Identification of three novel SNPs and association with carcass traits in porcine <Emphasis Type="Italic">TNNI1</Emphasis> and <Emphasis Type="Italic">TNNI2</Emphasis>

In this study, two novel SNPs (EU743939:g.5174T>C in intron 4 and EU743939:g.8350C>A in intron 7) in TNNI1 and one SNP (EU696779:g.1167C>T in intron 3) in TNNI2 were identified by PCR–RFLP (PCR restriction fragment length polymorphism) using XbaI, MspI and SmaI restriction enzyme, respectively. The allele frequencies of three novel SNPs were determined in the genetically diverse pig breeds including ten Chinese indigenous pigs and three Western commercial pig breeds. Association analysis of the SNPs with the carcass traits were conducted in a Large White × Meishan F₂ pig population. The linkage of two SNPs (g.5174T>C and g.8350C>A) in TNNI1 gene had significant effect on fat percentage. Besides these, the g.5174T>C polymorphism was also significantly associated with skin percentage (P < 0.05), shoulder fat thickness (P < 0.05) and backfat thickness between sixth and seventh ribs (P < 0.05). The significant effects of g.1167C>T polymorphism in TNNI2 gene on fat percentage (P < 0.01), lean meat percentage (P < 0.05), lion eye area (P < 0.05), thorax–waist backfat thickness (P < 0.01) and average backfat thickness (P < 0.05) were also found.     

Identification of <Emphasis Type="Italic">Elymus</Emphasis> (Triticeae,Poaceae) and its related genera genomes by RFLP analysis of PCR-amplified <Emphasis Type="Italic">Adh</Emphasis> genes

Elymus L. is the largest genus in Triticeae, containing about 150 species with four recognized genome donors (St, H, P, and W). Traditionally, the genome compound of this genus is identified based on cytological data. Recently, molecular phylogenetic analysis was used to investigate its genomic combination. Here we describe a restriction fragment length polymorphism (RFLP) assay based on digesting alcohol dehydrogenase (Adh) amplicons with two restriction enzyme combinations, EcoRI–HindIII and EcoRI–PstI, which easily can be used to distinguish Elymus and its closely related genera genomes. The method includes only four steps: (1) amplifying nuclear Adh genes with universal primers; (2) purifying and cloning PCR products; (3) digesting plasmids with restriction enzymes that identify a given genome; (4) running the digested products on an agarose gel and identify the sample based on the restriction profiles. Results showed that: (1) PCR products ranged from 1,200 to 2,000 bp; (2) Adh2 gene was amplified from all the tested genomes; Adh1 gene was amplified from almost all of the tested genomes except the W genome; Adh3 gene was amplified only from the St genome; (3) the EcoRI–HindIII combination was effective to distinguish different Adh gene types (Adh1, Adh2, and Adh3); (4) the Adh2–EcoRI–PstI fragments could be used to distinguish Elymus and its closely related genera genomes. Therefore, This RFLP assay provides an inexpensive and simple means of identifying Elymus genomes.     

Optimizing nucleotide sequence ensembles for combinatorial protein libraries using a genetic algorithm

Protein libraries are essential to the field of protein engineering. Increasingly, probabilistic protein design is being used to synthesize combinatorial protein libraries, which allow the protein engineer to explore a vast space of amino acid sequences, while at the same time placing restrictions on the amino acid distributions. To this end, if site-specific amino acid probabilities are input as the target, then the codon nucleotide distributions that match this target distribution can be used to generate a partially randomized gene library. However, it turns out to be a highly nontrivial computational task to find the codon nucleotide distributions that exactly matches a given target distribution of amino acids. We first showed that for any given target distribution an exact solution may not exist at all. Formulated as a constrained optimization problem, we then developed a genetic algorithm-based approach to find codon nucleotide distributions that match as closely as possible to the target amino acid distribution. As compared with the previous gradient descent method on various objective functions, the new method consistently gave more optimized distributions as measured by the relative entropy between the calculated and the target distributions. To simulate the actual lab solutions, new objective functions were designed to allow for two separate sets of codons in seeking a better match to the target amino acid distribution.     

Composition and variability of essential oils of Platycladus orientalis growing in China

Essential oils were isolated from the leaves of Platycladus orientalis growing in 16 areas of China. The essential oils were analyzed by gas chromatography and gas chromatography-mass spectrometry. In total, 98 volatile compounds were identified. Chemical variability in essential oil composition was evaluated using cluster analysis and principal component analysis. The two analyses led to the identification of four chemotypes: α-pinene, α-pinene/3-carene, cedrol, and cedrol/terpinyl acetate. Geographically, the populations growing in close proximity had similar essential oil composition. The chemical variability could possibly be attributed to genetic and environmental factors.     

