Sequence analysis of bacterial DNA in the colon and stomach of the Tyrolean Iceman

The male human body found in an Alpine glacier on September 19, 1991 ("Tyrolean Iceman") has, for the first time in history, given scientists a chance to perform detailed anatomical, histological, and molecular investigations on the organs of a person from the Neolithic Age (5350-5100 B.P.). In the present study, tissue samples aseptically taken from the stomach and the colon of the mummy were utilized for DNA extraction, and the DNA was PCR-amplified, using primer pairs designed to bind to fragments of the 16s ribosomal RNA gene (16s rDNA) of a broad range of bacteria. The PCR products were cloned in plasmid vectors, and the recombinant clones (amplicons) were sequenced. The sequence data were finally used for scanning data libraries containing the corresponding sequences of present-day bacteria, to infer the putative ecophysiology of the ancient ones. The same procedure was repeated on some fragments of grass from the clothing found near the corpse. These fragments were taken as a control of the microbiological situation of the glacier. The results show that the flora of the Iceman's stomach is entirely composed of Burkholderia pickettii, an organism commonly found in aquatic habitats. The colon, on the other hand, contains several members of the fecal flora of humans, such as Clostridium perfringens, C. ghonii, C. sordellii, Eubacterium tenue, and Bacteroides sp. The Iceman's colon, however, was found to contain, rather unexpectedly, also some members of the genus Vibrio. The results are discussed in light of what is known about the preservation of microbial DNA at the Iceman's site and of previous parasitological studies performed on the Iceman himself and on human coprolites.     

Complete mitochondrial genome sequence of the Tyrolean Iceman

The Tyrolean Iceman was a witness to the Neolithic-Copper Age transition in Central Europe 5350-5100 years ago, and his mummified corpse was recovered from an Alpine glacier on the Austro-Italian border in 1991 [1]. Using a mixed sequencing procedure based on PCR amplification and 454 sequencing of pooled amplification products, we have retrieved the first complete mitochondrial-genome sequence of a prehistoric European. We have then compared it with 115 related extant lineages from mitochondrial haplogroup K. We found that the Iceman belonged to a branch of mitochondrial haplogroup K1 that has not yet been identified in modern European populations. This is the oldest complete Homo sapiens mtDNA genome generated to date. The results point to the potential significance of complete-ancient-mtDNA studies in addressing questions concerning the genetic history of human populations that the phylogeography of modern lineages is unable to tackle.     

脂肪酸对红火蚁搬尸行为的影响

【目的】工蚁死亡后易受病原菌的侵染,进而危害蚁巢的健康。为了避免病菌横向传播,活工蚁根据尸体体内特定的化学物质的变化来识别尸体并将其搬运到弃尸堆。本实验旨在研究6种脂肪酸(油酸、亚油酸、棕榈油酸、棕榈酸、硬脂酸和肉豆蔻酸)对红火蚁Solenopsis invicta工蚁搬尸行为的影响,明确不同脂肪酸在其搬尸行为中发挥的作用。【方法】本实验利用GC-MS分析了工蚁活体和尸体提取物的脂肪酸成分,并在室内用滤纸片法测定了红火蚁对6种脂肪酸(10 μg/μL)、不同浓度(0.75和3 μg/μL)的单组分油酸或亚油酸以及不同浓度(0.01, 0.1, 1和10 μg/μL)的这两种酸的混合液的反应。【结果】结果表明,红火蚁尸体仅含有亚油酸和油酸两种脂肪酸;另外4种脂肪酸(棕榈油酸、棕榈酸、硬脂酸和肉豆蔻酸)对红火蚁的搬尸行为无显著影响;单组分的油酸和亚油酸均能促进红火蚁的搬尸行为,浓度越高,搬尸行为越显著。10 μg/μL的油酸和亚油酸混合液对工蚁的搬尸行为也具有显著的促进效果,低浓度的混合液对其无明显的促进作用(P>0.05)。【结论】结果提示油酸和亚油酸可调控红火蚁的搬尸行为,其他脂肪酸对红火蚁搬尸行为不产生影响。     

