Unraveling the evolutionary origin of the complex Nuclear Receptor Element (cNRE), a cis-regulatory module required for preferential expression in the atrial chamber.

Cardiac function requires appropriate proteins in each chamber. Atria requires slow myosin to act as reservoirs, while ventricles demand fast myosin for swift pumping. Myosins are thus under chamber-biased cis-regulation, with myosin gene expression imbalances leading to congenital heart dysfunction. To identify regulatory inputs leading to cardiac chamber-biased expression, we computationally and molecularly dissected the quail Slow Myosin Heavy Chain III (SMyHC III) promoter that drives preferential expression to the atria. We show that SMyHC III gene states are orchestrated by a complex Nuclear Receptor Element (cNRE) of 32 base pairs. Using transgenesis in zebrafish and mice, we demonstrate that preferential atrial expression is achieved by a combinatorial regulatory input composed of atrial activation motifs and ventricular repression motifs. Using comparative genomics, we show that the cNRE might have emerged from an endogenous viral element through infection of an ancestral host germline, revealing an evolutionary pathway to cardiac chamber-specific expression.

The novel HLA-C*17:69 allele, identified by Sanger dideoxy nucleotide sequencing in a Chinese individual.

HLA-C*17:69 differs from HLA-C*17:01:01:02 by one nucleotide in exon 4.

Rice kinase OsMRLK63 contributes to drought tolerance by regulating reactive oxygen species production.

Drought is a major adverse environmental factor that plants face in nature but the molecular mechanism by which plants transduce stress signals and further endow themselves with tolerance remains unclear. Malectin/malectin-like domains containing receptor-like kinases (MRLKs) have been proposed to act as receptors in multiple biological signaling pathways, but limited studies show their roles in drought-stress signaling and tolerance. In this study, we demonstrate OsMRLK63 in rice (Oryza sativa L.) functions in drought tolerance by acting as the receptor of 2 rapid alkalization factors, OsRALF45 and OsRALF46. We show OsMRLK63 is a typical receptor-like kinase that positively regulates drought tolerance and reactive oxygen species (ROS) production. OsMRLK63 interacts with and phosphorylates several nicotinamide adenine dinucleotide phosphate (NADPH) oxidases with the primarily phosphorylated site at Ser26 in the N-terminal of RESPIRATORY BURST OXIDASE HOMOLOGUE A (OsRbohA). The application of the 2 small signal peptides (OsRALF45/46) on rice can greatly alleviate the dehydration of plants induced by mimic drought. This function depends on the existence of OsMRLK63 and the NADPH oxidase-dependent ROS production. The 2 RALFs interact with OsMRLK63 by binding to its extracellular domain, suggesting they may act as drought/dehydration signal sensors for the OsMRLK63-mediated process. Our study reveals a OsRALF45/46-OsMRLK63-OsRbohs module which contributes to drought-stress signaling and tolerance in rice.

Rice Carbohydrate-Binding Malectin-Like Protein, OsCBM1, Contributes to Drought-Stress Tolerance by Participating in NADPH Oxidase-Mediated ROS Production.

Carbohydrate-binding malectin/malectin-like domain-containing proteins (CBMs) are a recently identified protein subfamily of lectins that participates various functional bioprocesses in the animal, bacterial, and plant kingdoms. However, little is known the roles of CBMs in rice development and stress response. In this study, OsCBM1, which encodes a protein containing only one malectin-like domain, was cloned and characterized. OsCBM1 is localized in both the endoplasmic reticulum and plasma membrane. Its transcripts are dominantly expressed in leaves and could be significantly stimulated by a number of phytohormone applications and abiotic stress treatments. Overexpression of OsCBM1 increased drought tolerance and reactive oxygen species production in rice, whereas the knockdown of the gene decreased them. OsCBM1 physically interacts with OsRbohA, a NADPH oxidase, and the expression of OsCBM1 in osrbohA, an OsRbohA-knockout mutant, is significantly downregulated under both normal growth and drought stress conditions. Meanwhile, OsCBM1 can also physically interacts with OsRacGEF1, a specific guanine nucleotide exchange factor for the Rop/Rac GTPase OsRac1, and transient coexpression of OsCBM1 with OaRacGEF1 significantly enhanced ROS production. Further transcriptome analysis showed that multiple signaling regulatory mechanisms are involved in the OsCBM1-mediated processes. All these results suggest that OsCBM1 participates in NADPH oxidase-mediated ROS production by interacting with OsRbohA and OsRacGEF1, contributing to drought stress tolerance of rice. Multiple signaling pathways are likely involved in the OsCBM1-mediated stress tolerance in rice.

