Docking of Antizyme to Ornithine Decarboxylase and Antizyme Inhibitor using Experimental Mutant and Double-Mutant Cycle Data

Antizyme (Az) is a highly conserved key regulatory protein bearing a major role in regulating polyamine levels in the cell. It has the ability to bind and inhibit ornithine decarboxylase (ODC), targeting it for degradation. Az inhibitor (AzI) impairs the activity of Az. In this study, we mapped the binding sites of ODC and AzI on Az using Ala scan mutagenesis and generated models of the two complexes by constrained computational docking. In order to scan a large number of mutants in a short time, we developed a workflow combining high-throughput mutagenesis, small-scale parallel partial purification of His-tagged proteins and their immobilization on a tris-nitrilotriacetic-acid-coated surface plasmon resonance chip. This combination of techniques resulted in a significant reduction in time for production and measurement of large numbers of mutant proteins. The data-driven docking results suggest that both proteins occupy the same binding site on Az, with Az binding within a large groove in AzI and ODC. However, single-mutant data provide information concerning the location of the binding sites only, not on their relative orientations. Therefore, we generated a large number of double-mutant cycles between residues on Az and ODC and used the resulting interaction energies to restrict docking. The model of the complex is well defined and accounts for the mutant data generated here, and previously determined biochemical data for this system. Insights on the structure and function of the complexes, as well as general aspects of the method, are discussed.     

Solanum Tuber-bearing Species Resistance Behavior Against Nacobbus aberrans

Naccobus aberrans is a major pest of the potato crop in the Andean regions of Argentina, Bolivia, and Perú. It is endemic in northwest Argentina and is also found in lowlands. The resistance of eleven Andean potato landraces and three accessions of the wild tuber-bearing species Solanum acaule, S. infundibuliforme, and S. megistacrolobum were evaluated against a population of N. aberrans from Coctaca, Jujuy province, while Solanum tuberosum ssp. tuberosum 'Spunta', 'Kennebec', and 'Frital INTA' were evaluated against a population from the southeast of Buenos Aires province. The presence, the number of galls, and the number of individuals were recorded. In addition, a reproduction factor was calculated and races were determined. Results showed that the N. aberrans population from Coctaca corresponded to race 2 and the population from the lowlands belonged to the sugar beet group. Landrace Azul, one genotype of S. megistacrolobum, and two genotypes of S. acaule showed resistance towards the race from Coctaca while no infection was recorded in potato cultivars with the Naccobus race from the lowland area.     

两种野生花卉的扦插繁殖研究

开展野生花卉车轮梅(Raphiolepis indica)和赤楠(Syzygium buxifolium)扦插试验,结果表明:车轮梅硬枝扦插需一定浓度的外源激素方能生根;对激素浓度大小不敏感;总体上NAA组合生根质量优于IBA组合。综合不同处理生根率、根数和不定根根长3个指标,以800 mg/L NAA或800 mg/L IBA作为车轮梅生产上扦插的激素种类和浓度。赤楠生根率较低,最高扦插率达66.7%,生根时间长,约需45 d始生根。综合生根率、不定根根数和不定根根长3个生根指标,试验的4种激素均能较好促进赤楠生根,200×根太阳在生根率和根数上效果最好,生产上可用200×根太阳浸泡2 h,也可用50-100 mg/L NAA或100-400 mg/L IBA浸泡2 h后进行扦插。     

γ-Irradiation induces P2X7 receptor-dependent ATP release from B16 melanoma cells

Background

Ionizing irradiation causes not only growth arrest and cell death, but also release of growth factors or signal transmitters, which promote cancer malignancy. Extracellular ATP controls cancer growth through activation of purinoceptors. However, there is no report of radiation-induced ATP release from cancer cells. Here, we examined γ-irradiation-induced ATP release and its mechanism in B16 melanoma.

Methods

Extracellular ATP was measured by luciferin–luciferase assay. To investigate mechanism of radiation-induced ATP release, we pharmacologically inhibited the ATP release and established stable P2X₇ receptor-knockdown B16 melanoma cells using two short hairpin RNAs targeting P2X₇ receptor.

Results

Cells were exposed to 0.5–8 Gy of γ-rays. Extracellular ATP was increased, peaking at 5 min after 0.5 Gy irradiation. A selective P2X₇ receptor channel antagonist, but not anion transporter inhibitors, blocked the release of ATP. Further, radiation-induced ATP release was significantly decreased in P2X₇ receptor-knockdown cells. Our results indicate that γ-irradiation evokes ATP release from melanoma cells, and P2X₇ receptor channel plays a significant role in mediating the ATP release.

General Significance

We suggest that extracellular ATP could be a novel intercellular signaling molecule released from cancer cells when cells are exposed to ionizing radiation.     

