Phototautomerism of the GC base pair of DNA

Electronic spectra and ground and excited state electronic structures of normal G and rare tautomeric G1z.sbnd;C1 base pairs as well as of the individual rare tautomeric bases (purines and pyrimidines) have been studied using the VE-PPP molecular orbital method. The nature and consequences of the lowest energy purine-localized and purine to pyrimidine charge transfer type π?π1 singlet excitations of the base pairs have been investigated. The results indicate that in these excited states, particularly in the charge transfer excited state, the probability for the GC base pair to change over to G1C1 would be larger than in the ground state. The likeliness of the relevance of results obtained experimentally by other workers from the study of a model system to the GC base pair is discussed.     

Synthesis and characterization of the anomeric pair of 17β-glucuronides of ethynylestradiol

The α- and β-anomers of the 17β-d-glucuronide conjugate of ethynylestradiol were synthesized by the SnCl₄-promoted reaction between β-acetoxy GAM and the t-17β-hydroxyl group of EE₂-3-acetate. The conjugates were resolved by crystallization and HPLC. Positive identification was established by u.v. spectrophotometry, i.r. and mass spectrometry and ¹H- and ¹³⁴C-n.m.r. The structure of the β-anomer was confirmed by X-ray crystallographic analysis. In addition, the α-anomer was refractory to hydrolysis by bovine β-glucuronidase, establishing a biochemical difference between the conjugate pair.     

Functional replacement of the endogenous tyrosyl-tRNA synthetase–tRNATyr pair by the archaeal tyrosine pair in Escherichia coli for genetic code expansion

Non-natural amino acids have been genetically encoded in living cells, using aminoacyl-tRNA synthetase–tRNA pairs orthogonal to the host translation system. In the present study, we engineered Escherichia coli cells with a translation system orthogonal to the E. coli tyrosyl-tRNA synthetase (TyrRS)–tRNA^Tyr pair, to use E. coli TyrRS variants for non-natural amino acids in the cells without interfering with tyrosine incorporation. We showed that the E. coli TyrRS–tRNA^Tyr pair can be functionally replaced by the Methanocaldococcus jannaschii and Saccharomyces cerevisiae tyrosine pairs, which do not cross-react with E. coli TyrRS or tRNA^Tyr. The endogenous TyrRS and tRNA^Tyr genes were then removed from the chromosome of the E. coli cells expressing the archaeal TyrRS–tRNA^Tyr pair. In this engineered strain, 3-iodo-l-tyrosine and 3-azido-l-tyrosine were each successfully encoded with the amber codon, using the E. coli amber suppressor tRNATyr and a TyrRS variant, which was previously developed for 3-iodo-l-tyrosine and was also found to recognize 3-azido-l-tyrosine. The structural basis for the 3-azido-l-tyrosine recognition was revealed by X-ray crystallography. The present engineering allows E. coli TyrRS variants for non-natural amino acids to be developed in E. coli, for use in both eukaryotic and bacterial cells for genetic code expansion.     

The effect of pair bonding in Cabrera vole’s scent marking

The Cabrera vole (Microtus cabrerae) is a rare rodent living in patchy grassy areas of the Iberian Peninsula where unpaired individuals of both sexes use scent marking primarily to increase their mate-finding likelihood. Cabrera voles establish long-term pair bonds with opposite-sex conspecifics constituting a breeding pair, which is expected to reduce the efforts in searching for a new mate. Under such circumstances, scent marking as a strategy to increase mate-finding likelihood became useless. Accordingly, we hypothesise that pair bonded Cabrera voles suppress mate-finding scent marking to reduce energetic costs and predation risk. To test this hypothesis, we compared scent-marking behaviour towards a clean substrate, in both paired and non-paired voles. No differences were found in the scent marks’ type and the amount of marks placed by voles in both conditions. We also analysed the scent-marking behaviour of both sex pair bonded voles when exposed simultaneously to a clean substrate, a substrate pre-marked by males and a substrate pre-marked by females. We found no significant differences in scent-marks (urine-marked area and number of faecal boli) across the three types of substrate types. In accordance with our prediction, these results suggest that pair bonded Cabrera voles did not use scent marking for mate finding, thus providing further support to the existence of a monogamous mating strategy. Furthermore, our results fail to support the use of scent marking for territorial defence purposes.     

