The Inhibitory Effect of Non-Substrate and Substrate DNA on the Ligation and Self-Adenylylation Reactions Catalyzed by T4 DNA Ligase

DNA ligases are essential both to in vivo replication, repair and recombination processes, and in vitro molecular biology protocols. Prior characterization of DNA ligases through gel shift assays has shown the presence of a nick site to be essential for tight binding between the enzyme and its dsDNA substrate, with no interaction evident on dsDNA lacking a nick. In the current study, we observed a significant substrate inhibition effect, as well as the inhibition of both the self-adenylylation and nick-sealing steps of T4 DNA ligase by non-nicked, non-substrate dsDNA. Inhibition by non-substrate DNA was dependent only on the total DNA concentration rather than the structure; with 1 μg/mL of 40-mers, 75-mers, or circular plasmid DNA all inhibiting ligation equally. A >15-fold reduction in T4 DNA ligase self-adenylylation rate when in the presence of high non-nicked dsDNA concentrations was observed. Finally, EMSAs were utilized to demonstrate that non-substrate dsDNA can compete with nicked dsDNA substrates for enzyme binding. Based upon these data, we hypothesize the inhibition of T4 DNA ligase by non-nicked dsDNA is direct evidence for a two-step nick-binding mechanism, with an initial, nick-independent, transient dsDNA-binding event preceding a transition to a stable binding complex in the presence of a nick site.     

The effect of lifestyle intervention in obesity on the soluble form of activated leukocyte cell adhesion molecule

Background

The aim of this study was to investigate the effect of a lifestyle intervention in obesity on the soluble form of the activated leukocyte cell adhesion molecule (sALCAM) and its association with metabolic parameters.

Methods

Twenty-nine obese subjects selected from the OPTIFAST®52 program. This program consisted into 2 crucial phases: an initial 12-week active weight reduction phase, followed by a 40-week weight maintenance phase. At baseline, after 12 weeks and at the end of the program, fasting glucose and insulin, total cholesterol, LDL-C, HDL-C, triglycerides, adiponectin, leptin, high sensitivity CRP, sALCAM, homeostasis model assessment-estimated insulin resistance (HOMA-IR) and leptin-to-adiponectin-ratio were determined. Oral glucose tolerance test (OGTT) was performed when indicated.

Results

At baseline, the serum concentration of sALCAM was increased and correlated positively with HOMA-IR and negatively with age. At the end of the program, sALCAM concentrations decreased significantly. Multivariate analysis showed that sALCAM significantly correlated with age, glucose concentration after 2 h OGTT and the HOMA-IR. A higher decrease of HOMA-IR during the study was observed in subjects with higher concentration of sALCAM at baseline.

Conclusions

sALCAM might be a novel biomarker in obesity that correlates and predicts insulin sensitivity improvement and that can be affected by lifestyle intervention.

     

Retrospective Analysis of the Incidence of Retained Placenta in 3 Large Colonies of NHP

