De Novo Assembly of the Polyhydroxybutyrate (PHB) Producer Strain H1 Genome and Genomic Analysis of PHB Production Machinery.

Polyhydroxybutyrate (PHB) is a biodegradable natural polymer produced by different prokaryotes as a valuable carbon and energy storage compound. Its biosynthesis pathway requires the sole expression of the operon, although auxiliary genes play a role in controlling polymer accumulation, degradation, granule formation and stabilization. Due to its biodegradability, PHB is currently regarded as a promising alternative to synthetic plastics for industrial/biotechnological applications.

REDIportal: toward an integrated view of the A-to-I editing.

A-to-I RNA editing is the most common non-transient epitranscriptome modification. It plays several roles in human physiology and has been linked to several disorders. Large-scale deep transcriptome sequencing has fostered the characterization of A-to-I editing at the single nucleotide level and the development of dedicated computational resources.

Bioinformatic survey of CRISPR loci across 15 Serratia species.

The Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated proteins (CRISPR-Cas) system of prokaryotes is an adaptative immune defense mechanism to protect themselves from invading genetic elements (e.g., phages and plasmids).

Evolutive emergence and divergence of an Ig regulatory node: An environmental sensor getting cues from the aryl hydrocarbon receptor?

One gene, the immunoglobulin heavy chain () gene, is responsible for the expression of all the different antibody isotypes. Transcriptional regulation of the gene is complex and involves several regulatory elements including a large element at the 3' end of the gene locus (3'RR). Animal models have demonstrated an essential role of the 3'RR in the ability of B cells to express high affinity antibodies and to express different antibody classes.

New insight of human-IgH 3'regulatory regions in immunoglobulins switch.

Background: Several studies in animal models have demonstrated the role of the 3' Regulatory Region (3'RR) in the B cell maturation in mammals. In healthy humans, the concentration of each class of circulating immunoglobulins (Igs) has stable but different levels, due to several control mechanisms that also involve a duplicated version of the 3'RR on the chromosome 14 (chr14). The classes' equilibrium can be altered during infections and in other pathological conditions.

A high-resolution map of small-scale inversions in the gibbon genome.

Gibbons are the most speciose family of living apes, characterized by a diverse chromosome number and rapid rate of large-scale rearrangements. Here we performed single-cell template strand sequencing (Strand-seq), molecular cytogenetics, and deep in silico analysis of a southern white-cheeked gibbon genome, providing the first comprehensive map of 238 previously hidden small-scale inversions. We determined that more than half are gibbon specific, at least fivefold higher than shown for other primate lineage-specific inversions, with a significantly high number of small heterozygous inversions, suggesting that accelerated evolution of inversions may have played a role in the high sympatric diversity of gibbons.

Analysis of Four New Phages and Modeling of a Hyaluronidase Catalytic Domain from .

Phage therapy (PT), as a method to treat bacterial infections, needs identification of bacteriophages targeting specific pathogenic host. , a Gram-positive coccus resident in the human gastrointestinal tract, may become pathogenic in hospitalized patients showing acquired resistance to vancomycin and thus representing a possible target for PT. We isolated four phages that infect and characterized them by host range screening, transmission electron microscopy, and genome sequencing.

Genome characterization and CRISPR-Cas9 editing of a human neocentromere.

The maintenance of genome integrity is ensured by proper chromosome inheritance during mitotic and meiotic cell divisions. The chromosomal counterpart responsible for chromosome segregation to daughter cells is the centromere, at which the spindle apparatus attaches through the kinetochore. Although all mammalian centromeres are primarily composed of megabase-long repetitive sequences, satellite-free human neocentromeres have been described.

The Organization of the Pig T-Cell Receptor γ (TRG) Locus Provides Insights into the Evolutionary Patterns of the Genes across Cetartiodactyla.

The domestic pig () is a species representative of the Suina, one of the four suborders within Cetartiodactyla. In this paper, we reported our analysis of the pig TRG locus in comparison with the loci of species representative of the Ruminantia, Tylopoda, and Cetacea suborders. The pig TRG genomic structure reiterates the peculiarity of the organization of Cetartiodactyla loci in TRGC "cassettes", each containing the basic V-J-J-C unit.

The Genomic Organisation of the TRA/TRD Locus Validates the Peculiar Characteristics of Dromedary δ-Chain Expression.

The role of γδ T cells in vertebrate immunity is still an unsolved puzzle. Species such as humans and mice display a low percentage of these T lymphocytes (i.e.

A genomic survey of Tc1-mariner transposons in nematodes suggests extensive horizontal transposon transfer events.

The number of reports concerning horizontal transposon transfers (HTT) in metazoan species is considerably increased, alongside with the exponential growth of genomic sequence data However, our understanding of the mechanisms of such phenomenon is still at an early stage. Nematodes constitute an animal phylum successfully adapted to almost every ecosystem and for this reason could potentially contribute to spreading the genetic information through horizontal transfer. To date, few studies describe HTT of nematode retrotransposons.

The establishment of a fungal consortium in a new winery.

The biodiversity and evolution of fungal communities were monitored over a period of 3 vintages in a new winery. Samples were collected before grape receipt and 3 months after fermentation from 3 different wine related environments (WRE): floor, walls and equipment and analyzed using Illumina Mi-Seq. Genera of mold and filamentous fungi (294), non-enological (10) and wine-associated yeasts (25) were detected on all WREs before the arrival of the first harvest.

