Genome-wide classification and expression analysis of nucleobase–ascorbate transporter (NAT) gene family in tomato

Ascorbic acid or vitamin C is a wide spectrum antioxidant and plays a crucial role in a many metal-containing enzymes essential for humans, which are unable to synthesize the vitamin C and must obtain it from dietary sources. Ascorbic acid is transported by sodium-coupled ascorbic acid transporters or SVCTs in humans. However, little information is available about the nucleobase–ascorbate transporters (NATs) in tomato (Solanum lycopersicum). In the current study, we identified 12 NAT genes by screening SGN genome databases in tomato. A complete overview of this gene family in tomato is presented, including gene structures, chromosome distribution and localization, phylogenies, motif analysis and expression profiles. The SlNAT genes contained 14 exons, mostly, and dispersed on all the chromosomes except chromosome 8 and 9. All the SlNATs were located to plasma membrane, chloroplast thylakoid membrane, Golgi body, and endoplasmic reticulum (membrane). The phylogenetic tree showed that the plant NATs were divided into 4 clades, well-supported by the distribution of conserved motifs, and the SlNAT proteins shared higher similarity and clustered more closely with AtNAT proteins. Furthermore, the expression profiles of SlNAT genes in various organs showed 9 out of 12 SlNAT genes were constituently expression with differential expression levels under normal growth conditions. Our systematic analysis will provide a useful platform for molecular clone and functional identification of NAT genes in tomato and probably other Solanaceae plants.     

Pre-diagnostic smoking behaviour and poorer prognosis in a German breast cancer patient cohort – Differential effects by tumour subtype,NAT2 status,BMI and alcohol intake

BackgroundInconsistent associations of smoking and breast cancer-specific mortality might be explained by subgroups of patients with different susceptibility to harmful effects of smoking.MethodsWe used a prospective cohort of 3340 postmenopausal breast cancer patients aged 50–74 and diagnosed with invasive tumours 2001–2005 in Germany, with a median follow-up time of 6 years. The effect of pre-diagnostic smoking behaviour on mortality outcomes and risk of recurrence was investigated using delayed entry Cox regression analysis. Differential effects according to N-acetyltransferase (NAT2) status, BMI, alcohol consumption, and tumour subtypes were assessed.ResultsOverall, smoking at time of breast cancer diagnosis versus never/former smoking was non-significantly associated with increased breast cancer-specific mortality and risk of recurrence (HR 1.23, 95% CI 0.93–1.64, and HR 1.29, 95% CI 0.95–1.75, respectively). Associations were consistently stronger in NAT2 slow than in fast acetylators for all mortality outcomes. Breast cancer-specific mortality was significantly increased in smokers with NAT2 slow acetylating status (HR 1.77, 95% CI 1.13–2.79) but not in those with fast acetylating status (HR 1.09, 95% CI 0.60–1.98; P_{heterogeneity} = 0.19). Smoking was associated with significantly poorer outcomes for triple negative and luminal A-like tumours (e.g. all-cause mortality: HR 1.93, 95% CI 1.02–3.65, and HR 2.08, 95% CI 1.40–3.10, respectively). Risk of recurrence was significantly increased for women with HER2 positive tumours (HR 3.64, 95% CI 1.22–10.8). There was significant heterogeneity by BMI for non-breast cancer-specific mortality (<25 kg/m²: HR 2.52, 95% CI 1.52–4.15 vs. ≥25 kg/m²: HR 0.94, 95% CI 0.38–2.36; P_{heterogeneity} = 0.04).ConclusionThe harmful effects of smoking may be particularly relevant for certain subgroups of breast cancer patients. This may include patients with NAT2 slow acetylation status or with tumour subtypes other than luminal B, such as luminal A tumours who usually have a rather good prognosis. Emphasis on smoking cessation programmes for all cancer patients should be strengthened.     

