CDCA7 is an evolutionarily conserved hemimethylated DNA sensor in eukaryotes.

Mutations of the SNF2 family ATPase HELLS and its activator CDCA7 cause immunodeficiency, centromeric instability, and facial anomalies syndrome, characterized by DNA hypomethylation at heterochromatin. It remains unclear why CDCA7-HELLS is the sole nucleosome remodeling complex whose deficiency abrogates the maintenance of DNA methylation. We here identify the unique zinc-finger domain of CDCA7 as an evolutionarily conserved hemimethylation-sensing zinc finger (HMZF) domain.

The Origin and Evolution of Sex Peptide and Sex Peptide Receptor Interactions.

Post-mating responses play a vital role in successful reproduction across diverse species. In fruit flies, sex peptide binds to the sex peptide receptor, triggering a series of post-mating responses. However, the origin of sex peptide receptor predates the emergence of sex peptide.

Structural insights into the recognition of the A/T-rich motif in target gene promoters by the LMX1a homeobox domain.

LIM homeodomain transcription factor 1-alpha (LMX1a) is a neuronal lineage-specific transcription activator that plays an essential role during the development of midbrain dopaminergic (mDA) neurons. LMX1a induces the expression of multiple key genes, which ultimately determine the morphology, physiology, and functional identity of mDA neurons. This function of LMX1a is dependent on its homeobox domain.

The origin and structural evolution of de novo genes in Drosophila.

Recent studies reveal that de novo gene origination from previously non-genic sequences is a common mechanism for gene innovation. These young genes provide an opportunity to study the structural and functional origins of proteins. Here, we combine high-quality base-level whole-genome alignments and computational structural modeling to study the origination, evolution, and protein structures of lineage-specific de novo genes.

CDCA7 is a hemimethylated DNA adaptor for the nucleosome remodeler HELLS.

Mutations of the SNF2 family ATPase HELLS and its activator CDCA7 cause immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome, characterized by hypomethylation at heterochromatin. The unique zinc-finger domain, zf-4CXXC_R1, of CDCA7 is widely conserved across eukaryotes but is absent from species that lack HELLS and DNA methyltransferases, implying its specialized relation with methylated DNA. Here we demonstrate that zf-4CXXC_R1 acts as a hemimethylated DNA sensor.

The Origin and Evolution of Sex Peptide and Sex Peptide Receptor Interactions.

Post-mating responses play a vital role in successful reproduction across diverse species. In fruit flies, sex peptide (SP) binds to the sex peptide receptor (SPR), triggering a series of post-mating responses. However, the origin of SPR predates the emergence of SP.

Autoregulatory control of mitochondrial glutathione homeostasis.

Mitochondria must maintain adequate amounts of metabolites for protective and biosynthetic functions. However, how mitochondria sense the abundance of metabolites and regulate metabolic homeostasis is not well understood. In this work, we focused on glutathione (GSH), a critical redox metabolite in mitochondria, and identified a feedback mechanism that controls its abundance through the mitochondrial GSH transporter, SLC25A39.

Fish Rhbdd3 positively regulates IFN response through RIG-I signaling pathway.

Rhomboid domain-containing protein 3 (Rhbdd3) is a member of the rhomboid family, which can modulate the innate immune response in mammals. Nonetheless, the function and regulatory mechanism of fish Rhbdd3 during viral infection have not been characterized. In this study, Rhbdd3 was firstly cloned from common carp (Cyprinus carpio) and nominated as CcRhbdd3.

Method for efficient calculating earth pressure of retaining wall considering plant transpiration.

An accurate estimation of earth pressure on retaining walls is imperative to achieving its design. This paper presents an analytical method framework that considers the effect of plant transpiration relative to the traditional calculation approaches. Specifically, a closed-form solution for one-dimensional steady unsaturated flow considering plant transpiration is incorporated into a representation of effective stress to obtain the changes in matric suction, and effective stress.

