Modeling robustness tradeoffs in yeast cell polarization induced by spatial gradients

Cells localize (polarize) internal components to specific locations in response to external signals such as spatial gradients. For example, yeast cells form a mating projection toward the source of mating pheromone. There are specific challenges associated with cell polarization including amplification of shallow external gradients of ligand to produce steep internal gradients of protein components (e.g. localized distribution), response over a broad range of ligand concentrations, and tracking of moving signal sources. In this work, we investigated the tradeoffs among these performance objectives using a generic model that captures the basic spatial dynamics of polarization in yeast cells, which are small. We varied the positive feedback, cooperativity, and diffusion coefficients in the model to explore the nature of this tradeoff. Increasing the positive feedback gain resulted in better amplification, but also produced multiple steady-states and hysteresis that prevented the tracking of directional changes of the gradient. Feedforward/feedback coincidence detection in the positive feedback loop and multi-stage amplification both improved tracking with only a modest loss of amplification. Surprisingly, we found that introducing lateral surface diffusion increased the robustness of polarization and collapsed the multiple steady-states to a single steady-state at the cost of a reduction in polarization. Finally, in a more mechanistic model of yeast cell polarization, a surface diffusion coefficient between 0.01 and 0.001 μm(2)/s produced the best polarization performance, and this range is close to the measured value. The model also showed good gradient-sensitivity and dynamic range. This research is significant because it provides an in-depth analysis of the performance tradeoffs that confront biological systems that sense and respond to chemical spatial gradients, proposes strategies for balancing this tradeoff, highlights the critical role of lateral diffusion of proteins in the membrane on the robustness of polarization, and furnishes a framework for future spatial models of yeast cell polarization.     

Pervanadate stabilizes desmosomes

Desmosomes are intercellular junctions responsible for strong cell-cell adhesion in epithelia and cardiac muscle. Numerous studies have shown that the other major type of epithelial cell adhesion, the adherens junction, is destabilized by src-induced tyrosine phosphorylation of two of its principal components, E-cadherin and β-catenin. Here we show that treatment of epithelial cells with the potent tyrosine phosphatase inhibitor sodium pervanadate causes tyrosine phosphorylation of the major desmosomal components desmoglein 2 and plakoglobin in both the non-ionic detergent soluble and insoluble cell fractions and, surprisingly, stabilizes desmosomal adhesion, inducing the hyper-adhesive form normally found in tissues and confluent cell sheets. Taken together with the few other studies on desmosomes these results suggest that the effects of tyrosine phosphorylation on desmosomal adhesion are complex.Key words: desmosome, cell-cell adhesion, intercellular junction, tyrosine phosphorylation, pervanadate, desmoglein, plakoglobin     

Functional characterization of two alkane hydroxylases in a versatile <Emphasis Type="Italic">Pseudomonas aeruginosa</Emphasis> strain NY3

Pseudomonas aeruginosa strain NY3 has an extraordinary capacity to utilize a wide range of substrates, including n–alkanes of lengths C₅ to C₃₄, aromatic compounds, phenols, diesel and crude oil, and it can produce a variety of small bioactive molecules, including rhamnolipids, which can enhance its metabolic capacity for hydrophobic organic pollutants. This capacity makes NY3 a good candidate for use in environmental pollution remediation. Alkane hydroxylases catalyze both the initial and rate-limiting step of the terminal oxidation of n–alkanes. To better understand the genetic mechanisms by which P. aeruginosa NY3 degrades such a wide range of n–alkanes, two putative coding genes of alkane hydroxylases were functionally characterized using a gene-knockout approach with three different degradation systems. The single n–alkane test indicated that the hydroxylase AlkB2 acted in the early growth phase and played a major role in the utilization of C₁₂–C₁₈. However, a double mutant showed a trend towards recovery when C₂₀–C₂₄ were used as sole carbon source. This suggests that there are other enzymes capable of utilizing n–alkanes longer than C₂₀. Tests of both artificial n–alkanes mixture and crude oil-containing waste water showed similar results, suggesting that both AlkB1 and AlkB2 are involved in n–alkane degradation, and, moreover, that AlkB2 plays a major role. Finally, given the wider functional range of both AlkBs in the mixture of n–alkanes compared to that of single n–alkanes, these results hint at co-metabolism.     