Population Genomic Analysis of Ancient and Modern Genomes Yields New Insights into the Genetic Ancestry of the Tyrolean Iceman and the Genetic Structure of Europe

Genome sequencing of the 5,300-year-old mummy of the Tyrolean Iceman, found in 1991 on a glacier near the border of Italy and Austria, has yielded new insights into his origin and relationship to modern European populations. A key finding of that study was an apparent recent common ancestry with individuals from Sardinia, based largely on the Y chromosome haplogroup and common autosomal SNP variation. Here, we compiled and analyzed genomic datasets from both modern and ancient Europeans, including genome sequence data from over 400 Sardinians and two ancient Thracians from Bulgaria, to investigate this result in greater detail and determine its implications for the genetic structure of Neolithic Europe. Using whole-genome sequencing data, we confirm that the Iceman is, indeed, most closely related to Sardinians. Furthermore, we show that this relationship extends to other individuals from cultural contexts associated with the spread of agriculture during the Neolithic transition, in contrast to individuals from a hunter-gatherer context. We hypothesize that this genetic affinity of ancient samples from different parts of Europe with Sardinians represents a common genetic component that was geographically widespread across Europe during the Neolithic, likely related to migrations and population expansions associated with the spread of agriculture.     

Production of 10-hydroxystearic acid from oleic acid by whole cells of recombinant Escherichia coli containing oleate hydratase from Stenotrophomonas maltophilia

A putative fatty acid hydratase from Stenotrophomonas maltophilia was cloned and expressed in Escherichia coli. The recombinant enzyme showed the highest hydration activity for oleic acid among the fatty acids tested, indicating that the enzyme is an oleate hydratase. The optimal conditions for the production of 10-hydroxystearic acid from oleic acid using whole cells of recombinant E. coli containing the oleate hydratase were pH 6.5, 35°C, 0.05% (w/v) Tween 40, 10 g l(-1) cells, and 50 g l(-1) oleic acid. Under these conditions, whole recombinant cells produced 49 g l(-1) 10-hydroxystearic acid for 4 h, with a conversion yield of 98% (w/w), a volumetric productivity of 12.3 g l(-1) h(-1), and a specific productivity of 1.23 g g-cells(-1) h(-1), which were 18%, 2.5-, and 2.5-fold higher than those of whole wild-type S. maltophilia cells, respectively. This is the first report of 10-hydroxystearic acid production using recombinant cells and the concentration and productivity are the highest reported thus far among cells.     

Ancient microorganisms offer new clues to the Iceman’s mummification

The DNA identification of the microorganisms that colonized the so-called Tyrolean Iceman in the ancient times can offer a clue to understanding the exact process through which the natural mummification of the 5.100–5.300 year-old body took place. The results suggest that this process was considerably more complex than previously assumed (wind desiccation followed by freezing) possibly involving also a prolonged stage of water immersion of the corpse.     

The effects of storage time of frozen pike (Esox lucius Linnaeus, 1758) fillets on the chemical composition as determined by various deterioration indicators

The study was designed to investigate the effects of frozen storage on the proximate composition and chemical indices of pike (Esox lucius) stored for a period of six months at ?20°C. During storage the moisture, protein and fatty acid contents decreased and the ash, total volatile basic nitrogen (TVB‐N) and peroxide value (PV) content increased significantly (P < 0.05). In the fresh samples the moisture, total protein and total lipid contents were 77.61%, 19.21%, and 2.3% respectively. At the end of the storage time the above‐mentioned parameters were measured as 75.98%, 16.95%, 0.9%, respectively. TVB‐N and PV contents changed from 1.30%, 6.27, 0.18 in fresh samples to 2.21%, 15.12 mg/100 g and 1.73 meq o₂ kg^?1 after six months frozen storage, respectively. Thirty fatty acids were found in pike fillets, with a higher percentage in fresh fish of polyunsaturated fatty acids (51.14%), saturated fatty acids (22.94%) and mono unsaturated fatty acids (22.61%). The PUFAs decreased to 31.67% at the end of the storage time. Although some changes in quality and nutritional value were observed in the pike fillets during frozen storage, the changes were within the acceptable range.     

