Are there insertions in the ribosomal DNA of vertebrates?

We have analysed the Eco RI restriction pattern of rDNA of the newt Triturus vulgaris and of some other amphibian species by Southern blotting and hybridization with nick-translated Xenopus rDNA prepared from the recombinant plasmids pXlr11 and pXlr12 (21). After hybridization with r11, the 28S coding fragments become visible in two bands, a prominent one of 5.3 kb and a weak band of 5.9 kb representing about 8% of the 28S genes. The evidence obtained so far by additional digestions with Bam HI and Bgl II indicates that in this species and in Triturus helveticus the coding regions of the 5.9 kb fragments are interrupted by an insertion 0.6 kb in length located in a 1.6 kb Bgl II fragment at the 3' end of the Eco RI fragment, which we believe to be the first described in a vertebrate.     

Are there specialized junctions in the pars maculata of the distal tubule?

Summary In the present study the tight junctions at the macula densa were compared to those of the adjacent straight and convoluted segments of the distal tubule using freeze fracturing and thin sectioning techniques. Only insignificant differences were found in the number of strands and the apico-basal depth of the tight junctions in the three distal tubular segments of rat, dog and tree shrew. In experiments with horseradish peroxidase on mice and tree shrews, the tracer did not penetrate the apical junctions in any of the distal tubular segments. Our findings do not support the concept of considerably higher permeability of the tight junctions at the macula densa, as previously reported. Gap junctions were never observed in the distal nephron. The present results suggest that the glomerulo-tubular feedback is more likely to be mediated by transcellular resorption of solutes than by passive diffusion through a leaky paracellular shunt pathway.These studies were supported by the German Research Foundation within the SFB 90 Cardiovasculäres System     

Are there Atlantic salmon in the River Tambre?

Genetic variability and assignment analyses demonstrate that the 60 returning adult salmon to the Tambre River in 2005 were not the product of an incipient wild population, but the result of straying from a neighbouring river.     

Intrinsic properties of the two replicative DNA polymerases of Pyrococcus abyssi in replicating abasic sites: possible role in DNA damage tolerance?

Spontaneous and induced abasic sites in hyperthermophiles DNA have long been suspected to occur at high frequency. Here, Pyrococcus abyssi was used as an attractive model to analyse the impact of such lesions onto the maintenance of genome integrity. We demonstrated that endogenous AP sites persist at a slightly higher level in P. abyssi genome compared with Escherichia coli. Then, the two replicative DNA polymerases, PabpolB and PabpolD, were characterized in presence of DNA containing abasic sites. Both Pabpols had abortive DNA synthesis upon encountering AP sites. Under running start conditions, PabpolB could incorporate in front of the damage and even replicate to the full-length oligonucleotides containing a specific AP site, but only when present at a molar excess. Conversely, bypassing activity of PabpolD was strictly inhibited. The tight regulation of nucleotide incorporation opposite the AP site was assigned to the efficiency of the proof-reading function, because exonuclease-deficient enzymes exhibited effective TLS. Steady-state kinetics reinforced that Pabpols are high-fidelity DNA polymerases onto undamaged DNA. Moreover, Pabpols preferentially inserted dAMP opposite an AP site, albeit inefficiently. While the template sequence of the oligonucleotides did not influence the nucleotide insertion, the DNA topology could impact on the progression of Pabpols. Our results are interpreted in terms of DNA damage tolerance.     

Are there age-related differences in the song repertoire size of Eurasian blackbirds?

Most oscine bird species possess a repertoire of different song patterns, and repertoire size is thought to signal aspects of male quality. As age is assumed to be related to male quality in terms of experience and/or viability, repertoire size may be expected to reflect male age. Here, we investigated the relationship between repertoire size and age (yearlings or older) in Eurasian blackbirds, Turdus merula, a species with a large repertoire delivered in a highly variable manner. We found that older males tended to have larger repertoires than yearlings though the two age groups overlapped considerably. Thus, compared to other species with large repertoires, age-related differences in repertoire size seem rather small in male Eurasian blackbirds. We also compared repertoires of three individuals in two successive years (as yearlings and in the year following) and found a large element turnover. Our investigation revealed that this turnover was almost complete in the quiet terminating twitter part of the song. Such turnover may allow a young bird to adjust his repertoire to his neighbours?? repertoires, which could be useful for song matching interactions.     

Is there a rate-limiting step in the catalytic cycle of [Ni-Fe] hydrogenases?

The question of the existence of a rate-limiting step in the catalytic cycle of Ni-Fe hydrogenases was taken up by using the sets of data available in the case of two specific enzymes: the hydrogenase from Thiocapsa roseopercisina, in which isotope effects have been systematically investigated over a wide pH range, and the enzyme from Desulfovibrio fructosovorans, for which the activities and the redox properties have been studied in two different forms, the wild type and the P238C mutant. When these data are analyzed in the light of appropriate kinetic models, it is concluded that electron transfer and proton transfer are rate limiting in the H2 uptake and H2 evolution reactions, respectively. This proposal is consistent with the data available from other Ni-Fe enzymes.     

