Colander: a probability-based support vector machine algorithm for automatic screening for CID spectra of phosphopeptides prior to database search

We developed a probability-based machine-learning program, Colander, to identify tandem mass spectra that are highly likely to represent phosphopeptides prior to database search. We identified statistically significant diagnostic features of phosphopeptide tandem mass spectra based on ion trap CID MS/MS experiments. Statistics for the features are calculated from 376 validated phosphopeptide spectra and 376 nonphosphopeptide spectra. A probability-based support vector machine (SVM) program, Colander, was then trained on five selected features. Data sets were assembled both from LC/LC-MS/MS analyses of large-scale phosphopeptide enrichments from proteolyzed cells, tissues and synthetic phosphopeptides. These data sets were used to evaluate the capability of Colander to select pS/pT-containing phosphopeptide tandem mass spectra. When applied to unknown tandem mass spectra, Colander can routinely remove 80% of tandem mass spectra while retaining 95% of phosphopeptide tandem mass spectra. The program significantly reduced computational time spent on database search by 60-90%. Furthermore, prefiltering tandem mass spectra representing phosphopeptides can increase the number of phosphopeptide identifications under a predefined false positive rate.     

不同耕作措施的温室气体排放日变化及最佳观测时间

在连续6 a耕作模式的基础上,利用静态箱-气相色谱法对常规耕作与免耕条件下小麦生育后期麦田CO2、CH4、N2O通量日变化进行了连续48 h观测,并确定1 d中最佳的观测时间。结果表明,常规耕作与免耕条件下小麦生育后期麦田CO2、CH4、N2O通量具有显著的日变化特征,常规耕作处理和免耕处理土壤表现为CH4的吸收汇、CO2、N2O的排放源。CH4日均吸收通量:常规耕作无秸秆还田处理(AC)>常规耕作秸秆还田处理(PC)>免耕(PZ);CO2日均排放通量:常规耕作秸秆还田处理(PC)>常规耕作无秸秆还田处理(AC)>免耕(PZ);N2O日均排放通量:常规耕作秸秆还田处理(PC)>常规耕作无秸秆还田处理(AC)>免耕(PZ)。相关性分析表明,常规耕作及免耕条件下CO2、CH4、N2O通量日变化与地表温度和5 cm地温呈极显著(P<0.01)或显著(P<0.05)的正相关关系,温度是决定温室气体日变化的主要决定因素。通过矫正系数和回归分析表明,在小麦生育后期(4—6月),CO2的最佳观测时间段在8:00—10:00,CH4为8:00—10:00,N2O为8:00—12:00。     

中国大阳岔寒武-奥陶系界线地层碳酸盐岩碳、氧同位素及其与牙形类演化序列相关性

采自吉林省太阳岔小羊桥寒武－奥陶系界线层型剖面１０１块泥晶灰岩的碳、氧稳定同位素分析数据表明：寒武－奥陶纪转换期间,δ１３Ｃ值曾发生了５次涨落现象,这些现象与牙形类演化序列具密切的相关性。它们被命名如下：１）ＰＣＭ低谷;２）ＴＣＭ低谷;３）ＨＳＳ峰;４）ＣＰＦ涨落,５）ＣＬＦ涨落。相同的涨落在澳大利亚黑山同期地层得到确认。碳同位素跨洲性同步涨落显然与全球环境变化有关,因此它是寒武－奥陶系界线地层洲际对比的一种有用工具。沉积岩石学和古生物学研究表明,δ１３Ｃ谷区与海平面低位和生物生产量下降有重要相关性。氧同位素值的分布区间为－９．８４％０—－６．６９‰,呈明显亏损现象,这种亏损现象表明样品均受到成岩作用影响。与碳同位素值对比研究发现,氧同位素值涨落与碳同位素涨落成正相关,或成负相关现象,这种相关性表明氧同位素原始信息并没有因成岩作用而全部丢失。     