CXCR6/CXCL16 functions as a regulator in metastasis and progression of cancer

Metastasis is considered the obvious mark for most aggressive cancers. However, little is known about the molecular mechanism of the regulation of cancer metastasis. Recent evidence increasingly suggests that the interaction between chemokines and chemokine receptors is pivotal in the process of metastasis. The chemokine receptor CXCR4 and its ligand CXCL12, for example, have been reported to play a vital role in cancer metastasis. Another chemokine and chemokine receptor pair, the CXCL16/CXCR6 axis, has been studied by several independent research groups. Here, we summarize recent advances in our knowledge of the function of CXC chemokine receptor CXCR6 and its ligand CXCL16 in regulating metastasis and invasion of cancer. CXCR6 and CXCL16 are up-regulated in multiple cancer tissue types and cancer cell lines relative to normal tissues and cell lines. In addition, both CXCR6 and CXCL16 levels increase as tumor malignancy increases. Trans-membranous CXCL16 chemokine reduces proliferation while soluble CXCL16 chemokine enhances proliferation and migration. TM-CXCL16 functions as an inducer for lymphocyte build-up around tumor sites. High trans-membranous CXCL16 expression correlates with a good prognosis. Moreover, the Akt/mTOR signal pathway is involved in activating the CXCR6/CXCL16 axis. These findings suggest multiple opportunities for blocking the CXCR6/CXCL16 axis and the Akt/mTOR signal pathway in novel cancer therapies.     

The Type II Arabidopsis Formin14 Interacts with Microtubules and Microfilaments to Regulate Cell Division

Formins have long been known to regulate microfilaments but have also recently been shown to associate with microtubules. In this study, Arabidopsis thaliana FORMIN14 (AFH14), a type II formin, was found to regulate both microtubule and microfilament arrays. AFH14 expressed in BY-2 cells was shown to decorate preprophase bands, spindles, and phragmoplasts and to induce coalignment of microtubules with microfilaments. These effects perturbed the process of cell division. Localization of AFH14 to microtubule-based structures was confirmed in Arabidopsis suspension cells. Knockdown of AFH14 in mitotic cells altered interactions between microtubules and microfilaments, resulting in the formation of an abnormal mitotic apparatus. In Arabidopsis afh14 T-DNA insertion mutants, microtubule arrays displayed abnormalities during the meiosis-associated process of microspore formation, which corresponded to altered phenotypes during tetrad formation. In vitro biochemical experiments showed that AFH14 bound directly to either microtubules or microfilaments and that the FH2 domain was essential for cytoskeleton binding and bundling. However, in the presence of both microtubules and microfilaments, AFH14 promoted interactions between microtubules and microfilaments. These results demonstrate that AFH14 is a unique plant formin that functions as a linking protein between microtubules and microfilaments and thus plays important roles in the process of plant cell division.     

Influence of bite force on jaw muscle activity ratios in subject-controlled unilateral isometric biting

Ratios of muscle activities in unilateral isometric biting are assumed to provide information on strategies of muscle activation independently from bite force. If valid, this assumption would facilitate experiments as it would justify subject-control instead of transducer-based force control in biting studies. As force independence of ratios is controversial, we tested whether activity ratios are associated with bite force and whether this could affect findings based on subject-controlled force. In 52 subjects, bite force and bilateral masseter and temporalis electromyograms were recorded during unilateral biting on a transducer with varying force levels and with uniform subject-controlled force. Working/balancing and temporalis/masseter ratios of activity peaks were related to bite force peaks. Activity ratios were significantly but weakly correlated with the bite force. The subject-controlled force varied within ±25% around the prescribed force in 95% of all bites. This scatter could cause a variation of group mean activity ratios of at most ±6% because of the weak correlation between bite force and ratios. As this small variation is negligible in most cases, subject-control of bite force can be considered an appropriate method to obtain group means of relative muscle activation in particular when force control with transducers is not feasible.     

Analysis of Determining Factors of the Public's Risk Acceptance Level in China

This work will characterize risk acceptance in China, based on the psychometric paradigm, and explore the determining factors that influence the risk acceptable level to the Chinese public. For this purpose, a survey was conducted including 12 hazards, 10 risk attributes (including risk acceptance), and demographic variables. First, the research attempted to explore Nanjing citizens’ average risk acceptable level for 12 hazards in China. Second, intercorrelation analysis and factor analysis of nine risk attributes were performed to obtain the suitable risk perception factors as independent variables. Three risk perception models of acceptance were constructed, which were named “Environmental risk model,” “Daily risk model,” and “Technical risk model,” that explained 59.0–69.6% of variance separately. In general, the variables of Knowledge, Benefit, and Trust were found to be significant in all models, implying that these variables are the main determining factors. However, in the environmental risk model, the variable of effect was also significant, which means the determining factors would change for different types of hazards. These results could help the Chinese government to improve the communication of risks with the public and make effective mitigation policies to improve people's rational judgment on the acceptability of risks.     

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.