The Potential of C4 Perennial Grasses for Developing a Global BIOHEAT Industry

Unprecedented opportunities for biofuel development are occurring as a result of rising fossil fuel prices, the need to reduce greenhouse gases, and growing energy security concerns. An estimated 250 million hectares (ha) of farmland could be utilized globally to develop a bioenergy industry if efficient and economical perennial biomass crops and bioenergy conversion systems are employed. In temperate zones, C₄ or warm-season grass research and development efforts have found switchgrass (Panicum virgatum) and Miscanthus capable of producing biomass yields of 10 to 20 oven dried tonnes (ODT)/ha/yr, while in tropical areas Erianthus and napier grass (Pennisetum purpureum) are producing 25 to 35 ODT/ha/yr. The potential to annually produce 100 barrels of oil energy equivalent/ha with a 25:1 energy output to input ratio appears achievable with high-yielding, N-fixing warm-season grasses grown on marginal lands in the tropics. Commercialization of densified herbaceous plant species has been slow because of the relatively high alkali and chlorine contents of the feedstocks, which leads to clinker formation and the fouling of boilers. This challenge can be overcome by improving biomass quality through advances in plant breeding and cultural management to reduce the chlorine, alkali, and silica content and through the use of new combustion technologies.

Warm-season grasses can be readily densified provided suitable grinding and densification equipment and pressure are utilized. The major advantages of producing densified warm-season grasses for BIOHEAT include: it is the most efficient strategy to use marginal farmlands in most temperate and tropical climates to collect solar radiation; it has an excellent energy balance; the feedstocks can be used conveniently in a variety of energy applications; and it is relatively environmentally friendly. Densified warm-season grass biofuels are poised to become a major global fuel source because they can meet some heating requirements at less cost than all other alternatives available today.     

Free flap from the flexor aspect of the wrist for resurfacing defects of the hand and fingers

The distal portion of the flexor aspect of the forearm has been used as the donor site of full-thickness skin grafts, venous skin grafts, and Chinese forearm flaps. This article describes the use of a free flap harvested from the flexor aspect of the wrist and based on the superficial palmar branch of the radial artery to repair skin defects of the hand and fingers. The advantages of this flap are as follows: (1) the operative field is the same; (2) the radial artery is preserved; (3) it is thin, pliable, and hairless and thus can supply a gliding surface for tendons beneath it; (4) when it involves a palmaris longus tendon and/or the palmar cutaneous branch of the median nerve, it can be used as a vascularized tendon or nerve graft; and (5) in view of the flow-through type of the pedicle of the flap, the digital artery can be reconstructed simultaneously. However, it should be noted that a hypesthesia in the proximal central carpal area remains when the palmar cutaneous branch of the median nerve is harvested as a vascularized nerve graft. The scar of the donor site should be left in the distal wrist crease. If it is not lying in the distal wrist crease, it may suggest that the patient has tried to commit suicide.     

Visualization and analysis of protein interactions

SUMMARY: We have developed a new program called InterViewer for drawing large-scale protein interaction networks in three-dimensional space. Unique features of InterViewer include (1) it is much faster than other recent implementations of drawing algorithms; (2) it can be used not only for visualizing protein interactions but also for analyzing them interactively; and (3) it provides an integrated framework for querying protein interaction databases and directly visualizes the query results. AVAILABILITY: http://wilab.inha.ac.kr/protein/     

Bridging between normal mode analysis and elastic network models

Normal mode analysis (NMA) has been a powerful tool for studying protein dynamics. Elastic network models (ENM), through their simplicity, have made normal mode computations accessible to a much broader research community and for many more biomolecular systems. The drawback of ENMs, however, is that they are less accurate than NMA. In this work, through steps of simplification that starts with NMA and ends with ENMs we build a tight connection between NMA and ENMs. In the process of bridging between the two, we have also discovered several high‐quality simplified models. Our best simplified model has a mean correlation with the original NMA that is as high as 0.88. In addition, the model is force‐field independent and does not require energy minimization, and thus can be applied directly to experimental structures. Another benefit of drawing the connection is a clearer understanding why ENMs work well and how it can be further improved. We discovered that can be greatly enhanced by including an additional torsional term and a geometry term. Proteins 2014; 82:2157–2168. © 2014 Wiley Periodicals, Inc.     

