Genomic insights into selection for heterozygous alleles and woody traits in Populus tomentosa

Heterozygous alleles are widespread in outcrossing and clonally propagated woody plants. The variation in heterozygosity that underlies population adaptive evolution and phenotypic variation, however, remains largely unknown. Here, we describe a de novo chromosome-level genome assembly of Populus tomentosa, an economic and ecologically important native tree in northern China. By resequencing 302 natural accessions, we determined that the South subpopulation (Pop_S) encompasses the ancestral strains of P. tomentosa, while the Northwest subpopulation (Pop_NW) and Northeast subpopulation (Pop_NE) experienced different selection pressures during population evolution, resulting in significant population differentiation and a decrease in the extent of heterozygosity. Analysis of heterozygous selective sweep regions (HSSR) suggested that selection for lower heterozygosity contributed to the local adaptation of P. tomentosa by dwindling gene expression and genetic load in the Pop_NW and Pop_NE subpopulations. Genome-wide association studies (GWAS) revealed that 88 single nucleotide polymorphisms (SNPs) within 63 genes are associated with nine wood composition traits. Among them, the selection for the homozygous AA allele in PtoARF8 is associated with reductions in cellulose and hemicellulose contents by attenuating PtoARF8 expression, and the increase in lignin content is attributable to the selection for decreases in exon heterozygosity in PtoLOX3 during adaptive evolution of natural populations. This study provides novel insights into allelic variations in heterozygosity associated with adaptive evolution of P. tomentosa in response to the local environment and identifies a series of key genes for wood component traits, thereby facilitating genomic-based breeding of important traits in perennial woody plants.     

Avicularin alleviates acute liver failure by regulation of the TLR4/MyD88/NF-κB and Nrf2/HO-1/GPX4 pathways to reduce inflammation and ferroptosis

Acute liver failure (ALF) is an inflammation-mediated hepatocyte death process associated with ferroptosis. Avicularin (AL), a Chinese herbal medicine, exerts anti-inflammatory and antioxidative effects. However, the protective effect of AL and the mechanism on ALF have not been reported. Our in vivo results suggest that AL significantly alleviated lipopolysaccharide (LPS)/D-galactosamine (D-GalN)-induced hepatic pathological injury, liver enzymes, inflammatory cytokines, reactive oxygen species and iron levels and increased the antioxidant enzyme activities (malondialdehyde and glutathione). Our further in vitro experiments demonstrated that AL suppressed inflammatory response in LPS-stimulated RAW 264.7 cells via blocking the toll-like receptor 4 (TLR4)/myeloid differentiation protein-88 (MyD88)/nuclear factor kappa B (NF-κB) pathway. Moreover, AL attenuated ferroptosis in D-GalN-induced HepG2 cells by activating the nuclear factor erythroid 2-related factor 2 (Nrf2)/heme oxygenase 1 (HO-1)/glutathione peroxidase 4 (GPX4) pathway. Therefore, AL can alleviate inflammatory response and ferroptosis in LPS/D-GalN-induced ALF, and its protective effects are associated with blocking TLR4/MyD88/NF-κB pathway and activating Nrf2/HO-1/GPX4 pathway. Moreover, AL is a promising therapeutic option for ALF and should be clinically explored.     

-cyano-substituted analogoues of decarboxylated S-adenosylmethionine as enzyme activated, irreversible inhibitors of S-adenosylmethionine decarboxylase

A pair of -cyano analogues of decarboxylated S-adenosylmethionine (2a and 2b) were synthesized as potential enzyme activated, irreversible inhibitors of the[pyruvoyl enzyme S-adenosylmethionine decarboxylase (AdoMet-DC). Each of these analogues acts as an irreversible inactivator for ADoMet-DC from Escherichia coli (IC₅₀ values of 9 and 50 μM, respectively). These analogues also inactivate human AdoMet-DC, with K_I values of 246.6 and 7.2 μM, and k_inact values of 0.29 and 0.03 min⁻¹, respectively.     

