Genetic relatedness analysis: modern data and new challenges

Individuals who belong to the same family or the same population are related because of their shared ancestry. Population and quantitative genetics theory is built with parameters that describe relatedness, and the estimation of these parameters from genetic markers enables progress in fields as disparate as plant breeding, human disease gene mapping and forensic science. The large number of multiallelic microsatellite loci and biallelic SNPs that are now available have markedly increased the precision with which relationships can be estimated, although they have also revealed unexpected levels of genomic heterogeneity of relationship measures.     

Queen recognition by brood-rearing workers of the ant Myrmica rubra L

The means by which queens communicate their presence to workers and so influence broodrearing, in particular caste determination, have been analysed; both chemical and topographical stimuli are used. This follows from the fact that though dead inseminated queens are effective, the following are not: dead virgins (same shape but different smell), lipid extracted mature queens (same shape but no smell), parts of inseminated queens alone or together (same smell but different shape). This also rules out a drug-like influence on workers or larvae. The chemicals are not produced in the two main head glands, the mandibular and the pharyngeal, as no loss of potency follows their excision. The abdomen is the most likely source of a substance, the emission of which must vary seasonally.     

Size of cardiomyocytes in different regions of the rat heart

In rats after alcaline dissociation of the heart at the state of systol and diastol, length and width of cardiomyocytes have been measured, their volume has been calculated. Statistical characteristics of distribution connected with the first four moments have been taken into consideration. Certain size differences of cardiomyocytes in five cardiac parts have been revealed, as well as peculiarites of their variability that is connected with an individual and internal changeability. In the atria predominates the first, in the ventricles--the second. If the internal changeability of the cardiomyocytes in all the cardiac parts is mainly the same, the individual one--is different (in the atrii it is 2 times as great, in the interventricular septum it is the same as in the atrii). The individual changeability of the cardiomyocytes volume is also greater than that of their size. This also proves the variability of their proportions. The degree of their contractility makes 11--20%, differences between the cardiac parts are not significant. The data obtained could be used as normatives for various experiments.     

Parallel evolution of ligand specificity between LacI/GalR family repressors and periplasmic sugar-binding proteins

The bacterial LacI/GalR family repressors such as lactose operon repressor (LacI), purine nucleotide synthesis repressor (PurR), and trehalose operon repressor (TreR) consist of not only the N-terminal helix-turn-helix DNA-binding domain but also the C-terminal ligand-binding domain that is structurally homologous to periplasmic sugar-binding proteins. These structural features imply that the repressor family evolved by acquiring the DNA-binding domain in the N-terminal of an ancestral periplasmic binding protein (PBP). Phylogenetic analysis of the LacI/GalR family repressors and their PBP homologues revealed that the acquisition of the DNA-binding domain occurred first in the family, and ligand specificity then evolved. The phylogenetic tree also indicates that the acquisition occurred only once before the divergence of the major lineages of eubacteria, and that the LacI/GalR and the PBP families have since undergone extensive gene duplication/loss independently along the evolutionary lineages. Multiple alignments of the repressors and PBPs furthermore revealed that repressors and PBPs with the same ligand specificity have the same or similar residues in their binding sites. This result, together with the phylogenetic relationship, demonstrates that the repressors and the PBPs individually acquired the same ligand specificity by homoplasious replacement, even though their genes are encoded in the same operon.     

Genotype-temperature interaction inDrosophila melanogaster. I. Viability

Some isogenic strains produced from a natural population at El Prat (Barcelona) were tested at different temperatures for total viability. Their hybrids were also tested at the same temperatures for the same trait. Hybrids proved to be more homcostatic than their isogenic parental strains. More efficient homeostasis in hybrids is suggested to be the cause of increased hybrid superiority with decreasing temperature.Genotype-temperature interaction was always significant for isogenic strains, but never for hybrids. These results are discussed in terms of coadaptation and homeostasis. Some maternal effects have also been detected.     

The formation and enzymatic repair of DNA modifications caused by the haloethylnitrosoureas and related compounds.

The haloethylnitrosoureas are both useful antitumor agents and known carcinogens. These biological activities are believed to be associated with DNA modification, and some biologically significant lesions have been identified in DNA exposed to these agents. At the same time, DNA repair is a cause of resistance to treatment by these agents, and may also serve as protection against their carcinogenic effects.     

日本菟丝子的生物防治研究初报危害性及寄生真菌的筛选

危害林木的菟丝子在广西主要是日本菟丝子(Cuscuta aponica Choisy),其危不仅表现在它寄生的普遍性和严重性。还表现在它寄生的持久性。其中以龙眼、柚子、桂花、台湾相思等被害严重。 在菟丝子寄生真菌的筛选中发现(1)对日本菟丝子有较强致病力的菌株是刺盘孢菌(Colletotrichum spp)。(2)这些菌株中的绝大多数对同种寄主上含不同色素的同种菟丝子有不同的致病力,仅有少数表现相近似的,但它们的致病力相对较弱。(3)对大多数菌株来说,同一菌株对来源于不同寄主上的同种色泽的同种菟丝子有不同的致病力。     

Antigenic relatedness of small ribonucleoprotein particles

We have examined the relationships among small ribonucleoprotein particles found in eucaryotic cells by an antigen depletion technique using autoimmune antibodies. We have confirmed that the (U1) ribonucleoprotein particle antigen is found on the same complex as the Sm antigen. We have also shown that the Ro antigen is found on the same complexes as the La antigen. However, both Sm and La antigens are also found on complexes that are never associated with (U1) ribonucleoprotein particle and Ro, respectively. Further, U1 containing complexes can exist that contain the Sm antigen but not the (U1) ribonucleoprotein particle antigen. In a similar manner, we find several La-Ro RNA containing complexes that carry the La antigen but do not always carry the Ro antigen. Sm and La antigen are quantitatively associated with their specific ribonucleoprotein complexes.     