N- 乙酰转移酶NAT10 在软组织肿瘤中的表达及意义

目的：观察N-乙酰转移酶NAT10蛋白在软组织肉瘤中的表达及与类型、分级的关系。方法：通过原核表达NAT10蛋白免疫制备特异性多克隆抗体,并经免疫印迹鉴定;以组织芯片一免疫组化检测166例软组织肉瘤和28例良性肿瘤及瘤样病变中NAT10蛋白的表达。结果：制备多克隆抗体经Western印迹鉴定与NAT10具有特异结合性。免疫组化显示166例软组织肉瘤中NAT10蛋白阳性95例,阳性率为57％（95／166）,28例良性肿瘤及瘤样病变中4例阳性14％（4／28）。两者间有显著性差异（P〈0．05）。NAT10表达的主要分布为：滑膜肉瘤76％（13／17）、恶性纤维组织细胞瘤75％（15／20）、原始神经外胚叶瘤（PNET）70％（16／23）、横纹肌肉瘤70％（7／10）、恶性外周神经鞘膜瘤50％（11,／22）、隆突性皮肤纤维肉瘤50％（7／14）、平滑肌肉瘤43％（6／14）、脂肪肉瘤42％（8／19）、黏液性纤维肉瘤38％（6／16）。统计比较显示：滑膜肉瘤与黏液性纤维肉瘤和脂肪肉瘤,以及恶性纤维组织细胞瘤与黏液性纤维肉瘤之间NAT10表达具有显著性差异（P〈0．05）;而其它各组间无明显差异（P〉0．05）。同时,NAT10蛋白强阳性表达（≥＋＋）多存在于滑膜肉瘤（53％,9／17）、横纹肌肉瘤（40％,4／10）及恶性纤维组织细胞瘤（40％,8／20）。在FNCLGC分级中,19例I级肉瘤中NAT10阳性表达率为42％（8／19）,44例Ⅱ级肉瘤为43％（19／44）,70例Ⅲ级肉瘤为73％（51／70）。Ⅲ级NAT10阳性率显著高于Ⅱ级组和Ⅰ级组（均为P〈0．05）。结论：研究表明N-乙酰转移酶NAT10表达于多种人软组织肉瘤,尤其在高度恶性肉瘤,因此有可能为软组织肉瘤的分级及预后因子。     

NAT对植物生长及生理活性调控作用的初步研究

以新合成的 N- (1-萘乙酰基 ) - N′- (4 -氨替吡啉基 )硫脲 (NAT)配制成不同浓度 (10、2 0、50mg.L-1)的水溶液 ,对大田扬花期小麦进行叶面喷洒和蜀葵叶片扦插基部的浸泡处理 ,并在分别含有 0 .1mg.L-1NAT与 NAA的培养基中对护颖分化期的小麦幼穗进行离体培养。测定了处理后小麦灌浆后期旗叶的生理指标 ,统计测量了扦插生根的效果 ,并观察记录了幼穗培养再分化的情况。结果表明 ,NAT可有效的延缓小麦旗叶的衰老 ,促进蜀葵叶柄的扦插生根和促进小麦幼穗离体培养的再分化作用。其效果比 NAA更为明显。     

Nucleic acid testing (NAT) in high prevalence–low resource settings

Blood screening by NAT for major transfusion transmitted viral infections (TTIs) was originally intended to complement serology for detection of infected donations. Reports from developed countries showed limited marginal value to NAT blood screening in improving blood safety. Reports on NAT results from Europe indicated yield of 1:0.6 million donations for HBV, <1:M for HCV and HIV-1-related to low prevalence of TTI. In contrast, prevalence of TTI in resource-limited countries is almost always high. As a result, more incident cases can be expected among first-time blood donors. Most reports of NAT blood donation screening in these countries showed NAT confirmed yield as high as 1/2800 for HBV and 1/3100 blood donations for HCV as reported from Thailand and Egypt, respectively. The issues for low resource countries are mostly the high cost of NAT but also the requirements of staff qualification, adequate facilities, reagent procurement and maintenance of delicate equipment. Alternatives to commercial NAT are the use of combos antigen-antibody for HIV and HCV, anti-HBc for HBV and in-house NAT. Most of these alternatives have been reported but very few comparisons are available. Once yield data is available, models for estimation of feasibility and cost-effectiveness are proposed to help decision-making.     

