Genome-wide selection footprints and deleterious variations in young Asian allotetraploid rapeseed

Brassica napus (AACC, 2n=38) is an important oilseed crop grown worldwide. However, little is known about the population evolution of this species, the genomic difference between its major genetic groups, such as European and Asian rapeseed, and the impacts of historical large-scale introgression events on this young tetraploid. In this study, we reported the de novo assembly of the genome sequences of an Asian rapeseed (B. napus), Ningyou 7 and its four progenitors and compared these genomes with other available genomic data from diverse European and Asian cultivars. Our results showed that Asian rapeseed originally derived from European rapeseed but subsequently significantly diverged, with rapid genome differentiation after hybridization and intensive local selective breeding. The first historical introgression of B. rapa dramatically broadened the allelic pool but decreased the deleterious variations of Asian rapeseed. The second historical introgression of the double-low traits of European rapeseed (canola) has reshaped Asian rapeseed into two groups (double-low and double-high), accompanied by an increase in genetic load in the double-low group. This study demonstrates distinctive genomic footprints and deleterious SNP (Single Nucleotide Polymorphism) variants for local adaptation by recent intra- and interspecies introgression events and provides novel insights for understanding the rapid genome evolution of a young allopolyploid cro

DeepSeek LLM: Scaling Open-Source Language Models with Longtermism

The rapid development of open-source large language models (LLMs) has been truly remarkable. However, the scaling law described in previous literature presents varying conclusions, which casts a dark cloud over scaling LLMs. We delve into the study of scaling laws and present our distinctive findings that facilitate scaling of large scale models in two commonly used open-source configurations, 7B and 67B. Guided by the scaling laws, we introduce DeepSeek LLM, a project dedicated to advancing open-source language models with a long-term perspective. To support the pre-training phase, we have developed a dataset that currently consists of 2 trillion tokens and is continuously expanding. We further conduct supervised fine-tuning (SFT) and Direct Preference Optimization (DPO) on DeepSeek LLM Base models, resulting in the creation of DeepSeek Chat models. Our evaluation results demonstrate that DeepSeek LLM 67B surpasses LLaMA-2 70B on various benchmarks, particularly in the domains of code, mathematics, and reasoning. Furthermore, open-ended evaluations reveal that DeepSeek LLM 67B Chat exhibits superior performance compared to GPT-3.5

Dietary Association with Midgut Microbiota Components of Eocanthecona furcellata (Wolff)

Eocanthecona furcellata is an important predatory stinkbug that attacks many lepidopteran pests. For mass-rearing, artificial diets are used to rear this predator in the laboratory; however, the fitness of the predators is reduced, and little is known about the cause. Since gut microbiota plays vital roles in the digestion and development of many hosts and can consequently affect host fitness, an understanding of the microbial community composition of E. furcellata may help to solve this unresolved problem. We compared the development and reproduction of E. furcellata reared on an artificial diet, and a natural (Spodoptera litura) or semi-natural (Tenebrio molitor) diet, and then the midgut microbiota were assessed using high-throughput 16S rRNA. The results of the high-throughput 16S rRNA show that the bacterial richness and diversity in the artificial diet gut samples increased considerably compared with the other samples. Proteobacteria and Firmicutes were the dominant phyla in E. furcellata. At the genus level, Serratia (however, the relative abundance was lower in the artificial diet gut samples), Enterococcus, and an uncultured bacterium genus of family Enterobacteriaceae, were dominant. The midgut microbiota components significantly differed among the diets, indicating that the gut bacteria had a dietary association with E. furcellata. This study provides a better understanding of midgut microbiota and the artificial diets that might affect them in E. furcellata

A Novel Form of Arginine-Chitosan as Nanoparticles Efficient for siRNA Delivery into Mouse Leukemia Cells

The modification of chitosan (CS) has greatly expanded its application in the field of medicine. In this study, low-molecular-weight chitosan was modified with arginine (Arg) by a simple method. The identification by the Fourier transform infrared spectra (FTIR) showed that Arg was successfully covalently attached to the CS. Interestingly, Arg-CS was identified as nanoparticles by atomic force microscopy (AFM) and transmission electron microscopy (TEM), whose particle size was 75.76 ± 12.07 nm based on Dynamic Light Scattering (DLS) characterization. Then, whether the prepared Arg-CS nanoparticles could encapsulate and deliver siRNA safely was investigated. Arg-CS was found to be able to encapsulate siRNAs in vitro via electrostatic interaction with siRNA; the Arg-CS/siRNA complex was safe for L1210 leukemia cells. Therefore, modification of chitosan by Arg produces novel nanoparticles to deliver siRNA into leukemia cells. This is the first time to identify Arg-CS as nanoparticles and explore their ability to deliver Rhoa siRNA into T-cell acute lymphoblastic leukemia (T-ALL) cells to advance therapies targeting Rhoa in the future

