Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data

Motivation: DNA assembly programs classically perform an all-against-all comparison of reads to identify overlaps, followed by a multiple sequence alignment and generation of a consensus sequence. If the aim is to assemble a particular segment, instead of a whole genome or transcriptome, a target-specific assembly is a more sensible approach. GenSeed is a Perl program that implements a seed-driven recursive assembly consisting of cycles comprising a similarity search, read selection and assembly. The iterative process results in a progressive extension of the original seed sequence. GenSeed was tested and validated on many applications, including the reconstruction of nuclear genes or segments, full-length transcripts, and extrachromosomal genomes. The robustness of the method was confirmed through the use of a variety of DNA and protein seeds, including short sequences derived from SAGE and proteome projects.

Atmosphere and hydrological controls of the evapotranspiration over a floodplain forest in the Bananal Island region, Amazonia

This article discusses seasonal and interannual variations of the evapotranspiration (ET) rates in Bananal Island floodplain, Brazil. Measurements included ET and sensible heat flux using the eddy covariance method, atmospheric forcings (net radiation, Rn, vapor pressure deficit, VPD, wind speed and air temperature), soil moisture profiles, groundwater level and flood height, taken from November 2003 to December 2006. For the hydrological years (October-September) of 2003/2004, 2004/2005 and 2005/2006, the accumulated precipitation was 1692, 1471, 1914 mm and the accumulated ET was 1361, 1318 and 1317 mm, respectively. Seasonal analyses indicated that ET decreased in the dry season (average 3.7 mm day(-1)), despite the simultaneous increase in Rn, air temperature and VPD. The increase of ET in the wet season and particularly in the flood period (average 4.1 mm day(-1)) showed that the free water surface evaporation strongly influenced the energy exchange. Soil moisture, which was substantially depleted during the dry season, and adaptative vegetation mechanisms such as leaf senescence contributed to limit the dry season ET. Strong drainage within permeable sandy soils helped to explain the soil moisture depletion. These results suggest that the Bananal flooding area shows a different pattern in relation to the upland Amazon forests, being more similar to the savanna strictu senso areas in central Brazil. For example, seasonal ET variation was not in phase with Rn; the wet season ET was higher than the dry season ET; and the system stored only a tiny memory of the flooding period, being sensitive to extended drought periods.

Patterns of water and heat flux across a biome gradient from tropical forest to savanna in Brazil

We investigated the seasonal patterns of water vapor and sensible heat flux along a tropical biome gradient from forest to savanna. We analyzed data from a network of flux towers in Brazil that were operated within the Large-Scale Biosphere-Atmosphere Experiment in Amazonia (LBA). These tower sites included tropical humid and semideciduous forest, transitional forest, floodplain (with physiognomies of cerrado), and cerrado sensu stricto. The mean annual sensible heat flux at all sites ranged from 20 to 38 Wm(-2), and was generally reduced in the wet season and increased in the late dry season, coincident with seasonal variations of net radiation and soil moisture. The sites were easily divisible into two functional groups based on the seasonality of evaporation: tropical forest and savanna. At sites with an annual precipitation above 1900 mm and a dry season length less than 4 months (Manaus, Santarem and Rondonia), evaporation rates increased in the dry season, coincident with increased radiation. Evaporation rates were as high as 4.0 mm d(-1) in these evergreen or semidecidous forests. In contrast, ecosystems with precipitation less than 1700 mm and a longer dry season (Mato Grosso, Tocantins and Sao Paulo) showed clear evidence of reduced evaporation in the dry season. Evaporation rates were as low as 2.5 mm d(-1) in the transitional forests and 1 mm d(-1) in the cerrado. The controls on evapotranspiration seasonality changed along the biome gradient, with evaporative demand (especially net radiation) playing a more important role in the wetter forests, and soil moisture playing a more important role in the drier savannah sites.

Chemoenzymatic synthesis of boron-containing chiral amines and amides

The first application of lipases as catalysts to obtain optically active boron-containing amines and amides is described. We studied several reaction conditions to achieve the kinetic resolution of boron-containing amines via enantioselective acylation mediated by Candida antarctica lipase B (CAL-B). Excellent enantioselectivity (E>200) and high enantiomeric excess (up to >99%) of both the remaining amines and amides were obtained. (C) 2010 Elsevier Ltd. All rights reserved.

