The tRNA A76 Hydroxyl Groups Control Partitioning of the tRNA-dependent Pre- and Post-transfer Editing Pathways in Class I tRNA Synthetase

Aminoacyl-tRNA synthetases catalyze ATP-dependent covalent coupling of cognate amino acids and tRNAs for ribosomal protein synthesis. Escherichia coli isoleucyl-tRNA synthetase (IleRS) exploits both the tRNA-dependent pre- and post-transfer editing pathways to minimize errors in translation. However, the molecular mechanisms by which tRNA^Ile organizes the synthetic site to enhance pre-transfer editing, an idiosyncratic feature of IleRS, remains elusive. Here we show that tRNA^Ile affects both the synthetic and editing reactions localized within the IleRS synthetic site. In a complex with cognate tRNA, IleRS exhibits a 10-fold faster aminoacyl-AMP hydrolysis and a 10-fold drop in amino acid affinity relative to the free enzyme. Remarkably, the specificity against non-cognate valine was not improved by the presence of tRNA in either of these processes. Instead, amino acid specificity is determined by the protein component per se, whereas the tRNA promotes catalytic performance of the synthetic site, bringing about less error-prone and kinetically optimized isoleucyl-tRNA^Ile synthesis under cellular conditions. Finally, the extent to which tRNA^Ile modulates activation and pre-transfer editing is independent of the intactness of its 3′-end. This finding decouples aminoacylation and pre-transfer editing within the IleRS synthetic site and further demonstrates that the A76 hydroxyl groups participate in post-transfer editing only. The data are consistent with a model whereby the 3′-end of the tRNA remains free to sample different positions within the IleRS·tRNA complex, whereas the fine-tuning of the synthetic site is attained via conformational rearrangement of the enzyme through the interactions with the remaining parts of the tRNA body.     

Shifting abundances of communities associated with nitrogen cycling in soils promoted by sugarcane harvest systems

Sugarcane cultivation supports Brazil as one of the largest world sugar and ethanol producer. In order to understand the impact of changing sugarcane harvest from manual to mechanized harvest, we studied the effect of machinery traffic on soil and consequently soil compaction upon soil microbial communities involved in nitrogen cycling. The impact of sugarcane harvest was dependent on soil depth and texture. At deeper soil layers, mechanized harvesting increases the abundance of nitrogen fixers and denitrifying communities (specifically nosZ clade I and II) while manual harvesting increases the abundance of ammonia oxidizers (specifically AOA) and increases denitrifying communities (nosZ clade I and II) on top and at intermediate depth. The effect of change on the harvest system is more evident on sandy soil than on clay soil, where soil indicators of compaction (bulk density and penetration resistance) were negatively correlated with soil microorganisms associated with the nitrogen cycle. Our results point to connections between soil compaction and N transformations in sugarcane fields, besides naming biological variables to be used as proxies for alterations in soil structure.     

Effects of nitrogen limitation on water relations of jack pine (Pinus banksiana Lamb.) seedlings

The water relations of shoots of young jack pine (Pinus banksiana Lamb.) seedlings were examined 6 and 15 weeks after the initiation of four different dynamic nitrogen (N) treatments using a pressure-volume analysis. The N treatments produced a wide range of needle N concentrations from 12 to 32 mg g^?1 dry mass and a 10-fold difference in total dry mass at 15 weeks. Osmotic potential at full turgor did not change over the range of needle N concentrations observed. Osmotic potential at turgor-loss point, however, declined as N concentrations decreased, indicating an increased ability of N-deficient jack pine plants to maintain turgor. The increase could be attributed largely to an increase in cell wall elasticity, suggesting that elasticity changes may be a common, significant adaptation of plants to environmental stresses. Dry mass per unit saturated water almost doubled as needle N level dropped from 32 to 12 mg g^?1 and was inversely correlated to the bulk modulus of elasticity. This suggests that cell wall elasticity is determined more by the nature of its cross-linking matrix than by the total amount of cell wall material present. Developmental change was evident in the response of some water relation variables to N limitation.     

气候变化下中国八种梧桐属树种潜在适生区模拟

中国梧桐属（Firmiana）在世界梧桐属中占比较大，且除梧桐外其余种均为中国特有且分布范围狭窄的植物种，灭绝风险大，研究气候变化对中国梧桐属树种的影响对于维护生物多样性具有重要的意义。结合多时期第六次国际气候耦合模式比较计划（CMIP6）气候变量数据和中国八种梧桐属树种的分布数据，基于R语言kuenm程序包优化的最大熵（Maxent）模型模拟分析中国八种梧桐属树种在多尺度下的潜在适生区，得出梧桐属最适宜的模拟尺度、潜在适生区的面积变化和迁移方向、梧桐属多样性保护关键区域及保护空缺。结果表明：（1）梧桐属最适宜的模拟尺度为亚洲；（2） Maxent模型的接收者操作特征曲线下面积（AUC）值均大于0.9，表明模型对梧桐属潜在适生区预测结果具有较高准确度；（3）气候变化影响下除云南梧桐（Firmiana major）外其它树种的潜在适生区都将在未来有所扩大；（4）中国八种梧桐属树种潜在适生区迁移方向主要为东西向，南北向大跨度迁移较少，纬度变化不大；（5）丹霞梧桐（Firmiana danxiaensis）的稳定潜在适生区最小；（6）中国梧桐属多样性保护关键区域主要分布于广西壮族自治区及云南、广东、海南等省区；（7）中国梧桐属多样性保护空缺区域主要分布于广西壮族自治区中部及海南省北部；（8）梧桐属多样性保护关键区域正在为人造地表所侵蚀。研究分析气候变化对中国八种梧桐属树种的影响及其潜在适生区变化、中国梧桐属多样性保护状态，可为中国梧桐属建立多样性保护廊道提供相关建议，为制定多样性保护规划及相应措施提供参考。     

