When secondary comes first – The importance of non-canonical DNA structures

Secondary structure-forming DNA motifs have achieved infamy because of their association with a variety of human diseases and cancer. The 3rd FASEB summer conference on dynamic DNA structures focused on the mechanisms responsible for the instabilities inherent to repetitive DNA and presented many exciting and novel aspects related to the metabolism of secondary structures. In addition, the meeting encompassed talks and posters on the dynamic structures that are generated during DNA metabolism including nicked DNA, Holliday junctions and RNA:DNA hybrids. New approaches for analysis and sequencing technologies put forth secondary structures and other DNA intermediates as vital regulators of a variety of cellular processes that contribute to evolution, polymorphisms and diseases.     

Structures composing protein domains

This review summarizes available data concerning intradomain structures (IS) such as functionally important amino acid residues, short linear motifs, conserved or disordered regions, peptide repeats, broadly occurring secondary structures or folds, etc. IS form structural features (units or elements) necessary for interactions with proteins or non-peptidic ligands, enzyme reactions and some structural properties of proteins. These features have often been related to a single structural level (e.g. primary structure) mostly requiring certain structural context of other levels (e.g. secondary structures or supersecondary folds) as follows also from some examples reported or demonstrated here. In addition, we deal with some functionally important dynamic properties of IS (e.g. flexibility and different forms of accessibility), and more special dynamic changes of IS during enzyme reactions and allosteric regulation. Selected notes concern also some experimental methods, still more necessary tools of bioinformatic processing and clinically interesting relationships.     

Genetic analysis of ORF5 porcine reproductive and respiratory syndrome virus isolated in Vietnam

Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most economically important swine pathogens because it is highly infectious and causes economic losses due to decreased pig productivity. In this study, the 603 bp complete major envelope protein encoding gene (ORF5) of 32 field PRRSV isolates from Vietnam collected during 2008–2012 were sequenced and analyzed. Multiple nucleotide (nt) and deduced amino acid (aa) alignments of ORF5 were performed on the 32 isolates: the representative strains (European and North American genotypes), Chinese strains available in GenBank and vaccine strains licensed for use in Vietnam. The results showed 94.8–100.0% nt identity and 94.0–100% aa similarity among the 32 isolates. These isolates shared similarities with the prototype of the North American PRRSV strain (VR‐2332; nt 87.8–89.3%, aa 87.5–90.0%), and Lelystat virus, the prototype of the European PRRSV strain (LV; nt 61.1–61.9%, aa 55.1‐57.0%). There was greater similarity with QN07 (nt 96.5‐98.5%, aa 96.0‐99.0%) from the 2007 PRRS outbreak in QuangNam Province, CH‐1a (nt 93.2–95.1%, 91.5–93.5%) isolated in China in 1995 and JXA1 (nt 96.5–98.6%, aa 95.0–98.0%), the highly pathogenic strain from China isolated in 2006. The Vietnamese isolates were more similar to JXA1‐R (nt 96.5–98.6%, aa 95.0–98.0%), the strain used in Chinese vaccines, than to Ingelvac MLV/BSL‐PS (nt 87.2–89.0%, aa 86.0–89.0%). Phylogenetic analysis showed that the 32 isolates were of the North American genotype and classified into sub‐lineage 8.7. This sub‐lineage contains highly pathogenic Chinese PRRSV strains. This study documents genetic variation in circulating PRRSV strains and could assist more effective use of PRRS vaccines in Vietnam.     

Crystal structure of the S187F variant of human liver alanine: Aminotransferase associated with primary hyperoxaluria type I and its functional implications

The substitution of Ser187, a residue located far from the active site of human liver peroxisomal alanine:glyoxylate aminotransferase (AGT), by Phe gives rise to a variant associated with primary hyperoxaluria type I. Unexpectedly, previous studies revealed that the recombinant form of S187F exhibits a remarkable loss of catalytic activity, an increased pyridoxal 5′‐phosphate (PLP) binding affinity and a different coenzyme binding mode compared with normal AGT. To shed light on the structural elements responsible for these defects, we solved the crystal structure of the variant to a resolution of 2.9 Å. Although the overall conformation of the variant is similar to that of normal AGT, we noticed: (i) a displacement of the PLP‐binding Lys209 and Val185, located on the re and si side of PLP, respectively, and (ii) slight conformational changes of other active site residues, in particular Trp108, the base stacking residue with the pyridine cofactor moiety. This active site perturbation results in a mispositioning of the AGT‐pyridoxamine 5′‐phosphate (PMP) complex and of the external aldimine, as predicted by molecular modeling studies. Taken together, both predicted and observed movements caused by the S187F mutation are consistent with the following functional properties of the variant: (i) a 300‐ to 500‐fold decrease in both the rate constant of L‐alanine half‐transamination and the k_cat of the overall transamination, (ii) a different PMP binding mode and affinity, and (iii) a different microenvironment of the external aldimine. Proposals for the treatment of patients bearing S187F mutation are discussed on the basis of these results. Proteins 2013; 81:1457–1465. © 2013 Wiley Periodicals, Inc.     