Stereospecificity of Microbial Hydrations of Oleic Acid to 10-Hydroxystearic Acid

We recently described a simple method for ascertaining the stereochemical purities of hydroxy fatty acids (S. H. El-Sharkawy, W. Yang, L. Dostal, and J. P. N. Rosazza, Appl. Environ. Microbiol. 58:2116-2122, 1992) based on the ¹H-nuclear magnetic resonance spectral analysis of diastereomeric S-(+)-O-acetylmandelate esters of hydroxystearates. This report describes the stereochemistries of microbial hydrations of oleic acid to 10-hydroxystearic acid by Nocardia aurantia (also known as Rhodococcus rhodochrous) ATCC 12674, Nocardia restrictus ATCC 14887, Mycobacterium fortuitum UI-53387, Pseudomonas species strain NRRL-2994, Pseudomonas species strain NRRL B-3266, and baker's yeast. 10(R)-hydroxystearic acid isolated from Pseudomonas species strain NRRL-2994 was the standard for use in the ¹H-nuclear magnetic resonance spectral technique to permit simple assignments of the absolute configurations of 10-hydroxystearic acid produced by different microorganisms. While the R. rhodochrous ATCC 12674-mediated hydration of oleic acid gave mixtures of enantiomers 10(R)-hydroxystearic acid and 10(S)-hydroxystearic acid, Pseudomonas species strain NRRL-B-3266 produced optically pure 10(R)-hydroxystearic acid. The remaining microorganisms stereoselectively hydrated oleic acid to 10(R)-hydroxystearic acid containing between 2 and 18% of the contaminating 10(S)-hydroxystearic acid.     

Biosynthesis of cutin monomers: involvement of a lipoxygenase/peroxygenase pathway

Cutin is synthesized from oxygenated fatty acids derived preponderantly from oleic acid. The enzymatic pathways involved in the biosynthesis of such cutin monomers have been studied, i.e. 18-hydroxyoleic acid, 9,10-epoxy-18-hydroxystearic acid (the major constituent) and 9,10,18-trihydroxystearic acid. This was approached by studying (i) the substrate specificity and stereoselectivity of purified peroxygenase, which epoxidizes unsaturated fatty acids, and fatty acid epoxide hydrolase, i.e. two enzyme activities that have been found recently in higher plants, and (ii) the transformation of oleic acid into cutin monomers by a cell free system, i.e. soybean microsomes. These two enzymes, along with a ω-hydroxylating activity, can account for the biosynthesis of the oleic acid-derived cutin monomers and their precursors. A new biosynthetic scheme is proposed, whose pathways take into account the dynamic aspects of the expression of the different enzyme activities involved. Importantly, since peroxygenase, for its activity, is strictly dependent on fatty acid hydroperoxides, which act as co-substrates, the biosynthesis of cutin monomers is also dependent on the activity of lipoxygenases.     

Conversion of fatty acids by Bacillus sphaericus-like organisms

Bacillus sphaericus species are mesophilic round-spored organisms that readily utilize fatty acid-based surfactants during growth, but their ability to modify fatty acids is unknown. Among 57 B. sphaericus-like strains tested for fatty acid transformation activity in Wallen fermentation (WF) medium, ten converted oleic acid to a new product determined by gas chromatography – mass spectrometry (GC-MS) to be 10-ketostearic acid (10-KSA). Additionally, a few other strains converted ricinoleic acid and linoleic acid to new products that remain to be characterized. Unlike most microbial hydrations of oleic acid, which produce a mixture of 10-KSA and 10-hydroxystearic acid, the conversion of oleic acid by B. sphaericus strains was unique in that 10-KSA was the sole reaction product. By replacing dextrose with sodium pyruvate in WF and adjusting to pH 6.5, conversion of oleic acid to 10-KSA by strain NRRL NRS-732 was improved from about 11% to more than 60%. Using the defined optimal conditions, the conversion reaction was scaled up in a stirred-batch reactor by using technical-grade oleic acid as substrate. This is the first report on the characterization of fatty acid conversions by B. sphaericus species. Received: 17 December 2001 / Accepted: 17 January 2002     

