Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry"

We used authentication tests developed for ancient DNA to evaluate claims by Asara et al. (Reports, 13 April 2007, p. 280) of collagen peptide sequences recovered from mastodon and Tyrannosaurus rex fossils. Although the mastodon samples pass these tests, absence of amino acid composition data, lack of evidence for peptide deamidation, and association of alpha1(I) collagen sequences with amphibians rather than birds suggest that T. rex does not.     

Diverse plant and animal genetic records from Holocene and Pleistocene sediments

Genetic analyses of permafrost and temperate sediments reveal that plant and animal DNA may be preserved for long periods, even in the absence of obvious macrofossils. In Siberia, five permafrost cores ranging from 400,000 to 10,000 years old contained at least 19 different plant taxa, including the oldest authenticated ancient DNA sequences known, and megafaunal sequences including mammoth, bison, and horse. The genetic data record a number of dramatic changes in the taxonomic diversity and composition of Beringian vegetation and fauna. Temperate cave sediments in New Zealand also yielded DNA sequences of extinct biota, including two species of ratite moa, and 29 plant taxa characteristic of the prehuman environment. Therefore, many sedimentary deposits may contain unique, and widespread, genetic records of paleoenvironments.     

Genomic sequencing of Pleistocene cave bears

Despite the greater information content of genomic DNA, ancient DNA studies have largely been limited to the amplification of mitochondrial sequences. Here we describe metagenomic libraries constructed with unamplified DNA extracted from skeletal remains of two 40,000-year-old extinct cave bears. Analysis of approximately 1 megabase of sequence from each library showed that despite significant microbial contamination, 5.8 and 1.1% of clones contained cave bear inserts, yielding 26,861 base pairs of cave bear genome sequence. Comparison of cave bear and modern bear sequences revealed the evolutionary relationship of these lineages. The metagenomic approach used here establishes the feasibility of ancient DNA genome sequencing programs.     

Rates of evolution in ancient DNA from Adélie penguins

Well-preserved subfossil bones of Adélie penguins, Pygoscelis adeliae, underlie existing and abandoned nesting colonies in Antarctica. These bones, dating back to more than 7000 years before the present, harbor some of the best-preserved ancient DNA yet discovered. From 96 radiocarbon-aged bones, we report large numbers of mitochondrial haplotypes, some of which appear to be extinct, given the 380 living birds sampled. We demonstrate DNA sequence evolution through time and estimate the rate of evolution of the hypervariable region I using a Markov chain Monte Carlo integration and a least-squares regression analysis. Our calculated rates of evolution are approximately two to seven times higher than previous indirect phylogenetic estimates.     

Molecular phylogenetics of mastodon and Tyrannosaurus rex

We report a molecular phylogeny for a nonavian dinosaur, extending our knowledge of trait evolution within nonavian dinosaurs into the macromolecular level of biological organization. Fragments of collagen alpha1(I) and alpha2(I) proteins extracted from fossil bones of Tyrannosaurus rex and Mammut americanum (mastodon) were analyzed with a variety of phylogenetic methods. Despite missing sequence data, the mastodon groups with elephant and the T. rex groups with birds, consistent with predictions based on genetic and morphological data for mastodon and on morphological data for T. rex. Our findings suggest that molecular data from long-extinct organisms may have the potential for resolving relationships at critical areas in the vertebrate evolutionary tree that have, so far, been phylogenetically intractable.     

5TH International Ancient DNA Conference. Divining diet and disease from DNA

Some 110 scientists from a range of disciplines gathered in the overcast British midlands for the 5th International Ancient DNA Conference, held here from 12 to 14 July. Among the attractions were new insights into the diets of early Americans gleaned from ancient human coprolites and intriguing reports of nuclear DNA and ancient viral sequences extracted from mammoth bones.     

The ginsberg experiment: modern and prehistoric evidence of a bone-flaking technology

The discovery of butchered and modified bones of extinct Pleistocene fauna from Old Crow Flats, Yukon Territory, and the Dutton and Selby sites, Colorado, provides some of the earliest evidence for man in the New World. However, the significance of these discoveries rests entirely on the ability to determine whether these remains were modified by man. The results of experiments of elephant butchering, bone fracturing, and bone tool manufacturing support the hypothesis that these modified bones can be used to identify the presence of cultural activities.     

