Here are some GOOD wordings that we should be proficient in. I apologize to the authors of each sentence for no citation.
While these results do not directly indicate a cause and effect relationship between genome rearrangement mutations and transcriptional deregulation, they do underscore the stochastic nature of genotoxic effects on cells and tissues and could provide a mechanism for age-related cellular degeneration in postmitotic tissue, such as heart or brain.
Like all exciting discoveries, the one described by Feng et al. (2) raises more questions than it answers.
In only-one-author paper, using “we” instead of “I“ makes your expression not too pretentious. One example is a PNAS paper written by an American physicist (104:19193-19198, Does the h index have predictive power?). Here we report results of an empirical study of the predictive power of the h index compared with other indicators. Our findings indicate that
Although it has been known for 20 years that there is selection on synonymous codon use to maximize some aspect of translation, it has remained unclear what the direct cause of selection for translational optimal codons is; is it to maximize the speed of elongation, minimize the costs of proofreading, or maximize the accuracy of translation
Third, if selection is acting to reduce the costs of missense errors, we expect longer genes to have higher codon bias because the
In our second test of accuracy, we
extended
We find a negative correlation of codon bias and dN per gene, which remains when we control for expression levels.
Such errors are likely to result in dysfunctional proteins.
Fig. 1—Comparisons of intron lengths between Drosophila melanogaster and Drosophila virilis (a, 115 introns) and between D. melanogaster and Drosophila pseudoobscura (b, 60 introns). The diagonal line is for reference only, to show where the intron lengths are identical between the two species.
The ribosome density (ribden) is the number of ribosomes on active mRNAs divided by the transcript length.
Patterns and degrees of codon usage bias vary not only among different organisms, but also among genes in the same genome.
… between genomes or along one genome
Patterns and bias in synonymous codon usage varies greatly among different organisms and also among genes in the same genome.
The correlation in the 25
ribosomal protein genes of D.melanogaster is also
positive, though not significant (r = - 0.13, P > 0.5 for ENC; r =
0.18, P > 0.3 for CAI). This may be simply due to
the relatively small sample size of this data set.
Synonymous codon usage bias thus depends on the gene length as much as on the expression level.
For most genes, proteins are the
actual players.
Gene expression in metabolic pathways also needs to be well-timed to be effective.
It is increasingly recognized that mRNA abundances are only a weak surrogate (proxy) for the corresponding protein concentrations.
I measured the percentage of sites in each protein occupied by the focal amino acid.
No significant correlation was found between ribosome density and mRNA abundance, codon usage, or half-life.
As the ORF length increased, the ribosome density dropped from an average of 1.2 ribosomes per 100 nts for ORFs shorter than 400 nts to an average of 0.14 ribosomes per 100 nts for ORFs longer than 3,600 nts.
The contributions of the individual alleles to the phenotype are often non-additive.
The difference between these functional categories of proteins, in terms of haplosufficiency, was highly statistically significant but far from all-or-none.
This result suggests intriguingly that the mature ….
On average, …
To further substantiate these results we deleted the introns from three….
In principle, the whole-fly transcriptome is made up of the sum of the transcriptomes of each tissue, multiplied by a coefficient that is effectively the fraction of organismal mRNA contributed by that tissue: (A equation followed in original paper, here it is omitted)
…, there is a potentially large variety of mechanisms that underlie it.
For the sake of generality, a
theoretical analysis of simple non-linear HI systems is also attempted.
Antisense regulation could be a way of governing the expression of stable transcripts more rapidly than by stopping the transcription [21]. The fact that antisenses have unusually short introns is in agreement with this theory [22] and [23]. In this respect, it is noticeable that Sp6os has a relatively short intron (476 bp).
Conversely, there might be little evolutionary conservation if the true biological function associated with an RNA is not the product itself but rather the act of transcription (and associated chromatin modifications), or if the RNA is the byproduct of a nearby enhancer that controls distal genes. Thus, the absence of evolutionary conservation is not a reliable indicator of transcriptional noise.
First, the L1 endonuclease domain had to be inactivated; in its presence, L1 insertions occurred at canonical endonuclease recognition sites, rather than at telomeres. Thus, addition of L1 sequences to chromosome ends is outcompeted by retrotransposition to 3’-OH sites created by the L1 endonuclease.
