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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.

Abstract 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.

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.

W ciągu ostatnich dekad przychodzące bezpośrednie inwestycje zagraniczne (BIZ) stały się istotnym elementem polskiej gospodarki. Ich wpływ na działające w Polsce przedsiębiorstwa został przeanalizowany pod wieloma względami, jednak stosunkowo niewiele uwagi poświęcono związkowi pomiędzy BIZ a wydatkami na badania i rozwój (B+R). Badania dokonywane w przeszłości nad tym zjawiskiem w krajach rozwijających się pokazały, że przedsiębiorstwa będące celem BIZ są bardziej konkurencyjne od innych działających na danym rynku i doprowadzić mogą do ich upadku i zmniejszenia się całkowitego wolumenu B+R w gospodarce. Istnieją badania, które wskazują na prawdziwość tej zależności w Polsce po transformacji rynkowej, aczkolwiek wydaje się interesujące zbadanie, czy zjawisko to ma dalej miejsce na trzydzieści lat po wprowadzeniu wolnego rynku. Celem artykułu jest odpowiedź na pytanie, czy w latach 2010–2016 wśród działających w Polsce przedsiębiorstw istniał pozytywny czy negatywny związek pomiędzy przychodzącymi BIZ a wydatkami na B+R. Po przeanalizowaniu danych statystycznych dostępnych m.in. w NBP, GUS i Banku Danych Lokalnych oraz stworzeniu modelu ekonometrycznego autorzy dowodzą, że wraz ze wzrostem przychodzących BIZ wzrasta również całkowity wolumen wydatków na B+R. Powodem odwrócenia się wcześniej opisanej zależności może być zmiana poziomu konkurencyjności polskich przedsiębiorstw oraz ich zdolności do absorpcji innowacji, jakie dokonały się w czasie od poprzedniego przeprowadzenia tego rodzaju badania.

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.

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).