Growth of a Molecular Base for Feeding: The Mind Body Dualism

It is often difficult to identify the ‘who, when, and where’ of advances in medicine and surgery because it's a rare advance indeed (such as the use of digitalis by William Withering) that can be clearly related to the astuteness of one person at one time and place.     

A Hidden Markov Model approach to variation among sites in rate of evolution

The method of Hidden Markov Models is used to allow for unequal and unknown evolutionary rates at different sites in molecular sequences. Rates of evolution at different sites are assumed to be drawn from a set of possible rates, with a finite number of possibilities. The overall likelihood of phylogeny is calculated as a sum of terms, each term being the probability of the data given a particular assignment of rates to sites, times the prior probability of that particular combination of rates. The probabilities of different rate combinations are specified by a stationary Markov chain that assigns rate categories to sites. While there will be a very large number of possible ways of assigning rates to sites, a simple recursive algorithm allows the contributions to the likelihood from all possible combinations of rates to be summed, in a time proportional to the number of different rates at a single site. Thus with three rates, the effort involved is no greater than three times that for a single rate. This "Hidden Markov Model" method allows for rates to differ between sites and for correlations between the rates of neighboring sites. By summing over all possibilities it does not require us to know the rates at individual sites. However, it does not allow for correlation of rates at nonadjacent sites, nor does it allow for a continuous distribution of rates over sites. It is shown how to use the Newton-Raphson method to estimate branch lengths of a phylogeny and to infer from a phylogeny what assignment of rates to sites has the largest posterior probability. An example is given using beta-hemoglobin DNA sequences in eight mammal species; the regions of high and low evolutionary rates are inferred and also the average length of patches of similar rates.      

ERRATUM: Effects of Loading on the Biomechanical Behavior of Molars of Homo,Pan, and Pongo. Am J Phys Anthropol 109:211–227.

ERRATUM: Macho GA and Spears IR. 1999. Effects of Loading on the Biomechanical Behavior of Molars of Homo, Pan, and Pongo. Am J Phys Anthropol 109:211–227. The correct title of the article is given above. The word “biochemical” should be read as “biomechanical.”     

一株石油降解菌培养基的优化

目的：有效降低石油降解菌株CT-6在工业生产中的培养成本,提高培养速度。方法：利用Minitab软件,采用中心组合设计、响应面分析,以葡萄糖、蔗糖、可溶性淀粉为碳源,以硝酸铵、尿素、氯化铵为氮源,对高效降解石油菌株CT-6的培养基进行了优化。结果：当碳源葡萄糖为5.6818g/L、氮源氯化铵为3.8030g/L时,菌株CT-6培养17h,OD600达到0.615。结论：优化前后,菌体CT-6的OD600分别为0.289和0.615,提高了112.8%,说明该培养基更有利于菌株CT-6的生长。     

Inferring functional modules of protein families with probabilistic topic models

Background  

Genome and metagenome studies have identified thousands of protein families whose functions are poorly understood and for which techniques for functional characterization provide only partial information. For such proteins, the genome context can give further information about their functional context.     

Presence of c-kit positive cells in fetal and adult bovine forestomachs

The interstitial cells of Cajal (ICC) have been reported to regulate gastrointestinal motility. We investigated the distribution and the morphological and morphometric characteristics of the immunohistochemical reaction against c-kit in the forestomachs of fetal, newborn and adult cows. The anti-c-kit reaction revealed different populations of ICC among age groups and organs. ICC were more numerous and smaller in fetuses. Larger ICC were identified in newborns, except for those in the rumen. During the earliest stages of development, ICC were abundant in the inner layer of the muscularis and were consistently associated with this layer. In all samples, ICC were found in the outer layer of the tunica muscularis. ICC were found between the two muscle layers in the omasum at all ages; however, they were identified only in the rumen of the adult. Our study demonstrated that ICC are present in the forestomach of bovines.     

新疆维吾尔自治区20年问胃癌的临床特点分析

目的：分析新疆地区近20年来胃癌流行病学特征,探讨其变化规律及发展趋势。方法：回顾性分析和比较1991年、2001年、2011年经新疆维吾自治区人民医院胃镜及病理学诊断确诊为胃癌的病例的一般资料、病理学及内镜下特点,包括性别、年龄、病理类型、发病部位。结果：1991年组：胃癌检出率为2．48％,中位年龄为54岁,男女之比为3-3：1．0,发病部位以胃窦部癌为主,占39．1％;2001年组：检出率为2．39％,中位年龄为61岁,男女之比为3．0：1．0,发病部位以胃体部癌为主,占42．1％;2011年组：检出率为1．48％,中位年龄为63岁,男女之比为3．9：1．0,发病部位以贵门胃底部为主,占34．8％。三组病理学类型均以腺癌为主,检出率有逐年升高趋势,但差异无统计学意义（P〉0．05）。结论：（1）近20年来胃癌发病部位有上移现象,且胃癌检发病率有下降趋势;（2）男性胃癌患者发病率明显高于女性,且近20年来胃癌患者男女比例无明显改变;（3）近20年来胃癌发病中位年龄逐渐增高,且随着年龄的增长发病率逐渐升高,以中老年发病率最高;（4）癌患者病理类型仍以腺癌为主,且近20年来腺癌所占比例无明显变化.     

Metabolomics reveals herbivore‐induced metabolites of resistance and susceptibility in maize leaves and roots

Plants respond to herbivory by reprogramming their metabolism. Most research in this context has focused on locally induced compounds that function as toxins or feeding deterrents. We developed an ultra‐high‐pressure liquid chromatography time‐of‐flight mass spectrometry (UHPLC‐TOF‐MS)‐based metabolomics approach to evaluate local and systemic herbivore‐induced changes in maize leaves, sap, roots and root exudates without any prior assumptions about their function. Thirty‐two differentially regulated compounds were identified from Spodoptera littoralis‐infested maize seedlings and isolated for structure assignment by microflow nuclear magnetic resonance (CapNMR). Nine compounds were quantified by a high throughput direct nano‐infusion tandem mass spectrometry/mass spectrometry (MS/MS) method. Leaf infestation led to a marked local increase of 1,3‐benzoxazin‐4‐ones, phospholipids, N‐hydroxycinnamoyltyramines, azealic acid and tryptophan. Only few changes were found in the root metabolome, but 1,3‐benzoxazin‐4‐ones increased in the vascular sap and root exudates. The role of N‐hydroxycinnamoyltyramines in plant–herbivore interactions is unknown, and we therefore tested the effect of the dominating p‐coumaroyltyramine on S. littoralis. Unexpectedly, p‐coumaroyltyramine was metabolized by the larvae and increased larval growth, possibly by providing additional nitrogen to the insect. Taken together, this study illustrates that herbivore attack leads to the induction of metabolites that can have contrasting effects on herbivore resistance in the leaves and roots.