气候变化导致青藏高原马鹿种群适应性分布退缩：以类乌齐马鹿国家级自然保护区为例

近50年青藏高原的气候变化速率是全球平均值的2倍,对高原有蹄类的种群分布和多样性维持带来严重影响。本研究以西藏类乌齐马鹿国家级自然保护区的马鹿种群为例,通过2013年和2021年对马鹿和牦牛种群数量、分布的调查,并整合了物种分布模型和种群动态模型,评估了当前和未来气候变化及人类活动(放牧、道路、居民点等)对马鹿种群适应性分布的影响。研究表明,马鹿种群在2013—2021年由890头增加到1 400头,根据种群增长模型预计在2050年马鹿种群数量将达到1 735头,但其适宜栖息地在2050年代下降43.4%,2070年代下降5.1%,表明马鹿种群增长与适宜栖息地缩小之间的冲突将不利于马鹿种群的可持续发展。同时,当前马鹿与牦牛栖息地重合率为19%,2050年代为60%,2070年代为37%,且牦牛与马鹿存在食物竞争,这在一定程度上减少了马鹿原有的适宜栖息地。为保护马鹿,建议减少牦牛的饲养量1 000～1 500头。本研究将种群增长模型、种间竞争关系与物种分布模型整合,把气候变化对物种的影响延伸到种群层面,对其他物种的保护具有借鉴意义。     

Metabolic engineering of Mannheimia succiniciproducens for malic acid production using dimethylsulfoxide as an electron acceptor

Microbial production of various TCA intermediates and related chemicals through the reductive TCA cycle has been of great interest. However, rumen bacteria that naturally possess strong reductive TCA cycle have been rarely studied to produce these chemicals, except for succinic acid, due to their dependence on fumarate reduction to transport electrons for ATP synthesis. In this study, malic acid (MA), a dicarboxylic acid of industrial importance, was selected as a target chemical for mass production using Mannheimia succiniciproducens, a rumen bacterium possessing a strong reductive branch of the TCA cycle. The metabolic pathway was reconstructed by eliminating fumarase to prevent MA conversion to fumarate. The respiration system of M. succiniciproducens was reconstructed by introducing the Actinobacillus succinogenes dimethylsulfoxide (DMSO) reductase to improve cell growth using DMSO as an electron acceptor. Also, the cell membrane was engineered by employing Pseudomonas aeruginosa cis-trans isomerase to enhance MA tolerance. High inoculum fed-batch fermentation of the final engineered strain produced 61 g/L of MA with an overall productivity of 2.27 g/L/h, which is the highest MA productivity reported to date. The systems metabolic engineering strategies reported in this study will be useful for developing anaerobic bioprocesses for the production of various industrially important chemicals.     

Subcellular Distribution and Chemical Forms of Cadmium in the Medicine Food Homology Plant <i>Platycodon grandiflorum</i> (Jacq.) A.DC.

Although Platycodon grandiflorum (Jacq.) A.DC. is a renowned medicine food homology plant, reports of excessive cadmium (Cd) levels are common, which affects its safety for clinical use and food consumption. To enable its Cd levels to be regulated or reduced, it is necessary to first elucidate the mechanism of Cd uptake and accumulation in the plant, in addition to its detoxification mechanisms. This present study used inductively couple plasma-mass-spectrometry to analyze the subcellular distribution and chemical forms of Cd in different tissues of P. grandiflorum. The experimental results showed that Cd was mainly accumulated in the roots [predominantly in the cell wall (50.96%–61.42%)], and it was found primarily in hypomobile and hypotoxic forms. The proportion of Cd in the soluble fraction increased after Cd exposure, and the proportion of insoluble phosphate Cd and oxalate Cd increased in roots and leaves, with a higher increase in oxalate Cd. Therefore, it is likely that root retention mechanisms, cell wall deposition, vacuole sequestration, and the formation of low mobility and low toxicity forms are tolerance strategies for Cd detoxification used by P. grandiflorum. The results of this study provide a theoretical grounding for the study of Cd accumulation and detoxification mechanisms in P. grandiflorum, and they can be used as a reference for developing Cd limits and standards for other medicine food homology plants.     