Effect of Precursor Solution Aging on the Crystallinity and Photovoltaic Performance of Perovskite Solar Cells

Perovskite materials due to their exceptional photophysical properties are beginning to dominate the field of thin‐film optoelectronic devices. However, one of the primary challenges is the processing‐dependent variability in the properties, thus making it imperative to understand the origin of such variations. Here, it is discovered that the precursor solution aging time before it is cast into a thin film, is a subtle but a very important factor that dramatically affects the overall thin‐film formation and crystallinity and therein factors such as grain growth, phase purity, surface uniformity, trap state density, and overall solar cell performance. It is shown that progressive aging of the precursor promotes efficient formation of larger seeds after the fast nucleation of a large density of small seeds. The hot‐casting method then leads to the growth of large grains in uniform thin‐films with excellent crystallinity validated using scanning microscopy images and X‐ray diffraction patterns. The high‐quality films cast from aged solution is ideal for thin‐film photovoltaic device fabrication with reduced shunt current and good charge transport. This observation is a significant step toward achieving highly crystalline thin‐films with reliability in device performance and establishes the subtle but dramatic effect of solution aging before fabricating perovskite thin‐films.     

大肠杆菌NAD+合成关键酶的克隆表达及发酵优化

【目的】烟酰胺腺嘌呤二核苷酸(NAD~+)在细胞基因表达、氧化还原反应、能量代谢以及调控细胞生命周期中具有重要的作用,其细胞内含量是能量效率的关键因素。强化辅因子合成策略,获得高产NAD~+菌株,对于NAD~+依赖型氧化还原反应的速率和调节相关生化合成途径的代谢流具有重要意义。【方法】首先通过内源性调节,对代谢途径中的关键酶基因进行强化,过量表达和共表达NAD~+合成途径中的关键酶基因pncB、nadD和nadE;其次,通过外源调节增加NAD~+前体物,优化诱导条件提高发酵过程中关键酶的表达量,增加NAD~+的合成量;最后在单因素优化试验的基础上,以NAD~+含量为响应值,采用Box-Bohnken试验设计方法,研究3个显著性影响因素相互作用对NAD~+积累量的影响,确定最佳的优化条件。【结果】根据关键酶基因强化策略,构建了7株重组菌,其中重组菌E.coli BL21/p ET-21a-nad E-pncB胞内NAD~+含量相比初始菌株E.coli BL21/pET-21a提高了405.2%。通过对该菌株诱导条件和NAD~+合成前体的优化,使用Design Expert 8.0分析实验数据,得出该重组菌株的最佳发酵条件为:诱导温度控制在15–20 oC,OD_(600)为0.6–0.8时添加IPTG 0.63 mmol/L、烟酸15.8 mg/L、诱导时长控制在24 h。NAD~+含量在最优条件下实验验证值可达43.16μmol/g DCW,与优化前相比提高了123.6%,与初始菌株相比提高了1029.8%。【结论】在大肠杆菌中共表达关键酶基因pncB和nadE,胞内NAD~+合成量明显增加,前体物以及诱导条件的外源调节使NAD~+积累量达到最佳优化值。实现了提高NAD~+含量的目标,胞内辅因子浓度的增加为提高生物催化效率奠定了可行性基础。     

Mapping of <Emphasis Type="BoldItalic">Id</Emphasis> locus for dermal shank melanin in a Chinese indigenous chicken breed

