A new test suggests hundreds of amino acid polymorphisms in humans are subject to balancing selection

The role that balancing selection plays in the maintenance of genetic diversity remains unresolved. Here, we introduce a new test, based on the McDonald–Kreitman test, in which the number of polymorphisms that are shared between populations is contrasted to those that are private at selected and neutral sites. We show that this simple test is robust to a variety of demographic changes, and that it can also give a direct estimate of the number of shared polymorphisms that are directly maintained by balancing selection. We apply our method to population genomic data from humans and provide some evidence that hundreds of nonsynonymous polymorphisms are subject to balancing selection.

What maintains genetic variation remains an unresolved mystery. This study describes the development of a new test and its application to human population genomic data, suggesting that natural selection may have a much more important role than previously thought, with hundreds of non-synonymous polymorphisms subject to balancing selection.     

FROM MORE TO FEWER? TESTING AN ALLEGEDLY PERVASIVE TREND IN THE EVOLUTION OF MORPHOLOGICAL STRUCTURE

While evolutionary trends have long received much attention and have been widely disputed, new methods are now allowing the testing of directional hypotheses with increased rigor. Here, we test a general hypothesis about the way many kinds of discrete characters are thought to evolve, termed oligomerization. This is the tendency for serial structures (such as arthropod body and appendage segments) or armature (such as spines) to evolve primarily through loss and fusion. Focusing on the Crustacea, we use maximum likelihood methods to test for directional evolution in a large sample (> 500) of discrete traits, analyzed against molecular-based phylogenies. We find evidence for a significant trend toward trait loss, in accordance with the reduction principle. However, this trend is far from ubiquitous, with many characters exhibiting a reconstructed bias toward gains. These results suggest that caution must be used before drawing conclusions about which taxa are "primitive" or about the directionality of morphological shifts in the absence of phylogenetic analysis. Nevertheless, oligomerization-as a trend rather than a law-may be an important process that influences evolutionary trajectories from both morphological and functional perspectives.     

Female genital cutting: a harmless practice?

A recent article in Medical Anthropology Quarterly (Obermeyer 1999) argues that the "facts" about the "harmful effects" of female genital cutting (FGC) are "not sufficiently supported by the evidence" (p. 79). The article suggests three further hypotheses, among others: (1) FGC may be of minimal harm because the more educated continue the practice just as much as the less educated; (2) FGC may be of minimal harm because it is so widespread and persistent; (3) FGC may be of minimal harm because the supposed link between the clitoris and female sexual pleasure is a social construction rather than a physiological reality. I challenge these hypotheses. I say that by appropriate standards of evaluation, FGC is harmful. Finally, I submit that most FGC is a proper matter of concern because it is the irreversible reduction of a human capacity in the absence of meaningful consent.     

Enzymatic generation of N-[4-dimethylamino)phenyl]acetohydroxamic acid by the action of pyruvate decarboxylase on 4-(dimethylamino)nitrosobenzene

The established ability of pyruvate decarboxylase to catalyze the conversion of nitroso aromatics to hydroxamic acids was utilized to generate the previously unknown hydroxamic acid 2. Although 2 could not be isolated in pure form from enzymatic reactions, evidence for its production is presented in this study. Under the conditions of the enzymatic reaction, 2 undergoes a slower reduction to give the corresponding acetanilide 3, which was isolated and characterized. The isomeric hydroxamic acid 4 was synthesized and its stability compared to that of 2. The much greater reactivity of the hydroxamic acid 2, particularly evidenced by its facile reduction to 3, was explained on the basis of the potential for the formation of the N-acylquinonediimine cation, 9.     

Nuclear genes resolve mesozoic-aged divergences in the insect order Lepidoptera

Compared to the number of genes available for study of both younger and older divergences, few genes have yet been identified that can strongly resolve phylogenetic splits of Mesozoic age ( approximately 65-250 mya). Thus, reconstruction of Mesozoic-age phylogenies, exemplified by basal divergences within the major orders of holometabolous insects, is likely to be especially dependent on combining multiple lines of evidence. This study tests the potential of the 18S ribosomal RNA gene for reconstructing Mesozoic-aged divergences within the insect order Lepidoptera and its ability when combined with a second, previously analyzed nuclear gene (phosphoenolpyruvate carboxykinase, PEPCK) to strongly resolve these relationships. 18S sequences were obtained for 21 taxa, representing major clades of Lepidoptera plus outgroups from the other "panorpoid orders. A well-corroborated morphology-based "test phylogeny was used to evaluate the effects of partitioning the 18S gene according to variable versus conserved domains, paired versus unpaired sites in the secondary structure, and transition versus transversion substitutions. Likelihood and unweighted parsimony analyses of the 18S data recover the "test phylogeny" almost completely, with no improvement of agreement or support provided by any form of weighting or partitioning. No conflict in signal between 18S and PEPCK was detected by the partition homogeneity test. Combined parsimony analysis yielded strong bootstrap support for nearly all relationships, much higher than for either gene alone, thereby also providing strong evidence on several hypotheses about the early evolution of lepidopteran-plant interactions. These genes in combination may be widely useful for resolving insect divergences of comparable age.     

