aim of this review is to appraise the data from available randomized clinical trials (RCT) regarding the possible combinations of neuroleptic and non-antipsychotic treatment which could enhance antipsychotic therapy efficacy whilst simultaneously addressing somatic symptoms in individuals with schizophrenia. A systematic search of the PubMed database up to February 2022 was conducted. Inclusion criteria: randomized controlled trials using augmentation therapy in chronic schizophrenia in adults, written in English, and only studies with psychometric assessments of schizophrenia were incorporated. Exclusion criteria: non-clinical, first episode of schizophrenia, patients on medication other than antipsychotics augmented, and not adjunctive therapy. Overall, 37 studies of 1931 patients with schizophrenia who received a combination of antipsychotic medication with other drugs were selected. A statistically significant reduction of negative and positive symptoms of schizophrenia, measured with the PANSS scale, when using a combination of antipsychotic treatment along with aspirin, simvastatin, N-acetylcysteine, or pioglitazone was found. A combination of antipsychotic medication with aspirin, simvastatin, N-acetylcysteine, or pioglitazone seems to be effective in the reduction of symptoms of schizophrenia in adults, but long-term studies are required to confirm this effect.

Analysis of Arabidopsis non-reference accessions reveals high diversity of metabolic gene clusters and discovers new candidate cluster members.

Metabolic gene clusters (MGCs) are groups of genes involved in a common biosynthetic pathway. They are frequently formed in dynamic chromosomal regions, which may lead to intraspecies variation and cause phenotypic diversity. We examined copy number variations (CNVs) in four Arabidopsis thaliana MGCs in over one thousand accessions with experimental and bioinformatic approaches. Tirucalladienol and marneral gene clusters showed little variation, and the latter was fixed in the population. Thalianol and especially arabidiol/baruol gene clusters displayed substantial diversity. The compact version of the thalianol gene cluster was predominant and more conserved than the noncontiguous version. In the arabidiol/baruol cluster, we found a large genomic insertion containing divergent duplicates of the CYP705A2 and BARS1 genes. The BARS1 paralog, which we named BARS2, encoded a novel oxidosqualene synthase. The expression of the entire arabidiol/baruol gene cluster was altered in the accessions with the duplication. Moreover, they presented different root growth dynamics and were associated with warmer climates compared to the reference-like accessions. In the entire genome, paired genes encoding terpene synthases and cytochrome P450 oxidases were more variable than their nonpaired counterparts. Our study highlights the role of dynamically evolving MGCs in plant adaptation and phenotypic diversity.

GeVaDSs - decision support system for novel Genetic Vaccine development process.

BACKGROUND: The lack of a uniform way for qualitative and quantitative evaluation of vaccine candidates under development led us to set up a standardized scheme for vaccine efficacy and safety evaluation. We developed and implemented molecular and immunology methods, and designed support tools for immunization data storage and analyses. Such collection can create a unique opportunity for immunologists to analyse data delivered from their laboratories. RESULTS: We designed and implemented GeVaDSs (Genetic Vaccine Decision Support system) an interactive system for efficient storage, integration, retrieval and representation of data. Moreover, GeVaDSs allows for relevant association and interpretation of data, and thus for knowledge-based generation of testable hypotheses of vaccine responses. CONCLUSIONS: GeVaDSs has been tested by several laboratories in Europe, and proved its usefulness in vaccine analysis. Case study of its application is presented in the additional files. The system is available at: http://gevads.cs.put.poznan.pl/preview/(login: viewer, password: password).

Iron Nitride Thin Films: Growth, Structure, and Properties.

The current state-of-the-art in the growth, structure, and physicochemical properties of iron nitride thin films is presented. First, different iron nitride phases are introduced based on their crystallographic structure and the Fe-N phase diagram. Second, preparation methods for thin iron nitride films are described. Next, the structure, electronic, and magnetic properties of the films are discussed. Finally, potential applications of iron nitride films, as well as the challenges to be faced in the field, are highlighted. This Review constitutes a starting point for anyone who would like to conduct research on these fascinating materials, the scientific and technological potential of which has not been fully explored to date.

Protein alignment algorithms with an efficient backtracking routine on multiple GPUs.

BACKGROUND: Pairwise sequence alignment methods are widely used in biological research. The increasing number of sequences is perceived as one of the upcoming challenges for sequence alignment methods in the nearest future. To overcome this challenge several GPU (Graphics Processing Unit) computing approaches have been proposed lately. These solutions show a great potential of a GPU platform but in most cases address the problem of sequence database scanning and computing only the alignment score whereas the alignment itself is omitted. Thus, the need arose to implement the global and semiglobal Needleman-Wunsch, and Smith-Waterman algorithms with a backtracking procedure which is needed to construct the alignment. RESULTS: In this paper we present the solution that performs the alignment of every given sequence pair, which is a required step for progressive multiple sequence alignment methods, as well as for DNA recognition at the DNA assembly stage. Performed tests show that the implementation, with performance up to 6.3 GCUPS on a single GPU for affine gap penalties, is very efficient in comparison to other CPU and GPU-based solutions. Moreover, multiple GPUs support with load balancing makes the application very scalable. CONCLUSIONS: The article shows that the backtracking procedure of the sequence alignment algorithms may be designed to fit in with the GPU architecture. Therefore, our algorithm, apart from scores, is able to compute pairwise alignments. This opens a wide range of new possibilities, allowing other methods from the area of molecular biology to take advantage of the new computational architecture. Performed tests show that the efficiency of the implementation is excellent. Moreover, the speed of our GPU-based algorithms can be almost linearly increased when using more than one graphics card.