Lanthanide induced shift as a tool for isomer assignment in esters of unsaturated fatty acids

Addition of Yb(fod)₃ to methyl oleate (cis) and methyl elaidate (trans) shifts the carboxylic lines of their ¹³C-NMR spectra to different extents; that of the cis isomer less than that of the trans isomer, as is to be expected.

On the same theoretical ground it can be anticipated that the opposite will occur for C-17: an effect that has been confirmed experimentally. The method is thus proposed as a means of aiding in the assignment of the cis and trans configuration in esters of fatty acids with one double bond.     

Evaluation of the surface-averaged load exerted on a blood element by the Reynolds shear stress field provided by artificial cardiovascular devices

Implantable prosthetic devices can often affect the recipient's hemostasis, with possible hemolysis and thrombus formation. Since such devices can produce turbulent flow, it is important to characterize it as accurately as possible, by means of the Reynolds stress tensor. Some parameters related to the latter have been often used to provide a quantity related to the possible damage to blood constituents: the TSS_max, for instance, has been associated with hemolysis. It can be expressed as TSS_max=(σ₁−σ₃)/2, σ₁ and σ₃ being the highest and lowest principal normal stresses (PNSs) in each point of the flow.

In the present work, the average value of the shear stress over a spherical surface, representative of a blood component, is derived. All three PNSs (σ₁, σ₂ and σ₃) are found to have an equal role in the determination of this parameter, since the relative formula shows a marked symmetry with respect to the PNSs. The average shear stress level, for a given (σ₁, σ₃) pair (hence, for a given TSS_max), has a minimum and maximum value, depending on the particular σ₂ value yielded by the local structure of the turbulent flow field. A numerical investigation on more complex geometries shows similar results. The role of the intermediate PNS is thus shown for the first time to have a physical relevance. The presented results can be useful whenever a spatial averaging of the shear field is important to be assessed, such as in the case of platelet activation. A new parameter is thus proposed, which can be correlated with prosthetic devices complications.     

Functional variability of the indices of ventilation and gas exchange in healthy young men in Western Siberia

The variability of standardized values of indices of the external respiration function (ERF) of healthy young men living in Western Siberia has been estimated. Three different states of ERF have been found: (i) normal respiration (normal ventilation efficiency at different levels); (ii) compensatory hyperventilation, during which the ventilation apparatus is strained, which indicates that there are some changes in the morphological structure of the respiratory regions of the lungs (this state can be considered a borderline between the normal state and pathology); and (iii) deep, highly effective respiration; it has no signs of the tension of the function or the apparatus of external respiration, and it can be considered a normal genotypic/phenotypic variant.     

Floquet theory: a useful tool for understanding nonequilibrium dynamics

Many ecological systems experience periodic variability. Theoretical investigation of population and community dynamics in periodic environments has been hampered by the lack of mathematical tools relative to equilibrium systems. Here, I describe one such mathematical tool that has been rarely used in the ecological literature but has widespread use: Floquet theory. Floquet theory is the study of the stability of linear periodic systems in continuous time. Floquet exponents/multipliers are analogous to the eigenvalues of Jacobian matrices of equilibrium points. In this paper, I describe the general theory, then give examples to illustrate some of its uses: it defines fitness of structured populations, it can be used for invasion criteria in models of competition, and it can test the stability of limit cycle solutions. I also provide computer code to calculate Floquet exponents and multipliers. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

An Escherichia coli system for assay of Flp site-specific recombination on substrate plasmids

