Homeobox genes encoding WOX transcription factors in the flowering parasitic plant Monotropa hypopitys

The formation and maintenance of plant stem cell populations are controlled by the WOX family of homeobox-containing transcription factors. The evolution of WOX genes is considered to be one of the main reasons for flower morphology and plant architecture diversity. The stem cell regulation mechanism is considered to be conserved among flowering plants and most thoroughly studied in Arabidopsis thaliana as a model. The angiosperms morphological diversity implies that there are species-specific features inherent to this mechanism, while the basic signaling is maintained. The unique flowering achlorophyllous mycoheterotrophic plant Monotropa hypopitys obtains nutrients from the tree roots through the mycorrhizal symbiosis. In inductive conditions, the reproductive stem with bracts and an inflorescence at the top is developed from an adventitious root bud. Like other plants, M. hypopitys forms the inflorescence, flower and root meristems, presumably using conserved mechanisms regulating stem cell niche. The study of M. hypopitys homeobox genes should contribute to the knowledge about the function of WOX transcription factors and further understanding of the stem cells control mechanisms in mycoheterotrophic species. The aim of the present study was to analyze M. hypopitys root, bracts and flower transcriptomes obtained from two individual flowering plants. In total, five WOX genes have been identified and characterized by their structure, phylogeny, expression pattern, and possible functions. The assumption is that the MhyWUS1 and MhyWUS2 genes maintain the stem cell population in the inflorescence and flower meristems, MhyWOX13 has a role in the control of root stem cell niche, seed pod formation, flowering initiation, and basic cellular processes, MhyWOX4 functions in the control of cambium stem cells, and MhyWOX2 participates in the differentiation of egg cells and zygotes

Identification and characterization of mRNAs of receptor-like kinases MhyGSO1 and MhyGSO2 in flowering parasitic plant Monotropa hypopitys

Plant organ formation is based on the balance of the programmed cell division and positional differentiation maintained by intercellular communication mediated by signaling molecules and receptors. In Arabidopsis thaliana, two paralogous leucine-rich repeat receptor-like kinases, GASSHO1 and GASSHO2, redundantly participate in the regulation of various root cells identity and functioning and the proper epidermis patterning. The GASSHO genes are characterized mainly in A. thaliana. Their significance in combination with the conservation of basic developmental processes justifies the study of GASSHO kinases in other plant species with different nutrition and developmental features. The aim of this work was to identify the GASSHO genes in an angiosperm plant, pinesap Monotropa hypopitys, which is a non-photosynthetic achlorophyllous mycoheterotroph. In different tissues (roots with buds, bracts, and flowers) of two individual plants at the late flowering stage, the transcriptomic data search identified 3’-partial mRNAs of two paralogous genes, MhyGASSHO1 (MhyGSO1) and MhyGSO2. Structural analysis of the encoded amino acid sequences revealed conserved domains, specific for leucine-rich repeat receptor-like kinases, in MhyGSO1, and the N-terminal leucine-rich domain in MhyGSO2. Phylogenetic analysis of MhyGASSHOs confirmed their homology with GSO1 and GSO2 kinases of the Rosids and Asterids representatives. The closest homologues of MhyGSO1 and MhyGSO2 were GSO1 and GSO2, respectively, of the Solanales members (Asterids). Quantification of the MhyGSO1 and MhyGSO2 transcripts revealed expression of both genes in flowers and bracts, and MhyGSO1 – also in roots with buds. In combination with known data about GSO1 and GSO2, it allowed us to assume the redundant activity of MhyGASSHO paralogues in signaling pathways, in particular, in response to exogenous sucrose and in development of reproductive organs and embryonic inflorescences

Specific features of telomerase RNA from Hansenula polymorpha.

