Metabolic profiles and aprE expression in anaerobic cultures of Bacillus subtilis using nitrate as terminal electron acceptor

Cultures using nitrate as the terminal electron acceptor were conducted in Schaeffer's medium to evaluate the growth performance and metabolic profiles of Bacillus subtilis, and its potential to express the aprE (subtilisin) gene under anoxic conditions. Nitrate was converted to ammonia through nitrite reduction; and different product profiles were observed during the growth phase when nitrate was added at various concentrations (4-24 mM) to Schaeffer's medium containing glucose (4 g l(-1)). If nitrate was not limiting, then acetic acid and acetoin were accumulated, suggesting a limitation of reduced cofactors but, if nitrate became limiting, then lactic acid and butanediol were accumulated, suggesting an excess of reduced cofactors. Due to a strong lysis at the onset of the end of the growth phase, sporulation frequency and aprE expression were negligible in anaerobic batch cultures. Fed-batch fermentation allowed the development of a stationary phase through a continuous supply of glucose and nitrate. In this case, sporulation frequency was almost null, but interestingly aprE expression was similar to that found in aerobic cultures.     

Aligning protein sequence and analysing substitution pattern using a class-specific matrix

Aligning protein sequences using a score matrix has became a routine but valuable method in modern biological research. However, alignment in the ‘twilight zone’ remains an open issue. It is feasible and necessary to construct a new score matrix as more protein structures are resolved. Three structural class-specific score matrices (all-alpha, allbeta and alpha/beta) were constructed based on the structure alignment of low identity proteins of the corresponding structural classes. The class-specific score matrices were significantly better than a structure-derived matrix (HSDM) and three other generalized matrices (BLOSUM30, BLOSUM60 and Gonnet250) in alignment performance tests. The optimized gap penalties presented here also promote alignment performance. The results indicate that different protein classes have distinct amino acid substitution patterns, and an amino acid score matrix should be constructed based on different structural classes. The class-specific score matrices could also be used in profile construction to improve homology detection.     

Aligning brains and minds

In this issue of Neuron, Haxby and colleagues describe a new method for aligning functional brain activity patterns across participants. Their study demonstrates that objects are similarly represented across different brains, allowing for reliable classification of one person's brain activity based on another's.     

Ultra-large alignments using phylogeny-aware profiles

Many biological questions, including the estimation of deep evolutionary histories and the detection of remote homology between protein sequences, rely upon multiple sequence alignments and phylogenetic trees of large datasets. However, accurate large-scale multiple sequence alignment is very difficult, especially when the dataset contains fragmentary sequences. We present UPP, a multiple sequence alignment method that uses a new machine learning technique, the ensemble of hidden Markov models, which we propose here. UPP produces highly accurate alignments for both nucleotide and amino acid sequences, even on ultra-large datasets or datasets containing fragmentary sequences. UPP is available at https://github.com/smirarab/sepp.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0688-z) contains supplementary material, which is available to authorized users.     

Aligning cells in arbitrary directions on a membrane sheet using locally formed microwrinkles

Sheets of cells can be used for tissue regenerative medicine. Cell alignment within the sheet is now a key factor in the next generation of this technology. Anisotropic cell sheets without random cell orientations have been conventionally produced with photolithographically, microfabricated substrates using special facilities and equipment. Here we demonstrate a more accessible approach to the fabrication of anisotropic substrates. We locally deformed part of an elastic membrane and simultaneously oxidized the surface to create microwrinkles as well as to enable adhesion to the extracellular matrix. The approach with the local loading made it possible to orient cells in controlled directions within a single membrane sheet depending on the strains determined by the controllable deformation. This technique potentially enables a versatile design of microwrinkles for target-compatible cell alignments.     

Protein structure alignment using environmental profiles

A new protein structure alignment procedure is described. An initial alignment is made by comparing a one-dimensional list of primary, secondary and tertiary structural features (profiles) of two proteins, without explicitly considering the three-dimensional geometry of the structures. The alignment is then iteratively refined in the second step, in which new alignments are found by three-dimensional superposition of the structures based on the current alignment. This new procedure is fast enough to do all-against-all structural comparisons routinely. The procedure sometimes finds an alignment that suggests an evolutionary relationship and which is not normally obtained if only geometry is considered. All pair-wise comparisons were made among 3539 protein structural domains that represent all known protein structures. The resulting 3539 z-scores were used to cluster the proteins. The number of main clusters increased continuously as the z-cutoff was raised, but the number of multiple-member clusters showed a maximum at z-cutoff values of 5.0 and 5.5. When a z-cutoff value of 5.0 was used, the total number of main clusters was 2043, of which only 336 clusters had more than one member.     