During 1999 through 2014, retained placenta was the most common cause of clinical admission for reproductive complications in breeding colonies of baboons (approximate colony size, 2000 animals), cynomolgus macaques (approximately 1000), and rhesus macaques (approximately 500) at the Southwest National Primate Research Center. Retained placentas occurred in 2.7% of baboons, 3.3% of cynomolgus macaques, and 1.0% of rhesus macaques. Apparent risk factors for retained placenta included stillbirth or abortion and at least one prior cesarean section. There was a significant association between stillbirth and retained placenta in all species. Cesarean sections were performed routinely for baboons to meet research objectives but occurred only as needed for cynomolgus and rhesus macaques. Having had at least one prior cesarean section was an incidence factor for retained placenta in 37.0% of baboons and 4.7% of cynomolgus macaques; none of the rhesus macaques with retained placentas had undergone cesarean section previously. More than 90% of dams with retained placenta returned to a successful reproductive life or assignment to a nonbreeding research protocol. Advances in reproductive management will benefit from prospective studies that capture additional data from all members of a breeding group prior to reproductive complications.Abbreviations: Southwest National Primate Research Center (SNPRC), retained placenta (RP), cesarean section (C-section)Retained placentas and other reproductive problems are unavoidable complications encountered in association with NHP production colonies and are difficult to diagnose, because most births occur at night, when human observation is minimal, and because the dams routinely consume the placenta.^41,44,45 There is extensive information regarding retained placentas in dairy cattle,^7,25,20 and humans,^{3,13,24,35,36,40} but little is documented about this problem''s health hazard and effect on future reproduction in NHP,^16,17,23,49 with 3 documented cases reported as isolated reports between 1991 and 2009.^16,17,23 The first documented case of a retained placenta in a NHP was that of a female chimpanzee (Pan troglodytes).¹⁷ Clinical signs for that case included depression, poor maternal care, and vaginal hemorrhage 1 wk after delivery. The chimpanzee was treated successfully, and the infant was returned to the dam with no further complications. Another documented case involved a golden lion tamarin (Leontopithecus rosalia),¹⁶ which had experienced prolonged labor resulting in a stillbirth. After continued placental retention, the tamarin was hysterectomized. Histopathologic evaluation revealed that placental infiltration into the myometrium was the cause of retention.¹⁶ The third documented case occurred in a bonobo (Pan paniscus) housed in a sanctuary in the Democratic Republic of Congo.²³ The animal was treated with oxytocin injections; after manual removal of the placenta, the dam and infant were reunited, and maternal recovery was uneventful.In addition, in an unpublished case, one of the current authors (TH) treated a mandrill (Mandrillus sphinx) by using oxytocin injection and manual removal of the placenta, after which the dam and infant were reunited, and maternal recovery was uneventful. Several other unpublished cases documented in the medical records of the breeding colonies at the Southwest National Primate Research Center (SNPRC) involved species baboons (Papio spp.), cynomolgus macaques (Macaca fascicularis), and rhesus macaques (Macaca mulatta). Clinical veterinarians had deemed all of these animals to be healthy prior to their placement into breeding groups and were rechecked semiannually concurrent with tuberculin testing. Body condition varied from lean to obese, but body condition score was not recorded. We retrospectively reviewed these records to determine the risk factors and incidence of retained placenta within the 3 NHP colonies over 15 y.     

Dual inhibition of Kif15 by oxindole and quinazolinedione chemical probes

The mitotic spindle is a microtubule-based machine that segregates a replicated set of chromosomes during cell division. Many cancer drugs alter or disrupt the microtubules that form the mitotic spindle. Microtubule-dependent molecular motors that function during mitosis are logical alternative mitotic targets for drug development. Eg5 (Kinesin-5) and Kif15 (Kinesin-12), in particular, are an attractive pair of motor proteins, as they work in concert to drive centrosome separation and promote spindle bipolarity. Furthermore, we hypothesize that the clinical failure of Eg5 inhibitors may be (in part) due to compensation by Kif15. In order to test this idea, we screened a small library of kinase inhibitors and identified GW108X, an oxindole that inhibits Kif15 in vitro. We show that GW108X has a distinct mechanism of action compared with a commercially available Kif15 inhibitor, Kif15-IN-1 and may serve as a lead with which to further develop Kif15 inhibitors as clinically relevant agents.     

Early‐breeding females experience greater telomere loss

Annual reproductive success is often highest in individuals that initiate breeding early, yet relatively few individuals start breeding during this apparently optimal time. This suggests that individuals, particularly females who ultimately dictate when offspring are born, incur costs by initiating reproduction early in the season. We hypothesized that increases in the ageing rate of somatic cells may be one such cost. Telomeres, the repetitive DNA sequences on the ends of chromosomes, may be good proxies of biological wear and tear as they shorten with age and in response to stress. Using historical data from a long‐term study population of dark‐eyed juncos (Junco hyemalis), we found that telomere loss between years was greater in earlier breeding females, regardless of chronological age. There was no relationship between telomere loss and the annual number of eggs laid or chicks that reached independence. However, telomere loss was greater when temperatures were cooler, and cooler temperatures generally occur early in the season. This suggests that environmental conditions could be the primary cause of accelerated telomere loss in early breeders.     

