[Ventilator-associated pneumonia among premature infants <34 weeks' gestational age in neonatal intensive care unit in China: a multicenter study]

Objective: To investigate the incidence and pathogen distribution of ventilator-associated pneumonia (VAP) among preterm infants admitted to level Ⅲ neonatal intensive care units (NICU) in China. Method: A prospective study was conducted in 25 level Ⅲ NICU, enrolling all preterm infants <34 weeks gestational age admitted to the participating NICU within the first 7 days of life from May 2015 to April 2016. Chi-square test, t test and Mann-Whitney U test were used for statistical analysis. Result: A total of 7 918 patients were enrolled, within whom 4 623(58.4%) were males. The birth weight was (1 639±415) g and the gestational age was (31.4±2.0) weeks; 4 654(58.8%) infants required non-invasive mechanical ventilation and 2 154(27.2%) required intubation. Of all the mechanically ventilated patients, VAP occurred in 95 patients. The overall VAP rate was 7.0 episodes per 1 000 ventilator days, varying from 0 to 34.4 episodes per 1 000 ventilator days in different centers. The incidence of VAP was 9.6 and 6.0 per 1 000 ventilator days in children's hospitals and maternity-infant hospitals respectively, without significant differences (t=1.002, P=0.327). Gram-negative bacilli (76 strains, 91.6%) were the primary VAP microorganisms, mainly Acinetobacter baumannii (24 strains, 28.9%), Klebsiella pneumonia (23 strains, 27.7%), and Pseudomonas aeruginosa (10 strains, 12.0%). Conclusion: The incidence of VAP in China is similar to that in developed counties, with substantial variability in different NICU settings. More efforts are needed to monitor and evaluate the preventable factors associated with VAP and conduct interventions that could effectively reduce the occurrence of VAP.

[A preliminary study on the molecular characteristics of D-cycloserine resistance of Mycobacterium tuberculosis]

Objective: To investigate the relationship between D-cycloserine resistance and the gene mutations of alrA, ddlA and cycA of Mycobacterium (M.) tuberculosis, as well as the association between D-cycloserine resistance and spoligotyping genotyping. Methods: A total of 145 M. tuberculosis strains were selected from the strain bank. D-cycloserine resistant phenotypes of the strains were determined by the proportion method and the minimal inhibitory concentration was determined by resazurin microtiter assay. PCR amplification and DNA direct sequencing methods were used for the analysis of gene mutations. Relationship between the resistance phenotype and genotype was analyzed by chi-square test. Results: Of the 145 clinically collected strains, 24 (16.6%) of them were D-cycloserine resistant and 121 (83.4%) were sensitive. There were only synonymous mutations noticed on alrA, ddlA and cycA in sensitive strains. Of the 24 D-cycloserine resistant strains, 3 (12.5%) isolates' cycA and 1 (4.2%) isolates' alrA happened to be non-synonymous mutations, in which the codes were 188, 318 and 508 of cycA, and 261 of alrA, respectively. Results on drug sensitivity tests confirmed the minimal inhibitory concentration of the mutant strains were all increased to some degrees. The D-cycloserine resistant rates of 88 Beijing genotype and 57 non-Beijing genotype strains were 20.5% and 10.5% , respectively, but with no statistically significant difference (χ(2) =2.47, P>0.05). Conclusions: The non-synonymous mutations of alrA and cycA might contribute to one of the mechanisms of M. tuberculosis D-cycloserine resistance. M. tuberculosis Beijing genotype or non-Beijing genotype was not considered to be associated with the D-cycloserine resistance.

[Prospects of hernia and abdominal wall surgery in China]

In recent 20 years, hernia and abdominal wall surgery has made great progress in China. However, what we've done still leaves much to be desired. Related guidelines of hernia disease had been conducted, but China is short of multi-center, prospective, and large-sample research evidence. These guidelines are still with low evidence level, and contents need additional modified to well meet Chinese real situation. In terms of treatment of inguinal and abdominal wall incisional hernia, some consensus has been reached from certain key issues globally, but further exploration are still needed. To stand at top of the world, we are a long distance. We should not only strengthen training and quality control but also establish patient registration system and overall management process.

