Rice's trajectory from wild to domesticated in East Asia.

Rice (Oryza sativa) serves as a staple food for more than one-third of the global population. However, its journey from a wild gathered food to domestication remains enigmatic, sparking ongoing debates in the biological and anthropological fields. Here, we present evidence of rice phytoliths sampled from two archaeological sites in China, Shangshan and Hehuashan, near the lower reaches of the Yangtze River. We demonstrate the growth of wild rice at least 100,000 years before present, its initial exploitation as a gathered resource at about 24,000 years before present, its predomestication cultivation at about 13,000 years before present, and eventually its domestication at about 11,000 years before present. These developmental stages illuminate a protracted process of rice domestication in East Asia and extend the continuous records of cereal evolution beyond the Fertile Crescent.

Fungal fermentation of Fuzhuan brick tea: A comprehensive evaluation of sensory properties using chemometrics, visible near-infrared spectroscopy, and electronic nose.

Fuzhuan brick tea (FBT) fungal fermentation is a key factor in achieving its unique dark color, aroma, and taste. Therefore, it is essential to develop a rapid and reliable method that could assess its quality during FBT fermentation process. This study focused on using electronic nose (e-nose) and spectroscopy combination with sensory evaluations and physicochemical measurements for building machine learning (ML) models of FBT. The results showed that the fused data achieved 100 % accuracy in classifying the FBT fermentation process. The SPA-MLR method was the best prediction model for FBT quality (R2 = 0.95, RMSEP = 0.07, RPD = 4.23), and the fermentation process was visualized. Where, it was effectively detecting the degree of fermentation relationship with the quality characteristics. In conclusion, the current study's novelty comes from the established real-time method that could sensitively detect the unique post-fermentation quality components based on the integration of spectral, and e-nose and ML approaches.

Retromer Proteins Reduced in Down Syndrome and the Dp16 Model: Impact of APP Dose and Preclinical Studies of a γ-Secretase Modulator.

OBJECTIVE: The retromer complex plays an essential role in intracellular endosomal sorting. Deficits in the retromer complex are linked to enhanced Aß production. The levels of the components of the retromer complex are reported to be downregulated in Alzheimer disease (AD). Down syndrome (DS) shares neuropathological features with AD. Recent evidence points to dysregulation of the retromer complex in DS. The mechanisms underlying retromer deficits in DS and AD are poorly understood. METHODS: We measured the levels of retromer components in the frontal cortex of cases of DS-AD (AD in DS) as well as DS; the frontal cortex of a person partially trisomic (PT-DS) for human chromosome 21 (HSA21), whose genome had only the normal 2 copies of the APP gene, was also examined. We also analyzed these proteins in the Dp16 mouse model of DS. To further explore the molecular mechanism for changes in the retromer complex, we treated Dp16 mice with a γ-secretase modulator (GSM; 776890), a treatment that reduces the levels of Aß42 and Aß40. RESULTS: We found VPS26A, VPS26B, and VPS29, but not VPS35, were significantly reduced in both DS and DS-AD, but not in PT-DS. Downregulation of VPS26A, VPS26B, and VPS29 was recapitulated in the brains of old Dp16 mice (at 16 months of age) and required increased App gene dose. Significantly, GSM treatment completely prevented reductions of the retromer complex. INTERPRETATION: Our studies point to increased APP gene dose as a compromising retromer function in DS and suggest a causal role for Aß42 and Aß40. ANN NEUROL 2023;94:245-258.

Reduced synaptic proteins and SNARE complexes in Down syndrome with Alzheimer's disease and the Dp16 mouse Down syndrome model: Impact of APP gene dose.

INTRODUCTION: Synaptic failure, a hallmark of Alzheimer's disease (AD), is correlated with reduced levels of synaptic proteins. Though people with Down syndrome (DS) are at markedly increased risk for AD (AD-DS), few studies have addressed synapse dysfunction. METHODS: Synaptic proteins were measured in the frontal cortex of DS, AD-DS, sporadic AD cases, and controls. The same proteins were examined in the Dp16 model of DS. RESULTS: A common subset of synaptic proteins were reduced in AD and AD-DS, but not in DS or a case of partial trisomy 21 lacking triplication of APP gene. Pointing to compromised synaptic function, the reductions in AD and AD-DS were correlated with reduced SNARE complexes. In Dp16 mice reductions in syntaxin 1A, SNAP25 and the SNARE complex recapitulated findings in AD-DS; reductions were impacted by both age and increased App gene dose. DISCUSSION: Synaptic phenotypes shared between AD-DS and AD point to shared pathogenetic mechanisms.

Effects of oxidation-based tea processing on the characteristics of the derived polysaccharide conjugates and their regulation of intestinal homeostasis in DSS-induced colitis mice.

