DECA,A Comprehensive,Automatic Post-processing Program for HDX-MS Data*

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Highlights

• •Open source software for comprehensive HDX-MS data analysis.
• •Automatic back-exchange correction options.
• •Rigorous statistical analysis of the significance of uptake differences.
• •High quality visualization tools.

     

Conditional gene inactivation by combining tetracycline-mediated transcriptional repression and auxin-inducible degron-mediated degradation

Characterizing the functions of essential cell cycle control genes requires tight and rapid inducible gene inactivation. Drawbacks of current conditional depletion approaches include slow responses and incomplete depletion. We demonstrated that by integrating the tetracycline-controlled promoter system and the auxin-inducible degron (AID) system together, AID-tagged proteins can be downregulated more efficiently than the individual technology alone. When used in conjunction with CRISPR-Cas9-mediated disruption of the endogenous locus, this system facilitates the analysis of essential genes by allowing rapid and tight conditional depletion, as we have demonstrated using several cell cycle-regulatory genes including cyclin A, CDK2, and TRIP13. The vectors constructed in this study allow expression of AID-fusion proteins under the control of tetracycline-controlled promoters and should be useful in studies requiring rapid and tight suppression of gene expression in mammalian cells.     

Species delimitation methods reveal cryptic diversity in the Hypnea cornuta complex (Cystocloniaceae,Rhodophyta)

The simple and convergent morphologies of many red algae make these species difficult to identify using traditional morphological characters. Many cryptic species have been described in recent years based on molecular datasets, and this has led to the application of an integrative taxonomy approach in species delimitation. Here, we performed several species delimitation methods (mBGD, ABGD, SPN, PTP, GMYCs and GMYCm) based on two different loci (COI-5P and rbcL) in species of the Hypnea cornuta complex. These methods were combined with morphological and phylogenetic data, extensive sampling, analysis of topotype material, and historically relevant herbarium samples. Our findings demonstrate that the groups morphologically assigned to H. cornuta and H. stellulifera consist of five different cryptic species. H. cornuta is a polyphyletic taxon composed of three well-separated lineages, thus requiring sequencing of type or topotype specimens to determine which one is Hypnea cornuta sensu stricto. We have revealed that the distribution of H. stellulifera is limited to Asia, while the Brazilian specimens initially assigned to this species were clarified as a new endemic species: Hypnea cryptica sp. nov. Our results indicated that only an integrative approach combining several lines of evidence, including morphology, nomenclature history, molecular data, biogeography and ecology can correctly solve the taxonomic status of widely distributed cryptic species.     

MotifAnalyzer‐PDZ: A computational program to investigate the evolution of PDZ‐binding target specificity

Recognition of short linear motifs (SLiMs) or peptides by proteins is an important component of many cellular processes. However, due to limited and degenerate binding motifs, prediction of cellular targets is challenging. In addition, many of these interactions are transient and of relatively low affinity. Here, we focus on one of the largest families of SLiM‐binding domains in the human proteome, the PDZ domain. These domains bind the extreme C‐terminus of target proteins, and are involved in many signaling and trafficking pathways. To predict endogenous targets of PDZ domains, we developed MotifAnalyzer‐PDZ, a program that filters and compares all motif‐satisfying sequences in any publicly available proteome. This approach enables us to determine possible PDZ binding targets in humans and other organisms. Using this program, we predicted and biochemically tested novel human PDZ targets by looking for strong sequence conservation in evolution. We also identified three C‐terminal sequences in choanoflagellates that bind a choanoflagellate PDZ domain, the Monsiga brevicollis SHANK1 PDZ domain (mbSHANK1), with endogenously‐relevant affinities, despite a lack of conservation with the targets of a homologous human PDZ domain, SHANK1. All three are predicted to be signaling proteins, with strong sequence homology to cytosolic and receptor tyrosine kinases. Finally, we analyzed and compared the positional amino acid enrichments in PDZ motif‐satisfying sequences from over a dozen organisms. Overall, MotifAnalyzer‐PDZ is a versatile program to investigate potential PDZ interactions. This proof‐of‐concept work is poised to enable similar types of analyses for other SLiM‐binding domains (e.g., MotifAnalyzer‐Kinase). MotifAnalyzer‐PDZ is available at http://motifAnalyzerPDZ.cs.wwu.edu .     

