Traveling wave solutions from microscopic to macroscopic chemotaxis models

In this paper, we study the existence and nonexistence of traveling wave solutions for the one-dimensional microscopic and macroscopic chemotaxis models. The microscopic model is based on the velocity jump process of Othmer et al. (SIAM J Appl Math 57:1044–1081, 1997). The macroscopic model, which can be shown to be the parabolic limit of the microscopic model, is the classical Keller–Segel model, (Keller and Segel in J Theor Biol 30:225–234; 377–380, 1971). In both models, the chemosensitivity function is given by the derivative of a potential function, Φ(v), which must be unbounded below at some point for the existence of traveling wave solutions. Thus, we consider two examples: F(v) = lnv{\Phi(v) = \ln v} and F(v) = ln[v/(1-v)]{\Phi(v) = \ln[v/(1-v)]}. The mathematical problem reduces to proving the existence or nonexistence of solutions to a nonlinear boundary value problem with variable coefficient on \mathbb R{\mathbb R}. The main purpose of this paper is to identify the relationships between the two models through their traveling waves, from which we can observe how information are lost, retained, or created during the transition from the microscopic model to the macroscopic model. Moreover, the underlying biological implications of our results are discussed.     

Mph1 requires mismatch repair-independent and -dependent functions of MutSα to regulate crossover formation during homologous recombination repair

In budding yeast the DNA helicase Mph1 prevents genome rearrangements during ectopic homologous recombination (HR) by suppressing the formation of crossovers (COs). Here we show that during ectopic HR repair, the anti-CO function of Mph1 is intricately associated with the mismatch repair (MMR) factor, MutSα. In particular, during HR repair using a completely homologous substrate, we reveal an MMR-independent function of MutSα in generating COs that is specifically antagonized by Mph1, but not Sgs1. In contrast, both Mph1 and MutSα are required to efficiently suppress COs in the presence of a homeologous substrate. Mph1 acts redundantly with Sgs1 in this respect since mph1Δ sgs1Δ double mutant cells pheno-copy MutSα mutants and completely fail to discriminate homologous and homeologous sequences during HR repair. However, this defect of mph1Δ sgs1Δ cells is not due to an inability to carry out MMR but rather is accompanied by elevated levels of gene conversion (GC) and bi-directional GC tracts specifically in non-crossover products. Models describing how Mph1, MutSα and Sgs1 act in concert to suppress genome rearrangements during ectopic HR repair are discussed.     

FragGeneScan: predicting genes in short and error-prone reads

The advances of next-generation sequencing technology have facilitated metagenomics research that attempts to determine directly the whole collection of genetic material within an environmental sample (i.e. the metagenome). Identification of genes directly from short reads has become an important yet challenging problem in annotating metagenomes, since the assembly of metagenomes is often not available. Gene predictors developed for whole genomes (e.g. Glimmer) and recently developed for metagenomic sequences (e.g. MetaGene) show a significant decrease in performance as the sequencing error rates increase, or as reads get shorter. We have developed a novel gene prediction method FragGeneScan, which combines sequencing error models and codon usages in a hidden Markov model to improve the prediction of protein-coding region in short reads. The performance of FragGeneScan was comparable to Glimmer and MetaGene for complete genomes. But for short reads, FragGeneScan consistently outperformed MetaGene (accuracy improved ∼62% for reads of 400 bases with 1% sequencing errors, and ∼18% for short reads of 100 bases that are error free). When applied to metagenomes, FragGeneScan recovered substantially more genes than MetaGene predicted (>90% of the genes identified by homology search), and many novel genes with no homologs in current protein sequence database.     

Insecticidal activity and chemical composition of the essential oil of Artemisia vestita from China against Sitophilus zeamais

In our screening program for new agrochemicals from local wild plants, essential oil of Artemisia vestita Wall (Asteraceae) was found to possess strong insecticidal activity against maize weevil, Sitophilus zeamais Motsch. Essential oil of aerial parts of A. vestita was obtained from hydrodistillation and was investigated by GC and GC–MS. The main components of essential oil were grandisol (40.29%), 1,8-cineol (14.88%) and camphor (11.37%). The essential oil of A. vestita possessed strong fumigant toxicity against S. zeamais adults with a LC₅₀ value of 13.42 mg/L air. The essential oil of A. vestita also showed contact toxicity against S. zeamais adults with a LD₅₀ value of 50.62 mg/adult.     

