Marker-free quantification of repair pathway utilization at Cas9-induced double-strand breaks

Genome integrity and genome engineering require efficient repair of DNA double-strand breaks (DSBs) by non-homologous end joining (NHEJ), homologous recombination (HR), or alternative end-joining pathways. Here we describe two complementary methods for marker-free quantification of DSB repair pathway utilization at Cas9-targeted chromosomal DSBs in mammalian cells. The first assay features the analysis of amplicon next-generation sequencing data using ScarMapper, an iterative break-associated alignment algorithm to classify individual repair products based on deletion size, microhomology usage, and insertions. The second assay uses repair pathway-specific droplet digital PCR assays (‘PathSig-dPCR’) for absolute quantification of signature DSB repair outcomes. We show that ScarMapper and PathSig-dPCR enable comprehensive assessment of repair pathway utilization in different cell models, after a variety of experimental perturbations. We use these assays to measure the differential impact of DNA end resection on NHEJ, HR and polymerase theta-mediated end joining (TMEJ) repair. These approaches are adaptable to any cellular model system and genomic locus where Cas9-mediated targeting is feasible. Thus, ScarMapper and PathSig-dPCR allow for systematic fate mapping of a targeted DSB with facile and accurate quantification of DSB repair pathway choice at endogenous chromosomal loci.     

The Robinson Protocol: a treadmill anaerobic performance test

The current investigation was designed to further examine the reliability of the Robinson protocol, which is a run-to-exhaustion treadmill test. Robinson (10) originally examined this protocol with 5 subjects. The significance of the initial exploratory study was the impetus for expanding the study to examine the reliability of the protocol with a larger sample. Fifteen male subjects participated in 3 trial runs on the treadmill. The first trial was a modified McConnell (7) test to determine the aerobic capacity of each subject. The second and third trials were identical Robinson protocols (10). The first trial run mean, in seconds (262.04 +/- 74.50), was not significantly different from the second trial run mean (257.30 +/- 72.65), p = 0.526 (2 tailed). As expected, trial 1 and trial 2 were highly correlated (intraclass) (r = 0.927, p < 0.001). These results provide additional support for the hypothesis that the Robinson protocol with a greater subject pool is a reliable protocol that can be used in research studies interested in examining various physiological interventions or anaerobic training.     

Crystal structure of the Escherichia coli dcm very-short-patch DNA repair endonuclease bound to its reaction product-site in a DNA superhelix

Very-short-patch repair (Vsr) enzymes occur in a variety of bacteria, where they initiate nucleotide excision repair of G:T mismatches arising by deamination of 5-methyl-cytosines in specific regulatory sequences. We have now determined the structure of the archetypal dcm-Vsr endonuclease from Escherichia coli bound to the cleaved authentic hemi-deaminated/hemi-methylated dcm sequence 5′-C-OH-3′ 5′-p-T-p-A-p-G-p-G-3′/3′-G-p-G-p-T-p^Me5C-p-C formed by self-assembly of a 12mer oligonucleotide into a continuous nicked DNA superhelix. The structure reveals the presence of a Hoogsteen base pair within the deaminated recognition sequence and the substantial distortions of the DNA that accompany Vsr binding to product sites.     

GSMN-TB: a web-based genome-scale network model of <Emphasis Type="Italic">Mycobacterium tuberculosis</Emphasis>metabolism

Background  

An impediment to the rational development of novel drugs against tuberculosis (TB) is a general paucity of knowledge concerning the metabolism of Mycobacterium tuberculosis, particularly during infection. Constraint-based modeling provides a novel approach to investigating microbial metabolism but has not yet been applied to genome-scale modeling of M. tuberculosis.     

Long-term effects of graduated compression stockings on cardiorespiratory performance

The use of graduated compression stockings (GCS) in sport has been increasing in the last years due to their potential positive effects for athletes. However, there is little evidence to support whether these types of garments actually improve cardiorespiratory performance. The aim of this study was to examine the cardiorespiratory responses of GCS during running after three weeks of regular use. Twenty recreational runners performed three tests on different days: test 1) – a 5-min maximal effort run in order to determine the participants’ maximal aerobic speed; and tests 2) and 3) – a fatigue running test of 30 minutes at 80% of their maximal aerobic speed with either GCS or PLACEBO stockings at random. Cardiorespiratory parameters (minute ventilation, heart rate, relative oxygen consumption, relative carbon dioxide production, ventilatory equivalents for oxygen and carbon dioxide, and oxygen pulse) were measured. Before each test in the laboratory, the participants trained with the randomly assigned stockings (GCS or PLACEBO) for three weeks. No significant differences between GCS and PLACEBO were found in any of the cardiorespiratory parameters. In conclusion, the present study provides evidence that running with GCS for three weeks does not influence cardiorespiratory parameters in recreational runners.     

Genetic characterization of Uruguayan Pampa Rocha pigs with microsatellite markers

In this study, we genetically characterized the Uruguayan pig breed Pampa Rocha. Genetic variability was assessed by analyzing a panel of 25 microsatellite markers from a sample of 39 individuals. Pampa Rocha pigs showed high genetic variability with observed and expected heterozygosities of 0.583 and 0.603, respectively. The mean number of alleles was 5.72. Twenty-four markers were polymorphic, with 95.8% of them in Hardy Weinberg equilibrium. The level of endogamy was low (F_IS = 0.0475). A factorial analysis of correspondence was used to assess the genetic differences between Pampa Rocha and other pig breeds; genetic distances were calculated, and a tree was designed to reflect the distance matrix. Individuals were also allocated into clusters. This analysis showed that the Pampa Rocha breed was separated from the other breeds along the first and second axes. The neighbour-joining tree generated by the genetic distances D_A showed clustering of Pampa Rocha with the Meishan breed. The allocation of individuals to clusters showed a clear separation of Pampa Rocha pigs. These results provide insights into the genetic variability of Pampa Rocha pigs and indicate that this breed is a well-defined genetic entity.     

Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals

Background  

In mammals, contrary to what is usually assumed, recent evidence suggests that synonymous mutations may not be selectively neutral. This position has proven contentious, not least because of the absence of a viable mechanism. Here we test whether synonymous mutations might be under selection owing to their effects on the thermodynamic stability of mRNA, mediated by changes in secondary structure.     

Oocyst shedding in cats vaccinated by the nasal and rectal routes with crude rhoptry proteins of Toxoplasma gondii

During this study, cats were immunized by the intranasal and rectal routes with crude rhoptry proteins of Toxoplasma gondii admixed with Quil-A. Twenty-five domestic short hair cats divided into five groups (n=5) were used during this evaluation: G1 and G3 cats received 200 μg of the rhoptry proteins with Quil-A (20 μg) by the intranasal and rectal routes, respectively; G2 and G4 cats received bovine serum albumin (BSA, 200 μg/dose) with Quil-A (20 μg); and G5 animals served as unvaccinated controls. All treatments were performed at days 0, 21, 42, and 63. The challenge was done with 800 cysts of the ME49 of T. gondii strain at day 70 (challenge day). The serum IgG, IgM, IgA, and fecal IgA antibody levels were evaluated by using the indirect enzyme-linked immunosorbent assay (ELISA). Some animals produced antibody levels beyond cut-off; however, two animals from G1 (OD(mean)=0.308, OD(cut-off)=0.200) and three from G3 (OD(mean)=0.254) demonstrated IgG levels on being challenged, with similar results occurring in two cats from G1 to IgM (OD(mean)=0.279, OD(cut-off)=0.200). Fecal IgA levels were detected in all G1 cats (OD(mean)=0.330, OD(cut-off)=0.065), and in one cat from G3 (OD(mean)=0.167). The serum and fecal humoral immune responses did not correlate with oocyst shedding. Oocyst shedding varied from 98.4% (G1), 87.5% (G2), 53.0% (G3), to 58% (G4), and was lower than that of G5 cats. The prepatent period of cats vaccinated intranasally (G1) was reduced from 6-9.6 to 2.8 days, suggesting protection of environmental contamination, considering cats as the primary source of contamination. The intranasally and rectally administered rhoptry vaccines were able to partially protect cats against T. gondii cysts on being challenged; however, the intranasal method of vaccination yielded better results relative to the rectal route.     

Effects of unilateral and bilateral lower-body heavy resistance exercise on muscle activity and testosterone responses

Unilateral and bilateral lower-body heavy resistance exercises (HREs) are used for strength training. Little research has examined whether muscle activation and testosterone (TES) responses differ between these exercises. Our purpose was to compare the effects of unilateral and bilateral lower-body HRE on muscle activity using surface electromyography (sEMG) and TES concentrations. Ten resistance-trained, college-aged male athletes (football, track and field) completed 5 testing sessions in which bilateral (back squat [BS]) and unilateral (pitcher squat [PS]) exercises were performed using a counterbalanced design. Sessions 1 and 2 determined estimated maximum strength (10 repetition maximum [10RM]) in the BS and PS. During testing session 3, muscle activation (sEMG) was measured in the right vastus lateralis, biceps femoris, gluteus maximus, and erector spinae (ES) during both BS and PS (stance leg) exercises. In sessions 4 and 5, total TES concentrations (nanomoles per liter) were measured via blood draws at baseline (preexercise), 0, 5, 10, 15, and 30 minutes postexercise after 4 sets of 10 repetitions at the 10RM. Separate repeated-measures analyses of variance examined differences in sEMG and TES between BS and PS (p < 0.05). The sEMG amplitudes were similar (p = 0.80) for BS (0.22 ± 0.06 mV) and PS (0.20 ± 0.07 mV). The TES responses were also similar (p = 0.15) between BS (21.8 ± 6.9 nmol·L(-1)) and PS (26.2 ± 10.1 nmol·L(-1)). The similar lower limb and back sEMG and TES responses may indicate that the neuromuscular and hormonal demands were comparable for both the BS and PS exercises despite the absolute work being less in the PS. The PS exercise may be an effective method for including unilateral exercise into lower-body resistance training when designing training programs for ground-based activities.     

血管内皮祖细胞与糖尿病微血管病变研究进展

糖尿病微血管病变严重影响了患者生活质量,是患者致死致残主要原因。微血管病变主要表现在视网膜、肾、神经、心肌组织。微血管病变的机制尚未完全清楚,近年越来越多研究发现血管内皮祖细胞(endothelial progenitor cells,EPCs)是该病发病重要原因。EPCs有分化为成熟的内皮细胞并且参与新血管形成和新生的能力。正常情况下内皮损失和EPCs对内皮的修复作用处于动态平衡状态,一旦EPCs受损,内皮损害和修复之间的平衡被打破,内皮层的完整性遭到破坏,必然参与糖尿病血管病变的发生发展。国内外大量研究证明糖尿病合并大血管病变EPCs数目功能改变,而糖尿病合并微血管病变EPCs的怎样变化?本文就EPCs与糖尿病微血管病变的关系进行系统综述。