Telomere Length Correlations among Somatic Tissues in Adult Zebra Finches

Telomeres are repetitive non coding DNA sequences located at the end of eukaryotic chromosomes, which maintain the integrity of the genome by hiding the chromosome ends from being recognised as double stranded breaks. Telomeres are emerging as biomarkers for ageing and survival, and are susceptible to reflect different individual life history trajectories. In particular, the telomere length with which one starts in life has been shown to be linked with individual life-long survival, suggesting that telomere dynamics can be a proxy for individual fitness and thereby be implicated in evolutionary trade-offs. As a consequence, an increasing number of studies were conducted on telomeres in the fields of ecology and evolutionary biology, in which telomere length was almost exclusively measured from blood samples. However, not only do the number of repeats of the telomeric sequences vary among species, but also within species with great inter-individual telomere lengths variability with age, tissues, and chromosomes. This raises the issue of the exact biological meaning of telomere measurement in blood cells and stimulated the study of the correlation of telomere lengths among tissues over age. By measuring telomere length in adult zebra finches (Taeniopygia guttata) in different somatic tissues displaying variable cell turnovers (bone marrow, brain, spleen, pectoral muscle, heart, liver and in red blood cells), we checked that the measure of telomere length in red blood cells is related to telomere lengths in the other tissues. Here we show significant relationships between the telomere lengths of red blood cells and several somatic tissues at adulthood. As red blood cells are easily accessible and suitable for the longitudinal monitoring of the individual rate of telomere loss, our study confirms that telomere length measured in red blood cells could serve as a surrogate for telomere length in the whole avian organism.     

2D:4D ratios predict hand grip strength (but not hand grip endurance) in men (but not in women)

In humans, the ratio of the second digit to the fourth digit — the 2D:4D ratio — is a sexually dimorphic trait (men, on average, exhibit lower 2D:4D ratios than do women) that is influenced by prenatal testosterone exposure, but not by circulating testosterone levels in adulthood. Consequently, 2D:4D ratios are commonly used as indirect measures of prenatal testosterone exposure. Many studies have examined the associations of 2D:4D ratios with sexually dimorphic adaptations that are thought to be influenced by such exposure, including physical prowess. The existing literature, however, remains unclear as to (1) whether 2D:4D ratios are more closely linked to strength or to endurance; and (2) whether 2D:4D ratios are linked with physical prowess for both men and women. In 100 men and 122 women, the relationship of 2D:4D ratios with maximum voluntary contraction (MVC) scores (hand grip strength) and maximum endurance time (MET) scores (local muscular endurance) using a hand dynamometer was examined. Controlling for age, height, weight, and average digit length, we found that 2D:4D ratios significantly predicted MVC scores in men, but not in women. 2D:4D ratios did not significantly predict MET scores for either sex. These results suggest that prenatal testosterone exposure in this sample is significantly related to hand grip strength in men, but not in women (and to local muscular endurance in neither sex), and, therefore, that strength, rather than local muscular endurance, potentially drives the relationship between 2D:4D ratios and physical prowess.     

Bacteriophage T4-Directed DNA Synthesis in Toluene-Treated Cells

DNA synthesis has been studied in T4-infected Escherichia coli cells made permeable to nucleotides by treatment with toluene. The rate of incorporation of labeled deoxyribonucleoside triphosphates into DNA at various times after infection is proportional to the in vivo rate. This in vitro incorporation is dependent on all four deoxyribonucleoside triphosphates (5-hydroxymethyldeoxy-cytidine triphosphate can substitute for dCTP) and Mg(2+). It is stimulated by rATP, partially inhibited by pancreatic DNase, and abolished by N-ethylmalei-mide and 1-beta-d-arabinofuranosylcytosine triphosphate. T4 amber DO (DNA negative) and temperature-sensitive DO mutants under nonpermissive conditions of infection fail to induce DNA synthesis in vitro. The synthesizing activity is intracellular and the DNA product is exclusively T4 DNA. The in vitro synthesis proceeds in a discontinuous manner involving synthesis and subsequent joining of small DNA fragments (about 10S in alkaline sucrose gradients) into larger molecules predominantly one-half the length of mature T4 DNA. No restriction of C-containing or nonglucosylated HMC-containing T4 DNA product is observed in this system.     