Transcript-Level Dysregulation of BCL2 Family Genes in Acute Myeloblastic Leukemia.

The expression of apoptosis-related BCL2 family genes, fine-tuned in normal cells, is dysregulated in many neoplasms. In acute myeloid leukemia (AML), this problem has not been studied comprehensively. To address this issue, RNA-seq data were used to analyze the expression of 26 BCL2 family members in 27 AML FAB M1 and M2 patients, divided into subgroups differently responding to chemotherapy. A correlation analysis, analysis of variance, and Kaplan-Meier analysis were applied to associate the expression of particular genes with other gene expression, clinical features, and the presence of mutations detected by exome sequencing. The expression of BCL2 family genes was dysregulated in AML, as compared to healthy controls. An upregulation of anti-apoptotic and downregulation of pro-apoptotic genes was observed, though only a decrease in BMF, BNIP1, and HRK was statistically significant. In a group of patients resistant to chemotherapy, overexpression of BCL2L1 was manifested. In agreement with the literature data, our results reveal that BCL2L1 is one of the key players in apoptosis regulation in different types of tumors. An exome sequencing data analysis indicates that BCL2 family genes are not mutated in AML, but their expression is correlated with the mutational status of other genes, including those recurrently mutated in AML and splicing-related. High levels of some BCL2 family members, in particular BIK and BCL2L13, were associated with poor outcome.

Translational and structural analysis of the shortest legume ENOD40 gene in Lupinus luteus.

Two early nodulin 40 (enod40) genes, ENOD40-1, the shortest legume ENOD40 gene, and ENOD40-2, were isolated from Lupinus luteus, a legume with indeterminate nodules. Both genes were expressed at similar levels during symbiosis with nitrogen-fixing bacteria. ENOD40 phylogeny clustered the L. luteus genes with legumes forming determinate nodules and revealed peptide similarities. The ENOD40-1 small ORF A fused to a reporter gene was efficiently expressed in plant cells, indicating that the start codon is recognized for translation. The ENOD40-1 RNA structure predicted based on Pb(II)-induced cleavage and modeling revealed four structurally conserved domains, an absence of domain 4 characteristic for legumes of indeterminate nodules, and interactions between the conserved region I and a region located upstream of domain 6. Domain 2 contains Mg(II) ion binding sites essential for organizing RNA secondary structure. The differences between L. luteus and Glycine max ENOD40 RNA models suggest the possibility of a switch between two structural states of ENOD40 transcript.

Altered Levels of Proteins and Phosphoproteins, in the Absence of Early Causative Transcriptional Changes, Shape the Molecular Pathogenesis in the Brain of Young Presymptomatic Ki91 SCA3/MJD Mouse.

Spinocerebellar ataxia type 3 (SCA3/MJD) is a polyQ neurodegenerative disease where the presymptomatic phase of pathogenesis is unknown. Therefore, we investigated the molecular network of transcriptomic and proteomic triggers in young presymptomatic SCA3/MJD brain from Ki91 knock-in mouse. We found that transcriptional dysregulations resulting from mutant ataxin-3 are not occurring in young Ki91 mice, while old Ki91 mice and also postmitotic patient SCA3 neurons demonstrate the late transcriptomic changes. Unlike the lack of early mRNA changes, we have identified numerous early changes of total proteins and phosphoproteins in 2-month-old Ki91 mouse cortex and cerebellum. We discovered the network of processes in presymptomatic SCA3 with three main groups of disturbed processes comprising altered proteins: (I) modulation of protein levels and DNA damage (Pabpc1, Ddb1, Nedd8), (II) formation of neuronal cellular structures (Tubb3, Nefh, p-Tau), and (III) neuronal function affected by processes following perturbed cytoskeletal formation (Mt-Co3, Stx1b, p-Syn1). Phosphoproteins downregulate in the young Ki91 mouse brain and their phosphosites are associated with kinases that interact with ATXN3 such as casein kinase, Camk2, and kinases controlled by another Atxn3 interactor p21 such as Gsk3, Pka, and Cdk kinases. We conclude that the onset of SCA3 pathology occurs without altered transcript level and is characterized by changed levels of proteins responsible for termination of translation, DNA damage, spliceosome, and protein phosphorylation. This disturbs global cellular processes such as cytoskeleton and transport of vesicles and mitochondria along axons causing energy deficit and neurodegeneration also manifesting in an altered level of transcripts at later ages.

