A molecular basis for natural selection at the timeless locus in Drosophila melanogaster

Diapause is a protective response to unfavorable environments that results in a suspension of insect development and is most often associated with the onset of winter. The ls-tim mutation in the Drosophila melanogaster clock gene timeless has spread in Europe over the past 10,000 years, possibly because it enhances diapause. We show that the mutant allele attenuates the photosensitivity of the circadian clock and causes decreased dimerization of the mutant TIMELESS protein isoform to CRYPTOCHROME, the circadian photoreceptor. This interaction results in a more stable TIMELESS product. These findings reveal a molecular link between diapause and circadian photoreception.     

High frequency of horizontal gene transfer in the oceans

Oceanic bacteria perform many environmental functions, including biogeochemical cycling of many elements, metabolizing of greenhouse gases, functioning in oceanic food webs (microbial loop), and producing valuable natural products and viruses. We demonstrate that the widespread capability of marine bacteria to participate in horizontal gene transfer (HGT) in coastal and oceanic environments may be the result of gene transfer agents (GTAs), viral-like particles produced by α-Proteobacteria. We documented GTA-mediated gene transfer frequencies a thousand to a hundred million times higher than prior estimates of HGT in the oceans, with as high as 47% of the culturable natural microbial community confirmed as gene recipients. These findings suggest a plausible mechanism by which marine bacteria acquire novel traits, thus ensuring resilience in the face of environmental change.     

The origins of genome complexity

Complete genomic sequences from diverse phylogenetic lineages reveal notable increases in genome complexity from prokaryotes to multicellular eukaryotes. The changes include gradual increases in gene number, resulting from the retention of duplicate genes, and more abrupt increases in the abundance of spliceosomal introns and mobile genetic elements. We argue that many of these modifications emerged passively in response to the long-term population-size reductions that accompanied increases in organism size. According to this model, much of the restructuring of eukaryotic genomes was initiated by nonadaptive processes, and this in turn provided novel substrates for the secondary evolution of phenotypic complexity by natural selection. The enormous long-term effective population sizes of prokaryotes may impose a substantial barrier to the evolution of complex genomes and morphologies.     

家蚕生物钟基因Bmtim2的克隆与序列分析

[目的]为进一步研究家蚕生物钟基因的功能提供依据。[方法]从家蚕品种p50未受精卵提取总RNA,利用快速扩增cDNA末端(RACE)技术克隆家蚕生物钟基因Bmtim2cDNA序列。最后运用实时定量RT-PCR对该基因在家蚕不同发育时期的表达情况进行初步分析。[结果]利用RACE扩增,获得长度为1867bp、包括完整3'非翻译区的家蚕生物钟基因timeless2(Bmtim2)cDNA序列。经推导,获得该基因序列编码的584个氨基酸残基的蛋白质序列。该蛋白序列具有TIM蛋白的C末端保守区,与黑腹果蝇、尖音库蚊的TIM2基因具有近缘进化关系。Bmtim2基因在家蚕生活周期各时点均有表达。[结论]该结果对研究Bmtim2基因在家蚕发育过程的时空表达差异及其与日周节律的关系具有参考价值。     

Influence of gene action across different time scales on behavior

Genes can affect natural behavioral variation in different ways. Allelic variation causes alternative behavioral phenotypes, whereas changes in gene expression can influence the initiation of behavior at different ages. We show that the age-related transition by honey bees from hive work to foraging is associated with an increase in the expression of the foraging (for) gene, which encodes a guanosine 3',5'-monophosphate (cGMP)-dependent protein kinase (PKG). cGMP treatment elevated PKG activity and caused foraging behavior. Previous research showed that allelic differences in PKG expression result in two Drosophila foraging variants. The same gene can thus exert different types of influence on a behavior.     