Testing Quasi-Independence in Stratified Triangular Contingency Tables

A special class of incomplete contingency tables has structural zeroes in one or more cells. Some of these tables have a triangular appearance in the sense that they are square and their cells are known a priori to contain zeroes above (or below) their main diagonals. We propose methods of analyzing log-linear models and testing quasi-independence in these triangular tables. We also offer a method for combining such tables that are stratified by a concomitant categorical variable. This strategy follows the same approach used in a Cochran-Mantel-Haenszel test.     

Microeconomic principles explain an optimal genome size in bacteria

Bacteria can clearly enhance their survival by expanding their genetic repertoire. However, the tight packing of the bacterial genome and the fact that the most evolved species do not necessarily have the biggest genomes suggest there are other evolutionary factors limiting their genome expansion. To clarify these restrictions on size, we studied those protein families contributing most significantly to bacterial-genome complexity. We found that all bacteria apply the same basic and ancestral 'molecular technology' to optimize their reproductive efficiency. The same microeconomics principles that define the optimum size in a factory can also explain the existence of a statistical optimum in bacterial genome size. This optimum is reached when the bacterial genome obtains the maximum metabolic complexity (revenue) for minimal regulatory genes (logistic cost).     

金华北山区部分绿色蔬菜的营养成分和有害物质测定

对马铃薯、菜豆、萝卜和番茄等４种绿色蔬菜进行营养成分和有害物质的全面测定。结果表明：绿色蔬菜具有高营养、无毒的特点。（１）４种绿色蔬菜的含钙量分别为一般蔬菜同一品种的２４０％、１９８．５％、１６３．７％和１５７．８％,含铁量分别为１７．４倍、８．７倍、１０．７倍和１２．７倍,含磷量分别为１１８．２％、１０２％、１６３．６％和１７７．８％,并具有较高的镁、锌、铜和锰等元素的含量。（２）４种绿色蔬菜的镉、砷、汞、氟、六六六、ＤＤＴ、敌敌畏、乐果、马拉硫磷、对硫磷、甲胺磷、杀螟硫和倍硫磷等１３项有害物质全部符合绿色食品标准。（３）４种绿色蔬菜的ＶＢ１含量分别增加２０％、２２．２％、１６．７％和６％,ＶＢ２分别增加３０％、１２％、１３５％和２６．７,Ｖc分别增加８．６％、６８．９％、１２．１％和１８．１％,胡萝卜素分别为一般同种蔬菜的１６倍、２．９倍、１３．５倍和４．５倍。（４）其蛋白质含量也分别增加１８．５％、１３．９％、７．５％和３０％,灰分分别为２．０８倍、３．１５倍、２．８５倍和２．９６倍,总糖分别为一般同种蔬菜的９１％、１０１．１％、１９１．３％和９５．２％,粗纤维分别为１１３．３％、８９．２％、８６．７％和１０５％。     

Look-up tables for protein solvent accessibility prediction and nearest neighbor effect analysis

We developed dictionaries of two-, three-, and five-residue patterns in proteins and computed the average solvent accessibility of the central residues in their native proteins. These dictionaries serve as a look-up table for making subsequent predictions of solvent accessibility of amino acid residues. We find that predictions made in this way are very close to those made using more sophisticated methods of solvent accessibility prediction. We also analyzed the effect of immediate neighbors on the solvent accessibility of residues. This helps us in understanding how the same residue type may have different accessible surface areas in different proteins and in different positions of the same protein. We observe that certain residues have a tendency to increase or decrease the solvent accessibility of their neighboring residues in C- or N-terminal positions. Interestingly, the C-terminal and N-terminal neighbor residues are found to have asymmetric roles in modifying solvent accessibility of residues. As expected, similar neighbors enhance the hydrophobic or hydrophilic character of residues. Detailed look-up tables are provided on the web at www.netasa.org/look-up/.     

All three Ca2+-binding loops of photoproteins bind calcium ions: the crystal structures of calcium-loaded apo-aequorin and apo-obelin

The crystal structures of calcium-loaded apo-aequorin and apo-obelin have been determined at resolutions 1.7A and 2.2 A, respectively. A calcium ion is observed in each of the three EF-hand loops that have the canonical calcium-binding sequence, and each is coordinated in the characteristic pentagonal bipyramidal configuration. The calcium-loaded apo-protein retain the same compact scaffold and overall fold as the unreacted photoproteins containing the bound substrate, 2-hyroperoxycoelenterazine, and also the same as the Ca2+-discharged obelin bound with product, coleneteramide. Nevertheless, there are easily discerned shifts in both helix and loop regions, and the shifts are not the same between the two proteins. It is suggested that these photoproteins to sense Ca2+ concentration transients and to produce their bioluminescence response on the millisecond timescale. A mechanism of intrastructural transmission of the calcium signal is proposed.     

