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

The Development of Biomimetic Spherical Hydroxyapatite/Polyamide 66 Biocomposites as Bone Repair Materials

A novel biomedical material composed of spherical hydroxyapatite (s-HA) and polyamide 66 (PA) biocomposite (s-HA/PA) was prepared, and its composition, mechanical properties, and cytocompatibility were characterized and evaluated. The results showed that HA distributed uniformly in the s-HA/PA matrix. Strong molecule interactions and chemical bonds were presented between the s-HA and PA in the composites confirmed by IR and XRD. The composite had excellent compressive strength in the range between 95 and 132 MPa, close to that of natural bone. In vitro experiments showed the s-HA/PA composite could improve cell growth, proliferation, and differentiation. Therefore, the developed s-HA/PA composites in this study might be used for tissue engineering and bone repair

Specific DNA-RNA Hybrid Recognition by TAL Effectors

SummaryThe transcription activator-like (TAL) effector targets specific host promoter through its central DNA-binding domain, which comprises multiple tandem repeats (TALE repeats). Recent structural analyses revealed that the TALE repeats form a superhelical structure that tracks along the forward strand of the DNA duplex. Here, we demonstrate that TALE repeats specifically recognize a DNA-RNA hybrid where the DNA strand determines the binding specificity. The crystal structure of a designed TALE in complex with the DNA-RNA hybrid was determined at a resolution of 2.5 Å. Although TALE repeats are in direct contact with only the DNA strand, the phosphodiester backbone of the RNA strand is inaccessible by macromolecules such as RNases. Consistent with this observation, sequence-specific recognition of an HIV-derived DNA-RNA hybrid by an engineered TALE efficiently blocked RNase H-mediated degradation of the RNA strand. Our study broadens the utility of TALE repeats and suggests potential applications in processes involving DNA replication and retroviral infections

High-Performance Multi-Mode Ptychography Reconstruction on Distributed GPUs

Ptychography is an emerging imaging technique that is able to provide wavelength-limited spatial resolution from specimen with extended lateral dimensions. As a scanning microscopy method, a typical two-dimensional image requires a number of data frames. As a diffraction-based imaging technique, the real-space image has to be recovered through iterative reconstruction algorithms. Due to these two inherent aspects, a ptychographic reconstruction is generally a computation-intensive and time-consuming process, which limits the throughput of this method. We report an accelerated version of the multi-mode difference map algorithm for ptychography reconstruction using multiple distributed GPUs. This approach leverages available scientific computing packages in Python, including mpi4py and PyCUDA, with the core computation functions implemented in CUDA C. We find that interestingly even with MPI collective communications, the weak scaling in the number of GPU nodes can still remain nearly constant. Most importantly, for realistic diffraction measurements, we observe a speedup ranging from a factor of $10$ to $10^3$ depending on the data size, which reduces the reconstruction time remarkably from hours to typically about 1 minute and is thus critical for real-time data processing and visualization.Comment: work presented in NYSDS 201

A qualitative exploration of perceptions and experiences of contraceptive use, abortion and post-abortion family planning services (PAFP) in three provinces in China

Background: The INPAC project aims to evaluate the effectiveness of integrated post-abortion family planning (PAFP) services into existing hospital based abortion services in China. A qualitative study was conducted in three provinces to contribute to developing effective PAFP services through understanding influences on contraceptive use, experiences of abortion and existing PAFP, and their effect on future contraceptive practices from the perspective of users, in the context of social and institutional change. Methods: Twenty-nine in-depth interviews (IDIs) were undertaken with women who had experienced abortion between 1 and 6 months prior to interview, recruited from three urban and two rural facilities in each province. Thirteen IDIs were also conducted with male partners. Six focus group discussions (FGDs) were carried out with community members from different social groups, including unmarried and married women and men, urban residents and rural-to-urban migrants. Results: Social networks and norms are important in shaping attitudes and behaviour towards abortion and contraception. Widespread concerns were expressed about side-effects, reliability and effects on future fertility of some modern contraceptives. The combination of limited information and choices and a lack of person-centred counselling in PAFP with anxieties about side effects underlies the widespread use of unreliable methods. Gendered power relations significantly influence contraceptive (non) use, with several examples illustrating women's relative lack of power to decide on a method, particularly in the case of condoms. Although the availability of contraceptive information from respected providers can offer impetus for individual behaviour change, social distance from providers reduces opportunities for clients to discuss their difficulties regarding contraceptive use; particularly, but not exclusively for young, unmarried clients. Conclusions: Increased access to non-commercial, reliable information on contraceptive methods is needed. PAFP services must go beyond simple information provision to ensure that providers take a more personcentred approach, which considers the most appropriate method for individual clients and probes for the underlying influences on contraceptive (non) use. More sensitive reflection on gender norms and relationships is required during counselling and, where women choose this, efforts should be made to include their male partners. Specific attention to provider positionality and skills for counselling young, unmarried clients is needed