NAT10 regulates the LPS-induced inflammatory response via the NOX2-ROS-NF-κB pathway in macrophages

Periodontitis is a chronic osteolytic inflammatory disease resulting from complex dynamic interactions among bacterial pathogens and the host immune response. Macrophages play a vital role in the pathogenesis of periodontitis by triggering periodontal inflammation and inducing periodontium destruction. N-Acetyltransferase 10 (NAT10) is an acetyltransferase that has been shown to catalyse N4-acetylcytidine (ac4C) mRNA modification and is related to cellular pathophysiological processes, including the inflammatory immune response. Nevertheless, whether NAT10 regulates the inflammatory response of macrophages in periodontitis remains unclear. In this study, the expression of NAT10 in macrophages was found to decrease during LPS-induced inflammation. NAT10 knockdown significantly reduced the generation of inflammatory factors, while NAT10 overexpression had the opposite effect. RNA sequencing revealed that the differentially expressed genes were enriched in the NF-κB signalling pathway and oxidative stress. Both the NF-κB inhibitor Bay11-7082 and the ROS scavenger N-acetyl-L-cysteine (NAC) could reverse the upregulation of inflammatory factors. NAC inhibited the phosphorylation of NF-κB, but Bay11-7082 had no effect on the production of ROS in NAT10-overexpressing cells, suggesting that NAT10 activated the LPS-induced NF-κB signalling pathway by regulating ROS generation. Furthermore, the expression and stability of Nox2 was promoted after NAT10 overexpression, indicating that Nox2 may be a potential target of NAT10. In vivo, the NAT10 inhibitor Remodelin reduced macrophage infiltration and bone resorption in ligature-induced periodontitis mice. In summary, these results showed that NAT10 accelerated LPS-induced inflammation via the NOX2-ROS-NF-κB pathway in macrophages and that its inhibitor Remodelin might be of potential therapeutic significance in periodontitis treatment.     

Syntheses and spectroscopic properties of α- and β-phosphatidylcholines and phosphatidylethanolamines

The widely used partial synthesis of phospholipids via deacylation of naturally occurring phospholipids, followed by reacylation with fatty acid anhydrides, is accompanied by phosphoryl migration. The resulting mixture of α- and β-phospholipids was separated by short-column chromatography. Milder acylation procedures in which no phosphoryl migration occurs, were developed. 1,2-Dilinoleoyl-sn-glycero-3-phosphocholine was prepared in 50% yield by acylation of sn-glycero-3-phosphocholine (GPC) with N-linoleoylimidazole. Detailed NMR and infrared spectra of α- and β-phosphatidylcholines (PCs) and -ethanolamines (PEs) are reported and the differences between isomers discussed.     

Phenotypic plasticity and longevity in plants and animals: cause and effect?

Immobile plants and immobile modular animals outlive unitary animals. This paper discusses competing but not necessarily mutually exclusive theories to explain this extreme longevity, especially from the perspective of phenotypic plasticity. Stem cell immortality, vascular autonomy, and epicormic branching are some important features of the phenotypic plasticity of plants that contribute to their longevity. Monocarpy versus polycarpy can also influence the kind of senescent processes experienced by plants. How density-dependent phenomena affecting the establishment of juveniles in these immobile organisms can influence the evolution of senescence, and consequently longevity, is reviewed and discussed. Whether climate change scenarios will favour long-lived or short-lived organisms, with their attendant levels of plasticity, is also presented.     

