Flexibility in the order of action and in the enzymology of the nuclease, polymerases, and ligase of vertebrate non-homologous DNA end joining： relevance to cancer, aging, and the immune system

Nonhomologous DNA end joining （NHEJ） is the primary pathway for repair of double-strand DNA breaks in human cells and in multicellular eukaryotes. The causes of double-strand breaks often fragment the DNA at the site of damage, resulting in the loss of information there. NHEJ does not restore the lost information and may resect additional nucleotides during the repair process. The ability to repair a wide range of overhang and damage configurations reflects the flexibility of the nuclease, polymerases, and ligase of NHEJ. The flexibility of the individual components also explains the large number of ways in which NHEJ can repair any given pair of DNA ends. The loss of information locally at sites of NHEJ repair may contribute to cancer and aging, but the action by NHEJ ensures that entire segments of chromosomes are not lost.     

The composition,structure, and dynamics of the nekton of the upper epipelagic layer in the Aleutian and Commander basins,western Bering Sea,in the fall seasons of 2002–2013

The data on the composition and abundance of nekton species and their interannual variations within the upper epipelagic layer (0–50 m) in the Aleutian and Commander basins in the western Bering Sea that are considered in the article were collected during complex surveys that were conducted by the Pacific Research Fisheries Center in September and October of 2002–2013. The core species structures of the nekton communities in these two areas were similar: the chum salmon Oncorhynchus keta and the boreopacific gonate squid Boreoteuthis borealis were the most abundant species. Simpson’s dominance index varied synchronously in both areas, with higher values in the Aleutian Basin, until 2009. In the subsequent years, the values of the index for the studied areas became equal and varied asynchronously. An analysis of abundance showed that two types of species structure most often prevailed (with the dominance of either chum salmon or squid); in some years the species structure differed from that in other years. Species of the low-boreal and low-boreal-subtropical complexes were more abundant in the Commander Basin, reaching particularly high proportions in 2006, 2008, and 2012. Certain species showed similarity in the year-to-year dynamics of their abundance; however, these coincidences were frequently accidental. After the climate regime shift in 2006–2007, the total biomass of nekton in the Aleutian Basin decreased from 3241 to 1736 kg/km² (46%); in the Komandorskiye Basin it decreased from 2459 to 1976 kg/km² (20%).     

Differences in the C age, δC and δO of Holocene tufa and speleothem in the Dinaric Karst

We studied Holocene speleothems and tufa samples collected in numerous caves and rivers in the Dinaric Karst of Croatia, Slovenia, Bosnia and Herzegovina, as well as Serbia and Montenegro. Differences in the formation process of tufa and speleothems are discussed in the context of their isotopic composition (¹⁴C, ¹³C and ¹⁸O), as well as the chemistry of surface water (rivers, lakes) and drip water (in caves). The physical and chemical parameters monitored in the surface water (tufa precipitation) and drip water (speleothem precipitation) show that more stable conditions accompany speleothem rather than tufa formation. This is particularly obvious in the water temperature variations (2-22°C in surface water and 7-12°C in drip water) and in saturation index variation (3-11 in surface water and 1-6 in drip water). The range of ¹⁴C ages recorded by Holocene speleothems (∼12?000 yr) is wider by several thousands years than that of Holocene tufa samples (∼6000 yr). δ¹³C values for tufa samples range from −12‰ to −6‰ and for speleothem samples from −12‰ to +3‰ reflecting higher soil carbon and/or vegetation impact on the process of tufa than on speleothem formation. The differences in δ¹⁸O values of tufa and speleothem samples from different areas reflect different temperature conditions and differing isotopic composition in the water. The study shows that speleothems from the Dinaric Karst can be used as global palaeoclimatic records, whereas tufa records changes in the local palaeoenvironment.     