Different cultivars and processing technologies involved in producing tea result in the high heterogeneity of derived polysaccharide conjugates, which limits the understanding of their composition and structure, and biological activity. Here, raw tea leaves from the same cultivar were used to produce dried fresh tea leaves, green tea, and black tea, and three polysaccharide conjugates derived from dried fresh tea leaves (FTPS), green tea (GTPS), and black tea (BTPS) were prepared accordingly. Their physiochemical characteristics and bioactivities were investigated. The results showed that the oxidation during tea processing increased the phenolics and proteins while decreasing the GalA in the derived TPS conjugates; meanwhile, it reduced the molecular weight and particle size of BTPS but enhanced their antioxidant activity in vitro. Furthermore, all three TPS conjugates improved intestinal homeostasis by reducing TJ protein loss and inflammation and alleviated DSS-induced colitis symptoms in mice. In addition, the three TPS conjugates showed differential regulation of the intestinal microbiome and altered the produced SCFAs, which contributed to the prevention of colitis. Our findings suggest that TPS conjugates could be applied in colitis prevention in association with the regulation of gut microbiota, and their efficacy could be optimized by employing suitable tea processing technologies.

Alternative polyadenylation by sequential activation of distal and proximal PolyA sites.

Analogous to alternative splicing, alternative polyadenylation (APA) has long been thought to occur independently at proximal and distal polyA sites. Using fractionation-seq, we unexpectedly identified several hundred APA genes in human cells whose distal polyA isoforms are retained in chromatin/nuclear matrix and whose proximal polyA isoforms are released into the cytoplasm. Global metabolic PAS-seq and Nanopore long-read RNA-sequencing provide further evidence that the strong distal polyA sites are processed first and the resulting transcripts are subsequently anchored in chromatin/nuclear matrix to serve as precursors for further processing at proximal polyA sites. Inserting an autocleavable ribozyme between the proximal and distal polyA sites, coupled with a Cleave-seq approach that we describe here, confirms that the distal polyA isoform is indeed the precursor to the proximal polyA isoform. Therefore, unlike alternative splicing, APA sites are recognized independently, and in many cases, in a sequential manner. This provides a versatile strategy to regulate gene expression in mammalian cells.

Detailed Avatar Recovery From Single Image.

This paper presents a novel framework to recover detailed avatar from a single image. It is a challenging task due to factors such as variations in human shapes, body poses, texture, and viewpoints. Prior methods typically attempt to recover the human body shape using a parametric-based template that lacks the surface details. As such resulting body shape appears to be without clothing. In this paper, we propose a novel learning-based framework that combines the robustness of the parametric model with the flexibility of free-form 3D deformation. We use the deep neural networks to refine the 3D shape in a Hierarchical Mesh Deformation (HMD) framework, utilizing the constraints from body joints, silhouettes, and per-pixel shading information. Our method can restore detailed human body shapes with complete textures beyond skinned models. Experiments demonstrate that our method has outperformed previous state-of-the-art approaches, achieving better accuracy in terms of both 2D IoU number and 3D metric distance.

O-GlcNAcylation of TDP-43 suppresses proteinopathies and promotes TDP-43's mRNA splicing activity.

Pathological TDP-43 aggregation is characteristic of several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD-TDP); however, how TDP-43 aggregation and function are regulated remain poorly understood. Here, we show that O-GlcNAc transferase OGT-mediated O-GlcNAcylation of TDP-43 suppresses ALS-associated proteinopathies and promotes TDP-43's splicing function. Biochemical and cell-based assays indicate that OGT's catalytic activity suppresses TDP-43 aggregation and hyperphosphorylation, whereas abolishment of TDP-43 O-GlcNAcylation impairs its RNA splicing activity. We further show that TDP-43 mutations in the O-GlcNAcylation sites improve locomotion defects of larvae and adult flies and extend adult life spans, following TDP-43 overexpression in Drosophila motor neurons. We finally demonstrate that O-GlcNAcylation of TDP-43 promotes proper splicing of many mRNAs, including STMN2, which is required for normal axonal outgrowth and regeneration. Our findings suggest that O-GlcNAcylation might be a target for the treatment of TDP-43-linked pathogenesis.

TDP-43 aggregation induced by oxidative stress causes global mitochondrial imbalance in ALS.

Amyotrophic lateral sclerosis (ALS) was initially thought to be associated with oxidative stress when it was first linked to mutant superoxide dismutase 1 (SOD1). The subsequent discovery of ALS-linked genes functioning in RNA processing and proteostasis raised the question of how different biological pathways converge to cause the disease. Both familial and sporadic ALS are characterized by the aggregation of the essential DNA- and RNA-binding protein TDP-43, suggesting a central role in ALS etiology. Here we report that TDP-43 aggregation in neuronal cells of mouse and human origin causes sensitivity to oxidative stress. Aggregated TDP-43 sequesters specific microRNAs (miRNAs) and proteins, leading to increased levels of some proteins while functionally depleting others. Many of those functionally perturbed gene products are nuclear-genome-encoded mitochondrial proteins, and their dysregulation causes a global mitochondrial imbalance that augments oxidative stress. We propose that this stress-aggregation cycle may underlie ALS onset and progression.

