New SHH and Known SIX3 Variants in a Series of Latin American Patients with Holoprosencephaly

Holoprosencephaly (HPE) is the failure of the embryonic forebrain to develop into 2 hemispheres promoting midline cerebral and facial defects. The wide phenotypic variability and causal heterogeneity make genetic counseling difficult. Heterozygous variants with incomplete penetrance and variable expressivity in the <i>SHH</i>, <i>SIX3</i>, <i>ZIC2</i>, and <i>TGIF1</i> genes explain ∼25% of the known causes of nonchromosomal HPE. We studied these 4 genes and clinically described 27 Latin American families presenting with nonchromosomal HPE. Three new <i>SHH</i> variants and a third known <i>SIX3</i> likely pathogenic variant found by Sanger sequencing explained 15% of our cases. Genotype-phenotype correlation in these 4 families and published families with identical or similar driver gene, mutated domain, conservation of residue in other species, and the type of variant explain the pathogenicity but not the phenotypic variability. Nine patients, including 2 with <i>SHH</i> pathogenic variants, presented benign variants of the <i>SHH</i>, <i>SIX3</i>, <i>ZIC2</i>, and <i>TGIF1</i> genes with potential alteration of splicing, a causal proposition in need of further studies. Finding more families with the same <i>SIX3</i> variant may allow further identification of genetic or environmental modifiers explaining its variable phenotypic expression.

Synapomorphic variations in the THAP domains of human THAP proteins and their homologs

The THAP (Thanatos-associated protein) domain is a DNA-binding domain which binds DNA via a zinc coordinating C2CH motif. Although THAP domains share a conserved structural fold, they bind different DNA sequences in different THAP proteins, which in turn perform distinct cellular functions. In this study, we investigate (using multiple sequence alignment, in silico motif and secondary structure prediction) THAP domain conservation within the homologs of the human THAP (hTHAP) protein family. We report that there is significant variation in sequence and predicted secondary structure elements across hTHAP homologs. Interestingly, we report that the THAP domain can be either longer or shorter than the conventional 90 residues and the amino terminal C2CH motif within the THAP domain serves as a hotspot for insertion or deletion. Our results lay the foundation for future studies which will further our understanding of the evolution of THAP domain and regulation of its function.

Synapomorphic variations in the THAP domains of the human THAP protein family and its homologs

The THAP (Thanatos-associated protein) domain is a DNA-binding domain which binds DNA via a zinc coordinating C2CH motif. Although THAP domains share a conserved structural fold, they bind different DNA sequences in different THAP proteins which in turn perform distinct cellular functions. In this study, we investigate (using multiple sequence alignment, in silico motif and secondary structure prediction) THAP domain conservation within the homologs of the human THAP (hTHAP) protein family. We report that there is significant variation in sequence and predicted secondary structure elements across hTHAP homologs. Interestingly, we report that the THAP domain can be either longer or shorter than the conventional 90 residues and the amino terminal C2CH motif within the THAP domain serves as a hotspot for insertion or deletion. Our results lay the foundation for future studies which will further our understanding of the evolution of THAP domain and regulation of its function.

EMS1 and BRI1 control separate biological processes via extracellular domain diversity and intracellular domain conservation

In flowering plants, EMS1 (Excess Microsporocytes 1) perceives TPD1 (Tapetum Determinant 1) to specify tapeta, the last somatic cell layer nurturing pollen development. However, the signaling components downstream of EMS1 are relatively unknown. Here, we use a molecular complementation approach to investigate the downstream components in EMS1 signaling. We show that the EMS1 intracellular domain is functionally interchangeable with that of the brassinosteroid receptor BRI1 (Brassinosteroid Insensitive 1). Furthermore, expressing EMS1 together with TPD1 in the BRI1 expression domain could partially rescue bri1 phenotypes, and led to the dephosphorylation of BES1, a hallmark of active BRI1 signaling. Conversely, expressing BRI1 in the EMS1 expression domain could partially rescue ems1 phenotypes. We further show that PpEMS1 and PpTPD1 from the early land plant Physcomitrella patens could completely rescue ems1 and tpd1 phenotypes, respectively. We propose that EMS1 and BRI1 have evolved distinct extracellular domains to control different biological processes but can act via a common intracellular signaling pathway.

chroGPS2: differential analysis of epigenome maps in R

1Abstract1.1BackgroundsIn the last years we have faced an unprecedented growth in the availability of high-throughput epigenomics data related to the genomic distribution of epigenetic marks, namely transcription factors, histone modifications and other DNA binding proteins. This also pointed out the need for efficient tools for integration, visualization and functional analysis of genomics and epigenomics data. On this subject, we previously developed a computational framework, chroGPS, to integrate and visualize the associations between epigenetic factors and their relation to functional genetic elements in low-dimensional maps. We demonstrated the usefulness of our approach with several practical case studies based on well-defined biological hypothesis.1.2ResultsHere we introduce chroGPS version 2, a major update of our previously developed software with new functionalities for differential analysis of epigenomes. Methods are provided for efficient integration and comparison of data from different conditions or biological backgrounds, accounting and adjusting for systematic biases in order to provide an efficient and statistically robust base for differential analysis. We also include new useful functionalities for general data assessment and quality control prior to comparing maps, such as functions to study chromatin domain conservation between epigenomic backgrounds, to detect gross technical outliers and also to help in the selection of candidate marks for de-novo epigenome mapping. Our software, implemented in R as a Bioconductor package, provides detailed reference and user manuals to allow the final user to reproduce the presented case studies and use them as a starting point for generating and exploring epigenetic maps according to their own experimental needs.1.3ConclusionchroGPS2 extends our previously developed software, providing now a complete, intuitive, efficient and statistically robust framework for generation, visualization, characterization and differential analysis of epigenomic maps, in a way which is easy to adapt to different biological and technical backgrounds allowing exploration and hypothesis testing in multiple biological scenarios.

Adjoint Aerodynamic Design Optimization for Blades in Multistage Turbomachines—Part I: Methodology and Verification

The adjoint method for blade design optimization will be described in this two-part paper. The main objective is to develop the capability of carrying out aerodynamic blading shape design optimization in a multistage turbomachinery environment. To this end, an adjoint mixing-plane treatment has been proposed. In the first part, the numerical elements pertinent to the present approach will be described. Attention is paid to the exactly opposite propagation of the adjoint characteristics against the physical flow characteristics, providing a simple and consistent guidance in the adjoint method development and applications. The adjoint mixing-plane treatment is formulated to have the two fundamental features of its counterpart in the physical flow domain: conservation and nonreflectiveness across the interface. The adjoint solver is verified by comparing gradient results with a direct finite difference method and through a 2D inverse design. The adjoint mixing-plane treatment is verified by comparing gradient results against those by the finite difference method for a 2D compressor stage. The redesign of the 2D compressor stage further demonstrates the validity of the adjoint mixing-plane treatment and the benefit of using it in a multi-bladerow environment.