Search

Background: Concerns have arisen that anterior cruciate ligament reconstruction (ACLR) with lateral extra-articular tenodesis (LET) may accelerate the development of posttraumatic osteoarthritis in the lateral compartment of the knee. Purpose/Hypothesis: The purpose of this study was to evaluate whether the augmentation of ACLR with LET affects the quality of lateral compartment articular cartilage on magnetic resonance imaging (MRI) at 2 years postoperatively. We hypothesized that there would be no difference in T1rho and T2 relaxation times when comparing ACLR alone with ACLR + LET. Study Design: Randomized controlled trial; Level of evidence, 1. Methods: A consecutive subgroup of patients at the Fowler Kennedy Sport Medicine Clinic participating in the STABILITY 1 Study underwent bilateral 3-T MRI at 2 years after surgery. The primary outcome was T1rho and T2 relaxation times. Articular cartilage in the lateral compartment was manually segmented into 3 regions of the tibia (lateral tibia [LT]–1 to LT-3) and 5 regions of the femur (lateral femoral condyle [LFC]–1 to LFC-5). Analysis of covariance was used to compare relaxation times between groups, adjusted for lateral meniscal tears and treatment, cartilage and bone marrow lesions, contralateral relaxation times, and time since surgery. Semiquantitative MRI scores according to the Anterior Cruciate Ligament OsteoArthritis Score were compared between groups. Correlations were used to determine the association between secondary outcomes (including results of the International Knee Documentation Committee score, Knee injury and Osteoarthritis Outcome Score, Lower Extremity Functional Scale, 4-Item Pain Intensity Measure, hop tests, and isokinetic quadriceps and hamstring strength tests) and cartilage relaxation. Results: A total of 95 participants (44 ACLR alone, 51 ACLR + LET) with a mean age of 18.8 years (61.1% female [58/95]) underwent 2-year MRI (range, 20-36 months). T1rho relaxation times were significantly elevated for the ACLR + LET group in LT-1 (37.3 ± 0.7 ms vs 34.1 ± 0.8 ms, respectively; P =.005) and LFC-2 (43.9 ± 0.9 ms vs 40.2 ± 1.0 ms, respectively; P =.008) compared with the ACLR alone group. T2 relaxation times were significantly elevated for the ACLR + LET group in LFC-1 (51.2 ± 0.7 ms vs 49.1 ± 0.7 ms, respectively; P =.03) and LFC-4 (45.9 ± 0.5 ms vs 44.2 ± 0.6 ms, respectively; P =.04) compared with the ACLR alone group. All effect sizes were small to medium. There was no difference in Anterior Cruciate Ligament OsteoArthritis Scores between groups (P =.99). Weak negative associations (rs = –0.27 to –0.22; P <.05) were found between relaxation times and quadriceps and hamstring strength in the anterolateral knee, while all other correlations were nonsignificant (P >.05). Conclusion: Increased relaxation times demonstrating small to medium effect sizes suggested early biochemical changes in articular cartilage of the anterolateral compartment in the ACLR + LET group compared with the ACLR alone group. Further evidence and long-term follow-up are needed to better understand the association between these results and the potential risk of the development of osteoarthritis in our patient cohort. [ABSTRACT FROM AUTHOR]

Purpose: To determine whether different regimens of multimodal analgesia will reduce postoperative pain scores, opioid consumption, costs and hospital length-of-stay following hip arthroscopy. Methods: From 2018 to 2021, 132 patients undergoing hip arthroscopy for femoroacetabular impingement syndrome (FAIS) were included in this prospective, single-center randomized controlled trial. Patients were randomized into four treatment groups: Group 1—Control: opioid medication (oxycodone-acetaminophen 5 mg/325 mg, 1–2 tabs q6H as needed), Heterotopic ossification prophylaxis—Naprosyn 500 mg twice daily × 3 weeks); Group 2—Control + postoperative sleeping aid (Zopiclone 7.5 mg nightly × 7 days); Group 3—Control + preoperative and postoperative Gabapentin (600 mg orally, 1 h preoperatively; 600 mg postoperatively, 8 h following pre-op dose); Group 4—Control + pre-medicate with Celecoxib (400 mg orally, 1 h preoperatively) The primary outcome was pain measured with a visual analog scale, monitored daily for the first week and every other day for 6 weeks. Secondary outcomes included opioid consumption, healthcare resource use, and hospital length of stay. Results: Patient characteristics were similar between groups. There were no statistically significant differences in pain scores between groups at any timepoint after adjusting for intra-operative traction time, intra-operative opioid administration and preoperative pain scores (p > 0.05). There were also no significant differences in the number of days that opioids were taken (n.s.) and the average daily morphine milligram equivalents consumed (n.s.). Similarly, there were no statistically significant differences in length of stay in the experimental groups, compared with the control group (n.s.). Finally, there were no differences in cost between groups (n.s.). Conclusion: The routine use of Zopiclone, Celecoxib and Gabapentin did not improve postoperative pain control or reduce length-of-stay following hip arthroscopy. Therefore, these medications are not recommended for routine postoperative pain control following hip arthroscopy. Level of evidence: l. [ABSTRACT FROM AUTHOR]

Osteoarthritis (OA) is the most prevalent joint disorder with increasing worldwide incidence. Mechanistic insights into OA pathophysiology are evolving and there are currently no disease-modifying OA drugs. An increase in protease activity is linked to progressive degradation of the cartilage in OA. Proteases also trigger inflammation through a family of G protein-coupled receptors (GPCRs) called the Proteinase-Activated Receptors (PARs). PAR signaling can trigger pro-inflammatory responses and targeting PARs is proposed as a therapeutic approach in OA. Several enzymes can cleave the PAR N-terminus, but the endogenous protease activators of PARs in OA remain unclear. Here we characterized PAR activating enzymes in knee joint synovial fluids from OA patients and healthy donors using genetically encoded PAR biosensor expressing cells. Calcium signaling assays were performed to examine receptor activation. The class and type of enzymes cleaving the PARs was further characterized using protease inhibitors and fluorogenic substrates. We find that PAR1, PAR2 and PAR4 activating enzymes are present in knee joint synovial fluids from healthy controls and OA patients. Compared to healthy controls, PAR1 activating enzymes are elevated in OA synovial fluids while PAR4 activating enzyme levels are decreased. Using enzyme class and type selective inhibitors and fluorogenic substrates we find that multiple PAR activating enzymes are present in OA joint fluids and identify serine proteinases (thrombin and trypsin-like) and matrix metalloproteinases as the major classes of PAR activating enzymes in the OA synovial fluids. Synovial fluid driven increase in calcium signaling was significantly reduced in cells treated with PAR1 and PAR2 antagonists, but not in PAR4 antagonist treated cells. OA associated elevation of PAR1 cleavage suggests that targeting this receptor may be beneficial in the treatment of OA. [ABSTRACT FROM AUTHOR]

Purpose: To assess how meniscal repair and excision impact short term patient-reported outcome measures (PROMs), knee stability, and early graft rupture rates following primary hamstring anterior cruciate ligament reconstruction (ACLR) with or without lateral extra-articular tenodesis (LET) in a group of young active patients where meniscal repair is commonly advocated. Methods: Six hundred and eighteen patients under 25 years of age at high-risk of graft failure following ACLR were recruited to the Stability 1 study. Multivariable regression models were developed to identify statistically and clinically significant surgical and demographic predictors of Knee Injury and Osteoarthritis Outcome Score (KOOS), International Knee Documentation Committee Subjective Knee Form (IKDC), ACL Quality of Life Questionnaire (ACL-QOL) and Marx Activity Rating Scale (MARS) scores. Chi-Square tests of independence were used to explore the association between meniscal status (torn, not torn), meniscal treatment (excision or repair), graft rupture, and rotatory knee laxity. Results: Medial meniscus repair was associated with worse outcomes on the KOOS (β = −1.32, 95% CI: −1.57 to −1.10, p = 0.003), IKDC (β = −1.66, 95% CI: −1.53 to −1.02, p = 0.031) and ACL-QOL (β = −1.25, 95% CI: −1.61 to 1.02, p = n.s.). However, these associations indicated small, clinically insignificant changes based on reported measures of clinical relevance. Other important predictors of post-operative PROMs included age, sex, and baseline scores. Medial meniscus excision and lateral meniscus treatment (repair or excision) did not have an important influence on PROMs. There was no significant association between meniscal treatment and graft rupture or rotatory knee laxity. Conclusion: While repairing the medial meniscus may result in a small reduction in PROM scores at two-year follow-up, these differences are not likely to be important to patients or clinicians. Any surgical morbidity associated with meniscal repair appears negligible in terms of PROMs. Meniscal repair does not affect rotatory laxity or graft failure rates in the short term. Therefore, meniscal repair should likely be maintained as the standard of care for concomitant meniscal tears with ACLR. Level of evidence: III. [ABSTRACT FROM AUTHOR]