Telomerase, a ribonucleoprotein, is responsible for the maintenance of eukaryotic genome integrity by replicating the ends of chromosomes. The core enzyme comprises the conserved protein TERT and an RNA subunit (TER) that, in contrast, displays large variations in size and structure. Here, we report the identification of the telomerase RNA from thermotolerant yeast Hansenula polymorpha (HpTER) and describe its structural features. We show further that the H. polymorpha telomerase reverse transcribes the template beyond the predicted boundary and adds a nontelomeric dT in vitro. Sequencing of the chromosomal ends revealed that this nucleotide is specifically present as a terminal nucleotide at the 3' end of telomeres. Mutational analysis of HpTER confirmed that the incorporation of dT functions to limit telomere length in this species

The low-temperature germinating spores of the thermophilic Desulfofundulus contribute to an extremely high sulfate reduction in burning coal seams

Burning coal seams, characterized by massive carbon monoxide (CO) emissions, the presence of secondary sulfates, and high temperatures, represent suitable environments for thermophilic sulfate reduction. The diversity and activity of dissimilatory sulfate reducers in these environments remain unexplored. In this study, using metagenomic approaches, in situ activity measurements with a radioactive tracer, and cultivation we have shown that members of the genus Desulfofundulus are responsible for the extremely high sulfate reduction rate (SRR) in burning lignite seams in the Altai Mountains. The maximum SRR reached 564 ± 21.9 nmol S cm−3 day−1 at 60°C and was of the same order of magnitude for both thermophilic (60°C) and mesophilic (23°C) incubations. The 16S rRNA profiles and the search for dsr gene sequences in the metagenome revealed members of the genus Desulfofundulus as the main sulfate reducers. The thermophilic Desulfofundulus sp. strain Al36 isolated in pure culture, did not grow at temperatures below 50°C, but produced spores that germinated into metabolically active cells at 20 and 15°C. Vegetative cells germinating from spores produced up to 0.738 ± 0.026 mM H2S at 20°C and up to 0.629 ± 0.007 mM H2S at 15°C when CO was used as the sole electron donor. The Al36 strain maintains significant production of H2S from sulfate over a wide temperature range from 15°C to 65°C, which is important in variable temperature biotopes such as lignite burning seams. Burning coal seams producing CO are ubiquitous throughout the world, and biogenic H2S may represent an overlooked significant flux to the atmosphere. The thermophilic spore outgrowth and their metabolic activity at temperatures below the growth minimum may be important for other spore-forming bacteria of environmental, industrial and clinical importance

Identification of O-Linked Glycoproteins Binding to the Lectin Helix pomatia Agglutinin as Markers of Metastatic Colorectal Cancer

Background Protein glycosylation is an important post-translational modification shown to be altered in all tumour types studied to date. Mucin glycoproteins have been established as important carriers of O-linked glycans but other glycoproteins exhibiting altered glycosylation repertoires have yet to be identified but offer potential as biomarkers for metastatic cancer. Methodology In this study a glycoproteomic approach was used to identify glycoproteins exhibiting alterations in glycosylation in colorectal cancer and to evaluate the changes in O-linked glycosylation in the context of the p53 and KRAS (codon 12/13) mutation status. Affinity purification with the carbohydrate binding protein from Helix pomatia agglutinin (HPA) was coupled to 2-dimensional gel electrophoresis with mass spectrometry to enable the identification of low abundance O-linked glycoproteins from human colorectal cancer specimens. Results Aberrant O-linked glycosylation was observed to be an early event that occurred irrespective of the p53 and KRAS status and correlating with metastatic colorectal cancer. Affinity purification using the lectin HPA followed by proteomic analysis revealed annexin 4, annexin 5 and CLCA1 to be increased in the metastatic colorectal cancer specimens. The results were validated using a further independent set of specimens and this showed a significant association between the staining score for annexin 4 and HPA and the time to metastasis; independently (annexin A4: Chi square 11.45, P = 0.0007; HPA: Chi square 9.065, P = 0.0026) and in combination (annexin 4 and HPA combined: Chi square 13.47; P = 0.0002). Conclusion Glycoproteins showing changes in O-linked glycosylation in metastatic colorectal cancer have been identified. The glycosylation changes were independent of p53 and KRAS status. These proteins offer potential for further exploration as biomarkers and potential targets for metastatic colorectal cancer

