Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2(T))

Thiothrix nivea (Rabenhorst 1865) Winogradsky 1888 (Approved Lists 1980) emend. Larkin and Shinabarger 1983 is the type species of the genus Thiothrix in the family Thiotrichaceae. The species is of interest not only because of its isolated location in the yet to be genomically characterized region of the tree of life, but also because of its life-style with gliding gonidia, the multilayer sheath, rosettes, and the embedded sulfur granules. Strain JP2(T) is the neotype strain of the species which was first observed by Rabenhorst in 1865 and later reclassified by Winogradsky in 1888 into the then novel genus Thiothrix. This is the first completed (improved-high-quality-draft) genome sequence to be published of a member of the family Thiotrichaceae. The genome in its current assembly consists of 15 contigs in four scaffolds with a total of 4,691,711 bp bearing 4,542 protein-coding and 52 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Frequency and Incidence of Pyrenochaeta terrestris in Root Internodes of Different Maize Hybrids

The frequency and incidence of Pyrenochaeta terrestris and symptom type on the roots of each internode of four maize hybrids of different maturity groups were studied 70 days after sowing. The fungus developed in the roots of all developed internodes (from the primary to the sixth or seventh internodes of all tested hybrids). The average frequency and incidence of P. terrestris in the roots of late and medium early maturity hybrids ranged from 29.5 to 55.2% and from 11.8 to 22.7%, respectively. The highest frequency of the fungus was at the 2nd root internode (93.3%), and its greatest incidence was detected in the mesocotyl of the medium early hybrid H‐1 (56.9%). Necrosis predominated in the roots of the medium early (i.e. medium late maturity hybrids, 44.5% and 44.3%, respectively), whereas reddish pink symptoms were recorded in the roots of the late hybrids (51% and 42.5%). Because the fungus always produces a distinctive red pigment on carnation leaf agar (CLA) in a light regime, these conditions can be recommended for the reliable identification of P. terrestris, even if pycnidia are not formed. These are the first reports of the successive distribution of the fungus in each maize root internode of different hybrids, as well as the use of CLA medium in the identification of the P. terrestris.     

Decreased Levels of BAG3 in a Family With a Rare Variant and in Idiopathic Dilated Cardiomyopathy

The most common cause of dilated cardiomyopathy and heart failure (HF) is ischemic heart disease; however, in a third of all patients the cause remains undefined and patients are diagnosed as having idiopathic dilated cardiomyopathy (IDC). Recent studies suggest that many patients with IDC have a family history of HF and rare genetic variants in over 35 genes have been shown to be causative of disease. We employed whole‐exome sequencing to identify the causative variant in a large family with autosomal dominant transmission of dilated cardiomyopathy. Sequencing and subsequent informatics revealed a novel 10‐nucleotide deletion in the BCL2‐associated athanogene 3 (BAG3) gene (Ch10:del 121436332_12143641: del. 1266_1275 [NM 004281]) that segregated with all affected individuals. The deletion predicted a shift in the reading frame with the resultant deletion of 135 amino acids from the C‐terminal end of the protein. Consistent with genetic variants in genes encoding other sarcomeric proteins there was a considerable amount of genetic heterogeneity in the affected family members. Interestingly, we also found that the levels of BAG3 protein were significantly reduced in the hearts from unrelated patients with end‐stage HF undergoing cardiac transplantation when compared with non‐failing controls. Diminished levels of BAG3 protein may be associated with both familial and non‐familial forms of dilated cardiomyopathy. J. Cell. Physiol. 229: 1697–1702, 2014. © 2014 The Authors. Journal of Cellular Physiology Published by Wiley Periodicals, Inc.     