Genetic evidence for inhibition of bacterial division protein FtsZ by berberine

Background

Berberine is a plant alkaloid that is widely used as an anti-infective in traditional medicine. Escherichia coli exposed to berberine form filaments, suggesting an antibacterial mechanism that involves inhibition of cell division. Berberine is a DNA ligand and may induce filamentation through induction of the SOS response. Also, there is biochemical evidence for berberine inhibition of the cell division protein FtsZ. Here we aimed to assess possible berberine mechanism(s) of action in growing bacteria using genetics tools.

Methodology/Principal Findings

First, we tested whether berberine inhibits bacterial growth through DNA damage and induction of the SOS response. The SOS response induced by berberine was much lower compared to that induced by mitomycin C in an SOS response reporter strain. Also, cell filamentation was observed in an SOS-negative E. coli strain. To test whether berberine inhibits FtsZ, we assessed its effects on formation of the cell division Z-rings, and observed a dramatic reduction in Z-rings in the presence of berberine. We next used two different strategies for RNA silencing of ftsZ and both resulted in sensitisation of bacteria to berberine, visible as a drop in the Minimum Inhibitory Concentration (MIC). Furthermore, Fractional Inhibitory Concentration Indices (FICIs) showed a high level of synergy between ftsZ silencing and berberine treatment (FICI values of 0.23 and 0.25 for peptide nucleic acid- and expressed antisense RNA-based silencing of ftsZ, respectively). Finally, over-expression of ftsZ led to a mild rescue effect in berberine-treated cells.

Conclusions

The results argue against DNA binding as the primary mechanism of action of berberine and support the hypothesis that its antibacterial properties are due to inhibition of the cell division protein FtsZ. In addition, the genetic approach used here provides a means to rapidly test the activity of other putative FtsZ inhibitors.     

系统发育和被子植物“多系-多期-多域”系统——兼答傅德志的评论

历史地回顾了谱系、系统发育、单系、多系概念的由来和发展。详细讨论了单系(monophyly )和多系(polyphyly)在叙述分类群起源和描述分类群内部系统发育线多样性的不同含义。以此为基础,说明在“多系_多2_多域”的八纲系统中“多系”和“单系”是指自然分类群内系统发育线的多样性,不等同于“多源”和“单源”。通过与近年来所发表的被子植物分类系统的比较,认为基于化石、形态、分子和地理分布证据提出的八纲系统所显示的预言性,必将在今后的科学实践中经受检验。     

Morphofunctional reconstruction of the brain of <Emphasis Type="Italic">Paroxyaena pavlovi</Emphasis> (Hyaenodontidae,Creodonta) based on a natural endocranial cast

The study of a natural endocranial cast of Paroxyaena has shown that its vision was an important system of afferentation, but did not prevail over others, unlike that of Neohyaenodon. The olfaction was much better developed than in Neohyaenodon. The large gyrus prorealis suggests the presence of a long mobile nose. The well-developed sensomotoric cortex is evidence that the forepaw of Paroxyaena showed a high mobility.     

The role of arginine 310 in catalysis and substrate specificity in xanthine dehydrogenase from Rhodobacter capsulatus

