The variability of the hepatitis B virus genome: statistical analysis and biological implications

A statistical analysis of the nucleotide sequence variability in 14 published hepatitis B virus (HBV) genomes was carried out using parametric and nonparametric methods. A parametric statistical model revealed that the different regions of the genome differed significantly in their variability. The conclusion was supported by a nonparametric kernel-density model of the HBV genome. Genes S, C, and P, region X, the precore region, and the pre-S2/pre-S1 regions were ranked in order of increasing variability. In many instances, conserved regions of the genome identified with sequences of known function in HBV biology. However, other characterized regions (such as pre-S) showed much variability despite the involvement of their encoded peptides in specific functions. Point mutations that may result in the formation of stop codons and amino acid changes may affect the clinical picture of HBV infection and may be reflected in atypical serological patterns.      

Influences of phylogenetic position and fertilization biology on spermatozoal ultrastructure exemplified by exocoetoid and poeciliid fish

In a cladistic analysis, poeciliids and zenarchopterids homoplasically show elongation and flattening of the nucleus at right angles to the plane of the central axonemal singlets; in both the tip of the nucleus appears rounded in the plane of flattening but pointed in the plane at right angles. The two families differ in the distribution of mitochondria in the .elongate midpiece: circumferential in poeciliids but bilateral in zenarchopterids. In poeciliid sperm and independently in Zenarchopterus, the individual mitochondria are considerably more extensive circumferentially than longitudinally; they differ in poeciliids in being C-shaped. In Hemirhamphodon they are moderately elongate. In Dermogenys and Nomorhamphus they have been modified monophyletically as a pair of elongate mitochondrial derivatives. A wide cytoplasmic periaxonemal sheath (not seen in poeciliids) appears to have developed monophyletically in the ancestry of Hemirhamphodon, Dermogenys and Nomorhamphus with acquisition of radial rodlets only in Hemirhamphodon. A distinctive development in poeciliids is the submitochondrial net. Poeciliids have greatly reduced the axonemal fins which are a synapomorphy of the Actinopteri. Exocoetoids have retained well developed fins in Arrhamphus, Dermogenys and Nomorhamphus but reduction has occurred in Zenarchopterus, in which the fins are small, and, apparently independently, in Hemirhamphodon in which fins are absent. A posterior extension of the nucleus over the base of the axoneme is C-shaped and embraces almost the entire circumference of the axoneme in poeciliids but, independently developed, in zenarchopterids is a dorsal plate. Its absence in Hemirhamphodon is computed as a loss. These modifications relative to the aquasperm condition are deduced to have been occasioned by the adoption of internal fertilization. To what extent they are constrained by features of the genome peculiar to poeciliids, zenarchopterids or atherinomorphs or are demanded by minute differences in fertilization biology, or by a combination of the two, is not at present determinable.Abbreviations a: axoneme - as: central axonemal singlet microtubules - ad: axonemal doublets - cc: cytoplasmic canal (periaxonemal space) - cca: centriolar cap - dc: distal centriole - f: flagellum - fi: axonemal fin - m: mitochondrion - n: nucleus - nf: basal nuclear fossa - ps: peri-axonemal cytoplasmic sheath - s: dorsal spur of nucleus - sl: submitochondrial dense layer - sr: satellite rays     

Definitive Evidence for the existence of tight junctions in invertebrates

Extensive and unequivocal tight junctions are here reported between the lateral borders of the cellular layer that circumscribes the arachnid (spider) central nervous system. This account details the features of these structures, which form a beltlike reticulum that is more complex than the simple linear tight junctions hitherto found in invertebrate tissues and which bear many of the characteristics of vertebrate zonulae occludentes. We also provide evidence that these junctions form the basis of a permeability barrier to exogenous compounds. In thin sections, the tight junctions are identifiable as punctate points of membrane apposition; they are seen to exclude the stain and appear as election- lucent moniliform strands along the lines of membrane fusion in en face views of uranyl-calcium-treated tissues. In freeze-fracture replicas, the regions of close membrane apposition exhibit P-face (PF) ridges and complementary E-face (EF) furrows that are coincident across face transitions, although slightly offset with respect to one another. The free inward diffusion of both ionic and colloidal lanthanum is inhibited by these punctate tight junctions so that they appear to form the basis of a circumferential blood-brain barrier. These results support the contention that tight junctions exist in the tissues of the invertebrata in spite of earlier suggestions that (a) they are unique to vertebrates and (b) septate junctions are the equivalent invertebrate occluding structure. The component tight junctional 8- to 10-nm-particulate PF ridges are intimately intercalated with, but clearly distinct from, inverted gap junctions possessing the 13-nm EF particles typical of arthropods. Hence, no confusion can occur as to which particles belong to each of the two junctional types, as commonly happens with vertebrate tissues, especially in the analysis of developing junctions. Indeed, their coexistance in this way supports the idea, over which there has been some controversy, that the intramembrane particles making up these two junctional types must be quite distinct entities rather than products of a common precursor.     