Male–male relationships in chimpanzees and the evolution of human pair bonds

The evolution of monogamy has been a central question in biological anthropology. An important avenue of research has been comparisons across “socially monogamous” mammals, but such comparisons are inappropriate for understanding human behavior because humans are not “pair living” and are only sometimes “monogamous.” It is the “pair bond” between reproductive partners that is characteristic of humans and has been considered unique to our lineage. I argue that pair bonds have been overlooked in one of our closest living relatives, chimpanzees. These pair bonds are not between mates but between male “friends” who exhibit enduring and emotional social bonds. The presence of such bonds in male–male chimpanzees raises the possibility that pair bonds emerged earlier in our evolutionary history. I suggest pair bonds first arose as “friendships” and only later, in the human lineage, were present between mates. The mechanisms for these bonds were co-opted for male-female bonds in humans.     

A pair of vicarious species of Epipactis（Orchidaceae）from western North America and Himalaya-central Asia

A pair of vicarious species disjunctly distributed in western North America and Himalaya-central　Asia,Epipactis gigantea Dougl.ex Hook.and E.royleana Lindl.,are illustrated and discussed taxonomically and phytogeographically.A distribution map is provided     

Role of terminal dipole charges in aggregation of α-helix pair in the voltage gated K+ channel

The voltage sensor domain (VSD) of the potassium ion channel KvAP is comprised of four (S1–S4) α-helix proteins, which are encompassed by several charged residues. Apart from these charges, each peptide α-helix having two inherent equal and opposite terminal dipolar charges behave like a macrodipole. The activity of voltage gated ion channel is electrostatic, where all the charges (charged residues and dipolar terminal charges) interact with each other and with the transmembrane potential. There are evidences that the role of the charged residues dominate the stabilization of the conformation and the gating process of the ion channel, but the role of the terminal dipolar charges are never considered in such analysis. Here, using electrostatic theory, we have studied the role of the dipolar terminal charges in aggregation of the S3b–S4 helix pair of KvAP in the absence of any external field (V = 0). A system attains stability, when its potential energy reaches minimum values. We have shown that the presence of terminal dipole charges (1) change the total potential energy of the charges on S3b–S4, affecting the stabilization of the α-helix pair within the bilayer lipid membrane and (2) the C- and the N-termini of the α-helices favor a different dielectric medium for enhanced stability. Thus, the dipolar terminal charges play a significant role in the aggregation of the two neighboring α-helices.     

Function of pair duets in the eastern whipbird: cooperative defense or sexual conflict?

Paired male and female eastern whipbirds, Psophodes olivaceus,sing precisely coordinated, male-led duets. Four broad explanationshave been proposed for the function of duets: 1) cooperativeresource defense, 2) prevention of partner usurpation, 3) defenseof an individual's own position within the partnership, or 4)mate identification and localization. These 4 hypotheses makedifferent predictions about how male and female residents shouldrespond to simulated intrusion by other pairs or individuals.We compared the behavioral and vocal responses of 20 pairs ofeastern whipbirds to simulated territorial intrusions by: 1)a solitary singing male, 2) a solitary singing female, and 3)a duetting pair. Males and females did not coordinate theirapproach to the playback speaker and showed sex-specific responsesto playback. Males did not respond differently to duetting versussolo singing intruders. By contrast, females approached moreclosely during solo female song than during solo male song orduet playback. Females also produced specific vocalizationsonly in response to duet and solo female playback. Both sexesapproached the speaker more closely and quickly during playbackof same-sex solo songs than opposite-sex solo songs. Finally,females answered more of their mate's songs during simulatedintrusion by a lone female than during simulated intrusion bya lone male. Our results suggest that duets in this speciesprimarily function to allow females to defend their exclusiveposition in a partnership. Mate defense by females is unusualin birds but may be promoted in eastern whipbirds by a female-biasedsex ratio and the need for exclusive access to male care. Thus,duets result from independent and conflicting strategies ofmate and territory defense in males and females.     