Identification of Altered Developmental Pathways in Human Juvenile HD iPSC With 71Q and 109Q Using Transcriptome Profiling.

In Huntington disease (HD) subtle symptoms in patients may occur years or even decades prior to diagnosis. HD changes at a molecular level may begin as early as in cells that are non-lineage committed such as stem cells or HD patients induced pluripotent stem cells (iPSCs) offering opportunity to enhance the understanding of the HD pathogenesis. In addition, juvenile HD non-linage committed cells were previously not directly investigated in detail by RNA-seq. In the present manuscript, we define the early HD and juvenile HD transcriptional alterations using 6 human HD iPS cell lines from two patients, one with 71 CAGs and one with 109 CAG repeats. We identified 107 (6 HD lines), 198 (3 HD71Q lines) and 217 (3 HD109Q lines) significantly dysregulated mRNAs in each comparison group. The analyses showed that many of dysregulated transcripts in HD109Q iPSC lines are involved in DNA damage response and apoptosis, such as CCND1, CDKN1A, TP53, BAX, TNFRSF10B, TNFRSF10C, TNFRSF10D, DDB2, PLCB1, PRKCQ, HSH2D, ZMAT3, PLK2, and RPS27L. Most of them were identified as downregulated and their proteins are direct interactors with TP53. HTT probably alters the level of several TP53 interactors influencing apoptosis. This may lead to accumulation of an excessive number of progenitor cells and potential disruption of cell differentiation and production of mature neurons. In addition, HTT effects on cell polarization also demonstrated in the analysis may result in a generation of incorrect progenitors. Bioinformatics analysis of transcripts dysregulated in HD71Q iPSC lines showed that several of them act as transcription regulators during the early multicellular stages of development, such as ZFP57, PIWIL2, HIST1H3C, and HIST1H2BB. Significant upregulation of most of these transcripts may lead to a global increase in expression level of genes involved in pathways critical for embryogenesis and early neural development. In addition, MS analysis revealed altered levels of TP53 and ZFP30 proteins reflecting the functional significance of dysregulated mRNA levels of these proteins which were associated with apoptosis and DNA binding. Our finding very well corresponds to the fact that mutation in the HTT gene may cause precocious neurogenesis and identifies pathways likely disrupted during development.

GRASShopPER-An algorithm for de novo assembly based on GPU alignments.

Next generation sequencers produce billions of short DNA sequences in a massively parallel manner, which causes a great computational challenge in accurately reconstructing a genome sequence de novo using these short sequences. Here, we propose the GRASShopPER assembler, which follows an approach of overlap-layout-consensus. It uses an efficient GPU implementation for the sequence alignment during the graph construction stage and a greedy hyper-heuristic algorithm at the fork detection stage. A two-part fork detection method allows us to identify repeated fragments of a genome and to reconstruct them without misassemblies. The assemblies of data sets of bacteria Candidatus Microthrix, nematode Caenorhabditis elegans, and human chromosome 14 were evaluated with the golden standard tool QUAST. In comparison with other assemblers, GRASShopPER provided contigs that covered the largest part of the genomes and, at the same time, kept good values of other metrics, e.g., NG50 and misassembly rate.

Symmetry-Induced Structuring of Ultrathin FeO and Fe3O4 Films on Pt(111) and Ru(0001).

Iron oxide films epitaxially grown on close-packed metal single crystal substrates exhibit nearly-perfect structural order, high catalytic activity (FeO) and room-temperature magnetism (Fe3O4). However, the morphology of the films, especially in the ultrathin regime, can be significantly influenced by the crystalline structure of the used support. This work reports an ultra-high vacuum (UHV) low energy electron/synchrotron light-based X-ray photoemission electron microscopy (LEEM/XPEEM) and electron diffraction (µLEED) study of the growth of FeO and Fe3O4 on two closed-packed metal single crystal surfaces: Pt(111) and Ru(0001). The results reveal the influence of the mutual orientation of adjacent substrate terraces on the morphology of iron oxide films epitaxially grown on top of them. On fcc Pt(111), which has the same mutual orientation of adjacent monoatomic terraces, FeO(111) grows with the same in-plane orientation on all substrate terraces. For Fe3O4(111), one or two orientations are observed depending on the growth conditions. On hcp Ru(0001), the adjacent terraces of which are 'rotated' by 180° with respect to each other, the in-plane orientation of initial FeO(111) and Fe3O4(111) crystallites is determined by the orientation of the substrate terrace on which they nucleated. The adaptation of three-fold symmetric iron oxides to three-fold symmetric substrate terraces leads to natural structuring of iron oxide films, i.e., the formation of patch-like magnetite layers on Pt(111) and stripe-like FeO and Fe3O4 structures on Ru(0001).