Background: Patients lost to follow-up (LTF) impact even the most meticulously planned randomized controlled trials. Identifying patients at high risk for becoming LTF and employing strategies to retain these patients may reduce attrition bias. Methods: A cohort of 618 young, active patients undergoing anterior cruciate ligament reconstruction in the STABILITY 1 study was analyzed. Patients completed clinical testing and 9 questionnaires at 3, 6, 12, and 24 months. Multivariable logistic regression was performed for 5 different definitions of LTF. Patient characteristics and study site were included as predictors. Results: The LTF rate was 8.3%. Current or previous smokers (odds ratio [OR] = 2.77; 95% confidence interval [CI]: 1.20 to 5.96), those employed part-time (OR = 2.31; 95% CI: 1.04 to 5.14), and those with body mass index (BMI) of >=25 kg/m2 had significantly greater odds of becoming LTF compared with nonsmokers, students, and those with BMI of <25 kg/m2, respectively. Those employed part-time were >8 times more likely (95% CI: 2.66 to 26.28) to become LTF compared with students within the first year. Postoperative BMI of >=25 kg/m2 was significantly associated with 2 times greater odds of missing the in-person clinical examination at any visit or becoming LTF after the first postoperative year. The clinical site was the single largest predictor of missing data at any visit. Conclusions: Current or previous smoking, part-time employment, and BMI of >=25 kg/m2 were significant predictors of becoming LTF, and part-time employment was significantly associated with early LTF. BMI of >=25 kg/m2 was also associated with late LTF and clinical LTF. The clinical site was significantly associated with missing data at any visit. While we cannot accurately predict who will become LTF, investigators should be aware of these factors to identify high-risk patients and focus retention strategies accordingly. Clinical Relevance: Understanding factors related to becoming LTF in young, active patients undergoing anterior cruciate ligament reconstruction can help investigators target retention strategies to reduce LTF in studies requiring clinical follow-up in similar populations. [ABSTRACT FROM AUTHOR]

Background: Anterior cruciate ligament (ACL) reconstruction (ACLR) has higher failure rates in young active patients returning to sports as compared with older, less active individuals. Augmentation of ACLR with an anterolateral procedure has been shown to reduce failure rates; however, indications for this procedure have yet to be clearly defined. Purpose/Hypothesis: The purpose of this study was to identify predictors of ACL graft failure in high-risk patients and determine key indications for when hamstring ACLR should be augmented by a lateral extra-articular tenodesis (LET). We hypothesized that different preoperative characteristics and surgical variables may be associated with graft failure characterized by asymmetric pivot shift and graft rupture. Study Design: Case-control study; Level of evidence, 3. Methods: Data were obtained from the Stability 1 Study, a multicenter randomized controlled trial of young active patients undergoing autologous hamstring ACLR with or without a LET. We performed 2 multivariable logistic regression analyses, with asymmetric pivot shift and graft rupture as the dependent variables. The following were included as predictors: LET, age, sex, graft diameter, tear chronicity, preoperative high-grade knee laxity, preoperative hyperextension on the contralateral side, medial meniscal repair/excision, lateral meniscal repair/excision, posterior tibial slope angle, and return-to-sports exposure time and level. Results: Of the 618 patients in the Stability 1 Study, 568 with a mean age of 18.8 years (292 female; 51.4%) were included in this analysis. Asymmetric pivot shift occurred in 152 (26.8%) and graft rupture in 43 (7.6%). The addition of a LET (odds ratio [OR], 0.56; 95% CI, 0.37-0.83) and increased graft diameter (OR, 0.62; 95% CI, 0.44-0.87) were significantly associated with lower odds of asymmetric pivot shift. The addition of a LET (OR, 0.40; 95% CI, 0.18-0.91) and older age (OR, 0.83; 95% CI, 0.72-0.96) significantly reduced the odds of graft rupture, while greater tibial slope (OR, 1.15; 95% CI, 1.01-1.32), preoperative high-grade knee laxity (OR, 3.27; 95% CI, 1.45-7.41), and greater exposure time to sport (ie, earlier return to sport) (OR, 1.18; 95% CI, 1.08-1.29) were significantly associated with greater odds of rupture. Conclusion: The addition of a LET and larger graft diameter were significantly associated with reduced odds of asymmetric pivot shift. Adding a LET was protective of graft rupture, while younger age, greater posterior tibial slope, high-grade knee laxity, and earlier return to sport were associated with increased odds of graft rupture. Orthopaedic surgeons should consider supplementing hamstring autograft ACLR with a LET in young active patients with morphological characteristics that make them at high risk of reinjury. [ABSTRACT FROM AUTHOR]

The −2/−1 programmed ribosomal frameshifting (−2/−1 PRF) mechanism in porcine reproductive and respiratory syndrome virus (PRRSV) leads to the translation of two additional viral proteins, nonstructural protein 2TF (nsp2TF) and nsp2N. This −2/−1 PRF mechanism is transactivated by a viral protein, nsp1β, and cellular poly(rC) binding proteins (PCBPs). Critical elements for −2/−1 PRF, including a slippery sequence and a downstream C-rich motif, were also identified in 11 simarteriviruses. However, the slippery sequences (XXXUCUCU instead of XXXUUUUU) in seven simarteriviruses can only facilitate −2 PRF to generate nsp2TF. The nsp1β of simian hemorrhagic fever virus (SHFV) was identified as a key factor that transactivates both −2 and −1 PRF, and the universally conserved Tyr111 and Arg114 in nsp1β are essential for this activity. In vitro translation experiments demonstrated the involvement of PCBPs in simarterivirus −2/−1 PRF. Using SHFV reverse genetics, we confirmed critical roles of nsp1β, slippery sequence, and C-rich motif in −2/−1 PRF in SHFV-infected cells. Attenuated virus growth ability was observed in SHFV mutants with impaired expression of nsp2TF and nsp2N. Comparative genomic sequence analysis showed that key elements of −2/−1 PRF are highly conserved in all known arteriviruses except equine arteritis virus (EAV) and wobbly possum disease virus (WPDV). Furthermore, −2/−1 PRF with SHFV PRF signal RNA can be stimulated by heterotypic nsp1βs of all non-EAV arteriviruses tested. Taken together, these data suggest that −2/−1 PRF is an evolutionarily conserved mechanism employed in non-EAV/-WPDV arteriviruses for the expression of additional viral proteins that are important for viral replication. IMPORTANCE Simarteriviruses are a group of arteriviruses infecting nonhuman primates, and a number of new species have been established in recent years. Although these arteriviruses are widely distributed among African nonhuman primates of different species, and some of them cause lethal hemorrhagic fever disease, this group of viruses has been undercharacterized. Since wild nonhuman primates are historically important sources or reservoirs of human pathogens, there is concern that simarteriviruses may be preemergent zoonotic pathogens. Thus, molecular characterization of simarteriviruses is becoming a priority in arterivirology. In this study, we demonstrated that an evolutionarily conserved ribosomal frameshifting mechanism is used by simarteriviruses and other distantly related arteriviruses for the expression of additional viral proteins. This mechanism is unprecedented in eukaryotic systems. Given the crucial role of ribosome function in all living systems, the potential impact of the in-depth characterization of this novel mechanism reaches beyond the field of virology. [ABSTRACT FROM AUTHOR]

The efficiency of start codon selection during ribosomal scanning in eukaryotic translation initiation is influenced by the context or flanking nucleotides surrounding the AUG codon. The levels of eukaryotic translation initiation factors 1 (eIF1) and 5 (eIF5) play critical roles in controlling the stringency of translation start site selection. The basic leucine zipper and W2 domain-containing proteins 1 and 2 (BZW1 and BZW2), also known as eIF5-mimic proteins, are paralogous human proteins containing C-terminal HEAT domains that resemble the HEAT domain of eIF5. We show that translation of mRNAs encoding BZW1 and BZW2 homologs in fungi, plants and metazoans is initiated by AUG codons in conserved unfavorable initiation contexts. This conservation is reminiscent of the conserved unfavorable initiation context that enables autoregulation of EIF1. We show that overexpression of BZW1 and BZW2 proteins enhances the stringency of start site selection, and that their poor initiation codons confer autoregulation on BZW1 and BZW2 mRNA translation. We also show that overexpression of these two proteins significantly diminishes the effect of overexpressing eIF5 on stringency of start codon selection, suggesting they antagonize this function of eIF5. These results reveal a surprising role for BZW1 and BZW2 in maintaining homeostatic stringency of start codon selection, and taking into account recent biochemical, genetic and structural insights into eukaryotic initiation, suggest a model for BZW1 and BZW2 function. [ABSTRACT FROM AUTHOR]

Most viruses in the genus Flavivirus are horizontally transmitted between hematophagous arthropods and vertebrate hosts, but some are maintained in arthropod- or vertebrate-restricted transmission cycles. Flaviviruses maintained by vertebrate-only transmission are commonly referred to as no known vector (NKV) flaviviruses. Fourteen species and two subtypes of NKV flaviviruses are recognized by the International Committee on Taxonomy of Viruses (ICTV), and Tamana bat virus potentially belongs to this group. NKV flaviviruses have been isolated in nature almost exclusively from bats and rodents; exceptions are the two isolates of Dakar bat virus recovered from febrile humans and the recent isolations of Sokoluk virus from field-collected ticks, which raises questions as to whether it should remain classified as an NKV flavivirus. There is evidence to suggest that two other NKV flaviviruses, Entebbe bat virus and Yokose virus, may also infect arthropods in nature. The best characterized bat- and rodent-associated NKV flaviviruses are Rio Bravo and Modoc viruses, respectively, but both have received limited research attention compared to many of their arthropod-infecting counterparts. Herein, we provide a comprehensive review of NKV flaviviruses, placing a particular emphasis on their classification, host range, geographic distribution, replication kinetics, pathogenesis, transmissibility and molecular biology. [ABSTRACT FROM AUTHOR]

