A method of dual-space molecular-replacement model completion has been proposed which involves the programs ARP/wARP, REFMAC, OASIS and DM. OASIS is used in reciprocal space for phase refinement based on models built by ARP/wARP. For this purpose, the direct-method probability formula of breaking SAD/SIR phase ambiguities has been redefined. During the phase refinement, phi(h)('') in the expression phi(h) = phi(h)('') +/- |Delta phi(h)| is redefined as a reference phase calculated from a randomly selected 5% of the atoms in the current structure model, while |Delta phi(h)| is defined as the absolute difference between the phase of the current model and phi(h)(''). The probability formula P(+)(Delta phi(h)) = (1/2) + (1/2) tanh {sin |Delta phi(h)| x [Sigma (h('))m(h('))m(h - h('))kappa(h,h(')) sin(Phi'(3) + Delta phi(h'best) + Delta phi(h - h'best)) + chi sin delta(h)]} is then used to derive the sign of Delta phi(h). In this way the '0-2pi' phase problem is reduced to a 'plus or minus' sign problem. The redefinition implies that during the refinement phases close to the true values will probably be kept unchanged, while those distant from the true values will probably undergo a large shift. This is the desired property of phase refinement. The procedure has been tested using protein diffraction data without SAD/SIR signals. The results show that dual-space MR-model completion making use of OASIS is much more efficient than that without.

A new version (2.0) of the pipeline IPCAS (Iterative Protein Crystal structure Automatic Solution) has been released, in which the program OASIS performs direct-method single-wavelength anomalous diffraction/single isomorphous replacement phasing and direct-method-aided partial-structure extension. IPCAS incorporates the widely used packages CCP4 and PHENIX for locating heavy atoms, density modification, molecular replacement, model building and refinement. Important extensions to the previous version of IPCAS include a resolution screening method for non-crystallographic symmetry searching, an alternate model-building protocol for avoiding premature convergence and direct-method image processing for electron microscopy maps, including singleparticle cryo-EM maps. Moreover, a new graphical user interface is provided for controlling and real-time monitoring of the whole dual-space iterative process, which works as a plugin to CCP4i. Applications of the new IPCAS to difficult cases have yielded promising results, including 'direct-method phasing and fragment extension' from weak anomalous diffraction signal data and 'directmethod-aided partial-structure extension' from low-homology models.

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Serial femtosecond crystallography (SFX) is capable of collecting threedimensional single-crystal diffraction data using polycrystalline samples. This may dramatically enhance the power of X-ray powder diffraction. In this paper a test has been performed using simulated diffraction patterns. The test sample is a mixture of two zeolites with crystal grain sizes from 100 to 300 nm. X-ray diffraction snapshots by SFX were simulated and processed using the program suite CrystFEL. Identification according to the primitive unit-cell volume determined from individual snapshots was able to separate the whole set of snapshots into two subsets, which correspond to the two zeolites in the sample. Monte Carlo integration in CrystFEL was then applied to them separately. This led to two sets of three-dimensional single-crystal diffraction intensities, based on which crystal structures of the two zeolites were solved easily by direct methods implemented in the program SHELXD.

A case study has been made on the treatment of the SIRAS (single isomorphous replacement with anomalous scattering) data of the originally unknown protein LegC3N. An alternative treatment has been proposed which led to improved results in this particular test case. The treatment involves iterative direct-method SAD (single-wavelength anomalous diffraction) phasing and direct-method-aided model completion, both of which are implanted in the IPCAS (Iterative Protein Crystal-structure Automatic Solution) pipeline. Apart from the experimental data, a simulated SIRAS data set for LegC3N with the derivative data truncated to 5.0 Å resolution has also been tested. SAD phasing and phase/model extension in PHENIX without direct methods failed to solve the structure using these simulated SIRAS data. However, the procedure proposed here involving direct methods in both SAD phasing and phase/model extension led to a nearly complete structure model. This shows the potential ability of treating SIRAS data with a derivative diffracting to lower resolution.

The genetic adaptation of Tibetans to high altitude hypoxia likely involves a group of genes in the hypoxic pathway, as suggested by earlier studies. To test the adaptive role of the previously reported candidate gene EP300 (histone acetyltransferase p300), we conducted resequencing of a 108.9 kb gene region of EP300 in 80 unrelated Tibetans. The allele-frequency and haplotype-based neutrality tests detected signals of positive Darwinian selection on EP300 in Tibetans, with a group of variants showing allelic divergence between Tibetans and lowland reference populations, including Han Chinese, Europeans, and Africans. Functional prediction suggested the involvement of multiple EP300 variants in gene expression regulation. More importantly, genetic association tests in 226 Tibetans indicated significant correlation of the adaptive EP300 variants with blood nitric oxide (NO) concentration. Collectively, we propose that EP300 harbors adaptive variants in Tibetans, which might contribute to high-altitude adaptation through regulating NO production.

Apart from solving the heavy-atom substructure in proteins and ab initio phasing of protein diffraction data at atomic resolution, direct methods have also been successfully combined with other protein crystallographic methods in dealing with diffraction data far below atomic resolution, leading to significantly improved results. In this respect, direct methods provide phase constraints in reciprocal space within a dual-space iterative framework rather than solve the phase problem independently. Applications of this type of direct methods to difficult SAD phasing, model completion and low-resolution phase extension will be described in detail.

The Qinghai-Tibet Plateau serves as an important ecological security shelter in China and across Asia. During the past two decades, the patterns of land development and conservation on the Qinghai-Tibet Plateau have undergone significant changes under the impacts of global climate change and human expansion. This paper analyzes the evolution of land development and conservation patterns and potential ecological implications on the Tibetan Plateau from 2000 to 2020 based on urbanization, agricultural and pastoral patterns with multi-source data, such as long-term time series land use data, ecological indices, environmental pollution, and population and economics. It was found that: (1) Coinciding with the agglomeration of population and economy, the urban development pattern on the Qinghai-Tibet Plateau has spatial-temporal differentiation. Urban development in the 2010s was more significant than that in the 2000s, with the intensity increased by 63.31%, and the development pattern varies spatially, which can be seen from the finding that central Tibet (the Yarlung Tsangpo, Lhasa river, and Nyangchu basins) and Huangshui River Basin in Qinghai Province were developed in a planar pattern, while other node cities and border towns in a dotted pattern. (2) The agricultural production pattern is relatively stable, the grain yields have increased by 34.68% in the past 20 years, but the total amount of arable land is shrinking, and the degree of fragmentation has increased. The pattern of pastoralism has changed greatly, showing a migration trend from west to east spatially, and there is a serious problem of pasture overload, with an increase of 18.4% in livestock products. Regardless of the pattern of urbanization or agricultural and livestock development, the intensity of human activities on the Qinghai-Tibet Plateau has shown an intensified trend in the past. (3) It shows that Lhasa City area and the middle and lower reaches of Huangshui show a trend of diffusion of atmospheric and water environmental pollution. The western part of the Ali region and the northern foothills of the Himalayas and other regions, under the combined impact of climate change and human activities, have undergone significant ecological degradation. Accordingly, this paper proposes policy recommendations for optimizing production and living space, advancing the establishment of national park clusters and nature reserve systems, and the integrated recovery of mountain, water, forest, lake, grass, sand, and ice with ecological value achievement.