Virtual reality 3D echocardiography in the assessment of tricuspid valve function after surgical closure of ventricular septal defect

Background

Chronic right ventricular apical pacing may have detrimental effect on left ventricular function and may promote to heart failure in adult patients with left ventricular dysfunction.

Methods

A group of 99 pediatric patients with previously implanted pacemaker was studied retrospectively. Forty-three patients (21 males) had isolated congenital complete or advanced atrioventricular block. The remaining 56 patients (34 males) had pacing indication in the presence of structural heart disease. Thirty-two of them (21 males) had isolated structural heart disease and the remaining 24 (13 males) had complex congenital heart disease. Patients were followed up for an average of 53 ± 41.4 months with 12-lead electrocardiogram and transthoracic echocardiography. Left ventricular shortening fraction was used as a marker of ventricular function. QRS duration was assessed using leads V₅ or II on standard 12-lead electrocardiogram.

Results

Left ventricular shortening fraction did not change significantly after pacemaker implantation compared to preimplant values overall and in subgroups. In patients with complex congenital heart malformations shortening fraction decreased significantly during the follow up period. (0.45 ± 0.07 vs 0.35 ± 0.06, p = 0.015). The correlation between the change in left ventricular shortening fraction and the mean increase of paced QRS duration was not significant. Six patients developed dilated cardiomyopathy, which was diagnosed 2 months to 9 years after pacemaker implantation.

Conclusion

Chronic right ventricular pacing in pediatric patients with or without structural heart disease does not necessarily result in decline of left ventricular function. In patients with complex congenital heart malformations left ventricular shortening fraction shows significant decrease.     

Storms may disrupt top-down control of algal turf on fringing reefs

Coral Reefs - Storms strongly affect coral reefs; one unstudied but potentially important outcome may be a decrease in herbivory, presumably through changes to freshwater, sediment and nutrient...     

Aspects of germinal cyst and sperm development in Poecilia latipinna (Teleostei: Poeciliidae).

The structure of the testis of Poecilia latipinna is described with particular reference to Sertoli cell-germ cell relationships during development and maturation of the germinal cyst. The cyst develops when primary spermatocytes become surrounded by a single layer of Sertoli cells at the testis periphery. As spermatogenesis and then spermiogenesis proceed, the cyst moves centrally in the testis toward the ducts comprising the vasa efferentia. In addition to being a structural part of the germinal cyst, the Sertoli cells phagocytize residual bodies cast off by developing spermatids and form an association with mature bodies cast off by developing spermatids and form an association with mature sperm, which resembles that observed in mammals, before the sperm are released into the vasa efferentia as a spermatozeugmata. The results of this investigation are discussed in view of what is known concerning testis structure in other teleosts and similarities between cell functions in teleosts and mammals. It is concluded that teleost Sertoli cells, teleost lobule boundary cells and mammalian Sertoli cells are homologous.     

The occurrence of spermatozoa in the ovary of the gynogenetic viviparous teleost Poecilia formosa (POECILIIDAE)

The reproductive mode of the female viviparous teleost Poecilia formosa (Poeciliidae) represents the phenomenon known as gynogenesis; that is, parthenogenetic development is initiated by spermatozoa which are needed for physiological activation of the egg and the initiation of gestation, but spermatozoa are prevented from contributing to the genome of the embryo. For the reason that no previous histological analyses of the ovary of this species during the reproductive cycle has been published the present study has been conducted. This study examined the histology of the ovary of P. formosa during nongestation and gestation phases and identified the presence of spermatozoa inside the ovary. Spermatozoa were observed in folds of the ovarian epithelium of P. formosa during both the nongestation and gestation phases. Sperm storage as documented in this study is a very important trait for the gynogenetic viviparous fish P. formosa contributing to the understanding of this species reproduction. J. Morphol. 277:341–350, 2016. © 2015 Wiley Periodicals, Inc.     