Kelvin-Helmholtz instability on the magnetopause, magnetohydrodynamic waveguide in the outer magnetosphere, and Alfvén resonance deep in the magnetosphere

Oscillations of the “magnetosphere-solar wind” system are studied analytically in the framework of a plane-stratified model of the medium. The properties of oscillations are determined by three phenomena: Kelvin-Helmholtz instability on the tangential discontinuity (magnetopause) separating the magnetosphere and the solar wind, the presence of a waveguide for fast magnetosonic waves in the magnetosphere, and the Alfvén resonance—a sharp increase in the amplitude of oscillations having the properties of Alfvén waves—in the inner magnetosphere. The oscillations of the system form a discrete spectrum of eigenmodes. Analytical expressions are obtained for the frequency and growth rate of instability of each mode, as well as for the functions describing the spatial structure of these modes. All these characteristics of the eigenmodes are shown to depend on the velocity of the solar wind as a parameter. The dependences of the main mode characteristics (such as the instability thresholds, the points of the maximum and minimum growth rate, and the spatial distributions of the oscillation energy) on this parameter are determined for each eigenmode.     

Ethnicity and biodemographic structure in the Arbëreshe of the province of Cosenza, southern Italy, in the XIX century

Cultural and environmental factors interact in determining the genetic structure of human populations. Bio-demographic investigations of ethnic minorities are able to disentangle the influences that these two components have on the evolution of the genetic structure of a population. The ethnic minority of the Arb?reshe of the province of Cosenza (Calabria, southern Italy) is analyzed in this paper and its bio-demographic structure in the early 1800s is compared with that of neighboring Italian populations. The data derive from surnames recorded in the birth registers of the 19 Arbdreshe municipalities of the province of Cosenza and in 5 non-Arb?reshe municipalities of the same province. Isonymy and repeated pairs of surnames are used to analyze the bio-demographic structure of these populations, while analysis of isonymic relationships is used to investigate the variability between populations. Higher values of marital isonymy and subdivision into subpopulations characterize the Arb?reshe populations with respect to their non-Arb?reshe neighbors. However, the high range of variability of these parameters suggests a strong influence of geographic location on the marriage pattern of each community. At the same time, cultural differences linked to group identity had a strong impact in limiting marriage exchanges between the different ethnic groups living in the province of Cosenza in the early 1800s. In fact, the analysis of isonymic relationships demonstrates that geographic location shaped kinship patterns among the Arbereshe communities, but it also shows that the non-Arb?reshe neighbors formed a clearly separate reproductive cluster.     

Long-term trends in water temperature and ice cover in the subalpine lake, Øvre Heimdalsvatn,and nearby lakes and rivers

Long-term data series of ice cover on lakes and river temperatures from the mountain areas of Norway are lacking. The present study analyses the last four decades of ice data from the subalpine lake, Øvre Heimdalsvatn, and water temperature data from its outlet river, Hinøgla. These data are compared to water temperature data from three neighbouring, quite different locations, the glacier-fed rivers Leirungsåi and Sjoa, and the alpine lake, Bessvatn. The study also examines the air temperature/river temperature relationships, and the air temperature/ice freeze-up and break-up dates. During the months of July, August and September, the water temperature in Hinøgla was well correlated to the air temperature, but the correlation was poor in the remaining months due to the ice cover and snow conditions. A significant temperature increase of 2–3°C has been observed in Hinøgla in the months August–October since 1984. There were only minor changes in the duration of the ice cover season during the last 40 years, but a delay of 9 days was found in the freeze-up date and a delay of 6 days in the break-up date, although the latter was not significant.     