Evaluation of automated analysis of 15N and total N in plant material and soil

Simultaneous determination of ¹⁵N and total N using an automated nitrogen analyser interfaced to a continuous-flow isotope ratio mass spectrometer (ANA-MS method) was evaluated. The coefficient of variation (CV) of repeated analyses of homogeneous standards and samples at natural abundance was lower than 0.1%. The CV of repeated analyses of ¹⁵N-labelled plant material and soil samples varied between 0.3% and 1.1%. The reproductibility of repeated total N analyses using the automated method was comparable to results obtained with a semi-micro Kjeldahl procedure. However, the automated method gave results which were 3% to 5% higher than those obtained with the Kjeldahl procedure. Since only small samples can be analysed, careful sample homogenization and fine grinding are very important. Evaluation of a diffusion method for preparing nitrate and ammonium in solution for automated ¹⁵N analysis showed that the recovery of inorganic N in the NH₃ trap was lower when the N was diffused from water than from 2 M KCl. The results also indicated that different proportions of the NO₃ ^- and the NH₄ ⁺ in aqueous solution were recovered in the trap after combined diffusion. The method is most suited for diffusing either NO₃ ^- or NH₄ ⁺ alone, but can be used for combined diffusion of the two ions.     

Dinitrogen fixation and infection of grass leaves byPseudomonas rubrisubalbicans andHerbaspirillum seropedicae

Bacteria causing mottled stripe disease in sugar cane, known asPseudomonas rubrisubalbicans, were shown to be able to fix molecular N₂ and to grow on it. The root associated diazotroph known asHerbaspirillum seropedicae, after artificial inoculation caused mottled stripe disease symptoms on sorghum and Napier grass but not on sugar cane. Both bacteria could be reisolated from leaves even 60 days after. Sugar cane leaves contained large numbers of these bacteria even in the uninoculated controls. Additional physiological characteristics of six strains ofP. rubrisubalbicans were compared with those of twoH. seropedicae strains and were shown to be very similar.     

The cellular pathway of photosynthate transfer in the developing wheat grain. II. A structural analysis and histochemical studies of the pathway from the crease phloem to the endosperm cavity

In the developing wheat grain, photosynthate is transferred longitudinally along the crease phloem and then laterally into the endosperm cavity through the crease vascular parenchyma, pigment strand and nucellar projection. In order to clarify this cellular pathway of photosynthate unloading, and hence the controlling mechanism of grain filling, the potential for symplastic and apoplastic transfer was examined through structural and histochemical studies on these tissue types. It was found that cells in the crease region from the phloem to the nucellar projection are interconnected by numerous plasmodesmata and have dense cytoplasm with abundant mitochondria. Histochemical studies confirmed that, at the stage of grain development studied, an apoplastic barrier exists in the cell walls of the pigment strand. This barrier is composed of lignin, phenolics and suberin. The potential capacity for symplastic transfer, determined by measuring plasmodesmatal frequencies and computing potential sucrose fluxes through these plasmodesmata, indicated that there is sufficient plasmodesmatal cross-sectional area to support symplastic unloading of photosynthate at the rate required for normal grain growth. The potential capacity for membrane transport of sucrose to the apoplast was assessed by measuring plasma membrane surface areas of the various cell types and computing potential plasma membrane fluxes of sucrose. These fluxes indicated that the combined plasma membrane surface areas of the sieve element–companion cell (se–cc) complexes, vascular parenchyma and pigment strand are not sufficient to allow sucrose transfer to the apoplast at the observed rates. In contrast, the wall ingrowths of the transfer cells in the nucellar projection amplify the membrane surface area up to 22-fold, supporting the observed rates of sucrose transfer into the endosperm cavity. We conclude that photosynthate moves via the symplast from the se–cc complexes to the nucellar projection transfer cells, from where it is transferred across the plasma membrane into the endosperm cavity. The apoplastic barrier in the pigment strand is considered to restrict solute movement to the symplast and block apoplastic solute exchange between maternal and embryonic tissues. The implications of this cellular pathway in relation to the control of photosynthate transfer in the developing grain are discussed.     

Effect of biceps-to-triceps transfer on rotator cuff stress during upper limb weight-bearing lift in tetraplegia: A modeling and simulation analysis

Rotator cuff stress during upper limb weight-bearing lifts presumably contribute to rotator cuff disease, which is the most common cause of shoulder pain in individuals with tetraplegia. Elbow extension strength appears to be a key determinant of rotator cuff stress during upper limb weight-bearing lifts since individuals with paraplegia who generate greater elbow extensor moments experience lower rotator cuff stress relative to individuals with tetraplegia. Biceps-to-triceps transfer surgery can increase elbow extension strength in individuals with tetraplegia. The purpose of this study was to determine whether active elbow extension via biceps transfer decreases rotator cuff stress during weight-bearing lifts in individuals with tetraplegia. A forward dynamics computational framework was used to estimate muscle stress during the lift; stress was computed as muscle force divided by the peak isometric muscle force. We hypothesized that rotator cuff stresses would be lower in simulated lifting with biceps transfer relative to simulated lifting without biceps transfer. We found that limited elbow extension strength in individuals with tetraplegia, regardless of whether elbow strength is enabled via biceps transfer or is residual after spinal cord injury, results in muscle stresses exceeding 85% of the peak isometric muscle stress in the supraspinatus, infraspinatus, and teres minor. The rotator cuff stresses we estimated suggest that performance of weight-bearing activities should be minimized or assisted in order to reduce the risk for shoulder pain. Our results also indicate that biceps transfer is unlikely to decrease rotator cuff stress during weight-bearing lifts in individuals with tetraplegia.