To address this question, we analyzed retrosequence formation from donor genes unrelated to telomere maintenance…
The impact factor for a journal in a particular year is declared to be a measure of the average number of times a paper published in the previous two years was cited during the year in question.
Compared with non-TAG genes, genes in TAGs are significantly shorter (P < 0.001) in terms of gene, coding sequence (CDS), and intron length, whereas their G/C content is significantly higher (table S11).
Sex is determined by the temperature of the incubating egg, and clutches can be all-male, all-female or somewhere in between.
Adaptive hypotheses explaining the evolution of regulatory networks assume that unneeded expression is costly and therefore decreases fitness, but the proximate cause (直接原因) of this cost is not clear.
These observations remained robust when using only genes with expression levels greater than the median, indicating that Rmax estimates were not biased by noise in array data.
each spliceosome can only catalyze the removal of its cognate introns, primarily because splice site recognition involves
At both its 5' and 3' splice sites and at its predicted branch-point sequence, the Acanthamoeba intron shares substantial sequence identity with conserved sequence elements diagnostic of U12-type minor spliceosomal introns (Fig. 2a).
When we combine the data from all the organisms in our analysis, there are 1.7 times more competing 3' splice sites than competing 5' splice sites.
The CE fraction is listed in Table 3 and illustrated in Figure 2 for each organism.
In Figure 3 we plot the fraction of constitutive introns greater than 200 bp versus the CE fraction, and demonstrate a direct correlation between the presence of long introns and high incidence of CEs (y = 0.84x + 0.00; R2 = 0.73). This correlation also holds within each kingdom (fungi, protists, plants, and animals), providing a phylogenetic control. As discussed below, this correlation is consistent with the hypothesis that splice site recognition differs within these groups.
…., in agreement with previous observations.
In general, CEs and RIs both tend to be shorter than their constitutively spliced counterparts, with the length difference most noticeable in organisms in which each splice variant was uncommon.
The prevalence of RIs in all organisms we analyzed provides an opportunity to assess the possibility of a
functional role for these observed events. Our analysis reveals that RIs do not
display a preference for preserving reading frames: the
lengths of all 11,925 observed RIs were roughly
equally distributed between intron lengths
evenly divisible by three (34%), and intron
lengths with remainders of one (34%) and two (33%) when
divided by three.
We thus see some evidence for coding potential in RIs, but taken together with previous observations of CEs, our results suggest that the majority of observed splice variants are unlikely to give rise to functional proteins.
Regarding your color confirmation, I can inform you that your e-mail is sufficient for us to proceed, as you have requested only black and white for print and color for the online version.
It is unquestionable that AS can generate mRNAs with important and distinct biological functions. The more difficult question is what fraction of the extensive transcript variation generated by AS is truly biological relevant and what fraction may be due to stochastic noise in the splicing process.
However, evidence accumulated through classical gene-by-gene studies and persuasive examples of coordinated regulation of biological processes through AS readily justify future systematic functional analyses of AS isoforms.
As illustrated by the examples below, a mounting body of evidence implicates splicing defects and altered splicing regulation as cause …
We should also question whether any advantage exists for the negative-feedback loop occurring at the posttranscriptional level or whether this simply reflects the most permissive evolutionary route for an RNA-binding protein.
A key implication of the formative view, as first recognized by Blake (1978), is that exons in protein-coding genes will tend to correspond to structural or functional units of proteins. A correspondence of exons to globular domains was anticipated originally (Blake 1978), but it soon became clear (Campbell and Porter 1983; Go 1983) that exons in animal genes are generally too short for such a correspondence.
If exon shuffling was a significant factor during evolution and contributed substantially to the increasing complexity of entire proteome, then we should expect to see significant correlation between exon borders and protein domain borders in this genome-wide study. The correlation would be manifested by higher than expected number of exon borders falling inside the domain border boxes.