The rapid reaction kinetics of wild-type xanthine dehydrogenase from Rhodobacter capsulatus and variants at Arg-310 in the active site have been characterized for a variety of purine substrates. With xanthine as substrate, k(red) (the limiting rate of enzyme reduction by substrate at high [S]) decreased approximately 20-fold in an R310K variant and 2 x 10(4)-fold in an R310M variant. Although Arg-310 lies on the opposite end of the substrate from the C-8 position that becomes hydroxylated, its interaction with substrate still contributed approximately 4.5 kcal/mol toward transition state stabilization. The other purines examined fell into two distinct groups: members of the first were effectively hydroxylated by the wild-type enzyme but were strongly affected by the exchange of Arg-310 to methionine (with a reduction in k(red) greater than 10(3)), whereas members of the second were much less effectively hydroxylated by wild-type enzyme but also much less significantly affected by the amino acid exchanges (with a reduction in k(red) less than 50-fold). The effect was such that the 4000-fold range in k(red) seen with wild-type enzyme was reduced to a mere 4-fold in the R310M variant. The data are consistent with a model in which "good" substrates are bound "correctly" in the active site in an orientation that allows Arg-310 to stabilize the transition state for the first step of the overall reaction via an electrostatic interaction at the C-6 position, thereby accelerating the reaction rate. On the other hand, "poor" substrates bound upside down relative to this "correct" orientation. In so doing, they are unable to avail themselves of the additional catalytic power provided by Arg-310 in wild-type enzyme but, for this reason, are significantly less affected by mutations at this position. The kinetic data thus provide a picture of the specific manner in which the physiological substrate xanthine is oriented in the active site relative to Arg-310 and how this residue is used catalytically to accelerate the reaction rate (rather than simply bind substrate) despite being remote from the position that is hydroxylated.     

Patterns of demographic change in the Americas.

Considerable scholarly debate has focused on the nature of demographic change in the Americas before and after 1492. Recent research on human skeletal samples and related archeological materials suggests that morbidity and mortality were increasing throughout much of the Western Hemisphere before 1492 in response to increased population density, increased sedentism, and changing subsistence. The evidence suggests that after 1492 population reduction was caused not by continental pandemics but by localized or regional epidemics augmented by social and economic disruption. The twentieth century has witnessed remarkable Native American population recovery, fueled both by improvements in health care and changing definitions of "being Indian."     

Selenium – an antioxidative protectant in soybean during senescence

Selenium (Se) is regarded as an antioxidant in animals and plants, even though considered as non-essential element in plants. To test its ability to counteract senescence related oxidative stress in soybean a pot culture experiment was conducted. The soybean plant was sprayed with sodium selenate (50ppm) at 78days after sowing (DAS). Soybean leaves were harvested at 80 and 90 DAS for analysis of oxidant production and antioxidative enzymes activity. Se positively promoted growth and acted as antioxidant by inhibiting lipid peroxidation and per cent injury of cell membrane. The antioxidative effect was associated with an increase in superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) enzymes activity. Significant increase in antioxidant enzyme activity was positively related to Se content. The decrease in antioxidative enzymes at 90 DAS was much faster in control plants than Se-sprayed plants. The reduction in SOD and GSH-Px may be associated with senescence-induced oxidative burst.     

Does Formate Reduce α-Ketoglutarate and Ammonia to Glutamate?

The reported reduction of -ketoglutarate and ammonia by formate is much slower than described (Morowitz et al., 1995). The formate reduction if any is small under these conditions. Glutamate is produced from a reduction by a second molecule of -ketoglutarate involving an oxidative decarboxylation.     

Physicochemical and biological characterizations of pregnant mare serum gonadotropin and its subunits.

Pregnant mare serum gonadotropin and its subunits have been further characterized. Ultracentrifugation of the gonadotropin at pH 1.3 and 11.5 showed little evidence of dissociation compared to pH 8.2. Highly purified subunits are obtained by urea dissociation and ion-exchange chromatography followed by gel-filtration. Circular dichroism spectra of the gonadotropin and its subunits are much like those of ovine lutropin and its subunits in that there is little evidence for secondary structure and one or more tyrosine residues are inaccessible in the intact gonadotropin compared to the subunits. The alpha-subunit possesses almost 3 times as much total carbohydrate as the beta-subunit; the individual sugar composition of each was determined as well as the amino acid composition. The alpha-subunit begins with the sequence NH2-Phe-Pro (Gly or Pro) ... and terminates with isoleucine. The beta-subunit has the sequence NH2-Ser-Pro-Gly ...; no C-terminal residue is detectable by either carboxypeptidase or hydrazinolysis. Biological studies show the gonadotropin to be active in assays specific for both lutropin and follitropin. Precipitin test in agar with rabbit antiserum against the gonadotropin show that the beta subunit cross-reacts whereas the alpha subunit does not.     