Tumor necrosis factor-α in macrophages of heart,liver, kidney,and in the pituitary gland

The relationship between myonuclear number, cellular size, succinate dehydrogenase activity, and myosin type was examined in single fiber segments (n=54; 9±3 mm long) mechanically dissected from soleus and plantaris muscles of adult rats. One end of each fiber segment was stained for DNA before quantitative photometric analysis of succinate dehydrogenase activity; the other end was double immunolabelled with fast and slow myosin heavy chain monoclonal antibodies. Mean±S.D. cytoplasmic volume/myonucleus ratio was higher in fast and slow plantaris fibers (112±69 vs. 34±21x10³ m³) than fast and slow soleus fibers (40±20 vs. 30±14x10³ m³), respectively. Slow fibers always had small volumes/myonucleus, regardless of fiber diameter, succinate dehydrogenase activity, or muscle of origin. In contrast, smaller diameter (<70 m) fast soleus and plantaris fibers with high succinate dehydrogenase activity appeared to have low volumes/myonucleus while larger diameter (>70 m) fast fibers with low succinate dehydrogenase activity always had large volume/myonucleus. Slow soleus fibers had significantly greater numbers of myonuclei/mm than did either fast soleus or fast plantaris fibers (116±51 vs. 55±22 and 44±23), respectively. These data suggest that the myonuclear domain is more limited in slow than fast fibers and in the fibers with a high, compared to a low, oxidative metabolic capability.     

Neuronal cholecystokinin,gastrin-releasing peptide,neurotensin, and β-endorphin in the intestine of the guinea pig

Summary The guinea-pig intestine was found to harbor nerve fibers containing immunoreactive cholecystokinin (CCK), gastrin-releasing peptide (GRP), neurotensin or - endorphin. Such fibers occurred in the myenteric and submucous ganglia and in the smooth muscle. GRP- and CCK-fibers, in addition, were found in the mucosa. Following colchicine treatment, neuronal perikarya in the myenteric ganglia displayed CCK-, GRP-, or -endorphin immunoreactivity. CCK-immunoreactive perikarya were located also in the submucous ganglia. Neurotensin-immunoreactive cell bodies could not be detected. The presence of immunoreactive neuronal perikarya in intramural ganglia indicates that CCK-, GRP- and -endorphin-containing fibers are intrinsic to the gut wall. GRP, neurotensin, and -endorphin were identified in extracts of smooth muscle by immunochemical and Chromatographic analysis.CCK-8, GRP and neurotensin contracted the isolated taenia coli. Tetrodotoxin reduced the response to CCK-8 but not that to GRP and neurotensin, suggesting that the two latter peptides act directly on smooth muscle receptors. The effect of CCK-8 is partly mediated by cholinergic nerves, since not only tetrodotoxin but also atropine greatly reduced the CCK-8-induced contractile response. The substance P (SP) antagonist, (d-Pro², d-Trp^7,9)-SP_1–11 had no effect on the CCK-8-induced contraction of the taenia. CCK-8 enhanced the SP-mediated (atropine-resistant) contractile response to electrical stimulation but not that mediated by acetylcholine. -Endorphin had no effect on the tension of the muscle but reduced the response to electrical stimulation (cholinergic as well as SP-mediated) through a naloxone-sensitive mechanism.While CCK-8 and -endorphin seem to play neuromodulatory roles in the taenia coli, the significance of GRP and neurotensin remains enigmatic.     

When, where, and in what environment could the RNA world appear and evolve?

The environment necessary for the existence, amplification, and evolution of the RNA world, the difficulties of the abiogenous synthesis of RNA, and paradoxical situations with the stability of RNA, its functions, and the place of RNA in the geological history of the Earth are discussed. The chemical instability of the covalent structure of RNA in the aqueous medium is incompatible with the necessity of water for formation of its functionally active conformations (“water paradox”). The stable double-helical structure of RNA required for replication is incompatible with the stable compact conformations of single-stranded RNA molecules that are necessary for catalytic functions (conformational paradox). There was a very short time gap (or no gap at all) between the end of the massive meteorite bombardment of the Earth (3.9 Ga ago) and the appearance of the first evidence of cellular life (bacteria) in the Earth’s rocks (3.8–3.85 Ga ago or even earlier) (geological paradox). It is concluded that the RNA world could not appear, exist, or evolve into cellular forms of life on the Earth. This paper briefly discusses the possibility of an extraterrestrial origin of the RNA world and its extraterrestrial evolution with a subsequent distribution in space (mainly by comets) of the cellular form of life as more resistant to the environment as compared with free RNA.     