Biotransformations on organic selenides and tellurides: synthetic applications

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Chemoselective screening for the reduction of a chiral functionalised (+/-)-2-(phenylthio)cyclohexanone by whole cells of Brazilian micro-organisms

The use of whole cells of micro-organisms to bring about the biotransformation of an organic compound offers a number of advantages, but problems caused by enzymatic Promiscuity may be encountered upon With Substrates hearing more than one functional group. A one-pot screening method, in which whole fungal cells were incubated with a Mixture of 4-rnethylcyclohexanone I and phenyl methyl Sulfide 2, has been employed to determine the chemoselectivity of various biocatalysts. The hyphomycetes, Aspergillus terreus CCT 3320 and A. terreus URM 3571, catalysed the oxidation of 2 accompanied by the reduction of I to 4-methylcyclohexanol 1a and, for strain A. terreus CCT 3320, the Baeyer-Villiger oxidation of 1. The Basidomycetes, Trametes versicolor CCB 202, Pycnoporus sanguineus CCB 501 and Trichaptum byssogenum CCB 203, catalysed the oxidation of 2 and the reduction 1, but no Baeyer-Villiger reaction products were detected. In contrast. Trametes rigida CCB 285 catalysed the biotransformation of 1 to 1a, exclusively, in the absence of any detectable Sulfide oxidation reactions. The chemoselective reduction Of (+/-)-2-(phenylthio)cyclohexanone 3 by T. rigida CCB 285 afforded exclusively the (+)-cis-(1R,2S) and (+)-trans-(1S,2S) diastereoisomers of 2-(phenylthio)cyclohexan-1-ol 3a in moderate yields (13% and 27%, respectively) and high enantiomeric excesses (>98%). Chemoselective screening for the reduction of a ketone and/or the oxidation Of a Sulfide group in one pot by whole cells of micro-organisms represents an attractive technique with applications in the development of synthesis of complex molecule hearing different functional groups. (C) 2008 Published by Elsevier Ltd.

First chemoenzymatic synthesis of organoselenium amines and amides

A series of organoselenium amines have been synthesized and submitted to the enzymatic kinetic resolution by acetylation mediated by CAL-B (Novozym 435) to give the corresponding chiral amides in an enantiomerically pure form. After evaluating the appropriate lipase, solvent, temperature,and lipase/substrate ratio in the kinetic resolution, the chiral organoselenium amides were obtained with enantiomeric excess of up to 99%. (C) 2008 Elsevier Ltd. All rights reserved.

Isosorbide Polyesters from Enzymatic Catalysis

The synthesis of isosorbide aliphatic polyesters is demonstrated by the use of Novozym 435, a catalyst consisting of Candida antarctica lipase B immobilized on a macroporous support Several experimental procedures were tested and azeotropic distillation was most effective in removing low mass byproduct Furthermore, the use of diethyl ester derivatives of diacid comonomers gave isosorbide copolyesters with highest Isolated yield and molecular weights The length of the diacid aliphatic chain was less restrictive, but with a clear preference for longer aliphatic chains The molecular mass values of the obtained products were equivalent or higher than those obtained by nonenzymatic polymerizations, a clear illustration of the potential of enzymatic over conventional catalysis The ability of Novozym 435 to catalyze the synthesis of isosorbide polyester with weight-average molecular weights in excess of 40000 Da was unexpected given that isosorbide has two chemically distinct secondary hydroxyl groups This is the first example in which isosorbide polyesters were synthesized by enzyme catalysis, opening a large array of possibilities for this important class of biomass-derived building blocks Because these polymers are potential biomaterials the total absence of conventional Lewis acid catalyst residues represents a major Improvement in the toxicity of the material

Physical Vapor Deposited Thin Films of Lignins Extracted from Sugar Cane Bagasse: Morphology, Electrical Properties, and Sensing Applications