红树林植物露兜树营养成分分析

本文对红树林植物露兜树的营养成分进行了分析,结果表明,露兜树中含有多种营养成分,丰富的矿质元素和维生素及其β-胡萝卜素。露兜树中至少含有17种氨基酸。旨在为开发利用植物资源提供科学依据。     

伊犁地区野生毛牛蒡和牛蒡的种群分布、生态和群落特性的研究

在充分踏察的基础上,选择具有代表性的样地,接线路调查法和样地调查法得出野生毛牛蒡和牛蒡种群的分布格局在伊犁地区总体上呈随机分布,占86．7％的调查样地;小范围内也有群聚分布的,占13．3％的调查样地;分布于喜光、低海拔、对土壤适应性高、生活力强等是牛蒡和毛牛蒡的生态习性;常与各类草本为伍,与菊科、禾本科、唇形科、藜科、蓼科、蒺藜科等常见科的植物均能共生于同一环境,是牛蒡和毛牛蒡的群落学特性;植被类型和人为因素是影响它们分布的环境因素。     

Distribution of Competition Potential Between Native Ungulates and Free-Roaming Equids on Western Rangelands

Free-roaming equids (i.e., feral horses [Equus caballus] and burros [Equus asinus]) are widely distributed and locally abundant across the rangelands of the western United States. The 1971 Wild Free Roaming Horse and Burro Act (WFRHBA) gave the Bureau of Land Management (BLM) and United States Forest Service (USFS) the legal authority to manage these animals on designated public lands. To fulfill this responsibility, federal agencies established an Appropriate Management Level (AML), defined as the number of horses or burros that can be sustained on a given management unit under prevailing environmental conditions and land uses. Although the WFRHBA specifies that feral equids must be managed in ecological balance with other land uses, including conservation of native wildlife, population control measures such as gathers, contraception, and adoptions have failed to keep pace with intrinsic growth rates. Over 80% of federally managed herds currently exceed prescribed population levels, making the potential for competition between native ungulates and feral equids a growing concern among state wildlife agencies. Mule deer (Odocoileus hemionus), pronghorn (Antilocapra americana), elk (Cervus canadensis), and bighorn sheep (Ovis canadensis) are of ecological and economic value to the states where they occur, and all exhibit some degree of distributional, habitat, or dietary overlap with horses or burros. Notwithstanding the scale of the problem, to date there have been no range-wide assessments of competition potential among native and feral ungulates for space, forage, or water. To address this need, we compiled demographic, jurisdictional, and species occurrence data collected from 2010–2019 by federal and state agencies. We used these data to map the distributions of 4 native ungulate species across federal equid management units (FEMUS) in 10 western states (n = 174). We then made within-state rankings of the 50 units that were ≥2 times over AML and encompassed ≥3 native ungulates. Collectively, FEMUs covered approximately 225,000 km², representing 18% of all BLM and USFS lands in affected states. Each FEMU supported ≥1 native ungulate and 14% contained all 4. The degree of overlap between native and feral species varied by state, ranging from <1% for mule deer in Montana, to 40% for bighorn sheep in Nevada. Oregon had the largest proportion of units that supported all 4 native ungulates (58%), whereas Montana and New Mexico had the fewest equids, but all populations were over target densities. Despite the perception that the problem of equid abundance is limited to the Great Basin states, high intrinsic growth rates and social constraints on management practices suggest all affected states should monitor range conditions and native ungulate demography in areas where forage and water resources are limited and expanding equid populations are a concern. © 2021 The Wildlife Society.     

野生动物分子水平研究中的取样方法进展

对野生动物进行分子水平研究时 ,在取材上经常存在野外找不到动物或得到的材料提取不到足够的DNA等困难。但随着PCR技术的产生和DNA提取技术的进步 ,研究材料也不再局限于新鲜的组织样本 ,从而取样的范围扩大到微量的血液、单根的毛发、羽毛、指甲、唾液、粪便、骨骼 ,甚至古代化石等样品 ,研究范围随之也不断扩大。     

Assembly and annotation of a draft genome sequence for Glycine latifolia,a perennial wild relative of soybean

Glycine latifolia (Benth.) Newell & Hymowitz (2n = 40), one of the 27 wild perennial relatives of soybean, possesses genetic diversity and agronomically favorable traits that are lacking in soybean. Here, we report the 939‐Mb draft genome assembly of G. latifolia (PI 559298) using exclusively linked‐reads sequenced from a single Chromium library. We organized scaffolds into 20 chromosome‐scale pseudomolecules utilizing two genetic maps and the Glycine max (L.) Merr. genome sequence. High copy numbers of putative 91‐bp centromere‐specific tandem repeats were observed in consecutive blocks within predicted pericentromeric regions on several pseudomolecules. No 92‐bp putative centromeric repeats, which are abundant in G. max, were detected in G. latifolia or Glycine tomentella. Annotation of the assembled genome and subsequent filtering yielded a high confidence gene set of 54 475 protein‐coding loci. In comparative analysis with five legume species, genes related to defense responses were significantly overrepresented in Glycine‐specific orthologous gene families. A total of 304 putative nucleotide‐binding site (NBS)‐leucine‐rich‐repeat (LRR) genes were identified in this genome assembly. Different from other legume species, we observed a scarcity of TIR‐NBS‐LRR genes in G. latifolia. The G. latifolia genome was also predicted to contain genes encoding 367 LRR‐receptor‐like kinases, a family of proteins involved in basal defense responses and responses to abiotic stress. The genome sequence and annotation of G. latifolia provides a valuable source of alternative alleles and novel genes to facilitate soybean improvement. This study also highlights the efficacy and cost‐effectiveness of the application of Chromium linked‐reads in diploid plant genome de novo assembly.     

贵州少数民族地区作物稀有种质资源和野生近缘植物

"贵州农业生物资源调查"项目于2012-2014年已对贵州省21个县(市)进行了系统调查。系统调查的21个县(市)均有少数民族集居,各民族有不同的传统文化和生活习俗,在世代相传中赋予了当地作物种质资源丰富的民族文化内涵。并且,当地的地形地貌复杂,气候类型多样。正因为这种多样的自然条件和各异的民族文化,造就了这里丰富的作物稀有种质资源和野生近缘植物。本次调查获得的作物稀有种质资源和野生近缘植物,对作物的分类研究和新品种选育以及商业开发,将会有一定的利用价值。