Many, but not all, lineage-specific genes can be explained by homology detection failure

Genes for which homologs can be detected only in a limited group of evolutionarily related species, called “lineage-specific genes,” are pervasive: Essentially every lineage has them, and they often comprise a sizable fraction of the group’s total genes. Lineage-specific genes are often interpreted as “novel” genes, representing genetic novelty born anew within that lineage. Here, we develop a simple method to test an alternative null hypothesis: that lineage-specific genes do have homologs outside of the lineage that, even while evolving at a constant rate in a novelty-free manner, have merely become undetectable by search algorithms used to infer homology. We show that this null hypothesis is sufficient to explain the lack of detected homologs of a large number of lineage-specific genes in fungi and insects. However, we also find that a minority of lineage-specific genes in both clades are not well explained by this novelty-free model. The method provides a simple way of identifying which lineage-specific genes call for special explanations beyond homology detection failure, highlighting them as interesting candidates for further study.

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Many but not all lineage-specific genes can be explained by homology detection failure

10.1101/2020.02.27.968420 ◽

2020 ◽

Cited By ~ 5

Author(s):

Caroline M. Weisman ◽

Andrew W. Murray ◽

Sean R. Eddy

Keyword(s):

Null Hypothesis ◽

Search Algorithms ◽

Homology Detection ◽

Simple Method ◽

Detection Failure ◽

Constant Rate ◽

Free Model ◽

Genetic Novelty ◽

Lineage Specific Genes ◽

Sizable Fraction

AbstractGenes for which homologs can be detected only in a limited group of evolutionarily related species, called “lineage-specific genes,” are pervasive: essentially every lineage has them, and they often comprise a sizable fraction of the group’s total genes. Lineage-specific genes are often interpreted as “novel” genes, representing genetic novelty born anew within that lineage. Here, we develop a simple method to test an alternative null hypothesis: that lineage-specific genes do have homologs outside of the lineage that, even while evolving at a constant rate in a novelty-free manner, have merely become undetectable by search algorithms used to infer homology. We show that this null hypothesis is sufficient to explain the lack of detected homologs of a large number of lineage-specific genes in fungi and insects. However, we also find that a minority of lineage-specific genes in both clades are not well-explained by this novelty-free model. The method provides a simple way of identifying which lineage-specific genes call for special explanations beyond homology detection failure, highlighting them as interesting candidates for further study.

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Mixing genome annotation methods in a comparative analysis inflates the apparent number of lineage-specific genes

10.1101/2022.01.13.476251 ◽

2022 ◽

Author(s):

Caroline M. Weisman ◽

Andrew M. Murray ◽

Sean R Eddy

Keyword(s):

Comparative Analysis ◽

Case Studies ◽

Dna Sequences ◽

Genome Annotation ◽

Gene Annotation ◽

Genome Sequences ◽

Gene Annotations ◽

Genetic Novelty ◽

The Impact ◽

Lineage Specific Genes

Comparisons of genomes of different species are used to identify lineage-specific genes, those genes that appear unique to one species or clade. Lineage-specific genes are often thought to represent genetic novelty that underlies unique adaptations. Identification of these genes depends not only on genome sequences, but also on inferred gene annotations. Comparative analyses typically use available genomes that have been annotated using different methods, increasing the risk that orthologous DNA sequences may be erroneously annotated as a gene in one species but not another, appearing lineage-specific as a result. To evaluate the impact of such 'annotation heterogeneity', we identified four clades of species with sequenced genomes with more than one publicly available gene annotation, allowing us to compare the number of lineage-specific genes inferred when differing annotation methods are used to those resulting when annotation method is uniform across the clade. In these case studies, annotation heterogeneity increases the apparent number of lineage-specific genes by up to 15-fold, suggesting that annotation heterogeneity is a substantial source of potential artifact.

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Numerical Simulation to Select Proper Strain Rates during CRS Consolidation Test

Periodica Polytechnica Civil Engineering ◽

10.3311/ppci.9650 ◽

2017 ◽

Author(s):

Abderrahmane Henniche ◽

Smain Belkacemi

Keyword(s):

Numerical Simulation ◽

Liquid Limit ◽

Strain Rates ◽

Relative Pressure ◽

Simple Method ◽

Initial Void Ratio ◽

Rate Dependent ◽

Constant Rate ◽

Good Agreement ◽

Incremental Loading

Constant rate of strain (CRS) and incremental loading (IL) consolidation tests are extensively used to measure consolidation properties of clayey soils. However, results of CRS test are usually strain rate dependent. In this study, a finite differences simulation of CRS test based on Terzaghi’s theory of consolidation is performed. The numerical simulation permits to evaluate a strain rates range satisfying a preset relative pressure criterion. Results of simulation show that the required relative pressure criterion can be verified, during the steady state stage of CRS test, only for particular types of soils and particular range of strain rates. Subsequently, a simple method is proposed to select, for a soil sample defined by its initial height, initial void ratio and liquid limit, an appropriate strain rates range satisfying the ASTM 4186-06 criterion. Comparison of previsions and experimental results reported in literature shows good agreement.