Gene symbol disambiguation using knowledge-based profiles

MOTIVATION: The ambiguity of biomedical entities, particularly of gene symbols, is a big challenge for text-mining systems in the biomedical domain. Existing knowledge sources, such as Entrez Gene and the MEDLINE database, contain information concerning the characteristics of a particular gene that could be used to disambiguate gene symbols. RESULTS: For each gene, we create a profile with different types of information automatically extracted from related MEDLINE abstracts and readily available annotated knowledge sources. We apply the gene profiles to the disambiguation task via an information retrieval method, which ranks the similarity scores between the context where the ambiguous gene is mentioned, and candidate gene profiles. The gene profile with the highest similarity score is then chosen as the correct sense. We evaluated the method on three automatically generated testing sets of mouse, fly and yeast organisms, respectively. The method achieved the highest precision of 93.9% for the mouse, 77.8% for the fly and 89.5% for the yeast. AVAILABILITY: The testing data sets and disambiguation programs are available at http://www.dbmi.columbia.edu/~hux7002/gsd2006     

Effective terminal sterilization using supercritical carbon dioxide

Gentle alternatives to existing sterilization methods are called for by rapid advances in biomedical technologies. Supercritical fluid technologies have found applications in a wide range of areas and have been explored for use in the inactivation of medical contaminants. In particular, supercritical CO(2) is appealing for sterilization due to the ease at which the supercritical state is attained, the non-reactive nature, and the ability to readily penetrate substrates. However, rapid inactivation of bacterial endospores has proven a barrier to the use of this technology for effective terminal sterilization. We report the development of a supercritical CO(2) based sterilization process capable of achieving rapid inactivation of bacterial endospores while in terminal packaging. Moreover, this process is gentle; as the morphology, ultrastructure, and protein profiles of inactivated microbes are maintained. These properties of the sterilization process suit it for possible use on a wide range of biomedical products including: materials derived from animal tissues, protein based therapies, and other sensitive medical products requiring gentle terminal sterilization.     

Aligning male and female linkage maps of apple (Malus pumila Mill.) using multi-allelic markers

 Linkage maps for the apple cultivars ‘Prima’ and ‘Fiesta’ were constructed using RFLP, RAPD, isozyme, AFLP, SCAR and microsatellite markers in a ‘Prima’בFiesta’ progeny of 152 individuals. Seventeen linkage groups, putatively corresponding to the seventeen haploid apple chromosomes, were obtained for each parent. These maps were aligned using 67 multi-allelic markers that were heterozygous in both parents. A large number of duplicate RFLP loci was observed and, in several instances, linked RFLP markers in one linkage group showed corresponding linkage in another linkage group. Distorted segregation was observed mainly in two regions of the genome, especially in the male parent alleles. Map positions were provided for resistance genes to scab and rosy leaf curling aphid (Vf and Sd ₁, respectively) for the fruit acidity gene Ma and for the self-incompatibility locus S. The high marker density and large number of mapped codominant RFLPs and some microsatellite markers make this map an ideal reference map for use in other progenies also and a valuable tool for the mapping of quantitative trait loci. Received: 17 November 1997 / Accepted: 9 December 1997     

Aligning demand and supply flexibility in custom product co-design

Flexibility of supply and demand is essential for successful implementation of a mass customization strategy that delivers sustained competitive advantage. Supply flexibility, i.e., a choice of alternative products designed to perform the same basic function, is made possible by the range of capabilities available in flexible and agile manufacturing systems and in supply chains. Demand flexibility is derived from the degree to which a customer is willing to compromise on product features or performance levels in order to meet budgetary (reflected in price) or schedule (reflected in delivery) constraints. Flexibility of both supply and demand can have significant strategic and financial value if they are properly aligned. However, customers are mostly unaware of mapping of demand flexibility on to supply flexibility and its impact on production cost and time. Recent advances in information technology have made it possible to co-design a product that involves customer on one end and the manufacturer on the other. This creates an aura and an opportunity where a middle ground between the supply and demand flexibility can be explored and a “deal” can be struck where both parties settle for a product that is beneficial to both through a negotiated settlement. In this paper, we develop a framework for such negotiations. The customer requirements are treated as a range of negotiable options instead of a set of fixed inputs. Demand and supply for customization is then matched by aligning the flexibility of manufacturing systems with customers’ requirement options. Based on this framework, a negotiation scheme is developed to assist customers and manufacturers in exploring and utilizing demand and supply flexibility information in co-design. The negotiation scheme is formulated using goal programming. Finally, an interactive problem-solving procedure is developed and implemented with an illustrative example.     

