Whole-genome shotgun sequencing of mitochondria from ancient hair shafts

Although the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized the study of ancient DNA, it has been plagued by large fractions of contaminating environmental DNA. The genetic analyses of hair shafts could be a solution: We present 10 previously unexamined Siberian mammoth (Mammuthus primigenius) mitochondrial genomes, sequenced with up to 48-fold coverage. The observed levels of damage-derived sequencing errors were lower than those observed in previously published frozen bone samples, even though one of the specimens was >50,000 14C years old and another had been stored for 200 years at room temperature. The method therefore sets the stage for molecular-genetic analysis of museum collections.     

Kepler-16: a transiting circumbinary planet

We report the detection of a planet whose orbit surrounds a pair of low-mass stars. Data from the Kepler spacecraft reveal transits of the planet across both stars, in addition to the mutual eclipses of the stars, giving precise constraints on the absolute dimensions of all three bodies. The planet is comparable to Saturn in mass and size and is on a nearly circular 229-day orbit around its two parent stars. The eclipsing stars are 20 and 69% as massive as the Sun and have an eccentric 41-day orbit. The motions of all three bodies are confined to within 0.5° of a single plane, suggesting that the planet formed within a circumbinary disk.     

Rice-related greenhouse gases in Japan, variations in scale and time and significance for the Kyoto Protocol

The contribution of rice production to the three major greenhouse gases CO₂, CH₄ and N₂O in 1990, the base year of the Kyoto protocol is investigated for Japan. For the CO₂ assessment, we use a top-down life cycle approach, CH₄ is assessed using the Japanese GHG emission inventory and N₂O is assessed according to the ratio of rice area divided by the total area of agricultural soils. In total, 1.6% of greenhouse gas (GHG) emissions in 1990 originated from rice production. Next, we assess regional variations in nine rice-producing regions, based on the CO₂ data of 1990. General trends in rice production from 1960 to 2000 and data from the Japanese GHG emission inventory since 1990 are used to assess variations in time. The rice-related GHG emissions decreased to 1.05% of the total GHG emissions in 2001 and will be less than half the 1990 level in 2012, mainly due to the decrease in rice production. Contrary to the trend in GHG emissions of rice, overall GHG emissions increased as rice production fulfils important roles, in mitigating global warming and in adapting to changing climates. The protection of rice production is required to counter the increase of GHG emissions in transportation, waste and domestic sectors and to minimize problems related to landscape, water and natural hazard management.     

Evidence for Parachlamydia in bovine abortion

Bovine abortion of unknown infectious aetiology still remains a major economic problem. In this study, we focused on a new possible abortigenic agent called Parachlamydia acanthamoebae. Retrospective samples (n=235) taken from late-term abortions in cattle were investigated by real-time diagnostic PCR for Chlamydiaceae and Parachlamydia spp., respectively. Histological sections of cases positive by real-time PCR for any Chlamydia-related agent were further examined by immunohistochemistry using specific antibodies. Chlamydophila abortus was detected only in three cases (1.3%) by real-time PCR and ArrayTube Microarray playing a less important role in bovine abortion compared to the situation in small ruminants in Switzerland. By real-time PCR as many as 43 of 235 (18.3%) cases turned out to be positive for Parachlamydia. The presence of Parachlamydia within placental lesions was confirmed in 35 cases (81.4%) by immunohistochemistry. The main histopathological feature in parachlamydial abortion was purulent to necrotizing placentitis (25/43). Parachlamydia should be considered as a new abortigenic agent in Swiss cattle. Since Parachlamydia may be involved in lower respiratory tract infections in humans, bovine abortion material should be handled with care given the possible zoonotic risk.     

