Low-fidelity DNA synthesis by the L979F mutator derivative of Saccharomyces cerevisiae DNA polymerase ζ

To probe Pol ζ functions in vivo via its error signature, here we report the properties of Saccharomyces cerevisiae Pol ζ in which phenyalanine was substituted for the conserved Leu-979 in the catalytic (Rev3) subunit. We show that purified L979F Pol ζ is 30% as active as wild-type Pol ζ when replicating undamaged DNA. L979F Pol ζ shares with wild-type Pol ζ the ability to perform moderately processive DNA synthesis. When copying undamaged DNA, L979F Pol ζ is error-prone compared to wild-type Pol ζ, providing a biochemical rationale for the observed mutator phenotype of rev3-L979F yeast strains. Errors generated by L979F Pol ζ in vitro include single-base insertions, deletions and substitutions, with the highest error rates involving stable misincorporation of dAMP and dGMP. L979F Pol ζ also generates multiple errors in close proximity to each other. The frequency of these events far exceeds that expected for independent single changes, indicating that the first error increases the probability of additional errors within 10 nucleotides. Thus L979F Pol ζ, and perhaps wild-type Pol ζ, which also generates clustered mutations at a lower but significant rate, performs short patches of processive, error-prone DNA synthesis. This may explain the origin of some multiple clustered mutations observed in vivo.     

Surprising negative association between IgG1 allotype disparity and anti-adalimumab formation: a cohort study

Introduction

The human monoclonal antibody adalimumab is known to induce an anti-globulin response in some adalimumab-treated patients. Antibodies against adalimumab (AAA) are associated with non-response to treatment. Immunoglobulins, such as adalimumab, carry allotypes which represent slight differences in the amino acid sequences of the constant chains of an IgG molecule. Immunoglobulins with particular IgG (Gm) allotypes are racially distributed and could be immunogenic for individuals who do not express these allotypes. Therefore, we investigated whether a mismatch in IgG allotypes between adalimumab and IgG in adalimumab-treated patients is associated with the development of AAA.

Methods

This cohort study consisted of 250 adalimumab-treated rheumatoid arthritis (RA) patients. IgG allotypes were determined for adalimumab and for all patients. Anti-idiotype antibodies against adalimumab were measured with a regular radio immunoassay (RIA), and a newly developed bridging enzyme linked immunosorbent assay (ELISA) was used to measure anti-allotype antibodies against adalimumab. The association between AAA and the G1m3 and the G1m17 allotypes was determined. For differences between groups we used the independent or paired samples t-test, Mann-Whitney test or Chi square/Fisher's exact test as appropriate. To investigate the influence of confounders on the presence or absence of AAA a multiple logistic regression-analysis was used.

Results

Adalimumab carries the G1m17 allotype. No anti-allotype antibodies against adalimumab were detected. Thirty-nine out of 249 patients had anti-idiotype antibodies against adalimumab (16%). IgG allotypes of RA patients were associated with the frequency of AAA: patients homozygous for G1m17 had the highest frequency of AAA (41%), patients homozygous for G1m3 the lowest frequency (10%), and heterozygous patients' AAA frequency was 14% (P = 0.0001).

Conclusions

An allotype mismatch between adalimumab and IgG in adalimumab-treated patients did not lead to a higher frequency of AAA. On the contrary, patients who carried the same IgG allotype as present on the adalimumab IgG molecule, had the highest frequency of anti-adalimumab antibodies compared to patients whose IgG allotype differed from adalimumab. This suggests that the allotype of adalimumab may not be highly immunogenic. Furthermore, patients carrying the G1m17-allotype might be more prone to antibody responses.     

Inhibition of L- and P-selectin by a rationally synthesized novel core 2-like branched structure containing GalNAc-Lewisx and Neu5Acalpha2- 3Galbeta1-3GalNAc sequences

