Back-translation for discovering distant protein homologies

Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of substitutions are additionally involved in the divergence, the homology detection becomes difficult even at the DNA level. To cope with this situation, we propose a novel method to infer distant homology relations of two proteins, that accounts for frameshift and point mutations that may have affected the coding sequences. We design a dynamic programming alignment algorithm over memory-efficient graph representations of the complete set of putative DNA sequences of each protein, with the goal of determining the two putative DNA sequences which have the best scoring alignment under a powerful scoring system designed to reflect the most probable evolutionary process. This allows us to uncover evolutionary information that is not captured by traditional alignment methods, which is confirmed by biologically significant examples.Comment: The 9th International Workshop in Algorithms in Bioinformatics (WABI), Philadelphia : \'Etats-Unis d'Am\'erique (2009

Study on Phylogenetic Relationships, Variability, and Correlated Mutations in M2 Proteins of Influenza Virus A

M2 channel, an influenza virus transmembrane protein, serves as an important target for antiviral drug design. There are still discordances concerning the role of some residues involved in proton transfer as well as the mechanism of inhibition by commercial drugs. The viral M2 proteins show high conservativity; about 3/4 of the positions are occupied by one residue in over 95%. Nine M2 proteins from the H3N2 strain and possibly two proteins from H2N2 strains make a phylogenic cluster closely related to 2RLF. The variability range is limited to 4 residues/position with one exception. The 2RLF protein stands out by the presence of 2 serines at the positions 19 and 50, which are in most other M2 proteins occupied by cysteines. The study of correlated mutations shows that there are several positions with significant mutational correlation that have not been described so far as functionally important. That there are 5 more residues potentially involved in the M2 mechanism of action. The original software used in this work (Consensus Constructor, SSSSg, Corm, Talana) is freely accessible as stand-alone offline applications upon request to the authors. The other software used in this work is freely available online for noncommercial purposes at public services on bioinformatics such as ExPASy or NCBI. The study on mutational variability, evolutionary relationship, and correlated mutation presented in this paper is a potential way to explain more completely the role of significant factors in proton channel action and to clarify the inhibition mechanism by specific drugs

Декодирование тензорного произведения MLD-кодов и приложения к кодовым криптосистемам

For the practical application of code cryptosystems such as McEliece, it is necessary that the code used in the cryptosystem should have a fast decoding algorithm. On the other hand, the code used must be such that finding a secret key from a known public key would be impractical with a relatively small key size. In this connection, in the present paper it is proposed to use the tensor product $C_1 \otimes C_2$ of group $\textrm{MLD}$ codes $C_1$ and $C_2$ in a McEliece-type cryptosystem. The algebraic structure of the code $C_1 \otimes C_2$ in the general case differs from the structure of the codes $C_1$ and $C_2$, so it is possible to build stable cryptosystems of the McEliece type even on the basis of codes $C_i$ for which successful attacks on the key are known. However, in this way there is a problem of decoding the code $C_1 \otimes C_2$. The main result of this paper is the construction and justification of a set of fast algorithms needed for decoding this code. The process of constructing the decoder relies heavily on the group properties of the code $C_1 \otimes C_2$. As an application, the McEliece-type cryptosystem is constructed on the code $C_1 \otimes C_2$ and an estimate is given of its resistance to attack on the key under the assumption that for code cryptosystems on codes $C_i$ an effective attack on the key is possible. The results obtained are numerically illustrated in the case when $C_1$, $C_2$ are Reed--Muller--Berman codes for which the corresponding code cryptosystem was hacked by L. Minder and A. Shokrollahi (2007).Для практического применения кодовой криптосистемы типа Мак-Элиса необходимо, чтобы используемый в основе криптосистемы код имел быстрый алгоритм декодирования. С другой стороны, используемый код должен быть таким, чтобы нахождение секретного ключа по известному открытому ключу было практически неосуществимо при относительно небольшом размере ключа. В связи с этим в настоящей работе  предлагается в криптосистеме типа Мак-Элиса использовать тензорное произведение $C_1\otimes C_2$ групповых $\textrm{MLD}$-кодов $C_1$ и $C_2$. Алгебраическая структура кода $C_1\otimes C_2$ в общем случае отличается от структуры кодов $C_1$ и $C_2$, поэтому представляется возможным построение стойких криптосистем типа Мак-Элиса даже на основе кодов $C_i$, для которых известны успешные атаки на ключ. Однако на этом пути возникает проблема декодирования кода $C_1\otimes C_2$. Основной результат настоящей работы -- построение и обоснование набора необходимых для декодирования этого кода быстрых алгоритмов. Процесс построения декодера существенно опирается на групповые свойства кода $C_1\otimes C_2$. В качестве приложения в работе построена криптосистема типа Мак-Элиса на коде $C_1\otimes C_2$ и приводится оценка ее стойкости к атаке на ключ в предположении, что для кодовых криптосистем на кодах $C_i$ возможна эффективная атака на ключ. Полученные результаты численно проиллюстрированы в случае, когда $C_1$, $C_2$  -- коды Рида--Маллера--Бермана, для которых соответствующая кодовая криптосистема взломана Л. Миндером и А. Шокроллахи (2007 г.)