ЭФФЕКТИВНОСТЬ КРОСС-ПРОТЕКТИВНОЙ РЕКОМБИНАНТНОЙ ПРОТИВОГРИППОЗНОЙ ВАКЦИНЫ, ВКЛЮЧАЮЩЕЙ КОНСЕРВАТИВНЫЕ ЭПИТОПЫ ВИРУСНЫХ БЕЛКОВ М2 И ГЕМАГГЛЮТИНИНА

The influenza virus is the most unique in the level of variability of antigenic and biological properties. Because of constant mutations into genes coding surface viral proteins, in modern vaccines it is necessary to replace 1–2 virus components annually. Traditional influenza vaccines are the strain – specific and have limited efficiency in prevention of new strains of influenza viruses. In this regard, creation of influenza vaccines based on conserved determinants of viral proteins with broad spectrum protection and the short period of production is one of priority tasks which decision will lead to real control of an influenza infection. A current trend in the design of universal flu vaccines is the construction of recombinant proteins based the combination of conserved viral proteins or peptides. The goals of this study: to develop the candidate recombinant flu vaccine based on the two conserved influenza proteins (М2 and НА); to investigate immune response; and to measure the protection activity in an animal model. Results: In this study we investigated the humoral and T-cell response in mice after intranasal immunization with recombinant proteins (Flg-4M2ehs and Flg-HA2-2-4M2ehs). Both proteins induce a robust M2e-specific humoral and CD4+ T-cell response in mice lung. The recombinant protein with two target antigens (M2e and HA2) induces virusspecific CD4+ and CD8+ T-cell response and full protection (100% survival) of mice from lethal challenge human and avian influenza viruses A (A/H3N2, A/H2N2, A/H5N1). In mice immunized with Flg-4M2ehs, the survival after lethal challenge was 60–75%. Conclusion: Our results show an essential role of a conserved fragment of the HA2 in the formation of protective T-cell response and protection of mice from lethal challenge with influenza viruses A of various subtypes. The prospects of the development of vaccine formulation based on two conserved antigenic determinants of influenza virus A are shown.Вирус гриппа является наиболее уникальным по уровню изменчивости антигенных и биологических свойств. Из-за постоянных мутаций в генах, кодирующих поверхностные белки вируса, в существующих «сезонных» вакцинах приходится ежегодно заменять 1–2 вирусных компонента. Кроме того, традиционные вакцины являются штамм-специфическими и обладают ограниченной эффективностью в предотвращении заболеваний, вызванных новыми штаммами вирусов гриппа. В связи с этим создание противогриппозных вакцин на основе консервативных детерминант вирусных белков с широким спектром защиты и коротким периодом производства является одной из приоритетных задач, решение которой приведет к реальному контролю гриппозной инфекции. Перспективной тенденцией в создании универсальных гриппозных вакцин является конструирование рекомбинантных белков на основе комбинации консервативных вирусных белков или пептидов. Цель: разработка кандидатной рекомбинантной гриппозной вакцины на основе двух консервативных белков вируса гриппа А (М2 и НА) и оценка ее иммуногенности и защитного эффекта на животной модели. Результаты: исследовали гуморальный и Т-клеточный ответ у мышей (Balb/c) после интраназальной иммунизации рекомбинантными белками (Flg4M2ehs и Flg-HA2-2-4M2ehs). Оба белка стимулировали формирование выраженного М2е-специфического гуморального и CD4+ Т-клеточного ответа в легких мышей. Рекомбинантный белок с двумя таргетными антигенами (М2е и полипептид 76–130 второй субъединицы гемагглютинина) стимулирует формирование вирус-специфического Т-клеточного ответа и полную защиту (100% выживаемость) мышей от летального заражения вирусами гриппа А человека и птиц (A/H3N2, A/H2N2, A/H5N1). У мышей, иммунизированных рекомбинантным белком с одним таргетным антигеном (Flg4M2ehs), выживаемость после летального заражения составила 60–75%. Заключение: полученные результаты демонстрируют существенную роль консервативного фрагмента второй субъединицы гемагглютинина в формировании протективного Т-клеточного иммунитета и защите мышей от летального заражения вирусами гриппа А различных субтипов. Показана перспективность разработки вакцинного препарата на основе двух консервативных антигенных детерминант вирусов гриппа А.