The oxidative metabolism of thioglycollate-elicited mouse peritoneal macrophages: the relationship between oxygen, superoxide and hydrogen peroxide and the effect of monolayer formation

The oxygen and glucose metabolism of peritoneal macrophages harvested from untreated mice (resident cells) and mice given an i.p. injection of thioglycollate broth (thioglycollate cells) were examined. Thioglycollate cells consumed approximately 3 times as much O2 at rest and during phagocytosis as resident cells, but oxygen reduction products (superoxide and hydrogen peroxide) could be recovered in only minimal amounts despite triggering by phagocytosis or exposure to PMA. Indirect evidence for the formation of oxygen reduction products such as O2- by thioglycollate cells was obtained by observation of the major pathways for glucose oxidation and NBT dye reduction. When thioglycollate cells were allowed to adhere to a glass surface O2- and H2O2 were easily recovered in the extracellular medium with a 20-fold increase above cells in suspension exposed to PMA. This study suggests that thioglycollate-elicited macrophages have a vigorous oxidative metabolism but that recovery, and perhaps utilization, of O2 reduction products formed will depend on the conditions of incubation. These events may be significant both for the study of parameters of macrophage "activation" in vitro as well as the function of these cells in vivo.     

Carbon monoxide-driven reduction of ferric heme and heme proteins

Oxidized cytochrome c oxidase in a carbon monoxide atmosphere slowly becomes reduced as shown by changes in its visible spectra and its reactivity toward oxygen. The "auto-reduction" of cytochrome c oxidase by this procedure has been used to prepare mixed valence hybrids. We have found that this process is a general phenomenon for oxygen-binding heme proteins, and even for isolated hemin in basic aqueous solution. This reductive reaction may have physiological significance. It also explains why oxygen-binding heme proteins become oxidized much more slowly and appear to be more stable when they are kept under a CO atmosphere. Oxidized alpha and beta chains of human hemoglobin become reduced under CO much more slowly than does cytochrome c oxidase, where the CO-binding heme is coupled with another electron accepting metal center. By observing the reaction in both the forward and reverse direction, we have concluded that the heme is reduced by an equivalent of the water-gas shift reaction (CO + H2O----CO2 + 2e- + 2H+). The reaction does not require molecular oxygen. However, when the CO-driven reduction of cytochrome c oxidase occurs in the presence of oxygen, there is a competition between CO and oxygen for the reduced heme and copper of cytochrome alpha 3. Under certain conditions when both CO and oxygen are present, a peroxide adduct derived from oxygen reduction can be observed. This "607 nm complex," described in 1981 by Nicholls and Chanady (Nicholls, P., and Chanady, G. (1981) Biochim. Biophys. Acta 634, 256-265), forms and decays with kinetics in accord with the rate constants for CO dissociation, oxygen association and reduction, and dissociation of the peroxide adduct. In the absence of oxygen, if a mixture of cytochrome c and cytochrome c oxidase is incubated under a CO atmosphere, auto-reduction of the cytochrome c as well as of the cytochrome c oxidase occurs. By our proposed mechanism this involves a redistribution of electrons from cytochrome alpha 3 to cytochrome alpha and cytochrome c.     

Again on language of biology]

Some time ago I proposed in an Editorial in this journal some considerations on the language of biology. I concluded that, to realize an autonomy of such a language (and therefore of biology), we have to develop a valid language for biology. In such a context, it seemed to me that the term "metaphors" referred to the concepts concerning the information carried by genetic code, was a reasonable one. However, Barbieri's article in this issue of Rivista di Biologia / Biology Forum calls for a reply. Of course, we do not know very much in this field, even if we have some evidence that a sequence of bases on a DNA is not determined only by chance. In any case we can exclude that nature in this occasion has "invented" a code. Nature doesn't "invent" anything: it only follows its rules, that we name "laws of nature". Barbieri quotes the Morse code, but forgets to say that such a code is "conventional" in the sense that it is valid only because it is the result of an "agreement" between Morse and the users of that code. There is nothing more unnatural than a "code": with whom nature should actually have to "reach an agreement"? As a matter of fact, we interpret as "information" what happens by law of nature. Also Barbieri's thesis that genes and proteins are molecular artifacts, assembled by external agents, whereas generally molecules are determined by their bonds, i.e. by internal factors, is a disputable one. It is examined how much an external structure plays a role in ordinary chemical reactions. The "information" of physics is not a semantic information. For such information we can refer to history of literature, telegraphic offices, genetics or biochemistry.     