Active RNA interference in mitochondria.

RNA interference (RNAi) has been thought to be a gene-silencing pathway present in most eukaryotic cells to safeguard the genome against retrotransposition. Small interfering RNAs (siRNAs) have also become a powerful tool for studying gene functions. Given the endosymbiotic hypothesis that mitochondria originated from prokaryotes, mitochondria have been generally assumed to lack active RNAi; however, certain bacteria have Argonaute homologs and various reports suggest the presence of specific microRNAs and nuclear genome (nDNA)-encoded Ago2 in the mitochondria. Here we report that transfected siRNAs are not only able to enter the matrix of mitochondria, but also function there to specifically silence targeted mitochondrial transcripts. The mitoRNAi effect is readily detectable at the mRNA level, but only recordable on relatively unstable proteins, such as the mtDNA-encoded complex IV subunits. We also apply mitoRNAi to directly determine the postulated crosstalk between individual respiratory chain complexes, and our result suggests that the controversial observations previously made in patient-derived cells might result from differential adaptation in different cell lines. Our findings bring a new tool to study mitochondrial biology.

Detailed Surface Geometry and Albedo Recovery from RGB-D Video under Natural Illumination.

This article presents a novel approach for depth map enhancement from an RGB-D video sequence. The basic idea is to exploit the photometric information in the color sequence to resolve the inherent ambiguity of shape from shading problem. Instead of making any assumption about surface albedo or controlled object motion and lighting, we use the lighting variations introduced by casual object movement. We are effectively calculating photometric stereo from a moving object under natural illuminations. One of the key technical challenges is to establish correspondences over the entire image set. We, therefore, develop a lighting insensitive robust pixel matching technique that out-performs optical flow method in presence of lighting variations. An adaptive reference frame selection procedure is introduced to get more robust to imperfect lambertian reflections. In addition, we present an expectation-maximization framework to recover the surface normal and albedo simultaneously, without any regularization term. We have validated our method on both synthetic and real datasets to show its superior performance on both surface details recovery and intrinsic decomposition.

Phytolith Radiocarbon Dating: A Review of Previous Studies in China and the Current State of the Debate.

Phytolith radiocarbon dating can be traced back to the 1960s. However, its reliability has recently been called into question. Piperno summarized recent dating evidence, but most phytolith dating results from China were not included in the review because they are written in Chinese. Herein, we summarize and evaluate previous phytolith dating results from China. We also review recent debates on the nature and origin of phytolith-occluded carbon (abbreviated as PhytOC), as well as the older age of phytoliths retrieved from modern plants. We conclude that although PhytOC includes a small amount of old carbon absorbed from the soil, this carbon fraction has not always biased phytolith ages, indicating that in certain situations, phytoliths can be tried as an alternative dating tool in archaeological and paleoecological research when other datable materials are not available.

Association of wheat chaff derived silica fiber and esophageal cancer in north China.

BACKGROUND: Despite decades of research and intervention programs, the epidemic of esophageal squamous cell carcinoma (ESCC) in the Taihang Mountain area of north China has not seen convincing explanation by any risk factor yet and the incidence has not seen a substantial decrease. Based on recently disclosed association of aridity and wheat consumption with esophageal cancer, we revisited the hypothesis of biogenic silica in esophageal cancer development. METHODS: From the archives of the Pathology Department of Heping Hospital, Changzhi Medical College, we selected three pairs of formalin-fixed samples, tumor tissues and distant normal tissues, of three patients operated for ESCC who had no history of workplace exposure to silica dust. Two pairs of dried tissue samples were used for phytolith (silica body) analysis and another pair for microanalysis with Transmission Electron Microscope (TEM). RESULTS: One of the phytoliths in ESCC tumor tissue was similar to the prickle hair on the surface of wheat bract. In the mineral particles detected in the tumor tissue the predominant elements were Si, Ca, and P, whereas Si signals were not obvious in the distant normal tissue. CONCLUSIONS: The preliminary findings on the detection of phytoliths and the higher than normal Si concentration in ESCC tumor tissue warrants further testing the role of biogenic silica in esophageal cancer.

A possible role of biogenic silica in esophageal cancer in North China?