Factors influencing QTL mapping accuracy under complicated genetic models by computer simulation

The accuracy of quantitative trait loci (QTLs) identified using different sample sizes and marker densities was evaluated in different genetic models. Model I assumed one additive QTL; Model II assumed three additive QTLs plus one pair of epistatic QTLs; and Model III assumed two additive QTLs with opposite genetic effects plus two pairs of epistatic QTLs. Recombinant inbred lines (RILs) (50-1500 samples) were simulated according to the Models to study the influence of different sample sizes under different genetic models on QTL mapping accuracy. RILs with 10-100 target chromosome markers were simulated according to Models I and II to evaluate the influence of marker density on QTL mapping accuracy. Different marker densities did not significantly influence accurate estimation of genetic effects with simple additive models, but influenced QTL mapping accuracy in the additive and epistatic models. The optimum marker density was approximately 20 markers when the recombination fraction between two adjacent markers was 0.056 in the additive and epistatic models. A sample size of 150 was sufficient for detecting simple additive QTLs. Thus, a sample size of approximately 450 is needed to detect QTLs with additive and epistatic models. Sample size must be approximately 750 to detect QTLs with additive, epistatic, and combined effects between QTLs. The sample size should be increased to >750 if the genetic models of the data set become more complicated than Model III. Our results provide a theoretical basis for marker-assisted selection breeding and molecular design breeding.

Impact of human activities on subaqueous topographic change in Lingding Bay of the Pearl River estuary, China, during 1955-2013

Estuaries have been sites of intensive human activities during the past century. Tracing the evolution of subaqueous topography in estuaries on a decadal timescale enables us to understand the effects of human activities on estuaries. Bathymetric data from 1955 to 2010 show that land reclamation decreased the subaqueous area of Lingding Bay, in the Pearl River estuary, by ~170 km² and decreased its water volume by 615 × 10⁶ m³, representing a net decrease of 11.2 × 10⁶m³ per year and indicating the deposition of approximately 14.5 Mt/yr of sediment in Lingding Bay during that period. Whereas Lingding Bay was mainly governed by natural processes with slight net deposition before 1980, subsequent dredging and large port engineering projects changed the subaqueous topography of the bay by shallowing its shoals and deepening its troughs. Between 2012 and 2013, continuous dredging and a surge of sand excavation resulted in local changes in water depth of ± 5 m/yr, far exceeding the magnitude of natural topographic evolution in Lingding Bay. Reclamation, dredging, and navigation-channel projects removed 8.4 Mt/yr of sediment from Lingding Bay, representing 29% of the sediment input to the bay, and these activities have increased recently.

[Protective effect of astragaloside IV against acute liver failure in experimental mice]

Objective: To investigate the clinical effect of astragaloside IV in the early treatment of mice with acute liver failure and possible mechanisms. Methods: A mouse model of acute liver failure induced by D-galactosamine/lipopolysaccharide (D-GalN/LPS) was established, and the mice were given astragaloside IV at different doses. The survival rate of mice, alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels, liver histopathological changes, apoptosis of hepatocytes, and the expression of superoxide dismutase (SOD) and malondialdehyde (MDA) were measured in each group. The least significant difference test was used for data with homogeneity of variances, the Dunnett's T3 test was used for data with heterogeneity of variance, and the Kaplan-Meier method was used for survival analysis. Results: Compared with the model group, the high-dose astragaloside IV group had a significant increase in the 48-hour survival rate [60% (9/15) vs 13.3% (2/15), P < 0.05], significant reductions in the serum ALT and AST levels (P < 0.01), and significant reductions in liver histopathological indices and the degree of apoptosis of hepatocytes (P < 0.01), as well as a significant reduction in the content of MDA in liver homogenate (P < 0.01) and a significant increase in the activity of SOD (P < 0.05). Conclusion: High-dose astragaloside IV has a significant protective effect against D-GalN/LPS-induced acute liver injury in mice, and its mechanisms may be associated with its effects against cell apoptosis and oxidative damage.