The coagulase of Staphylococcus aureus 8325-4. Sequence analysis and virulence of site-specific coagulase-deficient mutants

The sequence of the coagulase gene (coa) from Staphylococcus aureus strain 8325-4 is reported. The deduced amino acid sequence of the coagulase protein is compared with previously reported sequences of coagulases from strains 213 and BB. The secreted mature forms of coagulase proteins are composed of three distinct segments: (i) the N-terminal 150-270 residues, which are c. 50% identical, (ii) a central region with high (greater than 90%) residue identities, and (iii) a C-terminal region composed of repeated 27-amino-acid residue sequences. The variable N-terminal sequences are probably responsible for antigenic differences among coagulases of different serotype. The region of coagulase which binds to prothrombin and activates it to form staphylothrombin is also located in the N-terminal half of the protein. A site-specific substitution mutation in the coa gene, which abolished plasma clotting activity, was isolated by recombinational allele-replacement in strains 8325-4 and M60. The Coa- mutants did not show diminished virulence in subcutaneous and intramammary infections of mice. No evidence for a role for coagulase in virulence of toxigenic or nontoxigenic strains was obtained. This contradicts findings of several groups using Coa- mutants generated by chemical mutagenesis and suggests that the earlier results were obtained with strains that had suffered additional mutations in virulence-related genes.     

Modeling the biomechanics of fetal movements

Fetal movements in the uterus are a natural part of development and are known to play an important role in normal musculoskeletal development. However, very little is known about the biomechanical stimuli that arise during movements in utero, despite these stimuli being crucial to normal bone and joint formation. Therefore, the objective of this study was to create a series of computational steps by which the forces generated during a kick in utero could be predicted from clinically observed fetal movements using novel cine-MRI data of three fetuses, aged 20–22 weeks. A custom tracking software was designed to characterize the movements of joints in utero, and average uterus deflection of \(6.95 \pm 0.41\) mm due to kicking was calculated. These observed displacements provided boundary conditions for a finite element model of the uterine environment, predicting an average reaction force of \(0.52 \pm 0.15\) N generated by a kick against the uterine wall. Finally, these data were applied as inputs for a musculoskeletal model of a fetal kick, resulting in predicted maximum forces in the muscles surrounding the hip joint of approximately 8 N, while higher maximum forces of approximately 21 N were predicted for the muscles surrounding the knee joint. This study provides a novel insight into the closed mechanical environment of the uterus, with an innovative method allowing elucidation of the biomechanical interaction of the developing fetus with its surroundings.     

Production of algae-based biodiesel using the continuous catalytic Mcgyan® process

This study demonstrates the production of algal biodiesel from Dunaliella tertiolecta, Nannochloropsis oculata, wild freshwater microalgae, and macroalgae lipids using a highly efficient continuous catalytic process. The heterogeneous catalytic process uses supercritical methanol and porous titania microspheres in a fixed bed reactor to catalyze the simultaneous transesterification and esterification of triacylglycerides and free fatty acids, respectively, to fatty acid methyl esters (biodiesel). Triacylglycerides and free fatty acids were converted to alkyl esters with up to 85% efficiency as measured by 300 MHz ¹H NMR spectroscopy. The lipid composition of the different algae was studied gravimetrically and by gas chromatography. The analysis showed that even though total lipids comprised upwards of 19% of algal dry weight the saponifiable lipids, and resulting biodiesel, comprised only 1% of dry weight. Thus highlighting the need to determine the triacylglyceride and free fatty acid content when considering microalgae for biodiesel production.     

