Ultrasimple size encoded microfluidic chip for rapid simultaneous multiplex detection of DNA sequences.

Simultaneous multiplexed analysis can provide comprehensive information for disease diagnosis. However, the current multiplex methods rely on sophisticated barcode technology, which hinders its wider application. In this study, an ultrasimple size encoding method is proposed for multiplex detection using a wedge-shaped microfluidic chip. Driving by negative pressure, microparticles are naturally arranged in distinct stripes based on their sizes within the chip. This size encoding method demonstrates a high level of precision, allowing for accuracy in distinguishing 3-5 sizes of microparticles with a remarkable accuracy rate of up to 99%, even the microparticles with a size difference as small as 0.5 µm. The entire size encoding process is completed in less than 5 min, making it ultrasimple, reliable, and easy to operate. To evaluate the function of this size encoding microfluidic chip, three commonly co-infectious viruses' nucleic acid sequences (including complementary DNA sequences of HIV and HCV, and DNA sequence of HBV) are employed for multiplex detection. Results indicate that all three DNA sequences can be sensitively detected without any cross-interference. This size-encoding microfluidic chip-based multiplex detection method is simple, rapid, and high-resolution, its successful application in serum samples renders it highly promising for potential clinical promotion.

Magnetic Microbead-Based Herringbone Chip for Sensitive Detection of Human Immunodeficiency Virus.

The microfluidic chip-based nucleic acid detection method significantly improves the sensitivity since it precisely controls the microfluidic flow in microchannels. Nonetheless, significant challenges still exist in improving the detection efficiency to meet the demand for rapid detection of trace substances. This work provides a novel magnetic herringbone (M-HB) structure in a microfluidic chip, and its advantage in rapid and sensitive detection is verified by taking complementary DNA (cDNA) sequences of human immunodeficiency virus (HIV) detection as an example. The M-HB structure is designed based on controlling the magnetic field distribution in the micrometer scale and is formed by accumulation of magnetic microbeads (MMBs). Hence, M-HB is similar to a nanopore microstructure, which has a higher contact area and probe density. All of the above is conducive to improving sensitivity in microfluidic chips. The M-HB chip is stable and easy to form, which can linearly detect cDNA sequences of HIV quantitatively ranging from 1 to 20 nM with a detection limit of 0.073 nM. Compared to the traditional herringbone structure, this structure is easier to form and release by controlling the magnetic field, which is flexible and helps in further study. Results show that this chip can sensitively detect the cDNA sequences of HIV in blood samples, demonstrating that it is a powerful platform to rapidly and sensitively detect multiple nucleic acid-related viruses of infectious diseases.

AAformer: Auto-Aligned Transformer for Person Re-Identification.

In person re-identification (re-ID), extracting part-level features from person images has been verified to be crucial to offer fine-grained information. Most of the existing CNN-based methods only locate the human parts coarsely, or rely on pretrained human parsing models and fail in locating the identifiable nonhuman parts (e.g., knapsack). In this article, we introduce an alignment scheme in transformer architecture for the first time and propose the auto-aligned transformer (AAformer) to automatically locate both the human parts and nonhuman ones at patch level. We introduce the "Part tokens (PARTs)", which are learnable vectors, to extract part features in the transformer. A PART only interacts with a local subset of patches in self-attention and learns to be the part representation. To adaptively group the image patches into different subsets, we design the auto-alignment. Auto-alignment employs a fast variant of optimal transport (OT) algorithm to online cluster the patch embeddings into several groups with the PARTs as their prototypes. AAformer integrates the part alignment into the self-attention and the output PARTs can be directly used as part features for retrieval. Extensive experiments validate the effectiveness of PARTs and the superiority of AAformer over various state-of-the-art methods.

Plant-on-chip: Core morphogenesis processes in the tiny plant Wolffia australiana.

A plant can be thought of as a colony comprising numerous growth buds, each developing to its own rhythm. Such lack of synchrony impedes efforts to describe core principles of plant morphogenesis, dissect the underlying mechanisms, and identify regulators. Here, we use the minimalist known angiosperm to overcome this challenge and provide a model system for plant morphogenesis. We present a detailed morphological description of the monocot Wolffia australiana, as well as high-quality genome information. Further, we developed the plant-on-chip culture system and demonstrate the application of advanced technologies such as single-nucleus RNA-sequencing, protein structure prediction, and gene editing. We provide proof-of-concept examples that illustrate how W. australiana can decipher the core regulatory mechanisms of plant morphogenesis.