Disaster nursing experiences of Chinese nurses responding to the Sichuan Ya'an earthquake

AIM

The aim of this study was to investigate the disaster experiences of nurses called to assist survivors one month after the 2013 Ya'an earthquake.

BACKGROUND

China has experienced an increasing number of earthquake disasters in the past four decades. Although a health and disaster management system was initiated after the 2008 Wenchuan earthquake, nurses' roles and experiences in a disaster have been overlooked.

METHODS

The researchers used qualitative descriptive design that included 16 participants. Data were collected using semi-structured interviews and observation notes, after which a qualitative content analysis was conducted.

FINDINGS

Three major themes emerged: the process of being dispatched from hospitals to the disaster zone, the effort involved in getting to and working in the affected site and reflecting on the challenges they encountered.

DISCUSSION

About half of the participants had received disaster nursing training before deploying to the disaster site, but they consistently expressed a lack of physical and psychological preparedness regarding the process of being dispatched from their hospitals to the disaster zone.

LIMITATIONS

This was a single-incident experience. Caution should be taken when trying to extend the findings to other parts of China.

CONCLUSION

These findings highlighted the need for disaster in-service training as well as for having disaster plans in place.

IMPLICATIONS FOR NURSING AND HEALTH POLICY

Hospital and nursing leaders should provide disaster training opportunities that included topics such as compiling resource inventories, formulating disaster drills and simulations, managing emergencies, and using emergency communication methods. Health policy-makers should be required to prioritize capacity-building training for front-line nurses as well as to develop and implement disaster management plans to better prepare nurses for future disasters.

The common CARD14 gene missense polymorphism rs11652075 (c.C2458T/p.Arg820Trp) is associated with psoriasis: a meta-analysis

Recent genetic evidence suggests a robust association of the CARD14 single nucleotide polymorphism rs11652075 (c.C2458T/p.Arg820Trp) and other rare mutations in this gene with psoriasis. To assess whether combined data support the relationship between CARD14 rs11652075 and susceptibility to this disease, we conducted a meta-analysis. PubMed (MEDLINE), EMBASE, Web of Science, and the Cochrane Library were searched for relevant papers published in English. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using random-effect models. Heterogeneity between studies was assessed using the Cochran's Q and I² statistics. A total of five published studies, including 32,807 psoriasis patients and 45,458 controls, met our inclusion criteria and were included in the meta-analysis. The pooled OR of the association between the minor allele of this polymorphism and psoriasis was 0.877 (95%CI = 0.834-0.922; P < 0.001). In a stratified analysis, pooled ORs relating to European and Asian ancestry were 0.883 (95%CI = 0.822-0.948) and 0.872 (95%CI = 0.812-0.936), respectively. Those calculated for studies with case sample sizes above and below 1000 were 0.912 (95%CI = 0.870- 0.956) and 0.824 (95%CI = 0.734-0.924), respectively. No publication bias was present, and the exclusion of any single dataset did not substantially alter the corresponding pooled ORs. Due to the limited data available regarding clinical classification of cases and genotypes, subgroup stratification by clinical type was not performed. Our results demonstrate a significant association between the CARD14 rs11652075 polymorphism and psoriasis.