Immunohistochemical detection of cathepsin D, K, and L in the process of endochondral ossification in the human

Cathepsins D, K, and L were immunolocalized in tissue undergoing endochondral ossification in the human. Cathepsins D, K, and L were localized in osteoclasts and chondroclasts attached to bone matrix and cartilage matrix, respectively. Cathepsins D and L were immunostained in chondrocytes. Immunolocalization of cathepsin D was limited to hypertrophic chondrocytes adjacent to the osteochondral junction. In contrast, cathepsin L was immunolocalized in both proliferating and hypertrophic chondrocytes. In the bone marrow space, cathepsins D, K, and L were localized in multinucleated cells. Cathepsin D was diffusely detected in mononuclear bone marrow cells which were negative for cathepsins K and L. The present findings indicated that cathepsins K, D, and L were associated with the process of endochondral ossification in the human, and suggested that these cathepsins share roles in bone and cartilage turnover in the human.     

Koffka, Köhler, and the "crisis" in psychology

This paper examines the claims of the Gestalt psychologists that there was a crisis in experimental psychology ca. 1900, which arose because the prevailing sensory atomism excluded meaning from among psychological phenomena. The Gestaltists claim that a primary motivation of their movement was to show, against the speculative psychologists and philosophers and Verstehen historians, that natural scientific psychology can handle meaning. Purportedly, they revealed this motivation in their initial German-language presentations but in English emphasized their scientific accomplishments for an American audience. The paper finds that: there was a recognized crisis in the new experimental psychology ca. 1900 pertaining especially to sensory atomism; that the Gestaltists responded to the crisis with new experimental findings and theoretical concepts (Gestalten) that challenged atomism; in both languages, they raised problems of meaning and discussed the contest with speculative psychology and philosophy only after presenting their scientific case; that they introduced phenomenological observations on meaning and perceptual organization into their psychology but did not develop a theory of meaning or solve philosophical problems; that they argued "philosophically," that is, using abstract, conceptual arguments; and that this aspect of their cognitive style was not received well by some prominent members of their American audience.     

Discriminations, reversals, and extra-dimensional shifts in the Göttingen minipig

G?ttingen minipigs were trained on a set-shifting procedure involving discriminations, reversals, and extra-dimensional shifts. The discriminations used were black-white discriminations and right-left discriminations. The initial visual and spatial discrimination seemed equally difficult, and only for the visual modality was reversal found to be more difficult than the initial discrimination. Visual reversal was more difficult than spatial reversal, and a larger number of perseverative sessions were found for visual reversal compared to spatial reversal. The acquisition of the extra-dimensional shift from the visual to the spatial dimension was not inferior to the learning of spatial reversal. Neither was the acquisition of the extra-dimensional shift from the spatial to the visual dimension inferior to the learning of visual reversal. Thus, no evidence was found for attention to stimulus dimensions in discrimination learning of the pigs.     

Serum LH,progesterone and estradiol-17β levels throughout the ovarian cycle,during the early stage of pregnancy and after the parturition and the abortion in the common marmoset,Callithrix jacchus

In the ovarian cycle of common marmosets, serum progesterone began to increase at two to three days after estradiol-17β or LH surge, attained a peak of 25–70 ng/ml and then declined to a level of under 2 ng/ml before the ensuing rise in estradiol-17β and LH. Serum estradiol-17β increased to 700–5,500 pg/ml during the luteal phase, synchronizing with progesterone. It is suggested that the corpus luteum secreted estradiol-17β as well as progesterone. The cycle length as determined from the interval between successive LH surges was approximately 28 days. During the luteal phase, the levels of progesterone and estradiol-17β were higher than in Old World monkeys and women, but marmosets were not accompanied by any clinical symptoms due to excessive progesterone and estradiol-17β. This suggests that such unresponsiveness to progesterone and estradiol-17β in marmosets reflects the small amount of estradiol-17β receptor and presumably also the lower function of the post receptor system. Recovery of the post-partum ovarian cycle in two marmosets differed from that observed in Old World monkeys and women. The first LH surge was found on the ninth and tenth day after parturition and the first ovulation led to the next pregnancy. This suggests that the suckling stimulus of newborns in the common marmoset does not cause any delay in recovery of the ovarian cycle. In three cases of abortion, the recovery of the ovarian cycle was almost the same as that in the case of normal parturition: the first LH surge appeared on the 10th, 14th, and 34th day after abortion.     