Structural insights of non-canonical U?U pair and Hoogsteen interaction probed with Se atom

Unlike DNA, in addition to the 2′-OH group, uracil nucleobase and its modifications play essential roles in structure and function diversities of non-coding RNAs. Non-canonical U•U base pair is ubiquitous in non-coding RNAs, which are highly diversified. However, it is not completely clear how uracil plays the diversifing roles. To investigate and compare the uracil in U-A and U•U base pairs, we have decided to probe them with a selenium atom by synthesizing the novel 4-Se-uridine (^SeU) phosphoramidite and Se-nucleobase-modified RNAs (^SeU-RNAs), where the exo-4-oxygen of uracil is replaced by selenium. Our crystal structure studies of U-A and U•U pairs reveal that the native and Se-derivatized structures are virtually identical, and both U-A and U•U pairs can accommodate large Se atoms. Our thermostability and crystal structure studies indicate that the weakened H-bonding in U-A pair may be compensated by the base stacking, and that the stacking of the trans-Hoogsteen U•U pairs may stabilize RNA duplex and its junction. Our result confirms that the hydrogen bond (O4^…H-C5) of the Hoogsteen pair is weak. Using the Se atom probe, our Se-functionalization studies reveal more insights into the U•U interaction and U-participation in structure and function diversification of nucleic acids.     

Thermodynamic signature of DNA damage: characterization of DNA with a 5-hydroxy-2'-deoxycytidine·2'-deoxyguanosine base pair

Oxidation of DNA due to exposure to reactive oxygen species is a major source of DNA damage. One of the oxidation lesions formed, 5-hydroxy-2'-deoxycytidine, has been shown to miscode by some replicative DNA polymerases but not by error prone polymerases capable of translesion synthesis. The 5-hydroxy-2'-deoxycytidine lesion is repaired by DNA glycosylases that require the 5-hydroxycytidine base to be extrahelical so it can enter into the enzyme's active site where it is excised off the DNA backbone to afford an abasic site. The thermodynamic and nuclear magnetic resonance results presented here describe the effect of a 5-hydroxy-2'-deoxycytidine·2'-deoxyguanosine base pair on the stability of two different DNA duplexes. The results demonstrate that the lesion is highly destabilizing and that the energy barrier for the unstacking of 5-hydroxy-2'-deoxycytidine from the DNA duplex may be low. This could provide a thermodynamic mode of adduct identification by DNA glycosylases that requires the lesion to be extrahelical.     

Assessing the preferred solution conformation of an interacting sense–antisense (complementary) peptide pair

Sense peptides and corresponding antisense peptides, are capable of making specific interactions. Such interactions may result from inter-peptide side-chain/side-chain contacts or because peptides adopt mutually complementary three-dimensional shapes. Using a combined ¹H NMR spectroscopy/molecular modeling approach to study the interactions between one sense peptide and its corresponding antisense peptide, data are produced that provide clear support for the former hypothesis.     

Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct?

Many existing derivations of knowledge-based statistical pair potentials invoke the quasichemical approximation to estimate the expected side-chain contact frequency if there were no amino acid pair-specific interactions. At first glance, the quasichemical approximation that treats the residues in a protein as being disconnected and expresses the side-chain contact probability as being proportional to the product of the mole fractions of the pair of residues would appear to be rather severe. To investigate the validity of this approximation, we introduce two new reference states in which no specific pair interactions between amino acids are allowed, but in which the connectivity of the protein chain is retained. The first estimates the expected number of side-chain contracts by treating the protein as a Gaussian random coil polymer. The second, more realistic reference state includes the effects of chain connectivity, secondary structure, and chain compactness by estimating the expected side-chain contrast probability by placing the sequence of interest in each member of a library of structures of comparable compactness to the native conformation. The side-chain contact maps are not allowed to readjust to the sequence of interest, i.e., the side chains cannot repack. This situation would hold rigorously if all amino acids were the same size. Both reference states effectively permit the factorization of the side-chain contact probability into sequence-dependent and structure-dependent terms. Then, because the sequence distribution of amino acids in proteins is random, the quasichemical approximation to each of these reference states is shown to be excellent. Thus, the range of validity of the quasichemical approximation is determined by the magnitude of the side-chain repacking term, which is, at present, unknown. Finally, the performance of these two sets of pair interaction potentials as well as side-chain contact fraction-based interaction scales is assessed by inverse folding tests both without and with allowing for gaps.     