The pro-life argument from substantial identity and the pro-choice argument from asymmetric value: a reply to Patrick Lee

Lee claims that foetuses and adult humans are phases of the same identical substance, and thus have the same moral status because: first, foetuses and adults are the same physical organism, and second, the development from foetus to adult is quantitative and thus not a change of substance. Versus the first argument, I contend that the fact that foetuses and adults are the same physical organism implies only that they are the same thing but not the same substance, much as living adults and their corpses are the same thing (same body) but not the same substance. Against Lee's second argument, I contend that Lee confuses the nature of a process with the nature of its result. A process of quantitative change can produce a change in substance. Lee also fails to show that foetuses are rational and thus have all the essential properties of adults, as required for them to be the same substance. Against the pro-choice argument from asymmetric value (that only the fact that a human has become conscious of its life and begun to count on its continuing can explain human life's asymmetric moral value, i.e. that it is vastly worse to kill a human than not to produce one), Lee claims that foetus's lives are asymmetrically valuable to them before consciousness. This leads to counterintuitive outcomes, and it confuses the goodness of life (a symmetric value that cannot account for why it is worse to kill a human than not produce one) with asymmetric value.     

How modeling can reconcile apparently discrepant experimental results: the case of pacemaking in dopaminergic neurons

Midbrain dopaminergic neurons are endowed with endogenous slow pacemaking properties. In recent years, many different groups have studied the basis for this phenomenon, often with conflicting conclusions. In particular, the role of a slowly-inactivating L-type calcium channel in the depolarizing phase between spikes is controversial, and the analysis of slow oscillatory potential (SOP) recordings during the blockade of sodium channels has led to conflicting conclusions. Based on a minimal model of a dopaminergic neuron, our analysis suggests that the same experimental protocol may lead to drastically different observations in almost identical neurons. For example, complete L-type calcium channel blockade eliminates spontaneous firing or has almost no effect in two neurons differing by less than 1% in their maximal sodium conductance. The same prediction can be reproduced in a state of the art detailed model of a dopaminergic neuron. Some of these predictions are confirmed experimentally using single-cell recordings in brain slices. Our minimal model exhibits SOPs when sodium channels are blocked, these SOPs being uncorrelated with the spiking activity, as has been shown experimentally. We also show that block of a specific conductance (in this case, the SK conductance) can have a different effect on these two oscillatory behaviors (pacemaking and SOPs), despite the fact that they have the same initiating mechanism. These results highlight the fact that computational approaches, besides their well known confirmatory and predictive interests in neurophysiology, may also be useful to resolve apparent discrepancies between experimental results.     

Structure and Development of Stomata on the Vegetative and Floral Organs in Some Members of Caesalpiniaceae

The structure and development of stomata in 19 species of thefamily Caesalpiniaceae are described. The study is mostly confinedto the leaves, but observations have also been made on othervegetative and floral organs of some species Stomata may beparacytic, anisocytic, anomocytic, and with one subsidiary cell.Occasionally a stoma is diacytic, cyclocytic, or actinocytic.Different types occur individually or may be found side by sideeven on the same surface of an organ. The most prevalent typein all the genera is paracytic except in Caesalpima where itis anomocytic. The development of an anomocytic stoma is perigenous,but those with subsidiary cells are largely mesogenous; rarelyparacytic stomata are mesoperigenous. In spite of diversityof stomata, different types of stomata have similar patternsof development in different organs of the same plant. The presentinvestigation also indicates that the inconstancy of stomatain the family is due to (a) their diversity and (b) an increasein the number of subsidiary cells either by their division orby the neighbouring perigenes becoming subsidiary cell-like.     

Class III peroxidases and ascorbate metabolism in plants

Class III peroxidases (PODs) have many functions in plant metabolism mainly dependent on their various physiological reducing substrates. Their involvement in plant differentiation and in the response against environmental stress is well known. Several evidences underline that ascorbate (ASC) levels affect POD reactions and, as a consequence, interfere with the metabolic pathways controlled by these isoenzymes. Ascorbate peroxidases (APXs), enzymes belonging to a different class of peroxidases (class I), are often present in the same cellular compartments in which PODs are also active. Since both APXs and PODs specifically utilise hydrogen peroxide as oxidising substrate they can compete, when co-present, for the same substrate. In this review, attention focuses on some of the physiological processes in which both ASC metabolism and PODs are involved. In particular, the scavenging of reactive oxygen species (ROS) during photosynthesis, cell elongation and wall stiffening as well as programmed cell death have been considered thoroughly. The relations between PODs and ASC metabolism have been discussed also in the attempt to outline their relevance for the correct plant development as well as for the perception/response of external stimuli allowing plants to cope with unfavourable conditions.