Microproblematica,calcareous algae,and microbialites at the Frasnian-Famennian boundary interval in the Šumbera section (Moravian Karst,Czech Republic) and their significance in the context of the Kellwasser Crisis

The Kellwasser Crisis represents one of the most severe extinction events in the Phanerozoic. The ?umbera section (Moravo-Silesian Basin, Moravian Karst) spans the Upper rhenana to Palmatolepis minuta minuta (or younger) conodont zones and corresponds to the upper part of a carbonate ramp with material derived from shallower areas. A rich association of calcareous algae, cyanobacteria, and microproblematica, comprising renalcids (Izhella), Girvanella, Rectangulina cf. tortuosa, Rothpletzella, “solenoporaceans”, “Keega”-like microfossils, udoteacean alga Paralitanaia, volvocean and radiospherid calcispheres, palaeoberesellids, Umbellina bella, and Wetheredella, is similar in diversity to associations known from China, Australia, Canada, and Belgium. The ?umbera section represents a unique locality where changes in shallow-water biota at the Frasnian-Famennian boundary are well calibrated by detailed conodont biostratigraphy. We track in detail the evolution of shallow-water biota and the features that are often discussed in the context of “anachronistic” facies, such as flourishing microbial structures, enhanced early marine cementation, and flat-pebble conglomerates. Some features which could be indicative of environmental stress such as flat-pebble conglomerates developed during the Frasnian part of the Kellwasser Crisis (Upper rhenana to linguiformis Zones), whereas a renalcid boom started at the Frasnian-Famennian boundary.     

Mammalian DSCAMs: roles in the development of the spinal cord,cortex, and cerebellum?

Central nervous system (CNS) development involves neural patterning, neuronal and axonal migrations, and synapse formation. DSCAM, a chromosome 21 axon guidance molecule, is expressed by CNS neurons during development and throughout adult life. We now report that DSCAM and its chromosome 11 paralog DSCAML1 exhibit inverse ventral-dorsal expression patterns in the developing spinal cord and distinct, partly inverse, expression patterns in the developing cortex, beginning in the Cajal-Retzius cells. In the adult cortex, DSCAM predominates in layer 3/5 pyramidal cells and DSCAML1 predominates in layer 2 granule cells. In the cerebellum, DSCAM is stronger in the Purkinje cells and DSCAML1 in the granule cells. Finally, we find that the predicted DSCAML1 protein contains 60 additional N-terminal amino acids which may contribute to its distinct expression pattern and putative function. We propose that the DSCAMs comprise novel elements of the pathways mediating dorsal-ventral patterning and cell-fate specification in the developing CNS.     

Na,K-ATPase and the role of α isoforms in behavior

The Na,K-ATPase is composed of multiple isoforms and the isoform distribution varies with the tissue and during development. The α1 isoform for example, is the major isoform in the kidney and many other tissues, while the α2 isoform is the predominate one in skeletal muscle. All three isoforms are found in the brain although in adult rodent brain, the α3 isoform is located essentially in neurons while the α2 isoform is found in astrocytes and some limited neuronal populations. Interestingly the α4 isoform is found exclusively in the mid region of the sperm tail. The distribution of the isoforms of the Na,K-ATPase has been extensively studied in many tissues and during development. The examples cited above provide some indication to the diversity of Na,K-ATPase isoform expression. In order to understand the significance of this distribution, we have developed animals which lack the α1, α2, and α3 isoforms. It is anticipated that these studies will provide insight into the role that these isoforms play in driving various biological processes in specific tissues. Here we describe some of our studies which deal with the behavioral aspects of the α1, α2, and α3 deficient mice, particularly those that are haploinsufficient in one isoform i.e. lacking one functional gene for the α1, α2, or α3 isoforms. Such studies are important as two human diseases are associated with deficiency in the α2 and α3 isoforms. These are Familial Hemiplegic Migraine type 2 and Rapid-Onset Dystonia Parkinsonism, these diseases result from α2 and α3 isoform haploinsufficiency, respectively. We find that the haploinsufficiency of both α2 and α3 isoforms result in behavioral defects.     