First insights into the metagenome of Egyptian mummies using next-generation sequencing

We applied, for the first time, next-generation sequencing (NGS) technology on Egyptian mummies. Seven NGS datasets obtained from five randomly selected Third Intermediate to Graeco-Roman Egyptian mummies (806 BC–124AD) and two unearthed pre-contact Bolivian lowland skeletons were generated and characterised. The datasets were contrasted to three recently published NGS datasets obtained from cold-climate regions, i.e. the Saqqaq, the Denisova hominid and the Alpine Iceman. Analysis was done using one million reads of each newly generated or published dataset. Blastn and megablast results were analysed using MEGAN software. Distinct NGS results were replicated by specific and sensitive polymerase chain reaction (PCR) protocols in ancient DNA dedicated laboratories. Here, we provide unambiguous identification of authentic DNA in Egyptian mummies. The NGS datasets showed variable contents of endogenous DNA harboured in tissues. Three of five mummies displayed a human DNA proportion comparable to the human read count of the Saqqaq permafrost-preserved specimen. Furthermore, a metagenomic signature unique to mummies was displayed. By applying a “bacterial fingerprint”, discrimination among mummies and other remains from warm areas outside Egypt was possible. Due to the absence of an adequate environment monitoring, a bacterial bloom was identified when analysing different biopsies from the same mummies taken after a lapse of time of 1.5 years. Plant kingdom representation in all mummy datasets was unique and could be partially associated with their use in embalming materials. Finally, NGS data showed the presence of Plasmodium falciparum and Toxoplasma gondii DNA sequences, indicating malaria and toxoplasmosis in these mummies. We demonstrate that endogenous ancient DNA can be extracted from mummies and serve as a proper template for the NGS technique, thus, opening new pathways of investigation for future genome sequencing of ancient Egyptian individuals.     

76株薄壳山核桃实生单株的果实品质差异及综合评价

对南京地区种植的76株薄壳山核桃〔Carya illinoinensis(Wangenh.)K.Koch〕实生单株的8项果实性状和种仁中5种脂肪酸含量的差异以及各指标的相关性进行分析,并筛选出单项性状优良的单株;在此基础上,结合主成分分析结果,对供试76株单株的果实品质进行综合评价.结果显示:8项果实性状(包括坚果质量、种仁鲜质量、坚果壳厚度、坚果纵径、坚果横径、果形指数、出仁率和含油率)以及种仁中5种脂肪酸(包括棕榈酸、硬脂酸、油酸、亚油酸和亚麻酸)的含量均有较大变异,变异系数为663%~2899%,其中,出仁率的变异系数最小,亚麻酸含量的变异系数最大,8项果实性状的变异系数总体上小于5种脂肪酸含量的变异系数.部分果实性状间极显著或显著正相关,少数果实性状间极显著或显著负相关,而5种脂肪酸含量间均极显著正相关,但脂肪酸含量与果实性状间总体上无显著相关性.主成分分析结果表明:在8项果实性状中,与坚果大小有关的性状较为重要;而5种脂肪酸含量均同等重要.对果实性状和脂肪酸含量的主成分分析结果显示:第1主成分的决定指标包括含油率以及棕榈酸、硬脂酸、油酸、亚油酸和亚麻酸的含量,第2主成分的决定指标包括坚果质量、种仁鲜质量、坚果壳厚度和坚果横径,说明薄壳山核桃果实评价的首要指标为种仁中脂肪酸含量,其次为果实大小.在利用坚果质量、种仁鲜质量、坚果壳厚度、出仁率、含油率、果形指数、油酸含量和不饱和脂肪酸含量8个单项指标优选单株的基础上,结合主成分分析结果,71号单株的综合得分较高,其种仁鲜质量、含油率以及油酸和不饱和脂肪酸的含量均较高,可作为优良品种选育的首选候选单株.根据上述研究结果,建议在薄壳山核桃不同育种目标的优良品种选育工作中,将主成分分析法作为单项性状筛选法的有效补充方法.     