Gonadal maturation,fecundity, spawning,and timing of reproduction in the mud snail,Cerithidea cingulata,a pest in milkfish ponds in the Philippines

Summary

Gonadal maturation, spawning, fecundity and timing of reproduction of the snail Cerithidea cingulata in a brackish water pond in Molo, Iloilo, Philippines, are described. Snails 4–41 mm in shell length were sampled monthly from May 1997 to May 1998; 25% were <25 mm, 67% were 20–30 mm, and 8% were >30 mm. The sexes are separate and could first be distinguished at 15 mm. Males are aphallic, have narrower shells than females of the same length, and have bright yellow-orange testes overlying the digestive gland deep inside the shell. Females have more robust shells, an ovipositor at the right side of the foot, and yellow-green ovaries overlying the digestive gland. The sex ratio was one male to two females in the pond population studied. Gonadal maturation was monitored by means of gonadosomatic index (GSI, gonad weight as a percent of visceral weight); maturation stages were based on the gonad appearance (immature, developing, mature) and histology (immature, developing, mature, redeveloping). GSI increased with snail size, and reached 16% in a 33-mm female. The smallest mature males and females were 18–19 mm, and most snails >20 mm were mature, spawning, or redeveloping. Histological sections showed all stages of gametogenesis in mature male snails. The oocyte size-frequency distributions in mature females showed mostly mature oocytes and secondary oocytes, but also oogonia and primary oocytes. GSI and the frequency of snails at different maturation stages varied over the year. Both GSI and the frequency of mature snails were highest during the summer months, April to August. Nevertheless, mature snails occurred throughout the whole year, as did mating and egg-laying. Fecundity (= number of oocytes >70 pμ) increased with size in mature females 2041 mm; an average 25-mm female produced about 1,500 oocytes and larger females produced a maximum of about 2,500 oocytes. Eggs strings laid on the pond bottom were 45–75 mm long; an average 64-mm string contained 2,000 eggs 210+20 pm in diameter. The density of eggs strings was highest (80–120/m²) during March-September. Eggs hatched after 6–7 d into planktonic veligers, which in turn settle on the pond bottom 11–12 d later as juveniles. Juveniles 2–6-mm long were most abundant in the pond during August-October.     

Community Structure and Role Analysis in Biological Networks

Abstract

Complex network analysis has received increasing interest in recent years, which provides a remarkable tool to describe complex systems of interacting entities, particular for biological systems. In this paper, we propose a methodology for identifying the significant nodes of the networks, including core nodes, bridge nodes and high-influential nodes, based on the idea of community and two new ranking measures, InterRank and IntraRank. The results show the significant nodes form a small number in biological networks, and uncover the relative small number of which has advantage for reducing the dimensions of the network and possibly help to define new biological targets.     

Nereis succinea nuptial behavior: Does size matter?

Summary

Although Darwin noted that size may affect sexual selection, the effect of size on reproduction is controversial. Mature Nereis succinea, a polychaete that mates in pheromone-mediated twilight nuptial swarms, varies greatly in size, ranging more than 10-fold in body weight from 30 mg to >300 mg. Swim speed of swarming male worms increases with worm size, with the fastest males swimming more than twice the speed of the slowest. The female-produced spawning pheromone, nereithione, stimulates both swimming speed and spawning in males at concentrations of 10^?6 M and above, and lower concentrations cause significant activation of swimming. Individual worms can be stimulated to release sperm up to 40 or more times in a single experimental session. Larger worms release cumulatively more sperm than smaller ones, resulting in significant loss of body mass from repetitive spawning activated by nereithione. Size may enhance mating success of male N. succinea due to encountering more females as a result of faster swimming speed and due to the higher sperm density and number of spawning responses of large animals.     

Organization,development, and effects of infraorbital nerve transection on galanin binding sites in the trigeminal brainstem complex

Previous experiments from this laboratory have indicated that transection of the infraorbital nerve (ION, the trigeminal \[V] branch that supplies the mystacial vibrissae follicles) at birth and in adulthood has markedly different effects on galanin immunoreactivity in the V brainstem complex. Adult nerve transection increases galanin immunoreactivity in the superficial layers of V subnucleus caudalis (SpC) only, while neonatal nerve transection results in increased galanin expression in vibrissae-related primary afferents throughout the V brainstem complex. The present study describes the distribution of binding sites for this peptide in the mature and developing V ganglion and brainstem complex and determines the effects of neonatal and adult ION damage and the associated changes in galanin levels upon their distribution and density. Galanin binding sites are densely distributed in all V brainstem subnuclei and are particularly dense in V subnucleus interpolaris and the superficial layers of SpC. They are present at birth (P-0) and their distribution is similar to that in adult animals. Transection of the ION in adulthood and examination of brainstem 7 days later indicated marked reductions in the density of galanin binding sites in the V brainstem complex. With the exception of the superficial laminae of SpC, the same reduction in density remained apparent in rats that survived 45 days after nerve cuts. Transection of the ION on P-0 resulted in no change in the density of galanin binding sites in the brainstem after either 7 or 60 days survival. These results indicate that densely distributed galanin binding sites are present in the V brainstem complex of both neonatal and adult rats, that they are located in regions not innervated by galanin-positive axons, and that their density is not significantly influenced by large lesion-induced changes in the primary afferent content of their natural ligand.     

Spatial summation of heat induced pain within and between dermatomes

The aim was to study spatial summation within and between ipsi- and contralateral dermatomes at different painful temperatures. For heat stimulation we used a computer controlled thermofoil based thermode. The thermode area could be varied in five discrete steps from 3.14 to 15.70 cm2. When we applied the stimuli within a dermatome, the mean heat pain threshold decreased significantly from 45.6 to 43.5 C as the area was increased from minimum (3.14 cm2) to maximum (15.70 cm2). When the areas were increased involving different dermatomes (both ipsi- or contralateral), we found similar decreases in pain threshold. Spatial summation was also found within and between dermatomes at supra-threshold temperatures (46, 48, 50 C).The study shows that spatial summation of pain is most likely a mechanism acting across segments and is existing from pain threshold to tolerance.