The selectins interact in important normal and pathological situations with certain sialylated, fucosylated glycoconjugate ligands containing sialyl Lewisx(Neu5Acalpha2-3Galbeta1-4(Fucalpha1-3)GlcN Ac). Much effort has gone into the synthesis of sialylated and sulfated Lewisxanalogs as competitive ligands for the selectins. Since the natural selectin ligands GlyCAM-1 and PSGL-1 carry sialyl Lewisxas part of a branched Core 2 O-linked structure, we recently synthesized Galbeta1-4(Fucalpha1-3)GlcNAcbeta1-6(SE-3Galbeta1++ +-3)GalNAc1alphaOMe and found it to be a moderately superior ligand for L and P-selectin (Koenig et al. , Glycobiology 7, 79-93, 1997). Other studies have shown that sulfate esters can replace sialic acid in some selectin ligands (Yeun et al. , Biochemistry, 31, 9126-9131, 1992; Imai et al. , Nature, 361, 555, 1993). Based upon these observations, we hypothesized that Neu5Acalpha2-3Galbeta1-3GalNAc might have the capability of interacting with L- and P-selectin. To examine this hypothesis, we synthesized Galbeta1-4(Fucalpha1-3)GlcNAcbeta1-6(Neu5Acalpha2++ +-3Galbeta1-3)- GalNAc alpha1-OB, which was found to be 2- to 3-fold better than sialyl Lexfor P and L selectin, respectively. We also report the synthesis of an unusual structure GalNAcbeta1-4(Fucalpha1- 3)GlcNAcbeta1-OMe (GalNAc- Lewisx-O-methyl glycoside), which also proved to be a better inhibitor of L- and P-selectin than sialyl Lewisx-OMe. Combining this with our knowledge of Core 2 branched structures, we have synthesized a molecule that is 5- to 6-fold better at inhibiting L- and P-selectin than sialyl Lewisx-OMe, By contrast to unbranched structures, substitution of a sulfate ester group for a sialic acid residue in such a molecule resulted in a considerable loss of inhibition ability. Thus, the combination of a sialic acid residue on the primary (beta1-3) arm, and a modified Lexunit on the branched (beta1-6) arm on an O-linked Core 2 structure generated a monovalent synthetic oliogosaccharide inhibitor superior to SLexfor both L- and P-selectin.      

Simultaneous measurement of three-dimensional joint kinematics and ligament strains with optical methods

The objective of this study was to assess the precision and accuracy of a nonproprietary, optical three-dimensional (3D) motion analysis system for the simultaneous measurement of soft tissue strains and joint kinematics. The system consisted of two high-resolution digital cameras and software for calculating the 3D coordinates of contrast markers. System precision was assessed by examining the variation in the coordinates of static markers over time. Three-dimensional strain measurement accuracy was assessed by moving contrast markers fixed distances in the field of view and calculating the error in predicted strain. Three-dimensional accuracy for kinematic measurements was assessed by simulating the measurements that are required for recording knee kinematics. The field of view (190 mm) was chosen to allow simultaneous recording of markers for soft tissue strain measurement and knee joint kinematics. Average system precision was between +/-0.004 mm and +/-0.035 mm, depending on marker size and camera angle. Absolute error in strain measurement varied from a minimum of +/-0.025% to a maximum of +/-0.142%, depending on the angle between cameras and the direction of strain with respect to the camera axes. Kinematic accuracy for translations was between +/-0.008 mm and +/-0.034 mm, while rotational accuracy was +/-0.082 deg to +/-0.160 deg. These results demonstrate that simultaneous optical measurement of 3D soft tissue strain and 3D joint kinematics can be performed while achieving excellent accuracy for both sets of measurements.     

Novel splice variants associated with one of the zebrafish <Emphasis Type="Italic">dnmt3</Emphasis>genes

Background  

DNA methylation and the methyltransferases are known to be important in vertebrate development and this may be particularly true for the Dnmt3 family of enzymes because they are thought to be the de novo methyltransferases. Mammals have three Dnmt3 genes; Dnmt3a, Dnmt3b, and Dnmt3L, two of which encode active enzymes and one of which produces an inactive but necessary cofactor. However, due to multiple promoter use and alternative splicing there are actually a number of dnmt3 isoforms present. Six different dnmt3 genes have recently been identified in zebrafish.     

Growth of Variants of Myxococcus virescens

Some observations on variant strains of Myxococcus virescens B2 with special emphasis on characteristics associated with the ability to grow in dispersion are reported. The isolated strains were divided into two major classes according to their mode of growth in shaken and static liquid cultures based on casitone and casamino acids media. Strains growing in dispersion were designated D⁺-strains and those growing in aggregates or as films, D^?-strains. Colony morphology, cell morphology, growth in liquid and on solid medium and morphogenesis were compared. The ability to grow in dispersion shown by D⁺-strains seemed to be associated with a smooth colony on casitone agar, inability to form typical fruiting bodies and a low linear growth rate of colonies on solid medium as compared with the D^?-strains. In contrast D^?-strains produced rough colonies on casitone agar, were able to fruit and evidently formed an adhesive slime in the form of fibrils extending from the cell surface. It is suggested that the observed differences depend on different envelopes of the cells in the two classes.     