Micropipette aspiration method for characterizing biological materials with surface energy.

Many soft biological tissues possess a considerable surface stress, which plays a significant role in their biophysical functions, but most previous methods for characterizing their mechanical properties have neglected the effects of surface stress. In this work, we investigate the micropipette aspiration method to measure the mechanical properties of soft tissues and cells with surface effects. The neo-Hookean constitutive model is adopted to describe the hyperelasticity of the measured biological material, and the surface effect is taken into account by the finite element method. It is found that when the pipette radius or aspiration length is comparable to the elastocapillary length, surface energy may distinctly alter the aspiration response. Generally, both the aspiration length and the bulk normal stress decrease with increasing surface energy, and thus neglecting the surface energy would lead to an overestimation of elastic modulus. Through dimensional analysis and numerical simulations, we provide an explicit relation between the imposed pressure and the aspiration length. This method can be applied to determine the mechanical properties of soft biological tissues and organs, e.g., livers, tumors and embryos.

Are elastic moduli of biological cells depth dependent or not? Another explanation using a contact mechanics model with surface tension.

Atomic force microscopy (AFM) has become the most commonly used tool to measure the mechanical properties of biological cells. In AFM indentation experiments, the Hertz and Sneddon models of contact mechanics are usually adopted to extract the elastic modulus by analyzing the load-indent depth curves for spherical and conical tips, respectively. However, the effects of surface tension, neglected in existing contact models, become more significant in indentation responses due to the lower elastic moduli of living cells. Here, we present two simple yet robust relations between load and indent depth considering surface tension effects for spherical and conical indentations, through dimensional analysis and finite element simulations. When the indent depth is smaller than the intrinsic length defined as the ratio of surface tension to elastic modulus, the elastic modulus obtained by classical contact mechanics theories would be overestimated. Contrary to the majority of reported results, we find that the elastic modulus of a cell could be independent of indent depths if surface tension is taken into account. Our model seems to be in agreement with experimental data available. A comprehensive comparison will be done in the future.

CLD1/SRL1 modulates leaf rolling by affecting cell wall formation, epidermis integrity and water homeostasis in rice.

Leaf rolling is considered as one of the most important agronomic traits in rice breeding. It has been previously reported that SEMI-ROLLED LEAF 1 (SRL1) modulates leaf rolling by regulating the formation of bulliform cells in rice (Oryza sativa); however, the regulatory mechanism underlying SRL1 has yet to be further elucidated. Here, we report the functional characterization of a novel leaf-rolling mutant, curled leaf and dwarf 1 (cld1), with multiple morphological defects. Map-based cloning revealed that CLD1 is allelic with SRL1, and loses function in cld1 through DNA methylation. CLD1/SRL1 encodes a glycophosphatidylinositol (GPI)-anchored membrane protein that modulates leaf rolling and other aspects of rice growth and development. The cld1 mutant exhibits significant decreases in cellulose and lignin contents in secondary cell walls of leaves, indicating that the loss of function of CLD1/SRL1 affects cell wall formation. Furthermore, the loss of CLD1/SRL1 function leads to defective leaf epidermis such as bulliform-like epidermal cells. The defects in leaf epidermis decrease the water-retaining capacity and lead to water deficits in cld1 leaves, which contribute to the main cause of leaf rolling. As a result of the more rapid water loss and lower water content in leaves, cld1 exhibits reduced drought tolerance. Accordingly, the loss of CLD1/SRL1 function causes abnormal expression of genes and proteins associated with cell wall formation, cuticle development and water stress. Taken together, these findings suggest that the functional roles of CLD1/SRL1 in leaf-rolling regulation are closely related to the maintenance of cell wall formation, epidermal integrity and water homeostasis.

On the determination of elastic moduli of cells by AFM based indentation.

