Reconsideration of the phylogenetic positions of three stichotrichous genera Holosticha, Anteholosticha and Pseudokeronopsis （Spirotrichea： Ciliophora） inferred from complete SSU rRNA gene sequences

The small subunit rRNA (SSU rRNA) gene for six marine stichotrichs, Pseudokeronopsis carnea, P. flava, Holosticha heterofoissneri, H. diademata, H. bradburyae and Anteholosticha manca, was sequenced and characterized. Using this molecular information, the phylogenetic positions of three related genera, Pseudokeronopsis, Holosticha and Anteholosticha were determined. The results indicate that the family Urostylidae is clearly separated from the family Pseudokeronopsidae. The present phylogenetic analyses unambiguously placed Pseudokeronopsis close to Holosticha, and support the conclusion that these genera should be regarded as the members of the order Urostylidae within the stichotrich clade. Furthermore, the results of this study also support the monophyly of the genus Pseudokeronopsis,the redefinition of Holosticha s. str. and the placement of Anteholosticha in a clade separate from Holosticha.     

The draft genome of the parasitic nematode Trichinella spiralis

Genome evolution studies for the phylum Nematoda have been limited by focusing on comparisons involving Caenorhabditis elegans. We report a draft genome sequence of Trichinella spiralis, a food-borne zoonotic parasite, which is the most common cause of human trichinellosis. This parasitic nematode is an extant member of a clade that diverged early in the evolution of the phylum, enabling identification of archetypical genes and molecular signatures exclusive to nematodes. We sequenced the 64-Mb nuclear genome, which is estimated to contain 15,808 protein-coding genes, at ～35-fold coverage using whole-genome shotgun and hierarchal map-assisted sequencing. Comparative genome analyses support intrachromosomal rearrangements across the phylum, disproportionate numbers of protein family deaths over births in parasitic compared to a non-parasitic nematode and a preponderance of gene-loss and -gain events in nematodes relative to Drosophila melanogaster. This genome sequence and the identified pan-phylum characteristics will contribute to genome evolution studies of Nematoda as well as strategies to combat global parasites of humans, food animals and crops.     

Rapid responses of British butterflies to opposing forces of climate and habitat change.

Habitat degradation and climate change are thought to be altering the distributions and abundances of animals and plants throughout the world, but their combined impacts have not been assessed for any species assemblage. Here we evaluated changes in the distribution sizes and abundances of 46 species of butterflies that approach their northern climatic range margins in Britain-where changes in climate and habitat are opposing forces. These insects might be expected to have responded positively to climate warming over the past 30 years, yet three-quarters of them declined: negative responses to habitat loss have outweighed positive responses to climate warming. Half of the species that were mobile and habitat generalists increased their distribution sites over this period (consistent with a climate explanation), whereas the other generalists and 89% of the habitat specialists declined in distribution size (consistent with habitat limitation). Changes in population abundances closely matched changes in distributions. The dual forces of habitat modification and climate change are likely to cause specialists to decline, leaving biological communities with reduced numbers of species and dominated by mobile and widespread habitat generalists.     

中国、澳大利亚小麦、蔬菜以及棉花根部土传病害生物防治研究进展

土传病害是作物产量的经常性限制因素。在禾谷类生产中,某些病害在少耕制度下异常严重。因此,有利于保护土壤侵蚀的管理措施(例如减少耕作、保留农作物残体等)能导致病害发生更为严重,从而造成作物减产,这要求研究新的病害防治措施,而不能依靠农业耕作措施或轮作进行防治。生物防治是病害防治措施的一种,在中国和澳大利亚都已进行了研究。蔬菜和棉花的苗期病害一般是利用化学杀菌剂进行防治,或者病害严重发生导致毁种后重新播种。在这些病害防治方面,人们探索了生物防治措施,旨在发展安全、无残留的防治方法,本文介绍的合作研究,主要是在田间和盆栽条件下筛选、评价一系列澳大利亚和中国的土壤细菌和真菌在中国和澳大利亚东南部对土传病害的防治作用,从而建立有效可靠的作物病害生物防治方法。在两国进行的实验研究中,对象作物为小麦、蔬菜(番茄、黄瓜和辣椒)以及棉花。另外,还对枯草芽孢杆菌的作用机理以及重要植物病原菌如腐霉菌的生态学进行了研究。     