Research on substances inactivating the X virus present in sap from potato leaves

The work ofJermoljev andBr?ák (1964) showed that the sap of potato leaves contains substances inactivating X, Y and S viruses and that there was an increasing trend in the content of these substances in varieties resistant to these viruses. In further research it was found that potato tubers of varieties which are resistant and susceptible to the viruses contained the same amounts of inactivating substances. Differences in the power of inactivating the viruses evidently appeared in the leaves. Inactivating substances could be removed by boiling, they did not pass through a dialysing membrane and were adsorbed by animal charcoal. On centrifuging sap from potato leaves in a Spinco L ultracentrifuge for 60 min. at 40,000 r.p.m., the inactivating substances remained in the supernatant. When sucrose gradient centrifugation for 60 min. at 24,000 r.p.m. was employed, the inactivating substances remained in the layer of sap and 10% sucrose. Inhibition of the activity of certain enzyme groups did not affect the power of sap to inactivate X virus. Inactivating substances could be isolated chemically. The best method of isolation, however, was fractionation of sap, after ultracentrifugation, on a Sephadex G 50 column, rinsing the column with McIlvaine buffer at pH 6·5. Inactivating substances can be isolated, concentrated and preserved by lyophilization by this method. It is difficult to say precisely to what chemical group the inactivating substances belong. Some reactions indicate that they may be low molecular proteins.     

Comparative studies between in vitro and in vivo effects of human beta-interferon on natural killer activity and its relevance to immunochemotherapy

Summary A good correlation was found between in vivo and in vitro responses of peripheral MNC from breast cancer patients and the NK boosting effect of human IFN. In vitro immunochemotherapy studies showed that marked antitumor effects were obtained against cultured cancer cells when a widely used chemotherapeutic agent such as 5-FU was combined with nonsensitized spontaneously cytolytic MNC, preactivated in vitro with IFN. These results suggest that the in vitro susceptibility assay of MNC to IFNs could be used for predicting favorable responses to immunochemotherapy regimens employing IFNs as immunomodulating agents. Abbreviations used: IFN, beta-interferon; CM, complete medium; CTX, cyclophosphamide; E:T ratio, effector target ratio; EDTA, ethylenediaminetetraacetic acid; FCS, fetal calf serum; 5-FU, 5-fluorouracil; IFN, gamma-interferon; Hepes, N-2-hydroxyethylpiperazine-N-2-ethanesulphonic acid IFNs, interferons; KC, killed cells; LDIF, low doses beta-interferon; LU, lytic unit; MAT macrotest; MIT, microtest; MNC, mononuclear cells; MNC/IFN, IFN-pretreated MNC; MTX, methotrexate; NB, no boosting; NK, natural killer; NKA, NK activity; NR, natural resistance; PM, positive modulation; SE, standard error; WM, washing medium     

All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons

Accurate discovery of somatic mutations in a cell is a challenge that partially lays in immaturity of dedicated analytical approaches. Approaches comparing a cell’s genome to a control bulk sample miss common mutations, while approaches to find such mutations from bulk suffer from low sensitivity. We developed a tool, All², which enables accurate filtering of mutations in a cell without the need for data from bulk(s). It is based on pair-wise comparisons of all cells to each other where every call for base pair substitution and indel is classified as either a germline variant, mosaic mutation, or false positive. As All² allows for considering dropped-out regions, it is applicable to whole genome and exome analysis of cloned and amplified cells. By applying the approach to a variety of available data, we showed that its application reduces false positives, enables sensitive discovery of high frequency mutations, and is indispensable for conducting high resolution cell lineage tracing.     

Determination of fumonisins in maize by HPLC with ultraviolet detection of <Emphasis Type="Italic">o</Emphasis>-phthaldialdehyde derivatives

Fumonisins are mycotoxins that are produced by various Fusarium species and occur naturally in maize and maize-based foods. Fumonisins are carcinogenic, causing liver cancer in rats, and are associated with oesophageal cancer and neural tube defects in humans. Analytical methods for individual fumonisin analogues in maize rely on reversed-phase high-performance liquid chromatographic (HPLC) separation after suitable extraction and clean-up. As fumonisins lack a useful chromophore or fluorophore, HPLC detection is achieved by suitable derivatization and sensitive, specific fluorescence detection. A widely used and validated method involves extract clean-up on strong anion exchange solid phase extraction cartridges and pre-column derivatization with o-phthaldialdehyde (OPA). However, many laboratories requiring infrequent fumonisin analysis are only equipped with HPLC with ultraviolet (UV) detection. A HPLC system equipped with both UV and fluorescence detectors connected in series was used to determine the extent to which UV offers an alternative to fluorescence detection in the above analytical method. Comparison of the detection systems using fumonisin standards indicated that fluorescence is about 20-times more sensitive than UV. Analysis of maize samples with differing fumonisin contamination levels indicated that, at fumonisin B₁ levels above 1,000 μg/kg, the two detection systems were comparable and gave repeatabilities equal or less than 10% on six replicate analyses. Although a sensitive fumonisin analysis requires fluorescence detection, UV may offer an alternative in certain circumstances.     