The atomic force microscopy (AFM) has been widely used to measure the mechanical properties of biological cells through indentations. In most of existing studies, the cell is supposed to be linear elastic within the small strain regime when analyzing the AFM indentation data. However, in experimental situations, the roles of large deformation and surface tension of cells should be taken into consideration. Here, we use the neo-Hookean model to describe the hyperelastic behavior of cells and investigate the influence of surface tension through finite element simulations. At large deformation, a correction factor, depending on the geometric ratio of indenter radius to cell radius, is introduced to modify the force-indent depth relation of classical Hertzian model. Moreover, when the indent depth is comparable with an intrinsic length defined as the ratio of surface tension to elastic modulus, the surface tension evidently affects the indentation response, indicating an overestimation of elastic modulus by the Hertzian model. The dimensionless-analysis-based theoretical predictions, which include both large deformation and surface tension, are in good agreement with our finite element simulation data. This study provides a novel method to more accurately measure the mechanical properties of biological cells and soft materials in AFM indentation experiments.

The plasma membrane NADPH oxidase OsRbohA plays a crucial role in developmental regulation and drought-stress response in rice.

Plasma membrane NADPH oxidases are major producers of reactive oxygen species (ROS) in plant cells under normal growth and stress conditions. In the present study the total activity of rice NADPH oxidases and the transcription of OsRbohA, which encodes an Oryza sativa plasma membrane NADPH oxidase, were stimulated by drought. OsRbohA was expressed in all tissues examined throughout development. Its mRNA was upregulated by a number of factors, including heat, drought, salt, oxidative stress and methyl jasmonate treatment. Compared with wild-type (WT), the OsRbohA-knockout mutant osrbohA exhibited upregulated expression of other respiratory burst oxidase homolog genes and multiple abnormal agronomic traits, including reduced biomass, low germination rate and decreased pollen viability and seed fertility. However, OsRbohA-overexpressing transgenic plants showed no differences in these traits compared with WT. Although osrbohA leaves and roots produced more ROS than WT, the mutant had lesser intracellular ROS. In contrast, OsRbohA-overexpressing transgenic plants exhibited higher ROS production at the intracellular level and in tissues. Ablation of OsRbohA impaired the tolerance of plants to various water stresses, whereas its overexpression enhanced the tolerance. In addition, a number of genes related to energy supply, substrate transport, stress response and transcriptional regulation were differentially expressed in osrbohA plants even under normal growth conditions, suggesting that OsRbohA has fundamental and broad functions in rice. These results indicate that OsRbohA-mediated processes are governed by complex signaling pathways that function during the developmental regulation and drought-stress response in rice.

Efficacy evaluation of fungus Syncephalastrum racemosum and nematicide avermectin against the root-knot nematode Meloidogyne incognita on cucumber.

The root-knot nematode (RKN) is one of the most damaging agricultural pests.Effective biological control is need for controlling this destructive pathogen in organic farming system. During October 2010 to 2011, the nematicidal effects of the Syncephalastrum racemosum fungus and the nematicide, avermectin, alone or combined were tested against the RKN (Meloidogyne incognita) on cucumber under pot and field condition in China. Under pot conditions, the application of S. racemosum alone or combined with avermectin significantly increased the plant vigor index by 31.4% and 10.9%, respectively compared to the M. incognita-inoculated control. However, treatment with avermectin alone did not significantly affect the plant vigor index. All treatments reduced the number of root galls and juvenile nematodes compared to the untreated control. Under greenhouse conditions, all treatments reduced the disease severity and enhanced fruit yield compared to the untreated control. Fewer nematodes infecting plant roots were observed after treatment with avermectin alone, S. racemosum alone or their combination compared to the M. incognita-inoculated control. Among all the treatments, application of avermectin or S. racemosum combined with avermectin was more effective than the S. racemosum treatment. Our results showed that application of S. racemosum combined with avermectin not only reduced the nematode number and plant disease severity but also enhanced plant vigor and yield. The results indicated that the combination of S. racemosum with avermectin could be an effective biological component in integrated management of RKN on cucumber.

Characterization of Rice NADPH oxidase genes and their expression under various environmental conditions.