低温贮存对椰心叶甲啮小蜂品质的影响

研究低温贮存椰心叶甲蛹Brontispa longissima(Gestro)和椰心叶甲僵蛹对椰心叶甲啮小蜂Tetrastichus brontispae Ferriere种群品质的影响。寄生10℃低温贮存1~4日龄椰心叶甲蛹结果表明,1日龄椰心叶甲蛹的寄生率、羽化率、出蜂率、单蛹出蜂数、后代寄生能力均优于其他日龄,其次为2、3日龄的椰心叶甲蛹,最差为4日龄的椰心叶甲蛹。1日龄椰心叶甲蛹在10℃下贮存5,10,15,20d后,上述生物学指标和种群参数均随贮存天数增加而降低,其中以5d和10d的净生殖率、内禀增长率和周限增长率较未经低温贮存的差异小。1~11日龄椰心叶甲僵蛹于10℃贮存10d的结果表明,8日龄椰心叶甲僵蛹的雌蜂寿命、羽化率、单蛹出蜂数、寄生能力均优于其他日龄僵蛹。8日龄椰心叶甲僵蛹在10℃下贮存5,10,15,20d后,上述生物学指标和种群参数均随贮存天数增加而显著低于对照。     

Conversion of oleic acid to 10-hydroxystearic acid by two species of ruminal bacteria

Bacteria able to convert oleic acid to 10-hydroxystearic acid were isolated from the ovine rumen. The solid hydroxy fatty acid produced from bacterial fermentations containing oleic acid was recovered by filtration, extraction into ether and crystallisation. The identity of the product was confirmed by HPLC and gas chromatography/mass spectrometry. One 10-hydroxystearic-acid-producing bacterial group was represented by two strains of an anaerobic gram-negative curved rod with tufts of flagella on the concave surface of the cell. The morphology and other characteristics enabled the strains to be tentatively identified as Selenomonas ruminantium. Another bacterium capable of the same transformation, represented by two strains of a facultatively anaerobic gram positive chain-forming coccus, was identified as Enterococcus faecalis. Since unsaturated fatty acids entering the rumen are normally hydrogenated, hydration of oleic acid represents an alternative fate of unknown significance in vivo.     

Effect of Fatty Acids on the Membrane Potential of an Alkaliphilic <Emphasis Type="Italic">Bacillus</Emphasis>

Effect of various fatty acids on the membrane potential of an alkaliphilic Bacillus, YN-2000, was examined. Addition of unsaturated fatty acids such as palmitoleic acid, oleic acid, linoleic acid, and linolenic acid at 30 M caused the instantaneous depolarization of the membrane potential of the bacterium, which appears to result in the drastic decrease of viability. On the other hand, no depolarization was detected by the addition of saturated acids such as palmitic acid, stearic acid, and 12-hydroxystearic acid even at 1 mM.     

The Ancient Chemistry of Avoiding Risks of Predation and Disease

Illness, death, and costs of immunity and injury strongly select for avoidance of predators or contagion. Ants, cockroaches, and collembola recognize their dead using unsaturated fatty acids (e.g., oleic or linoleic acid) as “necromone” cues. Ants, bees, and termites remove dead from their nests (necrophoric behavior) whereas semi-social species seal off corpses or simply avoid their dead or injured (necrophobic behavior). Alarm and avoidance responses to exudates from injured conspecifics are widespread. This involves diverse pheromones, complex chemistry and learning. We hypothesized that necromones are a phylogenetically ancient class of related signals and predicted that terrestrial Isopoda (that strongly aggregate and lack known dispersants) would avoid body fluids and corpses using fatty acid “necromones.” Isopods were repelled by crushed conspecifics (blood), intact corpses, and alcohol extracts of bodies. As predicted, the repellent fraction contained oleic and linoleic acids and authentic standards repelled several isopod species. We further predicted a priori that social caterpillars (lacking known dispersants) would be repelled by their own body fluids and unsaturated fatty acids. Both tent caterpillars and fall webworms avoided branches treated with conspecific body fluid. Oleic and linoleic acids were also strongly avoided by both species. Necromone signaling appears widespread and likely traces to aquatic ancestors pre-dating the divergence of the Crustacea and Hexapoda at least 420 million years ago.     

