The use of a hybrid linear trap/FT-ICR mass spectrometer for on-line high resolution/high mass accuracy bottom-up sequencing.

In this work we present a hybrid linear trap/Fourier transform ion cyclotron resonance (ICR) mass spectrometer to perform protein sequencing using the bottom-up approach. We demonstrate that incorporation of the linear trap greatly enhances the overall performance of the hybrid system for the study of complex peptide mixtures separated by fast high-performance liquid chromatography gradients. The ability to detect in the linear trap enables employment of automatic gain control to greatly reduce space charging in the ICR cell irregardless of ion flux. Resulting accurate mass measurements of 2 ppm or better using external calibration are achieved for the base peak as well as ions at 2% relative abundance. The linear trap is used to perform ion accumulation and activation prior to detection in the ICR cell which increases the scan rate. The increased duty cycle allows for data-dependent mass analysis of coeluting peptides to be acquired increasing protein sequence coverage without increasing the gradient length. In addition, the linear trap could be used as an ion detection device to perform simultaneous detection of tandem mass spectra with full scan mass spectral detection in the ICR cell resulting in the fastest scan cycles for performing bottom-up sequencing of protein digests. Comparisons of protein sequence coverage are presented for product ion detection in the linear trap and ICR cell.     

A miniature Wright peak-flow meter.

A new miniature Wright peak-flow meter has been designed and produced. The meter is tubular with a spring-loaded piston and a longitudinal slot through which air escapes. Its dynamic characteristics have been carefully designed to make it respond only to peak flow and not to rate of rise. Performance tests on early instruments showed fairly close correlation with the Wright peak-flow meter but with a constant error of + 38 1/min. On later models the correlation was increased to 0.990 and the error reduced to + 3%. The mini-meter correlates as well with the standard instrument as two standard instruments correlate with each other and should prove useful clinically.     

A simple method for the determination of section thickness with high accuracy.

Using the partial carbon-coating of histological sections their thickness was determined by a relatively simple and accurate method. Calculations were based on the instrumental recording of the distance of focus change between the upper and lower section-surfaces. Determination of tissue refractive index was not required. Results compared favourably with those of more complicated techniques.     

Probe-level linear model fitting and mixture modeling results in high accuracy detection of differential gene expression

Background  

The identification of differentially expressed genes (DEGs) from Affymetrix GeneChips arrays is currently done by first computing expression levels from the low-level probe intensities, then deriving significance by comparing these expression levels between conditions. The proposed PL-LM (Probe-Level Linear Model) method implements a linear model applied on the probe-level data to directly estimate the treatment effect. A finite mixture of Gaussian components is then used to identify DEGs using the coefficients estimated by the linear model. This approach can readily be applied to experimental design with or without replication.     

剂量精确的大鼠无创气管滴注方法

目的建立一种滴注剂量精确的大鼠无创气管滴注方法。方法选用一次性使用静脉输液针的胶管制作套管,透射光插管法行大鼠气管插管,微量进样器平头针经由套管插入气管进行滴注。滴注液体为生理盐水,滴注剂量5～200μL,精确度为1μL。结果在体重200—350g的10只大鼠上共完成50次气管滴注操作,实验过程中和实验之后大鼠均无异常表现。结论套管微量进样器法具有无创、精确、安全的特点,可广泛应用于大鼠经气管给药或染毒的各类研究。     

California's male suicide rate at record high.

Breast cancer is the most commonly occurring cancer in women and, until recently surpassed by lung cancer, was the leading cause of cancer-related death in women. It is the leading cause of death in women aged 39 to 44 years. The American Cancer Society has estimated that there will be 135,000 new cases of breast cancer and 42,300 breast cancer-related deaths in 1988. It is now predicted that breast cancer will develop in one out of every ten women in the United States. Given the clinical and public health significance of breast cancer, annual screening with mammography and clinical breast examination is recommended for women aged 50 and older to reduce breast cancer mortality.     