Dogmatisms and Catechisms — Ethics and Companion Animals

Abstract

The current reconsideration of the place in nature of human beings unfortunately continues to be an acrimonious one. All too often the debate is more akin to a warlike encounter where each side attempts to gain control or the upper hand than a search for points of agreement. Given this context, it is important to entertain views that emanate from different cultural traditions as a way to infuse the debate with new life. Students of Native American culture have consistently pointed out that the essential concepts of life balance and reciprocity represented there may serve as useful points of consideration as we struggle with the appropriate relationships with animals and nature. This article presents a representative Zuni story, told by Governor Robert E. Lewis, that illustrates these notions.     

DCCP and DICP： Construction and Analyses of Databases for Copper- and Iron-Chelating Proteins

Copper and iron play important roles in a variety of biological processes, especially when being chelated with proteins. The proteins involved in the metal binding, transporting and metabolism have aroused much interest. To facilitate the study on this topic, we constructed two databases （DCCP and DICP） containing the known copper- and iron-chelating proteins~ which are freely available from the website http：//sdbi.sdut.edu.cn/en. Users can conveniently search and browse all of the entries in the databases. Based on the two databases, bioinformatic analyses were performed, which provided some novel insights into metalloproteins.     

Biosynthesis of geraniol and nerol and their β-d-glucosides in Perlargonium graveolens and Rosa dilecta

1. 3R-[2-(14)C]Mevalonate was incorporated into geranyl and neryl beta-d-glucosides in petals of Rosa dilecta in up to 10.6% yield, and the terpenoid part was specifically and equivalently labelled in the moieties derived from isopentenyl pyrophosphate and 3,3-dimethylallyl pyrophosphate. A similar labelling pattern, with incorporations of 0.06-0.1% was found for geraniol or nerol formed in leaves of Pelargonium graveolens The former results provide the best available evidence for the mevalonoid route to regular monoterpenes in higher plants. 2. Incorporation studies with 3RS-[2-(14)C,(4R)-4-(3)H(1)]-mevalonate and its (4S)-isomer showed that the pro-4R hydrogen atom of the precursor was retained and the pro-4S hydrogen atom was eliminated in both alcohols and both glucosides. These results suggest that the correlation of retention of the pro-4S hydrogen atom of mevalonate with formation of a cis-substituted double bond, such as has been found in certain higher terpenoids, does not apply to the biosynthesis of monoterpenes. It is proposed that either nerol is derived from isomerization of geraniol or the two alcohols are directly formed by different prenyltransferases. Possible mechanisms for these processes are discussed. 3. The experiments with [(14)C,(3)H]mevalonate also show that in these higher plants, as has been previously found in animal tissue and yeast, the pro-4S hydrogen atom of mevalonate was lost in the conversion of isopentenyl pyrophosphate into 3,3-dimethylallyl pyrophosphate.     

Zinc and diabetes — clinical links and molecular mechanisms

Zinc is an essential trace element crucial for the function of more than 300 enzymes and it is important for cellular processes like cell division and apoptosis. Hence, the concentration of zinc in the human body is tightly regulated and disturbances of zinc homeostasis have been associated with several diseases including diabetes mellitus, a disease characterized by high blood glucose concentrations as a consequence of decreased secretion or action of insulin. Zinc supplementation of animals and humans has been shown to ameliorate glycemic control in type 1 and 2 diabetes, the two major forms of diabetes mellitus, but the underlying molecular mechanisms have only slowly been elucidated. Zinc seems to exert insulin-like effects by supporting the signal transduction of insulin and by reducing the production of cytokines, which lead to beta-cell death during the inflammatory process in the pancreas in the course of the disease. Furthermore, zinc might play a role in the development of diabetes, since genetic polymorphisms in the gene of zinc transporter 8 and in metallothionein (MT)-encoding genes could be demonstrated to be associated with type 2 diabetes mellitus. The fact that antibodies against this zinc transporter have been detected in type 1 diabetic patients offers new diagnostic possibilities. This article reviews the influence of zinc on the diabetic state including the molecular mechanisms, the role of the zinc transporter 8 and MT for diabetes development and the resulting diagnostic and therapeutic options.     