Learning Semantics-Consistent Stripes With Self-Refinement for Person Re-Identification.

Aligning human parts automatically is one of the most challenging problems for person re-identification (re-ID). Recently, the stripe-based methods, which equally partition the person images into the fixed stripes for aligned representation learning, have achieved great success. However, the stripes with fixed height and position cannot well handle the misalignment problems caused by inaccurate detection and occlusion and may introduce much background noise. In this article, we aim at learning adaptive stripes with foreground refinement to achieve pixel-level part alignment by only using person identity labels for person re-ID and make two contributions. 1) A semantics-consistent stripe learning method (SCS). Given an image, SCS partitions it into adaptive horizontal stripes and each stripe is corresponding to a specific semantic part. Specifically, SCS iterates between two processes: i) clustering the rows to human parts or background to generate the pseudo-part labels of rows and ii) learning a row classifier to partition a person image, which is supervised by the latest pseudo-labels. This iterative scheme guarantees the accuracy of the learned image partition. 2) A self-refinement method (SCS+) to remove the background noise in stripes. We employ the above row classifier to generate the probabilities of pixels belonging to human parts (foreground) or background, which is called the class activation map (CAM). Only the most confident areas from the CAM are assigned with foreground/background labels to guide the human part refinement. Finally, by intersecting the semantics-consistent stripes with the foreground areas, SCS+ locates the human parts at pixel-level, obtaining a more robust part-aligned representation. Extensive experiments validate that SCS+ sets the new state-of-the-art performance on three widely used datasets including Market-1501, DukeMTMC-reID, and CUHK03-NP.

Rice Cell Division Cycle 20s are required for faithful chromosome segregation and cytokinesis during meiosis.

Chromosome segregation must be under strict regulation to maintain chromosome euploidy and stability. Cell Division Cycle 20 (CDC20) is an essential cell cycle regulator that promotes the metaphase-to-anaphase transition and functions in the spindle assembly checkpoint, a surveillance pathway that ensures the fidelity of chromosome segregation. Plant CDC20 genes are present in multiple copies, and whether CDC20s have the same functions in plants as in yeast and animals is unclear, given the potential for divergence or redundancy among the multiple copies. Here, we studied all three CDC20 genes in rice (Oryza sativa) and constructed two triple mutants by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9-mediated genome editing to explore their roles in development. Knocking out all three CDC20 genes led to total sterility but did not affect vegetative development. Loss of the three CDC20 proteins did not alter mitotic division but severely disrupted meiosis as a result of asynchronous and unequal chromosome segregation, chromosome lagging, and premature separation of chromatids. Immunofluorescence of tubulin revealed malformed meiotic spindles in microsporocytes of the triple mutants. Furthermore, cytokinesis of meiosis I was absent or abnormal, and cytokinesis II was completely prevented in all mutant microsporocytes; thus, no tetrads or pollen formed in either cdc20 triple mutant. Finally, the subcellular structures and functions of the tapetum were disturbed by the lack of CDC20 proteins. These findings demonstrate that the three rice CDC20s play redundant roles but are indispensable for faithful meiotic chromosome segregation and cytokinesis, which are required for the production of fertile microspores.

Two-Level Attention Network With Multi-Grain Ranking Loss for Vehicle Re-Identification.

Vehicle re-identification (re-ID) aims to identify the same vehicle across multiple non-overlapping cameras, which is rather a challenging task. On the one hand, subtle changes in viewpoint and illumination condition can make the same vehicle look much different. On the other hand, different vehicles, even different vehicle models, may look quite similar. In this paper, we propose a novel Two-level Attention network supervised by a Multi-grain Ranking loss (TAMR) to learn an efficient feature embedding for the vehicle re-ID task. The two-level attention network consisting of hard part-level attention and soft pixel-level attention can adaptively extract discriminative features from the visual appearance of vehicles. The former one is designed to localize the salient vehicle parts, such as windscreen and car head. The latter one gives an additional attention refinement at pixel level to focus on the distinctive characteristics within each part. In addition, we present a multi-grain ranking loss to further enhance the discriminative ability of learned features. We creatively take the multi-grain relationship between vehicles into consideration. Thus, not only the discrimination between different vehicles but also the distinction between different vehicle models is constrained. Finally, the proposed network can learn a feature space, where both intra-class compactness and inter-class discrimination are well guaranteed. Extensive experiments demonstrate the effectiveness of our approach and we achieve state-of-the-art results on two challenging datasets, including VehicleID and Vehicle-1M.