We have developed an Escherichia coli system for testing the behaviour of plasmids carrying target sites for the Flp site-specific recombinase. The E. coli strain BL-FLP is described, which carries a chromosomally integrated bacteriophage T7 RNA polymerase gene expressed from a lac promoter, and harbours the plasmid pMS40. pMS40 has the features: (i) it carries the FLP recombinase gene under the control of a bacteriophage T7 promoter, (ii) it confers kanamycin resistance, and (iii) it uses an R6K origin of replication; these two latter features make it compatible with most conventional cloning vectors. Substrate plasmids carrying Flp-recognition targets (FRT) are transformed into BL-FLP, and the consequences of Flp-mediated recombination can be analysed after subsequent extraction of plasmid DNA. We show that this system is capable of base-perfect Flp-mediated recombination on plasmid substrates. We also present a corrected sequence of the commonly used Flp substrate plasmid, pNEOβGAL (O'Gorman et al. (1991) Science 251, 1351–1355).     

A novel expression vector, designated as pHisJM, for producing recombinant His-fusion proteins

Compared to glutathione S -transferase (GST), tagging with hexahistidine residues (His) has several merits: low levels of toxicity and immunogenicity, a smaller size and no electric charge. We have constructed a novel expression vector, designated as pHisJM (EMBL/GenBank/DDJB accession no. AB116367), for producing recombinant His-fusion proteins. This vector was constructed by replacing GST and multiple cloning site (MCS) cassettes in pGEX-5X-3 with those of hexahistidine and MCS derived from pRSET C vector. Human annexin IV (Anx IV) was used as target protein. His-Anx IV fusion protein was expressed using pHisJM and gave a 40 kDa band when immuno-stained with anti-His mAb or anti-Anx IV mAb as predicted. To compare expression efficiency, a Anx IV cDNA inserted-pHisJM or pGEX-5X-3 was transformed into Escherichia coli DH5alpha, JM109, BL21 and BL21(DE3). Using pHisJM, Anx IV protein was highly expressed in all cell strains. In addition to the merits of using His-tag, pHisJM has several advantages: 1) it has high expression efficiency; 2) it can be used in any Escherichia coli strain; and 3) it can be used in a single strain of Escherichia coli in all steps from plasmid construction to the expression of the target gene.     

A Model-Based Clustering Method for Genomic Structural Variant Prediction and Genotyping Using Paired-End Sequencing Data

Structural variation (SV) has been reported to be associated with numerous diseases such as cancer. With the advent of next generation sequencing (NGS) technologies, various types of SV can be potentially identified. We propose a model based clustering approach utilizing a set of features defined for each type of SV events. Our method, termed SVMiner, not only provides a probability score for each candidate, but also predicts the heterozygosity of genomic deletions. Extensive experiments on genome-wide deep sequencing data have demonstrated that SVMiner is robust against the variability of a single cluster feature, and it significantly outperforms several commonly used SV detection programs. SVMiner can be downloaded from http://cbc.case.edu/svminer/.     

In vitro studies of the transmission barrier

Protein Misfolding Cyclic Amplification (PMCA) has proved to be an efficient method mimicking in vitro some of the fundamental steps involved in prion replication in vivo. Thus, it can be used to efficiently replicate a variety of prion strains/species. The in vitro generated prions possess key prion features, i.e., they are infectious in vivo and maintain their strain specificity. One of the big challenges is its use for studying prion transmission barriers. PMCA has been efficiently used for adapting different prion species through a range of species barriers; however its capacity for overcoming purportedly unbreakable species barriers compels us to adapt it in order to use it as a reliable technique. In addition, this in vitro method might be a crucial tool in evaluating the potential risks of different prion strains (natural or experimentally generated in vitro) to humans and animals.Key words: TSE (transmissible spongiform encephalopathy), prion, transmission barrier, PMCA, in vitro replication     

iSuc-PseOpt: Identifying lysine succinylation sites in proteins by incorporating sequence-coupling effects into pseudo components and optimizing imbalanced training dataset

