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Most spatial transcriptomics technologies are limited by their resolution, with spot sizes larger than that of a single cell. Although joint analysis with single-cell RNA sequencing can alleviate this problem, current methods are limited to assessing discrete cell types, revealing the proportion of cell types inside each spot. To identify continuous variation of the transcriptome within cells of the same type, we developed Deconvolution of Spatial Transcriptomics profiles using Variational Inference (DestVI). Using simulations, we demonstrate that DestVI outperforms existing methods for estimating gene expression for every cell type inside every spot. Applied to a study of infected lymph nodes and of a mouse tumor model, DestVI provides high-resolution, accurate spatial characterization of the cellular organization of these tissues and identifies cell-type-specific changes in gene expression between different tissue regions or between conditions. DestVI is available as part of the open-source software package scvi-tools ( https://scvi-tools.org ).

【Objective】 Wheat is the most important crop in North China. However, the scarcity of freshwater resources in this region cannot sustain its production. Optimizing wheat planting area to balance wheat production and its water requirement is hence essential to conserving irrigation water and alleviating water shortage pressure. 【Method】 Evapotranspiration and wheat yield were used as indicators to establish the objective of the wheat planting areas at county scale in the region. Optimization for wheat production was established from the trade-off between wheat production and its water consumption. 【Result】 From 2001 to 2009, evapotranspiration in the wheat season exhibited an increasing trend, followed by a significant decrease from 2010 to 2018 (p

Intercropping creates a heterogeneous canopy and triggers plastic responses in plant growth and structural development. In order to quantify the effect of planting pattern, strip width and row position on the structural development and light capture of maize and soybean in simultaneous intercropping, both experimental and modelling approaches were used. Field experiments were conducted in 2017－2018 with two sole crops (maize and soybean) and two intercrops: Two rows of maize alternating with two rows of soybeans (2:2 MS) and three rows of maize alternating with six rows of soybean (3:6 MS). The morphological traits of maize and soybean e.g., leaf length and width, internode length and diameter, leaf and petiole declination angle in different rows and different planting patterns, and photosynthetically active radiation (PAR) above and below the canopy of 2:2 MS were measured throughout the growing season. A functional-structural plant model of maize-soybean intercropping was developed in the GroIMP platform. The model was parameterized based on the morphological data set of 2017, and was validated with the leaf area index (LAI), plant height and PAR data set of 2018. The model simulated the morphological development of individual organs based on growing degree days (thermal time) and calculated the light capture at leaf level. The model well reproduced the observed dynamics of leaf area index and plant height (RMSE: 0.24－0.70 m2/m2 for LAI and 0.06－0.17 m for plant height), and the fraction of light capture in the 2:2 MS intercropping (RMSE: 0.06－0.10). Maize internode diameter in intercrops increased, but the internode length did not change. Soybean internodes in intercrops became longer and thinner compared to sole soybean probably caused by the shading imposed by maize, and the 2:2 MS had longer internodes than the 3:6 MS, indicating the effects of strip width. Simulated light capture of maize in 2:2 MS intercropping was 35.6% higher than sole maize. For maize in 3:6 MS intercropping, the light capture of the border rows and inner row were 27.8% and 20.3% higher than sole maize, respectively. Compared to sole soybean, the simulated light capture of soybean in border rows was 36.0% lower in 2:2 MS intercropping, and was 28.8% lower in 3:6 MS intercropping. For 3:6 MS intercropping, light capture of soybean in inner rows I and inner rows II were 4.1% and 1.8% lower than sole soybean, respectively. In the future, the model could be further developed and used to explore and optimize the planting patterns of maize soybean intercropping under different environmental conditions using light capture as an indicator.

Small and isolated populations face several intrinsic risks, such as genetic drift, inbreeding depression, and reduced gene flow. Thus, patterns of genetic diversity and differentiation have become an important focus of conservation genetics research. The golden snub-nosed monkey Rhinopithecus roxellana , an endangered species endemic to China, has experienced rapid reduction in population size and severe population fragmentation over the past few decades. We measured the patterns of genetic diversity and population differentiation using both neutral microsatellites and adaptive major histocompatibility complex (MHC) genes in 2 R. roxellana populations (DPY and GNG) distributed on the northern and southern slopes of the Qinling Mountains, respectively. Eight MHC-linked haplotypes formed by 5 DQA1 alleles, 5 DQB1 alleles, 5 DRB1 alleles, and 4 DRB2 alleles were detected in the 2 populations. The larger GNG population showed higher genetic variation for both MHC and microsatellites than the smaller DPY population, suggesting an effect of genetic drift on genetic variation. Genetic differentiation index (F ST) outlier analyses, principal coordinate analysis (PCoA), and inferred population genetic structure showed lower genetic differentiation in the MHC variations than microsatellites, suggesting that pathogen-mediated balancing selection, rather than local adaptation, homogenized the MHC genes of both populations. This study indicates that both balancing selection and genetic drift may shape genetic variation and differentiation in small and fragmented populations. [ABSTRACT FROM AUTHOR]

The evolutionary development and phylogenetic division between Asian and African cercopithecoids (Cercopithecidae) have attracted significant attention in genetics, molecular biology, behavior, and morphology. However, less emphasis has been placed on how they have evolved morphologically after divergence, approximately 10 million years ago (mya) for Colobinae and 5–7 mya for Cercopithecinae, corresponding to the significant variation and diversity in landscape, climate, habitat, and ecologies between the two continents. This study examines whether such variation and diversity have been reflected in dental morphology. Our findings reveal substantial differences between Hylobatidae and Cercopithecidae, as well as between Colobinae and Cercopithecinae, indicating that size-adjusted dental variation mainly reveals the diversity associated with evolution and phylogenetic inertia. Interestingly, despite the earlier divergence of Afro-Asian colobines, their Euclidean Distance is comparable to that of Afro-Asian cercopithecines. This implies that latecomers (macaques) demonstrate equivalent diversity to colobines due to their extensive dispersion and broader adaptative radiation on the same continent. Colobinae exhibit more developed premolar and molar regions. However, when post-canine teeth are considered alone, Colobinae present a significantly larger molar size than Asian Cercopithecinae but not with the African Cercopihecinae. This contradicts the hypothesis that folivorous primates (Colobinae) have larger post-canine molars than frugivorous ones (Cercopithecinae). The considerable molar size in African Cercopithecinae must be associated with their more protrusive and larger facial structure rather than a specific dietary preference, being less diverse than their Asian counterparts—a trait that has evolved phylogenetically. This study also paves the way for further exploration of facial and cranial differences between the continental groups of Cercopithecinae and Colobinae, delving deeply into diversity variation due to geographical and climatic adaptations. [ABSTRACT FROM AUTHOR]