X-ray tomography study of the random packing structure of ellipsoids.

We present an X-ray tomography study for the random packing of ellipsoids. The local structure displays short-range correlations. In addition to the contact number Z, we introduce ρshell, the average contact radius of curvature for contacting neighbors, as an additional parameter to characterize the local orientational geometry. In general, the local free volume w is affected by both Z and ρshell. We believe that the particle asphericity induces a polydispersity effect to influence the packing properties. A model is introduced which explicitly maps the ellipsoid packing onto a polydispersed sphere one, and it reproduces most of the experimental observations.

Sll1466, a glycosyl transferase homolog involved in global cellular regulation and high-light tolerance of Synechocystis PCC6803.

In Synechocystis sp. PCC 6803, the loop domain (aa 1-70) of the phycobilisome core-membrane linker, L(CM), was found to interact with the glycosyl transferase homolog, Sll1466. Growth of a Sll1466 knock-out mutant was slightly faster in low light, but strongly inhibited in high light; the phenotype is discussed in relation to the regulation of light energy transfer to photosystem II. At the molecular level, the mutant shows the following changes compared to the wild type: (1) a smaller size and higher mobility of phycobilisomes on the thylakoid membrane, and (2) a changed lipid composition of the thylakoid membrane, especially decreased amounts of digalactosyl diacylglycerol. These results indicate a profound regulatory role for Sll1466 in regulating photosynthetic energy transfer.

Rice OsGL1-1 is involved in leaf cuticular wax and cuticle membrane.

Cuticular wax forms a hydrophobic barrier on aerial plant organs; it plays an important role in protecting a plant from damage caused by many forms of environmental stress. In the present study, we characterized a rice leaf wax-deficient mutant osgl1-1 derived from a spontaneous mutation, which exhibited a wax-deficient and highly hydrophilic leaf phenotype. We cloned the OsGL1-1 gene by the map-based cloning method and performed a complementation test to confirm the function of the candidate gene. Molecular studies revealed that OsGL1-1 was a member of the OsGL1 family, and contained regions that were homologous to some regions in sterol desaturases and short-chain dehydrogenases/reductases. Compared to the wild-type, the osgl1-1 mutant showed decreased cuticular wax deposition, thinner cuticular membrane, decreased chlorophyll leaching, increased rate of water loss, and enhanced sensitivity to drought. OsGL1-1 is expressed ubiquitously in rice. The transient expression of OsGL1-1-green fluorescent protein fusion protein indicated that OsGL1-1 is localized in the cytoplasm, plasma membrane, and nucleus.

ROLLED LEAF 9, encoding a GARP protein, regulates the leaf abaxial cell fate in rice.

Leaves, the collective organ produced by the shoot apical meristem (SAM), are polarized along their adaxial-abaxial axis. In this study, we characterized two rice (Oryza sativa) allelic rolled-leaf mutants, rolled leaf 9-1 (rl9-1) and rl9-2, which display very similar phenotypes with completely adaxialized leaves and malformed spikelets. We cloned the RL9 gene by way of a map-based cloning strategy. Molecular studies have revealed that RL9 encodes a GARP protein, an orthologue of Arabidopsis KANADIs. RL9 is mainly expressed in roots, leaves, and flowers. The transient expression of a RL9-GFP (green fluorescent protein) fusion protein has indicated that RL9 protein is localized in the nucleus, suggesting that RL9 acts as a putative transcription factor.

Integration of cytological features with molecular and epigenetic properties of rice chromosome 4.