Succinylation is a posttranslational modification (PTM) where a succinyl group is added to a Lys (K) residue of a protein molecule. Lysine succinylation plays an important role in orchestrating various biological processes, but it is also associated with some diseases. Therefore, we are challenged by the following problem from both basic research and drug development: given an uncharacterized protein sequence containing many Lys residues, which one of them can be succinylated, and which one cannot? With the avalanche of protein sequences generated in the postgenomic age, the answer to the problem has become even more urgent. Fortunately, the statistical significance experimental data for succinylated sites in proteins have become available very recently, an indispensable prerequisite for developing a computational method to address this problem. By incorporating the sequence-coupling effects into the general pseudo amino acid composition and using KNNC (K-nearest neighbors cleaning) treatment and IHTS (inserting hypothetical training samples) treatment to optimize the training dataset, a predictor called iSuc-PseOpt has been developed. Rigorous cross-validations indicated that it remarkably outperformed the existing method. A user-friendly web-server for iSuc-PseOpt has been established at http://www.jci-bioinfo.cn/iSuc-PseOpt, where users can easily get their desired results without needing to go through the complicated mathematical equations involved.     

Sequence-based analysis of mutagenized mice

Treating mice with ethylnitrosourea (ENU) is an efficient means for mutagenizing spermatogonial cells, and this treatment has been proven effective in a variety of screens for both dominant and recessive mutations. However, a significant problem for this technology is that the efficiency of mutagenesis is assessed most often by the empiric determination of a per-locus mutation frequency by using the specific locus test, which is expensive, time-consuming, and logistically difficult. To approach this question more directly and more efficiently, one can utilize methods of PCR-based mutation detection for the characterization of progeny of mutagenized mice. Since this analysis can be done after a single generation of breeding, it is useful as a rapid means for the assessment of the efficiency of mutagen treatment. Furthermore, it is readily imaginable that this strategy can be applied for the general determination of gene function in a systematic manner. Theoretical considerations and empirical analysis suggest that the per-base mutation frequency for a fractionated-dose treatment protocol is on the order of 1 sequence change per 10⁵ bp. Received: 15 February 2000 / Accepted: 15 February 2000     

Trx/TXNIP在脑卒中的研究进展

脑卒中是导致中老年人群死亡最主要原因之一,其具有较高的致死率和致残率,且每年的发病率呈逐年上升的趋势,严重危害人类的生命和健康,因此寻找有效的诊断及治疗脑卒中的靶点具有重要意义。硫氧还蛋白(Trx)是细胞内主要的硫醇还原剂,通过调节细胞内氧化还原状态,参与细胞内多种信号通路转导过程,具有二硫化物还原酶活性,通过抗氧化效应,减轻脑卒中后神经元氧化应激损伤。硫氧还原蛋白相互作蛋白(TXNIP)是Trx的内源性抑制剂,通过绑定/抑制Trx的活性,破坏细胞内氧化还原平衡,促进氧化应激,而抑制或敲除TXNIP具有明显的神经保护作用。最新研究表明Trx/TXNIP可经多种途径参与脑卒中病理生理过程。本文通过分析Trx和TXNIP的研究现状,以及探讨Trx系统在中枢神经系统中的定位和Trx系统在缺血性脑卒中的研究进展,展望Trx/TXNIP参与脑卒中的病理生理过程的信号途径,拟对Trx/TXNIP在脑卒中的作用机制进行综述,为脑卒中的治疗提供新思路。     

Parallel implementation of 3D protein structure similarity searches using a GPU and the CUDA