Discovery of clubroot-resistant genes in Brassica napus by transcriptome sequencing

Clubroot significantly affects plants of the Brassicaceae family and is one of the main diseases causing serious losses in B. napus yield. Few studies have investigated the clubroot-resistance mechanism in B. napus. Identification of clubroot-resistant genes may be used in clubroot-resistant breeding, as well as to elucidate the molecular mechanism behind B. napus clubroot-resistance. We used three B. napus transcriptome samples to construct a transcriptome sequencing library by using Illumina HiSeq™ 2000 sequencing and bioinformatic analysis. In total, 171 million high-quality reads were obtained, containing 96,149 unigenes of N50-value. We aligned the obtained unigenes with the Nr, Swiss-Prot, clusters of orthologous groups, and gene ontology databases and annotated their functions. In the Kyoto encyclopedia of genes and genomes database, 25,033 unigenes (26.04%) were assigned to 124 pathways. Many genes, including broad-spectrum disease-resistance genes, specific clubroot-resistant genes, and genes related to indole-3-acetic acid (IAA) signal transduction, cytokinin synthesis, and myrosinase synthesis in the Huashuang 3 variety of B. napus were found to be related to clubroot-resistance. The effective clubroot-resistance observed in this variety may be due to the induced increased expression of these disease-resistant genes and strong inhibition of the IAA signal transduction, cytokinin synthesis, and myrosinase synthesis. The homology observed between unigenes 0048482, 0061770 and the Crr1 gene shared 94% nucleotide similarity. Furthermore, unigene 0061770 could have originated from an inversion of the Crr1 5'-end sequence.

The functional response of bioactive titania-modified three-dimensional Ti-6Al-4V mesh structure toward providing a favorable pathway for intercellular communication and osteoincorporation

The objective of the study is to fundamentally elucidate the biological response of 3D printed mesh structures subjected to plasma electrolytic oxidation process through the study of osteoblast functions. The cellular activity of plasma electrolytic-oxidized mesh structure was explored in terms of cell-to-cell communication involving proliferation, synthesis of extracellular and intracellular proteins, and mineralization. Upon plasma electrolytic oxidation of the mesh structure, a thin layer of bioactive titania with pore size 1-3 µm was nucleated on the surface. The combination of microporous bioactive titania and interconnected porous architecture provided the desired pathway for supply of nutrients and oxygen to cells and tissue and a favorable osteogenic microenvironment for tissue on-growth and in-growth, in relation to the unmodified mesh structure. The formation of a confluent layer as envisaged via electron microscopy and quantitative assessment of the expression level of proteins (actin, vinculin, and fibronectin) point toward the determining role of surface-modified mesh structure in modulating osteoblasts functions. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 2488-2501, 2016.

Estrogen/ERR-α signaling axis is associated with fiber-type conversion of upper airway muscles in patients with obstructive sleep apnea hypopnea syndrome

Estrogen is related with the low morbidity associated with obstructive sleep apnea hypopnea syndrome (OSAS) in women, but the underlying mechanisms remain largely unknown. In this study, we examined the relationship between OSAS and estrogen related receptor-α (ERR-α). We found that the expression levels of ERR-α and Myh7 were both downregulated in palatopharyngeal tissues from OSAS patients. In addition, we report that ERR-α is dynamically expressed during differentiation of C2C12 myoblasts. Knockdown of ERR-α via instant siRNA resulted in reduced expression of Myh7, but not Myh4. Furthermore, differentiation of C2C12 cells under 3% chronic intermittent hypoxia, a model resembling human OSAS, was impaired and accompanied by a obvious reduction in Myh7 expression levels. Moreover, activation of ERR-α with 17β-estradiol (E2) increased the expression of Myh7, whereas pretreatment with the ERR-α antagonist XCT790 reversed the E2-induced slow fiber-type switch. A rat ovariectomy model also demonstrated the switch to fast fiber type. Collectively, our findings suggest that ERR-α is involved in estrogen-mediated OSAS by regulating Myhc-slow expression. The present study illustrates an important role of the estrogen/ERR-α axis in the pathogenesis of OSAS, and may represent an attractive therapeutic target, especially in postmenopausal women.

