<Emphasis Type="Italic">Arabidopsis thaliana</Emphasis> outer ovule integument morphogenesis: Ectopic expression of <Emphasis Type="Italic">KNAT1</Emphasis>reveals a compensation mechanism

Background  

The Arabidopsis outer ovule integument is a simple two-cell layered structure that grows around the developing embryo and develops into the outer layer of the seed coat. As one of the functions of the seed coat is the protection of the plant embryo, the outer ovule integument is an example for a plant organ whose morphogenesis has to be precisely regulated.     

Evolution of the leukotoxin promoter in genus Mannheimia

Background  

The Mannheimia species encompass a wide variety of bacterial lifestyles, including opportunistic pathogens and commensals of the ruminant respiratory tract, commensals of the ovine rumen, and pathogens of the ruminant integument. Here we present a scenario for the evolution of the leukotoxin promoter among representatives of the five species within genus Mannheimia. We also consider how the evolution of the leukotoxin operon fits with the evolution and maintenance of virulence.     

Recognition and binding of mismatch repair proteins at an oncogenic hot spot

Background  

The current investigation was undertaken to determine key steps differentiating G:T and G:A repair at the H-ras oncogenic hot spot within the nuclear environment because of the large difference in repair efficiency of these two mismatches.     

An algorithm for automatic evaluation of the spot quality in two-color DNA microarray experiments

Background  

Although DNA microarray technologies are very powerful for the simultaneous quantitative characterization of thousands of genes, the quality of the obtained experimental data is often far from ideal. The measured microarrays images represent a regular collection of spots, and the intensity of light at each spot is proportional to the DNA copy number or to the expression level of the gene whose DNA clone is spotted. Spot quality control is an essential part of microarray image analysis, which must be carried out at the level of individual spot identification. The problem is difficult to formalize due to the diversity of instrumental and biological factors that can influence the result.     

A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics

Background  

In current comparative proteomics studies, the large number of images generated by 2D gels is currently compared using spot matching algorithms. Unfortunately, differences in gel migration and sample variability make efficient spot alignment very difficult to obtain, and, as consequence most of the software alignments return noisy gel matching which needs to be manually adjusted by the user.     

In situ evaluation of surface roughness and micromorphology of temporary soft denture liner materials at different time intervals

Objective

To perform an in situ evaluation of surface roughness and micromorphology of two soft liner materials for dentures at different time intervals.

Background

The surface roughness of materials may influence the adhesion of micro‐organisms and inflammation of the mucosal tissues. The in situ evaluation of surface roughness and the micromorphology of soft liner materials over the course of time may present results different from those of in vitro studies, considering the constant presence of saliva and food, the changes in temperature and the pH level in the oral cavity.

Materials and methods

Forty‐eight rectangular specimens of each of the two soft liner materials were fabricated: a silicone‐based material (Mucopren Soft) and an acrylic resin‐based material (Trusoft). The specimens were placed in the dentures of 12 participants (n = 12), and the materials were evaluated for surface roughness and micromorphology at different time intervals: 0, 7, 30 and 60 days. Roughness (Ra) was evaluated by means of a roughness tester. Surface micromorphology was evaluated by scanning electron microscopy.

Results

Analysis of variance for randomised block design and Tukey's test showed that surface roughness values were lower in the groups using the silicone‐based material at all the time intervals (P < .0001). The average surface roughness was higher at time interval 0 than at the other intervals, for both materials (P < .0001). The surface micromorphology showed that the silicone material presented a more regular and smoother surface than the acrylic resin‐based material.

Conclusion

The surface roughness of acrylic resin‐based and silicone‐based denture soft liner materials decreased after 7 days of evaluation, leading to a smoother surface over time. The silicone‐based material showed lower roughness values and a smoother surface than the acrylic resin‐based material, thereby making it preferred when selecting more appropriate material, due its tendency to promote less biofilm build‐up.     

