Secondary Structure of Chloroplast mRNAs In Vivo and In Vitro

mRNA secondary structure can influence gene expression, e.g., by influencing translation initiation. The probing of in vivo mRNA secondary structures is therefore necessary to understand what determines the efficiency and regulation of gene expression. Here, in vivo mRNA secondary structure was analyzed using dimethyl sulfate (DMS)-MaPseq and compared to in vitro-folded RNA. We used an approach to analyze specific, full-length transcripts. To test this approach, we chose low, medium, and high abundant mRNAs. We included both monocistronic and multicistronic transcripts. Because of the slightly alkaline pH of the chloroplast stroma, we could probe all four nucleotides with DMS. The structural information gained was evaluated using the known structure of the plastid 16S rRNA. This demonstrated that the results obtained for adenosines and cytidines were more reliable than for guanosines and uridines. The majority of mRNAs analyzed were less structured in vivo than in vitro. The in vivo secondary structure of the translation initiation region of most tested genes appears to be optimized for high translation efficiency

Using genic sequence capture in combination with a syntenic pseudo genome to map a deletion mutant in a wheat species

Mapping‐by‐sequencing analyses have largely required a complete reference sequence and employed whole genome re‐sequencing. In species such as wheat, no finished genome reference sequence is available. Additionally, because of its large genome size (17 Gb), re‐sequencing at sufficient depth of coverage is not practical. Here, we extend the utility of mapping by sequencing, developing a bespoke pipeline and algorithm to map an early‐flowering locus in einkorn wheat (Triticum monococcum L.) that is closely related to the bread wheat genome A progenitor. We have developed a genomic enrichment approach using the gene‐rich regions of hexaploid bread wheat to design a 110‐Mbp NimbleGen SeqCap EZ in solution capture probe set, representing the majority of genes in wheat. Here, we use the capture probe set to enrich and sequence an F2 mapping population of the mutant. The mutant locus was identified in T. monococcum, which lacks a complete genome reference sequence, by mapping the enriched data set onto pseudo‐chromosomes derived from the capture probe target sequence, with a long‐range order of genes based on synteny of wheat with Brachypodium distachyon. Using this approach we are able to map the region and identify a set of deleted genes within the interval

The Heider balance - a continuous approach

The Heider balance (HB) is investigated in a fully connected graph of $N$ nodes. The links are described by a real symmetric array r(i,j), i,j=1,...,N. In a social group, nodes represent group members and links represent relations between them, positive (friendly) or negative (hostile). At the balanced state, r(i,j)r(j,k)r(k,i)>0 for all the triads (i,j,k). As follows from the structure theorem of Cartwright and Harary, at this state the group is divided into two subgroups, with friendly internal relations and hostile relations between the subgroups. Here the system dynamics is proposed to be determined by a set of differential equations. The form of equations guarantees that once HB is reached, it persists. Also, for N=3 the dynamics reproduces properly the tendency of the system to the balanced state. The equations are solved numerically. Initially, r(i,j) are random numbers distributed around zero with a symmetric uniform distribution of unit width. Calculations up to N=500 show that HB is always reached. Time to get the balanced state varies with the system size N as N^{-1/2}. The spectrum of relations, initially narrow, gets very wide near HB. This means that the relations are strongly polarized. In our calculations, the relations are limited to a given range around zero. With this limitation, our results can be helpful in an interpretation of somestatistical data.Comment: 9 pages, 4 figures. Int. J. Mod. Phys. C (2005), in prin

Selective sweeps identification in distinct groups of cultivated rye (Secale cereale L.) germplasm provides potential candidate genes for crop improvement

Background: During domestication and subsequent improvement plants were subjected to intensive positive selection for desirable traits. Identification of selection targets is important with respect to the future targeted broadening of diversity in breeding programmes. Rye (Secale cereale L.) is a cereal that is closely related to wheat, and it is an important crop in Central, Eastern and Northern Europe. The aim of the study was (i) to identify diverse groups of rye accessions based on high-density, genome-wide analysis of genetic diversity within a set of 478 rye accessions, covering a full spectrum of diversity within the genus, from wild accessions to inbred lines used in hybrid breeding, and (ii) to identify selective sweeps in the established groups of cultivated rye germplasm and putative candidate genes targeted by selection.Results: Population structure and genetic diversity analyses based on high-quality SNP (DArTseq) markers revealed the presence of three complexes in the Secale genus: S. sylvestre, S. strictum and S. cereale/vavilovii, a relatively narrow diversity of S. sylvestre, very high diversity of S. strictum, and signatures of strong positive selection in S. vavilovii. Within cultivated ryes we detected the presence of genetic clusters and the influence of improvement status on the clustering. Rye landraces represent a reservoir of variation for breeding, and especially a distinct group of landraces from Turkey should be of special interest as a source of untapped variation. Selective sweep detection in cultivated accessions identified 133 outlier positions within 13 sweep regions and 170 putative candidate genes related, among others, to response to various environmental stimuli (such as pathogens, drought, cold), plant fertility and reproduction (pollen sperm cell differentiation, pollen maturation, pollen tube growth), and plant growth and biomass production.Conclusions: Our study provides valuable information for efficient management of rye germplasm collections, which can help to ensure proper safeguarding of their genetic potential and provides numerous novel candidate genes targeted by selection in cultivated rye for further functional characterisation and allelic diversity studies