EjMYB8 Transcriptionally Regulates Flesh Lignification in Loquat Fruit

Transcriptional regulatory mechanisms underlying lignin metabolism have been widely studied in model plants and woody trees, but seldom in fruits such as loquat, which undergo lignification. Here, twelve EjMYB genes, designed as EjMYB3-14, were isolated based on RNA-seq. Gene expression indicated that EjMYB8 and EjMYB9 were significantly induced in fruit with higher lignin content resulting from storage at low temperature (0°C), while two treatments (low temperature conditioning, LTC; heat treatment, HT) both alleviated fruit lignification and inhibited EjMYB8 and EjMYB9 expression. Dual-luciferase assays indicated that EjMYB8, but not EjMYB9, could trans-activate promoters of lignin-related genes EjPAL1, Ej4CL1 and Ej4CL5. Yeast one-hybrid assay indicated that EjMYB8 physically bind to Ej4CL1 promoter. Furthermore, the putative functions of EjMYB8 were verified using transient over-expression in both N. tabacum and loquat leaves, which increased lignin content. Moreover, combination of EjMYB8 and previously isolated EjMYB1 generated strong trans-activation effects on the Ej4CL1 promoter, indicating that EjMYB8 is a novel regulator of loquat fruit lignification.

The Citrus transcription factor, CitERF13, regulates citric acid accumulation via a protein-protein interaction with the vacuolar proton pump, CitVHA-c4

Organic acids are essential to fruit flavor. The vacuolar H(+) transporting adenosine triphosphatase (V-ATPase) plays an important role in organic acid transport and accumulation. However, less is known of V-ATPase interacting proteins and their relationship with organic acid accumulation. The relationship between V-ATPase and citric acid was investigated, using the citrus tangerine varieties 'Ordinary Ponkan (OPK)' and an early maturing mutant 'Zaoshu Ponkan (ZPK)'. Five V-ATPase genes (CitVHA) were predicted as important to citric acid accumulation. Among the genes, CitVHA-c4 was observed, using a yeast two-hybrid screen, to interact at the protein level with an ethylene response factor, CitERF13. This was verified using bimolecular fluorescence complementation assays. A similar interaction was also observed between Arabidopsis AtERF017 (a CitERF13 homolog) and AtVHA-c4 (a CitVHA-c4 homolog). A synergistic effect on citric acid levels was observed between V-ATPase proteins and interacting ERFs when analyzed using transient over-expression in tobacco and Arabidopsis mutants. Furthermore, the transcript abundance of CitERF13 was concomitant with CitVHA-c4. CitERF13 or AtERF017 over-expression leads to significant citric acid accumulation. This accumulation was abolished in an AtVHA-c4 mutant background. ERF-VHA interactions appear to be involved in citric acid accumulation, which was observed in both citrus and Arabidopsis.

Genetic polymorphisms of the FATP1 gene and their associations with meat quality traits in Chinese Qinchuan cattle

Fatty acid transport protein 1 (FATP1), an integral membrane protein that facilitates long-chain fatty acid influx, is involved in the genetic network for oleic acid synthesis. The aim of this study was to examine the association of FATP1 polymorphisms with live animal meat quality traits in Chinese Qinchuan cattle. Quantitative real-time PCR analysis demonstrated that FATP1 has a broad tissue distribution in Qinchuan cattle and is highly expressed in longissimus dorsi muscle and back fat. Using direct DNA sequencing of the FATP1 gene in 458 Qinchuan cattle, four single nucleotide polymorphisms (SNPs; g.28265 G>C, g.28381 G>A, g.28470 T>C, and g.28672 G>A) were identified for genotyping within a 671-bp region, including exon 3, intron 3, exon 4, intron 4, and part of exon 5 of the FATP1 gene. Positive effects of genotypes CC (g.28470 T>C locus) and AA (g.28672 G>A locus) on meat quality traits were obtained by association analysis. These results indicate the associations of g.28470 T>C and g.28672 G>A with meat quality traits in Qinchuan cattle. Thus, the FATP1 gene may be used in marker-assisted selection of beef cattle in breeding programs.