Protein binding hot spots and the residue-residue pairing preference: a water exclusion perspective

Background  

A protein binding hot spot is a small cluster of residues tightly packed at the center of the interface between two interacting proteins. Though a hot spot constitutes a small fraction of the interface, it is vital to the stability of protein complexes. Recently, there are a series of hypotheses proposed to characterize binding hot spots, including the pioneering O-ring theory, the insightful 'coupling' and 'hot region' principle, and our 'double water exclusion' (DWE) hypothesis. As the perspective changes from the O-ring theory to the DWE hypothesis, we examine the physicochemical properties of the binding hot spots under the new hypothesis and compare with those under the O-ring theory.     

Profound influence of microarray scanner characteristics on gene expression ratios: analysis and procedure for correction

Background  

High throughput gene expression data from spotted cDNA microarrays are collected by scanning the signal intensities of the corresponding spots by dedicated fluorescence scanners. The major scanner settings for increasing the spot intensities are the laser power and the voltage of the photomultiplier tube (PMT). It is required that the expression ratios are independent of these settings. We have investigated the relationships between PMT voltage, spot intensities, and expression ratios for different scanners, in order to define an optimal scanning procedure.     

Cytomegalovirus antibodies in dried blood spots: a minimally invasive method for assessing stress,immune function,and aging

Background  

Cytomegalovirus (CMV) is a prevalent herpesvirus with links to both stress and aging. This paper describes and validates a minimally invasive method for assessing antibodies against CMV in finger stick whole blood spot samples for use as an indirect marker of an aspect of cell-mediated immunity.     

Microarray image analysis: background estimation using quantile and morphological filters

Background  

In a microarray experiment the difference in expression between genes on the same slide is up to 10³ fold or more. At low expression, even a small error in the estimate will have great influence on the final test and reference ratios. In addition to the true spot intensity the scanned signal consists of different kinds of noise referred to as background. In order to assess the true spot intensity background must be subtracted. The standard approach to estimate background intensities is to assume they are equal to the intensity levels between spots. In the literature, morphological opening is suggested to be one of the best methods for estimating background this way.     

Hot spot prediction in protein-protein interactions by an ensemble system

Background

Hot spot residues are functional sites in protein interaction interfaces. The identification of hot spot residues is time-consuming and laborious using experimental methods. In order to address the issue, many computational methods have been developed to predict hot spot residues. Moreover, most prediction methods are based on structural features, sequence characteristics, and/or other protein features.

Results

This paper proposed an ensemble learning method to predict hot spot residues that only uses sequence features and the relative accessible surface area of amino acid sequences. In this work, a novel feature selection technique was developed, an auto-correlation function combined with a sliding window technique was applied to obtain the characteristics of amino acid residues in protein sequence, and an ensemble classifier with SVM and KNN base classifiers was built to achieve the best classification performance.

Conclusion

The experimental results showed that our model yields the highest F1 score of 0.92 and an MCC value of 0.87 on ASEdb dataset. Compared with other machine learning methods, our model achieves a big improvement in hot spot prediction.

Availability

http://deeplearner.ahu.edu.cn/web/HotspotEL.htm.

     

Extended morphological processing: a practical method for automatic spot detection of biological markers from microscopic images

Background  

A reliable extraction technique for resolving multiple spots in light or electron microscopic images is essential in investigations of the spatial distribution and dynamics of specific proteins inside cells and tissues. Currently, automatic spot extraction and characterization in complex microscopic images poses many challenges to conventional image processing methods.     

Characterization and simulation of cDNA microarray spots using a novel mathematical model

Background  

The quality of cDNA microarray data is crucial for expanding its application to other research areas, such as the study of gene regulatory networks. Despite the fact that a number of algorithms have been suggested to increase the accuracy of microarray gene expression data, it is necessary to obtain reliable microarray images by improving wet-lab experiments. As the first step of a cDNA microarray experiment, spotting cDNA probes is critical to determining the quality of spot images.     

MASQOT: a method for cDNA microarray spot quality control

Background  

cDNA microarray technology has emerged as a major player in the parallel detection of biomolecules, but still suffers from fundamental technical problems. Identifying and removing unreliable data is crucial to prevent the risk of receiving illusive analysis results. Visual assessment of spot quality is still a common procedure, despite the time-consuming work of manually inspecting spots in the range of hundreds of thousands or more.     