Ammoglanis natgeorum,a new miniature pencil catfish (Siluriformes: Trichomycteridae) from the lower Atabapo River,Amazonas, Venezuela

A new species of the sand-dwelling catfish genus Ammoglanis is described from a marginal habitat of the lower Atabapo River, a left-bank blackwater tributary of the upper Orinoco River in Amazonas, Venezuela, adjacent to the border with Colombia. Ammoglanis natgeorum is distinguished from all congeners by trunk pigmentation pattern consisting of scattered ventral chromatophores concentrated around the anal-fin base and numerous additional meristic and anatomical characteristics. A. natgeorum is the second species of Ammoglanis described from the Orinoco River basin after Ammoglanis pulex, and several shared character states (e.g., eight total dorsal-fin rays, overall coloration pattern and presence of two finger-like papillae posterior to chin) suggest that it is more closely related to Ammoglanis obliquus (from the central Amazon basin) and A. pulex than to other congeners.     

Does sex (female versus male) influence the impact of class attendance on examination performance?

The "conventional wisdom" is that grades are related to class attendance, i.e., students who attend classes more frequently obtain better grades and class attendance dramatically contributes to enhanced learning. However, the influence of sex (female vs. male) on this relationship is understudied. Furthermore, there have been several studies examining the impact of attendance on course grades that challenge the conventional wisdom. To address these issues, we determined the effect of class attendance on examination scores for female and male students enrolled in our undergraduate exercise physiology class of 51 students (20 female students and 31 male students). The experiment was designed not to interfere with the normal conduct of the course. Attendance was recorded in each class, and, although regular attendance was encouraged, it was not required and did not factor into the final grades. The final grade reflected the average days of attendance for female students only. Specifically, female students earning a grade above the class average attended 89 ± 4% of the classes; however, female students earning a grade below the class average attended only 64 ± 6% of the classes. In sharp contrast, there was no difference in the number of classes attended for male students earning grades above or below the class average (84 ± 3% vs. 79 ± 5%). Accordingly, some male students were absent frequently but scored above the class average, whereas other male students attended many classes but scored below the class average. Thus, the influence of regular attendance on examination performance is more important for female students than male students.     

Effect of ACL deficiency on MCL strains and joint kinematics

The knee joint is partially stabilized by the interaction of multiple ligament structures. This study tested the interdependent functions of the anterior cruciate ligament (ACL) and the medial collateral ligament (MCL) by evaluating the effects of ACL deficiency on local MCL strain while simultaneously measuring joint kinematics under specific loading scenarios. A structural testing machine applied anterior translation and valgus rotation (limits 100 N and 10 N m, respectively) to the tibia of ten human cadaveric knees with the ACL intact or severed. A three-dimensional motion analysis system measured joint kinematics and MCL tissue strain in 18 regions of the superficial MCL. ACL deficiency significantly increased MCL strains by 1.8% (p<0.05) during anterior translation, bringing ligament fibers to strain levels characteristic of microtrauma. In contrast, ACL transection had no effect on MCL strains during valgus rotation (increase of only 0.1%). Therefore, isolated valgus rotation in the ACL-deficient knee was nondetrimental to the MCL. The ACL was also found to promote internal tibial rotation during anterior translation, which in turn decreased strains near the femoral insertion of the MCL. These data advance the basic structure-function understanding of the MCL, and may benefit the treatment of ACL injuries by improving the knowledge of ACL function and clarifying motions that are potentially harmful to secondary stabilizers.     

Ichthyoplankton metabarcoding: An efficient tool for early detection of invasive species establishment

Detection of invasive species is critical for management but is often limited by challenges associated with capture, processing and identification of early life stages. DNA metabarcoding facilitates large-scale monitoring projects to detect establishment early. Here, we test the use of DNA metabarcoding to monitor invasive species by sequencing over 5000 fishes in bulk ichthyoplankton samples (larvae and eggs) from four rivers of ecological and cultural importance in southern Canada. We were successful in detecting species known from each river and three invasive species in two of the four rivers. This includes the first detection of early life-stage rudd in the Credit River. We evaluated whether sampling gear affected the detection of invasive species and estimates of species richness, and found that light traps outperform bongo nets in both cases. We also found that the primers used for the amplification of target sequences and the number of sequencing reads generated per sample affect the consistency of species detections. However, these factors have less impact on detections and species richness estimates than the number of samples collected and analysed. Our analyses also show that incomplete reference databases can result in incorrectly attributing DNA sequences to invasive species. Overall, we conclude that DNA metabarcoding is an efficient tool for monitoring the early establishment of invasive species by detecting evidence of reproduction but requires careful consideration of sampling design and the primers used to amplify, sequence and classify the diversity of native and potentially invasive species.