smalldisco, a pipeline for siRNA discovery and 3' tail identification.

Capturing and sequencing small RNAs is standard practice; however, identification of a group of these small RNAs-small interfering RNAs (siRNAs)-has been more difficult. We present smalldisco, a command-line tool for small interfering RNA discovery and annotation from small RNA-seq datasets. smalldisco can distinguish short reads that map antisense to an annotated genomic feature (e.g. exons or mRNAs), annotate these siRNAs, and quantify their abundance. smalldisco also uses the program Tailor to quantify 3' nontemplated nucleotides of siRNAs or any small RNA species. smalldisco and supporting documentation are available for download from GitHub (https://github.com/ianvcaldas/smalldisco) and archived in Zenodo (https://doi.org/10.5281/zenodo.7799621).

Screening by deep sequencing reveals mediators of microRNA tailing in C. elegans.

microRNAs are frequently modified by addition of untemplated nucleotides to the 3' end, but the role of this tailing is often unclear. Here we characterize the prevalence and functional consequences of microRNA tailing in vivo, using Caenorhabditis elegans. MicroRNA tailing in C. elegans consists mostly of mono-uridylation of mature microRNA species, with rarer mono-adenylation which is likely added to microRNA precursors. Through a targeted RNAi screen, we discover that the TUT4/TUT7 gene family member CID-1/CDE-1/PUP-1 is required for uridylation, whereas the GLD2 gene family member F31C3.2-here named GLD-2-related 2 (GLDR-2)-is required for adenylation. Thus, the TUT4/TUT7 and GLD2 gene families have broadly conserved roles in miRNA modification. We specifically examine the role of tailing in microRNA turnover. We determine half-lives of microRNAs after acute inactivation of microRNA biogenesis, revealing that half-lives are generally long (median = 20.7 h), as observed in other systems. Although we observe that the proportion of tailed species increases over time after biogenesis, disrupting tailing does not alter microRNA decay. Thus, tailing is not a global regulator of decay in C. elegans. Nonetheless, by identifying the responsible enzymes, this study lays the groundwork to explore whether tailing plays more specialized context- or miRNA-specific regulatory roles.

Evolution of Transcriptional Repressors Impacts Caenorhabditis Vulval Development.

Comparative genomic sequence analysis has found that the genes for many chromatin-associated proteins are poorly conserved, but the biological consequences of these sequence changes are not understood. Here, we show that four genes identified for an Inappropriate Vulval cell Proliferation (ivp) phenotype in the nematode Caenorhabditis briggsae exhibit distinct functions and genetic interactions when compared with their orthologs in C. elegans. Specifically, we show that the four C. briggsae ivp genes encode the noncanonical histone HTZ-1/H2A.z and three nematode-specific proteins predicted to function in the nucleus. The mutants exhibit ectopic vulval precursor cell proliferation (the multivulva [Muv] phenotype) due to inappropriate expression of the lin-3/EGF gene, and RNAseq analysis suggests a broad role for these ivp genes in transcriptional repression. Importantly, although the C. briggsae phenotypes have parallels with those seen in the C. elegans synMuv system, except for the highly conserved HTZ-1/H2A.z, comparable mutations in C. elegans ivp orthologs do not exhibit synMuv gene interactions or phenotypes. These results demonstrate the evolutionary changes that can underlie conserved biological outputs and argue that proteins critical to repress inappropriate expression from the genome participate in a rapidly evolving functional landscape.

Periprosthetic Distal Femur Fracture after Total Knee Arthroplasty: A Systematic Review.

This study was designed to itemize and analyze the classification of fracture types and their corresponding outcomes in an attempt to provide a better understanding of the current treatment methods. Two PubMed searches were performed using the words "periprosthetic distal femur fracture" and "periprosthetic supracondylar femur fracture" in studies that were published in the previous 10 years (2004-2014). Data from 41 articlesthat met the general inclusion criteria, were collected and categorized into fracture type and treatment method groupings. Healing outcome and complications were the two parameters used to analyze the data. Treatment techniques were grouped in the following categories: locking plate, non-locking plate, intramedullary nail/rod, screw, blade plate, cerclage wires, allograft, external fixation, revision arthroplasty, non-operative, and other. Classification systems by Lewis and Rorabeck, the Association for Osteosynthesis/Orthopedic Trauma Association (AO/OTA), Su et al., Neer et al., Kim et al., Backstein et al., and the Société Française de Chirurgie Orthopédique et Traumatologique were reported. In total 448 fractures were identified, of which Rorabeck type II was the most common fracture studied. The two most successful treatment options for periprosthetic distal femur fractures were locking plate (87%) and intramedullary nail/rod (84%). The most frequent complications associated with periprosthetic distal femur fractures included non/mal/delayed union and the need for revision. Locking plates used to treat Rorabeck type II fractures had a complication rate of 35% and those treated with intramedullary nailing had a higher complication rate of 53%. In conclusion, the most frequent type of periprosthetic distal femur fracture after total knee arthroplasty was Rorabeck type II. The most common treatments for these types of fractures are locked plating and intramedullary nailing, with similar healing rates of 87% and 84%, respectively. However, the complication rate for locked plating was lower than for intramedullary nailing.