Plasma membrane NADPH oxidases (Noxs) are key producers of reactive oxygen species under both normal and stress conditions in plants. We demonstrate that at least eleven genes in the genome of rice (Oryza sativa L.) were predicted to encode Nox proteins, including nine genes (OsNox1-9) that encode typical Noxs and two that encode ancient Nox forms (ferric reduction oxidase 1 and 7, OsFRO1 and OsFRO7). Phylogenetic analysis divided the Noxs from nine plant species into six subfamilies, with rice Nox genes distributed among subfamilies I to V. Gene expression analysis using semi-quantitative RT-PCR and real-time qRT-PCR indicated that the expression of rice Nox genes depends on organs and environmental conditions. Exogenous calcium strongly stimulated the expression of OsNox3, OsNox5, OsNox7, and OsNox8, but depressed the expression of OsFRO1. Drought stress substantially upregulated the expression of OsNox1-3, OsNox5, OsNox9, and OsFRO1, but downregulated OsNox6. High temperature upregulated OsNox5-9, but significantly downregulated OsNox1-3 and OsFRO1. NaCl treatment increased the expression of OsNox2, OsNox8, OsFRO1, and OsFRO7, but decreased that of OsNox1, OsNox3, OsNox5, and OsNox6. These results suggest that the expression profiles of rice Nox genes have unique stress-response characteristics, reflecting their related but distinct functions in response to different environmental stresses.

Surface effects on the superelasticity of nanohelices.

Helical nanomaterials with superelasticity have a wide range of promising applications in micro-/nanoelectromechanical systems. Based on the theory of surface elasticity, we present a nonlinear rod model to investigate the superelasticity of nanohelices. Our results demonstrate that the superelasticity of nanohelices exhibits a distinct size dependence due to the increased ratio of surface area to volume. The superelasticity can effectively enhance the efficiency of energy storage and retrieval of nanohelices. This study is helpful for the characterization of the mechanical properties of nanosized helical materials and the optimal design of nanohelix-based devices.

Timoshenko beam model for buckling of piezoelectric nanowires with surface effects.

This paper investigates the buckling behavior of piezoelectric nanowires under distributed transverse loading, within the framework of the Timoshenko beam theory, and in the presence of surface effects. Analytical relations are given for the critical force of axial buckling of nanowires by accounting for the effects of surface elasticity, residual surface tension, and transverse shear deformation. Through an example, it is shown that the critical electric potential of buckling depends on both the surface stresses and piezoelectricity. This study may be helpful in the characterization of the mechanical properties of nanowires and in the calibration of the nanowire-based force sensors.

Surface effects in various bending-based test methods for measuring the elastic property of nanowires.

The size-dependent elastic property of nanowires induced by the surface effect is investigated by using the core-shell model. The overall effective elastic moduli of nanowires with regular polygonal cross-sections are unified into a simple and explicit relation. It is found that the effect of surface elasticity on the elastic moduli can be well characterized by two dimensionless material and geometric parameters with clear physical meaning. Finite element simulations demonstrate that the derived theoretical relation is applicable for all the vibration, bending, and buckling test methods for measuring the mechanical properties of nanowires. The analytical result is also validated by comparing it with relevant experimental measurements. This study is helpful not only for interpreting various phenomena associated with size-dependent mechanical properties of nanowires but also for developing and evaluating test techniques for material characterization at the nanoscale.

Buoyant force and sinking conditions of a hydrophobic thin rod floating on water.

Owing to the superhydrophobicity of their legs, such creatures as water striders and fisher spiders can stand effortlessly, walk and jump quickly on water. Directed toward understanding their superior repellency ability, we consider hydrophobic thin rods of several representative cross sections pressing a water surface. First, the shape function of the meniscus surrounding a circular rod is solved analytically, and thereby the maximal buoyant force is derived as a function of the Young's contact angle and the rod radius. Then we discuss the critical conditions for a rod to sink into water, including the maximal volume condition and the meniscus-contact condition. Furthermore, we study the sinking conditions and the maximal buoyant forces of hydrophobic long rods with elliptical, triangular, or hexagonal cross-section shapes. The theoretical solutions are quantitatively consistent with existing experimental and numerical results. Finally, the optimized structures of water strider legs are analyzed to elucidate why they can achieve a very big buoyant force on water.