Mechanisms of Infertility Associated with Clinical and Subclinical Endometritis in High Producing Dairy Cattle

Clinical and subclinical endometritis are common causes of infertility and subfertility in high producing dairy cattle, delaying the onset of ovarian cyclic activity after parturition, extending luteal phases and reducing conception rates. Escherichia coli and Arcanobacterium pyogenes cause endometrial damage and inflammation. Components of microbes, such as lipopolysaccharide (LPS), are detected by Toll-like receptors on endometrial cells, leading to secretion of cytokines, chemokines and antimicrobial peptides. Long luteal phases associated with endometritis are probably caused by a switch in endometrial prostaglandin production from prostaglandin F_2a (PGF) to prostaglandin E₂. In addition, LPS impairs the function of the hypothalamus and pituitary, and directly perturbs ovarian granulosa cells steroidogenesis, providing mechanisms to explain the association between uterine disease and anovulatory anoestrus. Cows with uterine disease that ovulate have lower peripheral plasma progesterone concentrations that may further reduce the chance of conception associated with endometritis.     

Trickle irrigation: Predominant bacteria in treated Colorado River water and biologically clogged emitters

Summary Bacterial numbers and predominant bacterial types were determined in trickle irrigation systems receiving treated Colorado River water. Fourteen bacterial genera were isolated and identified from 86 water and sediment samples collected from trickle emitter systems receiving six water treatments. The bacteria identified were common aquatic and soil microbes and the genera in order of prevalence were Pseudomonas, Flavobacterium, Vibrio, Brevibacterium, Micrococcus, and Bacillus. A greater diversity of bacterial types was found in water that was sand filtered and received no chemical treatment. Regardless of the water treatment, Pseudomonas stutzeri was the predominant bacterium followed by Flavobacterium lutescens. The data indicated that pigmented bacteria, F. lutescens and ytophaga hutchinsonii caused the yellow color of the slime deposits in biologically clogged emitters; and, their growth was presumably supported by P. stutzeri., a nonpigmented bacterium. The occurrence of Bacillus sp. was enhanced by sand and screen filtration and markedly reduced by chemical conditioning the water with either chlorine and acid or acid alone. No strictly anaerobic bacteria, such as Clostridium sp., were detected in water treated with chlorine and acid. Iron bacteria, Sphaerotilus spp., were not detected in any water or sediment samples from trickle irrigation systems.Contribution from the U.S. Department of Agriculture, Science and Education Administration, Agricultural Research     

Genetic relationships between efficiency traits and gut microbiota traits in growing pigs being fed with a conventional or a high-fiber diet

In pigs, the gut microbiota composition plays a major role in the process of digestion, but is influenced by many external factors, especially diet. To be used in breeding applications, genotype by diet interactions on microbiota composition have to be quantified, as well as their impact on genetic covariances with feed efficiency (FE) and digestive efficiency (DE) traits. This study aimed at determining the impact of an alternative diet on variance components of microbiota traits (genera and alpha diversity indices) and estimating genetic correlations between microbiota and efficiency traits for pigs fed a conventional (CO) or a high-fiber (HF) diet. Fecal microbes of 812 full-siblings fed a CO diet and 752 pigs fed the HF diet were characterized at 16 weeks of age by sequencing the V3-V4 region of the 16S rRNA gene. A total of 231 genera were identified. Digestibility coefficients of nitrogen, organic matter, and energy were predicted analyzing the same fecal samples with near infrared spectrometry. Daily feed intake, feed conversion ratio, residual feed intake and average daily gain (ADG) were also recorded. The 71 genera present in more than 20% of individuals were retained for genetic analyses. Heritability (h²) of microbiota traits were similar between diets (from null to 0.38 ± 0.12 in the CO diet and to 0.39 ± 0.12 in the HF diet). Only three out of the 24 genera and two alpha diversity indices with significant h² in both diets had genetic correlations across diets significantly different from 0.99 (P < 0.05), indicating limited genetic by diet interactions for these traits. When both diets were analyzed jointly, 59 genera had h² significantly different from zero. Based on the genetic correlations between these genera and ADG, FE, and DE traits, three groups of genera could be identified. A group of 29 genera had abundances favorably correlated with DE and FE traits, 14 genera were unfavorably correlated with DE traits, and the last group of 16 genera had abundances with correlations close to zero with production traits. However, genera abundances favorably correlated with DE and FE traits were unfavorably correlated with ADG, and vice versa. Alpha diversity indices had correlation patterns similar to the first group. In the end, genetic by diet interactions on gut microbiota composition of growing pigs were limited in this study. Based on this study, microbiota-based traits could be used as proxies to improve FE and DE in growing pigs.