Role of the DinB Homologs Rv1537 and Rv3056 in Mycobacterium tuberculosis

The environment encountered by Mycobacterium tuberculosis during infection is genotoxic. Most bacteria tolerate DNA damage by engaging specialized DNA polymerases that catalyze translesion synthesis (TLS) across sites of damage. M. tuberculosis possesses two putative members of the DinB class of Y-family DNA polymerases, DinB1 (Rv1537) and DinB2 (Rv3056); however, their role in damage tolerance, mutagenesis, and survival is unknown. Here, both dinB1 and dinB2 are shown to be expressed in vitro in a growth phase-dependent manner, with dinB2 levels 12- to 40-fold higher than those of dinB1. Yeast two-hybrid analyses revealed that DinB1, but not DinB2, interacts with the β-clamp, consistent with its canonical C-terminal β-binding motif. However, knockout of dinB1, dinB2, or both had no effect on the susceptibility of M. tuberculosis to compounds that form N²-dG adducts and alkylating agents. Similarly, deletion of these genes individually or in combination did not affect the rate of spontaneous mutation to rifampin resistance or the spectrum of resistance-conferring rpoB mutations and had no impact on growth or survival in human or mouse macrophages or in mice. Moreover, neither gene conferred a mutator phenotype when expressed ectopically in Mycobacterium smegmatis. The lack of the effect of altering the complements or expression levels of dinB1 and/or dinB2 under conditions predicted to be phenotypically revealing suggests that the DinB homologs from M. tuberculosis do not behave like their counterparts from other organisms.The emergence and global spread of multi- and extensively drug-resistant strains of Mycobacterium tuberculosis have further complicated the already daunting challenge of controlling tuberculosis (TB) (15). The mechanisms that underlie the evolution of drug resistance in M. tuberculosis by chromosomal mutagenesis and their association with the conditions that tubercle bacilli encounter during the course of infection are poorly understood (6). It has been postulated that hypoxia, low pH, nutrient deprivation, and nitrosative and oxidative stress impose environmental and host immune-mediated DNA-damaging insults on infecting bacilli (64). In addition, the observed importance of excision repair pathways for the growth and survival of M. tuberculosis in murine models of infection (13, 55) and the upregulation of M. tuberculosis genes involved in DNA repair and modification in pulmonary TB in humans provide compelling evidence that the in vivo environment is DNA damaging (51).Damage tolerance constitutes an integral component of an organism''s response to genotoxic stress, preventing collapse of the replication fork at persisting, replication-blocking lesions through the engagement of specialized DNA polymerases that are able to catalyze translesion synthesis (TLS) across the sites of damage (19, 21, 60). Most TLS polymerases belong to the Y family, which comprises a wide range of structurally related proteins present in bacteria, archaea, and eukaryotes (44). Of these, the DinB subfamily of Y family polymerases, whose founder member is Escherichia coli Pol IV (63), is conserved among all domains of life (44). The association of Y family polymerases with inducible mutagenesis has implicated these enzymes in the adaptation of bacteria to environmental stress (17, 20, 39, 54, 58, 59, 66). Their key properties are exemplified in E. coli Pol IV: the polymerase catalyzes efficient and accurate TLS across certain N²-dG adducts (27, 28, 34, 40, 45, 67) and has been implicated in the tolerance of alkylation damage (4); furthermore, overexpression of Pol IV significantly increases mutation rates in E. coli (reviewed in references 21 and 26), and dinB is the only SOS-regulated gene required at induced levels for stress-induced mutagenesis in this organism (20). Furthermore, overproduction of E. coli Pol IV inhibits replication fork progression through replacement of the replicative polymerase to form an alternate replisome in which Pol IV modulates the rate of unwinding of the DnaB helicase (25) and also reduces colony-forming ability (61).The M. tuberculosis genome encodes two Y family polymerase homologs belonging to the DinB subfamily, designated herein as DinB1 (DinX, encoded by Rv1537) and DinB2 (DinP, encoded by Rv3056), as well as a third, distantly related homolog encoded by Rv3394c (see Fig. S1 in the supplemental material) (9). On the basis of sequence similarity with their counterparts from E. coli (63) and Pseudomonas aeruginosa (54), including the complete conservation of key acidic residues essential for catalysis, DinB1 and DinB2 may be functional DNA polymerases (see Fig. S1). In contrast, Rv3394c lacks these residues and as such is unlikely to have polymerase activity (see Fig. S1). Unlike most Y family polymerase-encoding genes investigated with other bacteria (17, 26, 54, 58), dinB1 and dinB2 expression in M. tuberculosis is not dependent on RecA, the SOS response, or the presence of DNA damage (5, 7, 52). That these genes are regulated by other mechanisms and so may serve distinct roles in DNA metabolism in M. tuberculosis is suggested by the observation that dinB1 is differentially expressed in pulmonary TB (51) and is a member of the SigH regulon (30), whereas expression of dinB2 is induced following exposure to novobiocin (5).In this study, we adopted a genetic approach to investigate the function of dinB1 and dinB2 in M. tuberculosis. Mutants with altered complements or expression levels of dinB1 and/or dinB2 were analyzed in vitro and in vivo under conditions predicted to be phenotypically revealing based on DinB function established with other model organisms. The lack of discernible phenotypes in any of the assays employed suggests that the DinB homologs from M. tuberculosis do not behave like their counterparts from other organisms.