Osteoblast functions in functionally graded Ti-6Al-4 V mesh structures

We describe here the combined efforts of engineering and biological sciences as a systemic approach to fundamentally elucidate osteoblast functions in functionally graded Ti-6Al-4 V mesh structures in relation to uniform/monolithic mesh arrays. First, the interconnecting porous architecture of functionally graded mesh arrays was conducive to cellular functions including attachment, proliferation, and mineralization. The underlying reason is that the graded fabricated structure with cells seeded from the large pore size side provided a channel for efficient transfer of nutrients to other end of the structure (small pore size), leading to the generation of mineralized extracellular matrix by differentiating pre-osteoblasts. Second, a comparative and parametric study indicated that gradient mesh structure had a pronounced effect on cell adhesion and mineralization, and strongly influenced the proliferation phase. High intensity and near-uniform distribution of proteins (actin and vinculin) on struts of the gradient mesh structure (cells seeded from large pore side) implied signal transduction during cell adhesion and was responsible for superior cellular activity, in comparison to the uniform mesh structure and non-porous titanium alloy. Cells adhered to the mesh struts by forming a sheet, bridging the pores through numerous cytoplasmic extensions, in the case of porous mesh structures. Intercellular interaction in porous structures provided a pathway for cells to communicate and mature to a differentiated phenotype. Furthermore, the capability of cells to migrate through the interconnecting porous architecture on mesh structures led to colonization of the entire structure. Cells were embedded layer-by-layer in the extracellular matrix as the matrix mineralized. The outcomes of the study are expected to address challenges associated with the treatment of segmental bone defects and bone-remodeling through favorable modulation of cellular response. Moreover, the study provides a foundation for a new branch of functionally graded materials with interconnected porous architecture.

Effects of choice of month of treatment and parity order on bovine superovulation traits

In this study, the performance of 300 Changbaishan Black cattle treated for superovulation from June to September was evaluated to determine the optimal conditions and herds for bovine embryo production. Data analysis revealed that cattle treated in July and August had higher numbers of available embryos (NAE), M1 embryos (NM1), and total embryos (NTE), as well as a higher percentage of M1 embryos (PM1). The temperature and precipitation observed during July and August were greater than those seen in the other two months; strong correlations were observed between these traits and the choice of month of treatment. In addition, multiparous cattle showed a better performance, higher NTE, NAE, NM1, and PM1 values, higher percentages of available embryos, and a lower percentage of degenerated embryos. The co-efficient correlation analysis showed that the month chosen for the treatment did not affect the superovulation traits of nulliparous cattle; however, the choice of the month affected multiparous cattle. Multiparous and nulliparous cattle exhibited many significant differences when treated in July and in August. In addition, the superovulatory traits of multiparous cattle, and not the nulliparous cattle, were strongly correlated to the choice of month of treatment. The results suggested that superovulation is more effective during a period with appropriate environmental temperature and humidity, and that multiparous cattle are more suitable for morula production.

Garlic for hypertension: A systematic review and meta-analysis of randomized controlled trials

BACKGROUND

In the past decade, garlic has become one of the most popular complementary therapies for blood pressure (BP) control used by hypertensive patients. Numerous clinical studies have focused on the BP-lowering effect of garlic, but results have been inconsistent. Overall, there is a dearth of information available to guide the clinical community on the efficacy of garlic in hypertensive patients.

AIM

To systematically review the medical literature to investigate the current evidence of garlic for the treatment of hypertension.

METHODS

PubMed, the Cochrane Library and EMBASE were searched for appropriate articles from their respective inceptions until August 2014. Randomized, placebo-controlled trials comparing garlic vs. a placebo in patients with hypertension were considered. Papers were independently reviewed by two reviewers and were analyzed using Cochrane software Revman 5.2.

