A universal trend of amino acid gain and loss in protein evolution

Amino acid composition of proteins varies substantially between taxa and, thus, can evolve. For example, proteins from organisms with (G + C)-rich (or (A + T)-rich) genomes contain more (or fewer) amino acids encoded by (G + C)-rich codons. However, no universal trends in ongoing changes of amino acid frequencies have been reported. We compared sets of orthologous proteins encoded by triplets of closely related genomes from 15 taxa representing all three domains of life (Bacteria, Archaea and Eukaryota), and used phylogenies to polarize amino acid substitutions. Cys, Met, His, Ser and Phe accrue in at least 14 taxa, whereas Pro, Ala, Glu and Gly are consistently lost. The same nine amino acids are currently accrued or lost in human proteins, as shown by analysis of non-synonymous single-nucleotide polymorphisms. All amino acids with declining frequencies are thought to be among the first incorporated into the genetic code; conversely, all amino acids with increasing frequencies, except Ser, were probably recruited late. Thus, expansion of initially under-represented amino acids, which began over 3,400 million years ago, apparently continues to this day.     

Structure and mobility of electron gain and loss centres in proteins

Radiation damage to proteins is a topic of intense interest to those involved in radiation effects in biology, and also to those involved in radiotherapy. Although it has been widely studied, fundamental processes in protein damage are very hard to specify because of the complexity of the final damage products. But the non-invasive technique of electron-spin resonance is ideally suited to the task of detecting and identifying the primary and secondary products as these are expected to contains unpaired electrons (that is, free-radicals) and such species are uniquely detected by this sensitive form of spectroscopy. Our present study shows that a major radical species formed by electron loss in a range of proteins is the backbone amido radical, -N.(CO)-, characterized by hyperfine coupling to one 14N nucleus. These centres are efficiently trapped in proteins at low temperatures. In contrast, the expected backbone electron-capture centres, -NH(CO.-)-, are not readily trapped and electron transfer occurs until the ejected electron is trapped by some electrophilic centre. Such electron mobility was in fact established in our previous work on oxyhaemoglobin (FeO2----FeO2-), superoxide dismutase (Cu(II)----Cu(I] haemocyanin (Cu(II)O2Cu(I)----Cu(I)O2Cu(II] and various proteins containing S-S bonds (-S-S-)----(-S.-S-) (refs 1-4 respectively). This is strongly supported by our observation that such electrons are captured by DNA molecules, giving T.- centres, when nucleohistones are irradiated, and that Fe(CN)3-(6) ions readily scavenge such electrons from proteins which are devoid of highly electrophilic centres.     

Coastal wetland in South China:Degradation trends,causes and protection countermeasures

There are abundant coastal wetlands in South China and their main characters are the tidal flats, mangroves and coral reefs. In this paper, the status quo of coastal wetlands in South China is introduced and their degradation trends in the last decades are analyzed based on the existing literatures and information. Their degradation trends are characterized by reduction of coastal wetlands’ area, pollution of seawater environment, degeneration of ecological environment, sharp decrease of biodiversity in the wetlands and so on. At the same time, the causes resulting in the above-mentioned degradations are discussed, mainly concluding imperfect systems of management and legislation, deficient property and assessment systems of the wetlands, weak consciousness of protecting coastal wetlands, shortage of basic study and backward management level and so on. Some countermeasures are put forward for the sake of a sustainable use of the coastal wetlands of South China, mainly including establishing and perfecting administrative and legal systems for the coastal wetlands, developing the study on assessment of coastal wetland, heightening the consciousness of public participation, and strengthening scientific research and establishment of wetland nature reserves.     

Protein dispensability and rate of evolution.

If protein evolution is due in large part to slightly deleterious amino acid substitutions, then the rate of evolution should be greater in proteins that contribute less to individual fitness. The rationale for this prediction is that relatively dispensable proteins should be subject to weaker purifying selection, and should therefore accumulate mildly deleterious substitutions more rapidly. Although this argument was presented over twenty years ago, and is fundamental to many applications of evolutionary theory, the prediction has proved difficult to confirm. In fact, a recent study showed that essential mouse genes do not evolve more slowly than non-essential ones. Thus, although a variety of factors influencing the rate of protein evolution have been supported by extensive sequence analysis, the relationship between protein dispensability and evolutionary rate has remained unconfirmed. Here we use the results from a highly parallel growth assay of single gene deletions in yeast to assess protein dispensability, which we relate to evolutionary rate estimates that are based on comparisons of sequences drawn from twenty-one fully annotated genomes. Our analysis reveals a highly significant relationship between protein dispensability and evolutionary rate, and explains why this relationship is not detectable by categorical comparison of essential versus non-essential proteins. The relationship is highly conserved, so that protein dispensability in yeast is also predictive of evolutionary rate in a nematode worm.     