Members of the family Coronaviridae have the largest genomes of all RNA viruses, typically in the region of 30 kilobases. Several coronaviruses, such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and Middle East respiratory syndrome-related coronavirus (MERS-CoV), are of medical importance, with high mortality rates and, in the case of SARS-CoV, significant pandemic potential. Other coronaviruses, such as Porcine epidemic diarrhea virus and Avian coronavirus, are important livestock pathogens. Ribosome profiling is a technique which exploits the capacity of the translating ribosome to protect around 30 nucleotides of mRNA from ribonuclease digestion. Ribosome-protected mRNA fragments are purified, subjected to deep sequencing and mapped back to the transcriptome to give a global “snap-shot” of translation. Parallel RNA sequencing allows normalization by transcript abundance. Here we apply ribosome profiling to cells infected with Murine coronavirus, mouse hepatitis virus, strain A59 (MHV-A59), a model coronavirus in the same genus as SARS-CoV and MERS-CoV. The data obtained allowed us to study the kinetics of virus transcription and translation with exquisite precision. We studied the timecourse of positive and negative-sense genomic and subgenomic viral RNA production and the relative translation efficiencies of the different virus ORFs. Virus mRNAs were not found to be translated more efficiently than host mRNAs; rather, virus translation dominates host translation at later time points due to high levels of virus transcripts. Triplet phasing of the profiling data allowed precise determination of translated reading frames and revealed several translated short open reading frames upstream of, or embedded within, known virus protein-coding regions. Ribosome pause sites were identified in the virus replicase polyprotein pp1a ORF and investigated experimentally. Contrary to expectations, ribosomes were not found to pause at the ribosomal frameshift site. To our knowledge this is the first application of ribosome profiling to an RNA virus. [ABSTRACT FROM AUTHOR]

Viruses in the family Luteoviridae have positive-sense RNA genomes of around 5.2 to 6.3 kb, and they are limited to the phloem in infected plants. The Luteovirus and Polerovirus genera include all but one virus in the Luteoviridae. They share a common gene block, which encodes the coat protein (ORF3), a movement protein (ORF4), and a carboxy-terminal extension to the coat protein (ORF5). These three proteins all have been reported to participate in the phloem-specific movement of the virus in plants. All three are translated from one subgenomic RNA, sgRNA1. Here, we report the discovery of a novel short ORF, termed ORF3a, encoded near the 5’ end of sgRNA1. Initially, this ORF was predicted by statistical analysis of sequence variation in large sets of aligned viral sequences. ORF3a is positioned upstream of ORF3 and its translation initiates at a non-AUG codon. Functional analysis of the ORF3a protein, P3a, was conducted with Turnip yellows virus (TuYV), a polerovirus, for which translation of ORF3a begins at an ACG codon. ORF3a was translated from a transcript corresponding to sgRNA1 in vitro, and immunodetection assays confirmed expression of P3a in infected protoplasts and in agroinoculated plants. Mutations that prevent expression of P3a, or which overexpress P3a, did not affect TuYV replication in protoplasts or inoculated Arabidopsis thaliana leaves, but prevented virus systemic infection (long-distance movement) in plants. Expression of P3a from a separate viral or plasmid vector complemented movement of a TuYV mutant lacking ORF3a. Subcellular localization studies with fluorescent protein fusions revealed that P3a is targeted to the Golgi apparatus and plasmodesmata, supporting an essential role for P3a in viral movement. [ABSTRACT FROM AUTHOR]

There has been a dramatic increase in the number of insect-specific flaviviruses (ISFs) discovered in the last decade. Historically, these viruses have generated limited interest due to their inability to infect vertebrate cells. This viewpoint has changed in recent years because some ISFs have been shown to enhance or suppress the replication of medically important flaviviruses in co-infected mosquito cells. Additionally, comparative studies between ISFs and medically important flaviviruses can provide a unique perspective as to why some flaviviruses possess the ability to infect and cause devastating disease in humans while others do not. ISFs have been isolated exclusively from mosquitoes in nature but the detection of ISF-like sequences in sandflies and chironomids indicates that they may also infect other dipterans. ISFs can be divided into two distinct phylogenetic groups. The first group currently consists of approximately 12 viruses and includes cell fusing agent virus, Kamiti River virus and Culex flavivirus. These viruses are phylogenetically distinct from all other known flaviviruses. The second group, which is apparently not monophyletic, currently consists of nine viruses and includes Chaoyang virus, Nounané virus and Lammi virus. These viruses phylogenetically affiliate with mosquito/vertebrate flaviviruses despite their apparent insect-restricted phenotype. This article provides a review of the discovery, host range, mode of transmission, superinfection exclusion ability and genomic organization of ISFs. This article also attempts to clarify the ISF nomenclature because some of these viruses have been assigned more than one name due to their simultaneous discoveries by independent research groups. [ABSTRACT FROM AUTHOR]

Abstract: Flaviviruses have a positive-sense, single-stranded RNA genome of ∼11 kb, encoding a large polyprotein that is cleaved to produce ∼10 mature proteins. Cell fusing agent virus, Kamiti River virus, Culex flavivirus and several recently discovered flaviviruses have no known vertebrate host and apparently infect only insects. We present compelling bioinformatic evidence for a 253–295 codon overlapping gene (designated fifo) conserved throughout these insect-specific flaviviruses and immunofluorescent detection of its product. Fifo overlaps the NS2A/NS2B coding sequence in the −1/+2 reading frame and is most likely expressed as a trans-frame fusion protein via ribosomal frameshifting at a conserved GGAUUUY slippery heptanucleotide with 3′-adjacent RNA secondary structure (which stimulates efficient frameshifting in vitro). The discovery bears striking parallels to the recently discovered ribosomal frameshifting site in the NS2A coding sequence of the Japanese encephalitis serogroup of flaviviruses and suggests that programmed ribosomal frameshifting may be more widespread in flaviviruses than currently realized. [Copyright &y& Elsevier]

Abstract: Programmed ribosomal frameshifting allows the synthesis of alternative, N-terminally coincident, C-terminally distinct proteins from the same RNA. Many viruses utilize frameshifting to optimize the coding potential of compact genomes, to circumvent the host cell''s canonical rule of one functional protein per mRNA, or to express alternative proteins in a fixed ratio. Programmed frameshifting is also used in the decoding of a small number of cellular genes. Recently, specific ribosomal −1 frameshifting was discovered at a conserved U_UUU_UUA motif within the sequence encoding the alphavirus 6K protein. In this case, frameshifting results in the synthesis of an additional protein, termed TF (TransFrame). This new case of frameshifting is unusual in that the −1 frame ORF is very short and completely embedded within the sequence encoding the overlapping polyprotein. The present work shows that there is remarkable diversity in the 3′ sequences that are functionally important for efficient frameshifting at the U_UUU_UUA motif. While many alphavirus species utilize a 3′ RNA structure such as a hairpin or pseudoknot, some species (such as Semliki Forest virus) apparently lack any intra-mRNA stimulatory structure, yet just 20 nt 3′-adjacent to the shift site stimulates up to 10% frameshifting. The analysis, both experimental and bioinformatic, significantly expands the known repertoire of −1 frameshifting stimulators in mammalian and insect systems. [Copyright &y& Elsevier]

Ornithine decarboxylase (ODC) catalyzes the first and rate limiting step in the biosynthesis of polyamines in most eukaryotes. Because polyamines have pleiotropic and often dramatic effects on cellular processes at both high and low concentrations, ODC expression is tightly controlled. ODC is regulated by a family of polyamine-induced proteins, antizymes, which bind to, and inactivate it. In mammals, and apparently most vertebrates, antizymes are in turn antagonized by proteins called antizyme inhibitors. Antizyme inhibitors are homologs of ODC that have lost their decarboxylation activity but have retained their ability to bind antizyme, in most cases even more tightly than ODC. We present a phylogenetic analysis of over 200 eukaryotic homologs of ODC and evaluate their potential to be either true ODCs or catalytically inactive proteins that might be analogs of the previously identified antizyme inhibitors. This analysis yielded several orthologous groups of putative novel antizyme inhibitors each apparently arising independently. In the process we also identify previously unrecognized ODC paralogs in several evolutionary branches, including a previously unrecognized ODC paralog in mammals, and we evaluate their biochemical potential based on their pattern of amino acid conservation. [ABSTRACT FROM AUTHOR]

Background: Overlapping genes are common in RNA viruses where they serve as a mechanism to optimize the coding potential of compact genomes. However, annotation of overlapping genes can be difficult using conventional gene-finding software. Recently we have been using a number of complementary approaches to systematically identify previously undetected overlapping genes in RNA virus genomes. In this article we gather together a number of promising candidate new overlapping genes that may be of interest to the community. Results: Overlapping gene predictions are presented for the astroviruses, seadornaviruses, cytorhabdoviruses and coronaviruses (families Astroviridae, Reoviridae, Rhabdoviridae and Coronaviridae, respectively). [ABSTRACT FROM AUTHOR]

The plant-infecting members of the genus Fijivirus (family Reoviridae) have linear dsRNA genomes divided into 10 segments, two of which contain two substantial and non-overlapping ORFs, while the remaining eight are apparently monocistronic. However, one of these - namely segment 5 - contains a second long ORF (~200+ codons) that overlaps the 3' end of the major ORF (~920-940 codons) in the +1 reading frame. In this report, we use bioinformatic techniques to analyze the pattern of base variations across an alignment of fijivirus segment 5 sequences, and show that this 3' ORF has a strong coding signature. Possible translation mechanisms for this unusually positioned ORF are discussed. [ABSTRACT FROM AUTHOR]