A monozygotic twin pair with β-thalassemia carrier status in a Dudh Kharia tribal family of Orissa

BACKGROUND:

The β-thalassemia syndrome is a genetically inherited commonly encountered hematological disorder in the state of Orissa. It causes high degree of morbidity, mortality and fetal wastage in the poor vulnerable people.

AIMS AND OBJECTIVES:

There is an equal probability (50% chance) in every singleton pregnancy that a carrier parent of β-thalassemia major would either bear normal or carrier offspring, but not two offspring with carrier of β-thalassemia major genotype together. For the first time, a carrier parent of β-thalassemia major gene has born progeny (three daughters and a twin male offspring) with a carrier status of β-thalassemia major in Dudh Kharia tribal family studied from Sundargarh district of Orissa.

MATERIALS AND METHODS:

We screened randomly selected population of Dudh Kharia tribe from Sundargarh district of Orissa for hemoglobinopathies to assess the extent of the problem, design possible interventions and provide genetic counseling to them. A family with twin children was identified during screening in Lata Gaon in Bargaon block of Sundargarh district of Orissa for the above-mentioned study. Background information for this family such as name, age, sex, tribe, native place, reproductive history, family pedigree and clinical signs and symptoms were also recorded. Standardized genetic and hematological procedures and techniques were followed for analysis.

RESULTS:

Laboratory investigations for alkaline electrophoresis of blood lysate on cellulose acetate membrane showed raised hemoglobin A₂ level in mother (Hb A₂ = 5.3%), in three daughters (Hb A₂ =6.5, 5.9, 5.5% in chronological and birth order), in two twin sons (Hb A₂ =5.9% and 6.0%) and normal (Hb A₂ = 3.3%) for father. Hence, all the children i.e., three daughters and two twin sons, including the mother were β-thalassemia carriers. Since all the hematological parameters i.e., red cell indices, G-6-PD enzyme activity, ABO and Rhesus blood groups and identical β-thalassemia (trait) genotypes with identical clinical manifestations and hematological profile of the twin sons under similar environmental conditions, hence they were labeled as identical monozygotic twins.

CONCLUSIONS:

It is a rare occasion when a single pregnancy carries either one or two abnormal genotypes at a time in a womb in human beings. Monozygotic twins are genetically alike and provide appraisal of the expression of identical genotype under the different environmental conditions.     

Is full physical contact necessary for buffering effects of pair housing on social stress in rats?

Our previous study showed that pair housing with a familiar male prevented an increase in anxiety caused by social defeat in male rats. The present study attempted to identify the aspects of social interactions with a familiar male that are needed for the emergence of such a pair-housing effect. In Experiment 1, the subject was repeatedly exposed to the cage and bedding used by a familiar pairmate, after two instances of social defeat. Mere exposure to the soiled cage and bedding did not prevent an increase in anxiety in the elevated plus-maze test performed two weeks after social defeat. In Experiment 2, the subject was separated from a familiar pairmate with a wire mesh partition, which allowed visual, auditory, and limited physical contact, in addition to olfactory contact with the pairmate. The separation with a wire mesh partition abolished the buffering effect of pair housing on anxiety. These results indicate that visual, auditory, and olfactory contact with a familiar male was not sufficient in reducing the anxiogenic effect of social defeat in male rats. It was suggested that full physical contact is necessary for the emergence of the buffering effect of pair housing on social stress.     