Cloning and expression of HSP70 gene of sipuncula Phascolosoma esculenta

In this study the gene encoding HSP70 was isolated from Phascoloma esculenta by homologous cloning and rapid amplification of cDNA ends (RACE). The full-length of cDNA (2520 bp) consists of a 5′-terminal untranslated region (UTR) (125 bp), a 3′-terminal UTR (421 bp) with a canonical polyadenylation signal sequence (AATAAA), a poly (A) tail, and an open reading frame (ORF) (1974 bp). The predicted molecular mass and isoelectric point for HSP70 is 71.6 kDa and 5.15, respectively. BLAST analysis showed that P. esculenta HSP70 gene shared high similarity. Classical HSP signature motifs, ATP/GTP-Binding Site Motif A, Bipartite Nuclear Targeting Sequence, the cytosolic HSP70 could be expressed in Escherichia coli BL21. After purification, the recombinant pET-HSP70 protein was used to produce the polyclonal antibody in mice and the specificity of the antibody was confirmed by Western blot analysis. Fluorescent real-time quantitative PCR analysis showed that expression of Hsp70 in sipuncula was increased significantly after exposure to 10 mM Zn for12 h, Cd for 24 h, Cu for 48 h, and was exposure to 37 °C for 24 h sea water.     

Multilocus sequence typing and virulence factors analysis of Escherichia coli O157 strains in China

Escherichia coli O157:H7, an important food-borne pathogen, has become a major public health concern worldwide. The aim of this study was to investigate the molecular epidemiologic feature of E. coli O157:H7 strains in China. 105 E. coli O157:H7 isolates were collected from various hosts and places over 9 years. A multilocus sequence typing scheme (MLST) was applied for bacteria genotyping and polymerase chain reaction (PCR) was used for virulence factor identification. Seven new MLST sequence types (STs), namely ST836, ST837, ST838, ST839, ST840, ST841, and ST842 were identified, which grouped into two lineages. Phylogenetic analysis suggested that the most two frequent STs in China, ST837 and ST836, may be the derivatives of E. coli O157:H7 Sakai or E. coli O157:H7 EDL933. Geographical diversity and host variety of E. coli O157:H7 were observed in China. In addition, the different distribution of tccp was detected. The data presented herein provide new insights into the molecular epidemiologic feature of E. coli O157:H7, and aid in the investigation of the transmission regularity and evolutionary mechanism of E. coli O157:H7.     

Comparative analysis of the genomes of <Emphasis Type="Italic">Bombyx mandarina</Emphasis> and <Emphasis Type="Italic">Bombyx mori</Emphasis> nucleopolyhedroviruses

The Bombyx mandarina nucleopolyhedrovirus (BomaNPV) S1 strain can infect the silkworm, Bombyx mori, but is significantly less virulent than B. mori nucleopolyhedrovirus (BmNPV) T3 strain. The complete nucleotide sequence of the S1 strain of BomaNPV was determined and compared with the BmNPV T3 strain. The circular, double stranded DNA genome of the S1 strain was 126,770 nucleotides long (GenBank accession no. FJ882854), with a G+C content of 40.23%. The genome contained 133 potential ORFs. Most of the putative proteins were more than 96% identical to homologs in the BmNPV T3 strain, except for bro-a, lef-12, bro-c, and bro-d. Compared with the BmNPV T3 strain, however, this genome did not encode the bro-b and bro-e genes. In addition, hr1 lacked two repeat units, while hr2L, hr2R, hr3, hr4L, hr4R, and hr5 were similar to the corresponding hrs in the T3 strain. The sequence strongly suggested that BomaNPV and BmNPV are variants with each other, and supported the idea that baculovirus strain heterogeneity may often be caused by variation in the hrs and bro genes.     