Nuclear and mitochondrial data reveal different evolutionary processes in the Lake Tanganyika cichlid genus <Emphasis Type="Italic">Tropheus</Emphasis>

Background  

Cichlid fishes are notorious for their wealth of intra- and interspecific colour pattern diversity. In Lake Tanganyika, the endemic genus Tropheus represents the most impressive example for geographic variation in the pattern and hue of integument colouration, but the taxonomy of the over 100 mostly allopatric colour morphs remains to a large degree unresolved. Previous studies of mitochondrial DNA sequence data revealed polyphyly of the six nominally described species and complex phylogeographic patterns influenced by lake level fluctuations and population admixture, and suggested the parallel evolution of similar colour patterns in divergent evolutionary lineages. A gene tree of a rapidly radiating group may be subject to incomplete and stochastic lineage sorting, and to overcome this problem we used multi-locus, nuclear AFLP data in comparison with mtDNA sequences to study diversification, migration and introgression in Tropheus colour morphs in Lake Tanganyika.     

Daily grazing time as a risk factor for alterations at the hock joint integument in dairy cows

Structural changes lead to increasing sizes of dairy herds and a reduction in grazing use. Thus, cows spend more time in the barn and become more exposed to the barn environment. The cubicle surface can result in damages of the cows’ hock joint integument. Pasture is generally seen as a beneficial environment for cows. We hypothesized that a higher number of daily grazing hours reduce the probability of hock joint alterations in dairy cows from large herds. In total, 3148 lactating cows from 36 grazing and 20 zero-grazing dairy herds, with an average herd size of 173 cows, were assessed individually on one randomly selected body side for alterations in hock integument (score 0 for no alterations or hairless areas <2 cm, 1 for at least one hairless area of ⩾2 cm, 2 for lesion or swelling). The cows were further assessed for lameness and cleanliness. Information on breed, parity and days in milk per cow was extracted from a national database. Cubicle surface was evaluated for each herd. Daily grazing hours 30 days before herd visits were recorded by the stockmen and later categorized as follows: zero hours (zero-grazing), few hours (3 to 9) and many hours (>9 to 21). The effects of daily grazing hours and other potential cow and herd-level risk factors were evaluated for their impact on hock integument alterations using a logistic analysis with a multi-level model structure. The probability for hock integument alterations such as hair loss, lesions or swellings decreased with increasing amount of grazing hours (odds of 3 to 9 h 2.2 times and odds of >9 to 21 h 4.8 times lower than of zero-grazing). The probability for only lesions or swellings decreased with >9 to 21 grazing hours (odds 2.1 times) but not with 3 to 9 h (odds 1.0 times) compared with zero-grazing. Lameness, hard cubicle surface and Danish Holstein v. other breeds showed an increasing effect on the probability for integument alterations. Increase in days in milk only showed an increasing effect on the probability for lesions and swellings. We concluded that a long daily stay on pasture is most beneficial for the hock joint integument of a dairy cow.     

APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility

Background  

It is well known that most of the binding free energy of protein interaction is contributed by a few key hot spot residues. These residues are crucial for understanding the function of proteins and studying their interactions. Experimental hot spots detection methods such as alanine scanning mutagenesis are not applicable on a large scale since they are time consuming and expensive. Therefore, reliable and efficient computational methods for identifying hot spots are greatly desired and urgently required.     

Improving missing value imputation of microarray data by using spot quality weights

Background  

Microarray technology has become popular for gene expression profiling, and many analysis tools have been developed for data interpretation. Most of these tools require complete data, but measurement values are often missing A way to overcome the problem of incomplete data is to impute the missing data before analysis. Many imputation methods have been suggested, some na?ve and other more sophisticated taking into account correlation in data. However, these methods are binary in the sense that each spot is considered either missing or present. Hence, they are depending on a cutoff separating poor spots from good spots. We suggest a different approach in which a continuous spot quality weight is built into the imputation methods, allowing for smooth imputations of all spots to larger or lesser degree.     

Scale-adaptive surface modeling of vascular structures

Background  

The effective geometric modeling of vascular structures is crucial for diagnosis, therapy planning and medical education. These applications require good balance with respect to surface smoothness, surface accuracy, triangle quality and surface size.