Effect of curarization on sensitivity of chicken latissimus dorsi to electric current]

(1.) To test the sensitivity to electric current of the latissimus dorsi and, therefore, its ability to yield action potential, we have studied the effect of curarisation on the amplitude of the isometric tetanus during "massive" stimulations by alternative current. (2.) Curarisation causes a considerable but reversible reduction of the tetanic tension of the latissimus dorsi anterior (L.D.A.) but has no effect on the tetanus of the latissimus dorsi posterior (L.D.P.). It is concluded that a part of the L.D.A. is not sensitive to electric current and is thus unable to yield action potentials, unlike the opinion of some authors. (3.) Rising the temperature has an inverse effect on the speed of the tetanus ascending phase, depending on whether the L.D.A. has been curarised or not. This show the existence of two types of excitation processes of very different nature in this muscle. (4.) Direct current is much less efficient than alternative current on the curarised L.D.A.     

Hypothesis testing in ecology: psychological aspects and the importance of theory maturation

Proper hypothesis testing is the subject of much debate in ecology. According to studies in cognitive psychology, confirmation bias (a tendency to seek confirming evidence) and theory tenacity (persistent belief in a theory in spite of contrary evidence) pervasively influence actual problem solving and hypothesis testing, often interfering with effective testing of alternative hypotheses. On the other hand, these psychological factors play a positive role in the process of theory maturation by helping to protect and nurture a new idea until it is suitable for critical evaluation. As a theory matures it increases in empirical content and its predictions become more distinct. Efficient hypothesis testing is often not possible when theories are in an immature state, as is the case in much of ecology. Problem areas in ecology are examined in light of these considerations, including failure to publish negative results, misuses of mathematical models, confusion resulting from ambiguous terms (such as "diversity" and "niche"), and biases against new ideas.     

Reduction and destruction rates of nitroxide spin probes

A series of nitroxides was tested for rates of one-electron reduction in a chemical, a photochemical, and two biological systems by ESR assays. In all cases, piperidine and hydropyridine nitroxides were reduced consistently more rapidly than pyrroline and pyrrolidine nitroxides. Substituents on the nitroxides also affected reduction rates, although not as greatly as ring structure. One of the reduction systems, consisting of the photosensitizer FMN and the photoreductant EDTA, was used to study both anaerobic reduction and O2-dependent reoxidation of some of the nitroxides. Reduced piperidine and hydropyridine nitroxides were also oxidized more rapidly than the reduced pyrroline and pyrrolidine nitroxides. Reoxidation subsequent to reduction was partially inhibited by superoxide dismutase, indicating that superoxide radicals are involved in the process. Even after prolonged reoxidation, not all of the probe molecules were returned to their oxidized form, implying an irreversible "destruction" of the spin probe concomitant with its chemical reduction. Probe destruction was studied more specifically with a photochemical system for generating methyl radicals, which showed that these carbon-centered radicals destroyed different nitroxides at rates which were much less influenced by the nitroxide structures than one-electron reduction was.     

Clustered genes related to sulfate respiration in uncultured prokaryotes support the theory of their concomitant horizontal transfer

The dissimilatory reduction of sulfate is an ancient metabolic process central to today's biogeochemical cycling of sulfur and carbon in marine sediments. Until now its polyphyletic distribution was most parsimoniously explained by multiple horizontal transfers of single genes rather than by a not-yet-identified "metabolic island." Here we provide evidence that the horizontal transfer of a gene cluster may indeed be responsible for the patchy distribution of sulfate-reducing prokaryotes (SRP) in the phylogenetic tree. We isolated three DNA fragments (32 to 41 kb) from uncultured, closely related SRP from DNA directly extracted from two distinct marine sediments. Fosmid ws39f7, and partially also fosmids ws7f8 and hr42c9, harbored a core set of essential genes for the dissimilatory reduction of sulfate, including enzymes for the reduction of sulfur intermediates and synthesis of the prosthetic group of the dissimilatory sulfite reductase. Genome comparisons suggest that encoded membrane proteins universally present among SRP are critical for electron transfer to cytoplasmic enzymes. In addition, novel, conserved hypothetical proteins that are likely involved in dissimilatory sulfate reduction were identified. Based on comparative genomics and previously published experimental evidence, a more comprehensive model of dissimilatory sulfate reduction is presented. The observed clustering of genes involved in dissimilatory sulfate reduction has not been previously found. These findings strongly support the hypothesis that genes responsible for dissimilatory sulfate reduction were concomitantly transferred in a single event among prokaryotes. The acquisition of an optimized gene set would enormously facilitate a successful implementation of a novel pathway.