Searching for similar 3D protein structures is one of the primary processes employed in the field of structural bioinformatics. However, the computational complexity of this process means that it is constantly necessary to search for new methods that can perform such a process faster and more efficiently. Finding molecular substructures that complex protein structures have in common is still a challenging task, especially when entire databases containing tens or even hundreds of thousands of protein structures must be scanned. Graphics processing units (GPUs) and general purpose graphics processing units (GPGPUs) can perform many time-consuming and computationally demanding processes much more quickly than a classical CPU can. In this paper, we describe the GPU-based implementation of the CASSERT algorithm for 3D protein structure similarity searching. This algorithm is based on the two-phase alignment of protein structures when matching fragments of the compared proteins. The GPU (GeForce GTX 560Ti: 384 cores, 2GB RAM) implementation of CASSERT (“GPU-CASSERT”) parallelizes both alignment phases and yields an average 180-fold increase in speed over its CPU-based, single-core implementation on an Intel Xeon E5620 (2.40GHz, 4 cores). In this paper, we show that massive parallelization of the 3D structure similarity search process on many-core GPU devices can reduce the execution time of the process, allowing it to be performed in real time. GPU-CASSERT is available at: http://zti.polsl.pl/dmrozek/science/gpucassert/cassert.htm.     

Human menopausal and pregnant mare serum gonadotrophins in murine superovulation regimens for transgenic applications

Superovulation is a fundamental procedure for generating transgenic rodents. While various methods exist, zygote yield/quality remain suboptimal, making these techniques open to refinement. All require a follicle stimulating and a luteinising effect. The former can be induced by pregnant mare serum gonadotrophin (PMSG) or other compounds like human menopausal gonadotrophin (HMG). While HMG can double zygote yield compared to PMSG, no study has compared their effects on embryo quality. Embryo yield could also be increased with PMSG: timing administration at estrus may further improve follicular recruitment. This study compared: (i) the efficacy of HMG/PMSG for producing viable embryos for microinjection; and (ii) the effect of HMG/PMSG administration at estrus on embryo yield. Whitten effect-induced estrous C57/Bl6xCBA F(1) hybrid mice were superovulated as follows: PMSG (day 1; 5 IU intraperitoneally) or HMG (days 1 and 2; 1 IU intramuscularly); all received human chorionic gonadotrophin (hCG) on day 3 (5 IU, intraperitoneally). Zygotes were retrieved following mating, morphologically assessed and microinjected with innocuous ZhAT1R construct (expressing LacZ reporter and human angiotensin II type 1 receptor) before transfer to pseudopregnant recipients. Pups were tested for the transgene by Southern blot. Neither HMG nor PMSG proved superior in improving embryo yield, morphology and short-term post-microinjection survival. However, HMG group micromanipulated embryos all failed to establish a pregnancy/generate transgenic pups, unlike their PMSG counterparts. While HMG can be used for superovulation, it appears to increase embryo vulnerability to the long-term effects of microinjection. Furthermore, the embryo yields associated with HMG can be replicated by timing PMSG injection to coincide with Whitten effect-induced estrus.     

Outcome signature genes in breast cancer: is there a unique set?

MOTIVATION: Predicting the metastatic potential of primary malignant tissues has direct bearing on the choice of therapy. Several microarray studies yielded gene sets whose expression profiles successfully predicted survival. Nevertheless, the overlap between these gene sets is almost zero. Such small overlaps were observed also in other complex diseases, and the variables that could account for the differences had evoked a wide interest. One of the main open questions in this context is whether the disparity can be attributed only to trivial reasons such as different technologies, different patients and different types of analyses. RESULTS: To answer this question, we concentrated on a single breast cancer dataset, and analyzed it by a single method, the one which was used by van't Veer et al. to produce a set of outcome-predictive genes. We showed that, in fact, the resulting set of genes is not unique; it is strongly influenced by the subset of patients used for gene selection. Many equally predictive lists could have been produced from the same analysis. Three main properties of the data explain this sensitivity: (1) many genes are correlated with survival; (2) the differences between these correlations are small; (3) the correlations fluctuate strongly when measured over different subsets of patients. A possible biological explanation for these properties is discussed. CONTACT: eytan.domany@weizmann.ac.il SUPPLEMENTARY INFORMATION: http://www.weizmann.ac.il/physics/complex/compphys/downloads/liate/