Thematic Content and Visualization Strategy for Map Design of City-Specific Culture Based on Local Chronicles: A Case Study of Dengfeng City, China

Local chronicles are a kind of historical record in China that are written in detail and play an important role in the transmission of local history and culture. Due to the single-text-carrier form of local chronicles, people have limited access to information on urban characteristics and culture; therefore, based on the cultural gene theory and Hofstede model, also known as the cultural onion model, this paper develops a “Spirit–Sign” content framework with the themes of urban characteristics and culture. Based on this framework, we map the urban characteristics and culture (visualization strategy and map design) of local chronicles. Taking the historic city of Dengfeng in the Central Plains as an example, the spatial information of the four historical city characteristics of Dengfeng was mined for the map design using the content framework of the city characteristics proposed in this study. The results of the study found that (1) there is a certain overlap in the spatial distribution of the four characteristic cultures of Dengfeng, indicating that the spiritual (traditional customs and famous people and events) and material (famous buildings and products) are complementary and mutually reinforcing to a certain extent; and (2) with the iterative development of Chinese dynasties, the material characteristic cultures of Dengfeng show strong temporal and spatial differences, which laterally reflect the changes in human activities and urban changes of each dynasty and also reflect the very important historical position occupied by Dengfeng in China. Compared with the traditional text-carrier form of local chronicles, the content construction and map visualization of the city’s historical and cultural information proposed in this study can effectively explore more potential cultural characteristics, as well as spatial and temporal connections of Dengfeng and thus help people better understand the historical characteristics of the city

Dietary Association with Midgut Microbiota Components of <i>Eocanthecona furcellata</i> (Wolff)

Eocanthecona furcellata is an important predatory stinkbug that attacks many lepidopteran pests. For mass-rearing, artificial diets are used to rear this predator in the laboratory; however, the fitness of the predators is reduced, and little is known about the cause. Since gut microbiota plays vital roles in the digestion and development of many hosts and can consequently affect host fitness, an understanding of the microbial community composition of E. furcellata may help to solve this unresolved problem. We compared the development and reproduction of E. furcellata reared on an artificial diet, and a natural (Spodoptera litura) or semi-natural (Tenebrio molitor) diet, and then the midgut microbiota were assessed using high-throughput 16S rRNA. The results of the high-throughput 16S rRNA show that the bacterial richness and diversity in the artificial diet gut samples increased considerably compared with the other samples. Proteobacteria and Firmicutes were the dominant phyla in E. furcellata. At the genus level, Serratia (however, the relative abundance was lower in the artificial diet gut samples), Enterococcus, and an uncultured bacterium genus of family Enterobacteriaceae, were dominant. The midgut microbiota components significantly differed among the diets, indicating that the gut bacteria had a dietary association with E. furcellata. This study provides a better understanding of midgut microbiota and the artificial diets that might affect them in E. furcellata

Inactivation and Membrane Damage Mechanism of Slightly Acidic Electrolyzed Water on <i>Pseudomonas deceptionensis</i> CM2

Pseudomonas is considered as the specific spoilage bacteria in meat and meat products. The purpose of this study was to evaluate the inactivation efficiency and mechanisms of slightly acidic electrolyzed water (SAEW) against Pseudomonas deceptionensis CM2, a strain isolated from spoiling chicken breast. SAEW caused time-dependent inactivation of P. deceptionensis CM2 cells. After exposure to SAEW (pH 5.9, oxidation–reduction potential of 945 mV, and 64 mg/L of available chlorine concentration) for 60 s, the bacterial populations were reduced by 5.14 log reduction from the initial load of 10.2 log10 CFU/mL. Morphological changes in P. deceptionensis CM2 cells were clearly observed through field emission-scanning electron microscopy as a consequence of SAEW treatment. SAEW treatment also resulted in significant increases in the extracellular proteins and nucleic acids, and the fluorescence intensities of propidium iodide and n-phenyl-1-napthylamine in P. deceptionensis CM2 cells, suggesting the disruption of cytoplasmic and outer membrane integrity. These findings show that SAEW is a promising antimicrobial agent