siRNA, miRNA and HIV： promises and challenges

Small interfering RNA （siRNA） and microRNA （miRNA） are small RNAs of 18-25 nucleotides （nt） in length that play important roles in regulating gene expression. They are incorporated into an RNA-induced silencing complex （RISC） and serve as guides for silencing their corresponding target mRNAs based on complementary base-pairing. The promise of gene silencing has led many researchers to consider siRNA as an anti-viral tool. However, in long-term settings, many viruses appear to escape from this therapeutical strategy. An example of this may be seen in the case of human immunodeficiency virus type-1 （HIV-1） which is able to evade RNA silencing by either mutating the siRNA-targeted sequence or by encoding for a partial suppressor of RNAi （RNA interference）. On the other hand, because miRNA targeting does not require absolute complementarity of base-pairing, mutational escape by viruses from miRNA-specified silencing may be more difficult to achieve. In this review, we discuss stratagems used by various viruses to avoid the cells＇ antiviral si/mi-RNA defenses and notions of how viruses might control and regulate host cell genes by encoding viral miRNAs （vmiRNAs）.     

Toxoplasmosis and Epilepsy — Systematic Review and Meta Analysis

Background

Toxoplasmosis is an important, widespread, parasitic infection caused by Toxoplasma gondii. The chronic infection in immunocompetent patients, usually considered as asymptomatic, is now suspected to be a risk factor for various neurological disorders, including epilepsy. We aimed to conduct a systematic review and meta-analysis of the available literature to estimate the risk of epilepsy due to toxoplasmosis.

Methods

A systematic literature search was conducted of several databases and journals to identify studies published in English or French, without date restriction, which looked at toxoplasmosis (as exposure) and epilepsy (as disease) and met certain other inclusion criteria. The search was based on keywords and suitable combinations in English and French. Fixed and random effects models were used to determine odds ratios, and statistical significance was set at 5.0%.

Principal findings

Six studies were identified, with an estimated total of 2888 subjects, of whom 1280 had epilepsy (477 positive for toxoplasmosis) and 1608 did not (503 positive for toxoplasmosis). The common odds ratio (calculated) by random effects model was 2.25 (95% CI 1.27–3.9), p = 0.005.

Conclusions

Despite the limited number of studies, and a lack of high-quality data, toxoplasmosis should continue to be regarded as an epilepsy risk factor. More and better studies are needed to determine the real impact of this parasite on the occurrence of epilepsy.     

Rise and Demise of Bioinformatics? Promise and Progress

The field of bioinformatics and computational biology has gone through a number of transformations during the past 15 years, establishing itself as a key component of new biology. This spectacular growth has been challenged by a number of disruptive changes in science and technology. Despite the apparent fatigue of the linguistic use of the term itself, bioinformatics has grown perhaps to a point beyond recognition. We explore both historical aspects and future trends and argue that as the field expands, key questions remain unanswered and acquire new meaning while at the same time the range of applications is widening to cover an ever increasing number of biological disciplines. These trends appear to be pointing to a redefinition of certain objectives, milestones, and possibly the field itself.     

Journal of Ethnobiology and Ethnomedicine – achievements and perspectives

Last summer we officially launched the Journal of Ethnobiology and Ethnomedicine, published by BioMedCentral, with the aim of establishing a serious, peer-reviewed, open-access online journal that focuses on the multidisciplinary, interdisciplinary, and transdisciplinary fields of ethnobiology and ethnomedicine, drawing on approaches and methods from both the social and biological sciences. The strong start vindicates the widely held belief that the journal responds to a real need within the research community. The success of the journal has been most gratifying. The steady influx of submissions of high scientific standards illustrates the strong demand for a dynamic, proactive, and open-minded scientific journal in these research areas. Our aim has been to dedicate JEE to the "scientific communities" worldwide, particularly those in the developing countries.