Are there changes in postural regulation across the lifespan?

Abstract

The purpose was to obtain parameters of postural regulation (n?=?1724) of asymptomatic subjects (6–97 years). The maximum postural stability and capacity of postural subsystems were calculated for the age ranges from 34 to 35 years (men) and from 38 to 44 years (women). A significant decline in postural performance was observed in the 40s (men) and 50s (women). Data can be used in the evaluation of dizziness and balance disorders in people of all ages.     

Are there molecules of nucleoprotamine?

A short critical review of the data related to protamine and nucleoprotamine (DNP) structure is given. A new model is proposed for DNP structure in which protamine molecules are located in channels between the DNA molecules. DNA molecules are arranged hexagonally in the x–y plane, whereas their relative positions with respect to the z-axis are shifted by 0, 1/3, and 2/3 of the pitch of the double helix. As a result, large cavities are formed in three out of six channels surrounding each DNA molecule where the large grooves are juxtaposed. Protamine molecules are also proposed to have some secondary/tertiary structure prior to complex formation. Inside the channels, a protamine molecule modifies its shape to fill the large grooves of all of the three surrounding DNA molecules simultaneously, and might possibly be in touch with other protamine molecules in neighbouring positions as well. This disposition allows the protamine molecules to be located between DNA molecules without a significant increase in the lattice parameters. BioEssays 21:440–448, 1999. © 1999 John Wiley & Sons, Inc.     

Are there subtypes of the inositol 1,4,5-trisphosphate receptor?

We have compared the properties of the [3H]Ins(1,4,5)P3-binding sites from a number of tissues in an attempt to determine if heterogeneity exists within the Ins(1,4,5)P3-receptor family. The binding of Ins(1,4,5)P3 was characterized in detail by using membranes prepared from human uterine smooth muscle and bovine adrenal cortex. Ins(1,4,5)P3 exhibited an approx. 5 times greater affinity for the binding site in adrenal cortex (KD = 9.81 +/- 1.92 nM) compared with uterine smooth muscle (KD = 37.1 +/- 1.8 nM). The binding was dependent on pH in both tissues, with a maximum at pH 8.3; at this pH various inositol phosphates and nucleotides competed for the binding sites with similar potencies on both tissues. However, the binding of Ins(1,4,5)P3 to the uterine smooth-muscle membranes was Ca2(+)-sensitive, whereas that to the bovine adrenal cortex was not; furthermore, heparin displaced the binding of Ins(1,4,5)P3 in the uterus with an IC50 value (concn. of displacer giving 50% inhibition of specific binding) of 3.9 micrograms/ml (2.5, 6.4; lower, upper range), compared with a value of 22 (13, 30) micrograms/ml in adrenal cortex. In view of the ability of Ins(1,4,5)P3 and heparin to distinguish between these binding sites, their effect on other tissues was examined. Ins(1,4,5)P3 showed a similar affinity for receptors located in the bovine cerebellum to those in the bovine adrenal cortex, but heparin displaced Ins(1,4,5)P3 binding with a 5-fold greater affinity from the cerebellum. Ins(1,4,5)P3 had a 2-fold greater affinity for its receptor with human platelets, as compared with human uterus, but heparin was unable to distinguish between these sites. In guinea-pig ileum, Ins(1,4,5)P3 displayed a similar affinity for the receptors in the longitudinal muscle compared with the circular muscle, but heparin could distinguish between these sites. These data show that small differences exist between tissues, but no clear picture is apparent. It is possible that these results reflect tissue-dependent factors such as phosphorylation, the presence of calmedin etc., rather than the presence of receptor subtypes or species difference.     

Are there pathological defects of interferon secretion in man?

Interferon is now recognized as an important biological mediator with both antiviral and non-antiviral (including immunoregulatory) functions. In some patients with repeated and severe infections, leucocytes appear to be unable to produce normal levels of interferon after stimulation with soluble antigens or allogeneic lymphoblastoid cells. This defect contrasts with normal immune functions, with the exception of "natural killer" non-specific cytotoxic activity which is usually impaired. This selective defect of interferon secretion may result in a special type of immuno-deficiency with multiple biological consequences, some of which can be reversed by interferon therapy.     

Are there geniuses among the apes?