We noticed that there could be considerable fluctuations in the significance of the exon-domain border correlation for species at similar evolutionary levels, as demonstrated by the difference between mouse and rat, and between Fugu and zebrafish. The same phenomenon exists for invertebrates (e.g. compare fruitfly and mosquito or compare C. elegans and C. briggsae). These differences could be due to either the different properties of the proteomes of the individual species or the different sequencing stages and quality of the respective genome-sequencing projects, or possibly both. Notwithstanding, it is clear that through the evolutionary distance represented by the nine species studied, there is a consistently more pronounced link between exon and domain borders observed as one moves from nematodes to mammals. This is possibly the direct result of extensive exon shuffling during species evolution accompanied by positive selection of domains correlating with exons.
The analysis here shows that there is an extremely strong statistical association between G-quadruplex forming sequences and RDR, but provides no evidence to suggest that the association is causal in any way; the RDR are predicted to form independently of the G-quadruplexes, and the high concentration of G bases to form RNA–DNA hybrids makes G-quadruplex formation much more likely.
One limitation of the approach described in this paper is that it neglects a number of factors present under physiological conditions, such as DNA supercoiling, protein interactions, especially the role of histones, and the detailed nature of the junction between the RNA–DNA hybrid and the flanking duplexes. These will require further experimental effort to determine the appropriate thermodynamic treatments. Another limitation is that this approach entirely neglects kinetic processes, examining only the most stable conformer of the strands.
With cutoff values of two, three, and four transcripts per cell to divide high- and low-expression classes, the numbers of functional categories with at least 10 genes in each expression class reduce to 21, 15 and 11, respectively. However, the main trends of amino acid usage are robust to these cutoff values; Mantel-Haenszel test statistics remain significantly positive for Val…and negative for Phe, …
Although the intron lengths are not normally distributed, the logarithm values of the intron lengths are almost normally distributed. Thus, we use ‘independent samples t-test’ to analyze the logarithm values of the intron lengths to determine significance (P-value) in difference of intron lengths between antisense and other categories of genes.
The interpretation of the slightly higher SF2/ASF and SC35 densities observed in retained introns is not straightforward.
However, the signals are too subtle to allow definite conclusions to be made.
Evolutionary conservation of given features is often taken as a signal of biological function, under the assumption that negative selection is acting on them.
These findings cannot disprove the intron-early theory, but they do point to the intron-late alternative as the most economical explanation of the available data.
L1 elements are mobilized through target-primed reverse transcription, in which ORF2 nicks target DNA, using the resultant 3’-OH to prime the reverse transcription of L1 RNA.
This more useful, albeit more ambiguous, criterion allows for some genetic exchange (gene flow) between species as long as they do not become homogenized.
noteworthy levels of reproductive isolation can begin to accumulate within only a few dozen generations;
（作为图表的附加说明）Total is greater than 100% because of rounding.
To determine whether the pattern of intron loss in these fungi might account for the observed bias in intron position, we examined the pattern of loss as a function of position within the gene.
Motivated by Drummond and Wilke’s (2008) hypothesis that translational accuracy selection minimizes the misfolding of mistranslated proteins, we test here whether
translationally optimal codons are associated with structurally sensitive sites, that is, sites at which translation errors are particularly likely to cause misfolding.
After combining the expression data with the structural data, we ended up with 698, 384, 123, and 569 genes for E. coli, S. cerevisiae, D. melanogaster, and M.musculus, respectively.
An alternative, and more direct, way of assessing whether a site is sensitive to mutation is to determine the distribution of free energy changes (ΔΔG values) that substitutions at this site effect.
Second, the existence of multiple weak correlations makes it hard to identify the primary or causative variables.
CTVS was first described and transmitted between dogs in 1876 by Novinski (reviewed in REF. 24). 实在查不到原始文献时，又必须引用，可以这样间接引用。
Mitochondria and plastids are the classic examples of organelles, although the term is sometimes used in reference to other cellular structures such as the Golgi apparatus, flagellar basal bodies and centrioles. Mitochondria and plastids are, however, unique in that they evolved from free-living prokaryotes through the process of endosymbiosis. Given this fundamental distinction, here we use organelle to refer only to permanent cellular inclusions of exogenous origin.
In this paper, we report the results of the analysis
at the more traditional lineage level, whereas the results
at the gene level are presented in the accompanying
paper.
On average, 86% of the sites in each gene are incapable of gaining introns (v = 0.86), in agreement with the protosplice sites hypothesis (Dibb and Newman 1989; Dibb 1991; Sverdlov et al. 2004b) and with the previous estimates of Nguyen et al. (2005).
