Motor Output Variability Impairs Driving Ability in Older Adults: Reply to Stinchcombe, Dickerson, Weaver, and Bedard

Driving is a complex skill, as indicated by Stinchcombe and colleagues in their letter. It requires the integration of sensory inputs, cognitive processing, and motor execution. Although our title is broad, we clearly indicate that our findings only address a single component of driving, namely reactive driving. We also indicate that these findings are based on a simulated task and recommend that future studies should examine the contribution of motor output variability to on-road driving performance (see Considerations in the Discussion section). Thus, we share the consideration of Stinchcombe and colleagues that the current results only address a small portion of the driving complexity

Sex Differences in Spatial Accuracy Relate to the Neural Activation of Antagonistic Muscles in Young Adults

Sex is an important physiological variable of behavior, but its effect on motor control remains poorly understood. Some evidence suggests that women exhibit greater variability during constant contractions and poorer accuracy during goal-directed tasks. However, it remains unclear whether motor output variability or altered muscle activation impairs accuracy in women. Here, we examine sex differences in endpoint accuracy during ankle goal-directed movements and the activity of the antagonistic muscles. Ten women (23.1 ± 5.1 years) and 10 men (23 ± 3.7 years) aimed to match a target (9° in 180 ms) with ankle dorsiflexion. Participants performed 50 trials and we recorded the endpoint accuracy and the electromyographic (EMG) activity of the primary agonist (Tibialis Anterior; TA) and antagonist (Soleus; SOL) muscles. Women exhibited greater spatial inaccuracy (Position error: t = −2.65, P = 0.016) but not temporal inaccuracy relative to men. The motor output variability was similar for the two sexes (P \u3e 0.2). The spatial inaccuracy in women was related to greater variability in the coordination of the antagonistic muscles (R 2 0.19, P = 0.03). These findings suggest that women are spatially less accurate than men during fast goal-directed movements likely due to an altered activation of the antagonistic muscles

Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations

<p>Abstract</p> <p>Background</p> <p>Folate synthesis and salvage pathways are relatively well known from classical biochemistry and genetics but they have not been subjected to comparative genomic analysis. The availability of genome sequences from hundreds of diverse bacteria, and from <it>Arabidopsis thaliana</it>, enabled such an analysis using the SEED database and its tools. This study reports the results of the analysis and integrates them with new and existing experimental data.</p> <p>Results</p> <p>Based on sequence similarity and the clustering, fusion, and phylogenetic distribution of genes, several functional predictions emerged from this analysis. For bacteria, these included the existence of novel GTP cyclohydrolase I and folylpolyglutamate synthase gene families, and of a trifunctional <it>p</it>-aminobenzoate synthesis gene. For plants and bacteria, the predictions comprised the identities of a 'missing' folate synthesis gene (<it>folQ</it>) and of a folate transporter, and the absence from plants of a folate salvage enzyme. Genetic and biochemical tests bore out these predictions.</p> <p>Conclusion</p> <p>For bacteria, these results demonstrate that much can be learnt from comparative genomics, even for well-explored primary metabolic pathways. For plants, the findings particularly illustrate the potential for rapid functional assignment of unknown genes that have prokaryotic homologs, by analyzing which genes are associated with the latter. More generally, our data indicate how combined genomic analysis of both plants and prokaryotes can be more powerful than isolated examination of either group alone.</p

Towards a Systems Approach in the Genetic Analysis of Archaea: Accelerating Mutant Construction and Phenotypic Analysis in Haloferax volcanii

With the availability of a genome sequence and increasingly sophisticated genetic tools, Haloferax volcanii is becoming a model for both Archaea and halophiles. In order for H. volcanii to reach a status equivalent to Escherichia coli, Bacillus subtilis, or Saccharomyces cerevisiae, a gene knockout collection needs to be constructed in order to identify the archaeal essential gene set and enable systematic phenotype screens. A streamlined gene-deletion protocol adapted for potential automation was implemented and used to generate 22 H. volcanii deletion strains and identify several potentially essential genes. These gene deletion mutants, generated in this and previous studies, were then analyzed in a high-throughput fashion to measure growth rates in different media and temperature conditions. We conclude that these high-throughput methods are suitable for a rapid investigation of an H. volcanii mutant library and suggest that they should form the basis of a larger genome-wide experiment