Urinary tract abnormalities in Chinese rural children who consumed melamine-contaminated dairy products: a population-based screening and follow-up study

Background

Kidney damage related to consumption of melamine-contaminated dairy products by young children in China has been described. However, no studies have reported on the population-based prevalence of kidney damage among exposed children or on the condition of affected children after follow-up.

Methods

We conducted an ultrasound-based screening in September 2008 of 7933 children younger than 36 months of age who lived in a rural area in China where the dairy products most highly contaminated with melamine were sold. We monitored children who had evidence of nephrolithiasis or hydronephrosis at screening using renal ultrasonography after one, three and six months. We also collected information from the mothers of affected children about consumption of melamine-contaminated products between June and August 2008.

Results

The overall prevalence of urinary tract abnormalities among screened children was 0.61% (95% confidence interval [CI] 0.45%–0.80%). The mean exposure dose of melamine was estimated to be 116 (range 36–220) mg per day. Of the 48 affected children, 43 (89.6%) were asymptomatic, 2 had symptoms and were hospitalized, and 3 had symptoms but treatment had been not sought for them. Of the 46 children for whom six-month follow-up information was available, renal abnormalities persisted in 5 children and resolved in the remaining 41.

Interpretation

Among children who underwent screening, 0.61% showed ultrasonographic evidence of nephrolithiasis or hydronephrosis. Most of the affected children were asymptomatic. The majority of the affected children recovered from the toxic effects of melamine over time without specific treatment. Renal abnormalities remained in 12% of the affected children.Contamination of dairy products with melamine in China has resulted in a widespread outbreak of serious kidney damage in children.^1–4 On Sept. 12, 2008, the Chinese government announced to the public that the outbreak had occurred and initiated various emergency responses, including the set-up of a high-level national coordinating group, free screening and treatment of affected children, thorough inspection of all dairy products and producers, timely release of information to the public, recalls of contaminated products, suspension of production of the contaminated milk and compensation to the families of affected children. More than 50 000 children have been hospitalized and six have died because of kidney damage.⁵Melamine is a nitrogen-containing compound commonly used in chemical industry. Because its addition to milk elevates apparent protein content, raw milk was intentionally adulterated with melamine in the production-chain, leading to contamination of dairy products and high-level exposure of thousands of children.⁶Melamine is known to cause formation of calculi in weanling rats and has led to acute renal failure in cats and dogs consuming melamine-contaminated pet foods.^7,8 In humans, melamine-related disease has been recognized only recently, and the full adverse effects of exposure remain unknown.^4,9 A clinicopathologic study suggests that the size of urinary stones is related to melamine concentration.⁹ A recent hospital-based study in Beijing reported the prevalence of nephrolithiasis was 8.5% among children who were exposed and referred by other hospitals.¹⁰However, no studies have reported on the population-based prevalence of kidney disease among exposed children, nor have follow-up reports been released about affected children. We performed a population-based screening and follow-up study involving residents of a rural area situated close to the manufacturer of Sanlu dairy products, which was the source of the most severely melamine-contaminated products in the mainland of China.¹¹ The study was approved by the Institutional Review Board of Peking University.     

Clinical application of the SurePath liquid-based Pap test in cytological screening of bronchial brushing for the diagnosis of lung cancer

The SurePath liquid-based Pap test (LPT) is successfully and widely used to assess sputum cytology. This study aimed to compare the cytological findings and diagnostic sensitivity of LPT with those of the conventional Pap smear (CPS) method for diagnosing lung cancer. Bronchial brushing specimens from 204 patients diagnosed with lung cancer were studied. LPT slides showed decreased areas of cell monolayers, a clearer background and distinct, stereoscopic cytological features. The LPT had a significantly higher diagnostic sensitivity for lung cancer (71.6%) than the CPS method (57.8%, p < 0.05), particularly for small cell lung carcinoma and >2 cm lesions (p < 0.05). Combination of the LPT with the CPS method showed obviously higher diagnostic sensitivity for the detection of adenocarcinoma (63.6%), central lesions (85.0%) and >2 cm lesions (81.4%) compared with the CPS method alone (p < 0.05, p < 0.01). Thus, LPT is a useful and easily performed technique that can be widely applied, and is suitable for the early diagnosis of lung cancer.