Identification of Mechanosensitive Genes during Embryonic Bone Formation

Although it is known that mechanical forces are needed for normal bone development, the current understanding of how biophysical stimuli are interpreted by and integrated with genetic regulatory mechanisms is limited. Mechanical forces are thought to be mediated in cells by “mechanosensitive” genes, but it is a challenge to demonstrate that the genetic regulation of the biological system is dependant on particular mechanical forces in vivo. We propose a new means of selecting candidate mechanosensitive genes by comparing in vivo gene expression patterns with patterns of biophysical stimuli, computed using finite element analysis. In this study, finite element analyses of the avian embryonic limb were performed using anatomically realistic rudiment and muscle morphologies, and patterns of biophysical stimuli were compared with the expression patterns of four candidate mechanosensitive genes integral to bone development. The expression patterns of two genes, Collagen X (ColX) and Indian hedgehog (Ihh), were shown to colocalise with biophysical stimuli induced by embryonic muscle contractions, identifying them as potentially being involved in the mechanoregulation of bone formation. An altered mechanical environment was induced in the embryonic chick, where a neuromuscular blocking agent was administered in ovo to modify skeletal muscle contractions. Finite element analyses predicted dramatic changes in levels and patterns of biophysical stimuli, and a number of immobilised specimens exhibited differences in ColX and Ihh expression. The results obtained indicate that computationally derived patterns of biophysical stimuli can be used to inform a directed search for genes that may play a mechanoregulatory role in particular in vivo events or processes. Furthermore, the experimental data demonstrate that ColX and Ihh are involved in mechanoregulatory pathways and may be key mediators in translating information from the mechanical environment to the molecular regulation of bone formation in the embryo.     

Small Changes in Climate Can Profoundly Alter the Dynamics and Ecosystem Services of Tropical Crater Lakes

African tropical lakes provide vital ecosystem services including food and water to some of the fastest growing human populations, yet they are among the most understudied ecosystems in the world. The consequences of climate change and other stressors on the tropical lakes of Africa have been informed by long-term analyses, but these studies have largely focused on the massive Great Rift Valley lakes. Our objective was to evaluate how recent climate change has altered the functioning and services of smaller tropical lakes, which are far more abundant on the landscape. Based on a paired analysis of 20 years of high-resolution water column data and a paleolimnological record from a small crater lake in western Uganda, we present evidence that even a modest warming of the air (∼0.9°C increase over 20 years) and changes in the timing and intensity of rainfall can have significant consequences on the dynamics of this common tropical lake type. For example, we observed a significant nonlinear increase (R²_adj = 0.23, e.d.f. = 7, p<0.0001) in thermal stability over the past 20 years. This resulted in the expansion of anoxic waters and consequent deterioration of fish habitat and appears to have abated primary production; processes that may impair ecosystem services for a vulnerable human population. This study on a system representative of small tropical crater lakes highlights the far-reaching effects of global climatic change on tropical waters. Increased research efforts into tropical aquatic ecosystem health and the development of sound management practices are necessary in order to strengthen adaptive capabilities in tropical regions.     

Self-organized segmentation of time series: separating growth hormone secretion in acromegaly from normal controls.

The pulsatile pattern of growth hormone (GH) secretion was assessed by sampling blood every 10 min over 24 h in healthy subjects (n = 10) under normal food intake and under fasting conditions (n = 6) and in patients with a GH-producing tumor (acromegaly, n = 6), before and after treatment with the somatostatin analog octreotide. Using autocorrelation, we found no consistent separation in the temporal dynamics of GH secretion in healthy controls and acromegalic patients. Time series prediction based on a single neural network has recently been demonstrated to separate the secretory dynamics of parathyroid hormone in healthy controls from osteoporotic patients. To better distinguish the differences in GH dynamics in healthy subjects and patients, we tested time series predictions based on a single neural network and a more refined system of multiple neural networks acting in parallel (adaptive mixtures of local experts). Both approaches significantly separated GH dynamics under the various conditions. By performing a self-organized segmentation of the alternating phases of secretory bursts and quiescence of GH, we significantly improved the performance of the multiple network system over that of the single network. It thus may represent a potential tool for characterizing alterations of the dynamic regulation associated with diseased states.