There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Industrial applications of microbial lipases

Interindividual variation in mean leukocyte telomere length (LTL) is associated with cancer and several age-associated diseases. We report here a genome-wide meta-analysis of 37,684 individuals with replication of selected variants in an additional 10,739 individuals. We identified seven loci, including five new loci, associated with mean LTL (P < 5 × 10−8). Five of the loci contain candidate genes (TERC, TERT, NAF1, OBFC1 and RTEL1) that are known to be involved in telomere biology. Lead SNPs at two loci (TERC and TERT) associate with several cancers and other diseases, including idiopathic pulmonary fibrosis. Moreover, a genetic risk score analysis combining lead variants at all 7 loci in 22,233 coronary artery disease cases and 64,762 controls showed an association of the alleles associated with shorter LTL with increased risk of coronary artery disease (21% (95% confidence interval, 5–35%) per standard deviation in LTL, P = 0.014). Our findings support a causal role of telomere-length variation in some age-related diseases.

Identification of seven loci affecting mean telomere length and their association with disease

Bacillus strains isolated from the rhizosphere soil of potato roots were evaluated for the potential antagonistic activity against fungal pathogens in vitro and in vivo. Two bacterial isolates were identified as new Bacillus subtilis strains by 16S rRNA and GyrB gene sequencing and were designated GM2 and GM5, respectively. Strains were characterized by their ability to inhibit growth of a number of phytopathogenic fungi. It was shown that GM5 strain inhibited growth of phytopathogenic fungi more effectively than GM2 strain. Both strains were capable of producing a number of hydrolytic enzymes as well as antimicrobial metabolites (ammonia and HCN). In addition, GM2 strain also produced siderophores. Four genes encoding antimicrobial peptides were identified in the genome of GM2 strain: ituC, bmyB, bacA and srfA. Genome of GM5 contained two genes encoding for antimicrobial peptides, srfA and fenD. Purified lipopeptide fraction from GM5 but not from GM2 strain was able to control Fusarium solani spread in the plate assay. Furthermore, Bacillus subtilis strain GM2 promoted growth of wheat but only GM5 strain was able to protect wheat seedlings from Fusarium oxysporum infection.

/pdf/bacillus-subtilis-strains-with-antifungal-activity-against-3hkotg9y81.pdf

Bacillus subtilis Strains with Antifungal Activity against the Phytopathogenic Fungi

Bacillus subtilis is a very important Gram-positive model organism of high biotechnological relevance, which is widely used as a host for the production of both secreted and cytoplasmic proteins. We developed a novel and efficient expression system, based on the liaI promoter (P
 liaI
 ) from B. subtilis, which is under control of the LiaRS antibiotic-inducible two-component system. In the absence of a stimulus, this promoter is kept tightly inactive. Upon induction by cell wall antibiotics, it shows an over 100-fold increase in activity within 10 min. Based on these traits of P
 liaI
 , we developed a novel LiaRS-controlled gene expression system for B. subtilis (the “LIKE" system). Two expression vectors, the integrative pLIKE-int and the replicative pLIKE-rep, were constructed. To enhance the performance of the P
 liaI
 -derived system, site-directed mutagenesis was employed to optimize the ribosome binding site and alter its spacing to the initiation codon used for the translational fusion. The impact of these genetic modifications on protein production yield was measured using GFP as a model protein. Moreover, a number of tailored B. subtilis expression strains containing different markerless chromosomal deletions of the liaIH region were constructed to circumvent undesired protein production, enhance the positive autoregulation of the LiaRS system and thereby increase target gene expression strength from the P
 liaI
 promoter. The LIKE protein expression system is a novel protein expression system, which offers a number of advantages over existing systems. Its major advantages are (i) a tightly switched-off promoter during exponential growth in the absence of a stimulus, (ii) a concentration-dependent activation of P
 liaI
 in the presence of suitable inducers, (iii) a very fast but transient response with a very high dynamic range of over 100-fold (up to 1,000-fold) induction, (iv) a choice from a range of well-defined, commercially available, and affordable inducers and (v) the convenient conversion of LIKE-derived inducible expression strains into strong constitutive protein production factories.

/pdf/the-like-system-a-novel-protein-expression-toolbox-for-40vkykaas1.pdf

The LIKE system, a novel protein expression toolbox for Bacillus subtilis based on the liaI promoter

Glutamyl endopeptidase of Bacillus intermedius, strain 3-19

Bacillus spp. are an affordable source of enzymes due to their wide distribution, safety in work, ease of cultivation, and susceptibility to genetic transformations. Researchers are particularly interested in proteolytic enzymes, which constitute one of the most diverse groups of microbial proteins in terms of properties. Despite the long history of their research, this group of enzymes continue to show great potential for practical application in the biomedical industry, as well as in the agricultural industry. Thus, the unique properties of bacillary proteinases, such as stability in a wide range of temperatures and pH, high specificity, biodegradability of a wide range of substrates, and the high potential of sequenced Bacillus genomes are a powerful foundation for the development of new biotechnologies. The current review aims to discuss recent studies on various enzymes in particular, proteinases produced by bacteria of the genus Bacillus, along with their prospective practical applications. This article also presents an interpretive summary of the recent developments on the usage of probiotic Bacillus strains as potential feed additives.

/pdf/the-practical-potential-of-bacilli-and-their-enzymes-for-53hlqvz63e.pdf

The Practical Potential of Bacilli and Their Enzymes for Industrial Production

Replenishing of the stores of inorganic phosphate is among the most urgent environmental problems. In soil, phosphorus within inorganic compounds is mostly (over 80%) present as insoluble, phytic acid-based conglomerates. Phytates are strong chelating agents, binding the cations of bivalent metals, as well as peptides and low-molecular metabolites into resilient poorly degradable compounds. Their hydrolysis in nature is carried out by microbial phytases, which may potentially be used for an innovative microbial technology. The review deals with microbial degradation of the derivatives of phytic acid. Bacterial species capable of phytase synthesis for stepwise specific cleaving of phytates and their derivatives are discussed. Information analysis was carried out in order to search for the genes encoding phytases in bacterial genomes. Directional modification of the genes of bacterial phytases in order to develop new biotechnologies for agriculture and forage industry is considered. Application of microbial enzymes in agriculture and medicine is analyzed. Bacteria phytases are concluded to have a high practical potential. Microbiology is capable of providing the theoretical and experimental basis for development of the new biotechnology.

Margarita R. Sharipova

Papers

Bacillus subtilis Strains with Antifungal Activity against the Phytopathogenic Fungi

The LIKE system, a novel protein expression toolbox for Bacillus subtilis based on the liaI promoter

Glutamyl endopeptidase of Bacillus intermedius, strain 3-19

The Practical Potential of Bacilli and Their Enzymes for Industrial Production

Microorganisms as phytase producers