Integrating Batteries in the Future Swiss Electricity Supply System: A Consequential Environmental Assessment

Stationary batteries are projected to play a role in the electricity system of Switzerland after 2030. By enabling the integration of surplus production from intermittent renewables, energy storage units displace electricity production from different sources and potentially create environmental benefits. Nevertheless, batteries can also cause substantial environmental impacts during their manufacturing process and through the extraction of raw materials. A prospective consequential life cycle assessment (LCA) of lithium metal polymer and lithium‐ion stationary batteries is undertaken to quantify potential environmental benefits and drawbacks. Projections are integrated into the LCA model: Energy scenarios are used to obtain marginal electricity supply mixes, and projections about the battery performances and the recycling process are sourced from the literature. The roles of key parameters and methodological choices in the results are systematically investigated. The results demonstrate that the displacement of marginal electricity sources determines the environmental implications of using batteries. In the reference scenario representing current policy, the displaced electricity mix is dominated by natural gas combined cycle units. In this scenario, the use of batteries generates environmental benefits in 12 of the 16 impact categories assessed. Nevertheless, there is a significant reduction in achievable environmental benefits when batteries are integrated into the power supply system in a low‐carbon scenario because the marginal electricity production, displaced using batteries, already has a reduced environmental impact. The direct impacts of batteries mainly originate from upstream manufacturing processes, which consume electricity and mining activities related to the extraction of materials such as copper and bauxite.     

When and where plant‐soil feedback may promote plant coexistence: a meta‐analysis

Plant‐soil feedback (PSF) theory provides a powerful framework for understanding plant dynamics by integrating growth assays into predictions of whether soil communities stabilise plant–plant interactions. However, we lack a comprehensive view of the likelihood of feedback‐driven coexistence, partly because of a failure to analyse pairwise PSF, the metric directly linked to plant species coexistence. Here, we determine the relative importance of plant evolutionary history, traits, and environmental factors for coexistence through PSF using a meta‐analysis of 1038 pairwise PSF measures. Consistent with eco‐evolutionary predictions, feedback is more likely to mediate coexistence for pairs of plant species (1) associating with similar guilds of mycorrhizal fungi, (2) of increasing phylogenetic distance, and (3) interacting with native microbes. We also found evidence for a primary role of pathogens in feedback‐mediated coexistence. By combining results over several independent studies, our results confirm that PSF may play a key role in plant species coexistence, species invasion, and the phylogenetic diversification of plant communities.     

Age-, gender-, and species-dependent mutagenicity in T cells of mice and rats exposed by inhalation to 1,3-butadiene

Experiments were performed: (i) to investigate potential age- and gender-dependent differences in mutagenic responses in T cells following exposures of B6C3F1 mice and F344 rats by inhalation for 2 weeks to 0 or 1250 ppm butadiene (BD), and (ii) to determine if exposures for 2 weeks to 62.5 ppm BD produce a mutagenic effect in female rats. To evaluate the effect of age on mutagenic response, mutant manifestation curves for splenic T cells of female mice exposed at 8-9 weeks of age were defined by measuring Hprt mutant frequencies (MFs) at multiple time points after BD exposure using a T cell cloning assay and comparing the resulting mutagenic potency estimate (calculated as the difference of areas under the mutant manifestation curves of treated versus control animals) to that reported for female mice exposed to BD in the same fashion beginning at 4-5 weeks of age. The shapes of the mutant T cell manifestation curves for spleens were different [e.g., the maximum BD-induced MFs in older mice (8.0+/-1.0 [S.D.]x10(-6)) and younger mice (17.8+/-6.1 x 10(-6)) were observed at 8 and 5 weeks post-exposure, respectively], but the mutagenic burden was the same for both age groups. To assess the effect of gender on mutagenic response, female and male rodents were exposed to BD at 4-5 weeks of age and Hprt MFs were measured when maximum MFs are expected to occur post-exposure. The resulting data demonstrated that the pattern for mutagenic susceptibility from high-level BD exposure is female mice>male mice>female rats>male rats. Exposures of female rats to 62.5 ppm BD caused a minor but significant mutagenic response compared with controls (n=16/group; P=0.03). These results help explain part of the differing outcomes/interpretations of data in earlier Hprt mutation studies in BD-exposed rodents.