Japanese encephalitis, West Nile, Usutu and Murray Valley encephalitis viruses form a tight subgroup within the larger Flavivirus genus. These viruses utilize a single-polyprotein expression strategy, resulting in ~10 mature proteins. Plotting the conservation at synonymous sites along the polyprotein coding sequence reveals strong conservation peaks at the very 5' end of the coding sequence, and also at the 5' end of the sequence encoding the NS2A protein. Such peaks are generally indicative of functionally important non-coding sequence elements. The second peak corresponds to a predicted stable pseudoknot structure whose biological importance is supported by compensatory mutations that preserve the structure. The pseudoknot is preceded by a conserved slippery heptanucleotide (Y CCU UUU), thus forming a classical stimulatory motif for - 1 ribosomal frameshifting. We hypothesize, therefore, that the functional importance of the pseudoknot is to stimulate a portion of ribosomes to shift -1 nt into a short (45 codon), conserved, overlapping open reading frame, termed foo. Since cleavage at the NS1-NS2A boundary is known to require synthesis of NS2A in cis, the resulting transframe fusion protein is predicted to be NS1- NS2AN-term-FOO. We hypothesize that this may explain the origin of the previously identified NS1 'extension' protein in JEV-group flaviviruses, known as NS1'. [ABSTRACT FROM AUTHOR]

The genus Waikavirus belongs to the order Picornavirales, whose members all use a polyprotein expression strategy. With the exception of Theiler’s virus, overlapping genes are essentially unknown in the order. Recently, we reported experimental verification for a new short overlapping coding sequence (CDS) in the Potyviridae—a family in which overlapping genes were previously unknown. Using the same bioinformatics software (MLOGD), we have identified an ~89-codon conserved open reading frame (ORF) with a strong coding signature in members of the genus Waikavirus. The ORF overlaps the polyprotein ORF but is in the +1 reading frame. Here, we describe the bioinformatic analysis. [ABSTRACT FROM AUTHOR]

Abstract: Reaction conditions facilitating the site-selective direct aryl functionalisation at the C-8 position of adenine nucleosides have been identified. Many different aromatic components may be effectively cross-coupled to provide a diverse array of arylated adenine nucleoside products without the need for ribose or adenine protecting groups. The optimal palladium catalyst loading lies between 0.5 and 5mol%. Addition of excess mercury to the reaction had a negligible affect on catalysis, suggesting the involvement of a homogeneous catalytic species. A study by transmission electron microscopy (TEM) shows that metal containing nanoparticles, ca. 3nm with good uniformity, are formed during the latter stages of the reaction. Stabilised PVP palladium colloids (PVP=N-polyvinylpyrrolidone) are catalytically active in the direct arylation process, releasing homogenous palladium into solution. The effect of various substituted 2-pyridine ligand additives has been investigated. A mechanism for the site-selective arylation of adenosine is proposed. [Copyright &y& Elsevier]

Members of the genus Cypovirus (family Reoviridae) are common pathogens of insects. These viruses have linear dsRNA genomes divided into 10-11 segments, which have generally been assumed to be monocistronic. Here, bioinformatic evidence is presented for a short overlapping coding sequence (CDS) in the cypovirus genome segment encoding the major core capsid protein VP1, overlapping the 5'-terminal region of the VP1 ORF in the +1 reading frame. In Cypovirus type 1 (CPV-1), a 62-codon AUG-initiated open reading frame (hereafter ORFX) is present in all four available segment 1 sequences. The pattern of base variations across the sequence alignment indicates that ORFX is subject to functional constraints at the amino acid level (even when the constraints due to coding in the overlapping VP1 reading frame are taken into account; MLOGD software). In fact the translated ORFX shows greater amino acid conservation than the overlapping region of VP1. The genomic location of ORFX is consistent with translation via leaky scanning. A 62-64 codon AUG-initiated ORF is present in a corresponding location and reading frame in other available cypovirus sequences (2 CPV-14, 1 CPV-15) and an 87-codon ORFX homologue may also be present in Aedes pseudoscutellaris reovirus. The ORFX amino acid sequences are hydrophilic and basic, with between 12 and 16 Arg/Lys residues in each though, at 7.5-10.2 kDa, the putative ORFX product is too small to appear on typical published protein gels. [ABSTRACT FROM AUTHOR]

Background: The genus Orbivirus includes several species that infect livestock -- including Bluetongue virus (BTV) and African horse sickness virus (AHSV). These viruses have linear dsRNA genomes divided into ten segments, all of which have previously been assumed to be monocistronic. Results: Bioinformatic evidence is presented for a short overlapping coding sequence (CDS) in the Orbivirus genome segment 9, overlapping the VP6 cistron in the +1 reading frame. In BTV, a 77-79 codon AUG-initiated open reading frame (hereafter ORFX) is present in all 48 segment 9 sequences analysed. The pattern of base variations across the 48-sequence alignment indicates that ORFX is subject to functional constraints at the amino acid level (even when the constraints due to coding in the overlapping VP6 reading frame are taken into account; MLOGD software). In fact the translated ORFX shows greater amino acid conservation than the overlapping region of VP6. The ORFX AUG codon has a strong Kozak context in all 48 sequences. Each has only one or two upstream AUG codons, always in the VP6 reading frame, and (with a single exception) always with weak or medium Kozak context. Thus, in BTV, ORFX may be translated via leaky scanning. A long (83-169 codon) ORF is present in a corresponding location and reading frame in all other Orbivirus species analysed except Saint Croix River virus (SCRV; the most divergent). Again, the pattern of base variations across sequence alignments indicates multiple coding in the VP6 and ORFX reading frames. Conclusion: At ∼9.5 kDa, the putative ORFX product in BTV is too small to appear on most published protein gels. Nonetheless, a review of past literature reveals a number of possible detections. We hope that presentation of this bioinformatic analysis will stimulate an attempt to experimentally verify the expression and functional role of ORFX, and hence lead to a greater understanding of the molecular biology of these important pathogens. [ABSTRACT FROM AUTHOR]

Background: The genus Alphavirus includes several potentially lethal human viruses. Additionally, species such as Sindbis virus and Semliki Forest virus are important vectors for gene therapy, vaccination and cancer research, and important models for virion assembly and structural analyses. The genome encodes nine known proteins, including the small '6K' protein. 6K appears to be involved in envelope protein processing, membrane permeabilization, virion assembly and virus budding. In protein gels, 6K migrates as a doublet -- a result that, to date, has been attributed to differing degrees of acylation. Nonetheless, despite many years of research, its role is still relatively poorly understood. Results: We report that ribosomal -1 frameshifting, with an estimated efficiency of ∼10-18%, occurs at a conserved UUUUUUA motif within the sequence encoding 6K, resulting in the synthesis of an additional protein, termed TF (TransFrame protein; ∼8 kDa), in which the Cterminal amino acids are encoded by the -1 frame. The presence of TF in the Semliki Forest virion was confirmed by mass spectrometry. The expression patterns of TF and 6K were studied by pulsechase labelling, immunoprecipitation and immunofluorescence, using both wild-type virus and a TF knockout mutant. We show that it is predominantly TF that is incorporated into the virion, not 6K as previously believed. Investigation of the 3' stimulatory signals responsible for efficient frameshifting at the UUUUUUA motif revealed a remarkable diversity of signals between different alphavirus species. Conclusion: Our results provide a surprising new explanation for the 6K doublet, demand a fundamental reinterpretation of existing data on the alphavirus 6K protein, and open the way for future progress in the further characterization of the 6K and TF proteins. The results have implications for alphavirus biology, virion structure, viroporins, ribosomal frameshifting, and bioinformatic identification of novel frameshift-expressed genes, both in viruses and in cellular organisms. [ABSTRACT FROM AUTHOR]

Abstract: A practical Sonogashira alkynylation protocol for the preparation of 8-alkynylated adenosines and guanosines has been developed. Protection of the sugar hydroxyl substituents is not required; protection hinders the purification of these products. A preliminary fluorescent study is reported, which shows that the presence of a substituent on the phenylene ring influences the fluorescent properties considerably, an outcome that could be utilized in biological applications. [Copyright &y& Elsevier]

Abstract: In the last decade, directed evolution has become a routine approach for engineering proteins with novel or altered properties. Concurrently, a trend away from purely ‘blind’ randomization strategies and towards more ‘semi-rational’ approaches has also become apparent. In this review, we discuss ways in which structural information and predictive computational tools are playing an increasingly important role in guiding the design of randomized libraries: web servers such as ConSurf-HSSP and SCHEMA allow the prediction of sites to target for producing functional variants, while algorithms such as GLUE, PEDEL and DRIVeR are useful for estimating library completeness and diversity. In addition, we review recent methodological developments that facilitate the construction of unbiased libraries, which are inherently more diverse than biased libraries and therefore more likely to yield improved variants. [Copyright &y& Elsevier]

ABSTRACT A new approach to estimating photometric redshifts – using artificial neural networks (ANNs) – is investigated. Unlike the standard template-fitting photometric redshift technique, a large spectroscopically-identified training set is required but, where one is available, ANNs produce photometric redshift accuracies at least as good as and often better than the template-fitting method. The Bayesian priors on the underlying redshift distribution are automatically taken into account. Furthermore, inputs other than galaxy colours – such as morphology, angular size and surface brightness – may be easily incorporated, and their utility assessed. Different ANN architectures are tested on a semi-analytic model galaxy catalogue and the results are compared with the template-fitting method. Finally, the method is tested on a sample of ∼20 000 galaxies from the Sloan Digital Sky Survey. The rms redshift error in the range z&lsim; 0.35 is σ[sub z]∼ 0.021 . [ABSTRACT FROM AUTHOR]