Molecular cloning of a pair of human pepsinogen A genes which differ by a Glu→Lys mutation in the activation peptide

Summary Three human cosmid clones containing pepsinogen A (PGA) encoding sequences were isolated from a genomic bank derived from a single individual. One cosmid contains two PGA genes in tandem in a head-to-tail orientation, while the other two cosmids each contain a single PGA gene. The three cosmids were characterized by restriction mapping and sequence analysis (exons 1 and 2 and flanking regions). As judged from these data, three of the four PGA genes isolated appear to be nearly identical, but one of the tandem genes is clearly different from the other genes. The first exon of all four genes codes for the same amino acid sequence. However, in the second exon of one of the tandem genes we found a nucleotide substitution giving rise to a GluLys substitution of the 43rd amino acid residue of the activation peptide, leading to a charge difference of the corresponding isozymogens. The presence of two distinct PGA genes in the isolated gene pair conclusively proves the multigene structure of the PGA system. These genes might be responsible for at least part of the electrophoretic polymorphism at the protein level.     

Thermodynamic and structural properties of the specific binding between Ag ion and C:C mismatched base pair in duplex DNA to form C–Ag–C metal-mediated base pair

Metal ion-nucleic acid interactions have attracted considerable interest for their involvement in structure formation and catalytic activity of nucleic acids. Although interactions between metal ion and mismatched base pair duplex are important to understand mechanism of gene mutations related to heavy metal ions, they have not been well-characterized. We recently found that the Ag⁺ ion stabilized a C:C mismatched base pair duplex DNA. A C–Ag–C metal-mediated base pair was supposed to be formed by the binding between the Ag⁺ ion and the C:C mismatched base pair to stabilize the duplex. Here, we examined specificity, thermodynamics and structure of possible C–Ag–C metal-mediated base pair. UV melting indicated that only the duplex with the C:C mismatched base pair, and not of the duplexes with the perfectly matched and other mismatched base pairs, was specifically stabilized on adding the Ag⁺ ion. Isothermal titration calorimetry demonstrated that the Ag⁺ ion specifically bound with the C:C base pair at 1:1 molar ratio with a binding constant of 10⁶ M⁻¹, which was significantly larger than those for nonspecific metal ion-DNA interactions. Electrospray ionization mass spectrometry also supported the specific 1:1 binding between the Ag⁺ ion and the C:C base pair. Circular dichroism spectroscopy and NMR revealed that the Ag⁺ ion may bind with the N3 positions of the C:C base pair without distorting the higher-order structure of the duplex. We conclude that the specific formation of C–Ag–C base pair with large binding affinity would provide a binding mode of metal ion-DNA interactions, similar to that of the previously reported T-Hg-T base pair. The C–Ag–C base pair may be useful not only for understanding of molecular mechanism of gene mutations related to heavy metal ions but also for wide variety of potential applications of metal-mediated base pairs in various fields, such as material, life and environmental sciences.     

Is one parasitoid enough? A test comparing one with a pair of parasitoid species in the biological control of arrowhead scales

In classic biological control using natural enemies, the question of whether a single species or multiple species should be introduced has been a matter of debate. The introduction of two parasitoids, Aphytis yanonensis and Coccobius fulvus (Hymenoptera: Aphelinidae), to control the arrowhead scale, Unaspis yanonensis (Hemoptera: Diaspididae), which is a serious pest in Japanese citrus orchards, has been one of the most successful biological control projects in Japan. The success of this program may be explained by two alternative hypotheses: (1) the parasitoid species work complementarily, or (2) only one of them plays a major role. To test which hypothesis is applicable to this host-parasitoid system, we conducted caging experiments and observed temporal changes in the proportion of the parasitisms and the densities of arrowhead scales enclosed with one of the following combinations of parasitoids: (1) A. yanonensis and C. fulvus together, (2) A. yanonensis alone, (3) C. fulvus alone, or (4) neither parasitoid. Parasitisms in the cohorts with A. yanonensis and C. fulvus together and C. fulvus alone rapidly increased to approximately 70%; parasitism with A. yanonensis alone also increased slightly, although it remained consistently lower that those with A. yanonensis and C. fulvus together and C. fulvus. At the end of the experiment, parasitisms with A. yanonensis and C. fulvus together and C. fulvus alone were significantly higher than that with A. yanonensis alone. Parasitism by C. fulvus constituted most of (74%) the parasitism in the cohort with A. yanonensis and C. fulvus together. Further, only C. fulvus suppressed the population growth rates of scales significantly. These results suggest that C. fulvus alone successfully suppresses scale populations as efficiently as both species together do.     