A high standard metabolic rate constrains juvenile growth

The allocation of energy to various components of an individual's energy budget is often viewed as a competitive process. As such, a tradeoff may exist between production (growth) and maintenance metabolism. One view of a potential tradeoff, termed “the principle of allocation”, suggests that individuals with lower maintenance metabolic expenditures may have higher growth rates. To determine whether such a tradeoff exists, I analyzed the relationship between growth rate and maintenance metabolism of 225 juvenile snapping turtles housed in the laboratory. I measured growth from hatching to 6 months of age, and then measured oxygen consumption and calculated standard metabolic rate. Mean growth rate was 0.19 g d⁻ and mean standard metabolic rate (SMR) was 1.41 kJ d⁻. Maintenance metabolism and growth were negatively correlated after both were adjusted for body mass. The results support the “principle of allocation” theory: individuals with higher standard metabolic rates tended to have low growth rates.     

A novel method for high accuracy sumoylation site prediction from protein sequences

Background

The use of novel algorithmic techniques is pivotal to many important problems in life science. For example the sequencing of the human genome [1] would not have been possible without advanced assembly algorithms. However, owing to the high speed of technological progress and the urgent need for bioinformatics tools, there is a widening gap between state-of-the-art algorithmic techniques and the actual algorithmic components of tools that are in widespread use.

Results

To remedy this trend we propose the use of SeqAn, a library of efficient data types and algorithms for sequence analysis in computational biology. SeqAn comprises implementations of existing, practical state-of-the-art algorithmic components to provide a sound basis for algorithm testing and development. In this paper we describe the design and content of SeqAn and demonstrate its use by giving two examples. In the first example we show an application of SeqAn as an experimental platform by comparing different exact string matching algorithms. The second example is a simple version of the well-known MUMmer tool rewritten in SeqAn. Results indicate that our implementation is very efficient and versatile to use.

Conclusion

We anticipate that SeqAn greatly simplifies the rapid development of new bioinformatics tools by providing a collection of readily usable, well-designed algorithmic components which are fundamental for the field of sequence analysis. This leverages not only the implementation of new algorithms, but also enables a sound analysis and comparison of existing algorithms.     

A comparison of three estimators of the population-scaled recombination rate: accuracy and robustness

We have performed simulations to assess the performance of three population genetics approximate-likelihood methods in estimating the population-scaled recombination rate from sequence data. We measured performance in two ways: accuracy when the sequence data were simulated according to the (simplistic) standard model underlying the methods and robustness to violations of many different aspects of the standard model. Although we found some differences between the methods, performance tended to be similar for all three methods. Despite the fact that the methods are not robust to violations of the underlying model, our simulations indicate that patterns of relative recombination rates should be inferred reasonably well even if the standard model does not hold. In addition, we assess various techniques for improving the performance of approximate-likelihood methods. In particular we find that the composite-likelihood method of Hudson (2001) can be improved by including log-likelihood contributions only for pairs of sites that are separated by some prespecified distance.     

MUSCLE: multiple sequence alignment with high accuracy and high throughput

We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.     

A pulsed diagonal-beam ultrasonic airflow meter

The construction and specific function of a new ultrasonic flowmeter are described. The mean velocity of the respiratory airflow is calculated by measuring the transit times of short ultrasonic pulse trains, simultaneously transmitted upstream and downstream at a 500-Hz rate. The flowmeter system consists of a control unit and a separate flow head. The former includes the power supplies, a controlling microprocessor, most of the signal-processing circuitry, and three analog outputs for flow, volume, and temperature. The flow head contains the respiratory tube with a constant circular cross section (length 90 mm, diam 20 mm, dead space 35 ml), a fast temperature sensor, two electronic circuits for processing of flow and temperature data, and a sound transmission channel with two capacitive ultrasonic wide-band transducers. This respiratory airflow meter, suitable for spirometric maneuvers (vital capacity, forced vital capacity) as well as for long-term breath-by-breath respiratory analysis, is extremely fast (response time 1-2 ms) and accurate (volume accuracy with room air +/- 0.7%), with low noise (below 9 ml/s), a wide flow range (bidirectional from 0 to 9 l/s), and a flat frequency response up to 70 Hz.