Large‐depth‐of‐field full‐field optical angiography

A large‐depth‐of‐field full‐field optical angiography (LD‐FFOA) method is developed to expand the depth‐of‐field (DOF) using a contrast pyramid fusion algorithm (CPFA). The absorption intensity fluctuation modulation effect is utilized to obtain full‐field optical angiography (FFOA) images at different focus positions. The CPFA is used to process these FFOA images with different focuses. By selecting high‐contrast areas, the CPFA can highlight the characteristics and details of blood vessels to obtain LD‐FFOA images. In the optimal case of the proposed method, the DOF for FFOA is more than tripled using 10 differently focused FFOA images. Both the phantom and animal experimental results show that the LD‐FFOA resolves FFOA defocusing issues induced by surface and thickness inhomogeneities in biological samples. The proposed method can be potentially applied to practical biological experiments.      

3D Printing: Applications in evolution and ecology

In the commercial and medical sectors, 3D printing is delivering on its promise to enable a revolution. However, in the fields of Ecology and Evolution we are only on the brink of embracing the advantages that 3D printing can offer. Here we discuss examples where the process has enabled researchers to develop new techniques, work with novel species, and to enhance the impact of outreach activities. Our aim is to showcase the potential that 3D printing offers in terms of improved experimental techniques, greater flexibility, reduced costs and promoting open science, while also discussing its limitations. By taking a general overview of studies using the technique from fields across the broad range of Ecology and Evolution, we show the flexibility of 3D printing technology and aim to inspire the next generation of discoveries.     

Computational methods in protein structure prediction

This review presents the advances in protein structure prediction from the computational methods perspective. The approaches are classified into four major categories: comparative modeling, fold recognition, first principles methods that employ database information, and first principles methods without database information. Important advances along with current limitations and challenges are presented.     

籼稻稻米蛋白质含量与外观品质性状间不同遗传体系的条件遗传相关分析

选用稻米蛋白质含量等品质差异较大的7个籼型不育系(A)及相应的保持系(B)与5个籼型恢复系(R)杂交,组成7×5不完全双列杂交组合。应用包括胚乳、细胞质和母体植株基因的遗传主效应以及基因型×环境互作效应的数量性状遗传模型及非条件和条件分析方法,研究了籼稻稻米蛋白质含量与外观品质性状间的遗传相关性,进一步揭示了籼稻糙米重、稻米直链淀粉含量对稻米蛋白质含量与外观品质性状间遗传相关性的影响。非条件分析的结果表明,除了与糙米厚的相关性未达到显著水平以外,蛋白质含量与其它稻米外观品质性状间的遗传相关性均达极显著水平,其中与糙米宽间的相关性表现为正值,其余为负向相关。条件分析的结果显示,糙米重和直链淀粉含量对稻米蛋白质含量与外观品质性状间的遗传相关性均可产生较大的影响。糙米重主要通过基因型×环境互作效应影响蛋白质含量与外观品质性状间的遗传相关性,其中对蛋白质含量与糙米长、糙米宽、糙米厚间遗传相关性的影响主要表现为负向作用,而对蛋白质含量与糙米长宽比、糙米长厚比间遗传相关性的影响则表现为正向作用。稻米直链淀粉主要通过细胞质遗传主效应和母体加性效应影响蛋白质含量与糙米长、糙米长宽比、糙米长厚比间的遗传相关性,而对蛋白质含量与糙米宽间的相关性影响主要表现为负向作用。