Hamming R (1986) You and your research. In: Kaiser JF Transcription of the Bell
Communications Research Colloquium Seminar; 7 March 1986; Morristown, New
Jersey, United States. Available: http://www.cs.virginia.edu/;robins/YouAndYourResearch. html. Accessed 24 September 2007. 引用网页的方式。
International Stratigraphic Chart" (pdf). International commission for Stratigraphy. 2009. http://www.stratigraphy.org/upload/ISChart2009.pdf. Retrieved 2009-09-22.
The excess of intronization over de-intronization echoes the case in Caenorhabditis nematodes found in our previous study [9], and contrasts with the excess of intron loss (by loss of the actual intron sequence) over insertion of new introns in the same species studied here [27].
These arguments suggest that intronization may not be a major overall contributor to modern gene structures. However, it is important to keep in mind that these estimates
are necessarily quite rough.
Cavalier-Smith’s
hypothesis rests on four propositions. First, that spliceosomal introns are really just
‘introns-in-pieces’ fragmented from a self-splicing Group II ancestor; second, that…..; third, that….; and, fourth, that ….
^ "International Stratigraphic Chart" (pdf). International commission for Stratigraphy. 2009. Retrieved 2009-09-22.
Our study has an ascertainment bias, making identification of intron presence preferential in TCO-related populations, because the exon boundaries used to detect intron absences were generated from the predicted annotations of the TCO genome. However, any polarizations as a gain or loss are not affected by this bias.
We used the annotation of Fg [5,6] as a reference to define the coding sequence versus intergenic (600 bp upstream of the start codon and 600 bases downstream of the stop codon) and intronic regions in the aligned regions.
These results correlate well with a recent report from the …laboratory that showed that ..
The fact that CFSs persist in widespread phyla suggests they serve a conserved purpose.
We distinguish between the passive dissipation of supercoils by diffusion and the active removal of supercoils by topoisomerase enzymes.
We suggest that genome size evolution is unlikely to be neatly explained by a single factor such as population size.
Furthermore, when coupled to nonsense-mediated decay, alternative splicing can function as an ‘‘on/off’’ switch by introducing premature termination codons, thereby directing mRNA degradation.
Nevertheless, the idea that Ne drives genome size and complexity seems to have gained acceptance [12–14], with some going so far as to characterize it as ‘‘the principal explanatory framework for understanding the evolution of genome organization’’ ([12], p.303). 引用原话不仅要注明出处，而且要用“”表明。
Such lack of resolution is often explained by a radiation event that would have left very little ancient signal in eukaryotic molecular markers. We suggest a complementary genomic approach that might help tackling this major issue. It rests on a hypothesis, the genome reduction hypothesis (GRH), suggesting that the divergence of major eukaryotic lineages might have been coupled with independent genomic reduction events, starting from a large and partially redundant chimerical genome. Thus, significant and coherent patterns
Almost 50 years following the discovery of the prokaryotic operon, the functional relevance of gene order within operons remains unclear. In this work, we take advantage of the eroded genome of Mycobacterium leprae to add evidence supporting the notion that functionally less important genes have a tendency to be located at the end of its operons.
The size distribution of introns was typically skewed with a mean intron size of 400 bp and a median of 96 bp (see Supplementary Note 3.4, Supplementary Fig. 2.4.3 and Supplementary Table 2.4.1).
There is a clear negative correlation between qs¢ and transcription levels (Fig. 3c), with the coldest genes (bottom5% qs¢) showing nearly fourfold higher transcription than the hottest (top 5% qs¢). 描述相关性时，可以参考此句子。除了告诉读者冷热（这里是指突变率高低，高的区域称为热点）与转录水平负相关外，比较一下最冷的和最热的基因的转录水平。这种故意重复同一个意思可以起到加深读者印象的效果，当然同时也给读者提供了更多信息。
They found nonrandom variation in the neutral mutation rate, with mutational hot spots and cold spots that inversely correlate to the degree of purifying selection acting on that particular region of the genome. 两个点对一条线的描述
We find that more than three per cent of the human genome is more closely related to either the bonobo or the chimpanzee genome than these are to each other. 三方比较还可以这样表述。