Concerted variation of the 3' regulatory region of Ig heavy chain and Gm haplotypes across human continental populations.

Objectives: The 3' regulatory region of the immunoglobulin heavy chain gene (IGH) includes the HS1.2 enhancer displaying length polymorphism with four known variants. The goal of the research was to provide an overview of this variability and of its evolutionary significance across human populations.

Characterization of CRISPR-Cas Systems in Isolated from (Olivier, 1790) (Coleoptera: Curculionidae).

The CRISPR-Cas adaptive immune system has been attracting increasing scientific interest for biological functions and biotechnological applications. Data on the system are scarce. Here, we report a comprehensive characterisation of CRISPR-Cas systems identified in strains isolated as secondary symbionts of , also known as Red Palm Weevil (RPW), one of the most invasive pests of major cultivated palms.

Correction: MYC-containing amplicons in acute myeloid leukemia: genomic structures, evolution, and transcriptional consequences.

In the original version of this Article, the affiliation details for Giovanni Martinelli were incorrectly given as 'Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy' and it should have been given as 'Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy and not Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy.'Furthermore, the original version of this Article contained an error in the spelling of the authors Alberto L'Abbate and Pietro D'Addabbo, an acute accent was used instead of an apostrophe for these authors names.These errors have now been corrected in both the PDF and HTML versions of the Article.

Myoblast Myogenic Differentiation but Not Fusion Process Is Inhibited via MyoD Tetraplex Interaction.

The presence of tetraplex structures in the promoter region of the myogenic differentiation 1 gene (MyoD1) was investigated with a specific tetraplex-binding porphyrin (TMPyP4), to test its influence on the expression of MyoD1 itself and downstream-regulated genes during myogenic differentiation. TMPyP4-exposed C2C12 myoblasts, blocking MyoD1 transcription, proliferated reaching confluence and fused forming elongated structures, resembling myotubes, devoid of myosin heavy chain 3 (MHC) expression. Besides lack of MHC, upon MyoD1 inhibition, other myogenic gene expressions were also affected in treated cells, while untreated control cell culture showed normal myotube formation expressing MyoD1, Myog, MRF4, Myf5, and MHC.

Association between Psoriasis and haplotypes of the IgH 3' Regulatory Region 1.

The association studies of several immune-diseases with the 3' Regulatory Region 1 (3'RR1) increased interest on the role that the region plays in the immune-regulation. The 3'RR1 is a polymorphic region on human chromosome 14q32, acting as a cis-regulative element on the Immunoglobulin constant-gene locus recently considered as super-enhancer. The human 3'RR1 share large sequences with its paralogous 3'RR2, at high level of similarity.

Inversion variants in human and primate genomes.

For many years, inversions have been proposed to be a direct driving force in speciation since they suppress recombination when heterozygous. Inversions are the most common large-scale differences among humans and great apes. Nevertheless, they represent large events easily distinguishable by classical cytogenetics, whose resolution, however, is limited.

MYC-containing amplicons in acute myeloid leukemia: genomic structures, evolution, and transcriptional consequences.

Double minutes (dmin), homogeneously staining regions, and ring chromosomes are vehicles of gene amplification in cancer. The underlying mechanism leading to their formation as well as their structure and function in acute myeloid leukemia (AML) remain mysterious. We combined a range of high-resolution genomic methods to investigate the architecture and expression pattern of amplicons involving chromosome band 8q24 in 23 cases of AML (AML-amp).

Association between IgH enhancer hs1.2 and type 1 diabetes.

Aim: To investigate the association of alleles of the 3' immunoglobulin heavy-chain regulatory region 1 (3'RR-1) enhancer hs1.2 in patients with type 1 diabetes (T1D).

Methods: Eighty-one patients with T1D [among which 12 had concomitant coeliac disease (CD) and 25 an autoimmune thyroid disease (AITD)] were compared to 248 healthy individuals.

Epigenetic origin of evolutionary novel centromeres.

Most evolutionary new centromeres (ENC) are composed of large arrays of satellite DNA and surrounded by segmental duplications. However, the hypothesis is that ENCs are seeded in an anonymous sequence and only over time have acquired the complexity of "normal" centromeres. Up to now evidence to test this hypothesis was lacking.

Inter-varietal structural variation in grapevine genomes.

Grapevine (Vitis vinifera L.) is one of the world's most important crop plants, which is of large economic value for fruit and wine production. There is much interest in identifying genomic variations and their functional effects on inter-varietal, phenotypic differences.

Evidence for a quadruplex structure in the polymorphic hs1.2 enhancer of the immunoglobulin heavy chain 3' regulatory regions and its conservation in mammals.

Regulatory regions in the genome can act through a variety of mechanisms that range from the occurrence of histone modifications to the presence of protein-binding loci for self-annealing sequences. The final result is often the induction of a conformational change of the DNA double helix, which alters the accessibility of a region to transcription factors and consequently gene expression. A ∼300 kb regulatory region on chromosome 14 at the 3' end (3'RR) of immunoglobulin (Ig) heavy-chain genes shows very peculiar features, conserved in mammals, including enhancers and transcription factor binding sites.