Can simple codon pair usage predict protein-protein interaction?

Deciphering functional interactions between proteins is one of the great challenges in biology. Sequence-based homology-free encoding schemes have been increasingly applied to develop promising protein-protein interaction (PPI) predictors by means of statistical or machine learning methods. Here we analyze the relationship between codon pair usage and PPIs in yeast. We show that codon pair usage of interacting protein pairs differs significantly from randomly expected. This motivates the development of a novel approach for predicting PPIs, with codon pair frequency difference as input to a Support Vector Machine predictor, termed as CCPPI. 10-fold cross-validation tests based on yeast PPI datasets with balanced positive-to-negative ratios indicate that CCPPI performs better than other sequence-based encoding schemes. Moreover, it ranks the best when tested on an unbalanced large-scale dataset. Although CCPPI is subjected to high false positive rates like many PPI predictors, statistical analyses of the predicted true positives confirm that the success of CCPPI is partly ascribed to its capability to capture proteomic co-expression and functional similarities between interacting protein pairs. Our findings suggest that codon pairs of interacting protein pairs evolve in a coordinated manner and consequently they provide additional information beyond amino acids-based encoding schemes. CCPPI has been made freely available at: http://protein.cau.edu.cn/ccppi.     

Neural mechanisms of mother–infant bonding and pair bonding: Similarities,differences, and broader implications

This article is part of a Special Issue “Parental Care”.Mother–infant bonding is a characteristic of virtually all mammals. The maternal neural system may have provided the scaffold upon which other types of social bonds in mammals have been built. For example, most mammals exhibit a polygamous mating system, but monogamy and pair bonding between mating partners occur in ~ 5% of mammalian species. In mammals, it is plausible that the neural mechanisms that promote mother–infant bonding have been modified by natural selection to establish the capacity to develop a selective bond with a mate during the evolution of monogamous mating strategies. Here we compare the details of the neural mechanisms that promote mother–infant bonding in rats and other mammals with those that underpin pair bond formation in the monogamous prairie vole. Although details remain to be resolved, remarkable similarities and a few differences between the mechanisms underlying these two types of bond formation are revealed. For example, amygdala and nucleus accumbens–ventral pallidum (NA–VP) circuits are involved in both types of bond formation, and dopamine and oxytocin actions within NA appear to promote the synaptic plasticity that allows either infant or mating partner stimuli to persistently activate NA–VP attraction circuits, leading to an enduring social attraction and bonding. Further, although the medial preoptic area is essential for maternal behavior, its role in pair bonding remains to be determined. Our review concludes by examining the broader implications of this comparative analysis, and evidence is provided that the maternal care system may have also provided the basic neural foundation for other types of strong social relationships, beyond pair bonding, in mammals, including humans.     

A haplotype-linked four base pair deletion upstream of the Aγ globin gene coincides with decreased gene expression

Summary During normal human development, a switch is classically observed in the relative expression of the two globin genes, the G/A ratio varying from 70/30 at birth to 40/60 by the end of the first year. An exception to this developmental pattern is linked to the presence of an XmnI restriction site at a position — 158 to the Cap site of the G gene. Another exception is observed in individuals homozygous for two easily detectable variations of the A gene: the presence of a threonine residue at codon 75 and a HindIII site within the second intron. A 4-bp deletion has been described around position — 225 in some thalassemic patients presenting with these variations. In this study, we find this deletion to be haplotypelinked in a series of 156 individuals of various ethnic origins and presenting with various normal and pathological phenotypes. In sickle cell patients heterozygous for this 4-bp deletion, the relative expression of the A genes on the two chromosomes can be measured by estimating the AT and AI chains, the former always being synthesized at a lower rate. These results suggest a functional role for the deleted sequence.