Background: The addition of an iliotibial band–based lateral extra-articular tenodesis (LET) to anterior cruciate ligament (ACL) reconstruction (ACLR) has been shown to reduce failure rates. However, there are concerns as to the potential overconstraint of tibiofemoral kinematics that may increase the risk of cartilage degradation. To date, no clinical study has investigated the effect of LET on patellofemoral joint articular cartilage health. Hypothesis: It was hypothesized that at 2 years postoperatively, (1) the addition of LET at the time of ACLR would have no effect on cartilage health on magnetic resonance imaging (MRI), and (2) higher cartilage relaxation values would be associated with worse patient-reported and functional outcomes. Study Design: Cohort study; Level of evidence, 3. Methods: A subset of patients from the STABILITY 1 randomized controlled trial were included. All patients underwent primary ACLR with a hamstring autograft. Patients were randomized to either LET augmentation or not. Cartilage status in the patellofemoral joint between the ACLR group and ACLR+LET group was compared using 2-year postoperative quantitative MRI and the ACL osteoarthritis scores of both the surgical and the contralateral nonsurgical knees. Objective functional outcomes and patient-reported outcome measures (PROMs) were attained. Results: A total of 92 patients (43 patients in the ACLR group; mean age, 18.9 ± 3.2 years; 60.5% female; and 49 patients in the ACLR+LET group; mean age, 18.7 ± 3.2 years, 63.3% female) were included. No significant differences were seen in the mean values (ms) for adjusted T1ρ/T2 relaxation times in the medial patella (47.8/42.2 vs 47.3/43.2), central patella (45.5/42.5 vs 44.1/42.7), lateral patella (48.2/43.5 vs 47.3/43.0), medial trochlea (54.7/50.9 vs 56.4/50.9), central trochlea (53.3/51.1 vs 53.1/52.0), and lateral trochlea (54.9/52.1 vs 53.9/52.6) between the ACLR and ACLR+LET groups. No difference in overall ACL osteoarthritis scores was observed (P =.99). An increase in medial patellar T2 relaxation times was associated with a decreasing International Knee Documentation Committee score (P =.046), Knee injury and Osteoarthritis Outcome Score (KOOS) Symptoms subscale score (P =.01), and total KOOS (P =.01). Conclusion: There was no statistical difference in patellofemoral cartilage health between knees 2 years after primary ACLR with hamstring tendon autograft with or without LET. Statistically significant correlations were found between quantitative MRI relaxation times, functional outcome scores, and PROMs; however, the correlations were weak and the clinical significance is unknown. Registration: NCT02018354 (ClinicalTrials.gov identifier). [ABSTRACT FROM AUTHOR]

Ilarviruses are a relatively understudied but important group of plant RNA viruses that includes a number of crop pathogens. Their genomes comprise three RNA segments encoding two replicase subunits, movement protein, coat protein (CP), and (in some ilarvirus subgroups) a protein that suppresses RNA silencing. Here we report that, in many ilarviruses, RNA3 encodes an additional protein (termed CP-RT) as a result of ribosomal readthrough of the CP stop codon into a short downstream readthrough (RT) ORF. Using asparagus virus 2 as a model, we find that CP-RT is expressed in planta where it functions as a weak suppressor of RNA silencing. CP-RT expression is essential for persistent systemic infection in leaves and shoot apical meristem. CP-RT function is dependent on a putative zinc-finger motif within RT. Replacing the asparagus virus 2 RT with the RT of an ilarvirus from a different subgroup restored the ability to establish persistent infection. These findings open up a new avenue for research on ilarvirus silencing suppression, persistent meristem invasion and vertical transmission. Author summary: Ilarviruses comprise a group of plant-infecting RNA viruses. Until now, ilarvirus genomes were thought to only encode two components of the viral replicase, a movement protein, the capsid protein, and the 2b suppressor of RNA silencing. Interestingly, whereas most plant viruses encode one or more proteins that suppress the host antiviral RNA silencing pathway, the gene encoding 2b is only present in some ilarviruses. Here, we identify an additional ilarvirus protein that is expressed via low efficiency ribosomal readthrough of the capsid protein (CP) stop codon. Readthrough ribosomes translate a short downstream readthrough (RT) domain to produce the capsid-readthrough fusion protein, CP-RT. We show that CP-RT is a second ilarvirus suppressor of silencing protein and is required for the model ilarvirus asparagus virus 2 to maintain persistent infection in the model plant Nicotiana benthamiana. These findings advance our understanding of ilarvirus molecular virology and virus-host interaction. Interestingly, there are substantial differences in the RT peptide between divergent groups of ilarviruses and, in at least two cases, a separate RT peptide appears to have evolved independently. Thus it will be of future interest to investigate the function of CP-RT in different ilarvirus lineages. [ABSTRACT FROM AUTHOR]

Purpose: The purpose of this study was to analyse adverse events encountered in medial opening wedge high tibial osteotomy (MOWHTO) utilizing contemporary surgical techniques with the Tomofix locking plate (DePuy Synthes, Raynham, MA, USA) and categorize them by their severity and need for further medical/surgical management. It was hypothesized that there would be low rates of serious complications after medial opening wedge high tibial osteotomy utilizing an internal locking plate fixator.Methods: This study included 169 consecutive patients (200 knees) who underwent MOWHTO with a Tomofix locking plate at a single center, completing a minimum 2-year follow-up. Types of intra- and post-operative adverse events were retrospectively identified by an independent observer and categorized by their severity and further need of management. Additional surgery due to elective hardware removal was not included in the adverse event classification.Results: There were in total 58 (29%) adverse events, the majority (13.5%) of which required no additional treatment (class 1). Class 1 events included lateral cortex hinge fractures that were observed in 8.5% (17 knees) and delayed wound healing 2% (4/200). Adverse events requiring additional or extended nonoperative management (class 2) were 9%. These included post-operative stiffness in 1% (2/200), low grade infection in 1.5% (3/200), delayed union in 5.4% (11/200), deep vein thrombosis 0.5% (1/200). One hundred and four knees (52%) underwent elective hardware removal. Serious adverse events requiring unplanned additional or revision surgery and/or long-term medical care (class 3) were the least reported (6.5%). Aseptic non-union was reported in 2.5%, deep infection requiring revision in 2% and limited hardware failure 1%.Conclusion: A low rate of serious complications (6.5%) requiring unplanned additional surgery (class 3) was found. The overall rate of complications following MOWHTO with Tomofix locking plate was 29% and the majority (13.5%) required no additional treatment (class 1). Lateral hinge fractures were the most common complication (8.5%) and these were associated with corrections over 12 mm. However, 52% knees required a further operation for elective hardware removal.Level Of Evidence: Level IV, prospective study without control group. [ABSTRACT FROM AUTHOR]

Background: The purpose of anterior cruciate ligament reconstruction (ACLR) is to restore stability to the knee. Persistent rotational laxity following ACLR has been correlated with poor outcome and graft failure. We hypothesize that anterolateral complex reconstruction by way of a Modified Lemaire Lateral Extra-articular Tenodesis (LET) in combination with single bundle ACLR would reduce the risk of persistent rotatory laxity in young individuals who are deemed as being at high risk of failure. We will conduct a pragmatic, multicenter, randomized clinical trial comparing standard single bundle hamstring ACLR with combined ACLR and LET.Methods: Six-hundred patients (300 per group) aged 25 years or less with an ACL deficient knee that meet two of the following three criteria will be included: 1) Grade 2 pivot shift or greater; 2) Returning to high risk cutting or pivoting sports; 3) Generalized ligamentous laxity. Participants will be seen at 3-months, 6-months, 12-months and 24-months post-operatively. The primary outcome measure is graft failure requiring revision ACLR or symptomatic instability associated with a positive asymmetric pivot shift indicating persistent rotational laxity. Patients will complete secondary outcome measures at each follow-up visit including patient-reported outcome measures, functional and biomechanical testing, and magnetic resonance imaging.Discussion: This protocol is the first adequately powered randomized clinical trial investigating the effects of augmenting ACLR with an LET in patients at high-risk of graft failure. The successful completion of this trial has the potential to change surgical practice and provide evidence for the role of the LET in ACLR.Trial Registration: The trial is registered at ClinicalTrials.gov: NCT02018354 , 23-12-2013. [ABSTRACT FROM AUTHOR]

The article presents a computational analysis which examines the molecular sequences of encephalomyocarditis virus (EMCV). It investigates the capacity of ribosomal frameshifting to control gene expression and develop overlapping genes. Findings reveal that the efficiency of frameshifting was observed in the cells infected with EMCV.