A genomic catalog of Earth’s microbiomes

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes

Genomic analysis and relatedness of P2-like phages of the Burkholderia cepacia complex

<p>Abstract</p> <p>Background</p> <p>The <it>Burkholderia cepacia </it>complex (BCC) is comprised of at least seventeen Gram-negative species that cause infections in cystic fibrosis patients. Because BCC bacteria are broadly antibiotic resistant, phage therapy is currently being investigated as a possible alternative treatment for these infections. The purpose of our study was to sequence and characterize three novel BCC-specific phages: KS5 (vB_BceM-KS5 or vB_BmuZ-ATCC 17616), KS14 (vB_BceM-KS14) and KL3 (vB_BamM-KL3 or vB_BceZ-CEP511).</p> <p>Results</p> <p>KS5, KS14 and KL3 are myoviruses with the A1 morphotype. The genomes of these phages are between 32317 and 40555 base pairs in length and are predicted to encode between 44 and 52 proteins. These phages have over 50% of their proteins in common with enterobacteria phage P2 and so can be classified as members of the <it>Peduovirinae </it>subfamily and the "P2-like viruses" genus. The BCC phage proteins similar to those encoded by P2 are predominantly structural components involved in virion morphogenesis. As prophages, KS5 and KL3 integrate into an AMP nucleosidase gene and a threonine tRNA gene, respectively. Unlike other P2-like viruses, the KS14 prophage is maintained as a plasmid. The P2 <it>E+E' </it>translational frameshift site is conserved among these three phages and so they are predicted to use frameshifting for expression of two of their tail proteins. The <it>lysBC </it>genes of KS14 and KL3 are similar to those of P2, but in KS5 the organization of these genes suggests that they may have been acquired via horizontal transfer from a phage similar to λ. KS5 contains two sequence elements that are unique among these three phages: an IS<it>Bmu</it>2-like insertion sequence and a reverse transcriptase gene. KL3 encodes an EcoRII-C endonuclease/methylase pair and Vsr endonuclease that are predicted to function during the lytic cycle to cleave non-self DNA, protect the phage genome and repair methylation-induced mutations.</p> <p>Conclusions</p> <p>KS5, KS14 and KL3 are the first BCC-specific phages to be identified as P2-like. As KS14 has previously been shown to be active against <it>Burkholderia cenocepacia in vivo</it>, genomic characterization of these phages is a crucial first step in the development of these and similar phages for clinical use against the BCC.</p

Genome Stability of Lyme Disease Spirochetes: Comparative Genomics of Borrelia burgdorferi Plasmids

Lyme disease is the most common tick-borne human illness in North America. In order to understand the molecular pathogenesis, natural diversity, population structure and epizootic spread of the North American Lyme agent, Borrelia burgdorferi sensu stricto, a much better understanding of the natural diversity of its genome will be required. Towards this end we present a comparative analysis of the nucleotide sequences of the numerous plasmids of B. burgdorferi isolates B31, N40, JD1 and 297. These strains were chosen because they include the three most commonly studied laboratory strains, and because they represent different major genetic lineages and so are informative regarding the genetic diversity and evolution of this organism. A unique feature of Borrelia genomes is that they carry a large number of linear and circular plasmids, and this work shows that strains N40, JD1, 297 and B31 carry related but non-identical sets of 16, 20, 19 and 21 plasmids, respectively, that comprise 33–40% of their genomes. We deduce that there are at least 28 plasmid compatibility types among the four strains. The B. burgdorferi ∼900 Kbp linear chromosomes are evolutionarily exceptionally stable, except for a short ≤20 Kbp plasmid-like section at the right end. A few of the plasmids, including the linear lp54 and circular cp26, are also very stable. We show here that the other plasmids, especially the linear ones, are considerably more variable. Nearly all of the linear plasmids have undergone one or more substantial inter-plasmid rearrangements since their last common ancestor. In spite of these rearrangements and differences in plasmid contents, the overall gene complement of the different isolates has remained relatively constant

ICAR: endoscopic skull‐base surgery

n/