The dermal shank pigmentation, one of the defining traits of chicken breeds, is caused by an abnormal deposition of melanin in the dermis of the shank. The abnormal deposition is controlled by the sex-linked inhibitor of dermal melanin (Id). In this study, we aim to locate the gene responsible for the dermal shank pigmentation in chickens by an association analysis and a differential expression analysis. Based on our results, 72 single-nucleotide polymorphisms (SNPs) located in Z chromosome (chrZ): 71–73 Mb (galGal3) were selected to further explore their relationships with the dermal shank pigmentation in pure lines of 96 Gushi hens and 96 Gushi hens with a yellow shank skin colour. The results of the association analysis showed that the SNPs located in chrZ: 72.58–72.99 Mb (galGal3) (chrZ: 79.02–79.44 Mb (galGal4)) are significantly associated with the dermal shank pigmentation. Based on the results of our previous studies and the present association analysis, the zinc-finger protein 608 (ZNF608), GRAM domain containing 3 (GRAMD3), aldehyde dehydrogenase 7 family member A1 (ALDH7A1), fem-1 homologue C (FEM1C), beta-1,4-galactosyltransferase 1 (B4GALT1) and versican (VCAN) genes were selected for the differential expression analysis. The gene expression profiles showed that the expression of GRAMD3 gene in the dermis tissues of the shank was significantly (\(P= 0.010738 < 0.05\)) higher in 350-day-old Gushi chickens characterized by the dermal shank pigmentation than in one-day-old Gushi chickens. The dermal shank pigmentation was not present in the one-day-old Gushi chickens. Additionally, the results of the association analysis and the expression analysis showed that GRAMD3 could be the most likely candidate gene for the Id locus. However, we did not detect a mutation, i.e. significantly associated with this trait within GRAMD3. Therefore, we concluded that the variations located in the flanking region of GRAMD3 led to the abnormal expression of GRAMD3, which requires further study.     

NaCl胁迫下交替呼吸途径对叶绿素含量及其荧光特性的影响

以菜豆幼苗作为试验材料,分析了NaCl胁迫下交替呼吸对叶绿素含量以及叶绿素荧光特性变化特征的影响,以探讨交替呼吸途径在逆境下的生理学作用以及植物在盐胁迫下光系统Ⅱ(PSⅡ)的调节作用机制。结果表明:(1)随着NaCl胁迫浓度(0、100、200、300mmol/L)的增高,菜豆幼苗叶片叶绿素含量显著下降,叶片光系统Ⅱ(PSⅡ)潜在最大光化学量子效率(Fv/Fm)、光适应下最大光化学效率(Fv′/Fm′)、PSⅡ光适应下实际光化学效率[Y(Ⅱ)]和光化学荧光猝灭(qP)与对照相比均显著性下降,而非光化学猝灭(NPQ)较对照组显著增加,同时交替呼吸容量在NaCl胁迫下也显著上升。(2)与单独NaCl胁迫相比,在NaCl胁迫下施加交替呼吸的抑制剂水杨基氧肟酸(SHAM)会导致菜豆幼苗叶片叶绿素含量、Fv/Fm、Fv′/Fm′、Y(Ⅱ)和qP进一步显著下降、NPQ进一步显著增加。研究认为,NaCl胁迫导致菜豆叶片光系统Ⅱ光化学效率下降和光能耗散增加,交替呼吸途径可有效缓解NaCl胁迫下菜豆叶绿素含量的减少以及光系统Ⅱ光化学反应效率的下降。     

Knockout of <Emphasis Type="Italic">OsACOS12</Emphasis> caused male sterility in rice

Pollen development in flowering plants is critical for male reproductive success. The pollen wall that protects the pollen from various environment stresses and bacterial infections plays an essential role in pollen development. The formation of pollen wall is associated with the biosynthesis and transport of sporopollenin components. ACOS5 in Arabidopsis encodes an acyl-CoA synthetase 5 required for sporopollenin biosynthesis. We identified the rice homolog of ACOS5 as OsACOS12. The CRISPR/Cas9-mediated OsACOS12 knockout mutant has complete male sterility due to a defect in pollen wall formation. β-Glucuronidase reporter gene analysis and RNA in situ hybridization indicated that OsACOS12 was specifically expressed in tapetum and microspores. The subcellular localization of OsACOS12-YFP demonstrated that OsACOS12 protein was primarily localized in the endoplasmic reticulum and nucleus. Our results suggest that OsACOS12 plays a critical and conserved role in pollen wall formation and pollen development and has implications in rice breeding.