Certain areas in North China have the highest incidence of esophageal squamous cell carcinoma (ESCC) in the world, which has not seen convincing explanation by any risk factor yet. Biogenic silica in millet bran was linked to ESCC in the early 1980s but the hypothesis was largely dismissed because of the lack of geographic correlation between millet consumption and ESCC. Later epidemiological studies disclosed the linkage of wheat consumption in North China to ESCC instead. Now, we hypothesize silica phytoliths (silicified bodies that have definite shapes) from wheat chaff are a major etiologic factor of ESCC in this region. This hypothesis is supported by the potentially high abundance of silica phytoliths on the bracts of wheat (Triticum aestivum) in North China due to favorable Si-accumulation genotype, arid climate, and siallitic soil with bioavailable Si. These silica phytoliths can contaminate wheat flour and cause repeated local injuries in the esophagus and stimulate proliferation by providing anchorage.

Dynamic Non-Rigid Objects Reconstruction with a Single RGB-D Sensor.

This paper deals with the 3D reconstruction problem for dynamic non-rigid objects with a single RGB-D sensor. It is a challenging task as we consider the almost inevitable accumulation error issue in some previous sequential fusion methods and also the possible failure of surface tracking in a long sequence. Therefore, we propose a global non-rigid registration framework and tackle the drifting problem via an explicit loop closure. Our novel scheme starts with a fusion step to get multiple partial scans from the input sequence, followed by a pairwise non-rigid registration and loop detection step to obtain correspondences between neighboring partial pieces and those pieces that form a loop. Then, we perform a global registration procedure to align all those pieces together into a consistent canonical space as guided by those matches that we have established. Finally, our proposed model-update step helps fixing potential misalignments that still exist after the global registration. Both geometric and appearance constraints are enforced during our alignment; therefore, we are able to get the recovered model with accurate geometry as well as high fidelity color maps for the mesh. Experiments on both synthetic and various real datasets have demonstrated the capability of our approach to reconstruct complete and watertight deformable objects.

Dating rice remains through phytolith carbon-14 study reveals domestication at the beginning of the Holocene.

Phytolith remains of rice (Oryza sativa L.) recovered from the Shangshan site in the Lower Yangtze of China have previously been recognized as the earliest examples of rice cultivation. However, because of the poor preservation of macroplant fossils, many radiocarbon dates were derived from undifferentiated organic materials in pottery sherds. These materials remain a source of debate because of potential contamination by old carbon. Direct dating of the rice remains might serve to clarify their age. Here, we first validate the reliability of phytolith dating in the study region through a comparison with dates obtained from other material from the same layer or context. Our phytolith data indicate that rice remains retrieved from early stages of the Shangshan and Hehuashan sites have ages of approximately 9,400 and 9,000 calibrated years before the present, respectively. The morphology of rice bulliform phytoliths indicates they are closer to modern domesticated species than to wild species, suggesting that rice domestication may have begun at Shangshan during the beginning of the Holocene.

Radiocarbon dating of prehistoric phytoliths: a preliminary study of archaeological sites in China.

Phytoliths can occlude some organic carbon during their deposition in plants. This carbon fraction is recognised as an ideal dating material because of its high resistance to decomposition and post-deposition contamination at the time of phytolith formation. However, the reliability of phytolith radiocarbon dating has recently been questioned. The development of a new extraction protocol for phytoliths, with paired dating between phytoliths and other materials from the same sediment, may provide further evidence for the reliability of phytolith dating. We present an improved method for extracting phytoliths from soils. We compared the dating of phytoliths and other materials (e.g., charcoal and plant seeds) recovered at the same depth from seven pits at six archaeological sites in China. The estimated ages of the phytoliths and other materials were generally consistent, except for one outlier. We attribute this inconsistency to the post-depositional processes of phytoliths in soil, rather than to the uptake of old carbon from the soil. Our results clearly show the potential for phytolith carbon dating at archaeological sites in the absence of other dating materials.

Bulliform Phytolith Research in Wild and Domesticated Rice Paddy Soil in South China.

Bulliform phytoliths play an important role in researching rice origins as they can be used to distinguish between wild and domesticated rice. Rice bulliform phytoliths are characterized by numerous small shallow fish-scale decorations on the lateral side. Previous studies have shown that domesticated rice has a larger number of these decorations than wild rice and that the number of decorations ≥9 is a useful feature for identifying domesticated rice. However, this standard was established based on limited samples of modern rice plants. In this study, we analyzed soil samples from both wild and domesticated rice paddies. Results showed that, in wild rice soil samples, the proportion of bulliform phytoliths with ≥9 decorations was 17.46% ± 8.29%, while in domesticated rice soil samples, the corresponding proportion was 63.70% ± 9.22%. This suggests that the proportion of phytoliths with ≥9 decorations can be adopted as a criterion for discriminating between wild and domesticated rice in prehistoric soil. This indicator will be of significance in improving the application of fish-scale decorations to research into rice origins and the rice domestication process.