Gray fox and coyote abundance and diet responses after a wildfire in central Arizona

There is a paucity of information on the effects of wildfire on carnivores. We studied the effects of a 237-km 2 catastrophic wildfire in the Mazatzal Mountains, Arizona, on gray foxes ( Urocyon cinereoargenteus ) and coyotes ( Canis latrans ). We indexed relative abundance 3 times each year from 1996 to1998 using scat transects in burned and unburned areas. We collected scats to estimate diet and measured small mammal abundance and mast availability in 1997 and 1998. We also measured vegetation cover in burned and unburned sites. Gray fox indices declined 3 months postfire, but after 30 months, indices returned to preburn levels. Coyote indices did not change. Primary foods for both species in burned and unburned sites were mast (fruits of shrubs) and rodents, and diet comparisons between sites became similar as plant succession continued. Scat indices did not correlate with seasonal small mammal abundance. We suspect that the lower abundance indices of gray foxes were related to reduction in cover and food availability, because indices increased as vertical cover and mast crop increased. These data indicate that the effects of this catastrophic fire were short-term but also highlight the importance of preserving shrub and vegetation diversity for gray fox.     

Some physiological variations of Agropyron smithii Rydb. (western wheatgrass) at different salinitylevels

The purpose of this study was to determine the physiological responses of Agropyron smithii Rydb. To various saline environments as evaluated in the laboratory. Agropyron smithii Rydb. (Rosana) seeds were germinated, transplanted into nutrient solutions with NaCl concentrations of 0, 50, 100, 150, and 200 m M , and grown for 80 days in a growth chamber. Results indicated that leaf water potential, relative water content of leaf tissue, and concentrations of Na, K, and Cl in plant tissue were significantly affected by increasing NaCl concentration. However, leaf chlorophyll concentration and concentrations of Ca and Mg in plant tissue were not significantly affected by the presence of NaCl.     

Bole volume growth in stems of Quercus gambelii

Shrub-form and tree-form Gambel oak ( Quercus gambelii ) stands contain a potentially significant fuelwood resource. Information on their growth characteristics can form a basis for future stand management. Stem analyses showed that height growth of shrub-form stems essentially ceased after age 50, while tree-form stems continued to increase in height until approximately age 100. Both stem forms continued to increase in basal area and volume at a relatively constant rate as the stems increased in age and size. Increases in all size measures were substantially greater in tree-form stems than in shrub-form stems. Mean bole volume for tree-form stems at age 100 was over 16 times that of shrub-form stems. Sprouts from tree-form stands would reach minimum size for fuelwood marketing in approximately 45 years.     

Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes

The human X and Y chromosomes evolved from an ordinary pair of autosomes during the past 200-300 million years. The human MSY (male-specific region of Y chromosome) retains only three percent of the ancestral autosomes' genes owing to genetic decay. This evolutionary decay was driven by a series of five 'stratification' events. Each event suppressed X-Y crossing over within a chromosome segment or 'stratum', incorporated that segment into the MSY and subjected its genes to the erosive forces that attend the absence of crossing over. The last of these events occurred 30 million years ago, 5 million years before the human and Old World monkey lineages diverged. Although speculation abounds regarding ongoing decay and looming extinction of the human Y chromosome, remarkably little is known about how many MSY genes were lost in the human lineage in the 25 million years that have followed its separation from the Old World monkey lineage. To investigate this question, we sequenced the MSY of the rhesus macaque, an Old World monkey, and compared it to the human MSY. We discovered that during the last 25 million years MSY gene loss in the human lineage was limited to the youngest stratum (stratum 5), which comprises three percent of the human MSY. In the older strata, which collectively comprise the bulk of the human MSY, gene loss evidently ceased more than 25 million years ago. Likewise, the rhesus MSY has not lost any older genes (from strata 1-4) during the past 25 million years, despite its major structural differences to the human MSY. The rhesus MSY is simpler, with few amplified gene families or palindromes that might enable intrachromosomal recombination and repair. We present an empirical reconstruction of human MSY evolution in which each stratum transitioned from rapid, exponential loss of ancestral genes to strict conservation through purifying selection.     