RESULTS

A total of seven randomized, placebo-controlled trials were identified. Compared with the placebo, this meta-analysis revealed a significant lowering effect of garlic on both systolic BP (WMD: -6.71 mmHg; 95% CI: -12.44 to -0.99; P = 0.02) and diastolic BP (WMD: -4.79 mmHg; 95% CI: -6.60 to -2.99; P < 0.00001). No serious adverse events were reported in any of the trials.

CONCLUSION

The present review suggests that garlic is an effective and safe approach for hypertension. However, more rigorously designed randomized controlled trials focusing on primary endpoints with long-term follow-up are still warranted before garlic can be recommended to treat hypertensive patients.

Involvement of CitCHX and CitDIC in developmental-related and postharvest-hot-air driven citrate degradation in citrus fruits

Citrate is the predominant organic acid associated with taste in citrus fruit. Although citrate metabolism has been widely studied in recent years, the potential contributions of transport proteins to citrate content remain unclear. In the present study, high-acid citrus fruit Gaocheng ('GC', Citrus sp.) and low-acid citrus fruit Satsuma mandarin ('SM', Citrus unshiu Marc.) were selected for study, and the degradation of citrate was deduced to be the main cause of the difference in acidity in fully mature fruits. RNA-seq analysis was carried out on 'GC' and 'SM' fruit samples over the same time course, and the results indicated that citrate degradation occurred mainly through the glutamine pathway, catalyzed by CitAco3-CitGS2-CitGDU1, and also two transport-related genes, CitCHX and CitDIC, were shown to be associated with citrate degradation. These results were confirmed by real-time PCR. In postharvest 'GC' fruit, the expressions of these two transport-related genes were induced by 2-fold under hot air treatment, accompanied by a reduction of 7%-9% in total acid degradation. Transient expression of CitCHX and CitDIC in tobacco leaves was performed, and the citrate content was reduced by 62%, 75% and 78% following CitCHX, CitDIC and CitCHX plus CitDIC treatments, respectively, as compared with expression of an empty vector. Overall, these data indicated that two transport proteins, CitCHX and CitDIC, are not only involved in citrate degradation during fruit development, but also involved in postharvest hot air triggered citrate reduction.

First Report of Fusarium solani Causing Root Rot of Juglans sigllata Dode in China

Juglans sigllata Dode, known as the iron walnut, is widely planted in Liangshan prefecture of southwest China for its nuts and wood. Liangshan prefecture is a major traditional growing area of J. sigllata and has unique advantages for walnut industrial development because of its good soil, climate, and availability of water. Currently there are 2.7 million hectares of walnut, contributing important incomes for farmers. In April 2013, numerous J. sigllata were found infected with root rot in the Muli county of Liangshan prefecture. Symptoms included dried leaves, dead branchcs, and even death. Rotted roots were collected and surface-sterilized in 2% NaOCl and 70% ethanol. The junction (1 cm) between infected and healthy regions was removed, plated on rose bengal-glycerin-urea medium, and incubated at 20°C for 12 h. A fungus was found and purified successively by transferring hyphal tips from the margin of a thinly growing colony on 2% water agar (3). Morphological characteristics were identified both on potato dextrose agar (PDA) and carnation leaf-piece agar. Evaluation of pigmentation and colony growth rate were also measured using PDA. Ovoid microconidia (average dimensions 10.6 × 9.1 μm) were observed after 2 to 3 days, and most of them had no septa or only one septum. Macroconidia (average dimensions 47.4 × 5.3 μm), with one to three septate sickle shapes, were found after 3 to 6 days. Single or paired chlamydospores (average dimensions 10.3 × 9.2 μm), which were circular to ovate, smooth or not smooth, were observed after 7 days of incubation in clean water. According to the cultural characteristics, the fungus was primarily identified as Fusarium solani (1). To better determine the species, universal primers ITS1/ITS4 for the ribosomal internal transcribed spacer (ITS) coupled with translation elongation factor (EF-1α) primers EF1/EF2 were used for PCR-based molecular identification. Against GenBank and the FUSARIUM-ID databases, our sequences shared 99 and 98% identities with ITS (FJ459973.1) and EF-1α (JX677562.1) of F. solani, respectively. Both sequences produced in this study have been deposited in GenBank under accession numbers KJ528277 for ITS and KJ528278 for EF-1α. Pathogenicity tests were conducted by drop inoculating 20 ml of microconidia suspension (10⁶ spores/ml) on the roots of 1-year-old healthy potted J.sigllata, Mianyang walnut, and Xinjiang walnut. Controls were not treated with F. solani. Fifteen plants were in each group. All materials, including pots and soil, were disinfected. After 12 days, all J. sigllata inoculated with F. solani exhibited dried leaves, and after 17 days, Mianyang walnut and Xinjiang walnut infected with F. solani also developed the same symptoms. After 24 days, the inoculated J. sigllata died. However, control plants remained asymptomatic. The fungus re-isolated from infected roots showed the same characteristics as described above and was totally identical in appearance to the isolates used to inoculate the plants. No colonies of F. solani were isolated from untreated plants. At present, F. solani has been reported in stem cankers on English walnut in South Africa (2). To our knowledge, this is the first report of root rot caused by F. solani in J. sigllata in China. References: (1) C. Booth. Fusarium Laboratory Guide to the Identification of the Major Species. CMI, Kew, England, 1977. (2) W. Chen and W. J. Swart. Plant Dis. 84:592, 2000. (3) J. F. Leslie and B. A. Summerell. The Fusarium Laboratory Manual. Blackwell Publishing, Ames, IA, 2006.

