Epidermal growth factor in Dupuytren's disease

The aim of this article was to show the participation of epidermal growth factor (EGF) in the pathogenesis of Dupuytren's disease (palmar contracture). The concentration of EGF in specimens obtained from 68 patients with Dupuytren's contracture and 14 controls was examined immunochemically with the use of enzyme-linked immunosorbent assay. The determined EGF concentration in pathologic aponeurosis with symptoms of Dupuytren's disease (median, 6.29 ng/g; range, 1.67 to 63.09 ng/g) showed significantly different values (p = 0.036) in comparison with the control group (median, 10.1 ng/g; range, 5.13 to 39.81 ng/g). The changes in EGF concentration were shown in tested groups of pathologic tissues that were formed according to the clinical stage of disease progression. The significantly lower concentration than that seen in the control group characterizes tissues with first and third degrees of palmar contracture progression (p = 0.025 and p = 0.018, respectively). In the group of patients with second-degree disease progression, the EGF level increased transiently. Nevertheless, in comparison with the other groups, the difference was not significant. The group with the fourth degree of the disease showed EGF concentrations that resembled the control values. The authors conclude that significant differences in levels of EGF concentration between contractured and normal fasciae may suggest the participation of this cytokine in the pathogenesis of Dupuytren's disease.     

The checkpoint clamp activates Mec1 kinase during initiation of the DNA damage checkpoint

Yeast Mec1/Ddc2 protein kinase, the ortholog of human ATR/ATRIP, plays a central role in the DNA damage checkpoint. The PCNA-like clamp Rad17/Mec3/Ddc1 (the 9-1-1 complex in human) and its loader Rad24-RFC are also essential components of this signal transduction pathway. Here we have studied the role of the clamp in regulating Mec1, and we delineate how the signal generated by DNA lesions is transduced to the Rad53 effector kinase. The checkpoint clamp greatly activates the kinase activity of Mec1, but only if the clamp is appropriately loaded upon partial duplex DNA. Activated Mec1 phosphorylates the Ddc1 and Mec3 subunits of the clamp, the Rad24 subunit of the loader, and the Rpa1 and Rpa2 subunits of RPA. Phosphorylation of Rad53, and of human PHAS-1, a nonspecific target, also requires a properly loaded clamp. Phosphorylation and binding studies with individual clamp subunits indicate that the Ddc1 subunit mediates the functional interactions with Mec1.     

Kinetic studies of ATP synthase: The case for the positional change mechanism

The mitochondrial ATP synthases shares many structural and kinetic properties with bacterial and chloroplast ATP synthases. These enzymes transduce the energy contained in the membrane's electrochemical proton gradients into the energy required for synthesis of high-energy phosphate bonds. The unusual three-fold symmetry of the hydrophilic domain, F₁, of all these synthases is striking. Each F₁ has three identical subunits and three identical subunits as well as three additional subunits present as single copies. The catalytic site for synthesis is undoubtedly contained in the subunit or an , interface, and thus each enzyme appears to contain three identical catalytic sites. This review summarizes recent isotopic and kinetic evidence in favour of the concept, originally proposed by Boyer and coworkers, that energy from the proton gradient is exerted not directly for the reaction at the catalytic site, but rather to release product from a single catalytic site. A modification of this binding change hypotheses is favored by recent data which suggest that the binding change is due to a positional change in all three subunits relative to the remaining subunits of F₁ and F₀ and that the vector of rotation is influenced by energy. The positional change, or rotation, appears to be the slow step in the process of catalysis and it is accelerated in all F₁F₀ ATPases studied by substrate binding and by the proton gradient. However, in the mammalian mitochondrial enzyme, other types of allosteric rate regulation not yet fully elucidated seem important as well.     

Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust

Background

The wheat stripe rust fungus (Puccinia striiformis f. sp. tritici, PST) is responsible for significant yield losses in wheat production worldwide. In spite of its economic importance, the PST genomic sequence is not currently available. Fortunately Next Generation Sequencing (NGS) has radically improved sequencing speed and efficiency with a great reduction in costs compared to traditional sequencing technologies. We used Illumina sequencing to rapidly access the genomic sequence of the highly virulent PST race 130 (PST-130).