Designer Dirac fermions and topological phases in molecular graphene

The observation of massless Dirac fermions in monolayer graphene has generated a new area of science and technology seeking to harness charge carriers that behave relativistically within solid-state materials. Both massless and massive Dirac fermions have been studied and proposed in a growing class of Dirac materials that includes bilayer graphene, surface states of topological insulators and iron-based high-temperature superconductors. Because the accessibility of this physics is predicated on the synthesis of new materials, the quest for Dirac quasi-particles has expanded to artificial systems such as lattices comprising ultracold atoms. Here we report the emergence of Dirac fermions in a fully tunable condensed-matter system-molecular graphene-assembled by atomic manipulation of carbon monoxide molecules over a conventional two-dimensional electron system at a copper surface. Using low-temperature scanning tunnelling microscopy and spectroscopy, we embed the symmetries underlying the two-dimensional Dirac equation into electron lattices, and then visualize and shape the resulting ground states. These experiments show the existence within the system of linearly dispersing, massless quasi-particles accompanied by a density of states characteristic of graphene. We then tune the quantum tunnelling between lattice sites locally to adjust the phase accrual of propagating electrons. Spatial texturing of lattice distortions produces atomically sharp p-n and p-n-p junction devices with two-dimensional control of Dirac fermion density and the power to endow Dirac particles with mass. Moreover, we apply scalar and vector potentials locally and globally to engender topologically distinct ground states and, ultimately, embedded gauge fields, wherein Dirac electrons react to 'pseudo' electric and magnetic fields present in their reference frame but absent from the laboratory frame. We demonstrate that Landau levels created by these gauge fields can be taken to the relativistic magnetic quantum limit, which has so far been inaccessible in natural graphene. Molecular graphene provides a versatile means of synthesizing exotic topological electronic phases in condensed matter using tailored nanostructures.     

Recent advances in the biosynthesis of modified tetrapyrroles: the discovery of an alternative pathway for the formation of heme and heme d 1

Hemes (a, b, c, and o) and heme d ₁ belong to the group of modified tetrapyrroles, which also includes chlorophylls, cobalamins, coenzyme F₄₃₀, and siroheme. These compounds are found throughout all domains of life and are involved in a variety of essential biological processes ranging from photosynthesis to methanogenesis. The biosynthesis of heme b has been well studied in many organisms, but in sulfate-reducing bacteria and archaea, the pathway has remained a mystery, as many of the enzymes involved in these characterized steps are absent. The heme pathway in most organisms proceeds from the cyclic precursor of all modified tetrapyrroles uroporphyrinogen III, to coproporphyrinogen III, which is followed by oxidation of the ring and finally iron insertion. Sulfate-reducing bacteria and some archaea lack the genetic information necessary to convert uroporphyrinogen III to heme along the “classical” route and instead use an “alternative” pathway. Biosynthesis of the isobacteriochlorin heme d ₁, a cofactor of the dissimilatory nitrite reductase cytochrome cd ₁, has also been a subject of much research, although the biosynthetic pathway and its intermediates have evaded discovery for quite some time. This review focuses on the recent advances in the understanding of these two pathways and their surprisingly close relationship via the unlikely intermediate siroheme, which is also a cofactor of sulfite and nitrite reductases in many organisms. The evolutionary questions raised by this discovery will also be discussed along with the potential regulation required by organisms with overlapping tetrapyrrole biosynthesis pathways.