Evaluating the annotation of protein-coding genes in bacterial genomes: Chloroflexus aurantiacus strain J-10-fl and Natrinema sp J7-2 as case studies

Gene annotation plays a key role in subsequent biochemical and molecular biological studies of various organisms. There are some errors in the original annotation of sequenced genomes because of the lack of sufficient data, and these errors may propagate into other genomes. Therefore, genome annotation must be checked from time to time to evaluate newly accumulated data. In this study, we evaluated the gene density of 2606 bacteria or archaea, and identified 2 with extreme values, the minimum value (Chloroflexus aurantiacus strain J-10-fl) and maximum value (Natrinema sp J7-2), to conduct genome re-annotation. In the genome of C. aurantiacus strain J-10-fl, we identified 17 new genes with definite functions and eliminated 34 non-coding open-reading frames; in the genome of Natrinema sp J7-2, we eliminated 118 non-coding open reading frames. Our re-annotation procedure may provide a reference for improving the annotation of other bacterial genomes.

Transcriptome and metabolome analyses of sugar and organic acid metabolism in Ponkan (Citrus reticulata) fruit during fruit maturation

Ponkan (Citrus reticulata Blanco cv. Ponkan) is an important mandarin citrus in China. However, the low ratio of sugars to organic acids makes it less acceptable for consumers. In this work, three stages (S120, early development stage; S195, commercial harvest stage; S205, delayed harvest stage) of Ponkan fruit were selected for study. Among 28 primary metabolites analyzed in fruit, sugars increased while organic acids in general decreased. RNA-Seq analysis was carried out and 19,504 genes were matched to the Citrus clementina genome, with 85 up-regulated and 59 down-regulated genes identified during fruit maturation. A sucrose phosphate synthase (SPS) gene was included in the up-regulated group, and this was supported by the transcript ratio distribution. Expression of two asparagine transferases (AST), and a specific ATP-citrate lyase (ACL) and glutamate decarboxylase (GAD) members increased during fruit maturation. It is suggested that SPS, AST, ACL and GAD coordinately contribute to sugar accumulation and organic acid degradation during Ponkan fruit maturation. Both the glycolysis pathway and TCA cycle were accelerated during later maturation, indicating the flux change from sucrose metabolism to organic acid metabolism was enhanced, with citrate degradation occurring mainly through the gamma-aminobutyric acid (GABA) and acetyl-CoA pathways.