Chemical and biological trends during lake evolution in recently deglaciated terrain

As newly formed landscapes evolve, physical and biological changes occur that are collectively known as primary succession. Although succession is a fundamental concept in ecology, it is poorly understood in the context of aquatic environments. The prevailing view is that lakes become more enriched in nutrients as they age, leading to increased biological production. Here we report the opposite pattern of lake development, observed from the water chemistry of lakes that formed at various times within the past 10,000 years during glacial retreat at Glacier Bay, Alaska. The lakes have grown more dilute and acidic with time, accumulated dissolved organic carbon and undergone a transient rise in nitrogen concentration, all as a result of successional changes in surrounding vegetation and soils. Similar trends are evident from fossil diatom stratigraphy of lake sediment cores. These results demonstrate a tight hydrologic coupling between terrestrial and aquatic environments during the colonization of newly deglaciated landscapes, and provide a conceptual basis for mechanisms of primary succession in boreal lake ecosystems.     

浅析青海省水土流失的成因及防护措施

阐述了造成青海省水土流失有气候干旱、植被稀疏、降雨集中等自然因素,也有土地利用不合理,过度开荒、过度放牧、过度采伐等人为因素。提出防治水土流失要全面规划,因地制宜,工程措施、生物措施并重,并且要依法加强管理,强化预防和监督。     

Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast

Under laboratory conditions 80% of yeast genes seem not to be essential for viability. This raises the question of what the mechanistic basis for dispensability is, and whether it is the result of selection for buffering or an incidental side product. Here we analyse these issues using an in silico flux model of the yeast metabolic network. The model correctly predicts the knockout fitness effects in 88% of the genes studied and in vivo fluxes. Dispensable genes might be important, but under conditions not yet examined in the laboratory. Our model indicates that this is the dominant explanation for apparent dispensability, accounting for 37-68% of dispensable genes, whereas 15-28% of them are compensated by a duplicate, and only 4-17% are buffered by metabolic network flux reorganization. For over one-half of those not important under nutrient-rich conditions, we can predict conditions when they will be important. As expected, such condition-specific genes have a more restricted phylogenetic distribution. Gene duplicates catalysing the same reaction are not more common for indispensable reactions, suggesting that the reason for their retention is not to provide compensation. Instead their presence is better explained by selection for high enzymatic flux.     

Analysis of variation trends and causes of aerosol optical depth in Shaanxi Province using MODIS data

The temporal and spatial variations and causes of aerosol optical depth （AOD） in Shaanxi Province were investigated based on the Moderate Resolution Imaging Spectroradiometer （MODIS） derived aerosol data for the period of March 2000-February 2012. The results showed that the distribution of aerosol was largely affected by topography and local economic activities. Heavy aero- sol loading and increasing tendency in AOD was observed in Guanzhong, Hanzhong and Ankang basin, while a reverse tendency was revealed in most other regions. The spatial distribution of aerosol Angstrom wavelength exponent was predominantly related to vegetation coverage in Shaanxi. Airborne dust from ground is an important source of coarse mode aerosols. Vegetation im- provement indicated by an increase in normalized difference vegetation index （NDVI） and a reduction in dust weather led to a gradual decrease in coarse mode AOD to the north of Qinling Mountains in Shaanxi, while anthropogenic activities led to an in- crease in fine mode AOD in other areas except those covered by forests. The main aerosol type gradually shifted to the urban industrial type in Shaanxi.     

Human-specific loss of regulatory DNA and the evolution of human-specific traits

Humans differ from other animals in many aspects of anatomy, physiology, and behaviour; however, the genotypic basis of most human-specific traits remains unknown. Recent whole-genome comparisons have made it possible to identify genes with elevated rates of amino acid change or divergent expression in humans, and non-coding sequences with accelerated base pair changes. Regulatory alterations may be particularly likely to produce phenotypic effects while preserving viability, and are known to underlie interesting evolutionary differences in other species. Here we identify molecular events particularly likely to produce significant regulatory changes in humans: complete deletion of sequences otherwise highly conserved between chimpanzees and other mammals. We confirm 510 such deletions in humans, which fall almost exclusively in non-coding regions and are enriched near genes involved in steroid hormone signalling and neural function. One deletion removes a sensory vibrissae and penile spine enhancer from the human androgen receptor (AR) gene, a molecular change correlated with anatomical loss of androgen-dependent sensory vibrissae and penile spines in the human lineage. Another deletion removes a forebrain subventricular zone enhancer near the tumour suppressor gene growth arrest and DNA-damage-inducible, gamma (GADD45G), a loss correlated with expansion of specific brain regions in humans. Deletions of tissue-specific enhancers may thus accompany both loss and gain traits in the human lineage, and provide specific examples of the kinds of regulatory alterations and inactivation events long proposed to have an important role in human evolutionary divergence.     

