Evidence that Accumulation of Mutants in a Biofilm Reflects Natural Selection Rather than Stress-Induced Adaptive Mutation

The accumulation of mutant genotypes within a biofilm evokes the controversy over whether the biofilm environment induces adaptive mutation or whether the accumulation can be explained by natural selection. A comparison of the virulence of two strains of the dental pathogen Streptococcus mutans showed that rats infected with one of the strains accumulated a high proportion (average, 22%) of organisms that had undergone a deletion between two contiguous and highly homologous genes. To determine if the accumulation of deletion mutants was due to selection or to an increased mutation rate, accumulations of deletion mutants within in vitro planktonic and biofilm cultures and within rats inoculated with various proportions of deletion organisms were quantified. We report here that natural selection was the primary force behind the accumulation of the deletion mutants.     

复合诱变选育高产GSH的菌株

目的:选育出GSH的高产菌株.方法:以产GSH的产朊假丝酵母(Candida utilis)为出发菌株,利用紫外-超声波复合诱变.结果:筛选得到ZnCl2抗性突变株UU3,GSH菌体含量为53.50mg·g-1,比出发菌株提高137.03%.结论:突变株UU3遗传性能稳定,可做进一步研究.     

利用Tn5定位诱变筛选紫云英根瘤菌Exo^—变种

利用Ｔｎ５定位诱变方法,对质粒ｐＪＢＢ５进行Ｔｎ５插入诱变,得到１０个Ｔｎ５在５９ｋｂＢ５外源片段上有不同插入位点的质粒ＴＮ１１,ＴＮ１１２,ＴＮ２２,ＴＮ２３,ＴＮ３１,ＴＮ４１,ＴＮ９１,ＴＮ１０１,ＴＮ１３１,ＴＮ１４１。将Ｔｎ１１等分别转移到已经含有不相容质粒ｐＰＨ１ＪＩ的紫云英根瘤菌１０７菌株中,使之发生同源变换。通过抗性选择及表型鉴别,筛选到３株菌落表型干燥（Ｍｕｃ－）的酸性胞外多糖（ＥＰＳ）合成缺陷菌株（Ｅｘｏ－）１０７（ＴＮ２２）,１０７（ＴＮ１０１）,１０７（ＴＮ１３１）。Ｓｏｕｔｈｅｒｎ杂交分析证明这３株变种的Ｔｎ５插入确实是同源交换而不是转座产生,表明经过适当改良的Ｔｎ５定位诱变法可以应用于紫云英根瘤菌Ｅｘｏ－变种的筛选。     

The Jackprot Simulation Couples Mutation Rate with Natural Selection to Illustrate How Protein Evolution Is Not Random

Protein evolution is not a random process. Views which attribute randomness to molecular change, deleterious nature to single-gene mutations, insufficient geological time, or population size for molecular improvements to occur, or invoke “design creationism” to account for complexity in molecular structures and biological processes, are unfounded. Scientific evidence suggests that natural selection tinkers with molecular improvements by retaining adaptive peptide sequence. We used slot-machine probabilities and ion channels to show biological directionality on molecular change. Because ion channels reside in the lipid bilayer of cell membranes, their residue location must be in balance with the membrane’s hydrophobic/philic nature; a selective “pore” for ion passage is located within the hydrophobic region. We contrasted the random generation of DNA sequence for KcsA, a bacterial two-transmembrane-domain (2TM) potassium channel, from Streptomyces lividans, with an under-selection scenario, the “jackprot,” which predicted much faster evolution than by chance. We wrote a computer program in JAVA APPLET version 1.0 and designed an online interface, The Jackprot Simulation , to model a numerical interaction between mutation rate and natural selection during a scenario of polypeptide evolution. Winning the “jackprot,” or highest-fitness complete-peptide sequence, required cumulative smaller “wins” (rewarded by selection) at the first, second, and third positions in each of the 161 KcsA codons (“jackdons” that led to “jackacids” that led to the “jackprot”). The “jackprot” is a didactic tool to demonstrate how mutation rate coupled with natural selection suffices to explain the evolution of specialized proteins, such as the complex six-transmembrane (6TM) domain potassium, sodium, or calcium channels. Ancestral DNA sequences coding for 2TM-like proteins underwent nucleotide “edition” and gene duplications to generate the 6TMs. Ion channels are essential to the physiology of neurons, ganglia, and brains, and were crucial to the evolutionary advent of consciousness. The Jackprot Simulation illustrates in a computer model that evolution is not and cannot be a random process as conceived by design creationists.     