New CZE-DAD method for honeybee venom analysis and standardization of the product

The aim of this study was to develop a new precise and accurate CZE-DAD method for honeybee venom analysis using cytochrome c as an internal standard. The 64.5 cm total length, 56 cm effective length, 75 μm ID, and 360 μm OD uncoated fused-silica capillary was used. The samples were injected into the capillary under a 50-mbar pressure for 7 s. There were 15 kV of electric field across the capillary applied. The current intensity was 26 μA. The separation was carried out at 25 °C. The analysis was run with the normal electrode polarity. The following steps and parameters were taken into account for the validation of the developed method: selectivity, precision, accuracy, linearity, limit of detection and limit of quantitation. All steps of the validation procedure proved that the developed analytical procedure was suitable for its intended purpose. Possibly this was the first study in which several honeybee venom components were separated and five of them were identified by capillary zone electrophoresis. In addition, the developed method was applied for quantitative analysis of 38 honeybee venom samples. The content (relative to the dry venom mass) of analyzed peptides in honeybee venom samples collected in 2002–2007 was as follows: apamine from 0.93% to 4.34% (mean, 2.85 ± 0.79%); mast cell degranulating peptide (MCDP) from 1.46% to 4.37% (mean, 2.82 ± 0.64%); phospholipase A2 from 7.41% to 20.25% (mean, 12.95 ± 3.09%); melittin from 25.40% to 60.27%, (mean, 45.91 ± 9.78%). The results were compared with the experimental data obtained for the same venom samples analyzed earlier by the HPLC method. It was stated that HPCE and HPLC data did not differ significantly and that the HPCE method was the alternative for the HPLC method. Moreover, using the results obtained principal component analysis (PCA) was applied to clarify the general distribution patterns or similarities of four major honeybee venom constituents collected from two different bee strains in various months and years. PCA has shown that the strain of bee appears to be the only criteria for bee venom sample classification. Strong correlations between apamine, MCDP, phospholipase A2, and melittin were confirmed. These correlations have to be taken into account in the honeybee venom standardization. The developed method due to its simplicity can be easily automated and incorporated into routine operations both in the bee venom identification, quality control, and standardization of the product