DArT Markers Effectively Target Gene Space in the Rye Genome

Large genome size and complexity hamper considerably the genomics research in relevant species. Rye (Secale cereale L.) has one of the largest genomes among cereal crops and repetitive sequences account for over 90% of its length. Diversity Arrays Technology is a high-throughput genotyping method, in which a preferential sampling of gene-rich regions is achieved through the use of methylation sensitive restriction enzymes. We obtained sequences of 6,177 rye DArT markers and following a redundancy analysis assembled them into 3,737 non-redundant sequences, which were then used in homology searches against five Pooideae sequence sets. In total 515 DArT sequences could be incorporated into publicly available rye genome zippers providing a starting point for the integration of DArT- and transcript-based genomics resources in rye. Using Blast2Go pipeline we attributed putative gene functions to 1101 (29.4%) of the non-redundant DArT marker sequences, including 132 sequences with putative disease resistance-related functions, which were found to be preferentially located in the 4RL and 6RL chromosomes. Comparative analysis based on the DArT sequences revealed obvious inconsistencies between two recently published high density consensus maps of rye. Furthermore we demonstrated that DArT marker sequences can be a source of SSR polymorphisms. Obtained data demonstrate that DArT markers effectively target gene space in the large, complex, and repetitive rye genome. Through the annotation of putative gene functions and the alignment of DArT sequences relative to reference genomes we obtained information, that will complement the results of the studies, where DArT genotyping was deployed, by simplifying the gene ontology and microcolinearity based identification of candidate genes

The Genome Sequence of the North-European Cucumber (Cucumis sativus L.) Unravels Evolutionary Adaptation Mechanisms in Plants

Cucumber (Cucumis sativus L.), a widely cultivated crop, has originated from Eastern Himalayas and secondary domestication regions includes highly divergent climate conditions e.g. temperate and subtropical. We wanted to uncover adaptive genome differences between the cucumber cultivars and what sort of evolutionary molecular mechanisms regulate genetic adaptation of plants to different ecosystems and organism biodiversity. Here we present the draft genome sequence of the Cucumis sativus genome of the North-European Borszczagowski cultivar (line B10) and comparative genomics studies with the known genomes of: C. sativus (Chinese cultivar – Chinese Long (line 9930)), Arabidopsis thaliana, Populus trichocarpa and Oryza sativa. Cucumber genomes show extensive chromosomal rearrangements, distinct differences in quantity of the particular genes (e.g. involved in photosynthesis, respiration, sugar metabolism, chlorophyll degradation, regulation of gene expression, photooxidative stress tolerance, higher non-optimal temperatures tolerance and ammonium ion assimilation) as well as in distributions of abscisic acid-, dehydration- and ethylene-responsive cis-regulatory elements (CREs) in promoters of orthologous group of genes, which lead to the specific adaptation features. Abscisic acid treatment of non-acclimated Arabidopsis and C. sativus seedlings induced moderate freezing tolerance in Arabidopsis but not in C. sativus. This experiment together with analysis of abscisic acid-specific CRE distributions give a clue why C. sativus is much more susceptible to moderate freezing stresses than A. thaliana. Comparative analysis of all the five genomes showed that, each species and/or cultivars has a specific profile of CRE content in promoters of orthologous genes. Our results constitute the substantial and original resource for the basic and applied research on environmental adaptations of plants, which could facilitate creation of new crops with improved growth and yield in divergent conditions

<i>Aux/IAA11</i> Is Required for UV-AB Tolerance and Auxin Sensing in <i>Arabidopsis thaliana</i>

In order to survive, plants have, over the course of their evolution, developed sophisticated acclimation and defense strategies governed by complex molecular and physiological, and cellular and extracellular, signaling pathways. They are also able to respond to various stimuli in the form of tropisms; for example, phototropism or gravitropism. All of these retrograde and anterograde signaling pathways are controlled and regulated by waves of reactive oxygen species (ROS), electrical signals, calcium, and hormones, e.g., auxins. Auxins are key phytohormones involved in the regulation of plant growth and development. Acclimation responses, which include programmed cell death induction, require precise auxin perception. However, our knowledge of these pathways is limited. The Aux/IAA family of transcriptional corepressors inhibits the growth of the plant under stress conditions, in order to maintain the balance between development and acclimation responses. In this work, we demonstrate the Aux/IAA11 involvement in auxin sensing, survival, and acclimation to UV-AB, and in carrying out photosynthesis under inhibitory conditions. The tested iaa11 mutants were more susceptible to UV-AB, photosynthetic electron transport (PET) inhibitor, and synthetic endogenous auxin. Among the tested conditions, Aux/IAA11 was not repressed by excess light stress, exclusively among its phylogenetic clade. Repression of transcription by Aux/IAA11 could be important for the inhibition of ROS formation or efficiency of ROS scavenging. We also hypothesize that the demonstrated differences in the subcellular localization of the two Aux/IAA11 protein variants might indicate their regulation by alternative splicing. Our results suggest that Aux/IAA11 plays a specific role in chloroplast retrograde signaling, since it is not repressed by high (excess) light stress, exclusively among its phylogenetic clade