Methodology/Principal Findings

We obtained nearly 80 million high quality paired-end reads (>50x coverage) that were assembled into 29,178 contigs (64.8 Mb), which provide an estimated coverage of at least 88% of the PST genes and are available through GenBank. Extensive micro-synteny with the Puccinia graminis f. sp. tritici (PGTG) genome and high sequence similarity with annotated PGTG genes support the quality of the PST-130 contigs. We characterized the transposable elements present in the PST-130 contigs and using an ab initio gene prediction program we identified and tentatively annotated 22,815 putative coding sequences. We provide examples on the use of comparative approaches to improve gene annotation for both PST and PGTG and to identify candidate effectors. Finally, the assembled contigs provided an inventory of PST repetitive elements, which were annotated and deposited in Repbase.

Conclusions/Significance

The assembly of the PST-130 genome and the predicted proteins provide useful resources to rapidly identify and clone PST genes and their regulatory regions. Although the automatic gene prediction has limitations, we show that a comparative genomics approach using multiple rust species can greatly improve the quality of gene annotation in these species. The PST-130 sequence will also be useful for comparative studies within PST as more races are sequenced. This study illustrates the power of NGS for rapid and efficient access to genomic sequence in non-model organisms.     

Changes of GABA(A)receptor activation kinetics in hippocampal neurons cultured for different periods of time

Cell culture is a convenient model for pharmacokinetic studies, but during the culture period, GABA(A)receptors are likely to undergo different modulatory processes. In this study, the current responses to ultrafast GABA applications were recorded from patches excised from neurons cultured for either up to two days (short-term culture) or for more than two weeks (long-term culture). The dose-dependencies of the current rising phases revealed significant differences between the two groups. In the short-term cultures, the responses to both saturating and non-saturating GABA concentrations were slower than in the case of the long-term cultures. We conclude that the GABA(A)receptors in cultured neurons undergo profound kinetic changes involving the modulation of the binding reaction and transitions between bound states.     

云南常见牛肝菌属真菌中汞含量及食用安全评价

汞(Hg)是危害人类健康的主要重金属元素之一,多数食用菌对Hg有很强的富集能力,测定食用菌中Hg含量,并对其进行食用安全性评价具有重要意义。采用冷原子吸收直接测汞仪系统测定85份云南常见牛肝菌属真菌菌盖、菌柄中总Hg含量;以同一牛肝菌子实体菌盖与菌柄总Hg含量比(Q(C/S))分析牛肝菌属真菌对Hg的富集特征;根据联合国粮农组织和世界卫生组织(FAO/WHO)现行每周Hg允许摄入量(provisional tolerable weekly intake,PTWI)标准和中国GB 2762—2012规定的食用菌中Hg限量标准评价样品的食用安全性。结果表明,菌盖和菌柄中总Hg含量分别在0.13~22.00、0.20~8.40 mg·kg-1DW,不同产地、种类及不同采集年份的样品中总Hg含量存在明显差异;同一牛肝菌菌盖、菌柄总Hg含量比(Q(C/S))在0.28~4.08,92%的样品Q(C/S)1,表明多数样品中菌盖对Hg的富集能力强于菌柄。根据GB 2762—2012规定的食用菌及其制品中总Hg含量限量标准(≤0.1 mg·kg-1),发现所有测试样品的总Hg含量均超标;根据PTWI标准,假设成年人(60 kg)每周食用300 g新鲜牛肝菌,则多数样品Hg摄入量低于允许摄入量,无安全风险,而少数样品Hg摄入量高于允许摄入量,食用有一定的潜在风险。同时,牛肝菌总Hg含量与种类、产地、采集时间等因素密切相关,采食及安全评价需综合考虑这些因素。     

Nonplanar DNA Base Pairs

Abstract

Three-dimensional structures of a representative set of more than 30 hydrogen-bonded nucleic acids base pairs have been studied by reliable ab initio quantum mechanical methods. We show that many hydrogen-bonded nucleic acid base pairs are intrinsically nonplanar, mainly due to the partial sp³ hybridization of nitrogen atoms of their amino groups and secondary electrostatic interactions. This finding extends the variability of intermolecular interactions of DNA bases in that i) flexibility of the base pairs is larger than has been assumed before, and ii) attractive proton-proton acceptor interactions oriented out of the base pair plane are allowed. For example, all four G…A mismatch base pairs are propeller twisted, and the energy preferences for the nonplanar structures range from less than 0.1 kcal/mol to 1.8 kcal/mol. We predict that nonplanarity of the amino group of guanine in the G(anti)…A(anti) pair of the ApG step of the d(CCAAGATTGG)₂ crystal structure is an important stabilizing factor that improves the energy of this structure by almost 3 kcal/mol. Currently used empirical potentials are not accurate enough to properly cover the interactions associated with amino-group and base-pair nonplanarity.