Gene flow and population differentiation

There are many possible spatial patterns of selection and gene flow that can produce a given cline structure; the actual geography of natural selection and gene flow must be worked out before an attempt is made to explain a given natural cline in terms of a model. The results of experimental and theoretical models show that it is possible for local differentiation to evolve parapatrically in spite of considerable gene flow if the selection gradients are relatively uniform. Irregularities in environmental gradients increase the sensitivity of clines to the effects of gene flow in proportion to the increase in the differences in gene frequencies between the emigrants and the demes receiving the immigrants. It is not necessary for a sharp spatial environmental change to be present for distinct differentiation to occur. In some cases even a gentle environmental gradient can give rise to marked spatial differentiation along a genetically continuous series of demes; such environmental differences may be below the practical limits of resolution in field studies. Any asymmetry in gene flow does not lead to dedifferentiation if the environmental gradient is smooth; it merely shifts the position of the transition zone between the differentiated areas from that which would be expected if there were no asymmetry. Abrupt geographic differences in gene, genotype, or morph frequencies should not, therefore, be interpreted as evidence for environmental changes in the immediate vicinity of the steepest part of the cline; neither should they be interpreted as evidence for geographic barriers, sharp environmental differences, or sexual isolation among the differentiated groups of populations when there are no other sources of evidence for these phenomena. Gene flow may be unimportant in the differentiation of populations along environmental gradients.     

A gain-of-function polymorphism controlling complex traits and fitness in nature

Identification of the causal genes that control complex trait variation remains challenging, limiting our appreciation of the evolutionary processes that influence polymorphisms in nature. We cloned a quantitative trait locus that controls plant defensive chemistry, damage by insect herbivores, survival, and reproduction in the natural environments where this polymorphism evolved. These ecological effects are driven by duplications in the BCMA (branched-chain methionine allocation) loci controlling this variation and by two selectively favored amino acid changes in the glucosinolate-biosynthetic cytochrome P450 proteins that they encode. These changes cause a gain of novel enzyme function, modulated by allelic differences in catalytic rate and gene copy number. Ecological interactions in diverse environments likely contribute to the widespread polymorphism of this biochemical function.     

Gene flow and the geographic structure of natural populations

There is abundant geographic variation in both morphology and gene frequency in most species. The extent of geographic variation results from a balance of forces tending to produce local genetic differentiation and forces tending to produce genetic homogeneity. Mutation, genetic drift due to finite population size, and natural selection favoring adaptations to local environmental conditions will all lead to the genetic differentiation of local populations, and the movement of gametes, individuals, and even entire populations--collectively called gene flow--will oppose that differentiation. Gene flow may either constrain evolution by preventing adaptation to local conditions or promote evolution by spreading new genes and combinations of genes throughout a species' range. Several methods are available for estimating the amount of gene flow. Direct methods monitor ongoing gene flow, and indirect methods use spatial distributions of gene frequencies to infer past gene flow. Applications of these methods show that species differ widely in the gene flow that they experience. Of particular interest are those species for which direct methods indicate little current gene flow but indirect methods indicate much higher levels of gene flow in the recent past. Such species probably have undergone large-scale demographic changes relatively frequently.     

A circadian output in Drosophila mediated by neurofibromatosis-1 and Ras/MAPK

Output from the circadian clock controls rhythmic behavior through poorly understood mechanisms. In Drosophila, null mutations of the neurofibromatosis-1 (Nf1) gene produce abnormalities of circadian rhythms in locomotor activity. Mutant flies show normal oscillations of the clock genes period (per) and timeless (tim) and of their corresponding proteins, but altered oscillations and levels of a clock-controlled reporter. Mitogen-activated protein kinase (MAPK) activity is increased in Nf1 mutants, and the circadian phenotype is rescued by loss-of-function mutations in the Ras/MAPK pathway. Thus, Nf1 signals through Ras/MAPK in Drosophila. Immunohistochemical staining revealed a circadian oscillation of phospho-MAPK in the vicinity of nerve terminals containing pigment-dispersing factor (PDF), a secreted output from clock cells, suggesting a coupling of PDF to Ras/MAPK signaling.     

Genetic properties influencing the evolvability of gene expression

Identifying the properties of gene networks that influence their evolution is a fundamental research goal. However, modes of evolution cannot be inferred solely from the distribution of natural variation, because selection interacts with demography and mutation rates to shape polymorphism and divergence. We estimated the effects of naturally occurring mutations on gene expression while minimizing the effect of natural selection. We demonstrate that sensitivity of gene expression to mutations increases with both increasing trans-mutational target size and the presence of a TATA box. Genes with greater sensitivity to mutations are also more sensitive to systematic environmental perturbations and stochastic noise. These results provide a mechanistic basis for gene expression evolvability that can serve as a foundation for realistic models of regulatory evolution.     