The concern related to the environmental degradation and to the exhaustion of natural resources has induced the research on biodegradable materials obtained from renewable sources, which involves fundamental properties and general application. In this context, we have fabricated thin films of lignins, which were extracted from sugar cane bagasse via modified organosolv process using ethanol as organic solvent. The films were made using the vacuum thermal evaporation technique (PVD, physical vapor deposition) grown up to 120 nm. The main objective was to explore basic properties such as electrical and surface morphology and the sensing performance of these lignins as transducers. The PVD film growth was monitored via ultraviolet-visible (UV-vis) absorption spectroscopy and quartz crystal microbalance, revealing a linear relationship between absorbance and film thickness. The 120 nm lignin PVD film morphology presented small aggregates spread all over the film surface on the nanometer scale (atomic force microscopy, AFM) and homogeneous on the micrometer scale (optical microscopy). The PVD films were deposited onto Au interdigitated electrode (IDE) for both electrical characterization and sensing experiments. In the case of electrical characterization, current versus voltage (I vs V) dc measurements were carried out for the Au IDE coated with 120 nm lignin PVD film, leading to a conductivity of 3.6 x 10(-10) S/m. Using impedance spectroscopy, also for the Au IDE coated with the 120 nm lignin PVD film, dielectric constant of 8.0, tan delta of 3.9 x 10(-3)) and conductivity of 1.75 x 10(-9) S/m were calculated at 1 kHz. As a proof-of-principle, the application of these lignins as transducers in sensing devices was monitored by both impedance spectroscopy (capacitance vs frequency) and I versus time dc measurements toward aniline vapor (saturated atmosphere). The electrical responses showed that the sensing units are sensible to aniline vapor with the process being reversible. AFM images conducted directly onto the sensing units (Au IDE coated with 120 nm lignin PVD film) before and after the sensing experiments showed a decrease in the PVD film roughness from 5.8 to 3.2 nm after exposing to aniline.

Energy Efficiency through Thermal Energy Storage : Possibilities for the Swedish Building Stock

The need for heating and cooling in buildings constitutes a considerable part of the total energy use in a country and reducing this need is of outmost importance in order to reach national and international goals for reducing energy use and emissions. One important way of reaching these goals is to increase the proportion of renewable energy used for heating and cooling of buildings. Perhaps the largest obstacle with this is the often occurring mismatch between the availability of renewable energy and the need for heating or cooling, hindering this energy to be used directly. This is one of the problems that can be solved by using thermal energy storage (TES) in order to save the heat or cold from when it is available to when it is needed. This thesis is focusing on the combination of TES techniques and buildings to achieve increased energy efficiency for heating and cooling. Various techniques used for TES as well as the combination of TES in buildings have been investigated and summarized through an extensive literature review. A survey of the Swedish building stock was also performed in order to define building types common in Sweden. Within the scope of this thesis, the survey resulted in the selection of three building types, two single family houses and one office building, out of which the two residential buildings were used in a simulation case study of passive TES with increased thermal mass (both sensible and latent). The second case study presented in the thesis is an evaluation of an existing seasonal borehole storage of solar heat for a residential community. In this case, real measurement data was used in the evaluation and in comparisons with earlier evaluations. The literature reviews showed that using TES opens up potential for reduced energy demand and reduced peak heating and cooling loads as well as possibilities for an increased share of renewable energy to cover the energy demand. By using passive storage through increased thermal mass of a building it is also possible to reduce variations in the indoor temperature and especially reduce excess temperatures during warm periods, which could result in avoiding active cooling in a building that would otherwise need it. The analysis of the combination of TES and building types confirmed that TES has a significant potential for increased energy efficiency in buildings but also highlighted the fact that there is still much research required before some of the technologies can become commercially available. In the simulation case study it was concluded that only a small reduction in heating demand is possible with increased thermal mass, but that the time with indoor temperatures above 24 °C can be reduced by up to 20%. The case study of the borehole storage system showed that although the storage system worked as planned, heat losses in the rest of the system as well as some problems with the system operation resulted in a lower solar fraction than projected. The work presented within this thesis has shown that TES is already used successfully for many building applications (e.g. domestic hot water stores and water tanks for storing solar heat) but that there still is much potential in further use of TES. There are, however, barriers such as a need for more research for some storage technologies as well as storage materials, especially phase change material storage and thermochemical storage.