Analyses of soft tissue from Tyrannosaurus rex suggest the presence of protein

We performed multiple analyses of Tyrannosaurus rex (specimen MOR 1125) fibrous cortical and medullary tissues remaining after demineralization. The results indicate that collagen I, the main organic component of bone, has been preserved in low concentrations in these tissues. The findings were independently confirmed by mass spectrometry. We propose a possible chemical pathway that may contribute to this preservation. The presence of endogenous protein in dinosaur bone may validate hypotheses about evolutionary relationships, rates, and patterns of molecular change and degradation, as well as the chemical stability of molecules over time.     

Gender-specific reproductive tissue in ratites and Tyrannosaurus rex

Unambiguous indicators of gender in dinosaurs are usually lost during fossilization, along with other aspects of soft tissue anatomy. We report the presence of endosteally derived bone tissues lining the interior marrow cavities of portions of Tyrannosaurus rex (Museum of the Rockies specimen number 1125) hindlimb elements, and we hypothesize that these tissues are homologous to specialized avian tissues known as medullary bone. Because medullary bone is unique to female birds, its discovery in extinct dinosaurs solidifies the link between dinosaurs and birds, suggests similar reproductive strategies, and provides an objective means of gender differentiation in dinosaurs.     

獭兔胃肠道乳酸菌的分离与鉴定

为探索獭兔胃肠道中固有的乳酸菌群,丰富乳酸菌应用,选择中性或偏酸性MRS培养基分离并培养健康獭兔胃肠道中的乳酸菌、16S rDNA测序对所获菌株进行种属鉴定、基因组DNA荧光定量PCR检测其在40、80日龄的獭兔胃肠道中的相对含量。结果从獭兔胃、空肠、盲肠、结肠、直肠中均分离出1株粪肠球菌;胃、十二指肠、空肠、回肠、盲肠中均分离出1株短乳杆菌;胃、十二指肠、回肠、盲肠、结肠、直肠中均分离出1株植物乳杆菌;十二指肠、空肠、盲肠、结肠中均分离出1株空肠肠球菌。所获菌株在獭兔胃肠道中普遍分布,并且其相对水平随獭兔日龄的增长而升高,这些菌类有待成为獭兔内源乳酸菌饲料添加剂的备用选择。     

家蚕幼虫关联基因在胚胎期的表达（英文）

    用蛋白质表达谱分析技术研究家蚕胚胎发育时期的基因表达.用蛋白质双向电泳技术(2-DE)分离蛋白质,用ImageMaster Elite图谱分析软件比较分析12个家蚕胚胎发育特异时期的2-DE图谱,发现一些蛋白斑点丰度高,并且一旦出现就在后续特异时期一直表达,推测这些蛋白可能在胚胎发育和代谢方面起重要作用,从中选择5个点分析它们的序列和功能.用基质辅助激光解吸电离质谱(MALDI-TOF-MS)和数据库检索鉴定蛋白质,发现5个幼虫期功能蛋白分别在4个胚胎发育特异时期表达:保幼激素结合蛋白(JHBP)基因在缩短期表达,表皮生长因子受体在头胸分化期表达,家蚕幼虫表皮蛋白和副腺特异肽在毛瘤发生期表达,淀粉酶在转青期表达.这些幼虫功能蛋白都在胚胎特定的生理期功能需要下出现,表明幼虫关联基因在胚胎期有序而及时地表达.     

植物羟基肉桂酰辅酶A还原酶的生物信息学分析

分析GenBank公布的68条蕨类、裸子、单子叶和双子叶植物的CCR蛋白,发现单子叶植物CCR基因的GC含量最高,CCR一级结构的理化性质基本一致,但主要氨基酸种类和含量不同;CCR是一类无导肽、信号肽及跨膜结构域的亲水性蛋白质,N-端存在3β-羟基类固醇脱氢酶/差向异构酶/NAD结合蛋白的结构域,存在9个功能保守区;进化树表明,该基因可用于植物高等级单元的分类;同源建模表明其三级结构稳定,建模结果可靠;CCR蛋白亚细胞定位于细胞质、叶绿体和内质网,除黑麦草和番茄外,同一物种CCR不同成员的亚细胞定位基本相同.     