Ochrona danych osobowych i (cyber) bezpieczeństwo sektora energetycznego

Czy atak socjotechniczny na jeden adres email pracownika podmiotu sektora energetycznego zagraża cyberbezpieczeństwu? Jeśli jest nieskuteczny, to pewnie nie. A jeśli zaatakowanych zostanie pięć tysięcy adresów? Wtedy to już nie ryzyko, tylko statystyka

Z-BEAM: a novel conditioning regimen in hematopoietic stem cell transplantation. Case report

Low-grade lymphomas pose a considerable therapeutic problem, as they yield to treatment very reluctantly. Not infrequently we are faced with resistance to chemotherapy. This type of lymphomas are usually seen in persons of middle or advanced age, rarely in people under 30. Due to the presence of CD20+ receptor on cell membranes of lymphoma originating from B-cells, monoclonal antibody anti-CD20+ (rituximab) has been introduced to the therapy. This has certainly resulted in improved outcomes. Of value in consolidation treatment of low-grade lymphomas is also autologous or allogenic hematopoietic cell transplantation (autoHSCT, alloHSCT). As escalation of dose of cytostatics as myeloablative treatment prior to autoHSCT or alloHSCT may not guarantee total eradication of residual lymphoma cells, research focuses on treatment modalities which might improve late outcomes in this tumor type. In this setting useful proved radioimmunotherapy with 90Y-ibritumomab tiuxetan (Zevalin). Zevalin combined with high-dose chemotherapy can be used now as a component of myeloablative treatment prior to autoHSCT. Reduced intensity conditioning (RIC) contributes to reduced mortality associated with standard conditioning protocol administered prior to transplantation, but may facilitate disease recurrence. Radioimmunotherapy using ibritumomab may reduce recurrence rate and, as a conditioning measure, may be initiated on the outpatient setting, prior to admission to bone marrow transplantation center. Labeling of antibodies and their application must take place at a Nuclear Medicine Unit, observing all necessary precautions and regulations concerning radiation protection. Administration of ibritumomab is preceded by application of two doses of rituximab: 250 mg/m2, 7 days and 4 hours prior to the RIT procedure. The dose of rituximab administered one week before, according to recommended protocol of ibritumomab use, initially preceded dosimetry (administration of indium-labeled antibodies).Chłoniaki o niskim stopniu złośliwości stanowią istotny problem terapeutyczny, gdyż bardzo trudno poddają się leczeniu. Nierzadko spotykamy się z opornością na chemioterapię. Zazwyczaj chłoniaki tego typu występują u ludzi w średnim lub starszym wieku. Rzadziej u chorych młodszych (poniżej 30. roku życia). W związku z obecnością ekspresji receptora CD20+ na błonach komórkowych komórek chłoniaka wywodzącego się z komórek B zaczęto stosować poza chemioterapią przeciwciało monoklonalne antyCD20+ (rytuksymab). Oczywiście udało się dzięki temu przeciwciału poprawić efekty terapeutyczne. Swoją wartość w leczeniu konsolidującym chłoniaków o niskim stopniu złośliwości ma też przeszczepienie autologicznych bądź alogenicznych komórek krwiotwórczych (autoHSCT i alloHSCT). Ponieważ eskalacja dawek cytostatyków jako leczenie mieloablacyjne przed autoHSCT i alloHSCT może nie zapewniać pełnej eradykacji resztkowych komórek chłoniaka, poszukuje się metod terapeutycznych, które poprawiłyby odległe efekty leczenia tego typu nowotworów. Tutaj swoje miejsce znalazła radioimmunoterapia za pomocą 90Y-ibrytumomabu tiuksetanu (Zevalin). Zevalin wraz z wysokodawkową chemioterapią można obecnie stosować jako jeden ze składników leczenia mieloablacyjnego przed autoHSCT. Kondycjonowanie o zredukowanej intensywności (RIC) zmniejsza śmiertelność związaną ze schematem przygotowawczym stosowanym przed podaniem przeszczepu, ale mogą zdarzać się nawroty choroby. Radioimmunoterapia z zastosowaniem ibrytumomabu jest procedurą, która może zmniejszyć częstość nawrotów choroby i może być jako kondycjonowanie rozpoczynana ambulatoryjnie, zanim chory zostanie przyjęty do ośrodka przeszczepiania szpiku. Samo przygotowanie (znakowanie) przeciwciał i ich podanie musi się odbyć w Zakładzie Medycyny Nuklearnej, z zachowaniem niezbędnych środków ochrony radiologicznej. Podanie ibrytumomabu poprzedza infuzja dwóch dawek rytuksymabu: 250 mg/m2, 7 dni i 4 godziny przed samą procedurą RIT. Dawka rytuksymabu podana tydzień wcześniej, zgodnie z zalecanym schematem podania ibrytumomabu, pierwotnie poprzedzała dozymetrię (podanie przeciwciała znakowanego indem)