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Modeling Boundary-Dominated Flow in Hydraulically-Fractured Wells

10.2118/206345-ms ◽

2021 ◽

Author(s):

Hafiz Mustafa Ud Din Sheikh ◽

W. J. Lee ◽

H. S. Jha

Keyword(s):

Horizontal Wells ◽

Drainage Area ◽

Hydraulic Fractures ◽

Simple Method ◽

Shape Factors ◽

Fracture Spacing ◽

Aspect Ratios ◽

Constant Rate ◽

Spacing Ratio ◽

Half Length

Abstract This paper presents a simple method to model boundary-dominated flow in hydraulically fractured wells, including horizontal wells with multiple fractures. While these wells are almost always producedat more nearly constant BHP rather than constant rate, use of material-balance time transforms variable-rate production profiles to constant-rate profiles, allowing us to use the pseudo-steady-state (PSS) flow equation for modeling. However, the PSS equation requires use of shape factors in applications, and shape factors available in the literature are available only for square-shaped bounded reservoirs with hydraulic fractures. In this work, we derived shape factors for wells centered in rectangular-shaped drainage areas with different length-to-width aspect ratios. The superposition principle can be used to transform transient radial flow and transient linear flow solutions into bounded reservoir solutions. At large times (when boundary-dominated flow is established), results from these solutions are similar to those obtained from the PSS equation. Therefore, for a pre-defined reservoir geometry, pressure drop values from superimposed transient flow equationscan be substituted back into the PSS equation to calculate shape factors for that reservoir geometry.We used shape factors previously presented by other authors for square drainage areas to validate themethod before applying it to calculate shape factors for more general drainage area configurations. We present shape factors for different fracture half-length to fracture-spacing ratios ranging from 0.2 to 10. Calculated shape factors, when plotted against the fracture half-length to fracture-spacing ratio, produced a smooth curve which can be used to interpolate shape factor values for other fracture configurations. We present applications of this methodology to example low-permeability wells. The use of the PSS equation for wells with vertical fracturescan be extended to multi-fractured horizontal wells (MFHWs) by incorporating the number of fractures in the equation; hence, shape factorsderived for wells with vertical fractures can also be used for MFHWs. Although our results are rigorously correct only for fluids with constant compressibility, use of pseudo-pressure and pseudo-time transformations extend application to compressible fluids, notably gases. Using the PSS equation in production data analysis allows us to calculate contributing reservoir volume and drainage area in a simple manner not requiring use of specialized software.

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A simple way for producing holographic filters suitable for image improvement

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100108271 ◽

1978 ◽

Vol 36 (1) ◽

pp. 226-227

Author(s):

K.-H. Herrmann ◽

E. Reuber ◽

P. Schiske

Keyword(s):

Transfer Functions ◽

Diffraction Order ◽

Lateral Position ◽

Simple Method ◽

Spatial Frequencies ◽

Resolution Electron ◽

Wiener Filters ◽

Image Improvement ◽

Optical Reconstruction ◽

Set Up

Aposteriori deblurring of high resolution electron micrographs of weak phase objects can be performed by holographic filters [1,2] which are arranged in the Fourier domain of a light-optical reconstruction set-up. According to the diffraction efficiency and the lateral position of the grating structure, the filters permit adjustment of the amplitudes and phases of the spatial frequencies in the image which is obtained in the first diffraction order.In the case of bright field imaging with axial illumination, the Contrast Transfer Functions (CTF) are oscillating, but real. For different imageforming conditions and several signal-to-noise ratios an extensive set of Wiener-filters should be available. A simple method of producing such filters by only photographic and mechanical means will be described here.A transparent master grating with 6.25 lines/mm and 160 mm diameter was produced by a high precision computer plotter. It is photographed through a rotating mask, plotted by a standard plotter.

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Rotary Beveling for In Situ Thin-Section Microscopy of Cell Cultures

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100099192 ◽

1981 ◽

Vol 39 ◽

pp. 550-551

Author(s):

Dean A. Handley ◽

Jack T. Alexander ◽

Shu Chien

Keyword(s):

Cell Growth ◽

Cell Cultures ◽

Molecular Interactions ◽

Convenient Method ◽

Petri Dish ◽

Simple Method ◽

Thin Section Microscopy ◽

Thin Sectioning ◽

Organic Fluids

In situ preparation of cell cultures for ultrastructural investigations is a convenient method by which fixation, dehydration and embedment are carried out in the culture petri dish. The in situ method offers the advantage of preserving the native orientation of cell-cell interactions, junctional regions and overlapping configurations. In order to section after embedment, the petri dish is usually separated from the polymerized resin by either differential cryo-contraction or solvation in organic fluids. The remaining resin block must be re-embedded before sectioning. Although removal of the petri dish may not disrupt the native cellular geometry, it does sacrifice what is now recognized as an important characteristic of cell growth: cell-substratum molecular interactions. To preserve the topographic cell-substratum relationship, we developed a simple method of tapered rotary beveling to reduce the petri dish thickness to a dimension suitable for direct thin sectioning.

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