猪OLR1基因克隆及生物信息学分析

设计猪氧化低密度脂蛋白受体1(OLR1)基因编码区全长引物,从猪脂肪组织中扩增OLR1基因编码区全长序列,对其蛋白质序列进行比对分析,预测蛋白质信号肽位点及结构域并研究该基因密码子使用偏好性。结果表明:猪OLR1基因编码区全长为825 bp,共编码273个氨基酸,猪OLR1基因与牛同源性最高(84%),其次是人(79%)、大鼠(51%)和小鼠(27%)。猪OLR1蛋白38~60位氨基酸为信号肽所在位置,144~256位氨基酸正是C型凝集素家族共有结构域;OLR1基因密码子A U含量(61.2%)远高于G C含量(38.8%),而且偏向使用A/U结尾的密码子(占76.53%),这可能影响到OLR1基因的表达水平。     

Fossilized viscera in primitive echinoderms

Fossilized visceral organs in ancient echinoderms have anatomical features that were not inferred from the anatomy of extant relatives. The unique visceral anatomy of extinct echinoderms demonstrates the need to integrate paleontological and neontological analyses in order to fully evaluate this and other morphologically complex phyla. Comparative analysis of the visceral anatomy of extinct and extant echinoderms necessitates regrouping these animals into three new subphyla. Similar analyses for other metazoan groups could yield equally significant results.     

Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry"

Asara et al. (Reports, 13 April 2007, p. 280) reported sequencing of Tyrannosaurus rex proteins and used them to establish the evolutionary relationships between birds and dinosaurs. We argue that the reported T. rex peptides may represent statistical artifacts and call for complete data release to enable experimental and computational verification of their findings.     

Primary structure of the beta subunit of the DHP-sensitive calcium channel from skeletal muscle

Complementary DNAs for the beta subunit of the dihydropyridine-sensitive calcium channel of rabbit skeletal muscle were isolated on the basis of peptide sequences derived from the purified protein. The deduced primary structure is without homology to other known protein sequences and is consistent with the beta subunit being a peripheral membrane protein associated with the cytoplasmic aspect of the sarcolemma. The protein contains sites that might be expected to be preferentially phosphorylated by protein kinase C and guanosine 3',5'-monophosphate-dependent protein kinase. A messenger RNA for this protein appears to be expressed in brain.     

A plant peptide encoded by CLV3 identified by in situ MALDI-TOF MS analysis

The Arabidopsis CLAVATA3 (CLV3) gene encodes a stem cell-specific protein presumed to be a precursor of a secreted peptide hormone. Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) applied to in situ Arabidopsis tissues determined the structure of a modified 12-amino acid peptide (MCLV3), which was derived from a conserved motif in the CLV3 sequence. Synthetic MCLV3 induced shoot and root meristem consumption as cells differentiated into other organs, displaying the typical phenotype of transgenic plants overexpressing CLV3. These results suggest that the functional peptide of CLV3 is MCLV3.     

不同粗蛋白、消化能水平对商品獭兔生产性能的影响

旨在研究粗蛋白、消化能对商品獭兔生产性能的影响,选择3月龄獭兔108只,随机分为9组,每组饲喂不同粗蛋白、消化能营养水平的日粮.结果表明:饲喂消化能为(DE)10 MJ/kg、粗蛋白(CP)为15%的日粮时,日采食量最小为129.01 g/d,日增体质量最高为23.15 g/d,料重比最小为5.57;饲喂消化能(DE)为10 MJ/kg、粗蛋白(CP)为17%的日粮时,半净膛率和全净膛率均达到最高,分别为69.46%、63.38%.     

Random peptide libraries: a source of specific protein binding molecules

Libraries of random peptide sequences were constructed and screened to identify peptides that specifically bind to proteins. In one of these about 2 X 10(7) different 15-residue peptide sequences were expressed on the surface of the coliphage M13. Each phage encoded a single random sequence and expressed it as a fusion complex with pIII, a minor coat protein present at five molecules per phage. Phage encoding nine different streptavidin-binding peptide sequences were isolated from this library. The core consensus sequence was His-Pro-Gln and binding of these phage to streptavidin was inhibited by biotin. This type of library makes it possible to identify peptides that bind to proteins (or other macromolecules) that have no previously known affinity for peptides.