We are often asked whether some apes are smarter than others. Here we used two individual-based datasets on cognitive abilities to answer this question and to elucidate the structure of individual differences. We identified some individuals who consistently scored well across multiple tasks, and even one individual who could be classified as exceptional when compared with her conspecifics. However, we found no general intelligence factor. Instead, we detected some clusters of certain abilities, including inferences, learning and perhaps a tool-use and quantities cluster. Thus, apes in general and chimpanzees in particular present a pattern characterized by the existence of some smart animals but no evidence of a general intelligence factor. This conclusion contrasts with previous studies that have found evidence of a g factor in primates. However, those studies have used group-based as opposed to the individual-based data used here, which means that the two sets of analyses are not directly comparable. We advocate an approach based on testing multiple individuals (of multiple species) on multiple tasks that capture cognitive, motivational and temperament factors affecting performance. One of the advantages of this approach is that it may contribute to reconcile the general and domain-specific views on primate intelligence.     

How Effective Are DNA Barcodes in the Identification of African Rainforest Trees?

Background

DNA barcoding of rain forest trees could potentially help biologists identify species and discover new ones. However, DNA barcodes cannot always distinguish between closely related species, and the size and completeness of barcode databases are key parameters for their successful application. We test the ability of rbcL, matK and trnH-psbA plastid DNA markers to identify rain forest trees at two sites in Atlantic central Africa under the assumption that a database is exhaustive in terms of species content, but not necessarily in terms of haplotype diversity within species.

Methodology/Principal Findings

We assess the accuracy of identification to species or genus using a genetic distance matrix between samples either based on a global multiple sequence alignment (GD) or on a basic local alignment search tool (BLAST). Where a local database is available (within a 50 ha plot), barcoding was generally reliable for genus identification (95–100% success), but less for species identification (71–88%). Using a single marker, best results for species identification were obtained with trnH-psbA. There was a significant decrease of barcoding success in species-rich clades. When the local database was used to identify the genus of trees from another region and did include all genera from the query individuals but not all species, genus identification success decreased to 84–90%. The GD method performed best but a global multiple sequence alignment is not applicable on trnH-psbA.

Conclusions/Significance

Barcoding is a useful tool to assign unidentified African rain forest trees to a genus, but identification to a species is less reliable, especially in species-rich clades, even using an exhaustive local database. Combining two markers improves the accuracy of species identification but it would only marginally improve genus identification. Finally, we highlight some limitations of the BLAST algorithm as currently implemented and suggest possible improvements for barcoding applications.     

Are there non‐catalytic functions of acetylcholinesterases? Lessons from mutant animal models

Acetylcholinesterase (AChE) hydrolyses acetylcholine (ACh) ensuring the fast clearance of released neurotransmitter at cholinergic synapses. Many studies led to the hypothesis that AChE and the closely related enzyme butyrylcholinesterase (BChE) may play other, non-hydrolytic roles during development. In this review, we compare data from in vivo studies performed on invertebrate and vertebrate genetic models. The loss of function of ache in these systems is responsible for the appearance of several phenotypes. In all aspects so far studied, the phenotypes can be explained by an excess of the undegraded substrate, ACh, leading to misfunction and pathological alterations. Thus, the lack of AChE catalytic activity in the mutants appears to be solely responsible for the observed phenotypes. None of them appears to require the postulated adhesive or other non-hydrolytic functions of AChE.     

Are there new possibilities in immunomorphology?

Immunomorphology, including immunohistochemistry and immunocytochemistry, forms a category of well known, reproducible, cost and environment saving immunodiagnostic methods based on immunological specificity. Both the accurate diagnosis and a better knowledge of biological parameters of diseases, especially of malignant tumors, result from the continual development of technologies and applications concerning at least 60 years of history of immunostaining. This review attempts to summarize the most important steps of development of immunomorphology.     

Why are complementary DNA strands symmetric?

MOTIVATION: Over sufficiently long windows, complementary strands of DNA tend to have the same base composition. A few reports have indicated that this first-order parity rule extends at higher orders to oligonucleotide composition, at least in some organisms or taxa. However, the scientific literature falls short of providing a comprehensive study of reverse-complement symmetry at multiple orders and across the kingdom of life. It also lacks a characterization of this symmetry and a convincing explanation or clarification of its origin. RESULTS: We develop methods to measure and characterize symmetry at multiple orders, and analyze a wide set of genomes, encompassing single- and double-stranded RNA and DNA viruses, bacteria, archae, mitochondria, and eukaryota. We quantify symmetry at orders 1 to 9 for contiguous sequences and pools of coding and non-coding upstream regions, compare the observed symmetry levels to those predicted by simple statistical models, and factor out the effect of lower-order distributions. We establish the universality and variability range of first-order strand symmetry, as well as of its higher-order extensions, and demonstrate the existence of genuine high-order symmetric constraints. We show that ubiquitous reverse-complement symmetry does not result from a single cause, such as point mutation or recombination, but rather emerges from the combined effects of a wide spectrum of mechanisms operating at multiple orders and length scales.