The Role of Natural Selection in the Origin of Life

It is commonly accepted among origin-of-life scientists that the emergence of life was an evolutionary process involving at one stage or other the working of natural selection. Researchers disagree, however, on the nature of the chemical infrastructure that could have formed prebiotically, enabling the evolutionary process. The division of the origin-of-life research community into ‘geneticists’ and ‘metabolists’ usually revolves around the issue whether the first to arise prebiotically was a genetic polymer or a primitive metabolic system. In this paper I offer an alternative classification based on the attitude to the onset of natural selection. From this perspective I add to the conventional division between gene-first and metabolism-first groups a position I call “preparatory metabolism”. By this line of thought, an RNA or an RNA-like polymer could not have emerged prebiotically. Nevertheless, the onset of natural selection had to wait until such a polymer had arised. This paper examines the RNA-first, RNA-later, metabolism-first and preparatory-metabolism scenarios, assessing the weaknesses and strengths of each. I conclude that despite the recent theoretical advances in all these lines of research, and despite experimental breakthroughs, especially in overcoming several RNA-first hurdles, none of the examined paradigms has yet attained decisive experimental support. Demonstrating the evolvability of a potentially prebiotic infrastructure, whether genetic or metabolic, is a most serious challenge. So is the experimental demonstration of the emergence of such an infrastructure under prebiotic conditions. The current agenda before origin-of-life researchers of all stripes and colors is the search for the experimental means to tackle all these difficulties.     

The Effects of Mutation and Natural Selection on Codon Bias in the Genes of Drosophila

Codon bias varies widely among the loci of Drosophila melanogaster, and some of this diversity has been explained by variation in the strength of natural selection. A study of correlations between intron and coding region base composition shows that variation in mutation pattern also contributes to codon bias variation. This finding is corroborated by an analysis of variance (ANOVA), which shows a tendency for introns from the same gene to be similar in base composition. The strength of base composition correlations between introns and codon third positions is greater for genes with low codon bias than for genes with high codon bias. This pattern can be explained by an overwhelming effect of natural selection, relative to mutation, in highly biased loci. In particular, this correlation is absent when examining fourfold degenerate sites of highly biased genes. In general, it appears that selection acts more strongly in choosing among fourfold degenerate codons than among twofold degenerate codons. Although the results indicate regional variation in mutational bias, no evidence is found for large scale regions of compositional homogeneity.     

Isolation of Neurospora Crassa a Mating Type Mutants by Repeat Induced Point (Rip) Mutation

In the filamentous fungus, Neurospora crassa, mating type is regulated by a single locus with alternate alleles, termed A and a. The mating type alleles control entry into the sexual cycle, but during vegetative growth they function to elicit heterokaryon incompatibility, such that fusion of A and a hypha results in death of cells along the fusion point. Previous studies have shown that the A allele consists of 5301 bp and has no similarity to the a allele; it is found as a single copy and only within the A genome. The a allele is 3235 bp in length and it, too, is found as a single copy within the a genome. Within the A sequence, a single open reading frame (ORF) of 288 amino acids (mt A-1) is thought to confer fertility and heterokaryon incompatibility. In this study, we have used repeat induced point (RIP) mutation to identify functional regions of the A idiomorph. RIP mutations in mt A-1 resulted in the isolation of sterile, heterokaryon-compatible mutants, while RIP mutations generated in a region outside of mt A-1 resulted in the isolation of mutants capable of mating, but deficient in ascospore formation.     