现代小区植物景观设计——以南京“东恒—阳光嘉园”小区为例

从植物设计的科学性、艺术性、经济性、技术性及时间性对南京＂东恒—阳光嘉园＂小区的植物景观设计进行了分析,并对该小区在植物景观设计中所出现的问题及缺点提出了一些看法和建议。     

Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios

Even though human and chimpanzee gene sequences are nearly 99% identical, sequence comparisons can nevertheless be highly informative in identifying biologically important changes that have occurred since our ancestral lineages diverged. We analyzed alignments of 7645 chimpanzee gene sequences to their human and mouse orthologs. These three-species sequence alignments allowed us to identify genes undergoing natural selection along the human and chimp lineage by fitting models that include parameters specifying rates of synonymous and nonsynonymous nucleotide substitution. This evolutionary approach revealed an informative set of genes with significantly different patterns of substitution on the human lineage compared with the chimpanzee and mouse lineages. Partitions of genes into inferred biological classes identified accelerated evolution in several functional classes, including olfaction and nuclear transport. In addition to suggesting adaptive physiological differences between chimps and humans, human-accelerated genes are significantly more likely to underlie major known Mendelian disorders.     

A similarity between viral defense and gene silencing in plants

Gene silencing in plants, in which an endogenous gene is suppressed by introduction of a related transgene, has been used for crop improvement. Observations that viruses are potentially both initiators and targets of gene silencing suggested that this phenomenon may be related to natural defense against viruses. Supporting this idea, it was found that nepovirus infection of nontransgenic plants induces a resistance mechanism that is similar to transgene-induced gene silencing.     

miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay

microRNAs (miRNAs) regulate gene expression through translational repression and/or messenger RNA (mRNA) deadenylation and decay. Because translation, deadenylation, and decay are closely linked processes, it is important to establish their ordering and thus to define the molecular mechanism of silencing. We have investigated the kinetics of these events in miRNA-mediated gene silencing by using a Drosophila S2 cell-based controllable expression system and show that mRNAs with both natural and engineered 3' untranslated regions with miRNA target sites are first subject to translational inhibition, followed by effects on deadenylation and decay. We next used a natural translational elongation stall to show that miRNA-mediated silencing inhibits translation at an early step, potentially translation initiation.     

Regulation of keystone predation by small changes in ocean temperature

Key species interactions that are sensitive to temperature may act as leverage points through which small changes in climate could generate large changes in natural communities. Field and laboratory experiments showed that a slight decrease in water temperature dramatically reduced the effects of a keystone predator, the sea star Pisaster ochraceus, on its principal prey. Ongoing changes in patterns of cold water upwelling, associated with El Nino events and longer term geophysical changes, may thus have far-reaching impacts on the composition and diversity of these rocky intertidal communities.     

Experience strengthening transmission by driving AMPA receptors into synapses

The mechanisms underlying experience-dependent plasticity in the brain may depend on the AMPA subclass of glutamate receptors (AMPA-Rs). We examined the trafficking of AMPA-Rs into synapses in the developing rat barrel cortex. In vivo gene delivery was combined with in vitro recordings to show that experience drives recombinant GluR1, an AMPA-R subunit, into synapses formed between layer 4 and layer 2/3 neurons. Moreover, expression of the GluR1 cytoplasmic tail, a construct that inhibits synaptic delivery of endogenous AMPA-Rs during long-term potentiation, blocked experience-driven synaptic potentiation. In general, synaptic incorporation of AMPA-Rs in vivo conforms to rules identified in vitro and contributes to plasticity driven by natural stimuli in the mammalian brain.     

Unsupervised natural experience rapidly alters invariant object representation in visual cortex

Object recognition is challenging because each object produces myriad retinal images. Responses of neurons from the inferior temporal cortex (IT) are selective to different objects, yet tolerant ("invariant") to changes in object position, scale, and pose. How does the brain construct this neuronal tolerance? We report a form of neuronal learning that suggests the underlying solution. Targeted alteration of the natural temporal contiguity of visual experience caused specific changes in IT position tolerance. This unsupervised temporal slowness learning (UTL) was substantial, increased with experience, and was significant in single IT neurons after just 1 hour. Together with previous theoretical work and human object perception experiments, we speculate that UTL may reflect the mechanism by which the visual stream builds and maintains tolerant object representations.