Maturation trends indicative of rapid evolution preceded the collapse of northern cod

Northern cod, comprising populations of Atlantic cod (Gadus morhua) off southern Labrador and eastern Newfoundland, supported major fisheries for hundreds of years. But in the late 1980s and early 1990s, northern cod underwent one of the worst collapses in the history of fisheries. The Canadian government closed the directed fishing for northern cod in July 1992, but even after a decade-long offshore moratorium, population sizes remain historically low. Here we show that, up until the moratorium, the life history of northern cod continually shifted towards maturation at earlier ages and smaller sizes. Because confounding effects of mortality changes and growth-mediated phenotypic plasticity are accounted for in our analyses, this finding strongly suggests fisheries-induced evolution of maturation patterns in the direction predicted by theory. We propose that fisheries managers could use the method described here as a tool to provide warning signals about changes in life history before more overt evidence of population decline becomes manifest.     

Paternal cyclophosphamide treatment of rats causes fetal loss and malformations without affecting male fertility

The use of cytotoxic, mutagenic and carcinogenic agents as treatment for various types of cancer may be particularly hazardous in men of reproductive age as there exists the possibility that this may lead to congenital malformations in the progeny. Such agents can affect fertility and other aspects of male reproductive function, for example, treatment with anti-cancer drugs such as cyclophosphamide has been associated with oligozoospermia, azoospermia and increased levels of serum follicle-stimulating hormone (FSH). Depending on the cumulative dose and the duration of treatment, spermatogenesis often returns but this may take years. The relevance of the effects of such chemicals on the male reproductive system to the offspring is poorly understood. We have set out to determine whether present tests of male reproductive function (that is, endocrine status, numbers of spermatozoa, fertility) can predict deleterious effects of a paternally administered agent on the offspring. Here, we report that chronic administration in rats of low doses of the widely used drug cyclophosphamide had minimal effects on the male reproductive system and fertility, but resulted in malformations and retardation of growth in the surviving fetuses and a high frequency of fetal death. Thus, adverse effects on the fetus cannot be predicted from the effects of a drug on the male reproductive system.     

The Ter mutation in the dead end gene causes germ cell loss and testicular germ cell tumours

In mice, the Ter mutation causes primordial germ cell (PGC) loss in all genetic backgrounds. Ter is also a potent modifier of spontaneous testicular germ cell tumour (TGCT) susceptibility in the 129 family of inbred strains, and markedly increases TGCT incidence in 129-Ter/Ter males. In 129-Ter/Ter mice, some of the remaining PGCs transform into undifferentiated pluripotent embryonal carcinoma cells, and after birth differentiate into various cells and tissues that compose TGCTs. Here, we report the positional cloning of Ter, revealing a point mutation that introduces a termination codon in the mouse orthologue (Dnd1) of the zebrafish dead end (dnd) gene. PGC deficiency is corrected both with bacterial artificial chromosomes that contain Dnd1 and with a Dnd1-encoding transgene. Dnd1 is expressed in fetal gonads during the critical period when TGCTs originate. DND1 has an RNA recognition motif and is most similar to the apobec complementation factor, a component of the cytidine to uridine RNA-editing complex. These results suggest that Ter may adversely affect essential aspects of RNA biology during PGC development. DND1 is the first protein known to have an RNA recognition motif directly implicated as a heritable cause of spontaneous tumorigenesis. TGCT development in the 129-Ter mouse strain models paediatric TGCT in humans. This work will have important implications for our understanding of the genetic control of TGCT pathogenesis and PGC biology.     

MIMO系统中空间分集增益与复用增益的权衡分析

MIMO系统由于在收发两端采用多天线,可以获得复用增益和分集增益,克服了无线信道的衰落,并提高了数据传输效率.然而,如何去权衡这两者之间的关系,是研究的重点.从简单的MIMO系统模型入手,在确定衡量其系统性能标准的基础上,研究2×2MIMO系统的3种发送策略,并对比分析其分集增益及复用增益,为MIMO系统在不同信道条件下如何权衡两者的关系提供一定的参考价值.     

Targeted disruption of mu chain membrane exon causes loss of heavy-chain allelic exclusion.

Burnet's clonal selection theory suggests that each B lymphocyte is committed to a single antibody specificity. This is achieved by a programme of somatic rearrangements of the gene segments encoding antibody variable (V) regions, in the course of B-cell development. Evidence from immunoglobulin-transgenic mice and immunoglobulin-gene-transfected transformed pre-B cells suggest that the membrane form of the immunoglobulin heavy (H) chain of class mu (microns), expressed from a rearranged H-chain (IgH) locus, may signal allelic exclusion of the homologous IgH locus in the cell and initiation of light (L)-chain gene rearrangement in the Ig kappa loci. We report here that targeted disruption of the membrane exon of the mu chain indeed results in the loss of H-chain allelic exclusion. But, some kappa chain gene rearrangement is still observed in the absence of micron expression.