Consensus design of a NOD receptor leucine rich repeat domain with binding affinity for a muramyl dipeptide,a bacterial cell wall fragment

Repeat proteins have recently emerged as especially well‐suited alternative binding scaffolds due to their modular architecture and biophysical properties. Here we present the design of a scaffold based on the consensus sequence of the leucine rich repeat (LRR) domain of the NOD family of cytoplasmic innate immune system receptors. Consensus sequence design has emerged as a protein design tool to create de novo proteins that capture sequence‐structure relationships and interactions present in nature. The multiple sequence alignment of 311 individual LRRs, which are the putative ligand‐recognition domain in NOD proteins, resulted in a consensus sequence protein containing two internal and N‐ and C‐capping repeats named CLRR2. CLRR2 protein is a stable, monomeric, and cysteine free scaffold that without any affinity maturation displays micromolar binding to muramyl dipeptide, a bacterial cell wall fragment. To our knowledge, this is the first report of direct interaction of a NOD LRR with a physiologically relevant ligand.     

Vanadate Influence on Metabolism of Sugar Phosphates in Fungus Phycomyces blakesleeanus

The biological and chemical basis of vanadium action in fungi is relatively poorly understood. In the present study, we investigate the influence of vanadate (V⁵⁺) on phosphate metabolism of Phycomyces blakesleeanus. Addition of V⁵⁺ caused increase of sugar phosphates signal intensities in ³¹P NMR spectra in vivo. HPLC analysis of mycelial phosphate extracts demonstrated increased concentrations of glucose 6 phosphate, fructose 6 phosphate, fructose 1, 6 phosphate and glucose 1 phosphate after V⁵⁺ treatment. Influence of V⁵⁺ on the levels of fructose 2, 6 phosphate, glucosamine 6 phosphate and glucose 1, 6 phosphate (HPLC), and polyphosphates, UDPG and ATP (³¹P NMR) was also established. Increase of sugar phosphates content was not observed after addition of vanadyl (V⁴⁺), indicating that only vanadate influences its metabolism. Obtained results from in vivo experiments indicate catalytic/inhibitory vanadate action on enzymes involved in reactions of glycolysis and glycogenesis i.e., phosphoglucomutase, phosphofructokinase and glycogen phosphorylase in filamentous fungi.     

Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (= HR1)

Saprospira grandis Gross 1911 is a member of the Saprospiraceae, a family in the class 'Sphingobacteria' that remains poorly characterized at the genomic level. The species is known for preying on other marine bacteria via 'ixotrophy'. S. grandis strain Sa g1 was isolated from decaying crab carapace in France and was selected for genome sequencing because of its isolated location in the tree of life. Only one type strain genome has been published so far from the Saprospiraceae, while the sequence of strain Sa g1 represents the second genome to be published from a non-type strain of S. grandis. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,495,250 bp long Improved-High-Quality draft of the genome with its 3,536 protein-coding and 62 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Complete genome sequence of Polynucleobacter necessarius subsp. asymbioticus type strain (QLW-P1DMWA-1(T))

Polynucleobacter necessarius subsp. asymbioticus strain QLW-P1DMWA-1(T) is a planktonic freshwater bacterium affiliated with the family Burkholderiaceae (class Betaproteobacteria). This strain is of interest because it represents a subspecies with cosmopolitan and ubiquitous distribution in standing freshwater systems. The 16S-23S ITS genotype represented by the sequenced strain comprised on average more than 10% of bacterioplankton in its home habitat. While all strains of the subspecies P. necessarius asymbioticus are free-living freshwater bacteria, strains belonging to the only other subspecies, P. necessarius subsp. necessarius are obligate endosymbionts of the ciliate Euplotes aediculatus. The two subspecies of P. necessarius are the instances of two closely related subspecies that differ in their lifestyle (free-living vs. obligate endosymbiont), and they are the only members of the genus Polynucleobacter with completely sequenced genomes. Here we describe the features of P. necessarius subsp. asymbioticus, together with the complete genome sequence and annotation. The 2,159,490 bp long chromosome with a total of 2,088 protein-coding and 48 RNA genes is the first completed genome sequence of the genus Polynucleobacter to be published and was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2006.