Revisiting the TALE repeat

Transcription activator-like (TAL) effectors specifically bind to double stranded (ds) DNA through a central domain of tandem repeats. Each TAL effector (TALE) repeat comprises 33–35 amino acids and recognizes one specific DNA base through a highly variable residue at a fixed position in the repeat. Structural studies have revealed the molecular basis of DNA recognition by TALE repeats. Examination of the overall structure reveals that the basic building block of TALE protein, namely a helical hairpin, is one-helix shifted from the previously defined TALE motif. Here we wish to suggest a structure-based re-demarcation of the TALE repeat which starts with the residues that bind to the DNA backbone phosphate and concludes with the base-recognition hyper-variable residue. This new numbering system is consistent with the α-solenoid superfamily to which TALE belongs, and reflects the structural integrity of TAL effectors. In addition, it confers integral number of TALE repeats that matches the number of bound DNA bases. We then present fifteen crystal structures of engineered dHax3 variants in complex with target DNA molecules, which elucidate the structural basis for the recognition of bases adenine (A) and guanine (G) by reported or uncharacterized TALE codes. Finally, we analyzed the sequence-structure correlation of the amino acid residues within a TALE repeat. The structural analyses reported here may advance the mechanistic understanding of TALE proteins and facilitate the design of TALEN with improved affinity and specificity. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s13238-014-0035-2) contains supplementary material, which is available to authorized users

Acoustic Tweezing Cytometry Induces Rapid Initiation of Human Embryonic Stem Cell Differentiation.

Mechanical forces play critical roles in influencing human embryonic stem cell (hESC) fate. However, it remains largely uncharacterized how local mechanical forces influence hESC behavior in vitro. Here, we used an ultrasound (US) technique, acoustic tweezing cytometry (ATC), to apply targeted cyclic subcellular forces to hESCs via integrin-bound microbubbles (MBs). We found that ATC-mediated cyclic forces applied for 30 min to hESCs near the edge of a colony induced immediate global responses throughout the colony, suggesting the importance of cell-cell connection in the mechanoresponsiveness of hESCs to ATC-applied forces. ATC application generated increased contractile force, enhanced calcium activity, as well as decreased expression of pluripotency transcription factors Oct4 and Nanog, leading to rapid initiation of hESC differentiation and characteristic epithelial-mesenchymal transition (EMT) events that depend on focal adhesion kinase (FAK) activation and cytoskeleton (CSK) tension. These results reveal a unique, rapid mechanoresponsiveness and community behavior of hESCs to integrin-targeted cyclic forces

Comparative phylogeography of the plateau zokor (Eospalax baileyi) and its host-associated flea (Neopsylla paranoma) in the Qinghai-Tibet Plateau

Background: Specific host-parasite systems often embody a particular co-distribution phenomenon, in which the parasite’s phylogeographic pattern is dependent on its host. In practice, however, both congruent and incongruent phylogeographic patterns between the host and the parasite have been reported. Here, we compared the population genetics of the plateau zokor (Eospalax baileyi), a subterranean rodent, and its host-associated flea species, Neopsylla paranoma, with an aim to determine whether the two animals share a similar phylogeographic pattern. Results: We sampled 130 host-parasite pairs from 17 localities in the Qinghai-Tibet Plateau (QTP), China, and sequenced a mitochondrial DNA (mtDNA) segment (~2,500 bp), including the complete COI and COII genes. We also detected 55 zokor and 75 flea haplotypes. AMOVA showed that the percentage of variation among the populations of zokors constituted 97.10%, while the within population variation was only 2.90%; for fleas, the values were 85.68% and 14.32%, respectively. Moreover, the flea Fst (fixation index) values were significantly smaller than in zokor. Although the Fst values between zokors and fleas were significantly and positively correlated (N =105, R =0.439, p =0.000), only a small amount (R2= 0.19) of the flea Fst variations could be explained by the zokor Fst variations. The two animals showed very distinct haplotype network structures from each other while co-phylogenetic analyses were unable to reject the hypothesis of an independence of speciation events. Conclusions: Zokors and fleas have very distinct population genetic patterns from each other, likely due to the influence of other sympatrically-distributed vertebrates on the transmission of fleas

Antiseismic response research of horizontal residual heat removal pump in different seismic spectrum input directions

A million kilowatt horizontal residual heat removal pump is an essential part of the first loop residual heat removal system in nuclear power plants; it is the second most significant piece of nuclear power equipment. The residual heat removal pump of a nuclear power plant is examined by using a multiseismic spectrum, multiinput direction method to analyze its dynamic characteristics and responses. The aim of this analysis was to determine the seismic responses and possible actions to reduce damage to the integral structure. The favorable and unfavorable spectra are investigated as well. The research focuses on avoiding the damaging effects caused by earthquakes. The maximum value of seismic effect and the corresponding seismic input direction are determined, laying a speculative foundation for structural design and installation. Utilizing a response spectrum method, the antiseismic performance of a pump at SSE seismic load has been analyzed according to an algorithm using the square root of the sum of the squares. The result shows that the deformation of the impeller surface fitted with a wear ring decreases along the direction of flow in different input directions of the seismic spectrum. The largest deformation occurs at an angle of approximately 135 degrees; thus, antiseismic analysis should be conducted at this input angle to conservatively evaluate the antiseismic performance, and the installation angle designed for frequent earthquakes should avoid 135 degrees to decrease the deformation caused by the seismic force. Calculation results prove that the clearance between the rotor and the stator of the horizontal residual heat removal pump shows satisfactory seismic response performance that fulfills the requirements for antiseismic design according to the RCC-M standard; this may reduce seismic damage and avoid environmental disasters

CD24 Expression as a Marker for Predicting Clinical Outcome in Human Gliomas

CD24 is overexpressed in glioma cells in vitro and in vivo. However, the correlation of its expression with clinicopathological parameters of gliomas and its prognostic significance in this tumor remain largely unknown. To address this problem, 151 glioma specimens and 10 nonneoplastic brain tissues were collected. Quantitative real-time PCR, immunochemistry assay, and Western blot analysis were carried out to investigate the expression of CD24. As per the results, CD24 was overexpressed in gliomas. Its expression levels in glioma tissues with higher grade (P < 0.001) and lower KPS (P < 0.001) were significantly higher than those with lower grade and higher KPS, respectively. Cox multifactor analysis showed that CD24 (P = 0.02) was an independent prognosis factor for human glioma. Our data provides convincing evidence for the first time that the overexpression of CD24 at gene and protein levels is correlated with advanced clinicopathological parameters and poor prognosis in patients with glioma

Multifunctional photonic integrated circuit for diverse microwave signal generation, transmission and processing

Microwave photonics (MWP) studies the interaction between microwave and optical waves for the generation, transmission and processing of microwave signals (i.e., three key domains), taking advantages of broad bandwidth and low loss offered by modern photonics. Integrated MWP using photonic integrated circuits (PICs) can reach a compact, reliable and green implementation. Most PICs, however, are recently developed to perform one or more functions restricted inside a single domain. In this paper, as highly desired, a multifunctional PIC is proposed to cover the three key domains. The PIC is fabricated on InP platform by monolithically integrating four laser diodes and two modulators. Using the multifunctional PIC, seven fundamental functions across microwave signal generation, transmission and processing are demonstrated experimentally. Outdoor field trials for electromagnetic environment surveillance along an in-service high-speed railway are also performed. The success to such a PIC marks a key step forward for practical and massive MWP implementations.Comment: 17 page