Adolescent sexuality and the HIV epidemic in Yaoundé, Cameroon

Adolescents are the focus of many interventions that aim to prevent HIV transmission. In order for these interventions to be effective, it is essential to understand adolescents' sexual behaviour. Using data collected in Yaoundé, Cameroon, in 1997, the study analysed risk exposure and HIV prevalence among 426 men and 510 women aged 15-24. Although risky behaviours seem to be more prevalent among young men, their HIV prevalence remains under 1%. In contrast, HIV prevalence is high among young women (7.5%), even those who report having had few sexual partners. Mixing patterns among sexual partners, and especially the age difference between men and women, do not seem to be sufficient to explain the large male-female discrepancy in HIV prevalence that is evident in these data. The results are therefore probably due to a greater susceptibility to infection of young women than men. This study highlights the necessity of reinforcing prevention campaigns among youth and fighting the obstacles that continue to impede the use of condoms in this population.     

β-catenin and early development in the gastropod, Crepidula fornicata

This study describes the early expression and function of β-catenin in the gastropod, Crepidula fornicata. In other bilaterians β-catenin functions in cell adhesion, gastrulation, and cell signaling, which is related to the establishment of the dorso-ventral axis and mesendoderm. Here, we studied the distribution of β-catenin mRNA and protein in C. fornicata via whole mount in situ hybridization and by expressing GFP-tagged β-catenin in vivo. During early cleavage, β-catenin mRNA and protein appear to be broadly localized to all cells in the early embryo. The mRNA tends to be concentrated at inter-phase centrosomes in these cells. At later stages, the mRNA is predominantly in the vegetal macromeres, and subsequently in the rudiment of the hindgut, stomodeum, and velar lobes. Expression of full-length GFP-tagged protein suggests that there is no active mechanism to degrade β-catenin within cells of the early embryos prior to the 25-cell stage. However, by the second day of development, when the fourth quartet micromeres have formed, β-catenin becomes selectively stabilized in the progeny of the 4d mesentoblast (e.g., ML and MR and their daughters) and is missing from most other blastomeres, including vegetal macromeres. Over the next 2 days of development, during subsequent divisions of 4d, β-catenin protein becomes progressively degraded, along the proximo-distal axes, within the progeny of the paired mesendodermal bands. The cells located at the tips of the mesodermal bands (2?mL2 and 2?mR2) are the last to contain this protein, which is no longer detected after 4 days of development. In animals like C. fornicata, which undergo a spiral cleavage program (e.g., molluscs, annelids, nemerteans, and polyclad flatworms), the mesentoblast or 4d cell represents the progenitor of endomesoderm (forming hindgut, internal and external kidneys, and various muscles). Therefore, the selective stabilization of β-catenin in the progeny of 4d in C. fornicata is consistent with arguments that a basic, ancestral role of β-catenin lies in the formation of endomesodermal fates. Experiments using a truncated β-catenin clone show that the regions located in the C-terminus, distal to the 11th armadillo repeat, are required for normal stabilization/degradation of β-catenin protein within the embryo. Microinjection of translation blocking β-catenin morpholinos into zygotes led to the down-regulation of β-catenin expression. This resulted in the subsequent failure of gastrulation, but did not interfere with the formation and early cleavage of 4d, although there were no discernable differentiated cell fates in these defective embryos. These results are compared with those obtained in other metazoans.