We determined the complete genomic sequences of two previously discovered insect-specific flaviviruses, Marisma mosquito virus (MMV) and Nanay virus (NANV), using a combination of high-throughput sequencing, reverse transcription-polymerase chain reaction, 5′ and 3′ rapid amplification of cDNA ends and Sanger sequencing. Complete polyprotein amino acid sequence alignments revealed that the closest known relatives of MMV and NANV are Donggang virus (89% identity, 95% similarity) and Nounané virus (53% identity, 70% similarity), respectively. Phylogenetic inference is in agreement with these findings. Potential programmed −1 ribosomal frameshifting sites were bioinformatically identified in the genomes of both viruses. [ABSTRACT FROM AUTHOR]

Background: Programmed ribosomal frameshifting (PRF) is a gene expression mechanism which enables the translation of two N-terminally coincident, C-terminally distinct protein products from a single mRNA. Many viruses utilize PRF to control or regulate gene expression, but very few phylogenetically conserved examples are known in vertebrate genes. Additional sex combs-like (ASXL) genes 1 and 2 encode important epigenetic and transcriptional regulatory proteins that control the expression of homeotic genes during key developmental stages. Here we describe an ~150-codon overlapping ORF (termed TF) in ASXL1 and ASXL2 that, with few exceptions, is conserved throughout vertebrates. Results: Conservation of the TF ORF, strong suppression of synonymous site variation in the overlap region, and the completely conserved presence of an EH[N/S]Y motif (a known binding site for Host Cell Factor-1, HCF-1, an epigenetic regulatory factor), all indicate that TF is a protein-coding sequence. A highly conserved UCC_UUU_CGU sequence (identical to the known site of +1 ribosomal frameshifting for influenza virus PA-X expression) occurs at the 5' end of the region of enhanced synonymous site conservation in ASXL1. Similarly, a highly conserved RG_GUC_UCU sequence (identical to a known site of -2 ribosomal frameshifting for arterivirus nsp2TF expression) occurs at the 5' end of the region of enhanced synonymous site conservation in ASXL2. Conclusions: Due to a lack of appropriate splice forms, or initiation sites, the most plausible mechanism for translation of the ASXL1 and 2 TF regions is ribosomal frameshifting, resulting in a transframe fusion of the N-terminal half of ASXL1 or 2 to the TF product, termed ASXL-TF. Truncation or frameshift mutants of ASXL are linked to myeloid malignancies and genetic diseases, such as Bohring-Opitz syndrome, likely at least in part as a result of gain-of-function or dominant-negative effects. Our hypothesis now indicates that these disease-associated mutant forms represent overexpressed defective versions of ASXL-TF. Reviewers: This article was reviewed by Laurence Hurst and Eugene Koonin. [ABSTRACT FROM AUTHOR]

Sequence accessions attributable to novel plant amalgaviruses have been found in the Transcriptome Shotgun Assembly database. Sixteen accessions, derived from 12 different plant species, appear to encompass the complete protein-coding regions of the proposed amalgaviruses, which would substantially expand the size of genus Amalgavirus from 4 current species. Other findings include evidence for UUU_CGN as a +1 ribosomal frameshifting motif prevalent among plant amalgaviruses; for a variant version of this motif found thus far in only two amalgaviruses from solanaceous plants; for a region of α-helical coiled coil propensity conserved in a central region of the ORF1 translation product of plant amalgaviruses; and for conserved sequences in a C-terminal region of the ORF2 translation product (RNA-dependent RNA polymerase) of plant amalgaviruses, seemingly beyond the region of conserved polymerase motifs. These results additionally illustrate the value of mining the TSA database and others for novel viral sequences for comparative analyses. [ABSTRACT FROM AUTHOR]

Background: Anterior cruciate ligament (ACL) reconstructions (ACLRs) with graft diameters <8mm have been shown to have higher revision rates. The 5-strand (5S) hamstring autograft configuration is a proposed option to increase graft diameter. Purpose: To investigate the differences in clinical outcomes between 4-strand (4S) and 5S hamstring autografts for ACLR in patients who underwent ACLR alone or concomitantly with a lateral extra-articular tenodesis (LET) procedure. Study Design: Cohort study; Level of evidence, 2. Methods: Data from the STABILITY study were analyzed to compare a subgroup of patients undergoing ACLR alone or with a concomitant LET procedure (ACLR + LET) with a minimum graft diameter of 8mm that had either a 4S or 5S hamstring autograft configuration. The primary outcome was clinical failure, a composite of rotatory laxity and/or graft failure. The secondary outcome measures consisted of 2 patient-reported outcome scores (PROs)—namely, the ACL Quality of Life Questionnaire (ACL-QoL) and the International Knee Documentation Committee (IKDC) score at 24 months postoperatively. Results: Of the 618 patients randomized in the STABILITY study, 399 (228 male; 57%) fit the inclusion criteria for this study. Of these, 191 and 208 patients underwent 4S and 5S configurations of hamstring ACLR, respectively, with a minimum graft diameter of 8mm. Both groups had similar characteristics other than differences in anthropometric factors—namely, sex, height, and weight, and Beighton scores. The primary outcomes revealed no difference between the 2 groups in rotatory stability (odds ratio [OR], 1.19; 95% CI, 0.77-1.84; P =.42) or graft failure (OR, 1.13; 95% CI, 0.51-2.50; P =.76). There was no significant difference between the groups in Lachman (P =.46) and pivot-shift (P =.53) test results at 24 months postoperatively. The secondary outcomes revealed no differences in the ACL-QoL (P =.67) and IKDC (P =.83) scores between the 2 subgroups. Conclusion: At the 24-month follow-up, there were no significant differences in clinical failure rates and PROs in an analysis of patients with 4S and 5S hamstring autografts of ≥8mm diameter for ACLR or ACLR + LET. The 5S hamstring graft configuration is a viable option to produce larger-diameter ACL grafts. [ABSTRACT FROM AUTHOR]

In this study, we characterized an emerging porcine reproductive and respiratory syndrome virus (PRRSV) isolate UIL21-0712, which is a lineage 1C variant with ORF5 restriction fragment length polymorphism (RFLP) cutting pattern of 1-4-4. The UIL21-0712 genome sequence has 85.3% nucleotide identity with the prototypic PRRSV-2 strain VR2332. The nsp2 region is the most variable, and the -2/-1 programmed ribosome frameshifting (PRF) signal therein is distinct from historical PRRSV strains. Analysis of PRRSV sequences in GenBank revealed that the majority of the emerging PRRSV variants contain substitutions that disrupt the -1 PRF stop codon to generate a nsp2N protein with a C-terminal extension. Two of the -1 PRF stop codon variant patterns were identified to be predominantly circulating in the field. They demonstrated higher growth kinetics than the other variants, suggesting that the most dominant -1 PRF stop codon variant patterns may provide enhanced growth fitness for the virus. • An emerging PRRSV RFLP1-4-4 L1C variant was isolated and characterized in cell culture. • The unique -1 PRF signal sequences express the PRRSV nsp2N protein with C-terminal extension. • The most dominant -1 PRF stop codon variants may provide enhanced growth fitness for the virus in the field. [ABSTRACT FROM AUTHOR]

The arterivirus porcine reproductive and respiratory syndrome virus (PRRSV) causes significant economic losses to the swine industry worldwide. Here we apply ribosome profiling (RiboSeq) and parallel RNA sequencing (RNASeq) to characterise the transcriptome and translatome of both species of PRRSV and to analyse the host response to infection. We calculated programmed ribosomal frameshift (PRF) efficiency at both sites on the viral genome. This revealed the nsp2 PRF site as the second known example where temporally regulated frameshifting occurs, with increasing -2 PRF efficiency likely facilitated by accumulation of the PRF-stimulatory viral protein, nsp1β. Surprisingly, we find that PRF efficiency at the canonical ORF1ab frameshift site also increases over time, in contradiction of the common assumption that RNA structure-directed frameshift sites operate at a fixed efficiency. This has potential implications for the numerous other viruses with canonical PRF sites. Furthermore, we discovered several highly translated additional viral ORFs, the translation of which may be facilitated by multiple novel viral transcripts. For example, we found a highly expressed 125-codon ORF overlapping nsp12, which is likely translated from novel subgenomic RNA transcripts that overlap the 3' end of ORF1b. Similar transcripts were discovered for both PRRSV-1 and PRRSV-2, suggesting a potential conserved mechanism for temporally regulating expression of the 3'-proximal region of ORF1b. We also identified a highly translated, short upstream ORF in the 5' UTR, the presence of which is highly conserved amongst PRRSV-2 isolates. These findings reveal hidden complexity in the gene expression programmes of these important nidoviruses. [ABSTRACT FROM AUTHOR]

Introduction: Anterior dislocations, the most common type of shoulder dislocation, are often complicated by subsequent instability. With recurrent dislocations there often is attrition of the labrum and progressive loss of the anterior bony contour of the glenoid. Treatment options for this pathology involve either soft tissue repair or bony augmentation procedure. The optimal management remains unknown and current clinical practice is highly varied. Methods and analysis: The Shoulder instability Trial comparing Arthroscopic stabilization Benefits compared with Latarjet procedure Evaluation (STABLE) is an ongoing multi-centre, pilot randomized controlled trial of 82 patients who have been diagnosed with recurrent anterior shoulder instability and subcritical glenoid bone loss. Patients are randomized to either soft tissue repair (Bankart + Remplissage) or bony augmentation (Latarjet procedure). The primary outcome for this pilot is to assess trial feasibility and secondary outcomes include recurrent instability as well as functional outcomes up to two years post-operatively. Conclusions: This trial will help to identify the optimal treatment for patients with recurrent shoulder instability with a focus on determining which treatment option results in reduced risk of recurrent dislocation and improved patient outcomes. Findings from this trial will guide clinical practice and improve care for patients with shoulder instability. Trial registration: This study has been registered on http://www.ClinicalTrials.gov with the following identifier: ClinicalTrials.gov Identifier: NCT03585491, registered 13 July 2018, https://www.clinicaltrials.gov/ct2/show/NCT03585491?term=NCT03585491&draw=2&rank=1. Ethics and dissemination: This study has ethics approval from the McMaster University/Hamilton Health Sciences Research Ethics Board (REB) (approval #4942). Successful completion will significantly impact the global management of patients with recurrent instability. This trial will develop a network of collaboration for future high-quality trials in shoulder instability. [ABSTRACT FROM AUTHOR]