The two-component system expression patterns and immune regulatory mechanism of with different genotypes at the early stage of infection in THP-1 cells.

must endure various challenging circumstances while being swallowed by phagocytes of the innate immune system. Moreover, bacteria should recognize and react to environmental signals quickly in host cells. Two-component system (TCS) is an important way for bacteria to perceive external environmental signals and transmit them to the interior to trigger the associated regulatory mechanism.

The origin and structural evolution of genes in .

Although previously thought to be unlikely, recent studies have shown that gene origination from previously non-genic sequences is a relatively common mechanism for gene innovation in many species and taxa. These young genes provide a unique set of candidates to study the structural and functional origination of proteins. However, our understanding of their protein structures and how these structures originate and evolve are still limited, due to a lack of systematic studies.

Graphene-based Pancharatnam-Berry phase metasurface in the terahertz domain for dynamically independent amplitude and phase manipulation.

Dynamic and independent amplitude and phase manipulation are the paramount demand for many advanced wavefronts engineering applications. Currently, the coupling issue between the amplitude and phase hinders the efficient modulation wavefront's further implementation. This paper proposes and numerically demonstrates the bi-layer stacked graphene Pancharatnam-Berry (P-B) phase metasurface and mono-layer graphene P-B phase metasurface to address the above problem.

Structures of a mobile intron retroelement poised to attack its structured DNA target.

Group II introns are ribozymes that catalyze their self-excision and function as retroelements that invade DNA. As retrotransposons, group II introns form ribonucleoprotein (RNP) complexes that roam the genome, integrating by reversal of forward splicing. Here we show that retrotransposition is achieved by a tertiary complex between a structurally elaborate ribozyme, its protein mobility factor, and a structured DNA substrate.

Terahertz quasi non-diffraction Bessel vortex beam generation using three lattice types reflective metasurface.

Bandwidth, orbital-angular momentum (OAM) divergence, and mode purity are the three critical issues for the practical terahertz orbital angular momentum manipulation, especially in the next sixth-generation (6G) communication system. Here we propose the broadband high-order Bessel vortex beam carrying multiple OAM modes reflective metasurface in the terahertz domain. The simulation results agree with the theoretical expectation, and the diffracting divergence of OAM vortex beam characteristics has been alleviated.

Intermolecular Interactions Drive Protein Adaptive and Coadaptive Evolution at Both Species and Population Levels.

Proteins are the building blocks for almost all the functions in cells. Understanding the molecular evolution of proteins and the forces that shape protein evolution is essential in understanding the basis of function and evolution. Previous studies have shown that adaptation frequently occurs at the protein surface, such as in genes involved in host-pathogen interactions.

Behavioral and Genomic Sensory Adaptations Underlying the Pest Activity of Drosophila suzukii.

Studying how novel phenotypes originate and evolve is fundamental to the field of evolutionary biology as it allows us to understand how organismal diversity is generated and maintained. However, determining the basis of novel phenotypes is challenging as it involves orchestrated changes at multiple biological levels. Here, we aim to overcome this challenge by using a comparative species framework combining behavioral, gene expression, and genomic analyses to understand the evolutionary novel egg-laying substrate-choice behavior of the invasive pest species Drosophila suzukii.

Molecular mechanism of histone variant H2A.B on stability and assembly of nucleosome and chromatin structures.

Background: H2A.B, the most divergent histone variant of H2A, can significantly modulate nucleosome and chromatin structures. However, the related structural details and the underlying mechanism remain elusive to date.

Three-site and five-site fixed-charge water models compatible with AMOEBA force field.

In a typical biomolecular simulation using Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field, the vast majority molecules in the simulation box consist of water, and these water molecules consume the most CPU power due to the explicit mutual induction effect. To improve the computational efficiency, we here develop two new nonpolarizable water models (with flexible bonds and fixed charges) that are compatible with AMOEBA solute: the 3-site AW3C and 5-site AW5C. To derive the force-field parameters for AW3C and AW5C, we fit to six experimental liquid thermodynamic properties: liquid density, enthalpy of vaporization, dielectric constant, isobaric heat capacity, isothermal compressibility and thermal expansion coefficient, at a broad range of temperatures from 261.