Der Mann aus dem Eis

New scientific findings on the Iceman The Iceman, commonly referred to as Ötzi, is the world's oldest glacier mummy and one of the best studied ancient humans in the world. Since the discovery of the 5300-year-old Copper Age individual in 1991, at the Tisenjoch in the Eastern Italian Alps, a variety of morphological, radiological, and molecular analyses have been applied that revealed important insights into his ancestry, his life habits and the circumstances surrounding his violent death. In more recent research, the mummy was subjected to modern research methodologies focusing on high-throughput sequence analysis of ancient biomolecules (DNA, proteins, lipids) that are still found to be preserved in his mummified tissues. Thereby, a genetic predisposition for increased risk for coronary heart disease and the stomach pathogen Helicobacter pylori were detected. This application of innovative “-omics” technologies have allowed the reconstruction of his last meal, that was mainly composed of fat and game meat from wild animals supplemented with cereals from einkorn.     

Kefir Grains Change Fatty Acid Profile of Milk during Fermentation and Storage

Several studies have reported that lactic acid bacteria may increase the production of free fatty acids by lipolysis of milk fat, though no studies have been found in the literature showing the effect of kefir grains on the composition of fatty acids in milk. In this study the influence of kefir grains from different origins [Rio de Janeiro (AR), Viçosa (AV) e Lavras (AD)], different time of storage, and different fat content on the fatty acid content of cow milk after fermentation was investigated. Fatty acid composition was determined by gas chromatography. Values were considered significantly different when p<0.05. The highest palmitic acid content, which is antimutagenic compost, was seen in AV grain (36.6g/100g fatty acids), which may have contributed to increasing the antimutagenic potential in fermented milk. Higher monounsaturated fatty acid (25.8g/100g fatty acids) and lower saturated fatty acid (72.7g/100g fatty acids) contents were observed in AV, when compared to other grains, due to higher Δ9-desaturase activity (0.31) that improves the nutritional quality of lipids. Higher oleic acid (25.0g/100g fatty acids) and monounsaturated fatty acid (28.2g/100g fatty acids) and lower saturated fatty acid (67.2g/100g fatty acids) contents were found in stored kefir relatively to fermented kefir leading to possible increase of antimutagenic and anticarcinogenic potential and improvement of nutritional quality of lipids in storage milk. Only high-lipidic matrix displayed increase polyunsaturated fatty acids after fermentation. These findings open up new areas of study related to optimizing desaturase activity during fermentation in order to obtaining a fermented product with higher nutritional lipid quality.     

The omnivorous Tyrolean Iceman: colon contents (meat, cereals, pollen, moss and whipworm) and stable isotope analyses

The contents of the colon of the Tyrolean Iceman who lived ca. 5300 years ago include muscle fibres, cereal remains, a diversity of pollen, and most notably that of the hop hornbeam (Ostrya carpinifolia) retaining cellular contents, as well as a moss leaf (Neckera complanata) and eggs of the parasitic whipworm (Trichuris trichiura). Based almost solely on stable isotope analyses and ignoring the work on the colon contents, two recently published papers on the Iceman's diet draw ill-founded conclusions about vegetarianism and even veganism. Neither the pollen nor the moss is likely to have been deliberately consumed as food by the Iceman. All the available evidence concerning the Iceman's broad-based diet is reviewed and the significance of the colon contents for matters other than assessment of food intake is outlined.     

Lipids of microorganisms from the family Vibrionaceae causing diseases in fishes]

Lipid fractional and fatty acid compositions of microorganisms from the genera Aeromonas, Pseudomonas, and Vibrio (the family Vibrionaceae), causing diseases of different fish species, were studied. Motile aeromonads and vibrios displayed higher relative contents of membrane lipids and oleic acid and lower relative contents of storage lipids compared with immotile aeromonads and pseudomonads, which is connected with the activities of their movements. Immotile aeromonads and vibrios exhibited higher levels of polyunsaturated fatty acids and higher absolute phospholipid contents compared to motile aeromonads and pseudomonads. This is likely to be related to host specificity of these bacteria and reflects the specific patterns of fatty acid compositions of the infected fish (salmonid and cyprinid) tissues.