First-principles study of symmetry lowering in relaxed BaTiO3/SrTiO3 superlattices

The crystal structure and local spontaneous polarization of (BaTiO3)m/(SrTiO3)n superlattices is calculated using a first-principles density functional theory method. The in-plane lattice constant is 1% larger than the SrTiO3 substrate to imitate the relaxed superlattice structure and the symmetry is lowered to monoclinic space group Cm which allows polarization to develop along the [110] and [001] directions. The polarization component in the [110] direction is found to develop only in the SrTiO3 layers and falls to zero in the BaTiO3 layers, whereas the polarization in the [001] direction is approximately uniform throughout the superlattice. These findings are consistent with recent experimental data and first-principles results for epitaxially strained BT and ST.Comment: 4 pages, 2 figure

The scale and evolutionary significance of horizontal gene transfer in the choanoflagellate

Background It is generally agreed that horizontal gene transfer (HGT) is common in phagotrophic protists. However, the overall scale of HGT and the cumulative impact of acquired genes on the evolution of these organisms remain largely unknown. Results Choanoflagellates are phagotrophs and the closest living relatives of animals. In this study, we performed phylogenomic analyses to investigate the scale of HGT and the evolutionary importance of horizontally acquired genes in the choanoflagellate Monosiga brevicollis. Our analyses identified 405 genes that are likely derived from algae and prokaryotes, accounting for approximately 4.4% of the Monosiga nuclear genome. Many of the horizontally acquired genes identified in Monosiga were probably acquired from food sources, rather than by endosymbiotic gene transfer (EGT) from obsolete endosymbionts or plastids. Of 193 genes identified in our analyses with functional information, 84 (43.5%) are involved in carbohydrate or amino acid metabolism, and 45 (23.3%) are transporters and/or involved in response to oxidative, osmotic, antibiotic, or heavy metal stresses. Some identified genes may also participate in biosynthesis of important metabolites such as vitamins C and K12, porphyrins and phospholipids. Conclusions Our results suggest that HGT is frequent in Monosiga brevicollis and might have contributed substantially to its adaptation and evolution. This finding also highlights the importance of HGT in the genome and organismal evolution of phagotrophic eukaryotes

Analyses of the oligopeptide transporter gene family in poplar and grape

<p>Abstract</p> <p>Background</p> <p>Oligopeptide transporters (OPTs) are a group of membrane-localized proteins that have a broad range of substrate transport capabilities and that are thought to contribute to many biological processes. The OPT proteins belong to a small gene family in plants, which includes about 25 members in Arabidopsis and rice. However, no comprehensive study incorporating phylogeny, chromosomal location, gene structure, expression profiling, functional divergence and selective pressure analysis has been reported thus far for Populus and Vitis.</p> <p>Results</p> <p>In the present study, a comprehensive analysis of the OPT gene family in Populus (<it>P. trichocarpa</it>) and Vitis (<it>V. vinifera</it>) was performed. A total of 20 and 18 full-length OPT genes have been identified in Populus and Vitis, respectively. Phylogenetic analyses indicate that these OPT genes consist of two classes that can be further subdivided into 11 groups. Gene structures are considerably conserved among the groups. The distribution of OPT genes was found to be non-random across chromosomes. A high proportion of the genes are preferentially clustered, indicating that tandem duplications may have contributed significantly to the expansion of the OPT gene family. Expression patterns based on our analyses of microarray data suggest that many OPT genes may be important in stress response and functional development of plants. Further analyses of functional divergence and adaptive evolution show that, while purifying selection may have been the main force driving the evolution of the OPTs, some of critical sites responsible for the functional divergence may have been under positive selection.</p> <p>Conclusions</p> <p>Overall, the data obtained from our investigation contribute to a better understanding of the complexity of the Populus and Vitis OPT gene family and of the function and evolution of the OPT gene family in higher plants.</p

OCTScenes: A Versatile Real-World Dataset of Tabletop Scenes for Object-Centric Learning

Humans possess the cognitive ability to comprehend scenes in a compositional manner. To empower AI systems with similar abilities, object-centric representation learning aims to acquire representations of individual objects from visual scenes without any supervision. Although recent advancements in object-centric representation learning have achieved remarkable progress on complex synthesis datasets, there is a huge challenge for application in complex real-world scenes. One of the essential reasons is the scarcity of real-world datasets specifically tailored to object-centric representation learning methods. To solve this problem, we propose a versatile real-world dataset of tabletop scenes for object-centric learning called OCTScenes, which is meticulously designed to serve as a benchmark for comparing, evaluating and analyzing object-centric representation learning methods. OCTScenes contains 5000 tabletop scenes with a total of 15 everyday objects. Each scene is captured in 60 frames covering a 360-degree perspective. Consequently, OCTScenes is a versatile benchmark dataset that can simultaneously satisfy the evaluation of object-centric representation learning methods across static scenes, dynamic scenes, and multi-view scenes tasks. Extensive experiments of object-centric representation learning methods for static, dynamic and multi-view scenes are conducted on OCTScenes. The results demonstrate the shortcomings of state-of-the-art methods for learning meaningful representations from real-world data, despite their impressive performance on complex synthesis datasets. Furthermore, OCTScenes can serves as a catalyst for advancing existing state-of-the-art methods, inspiring them to adapt to real-world scenes. Dataset and code are available at https://huggingface.co/datasets/Yinxuan/OCTScenes

No miRNA were found in Plasmodium and the ones identified in erythrocytes could not be correlated with infection

<p>Abstract</p> <p>Background</p> <p>The transcriptional regulation of <it>Plasmodium </it>during its complex life cycle requires sequential activation and/or repression of different genetic programmes. MicroRNAs (miRNAs) are a highly conserved class of non-coding RNAs that are important in regulating diverse cellular functions by sequence-specific inhibition of gene expression. What is know about double-stranded RNA-mediated gene silencing (RNAi) and posttranscriptional gene silencing (PTGS) in <it>Plasmodium </it>parasites entice us to speculate whether miRNAs can also function in <it>Plasmodium</it>-infected RBCs.</p> <p>Results</p> <p>Of 132 small RNA sequences, no <it>Plasmodium</it>-specific miRNAs have been found. However, a human miRNA, miR-451, was highly expressed, comprising approximately one third of the total identified miRNAs. Further analysis of miR-451 expression and malaria infection showed no association between the accumulation of miR-451 in <it>Plasmodium falciparum</it>-iRBCs, the life cycle stage of <it>P. falciparum </it>in the erythrocyte, or of <it>P. berghei </it>in mice. Moreover, treatment with an antisense oligonucleotide to miR-451 had no significant effect on the growth of the erythrocytic-stage <it>P. falciparum</it>.</p> <p>Methods</p> <p>Short RNAs from a mixed-stage of <it>P. falciparum</it>-iRBC were separated in a denaturing polyacrylamide gel and cloned into T vectors to create a cDNA library. Individual clones were then sequenced and further analysed by bioinformatics prediction to discover probable miRNAs in <it>P. falciparum</it>-iRBC. The association between miR-451 expression and the parasite were analysed by Northern blotting and antisense oligonucleotide (ASO) of miR-451.</p> <p>Conclusion</p> <p>These results contribute to eliminate the probability of miRNAs in <it>P. falciparum</it>. The absence of miRNA in <it>P. falciparum </it>could be correlated with absence of argonaute/dicer genes. In addition, the miR-451 accumulation in <it>Plasmodium</it>-infected RBCs is independent of parasite infection. Its accumulation might be only the residual of erythroid differentiation or a component to maintain the normal function of mature RBCs.</p