It has been reported that rice chromosome 4 has eight major heterochromatic knobs within the heterochromatic half and that this organization correlates with chromosomal-level transcriptional activity. To better understand this chromosomal organization, we created a model based on the statistical distribution of various types of gene models to divide chromosome 4 into 17 euchromatic and heterochromatic regions that correspond with the cytological staining. Fluorescence in-situ hybridization (FISH) experiments using a set of bacterial artificial chromosome (BAC) clones from chromosome 4 placed all 18 clones in the region predicted by the model. Elevated levels of H3K4 di- and tri-methylation detected by chromatin-immunoprecipitation (ChIP) on chip were correlated with euchromatic regions whereas lower levels of these two modifications were detected in heterochromatic regions. Small RNAs were more abundant in the heterochromatic regions. To validate these findings, H3K4 trimethylation, H3K9 acetylation, H4K12 acetylation, and H3K9 di- and tri-methylation of 19 individual genes were measured by ChIP-PCR. Genes in heterochromatic regions had elevated H3K9 di- and tri-methylation while genes in euchromatic regions had elevated levels of the other three modifications. We also assayed cytosine methylation of these genes using the restriction enzymes McrBC, HapII, and Msp I. This analysis indicated that cytosines of transposable elements and some genes located in heterochromatic regions were methylated while cytosines of the other genes were unmethylated. These results suggest that local transcriptional activity may reflect the organization of the corresponding part of the chromosome. They also indicate that epigenetic regulation plays an important role in correlating chromosomal organization with transcriptional activity.

[Genetic analysis of two extremely segregation distorted populations in rice (Oryza sativa L.)].

Segregation distortion is a quite common phenomenon in living species and thought to be a potent evolutional force. The main reasons of distorted segregation ratios are responsible for the selection of gametes or sporophytes. In this study, two extreme segregation distortions from the progenies of lmi x 02428 and d6 x 93-11 were identified. The segregation ratio of molecular markers tightly linked with LMI and D6 genes were analyzed and skew segregation were found in the markers tested which were indicated by significant deviation from the expected Mendelian segregation ratio(1:2:1). The segregation distorted regions were detected between molecular markers ST8 and ST8-2 near the centromere of chromosome 8, and ST7-1 and ST7-3 near telomere of chromosome 7, respectively. Meanwhile, the results indicated that segregation distortion had related with the different crossed combinations.

[Meiotic recombination hotspots in eukaryotes].

Meiotic recombination may occur more frequently in some regions of the eukaryotic genome. These regions are referred to as meiotic recombination hotspot loci. Genetic studies in the yeast have revealed that these hotspots contain special sites for recombination initiation and result in heterogeneous distribution of recombination (along the chromosome length or across the genome). However, the data for recombination hotspot is so far limited to organisms such as fungi, maize and human. In the present paper, we listed several typical approaches to characterizing recombination hotspots in different organisms, summarizing current progress in mapping of the meiotic recombination hotspots and discussing the factors and mechanisms for activation of eukaryotic meiotic recombination. Some unresolved questions and future prospects were also discussed.

[Analysis of the transgenic rice plants derived from transformed anther calli].

Rice calli derived from anther culture were used as recipient to transfer a rice blight resistance gene, Xa21, into a japonica rice variety, Taipei 309, via Agrobacterium-mediated transformation. Seven green transgenic plants, including one mixoploid, two haploid, and four diploid plants, were regenerated. PCR, Southern blot, FISH and blight resistance analysis all indicated that Xa21 gene has been integrated into the T0 plant genomes. T1 generations of the four diploid T0 plants were further investigated for resistance segregation. Chi2 test showed that two T1 populations segregated with a ratio of 3:1, indicating that a single copy of Xa21 gene was integrated into the genome, whereas the segregation ratios of the other two T1 populations were non-Mendelian. Therefore, the four diploid transgenic plants should be heterozygous diploids.

[Physical mapping of the 45S rDNA and 5S rDNA to rice prometaphase chromosome].

Rice (Oryza sativa L.) is one of the most important cereal crops in the world. The chromosomes of rice are relatively small in size. With the help of fluorescence in situ hybridization (FISH), several rice DNAs have been localized on rice chromosomes. 45S rDNA and 5S rDNA are encoding sequences for ribosomal RNA synthesis. For detecting the chromosomes related to 45S rDNA and 5S rDNA, the digoxigenin-dUTP labeled probe DNA was probed to the prometaphase chromosomes which were prepared from the root tips harvested from an indica rice variety, Zhongxian 3037. For identification of the chromosomes, slides were stained with Giemsa before FISH. With the improved FISH protocol 45S rDNA was clearly detected on two pairs of chromosomes which are usually found to be attached to nucleolus. The signal size between two pairs of the chromosomes was different. According to the characteristics of the chromosomes, the chromosomes with bigger signal were chromosome 9 and the other pair were chromosome 10. They were also discriminated from arm ratio. The signals of 5S rDNA were relatively small but clear. According to the size and arm ratio of the chromosome with FISH signals, the 5S rDNA was mapped on the short arm of chromosome 11, very close to the centromere region.