Targeted Mutagenesis by Duplication Insertion in the Radioresistant Bacterium Deinococcus radiodurans: Radiation Sensitivities of Catalase (katA) and Superoxide Dismutase (sodA) Mutants

Deinococcus radiodurans R1 is extremely resistant to both oxidative stress and ionizing radiation. A simple and general targeted mutagenesis method was developed to generate catalase (katA) and superoxide dismutase (sodA) mutants. Both mutants were shown to be more sensitive to ionizing radiation than the wild type.     

Histidine Mutants Requiring Adenine: Selection of Mutants with Reduced hisG Expression in SALMONELLA TYPHIMURIUM

A method is described for the selection of Salmonella typhimurium mutants with reduced levels of hisG enzyme activity. This method is based on the fact that the hisG enzyme catalyzes the consumption of ATP in the first step of histidine biosynthesis. Normally, this reaction is closely regulated, both by feedback inhibition and by repression of the operon. However, conditions can be set up that result in the uncontrolled use of adenine in histidine biosynthesis. Cells grown under these conditions become phenotypic adenine auxotrophs. Some revertant clones that no longer require adenine contain mutations in hisG, hisE, or the his-control region. The hisG mutations are of all types (nonsense, frameshift, missense, deletion and leaky types), and they map throughout the hisG gene.     

玉米体细胞突变体筛选研究

综述了近10多年来在玉米体细胞突变体筛选研究方面的研究进展;玉米突变体筛选程序的改进;产生能稳定遗传突变的机理等。指出开展玉米突变体筛选育种更具可行性与必要性。     

Incipient Balancing Selection through Adaptive Loss of Aquaporins in Natural Saccharomyces cerevisiae Populations

A major goal in evolutionary biology is to understand how adaptive evolution has influenced natural variation, but identifying loci subject to positive selection has been a challenge. Here we present the adaptive loss of a pair of paralogous genes in specific Saccharomyces cerevisiae subpopulations. We mapped natural variation in freeze-thaw tolerance to two water transporters, AQY1 and AQY2, previously implicated in freeze-thaw survival. However, whereas freeze-thaw–tolerant strains harbor functional aquaporin genes, the set of sensitive strains lost aquaporin function at least 6 independent times. Several genomic signatures at AQY1 and/or AQY2 reveal low variation surrounding these loci within strains of the same haplotype, but high variation between strain groups. This is consistent with recent adaptive loss of aquaporins in subgroups of strains, leading to incipient balancing selection. We show that, although aquaporins are critical for surviving freeze-thaw stress, loss of both genes provides a major fitness advantage on high-sugar substrates common to many strains'' natural niche. Strikingly, strains with non-functional alleles have also lost the ancestral requirement for aquaporins during spore formation. Thus, the antagonistic effect of aquaporin function—providing an advantage in freeze-thaw tolerance but a fitness defect for growth in high-sugar environments—contributes to the maintenance of both functional and nonfunctional alleles in S. cerevisiae. This work also shows that gene loss through multiple missense and nonsense mutations, hallmarks of pseudogenization presumed to emerge after loss of constraint, can arise through positive selection.     

The Adaptive Significance of Tetrapod Gait Selection

At the slow walk tetrapods avoid lateral couplets gaits to minimizesupport by ipsilateral bipods. Most of them use the lateralsequence because tripods then make larger triangles than forthe diagonal sequence. Of the running symmetrical gaits thesingle foots (in each sequence) permit the smoothest and fastesttravel without suspensions. The trot and pace allow two legsto thrust in unison, the former giving the most stability toanimals not placing the feet well under the body and the latteravoiding interference for long legged runners. The bound andhalf bound are most used by small agile mammals for bursts ofspeed and for maneuvering on rough terrain by a series of leaps.Such animals use the extended suspension. Large cursors on openterrain usually select the shorter more economical, gatheredsuspension. The fastest runners use both suspensions to gainlong strides. At moderate speed the transverse gallop has theadvantages over the rotary gallop that both bipods and tripodsare more stable and that interference may be avoided. At highspeed using both suspensions, none of these advantages pertains.The rotary gallop may then increase maneuverability.