Thermal energy storage in Swedish single family houses : a case study

In a Nordic climate, space heating (SH) and domestic hot water (DHW) used in buildings constitute a considerable part of the total energy use in the country. For 2010, energy used for SH and DHW amounted to almost 90 TWh in Sweden which corresponds to 60 % of the energy used in the residential and service sector, or almost 24 % of the total final energy use for the country. Storing heat and cold with the use of thermal energy storage (TES) can be one way of increasing the energy efficiency of a building by opening up possibilities for alternative sources of heat or cold through a reduced mismatch between supply and demand. Thermal energy storage without the use of specific control systems are said to be passive and different applications using passive TES have been shown to increase energy efficiency and/or reduce power peaks of systems supplying the heating and cooling needs of buildings, as well as having an effect on the indoor climate. Results are however not consistent between studies and focus tend to be on the reduction of cooling energy or cooling power peaks. In this paper, passive TES introduced through an increased thermal mass in the building envelope to two single family houses with different insulation standard is investigated with building energy simulations. A Nordic climate is used and the focus of this study is both on the reduction of space heating demand and space heating power, as well as on reduction of excess temperatures in residential single family houses without active cooling systems. Care is taken to keep the building envelope characteristics other than the thermal mass equal for all cases so that any observations made can be derived to the change in thermal mass. Results show that increasing the sensible thermal mass in a single family house can reduce the heating demand only slightly (1-4 %) and reduce excess temperatures (temperatures above 24 degrees C) by up to 20 %. Adding a layer of PCM (phase change materials) to the light building construction can give similar reduction in heating demand and excess temperatures, however the phase change temperature is important for the results.

Ethics in a capitalistic society

The problem of semantics is inherent in any discussion of ethics. The general term "ethics" is itself commonly confused. In addition, systems of ethics must be built upon assumptions, and assumptions are necessarily subject to lengthy debate. These two problems are encountered in my investigation of the ethical practices of the modern business community and to remedy the situation I have taken two steps: the first being an attempt to clarify the meaning of terms used therein;-and the second being a clear description of the assumptions utilized to further my analysis. To satisfy those who would disagree with these assumptions, I have attempted to outline the consequences of differing premises. The first assumption in my discussion is that the capitalistic economy is powered by the motivation supplied by man's self-interest. We are conditioned to basing our courses of action upon an orientation toward gratifying this self-interest. Careers are chosen by blending aptitude, interest, and remuneration. of course, some people are less materially inclined than others, but the average member of our capitalistic society is concerned with the physical rewards derived from his employment. Status and happiness are all-important considerations in pursuing a chosen course of action, yet all too often they are measured in physical terms. The normal self-interest natural to mankind is heightened in capitalism, due to the emphasis placed upon material compensation. Our thinking becomes mechanistic as life devolves into a complex game played by the rules. We are accustomed to performing meaningless or unpleasant duties to fulfill our gratifications. Thought, consequently, interferes with the completion of our everyday routines. We learn quickly not to be outspoken, as the outspoken one threatens the security of his fellow man. The majority of the people are quite willing to accept others views on morality, and indeed this is the sensible thing to do as one does not risk his own neck. The unfortunate consequence of this situation has been the substitution of the legal and jural for the moral and ethical. Our actions are guided by legal considerations and nowhere has this been more evident than in the business community. The large legal departments of modern corporations devote full time to inspecting the legality of corporate actions. The business community has become preoccupied with the law, yet this is necessarily so. Complex, modern, capitalistic society demands an elaborate framework of rules and regulations. Without this framework it would be impossible to have an orderly economy, to say nothing of protecting the best interests of the people. However, the inherent complexities, contradictions, and sometimes unfair aspects of our legal system can tempt men to take things into their own hands. From time to time cases arise where men have broken laws while acting in good faith, and other cases where men have been extremely unethical without being illegal. Examples such as these foster the growth of cynicism, and generally create an antagonistic attitude toward the law on the part of business. My second assumption is that the public, on the whole, has adopted an apathetic attitude toward business morality. when faced with an ethical problem, far too many people choose to cynically assume that, if I don't do it someone else will. "The danger of such an assumption lies in that it eliminates many of the inhibitions that normally would preclude unethical action. The preventative factor in contemplating an unethical act not only lies in it going against the "right course of action", but also in that it would display the actor as one of the few, immoral practitioners. However, if the contemplator feels that many other people follow the same course of action, he would not feel himself to be so conspicuous. These two assumptions underly my entire discussion of modern business ethics., and in my judgment are the two most important causal factors in unethical acts perpetrated by the business community. The future elimination of these factors seems improbable, if not futile, yet there is no reason to consider things worse than they ever have been before. The heightened public interest in business morality undoubtedly lies in part in the fact that examples of corporate malpractice are of such magnitude in scope, and hence more newsworthy.