Structure and ultrastructure of the testis and sperm formation in goodeid teleosts

Testis structure in four species of goodeid teleosts is described. Testicular tubules terminate blindly at the testis periphery where spermatogonia are located. In goodeid teleosts, development of sperm takes place synchronously within cysts whose periphery is made up of a single layer of Sertoli cells. Upon completion of spermiogenesis, spermiation ensues wherein sperm are shed, as spermatozeugmata, into the testis efferent duct system. Subsequently, Sertoli cells, which comprised the cyst periphery, transform into efferent duct cells. Sertoli cells phagocytize residual bodies and are involved in the formation of spermatozeugmata. The structure of the goodeid spermatozeugmatum is quite different from that observed in the related poeciliids. It is concluded, in view of this and other considerations, that the goodeids and poeciliids have independently evolved solutions to the problems of internal fertilization and gestation.     

Conserved form and function of the germinal epithelium through 500 million years of vertebrate evolution

The germinal epithelium, i.e., the site of germ cell production in males and females, has maintained a constant form and function throughout 500 million years of vertebrate evolution. The distinguishing characteristic of germinal epithelia among all vertebrates, males, and females, is the presence of germ cells among somatic epithelial cells. The somatic epithelial cells, Sertoli cells in males or follicle (granulosa) cells in females, encompass and isolate germ cells. Morphology of all vertebrate germinal epithelia conforms to the standard definition of an epithelium: epithelial cells are interconnected, border a body surface or lumen, are avascular and are supported by a basement membrane. Variation in morphology of gonads, which develop from the germinal epithelium, is correlated with the evolution of reproductive modes. In hagfishes, lampreys, and elasmobranchs, the germinal epithelia of males produce spermatocysts. A major rearrangement of testis morphology diagnoses osteichthyans: the spermatocysts are arranged in tubules or lobules. In protogynous (female to male) sex reversal in teleost fishes, female germinal epithelial cells (prefollicle cells) and oogonia transform into the first male somatic cells (Sertoli cells) and spermatogonia in the developing testis lobules. This common origin of cell types from the germinal epithelium in fishes with protogynous sex reversal supports the homology of Sertoli cells and follicle cells. Spermatogenesis in amphibians develops within spermatocysts in testis lobules. In amniotes vertebrates, the testis is composed of seminiferous tubules wherein spermatogenesis occurs radially. Emerging research indicates that some mammals do not have lifetime determinate fecundity. The fact emerged that germinal epithelia occur in the gonads of all vertebrates examined herein of both sexes and has the same form and function across all vertebrate taxa. Continued study of the form and function of the germinal epithelium in vertebrates will increasingly clarify our understanding of vertebrate reproduction. J. Morphol. 277:1014–1044, 2016. © 2016 Wiley Periodicals, Inc.     

Assessment of Genotype Imputation Performance Using 1000 Genomes in African American Studies

Genotype imputation, used in genome-wide association studies to expand coverage of single nucleotide polymorphisms (SNPs), has performed poorly in African Americans compared to less admixed populations. Overall, imputation has typically relied on HapMap reference haplotype panels from Africans (YRI), European Americans (CEU), and Asians (CHB/JPT). The 1000 Genomes project offers a wider range of reference populations, such as African Americans (ASW), but their imputation performance has had limited evaluation. Using 595 African Americans genotyped on Illumina’s HumanHap550v3 BeadChip, we compared imputation results from four software programs (IMPUTE2, BEAGLE, MaCH, and MaCH-Admix) and three reference panels consisting of different combinations of 1000 Genomes populations (February 2012 release): (1) 3 specifically selected populations (YRI, CEU, and ASW); (2) 8 populations of diverse African (AFR) or European (AFR) descent; and (3) all 14 available populations (ALL). Based on chromosome 22, we calculated three performance metrics: (1) concordance (percentage of masked genotyped SNPs with imputed and true genotype agreement); (2) imputation quality score (IQS; concordance adjusted for chance agreement, which is particularly informative for low minor allele frequency [MAF] SNPs); and (3) average r2hat (estimated correlation between the imputed and true genotypes, for all imputed SNPs). Across the reference panels, IMPUTE2 and MaCH had the highest concordance (91%–93%), but IMPUTE2 had the highest IQS (81%–83%) and average r2hat (0.68 using YRI+ASW+CEU, 0.62 using AFR+EUR, and 0.55 using ALL). Imputation quality for most programs was reduced by the addition of more distantly related reference populations, due entirely to the introduction of low frequency SNPs (MAF≤2%) that are monomorphic in the more closely related panels. While imputation was optimized by using IMPUTE2 with reference to the ALL panel (average r2hat = 0.86 for SNPs with MAF>2%), use of the ALL panel for African American studies requires careful interpretation of the population specificity and imputation quality of low frequency SNPs.