Suppression of Nonsense Mutations Induced by Expression of an RNA Complementary to a Conserved Segment of 23S rRNA

We identified a short RNA fragment, complementary to the Escherichia coli 23S rRNA segment comprising nucleotides 735 to 766 (in domain II), which when expressed in vivo results in the suppression of UGA nonsense mutations in two reporter genes. Neither UAA nor UAG mutations, examined at the same codon positions, were suppressed by the expression of this antisense rRNA fragment. Our results suggest that a stable phylogenetically conserved hairpin at nucleotides 736 to 760 in 23S rRNA, which is situated close to the peptidyl transferase center, may participate in one or more specific interactions during peptide chain termination.     

merlin,an improved framework for the reconstruction of high-quality genome-scale metabolic models

Genome-scale metabolic models have been recognised as useful tools for better understanding living organisms’ metabolism. merlin (https://www.merlin-sysbio.org/) is an open-source and user-friendly resource that hastens the models’ reconstruction process, conjugating manual and automatic procedures, while leveraging the user''s expertise with a curation-oriented graphical interface. An updated and redesigned version of merlin is herein presented. Since 2015, several features have been implemented in merlin, along with deep changes in the software architecture, operational flow, and graphical interface. The current version (4.0) includes the implementation of novel algorithms and third-party tools for genome functional annotation, draft assembly, model refinement, and curation. Such updates increased the user base, resulting in multiple published works, including genome metabolic (re-)annotations and model reconstructions of multiple (lower and higher) eukaryotes and prokaryotes. merlin version 4.0 is the only tool able to perform template based and de novo draft reconstructions, while achieving competitive performance compared to state-of-the art tools both for well and less-studied organisms.     

Sequence-ready physical map of the mouse Chromosome 16 region with conserved synteny to the human Velocardiofacial syndrome region on 22q11.2

Proximal mouse Chromosome (Chr) 16 shows conserved synteny with human Chrs 16, 8, 22, and 3. The mouse Chr 16/human Chr 22 conserved synteny region includes the DiGeorge/Velocardiofacial syndrome region of human Chr 22q11.2. A physical map of the entire mouse Chr 16/human Chr 22 region of conserved synteny has been constructed to provide a substrate for gene discovery, genomic sequencing, and animal model development. A YAC contig was constructed that extends ca. 5.4 Mb from a region of conserved synteny with human Chr 8 at Prkdc through the region conserved with human Chr 3 at DVL3. Sixty-one markers including 37 genes are mapped with average marker spacing of 90 kb. Physical distance was determined across the 2.6-Mb region from D16Mit74 to Hira with YAC fragmentation. The central region from D16Jhu28 to Igl-C1 was converted into BAC and PAC clones, further refining the physical map and providing sequence-ready template. The gene content and borders of three blocks of conserved linkage between human Chr 22q11.2 mouse Chr 16 are refined. Received: 4 November 1998 / Accepted: 21 December 1998     

Dense cold‐water coral garden of Paragorgia johnsoni suggests the importance of the Mid‐Atlantic Ridge for deep‐sea biodiversity

Mid‐ocean ridges generate a myriad of physical oceanographic processes that favor the supply of food and nutrients to suspension‐ and filter‐feeding organisms, such as cold‐water corals and deep‐sea sponges. However, the pioneering work conducted along the Mid‐Atlantic Ridge failed to report the presence of large and dense living coral reefs, coral gardens, or sponge aggregations. Here, we describe the densest, near‐natural, and novel octocoral garden composed of large red and white colonies of Paragorgia johnsoni Gray, 1862 discovered at 545–595 m depth on the slopes of the Mid‐Atlantic Ridge, in the Azores region. This newly discovered octocoral garden is a good candidate for protection since it fits many of the FAO criteria that define what constitutes a Vulnerable Marine Ecosystem. The observations described here corroborate the existence of a close relationship between the octocoral structure and the ambient currents on ridge‐like topographies, providing new insights into the functioning of mid‐ocean ridges'' ecosystems. The ubiquitous presence of biogenic and geological topographies associated with mid‐ocean ridges, which could act as climate refugia, suggests their global importance for deep‐sea biodiversity. A better understanding of the processes involved is, therefore, required. Our observations may inspire future deep‐sea research initiatives to narrow existing knowledge gaps of biophysical connections with benthic fauna at small spatial scales along mid‐ocean ridges.     

Adventitious root induction in Ophiorrhiza prostrata: a tool for the production of camptothecin (an anticancer drug) and rapid propagation

Roots of Ophiorrhiza prostrata D. Don serve as a rich source of camptothecin (CPT), an anticancer drug. Because of the large-scale collection of its roots, the plant has become a threatened species. The present study accomplishes the induction of adventitious roots as a means for the production of CPT as well as for the large-scale propagation of this anticancer drug plant using leaf and internode explants. The biomass yield and CPT content of adventitious roots induced from different explants were compared to roots developed on ex vitro rooted stem cuttings. Adventitious roots were produced on half-strength Murashige and Skoog (MS) medium supplemented with 10.74 μM α-naphthaleneacetic acid and 2.32 μM kinetin at mean fresh weights of 0.753, 0.739 and 0.748 g roots from leaf, internode and shoot, respectively. CPT yield from in vitro derived roots after 50, 80 and 120 days of incubation (0.028, 0.06 and 0.1% dry weight, respectively) was not significantly different from those harvested at the same age from ex vitro rooted (0.03, 0.06 and 0.13%, respectively) stem cuttings. CPT from subcultured roots derived from solid (0.08%) medium was lower than from suspension culture medium (0.12%). Subsequent cultures of the adventitious roots showed a stable production of CPT (0.16%). The yield of CPT from 360-day-old plant-derived roots was 0.19%. Elicitation using methyl jasmonate and acetyl salicylic acid exhibited no enhancement in CPT yield. In vitro propagation through direct shoot regeneration was achieved from the adventitious roots upon transfer to MS medium with 8.87 μM N ⁶-benzyladenine (BA) and 2.46 μM indole-3-butyric acid (IBA) with a mean of 21.2 shoots per culture in 50 days. The shoots upon subculture on medium having the same level of BA and IBA underwent rapid proliferation. The shoots transferred to field conditions after in vitro rooting exhibited 95% survival. Adventitious root induction, from leaf and internode explants, enables the feasible production of CPT as well as the large-scale rapid propagation of this species which can safeguard it from extinction.     

Application of sector protein microarrays to clinical samples

Many protein functions are conferred by posttranslational modifications, which allow proteins to perform specific cellular tasks. Protein microarrays enable specific detection of posttranslational modifications not attainable by gene arrays. Reverse-phase protein microarrays have been widely adopted for use with clinical biopsy specimens because they have many advantages including highly reproducible printing of cellular lysates onto array surfaces, buit-in dilution curves, and direct detection using one antibody per analyte. This results in high-sensitivity, broad dynamic range, and favorable precision. Reverse-phase arrays have been restricted to a one slide/one antibody format. Although this is suitable for analyzing treatment effects over populations of samples, it is not well suited to individual patient assessments. One means of reaching this goal is the sector array format. Through the sector array, multiple antibody probes can be multiplexed on a single slide containing replicate immobilized aliquots from one patient. Thus, on one slide, a complete set of analytes can be characterized and used to support a therapy decision. This article describes a method for constructing sector arrays and demonstrates feasibility and adequate sensitivity applied to apoptosis related pathways.