Sub-Cellular Distribution of Zinc in Different Vegetative Organs and Their Contribution to Grains Zinc Accumulation in Rice Under Different Nitrogen and Zinc Supply

Journal of Plant Growth Regulation - Zinc is an important micronutrient for the growth and development of human body and plants. Proper use of nitrogen fertilizer and foliar application of Zn have...     

采用Reichardt运动检测器和Boltzmann Machine神经网络的运动计算

建立了一个探讨灵长类视皮层从Ｖ１区到ＭＴ区的运动信息加工原理的计算模型,这个过程的突出特征是视觉运动信息经过了从局部检测进步到整体感知。模型的第一层由用于抽提运动模式的局部速度以及结构性质的Ｒｅｉｃｈａｒｄｔ运动检测器组成,进一步的加工是通过Ｂｏｌｔｚｍａｎｎ Ｍａｃｈｉｎｅ神经网络来实现的。这种网络的学习算法具有局部更新的显著性质,在学习阶段,网络不断地修改联结权重以形成对于记录在网络的显单元上     

应用PCR对尖锐湿疣和外耳道乳头状瘤中HPV DNA的分型检测

从手术切除的24例女性和12例男性尖锐湿疣新鲜标本中,以及42例女性尖锐湿疣、16例男性外耳道乳头状瘤和4例女性假性湿疣的石蜡包埋标本中,提取组织的基因组DNA,用人工合成的人乳头瘤病毒6.11和16型E6区特异性寡聚核苷酸引物,通过PCR进行HPV DNA的分型检测。结果66例女性尖锐湿疣中,感染HPV6型者4例,感染11型者12例,6+11型混合感染者49例;阴性1例,总检出率达98.4％。4例女性假性湿疣中1例为HPV6型感染,阳性率25％。16例男性外耳道乳头状瘤中HPV6+11型感染者5例,6+16型感染者3例,6+11+16型多重感染者8例,阳性率100％。12例男性尖锐湿疣中,HPV11型感染者7例,6+11型4例,阴性1例,总阳性率91.6％。还对细胞学上空泡化和非典型空泡化尖锐湿疣标本的HPV感染做了比较,未发现差异。     

谷类作物β-葡聚糖合成酶基因家族的研究进展

Beta-葡聚糖是由β-(1,3)和β-(1,4)糖苷键连接的非纤维素多糖,主要分布在谷类作物籽粒胚乳及糊粉层中,在高尔基体合成,经由囊泡运输到质膜,最终在细胞壁上沉积。通过增加胆汁酸排泄,延迟葡萄糖吸收,β-葡聚糖可有效降低胆固醇及血糖水平。Beta-葡聚糖合成酶基因家族成员最早在水稻(Oryza sativa)中得到鉴定,后在其他作物中陆续被发现。该基因家族包括3个主要成员：CslF、CslH和CslJ亚基因家族,起源于不同分支,经过趋同演化,执行合成β-葡聚糖的功能。Beta-葡聚糖基因家族成员均受到负选择压力,演化过程中序列高度保守。CslF亚家族基因成员相对较多,常在染色体上形成基因簇,CslF6是介导β-葡聚糖合成的主效基因。CslF亚家族在叶基部等幼嫩组织中表达水平相对较高,且明显受到光照强度的影响;CslH和CslJ亚家族成员较少,其中CslH亚家族在叶尖等成熟组织中的表达水平高,而CslJ亚家族在籽粒中有较高的表达水平。该文综述了β-葡聚糖合成酶基因家族成员的系统发育关系、表达模式,β-葡聚糖合成酶的亚细胞定位,以及作物中的定向育种研究进展,提出β-葡聚糖合成酶基因家...