Identification ofArcobacter species using phospholipid and total fatty acid profiles

High-performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry (GC-MS) were used to analyze the phospholipids and fatty acids of four Arcobacter species (becoming routinely isolated from a wide variety of food sources, especially of animal origin) to provide information for the identification within these species. Phospholipid differences were observed in the HPLC profiles. GC-MS analysis provided a complete fatty acid composition for each arcobacter that after pattern recognition analysis allows taxonomic classification of each species.     

T-Align, a web-based tool for comparison of multiple terminal restriction fragment length polymorphism profiles

Terminal restriction fragment length polymorphism (tRFLP) is a potentially high-throughput method for the analysis of complex microbial communities. Comparison of multiple tRFLP profiles to identify shared and unique components of microbial communities however, is done manually, which is both time consuming and error prone. This paper describes a freely accessible web-based program, T-Align (http://inismor.ucd.ie/~talign/), which addresses this problem. Initially replicate profiles are compared and used to generate a single consensus profile containing only terminal restriction fragments that occur in all replicate profiles. Subsequently consensus profiles representing different communities are compared to produce a list showing whether a terminal restriction fragment (TRF) is present in a particular sample and its relative fluorescence intensity. The use of T-Align thus allows rapid comparison of numerous tRFLP profiles. T-Align is demonstrated by alignment of tRFLP profiles generated from bacterioplankton communities collected from the Irish and Celtic Seas in November 2000. Ubiquitous TRFs and site-specific TRFs were identified using T-Align.     

The POPPs: clustering and searching using peptide probability profiles

The POPPs is a suite of inter-related software tools which allow the user to discover what is statistically 'unusual' in the composition of an unknown protein, or to automatically cluster proteins into families based on peptide composition. Finally, the user can search for related proteins based on peptide composition. Statistically based peptide composition provides a view of proteins that is, to some extent, orthogonal to that provided by sequence. In a test study, the POPP suite is able to regroup into their families sets of approximately 100 randomised Pfam protein domains. The POPPs suite is used to explore the diverse set of late embryogenesis abundant (LEA) proteins.     

Analysis of confocal images using variable-width line profiles

A line profile of fluorescent intensities in confocal images is frequently examined. We have developed the computer software tool to analyse the profiles of intensities of fluorescent probes in confocal images. The software averages neighbouring pixels, adjacent to the central line, without reducing the spatial resolution of the image. As an experimental model, we have used the skeletal muscle fibre isolated from the rat skeletal muscle extensor digitorum brevis. As a marker of myofibrils' structure, we have used phalloidin–rhodamine staining and the anti-TIM antibody to label mitochondria. We also tested the distribution of the protein kinase B/Akt. Since signalling is ordered in modules and large protein complexes appear to direct signalling to organelles and regulate specific physiological functions, a software tool to analyse such complexes in fluorescent confocal images is required. The software displays the image, and the user defines the line for analysis. The image is rotated by the angle of the line. The line profile is calculated by averaging one dimension of the cropped rotated image matrix. The spatial resolution in averaged line profile is not decreased compared with single-pixel line profile, which was confirmed by the discrete Fourier transform computed with a fast Fourier transform algorithm. We conclude that the custom software tool presented here is a useful tool to analyse line profiles of fluorescence intensities in confocal images.     

Predicting renal graft failure using multivariate longitudinal profiles

Patients who have undergone renal transplantation are monitored longitudinally at irregular time intervals over 10 years or more. This yields a set of biochemical and physiological markers containing valuable information to anticipate a failure of the graft. A general linear, generalized linear, or nonlinear mixed model is used to describe the longitudinal profile of each marker. To account for the correlation between markers, the univariate mixed models are combined into a multivariate mixed model (MMM) by specifying a joint distribution for the random effects. Due to the high number of markers, a pairwise modeling strategy, where all possible pairs of bivariate mixed models are fitted, is used to obtain parameter estimates for the MMM. These estimates are used in a Bayes rule to obtain, at each point in time, the prognosis for long-term success of the transplant. It is shown that allowing the markers to be correlated can improve this prognosis.