A Gateway platform for functional genomics in Haloferax volcanii

In part due to the existence of simple methods for its cultivation and genetic manipulation, Haloferax volcanii is a major archaeal model organism. It is the only archaeon for which the whole set of post-transcriptionally modified tRNAs has been sequenced, allowing for an in silico prediction of all RNA modification genes present in the organism. One approach to check these predictions experimentally is via the construction of targeted gene deletion mutants. Toward this goal, an integrative “Gateway vector” that allows gene deletion in H. volcanii uracil auxotrophs was constructed. The vector was used to delete three predicted tRNA modification genes: HVO_2001 (encoding an archaeal transglycosyl tranferase or arcTGT), which is involved in archeosine biosynthesis; HVO_2348 (encoding a newly discovered GTP cyclohydrolase I), which catalyzes the first step common to archaeosine and folate biosynthesis; and HVO_2736 (encoding a member of the COG1444 family), which is involved in N4-acetylcytidine (ac4C) formation. Preliminary phenotypic analysis of the deletion mutants was conducted, and confirmed all three predictions

Distribution of HLA-DRB1/DQB1 alleles and DRB1-DQB1 haplotypes among Tunisian patients with autoimmune hepatitis

Background: Autoimmune hepatitis (AIH) is a chronic inflammatory disease characterized by necrotic inflammation leading to hepatocyte destruction. The association of human leukocyte antigens (HLA) with AIH development and onset is not fully elucidated especially in the Tunisian population.Objectives: The aim of this study was to determine the association of HLA class II alleles and DRB1-DQB1 haplotypes with AIH in Tunisian population.Patients and Methods: A total of 30 AIH patients and 60 healthy controls were included in the study. HLA class II typing was performed by Single-specific-primer polymerase chain reaction (PCR-SSP) technique.Results: Among 13 DRB1 and 5 DQB1 alleles resolved, our results show a positive association of HLADRB1 ⁄03 (38.3% vs. 21.6%, OR = 2.24, P = 0.028) and negative association of HLA-DRB1⁄11 (3.3% vs. 16.7%, P = 0.019). The analysis of DRB1-DQB1 haplotypes in cases and controls revealed 11-shared haplotypes with a frequency exceeding 1%. HLA-DRB1⁄11-DQB1⁄03 haplotype showed a decreased frequency in AIH patients (1.6% vs. 15.8%, P = 0.009) and may be considered as an haplotype of resistance to AIH.Conclusions: To our Knowledge, this is the first study performed to detect the HLA-DRB1 and DQB1 alleles associated with predisposition to AIH in Tunisian patients. The search for HLA predisposing genes to AIH may permit an earlier diagnosis allowing a better management and treatment of the disease in order to avoid liver transplantation

The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA

Threonylcarbamoyladenosine (t6A) is a universal modification found at position 37 of ANN decoding tRNAs, which imparts a unique structure to the anticodon loop enhancing its binding to ribosomes in vitro. Using a combination of bioinformatic, genetic, structural and biochemical approaches, the universal protein family YrdC/Sua5 (COG0009) was shown to be involved in the biosynthesis of this hypermodified base. Contradictory reports on the essentiality of both the yrdC wild-type gene of Escherichia coli and the SUA5 wild-type gene of Saccharomyces cerevisiae led us to reconstruct null alleles for both genes and prove that yrdC is essential in E. coli, whereas SUA5 is dispensable in yeast but results in severe growth phenotypes. Structural and biochemical analyses revealed that the E. coli YrdC protein binds ATP and preferentially binds RNAThr lacking only the t6A modification. This work lays the foundation for elucidating the function of a protein family found in every sequenced genome to date and understanding the role of t6A in vivo