A simple and fast heuristic for protein structure comparison

Background Protein structure comparison is a key problem in bioinformatics. There exist several methods for doing protein comparison, being the solution of the Maximum Contact Map Overlap problem (MAX-CMO) one of the alternatives available. Although this problem may be solved using exact algorithms, researchers require approximate algorithms that obtain good quality solutions using less computational resources than the formers. Results We propose a variable neighborhood search metaheuristic for solving MAX-CMO. We analyze this strategy in two aspects: 1) from an optimization point of view the strategy is tested on two different datasets, obtaining an error of 3.5%(over 2702 pairs) and 1.7% (over 161 pairs) with respect to optimal values; thus leading to high accurate solutions in a simpler and less expensive way than exact algorithms; 2) in terms of protein structure classification, we conduct experiments on three datasets and show that is feasible to detect structural similarities at SCOP's family and CATH's architecture levels using normalized overlap values. Some limitations and the role of normalization are outlined for doing classification at SCOP's fold level. Conclusion We designed, implemented and tested.a new tool for solving MAX-CMO, based on a well-known metaheuristic technique. The good balance between solution's quality and computational effort makes it a valuable tool. Moreover, to the best of our knowledge, this is the first time the MAX-CMO measure is tested at SCOP's fold and CATH's architecture levels with encouraging results. Software is available for download at http://modo.ugr.es/jrgonzalez/msvns4maxcmo webcite.This work is supported by Projects HeuriCosc TIN2005-08404-C04-01, HeuriCode TIN2005-08404-C04-03, both from the Spanish Ministry of Education and Science. JRG acknowledges financial support from Project TIC2002-04242-C03-02. Authors thank N. Krasnogor and ProCKSi project (BB/C511764/1) for their support

The venom composition of the parasitic wasp Chelonus inanitus resolved by combined expressed sequence tags analysis and proteomic approach

<p>Abstract</p> <p>Background</p> <p>Parasitic wasps constitute one of the largest group of venomous animals. Although some physiological effects of their venoms are well documented, relatively little is known at the molecular level on the protein composition of these secretions. To identify the majority of the venom proteins of the endoparasitoid wasp <it>Chelonus inanitus </it>(Hymenoptera: Braconidae), we have randomly sequenced 2111 expressed sequence tags (ESTs) from a cDNA library of venom gland. In parallel, proteins from pure venom were separated by gel electrophoresis and individually submitted to a nano-LC-MS/MS analysis allowing comparison of peptides and ESTs sequences.</p> <p>Results</p> <p>About 60% of sequenced ESTs encoded proteins whose presence in venom was attested by mass spectrometry. Most of the remaining ESTs corresponded to gene products likely involved in the transcriptional and translational machinery of venom gland cells. In addition, a small number of transcripts were found to encode proteins that share sequence similarity with well-known venom constituents of social hymenopteran species, such as hyaluronidase-like proteins and an Allergen-5 protein.</p> <p>An overall number of 29 venom proteins could be identified through the combination of ESTs sequencing and proteomic analyses. The most highly redundant set of ESTs encoded a protein that shared sequence similarity with a venom protein of unknown function potentially specific of the <it>Chelonus </it>lineage. Venom components specific to <it>C. inanitus </it>included a C-type lectin domain containing protein, a chemosensory protein-like protein, a protein related to yellow-e3 and ten new proteins which shared no significant sequence similarity with known sequences. In addition, several venom proteins potentially able to interact with chitin were also identified including a chitinase, an imaginal disc growth factor-like protein and two putative mucin-like peritrophins.</p> <p>Conclusions</p> <p>The use of the combined approaches has allowed to discriminate between cellular and truly venom proteins. The venom of <it>C. inanitus </it>appears as a mixture of conserved venom components and of potentially lineage-specific proteins. These new molecular data enrich our knowledge on parasitoid venoms and more generally, might contribute to a better understanding of the evolution and functional diversity of venom proteins within Hymenoptera.</p

Cold Plasma Surface Modification of PLA and LDPE Polymer Plastics

Low-density polyethylene (LDPE) and polylactic acid (PLA) plastic films were subjected to modification using different plasma sources. Argon, nitrogen, air and oxygen were used as a gas phase throughout the process, and their impact on the material's surface properties was verified. The surface activation rate was measured via atomic force microscopy regarding the porosity factor and using the water contact angle technique. The last method – being feasible, agile and of high sensitivity to alternating physicochemical surface character – was utilised to verify the post-process stability of the modified surface. Those tests were performed extensively, up to 160 hours (contact angle) and 240 hours (atomic force microscopy)

An openwork like structures of polylactide – manufacturing and properties

Poly(lactic acid) electrospinning tests were carried out under various process conditions. Openwork structures with a high surface area to weight ratio have been obtained. Changing the parameters of the PLA electrospinning process resulted in products with different fiber morphology