Translation start site selection in eukaryotes is influenced by context nucleotides flanking the AUG codon and by levels of the eukaryotic translation initiation factors eIF1 and eIF5. In a search of mammalian genes, we identified five homeobox (Hox) gene paralogs initiated by AUG codons in conserved suboptimal context as well as 13 Hox genes that contain evolutionarily conserved upstream open reading frames (uORFs) that initiate at AUG codons in poor sequence context. An analysis of published cap analysis of gene expression sequencing (CAGE-seq) data and generated CAGE-seq data for messenger RNAs (mRNAs) from mouse somites revealed that the 50 leaders of Hox mRNAs of interest contain conserved uORFs, are generally much shorter than reported, and lack previously proposed internal ribosome entry site elements. We show that the conserved uORFs inhibit Hox reporter expression and that altering the stringency of start codon selection by overexpressing eIF1 or eIF5 modulates the expression of Hox reporters. We also show that modifying ribosome homeostasis by depleting a large ribosomal subunit protein or treating cells with sublethal concentrations of puromycin leads to lower stringency of start codon selection. Thus, altering global translation can confer genespecific effects through altered start codon selection stringency [ABSTRACT FROM AUTHOR]

Solenopsis invicta colonies were exposed to purified preparations of Solenopsis invicta virus 3 (SINV-3) to investigate virus pathogenesis at the colony level. Time course experiments revealed an infection exhibiting specificity for the adult stage (workers). SINV-3 genome and a capsid protein were increasingly present in worker ants with time. Northern blot analysis revealed two bands in RNA preparations from worker ants infected with SINV-3 corresponding to the genomic and sub-genomic species. Conversely, larval RNA preparations from SINV-3-infected colonies showed a near-complete absence of SINV-3 genome or sub-genome. The data confirm that SINV-3 is the etiological agent causing mortality among S. invicta colonies in the laboratory. We propose that SINV-3 infection somehow alters worker ant behavior, which may prevent them from acquiring and/or distributing solid food to the larvae. Consequently, larval mortality and impaired queen health occur as a result of starvation or neglect by the worker caste. [ABSTRACT FROM AUTHOR]

Solenopsis invicta virus 3 (SINV-3) is a positive-sense single-stranded RNA virus that infects the red imported fire ant, Solenopsis invicta. We show that the second open reading frame (ORF) of the dicistronic genome is expressed via a frameshifting mechanism and that the sequences encoding the structural proteins map to both ORF2 and the 3' end of ORF1, downstream of the sequence that encodes the RNA-dependent RNA polymerase. The genome organization and structural protein expression strategy resemble those of Acyrthosiphon pisum virus (APV), an aphid virus. The capsid protein that is encoded by the 3' end of ORF1 in SINV-3 and APV is predicted to have a jelly-roll fold similar to the capsid proteins of picornaviruses and caliciviruses. The capsid-extension protein that is produced by frameshifting, includes the jelly-roll fold domain encoded by ORF1 as its N-terminus, while the C-terminus encoded by the 5' half of ORF2 has no clear homology with other viral structural proteins. A third protein, encoded by the 3' half of ORF2, is associated with purified virions at sub-stoichiometric ratios. Although the structural proteins can be translated from the genomic RNA, we show that SINV-3 also produces a subgenomic RNA encoding the structural proteins. Circumstantial evidence suggests that APV may also produce such a subgenomic RNA. Both SINV-3 and APV are unclassified picorna-like viruses distantly related to members of the order Picornavirales and the family Caliciviridae. Within this grouping, features of the genome organization and capsid domain structure of SINV-3 and APV appear more similar to caliciviruses, perhaps suggesting the basis for a "Calicivirales" order. [ABSTRACT FROM AUTHOR]

The recently developed ribosome profiling technique (Ribo-Seq) allows mapping of the locations of translating ribosomes on mRNAs with subcodon precision. When ribosome protected fragments (RPFs) are aligned to mRNA, a characteristic triplet periodicity pattern is revealed. We utilized the triplet periodicity of RPFs to develop a computational method for detecting transitions between reading frames that occur during programmed ribosomal frameshifting or in dual coding regions where the same nucleotide sequence codes for multiple proteins in different reading frames. Application of this method to ribosome profiling data obtained for human cells allowed us to detect several human genes where the same genomic segment is translated in more than one reading frame (from different transcripts as well as from the same mRNA) and revealed the translation of hitherto unpredicted coding open reading frames. [ABSTRACT FROM AUTHOR]

The genus Orbivirus includes both insect and tick-borne viruses. The orbivirus genome, composed of 10 segments of dsRNA, encodes 7 structural proteins (VP1-VP7) and 3 non-structural proteins (NS1-NS3). An open reading frame (ORF) that spans almost the entire length of genome segment-9 (Seg-9) encodes VP6 (the viral helicase). However, bioinformatic analysis recently identified an overlapping ORF (ORFX) in Seg-9. We show that ORFX encodes a new non-structural protein, identified here as NS4. Western blotting and confocal fluorescence microscopy, using antibodies raised against recombinant NS4 from Bluetongue virus (BTV, which is insect-borne), or Great Island virus (GIV, which is tick-borne), demonstrate that these proteins are synthesised in BTV or GIV infected mammalian cells, respectively. BTV NS4 is also expressed in Culicoides insect cells. NS4 forms aggregates throughout the cytoplasm as well as in the nucleus, consistent with identification of nuclear localisation signals within the NS4 sequence. Bioinformatic analyses indicate that NS4 contains coiled-coils, is related to proteins that bind nucleic acids, or are associated with membranes and shows similarities to nucleolar protein UTP20 (a processome subunit). Recombinant NS4 of GIV protects dsRNA from degradation by endoribonucleases of the RNAse III family, indicating that it interacts with dsRNA. However, BTV NS4, which is only half the putative size of the GIV NS4, did not protect dsRNA from RNAse III cleavage. NS4 of both GIV and BTV protect DNA from degradation by DNAse. NS4 was found to associate with lipid droplets in cells infected with BTV or GIV or transfected with a plasmid expressing NS4. [ABSTRACT FROM AUTHOR]

Background: The many Hepadnaviridae sequences available have widely varied functional annotation. The genomes are very compact (∼3.2 kb) but contain multiple layers of functional regulatory elements in addition to coding regions. Key regions are subject to purifying selection, as mutations in these regions will produce non-functional viruses. Results: These genomic sequences have been organized into a structured database to facilitate research at the molecular level. HBVRegDB is a comparative genomic analysis tool with an integrated underlying sequence database. The database contains genomic sequence data from representative viruses. In addition to INSDC and RefSeq annotation, HBVRegDB also contains expert and systematically calculated annotations (e.g. promoters) and comparative genome analysis results (e.g. blastn, tblastx). It also contains analyses based on curated HBV alignments. Information about conserved regions -- including primary conservation (e.g. CDS-Plotcon) and RNA secondary structure predictions (e.g. Alidot) -- is integrated into the database. A large amount of data is graphically presented using the GBrowse (Generic Genome Browser) adapted for analysis of viral genomes. Flexible query access is provided based on any annotated genomic feature. Novel regulatory motifs can be found by analysing the annotated sequences. Conclusion: HBVRegDB serves as a knowledge database and as a comparative genomic analysis tool for molecular biologists investigating HBV. It is publicly available and complementary to other viral and HBV focused datasets and tools http://hbvregdb.otago.ac.nz. The availability of multiple and highly annotated sequences of viral genomes in one database combined with comparative analysis tools facilitates detection of novel genomic elements. [ABSTRACT FROM AUTHOR]

Background: The majority of introns in gene transcripts are found within the coding sequences (CDSs). A small but significant fraction of introns are also found to reside within the untranslated regions (5'UTRs and 3'UTRs) of expressed sequences. Alignment of the whole genome and expressed sequence tags (ESTs) of the model plant Arabidopsis thaliana has identified introns residing in both coding and non-coding regions of the genome. Results: A bioinformatic analysis revealed some interesting observations: (1) the density of introns in 5'UTRs is similar to that in CDSs but much higher than that in 3'UTRs; (2) the 5'UTR introns are preferentially located close to the initiating ATG codon; (3) introns in the 5'UTRs are, on average, longer than introns in the CDSs and 3'UTRs; and (4) 5'UTR introns have a different nucleotide composition to that of CDS and 3'UTR introns. Furthermore, we show that the 5'UTR intron of the A. thaliana EF1α -A3 gene affects the gene expression and the size of the 5'UTR intron influences the level of gene expression. Conclusion: Introns within the 5'UTR show specific features that distinguish them from introns that reside within the coding sequence and the 3'UTR. In the EF1α -A3 gene, the presence of a long intron in the 5'UTR is sufficient to enhance gene expression in plants in a size dependent manner. [ABSTRACT FROM AUTHOR]