Gray Correlation Analysis and Prediction on Permanent Deformation of Subgrade Filled with Construction and Demolition Materials.

Construction and demolition (C&D) materials obtained from the demolition of buildings are proven to be qualified and sustainable subgrade fillers. The permanent deformation response of subgrade C&D materials under different moisture contents, degrees of compaction, deviator stresses, and confining pressures was revealed by carrying out dynamic triaxial texts. Then, using a four-factor and three-level orthogonal test and by calculating the Gray correlation degree of each factor, the influence degree of each factor on the permanent deformation was determined.

The facile and visualizable identification of broad-spectrum inhibitors of MDM2/p53 using co-expressed protein complexes.

MDM2 is a well-known oncoprotein overexpressed in a variety of cancers, and the identification of inhibitors that disrupt the MDM2/p53 interaction is of great interest in anticancer drug development. Here we designed a platform for the facile and visualizable identification of inhibitors of MDM2 using co-expressed protein complexes of MDM2/p53. A hexahistidine-tag on MDM2 allows the binding of the protein complex to the Ni-NTA affinity resin, while the fluorescent protein fused to p53 enables the direct visualization of the interaction of p53 with MDM2.

Backmapping from Multiresolution Coarse-Grained Models to Atomic Structures of Large Biomolecules by Restrained Molecular Dynamics Simulations Using Bayesian Inference.

Coarse-grained (CG) simulations have allowed access to larger length scales and longer time scales in the study of the dynamic processes of large biomolecules than all-atom (AA) molecular dynamics (MD) simulations. Backmapping from CG models to AA structures has long been studied because it enables us to gain detailed structure insights from CG simulations. Many methods first construct an AA structure from the CG model by fragments, random placement, or geometrical rules and subsequently optimize the solution via energy minimization, simulated annealing or position-restrained simulations.

Real-Time Monitoring of Hierarchical Self-Assembly and Induction of Circularly Polarized Luminescence from Achiral Luminogens.

Constructing artificial helical structures through hierarchical self-assembly and exploring the underlying mechanism are important, and they help gain insight from the structures, processes, and functions from the biological helices and facilitate the development of material science and nanotechnology. Herein, the two enantiomers of chiral Au(I) complexes ( S)-1 and ( R)-1 were synthesized, and they exhibited impressive spontaneous hierarchical self-assembly transitions from vesicles to helical fibers. An impressive chirality inversion and amplification was accompanied by the assembly transition, as elucidated by the results of in situ and time-dependent circular dichroism spectroscopy and scanning electron microscope imaging.

Dynamic Nature of CTCF Tandem 11 Zinc Fingers in Multivalent Recognition of DNA As Revealed by NMR Spectroscopy.

The 11 zinc fingers (ZFs) of the transcription factor CTCF play a versatile role in the regulation of gene expression. CTCF binds to numerous genomic sites to form chromatin loops and topologically associated domains and thus mediates the 3D architecture of chromatin. Although CTCF inter-ZF plasticity is essential for the recognition of multiple genomic sites, the dynamic nature of its 11 ZFs remains unknown.

Insights into the Structure of Dimeric RNA Helicase CsdA and Indispensable Role of Its C-Terminal Regions.

CsdA has been proposed to be essential for the biogenesis of ribosome and gene regulation after cold shock. However, the structure of CsdA and the function of its long C-terminal regions are still unclear. Here, we solved all of the domain structures of CsdA and found two previously uncharacterized auxiliary domains: a dimerization domain (DD) and an RNA-binding domain (RBD).

SAXS-Oriented Ensemble Refinement of Flexible Biomolecules.

The conformational flexibility of a biomolecule may play a crucial role in its biological function. Small-angle x-ray scattering (SAXS) is a very popular technique for characterizing biomolecule flexibility. It can be used to determine a possible structural ensemble of the biomolecule in solution with the aid of a computer simulation.