Functional Promiscuity of the COG0720 Family

The biosynthesis of GTP derived metabolites such as tetrahydrofolate (THF), biopterin (BH4), and the modified tRNA nucleosides queuosine (Q) and archaeosine (G+) relies on several enzymes of the Tunnel-fold superfamily. A subset of these proteins include the 6-pyruvoyl-tetrahydropterin (PTPS-II), PTPS-III, and PTPS-I homologs, all members of the COG0720 family, that have been previously shown to transform 7,8-dihydroneopterin triphosphate (H2NTP) into different products. PTPS-II catalyzes the formation of 6-pyruvoyltetrahydropterin in the BH4 pathway. PTPS-III catalyzes the formation of 6-hydroxylmethyl-7,8-dihydropterin in the THF pathway. PTPS-I catalyzes the formation of 6-carboxy-5,6,7,8-tetrahydropterin in the Q pathway. Genes of these three enzyme families are often misannotated as they are difficult to differentiate by sequence similarity alone. Using a combination of physical clustering, signature motif, and phylogenetic codistribution analyses, in vivo complementation studies, and in vitro enzymatic assays, a complete reannotation of the COG0720 family was performed in prokaryotes. Notably, this work identified and experimentally validated dual function PTPS-I/III enzymes involved in both THF and Q biosynthesis. Both in vivo and in vitro analyses showed that the PTPS-I family could tolerate a translation of the active site cysteine and was inherently promiscuous, catalyzing different reactions on the same substrate, or the same reaction on different substrates. Finally, the analysis and experimental validation of several archaeal COG0720 members confirmed the role of PTPS-I in archaeosine biosynthesis, and resulted in the identification PTPS-III enzymes with variant signature sequences in Sulfolobus species. This study reveals an expanded versatility of the COG0720 family members and illustrates that for certain protein families, extensive comparative genomic analysis beyond homology is required to correctly predict function

Synergistic use of plant-prokaryote comparative genomics for functional annotations

<p>Abstract</p> <p>Background</p> <p>Identifying functions for all gene products in all sequenced organisms is a central challenge of the post-genomic era. However, at least 30-50% of the proteins encoded by any given genome are of unknown or vaguely known function, and a large number are wrongly annotated. Many of these ‘unknown’ proteins are common to prokaryotes and plants. We set out to predict and experimentally test the functions of such proteins. Our approach to functional prediction integrates comparative genomics based mainly on microbial genomes with functional genomic data from model microorganisms and post-genomic data from plants. This approach bridges the gap between automated homology-based annotations and the classical gene discovery efforts of experimentalists, and is more powerful than purely computational approaches to identifying gene-function associations.</p> <p>Results</p> <p>Among Arabidopsis genes, we focused on those (2,325 in total) that (i) are unique or belong to families with no more than three members, (ii) occur in prokaryotes, and (iii) have unknown or poorly known functions. Computer-assisted selection of promising targets for deeper analysis was based on homology-independent characteristics associated in the SEED database with the prokaryotic members of each family. In-depth comparative genomic analysis was performed for 360 top candidate families. From this pool, 78 families were connected to general areas of metabolism and, of these families, specific functional predictions were made for 41. Twenty-one predicted functions have been experimentally tested or are currently under investigation by our group in at least one prokaryotic organism (nine of them have been validated, four invalidated, and eight are in progress). Ten additional predictions have been independently validated by other groups. Discovering the function of very widespread but hitherto enigmatic proteins such as the YrdC or YgfZ families illustrates the power of our approach.</p> <p>Conclusions</p> <p>Our approach correctly predicted functions for 19 uncharacterized protein families from plants and prokaryotes; none of these functions had previously been correctly predicted by computational methods. The resulting annotations could be propagated with confidence to over six thousand homologous proteins encoded in over 900 bacterial, archaeal, and eukaryotic genomes currently available in public databases.</p