The herpes simplex virus (HSV)-1 protein pUL21 is essential for efficient virus replication and dissemination. While pUL21 has been shown to promote multiple steps of virus assembly and spread, the molecular basis of its function remained unclear. Here we identify that pUL21 is a virus-encoded adaptor of protein phosphatase 1 (PP1). pUL21 directs the dephosphorylation of cellular and virus proteins, including components of the viral nuclear egress complex, and we define a conserved non-canonical linear motif in pUL21 that is essential for PP1 recruitment. In vitro evolution experiments reveal that pUL21 antagonises the activity of the virus-encoded kinase pUS3, with growth and spread of pUL21 PP1-binding mutant viruses being restored in adapted strains where pUS3 activity is disrupted. This study shows that virus-directed phosphatase activity is essential for efficient herpesvirus assembly and spread, highlighting the fine balance between kinase and phosphatase activity required for optimal virus replication. Author summary: Herpes simplex virus (HSV)-1 is a highly prevalent human virus that causes life-long infections. While the most common symptom of HSV-1 infection is orofacial lesions ('cold sores'), HSV-1 infection can also cause fatal encephalitis and it is a leading cause of infectious blindness. The HSV-1 genome encodes many proteins that dramatically remodel the environment of infected cells to promote virus replication and spread, including enzymes that add phosphate groups (kinases) to cellular and viral proteins in order to fine-tune their function. Here we identify that pUL21 is an HSV-1 protein that binds directly to protein phosphatase 1 (PP1), a highly abundant cellular enzyme that removes phosphate groups from proteins. We demonstrate that pUL21 stimulates the specific dephosphorylation of both cellular and viral proteins, including a component of the viral nuclear egress complex that is essential for efficient assembly of new HSV-1 particles. Furthermore, our in vitro evolution experiments demonstrate that pUL21 antagonises the activity of the HSV-1 kinase pUS3. Our work highlights the precise control that herpesviruses exert upon the protein environment within infected cells, and specifically the careful balance of kinase and phosphatase activity that HSV-1 requires for optimal replication and spread. [ABSTRACT FROM AUTHOR]

RNA structural elements occur in numerous single-stranded positive-sense RNA viruses. The stem-loop 2 motif (s2m) is one such element with an unusually high degree of sequence conservation, being found in the 39 untranslated region (UTR) in the genomes of many astroviruses, some picornaviruses and noroviruses, and a variety of coronaviruses, including severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2. The evolutionary conservation and its occurrence in all viral subgenomic transcripts imply a key role for s2m in the viral infection cycle. Our findings indicate that the element, while stably folded, can nonetheless be invaded and remodeled spontaneously by antisense oligonucleotides (ASOs) that initiate pairing in exposed loops and trigger efficient sequence-specific RNA cleavage in reporter assays. ASOs also act to inhibit replication in an astrovirus replicon model system in a sequence-specific, dose-dependent manner and inhibit SARS-CoV-2 replication in cell culture. Our results thus permit us to suggest that the s2m element is readily targeted by ASOs, which show promise as antiviral agents. IMPORTANCE The highly conserved stem-loop 2 motif (s2m) is found in the genomes of many RNA viruses, including SARS-CoV-2. Our findings indicate that the s2m element can be targeted by antisense oligonucleotides. The antiviral potential of this element represents a promising start for further research into targeting conserved elements in RNA viruses. [ABSTRACT FROM AUTHOR]

Coronavirus infection induces the unfolded protein response (UPR), a cellular signalling pathway composed of three branches, triggered by unfolded proteins in the endoplasmic reticulum (ER) due to high ER load. We have used RNA sequencing and ribosome profiling to investigate holistically the transcriptional and translational response to cellular infection by murine hepatitis virus (MHV), often used as a model for the Betacoronavirus genus to which the recently emerged SARS-CoV-2 also belongs. We found the UPR to be amongst the most significantly up-regulated pathways in response to MHV infection. To confirm and extend these observations, we show experimentally the induction of all three branches of the UPR in both MHV- and SARS-CoV-2-infected cells. Over-expression of the SARS-CoV-2 ORF8 or S proteins alone is itself sufficient to induce the UPR. Remarkably, pharmacological inhibition of the UPR greatly reduced the replication of both MHV and SARS-CoV-2, revealing the importance of this pathway for successful coronavirus replication. This was particularly striking when both IRE1α and ATF6 branches of the UPR were inhibited, reducing SARS-CoV-2 virion release (~1,000-fold). Together, these data highlight the UPR as a promising antiviral target to combat coronavirus infection. Author summary: SARS-CoV-2 is the novel coronavirus responsible for the COVID-19 pandemic which has resulted in over 150 million cases since the end of 2019. Most people infected with the virus will experience mild to moderate respiratory illness and recover without any special treatment. However, older people, and those with underlying medical problems like chronic respiratory disease are more likely to develop a serious illness. So far, more than 3 million people have died of COVID-19. Unfortunately, there is no specific medication for this viral disease. In order to produce viral proteins and to replicate their genetic information, all coronaviruses use a cellular structure known as the endoplasmic reticulum or ER. However, the massive production and modification of viral proteins stresses the ER and this activates a compensatory cellular response that tries to reduce ER protein levels. This is termed the unfolded protein response or UPR. We believe that coronaviruses take advantage of the activation of the UPR to enhance their replication. The UPR is also activated in some types of cancer and neurodegenerative disorders and UPR inhibitor drugs have been developed to tackle these diseases. Here, we show also that these compounds can significantly reduce SARS-CoV-2 replication in human lung cells. [ABSTRACT FROM AUTHOR]

At least six small alternative-frame open reading frames (ORFs) overlapping well-characterized SARS-CoV-2 genes have been hypothesized to encode accessory proteins. Researchers have used different names for the same ORF or the same name for different ORFs, resulting in erroneous homological and functional inferences. We propose standard names for these ORFs and their shorter isoforms, developed in consultation with the Coronaviridae Study Group of the International Committee on Taxonomy of Viruses. We recommend calling the 39 codon Spike-overlapping ORF ORF2b; the 41, 57, and 22 codon ORF3a-overlapping ORFs ORF3c, ORF3d, and ORF3b; the 33 codon ORF3d isoform ORF3d-2; and the 97 and 73 codon Nucleocapsid-overlapping ORFs ORF9b and ORF9c. Finally, we document conflicting usage of the name ORF3b in 32 studies, and consequent erroneous inferences, stressing the importance of reserving identical names for homologs. We recommend that authors referring to these ORFs provide lengths and coordinates to minimize ambiguity caused by prior usage of alternative names. [Display omitted] • Small SARS-CoV-2 ORFs in alternative reading frames may encode accessory proteins. • Conflicting names of these ORFs are widely used in the rapidly-growing literature. • The names ORF3b and ORF9b have been used inconsistently and ambiguously in the literature. • These name conflicts have caused erroneous functional and evolutionary inferences. • We use species-based homology to recommend the names ORF2b, ORF3c, ORF3d, ORF3b, ORF9b, ORF9c. [ABSTRACT FROM AUTHOR]

Arteriviruses are enveloped positive-strand RNA viruses that assemble and egress using the host cell's exocytic pathway. In previous studies, we demonstrated that most arteriviruses use a unique -2 ribosomal frameshifting mechanism to produce a C-terminally modified variant of their nonstructural protein 2 (nsp2). Like full-length nsp2, the N-terminal domain of this frameshift product, nsp2TF, contains a papain-like protease (PLP2) that has deubiquitinating (DUB) activity, in addition to its role in proteolytic processing of replicase polyproteins. In cells infected with porcine reproductive and respiratory syndrome virus (PRRSV), nsp2TF localizes to compartments of the exocytic pathway, specifically endoplasmic reticulum-Golgi intermediate compartment (ERGIC) and Golgi complex. Here, we show that nsp2TF interacts with the two major viral envelope proteins, the GP5 glycoprotein and membrane (M) protein, which drive the key process of arterivirus assembly and budding. The PRRSV GP5 and M proteins were found to be poly-ubiquitinated, both in an expression system and in cells infected with an nsp2TF-deficient mutant virus. In contrast, ubiquitinated GP5 and M proteins did not accumulate in cells infected with the wild-type, nsp2TF-expressing virus. Further analysis implicated the DUB activity of the nsp2TF PLP2 domain in deconjugation of ubiquitin from GP5/M proteins, thus antagonizing proteasomal degradation of these key viral structural proteins. Our findings suggest that nsp2TF is targeted to the exocytic pathway to reduce proteasome-driven turnover of GP5/M proteins, thus promoting the formation of GP5-M dimers that are critical for arterivirus assembly. Author summary: Arteriviruses are a rapidly expanding family of positive-stranded RNA viruses, which includes economically important veterinary pathogens like equine arteritis virus (EAV) and two species of porcine reproductive and respiratory syndrome virus (PRRSV-1 and PRRSV-2). In our previous studies, we uncovered an unprecedented arterivirus gene expression mechanism: a highly efficient -2 programmed ribosomal frameshift (PRF) that is controlled by an interaction of viral protein nsp1ß with specific RNA sequences and host poly(C) binding proteins. It is used by PRRSVs, and most other arteriviruses, to efficiently produce a previously unknown nonstructural protein variant, nsp2TF. In this study, we demonstrate that PRRSV nsp2TF interacts with the two major arteriviral envelope proteins, GP5 and M, whose heterodimerization in the secretory pathway is a key step in envelope protein trafficking and virus assembly. Our findings suggest that nsp2TF promotes arterivirus assembly by antagonizing the ubiquitination-dependent proteasomal degradation of GP5 and M proteins. This mechanism is based on the DUB activity of the PLP2 protease domain located within the N-terminal region of nsp2TF. To our knowledge, this is the first study to demonstrate that viruses can express a DUB that functions specifically to counteract the ubiquitination and degradation of key viral structural proteins. [ABSTRACT FROM AUTHOR]