Machine learning for design of degenerate Cas13a crRNAs using lassa virus as a model of highly variable RNA target.

The design of minimum CRISPR RNA (crRNA) sets for detection of diverse RNA targets using sequence degeneracy has not been systematically addressed. We tested candidate degenerate Cas13a crRNA sets designed for detection of diverse RNA targets (Lassa virus). A decision tree machine learning (ML) algorithm (RuleFit) was applied to define the top attributes that determine the specificity of degenerate crRNAs to elicit collateral nuclease activity. Although the total number of mismatches (0-4) is important, the specificity depends as well on the spacing of mismatches, and their proximity to the 5' end of the spacer. We developed a predictive algorithm for design of candidate degenerate crRNA sets, allowing improved discrimination between "included" and "excluded" groups of related target sequences. A single degenerate crRNA set adhering to these rules detected representatives of all Lassa lineages. Our general ML approach may be applied to the design of degenerate crRNA sets for any CRISPR/Cas system.

Large scale screening of CRISPR guide RNAs using an optimized high throughput robotics system.

All CRISPR/CAS systems utilize CRISPR guide RNAs (crRNAs), the design of which depend on the type of CAS protein, genetic target and the environment/matrix. While machine learning approaches have recently been developed to optimize some crRNA designs, candidate crRNAs must still be screened for efficacy under relevant conditions. Here, we demonstrate a high-throughput method to screen hundreds of candidate crRNAs for activation of Cas13a collateral RNA cleavage. Entire regions of a model gene transcript (Y. pestis lcrV gene) were tiled to produce overlapping crRNA sets. We tested for possible effects that included crRNA/target sequence, size and secondary structures, and the commercial source of DNA oligomers used to generate crRNAs. Detection of a 981 nt target RNA was initially successful with 271 out of 296 tested guide RNAs, and that was improved to 287 out of 296 (97%) after protocol optimizations. For this specific example, we determined that crRNA efficacy did not strongly depend on the target region or crRNA physical properties, but was dependent on the source of DNA oligomers used for RNA preparation. Our high-throughput methods for screening crRNAs has general applicability to the optimization of Cas12 and Cas13 guide RNA designs.

Amlodipine accelerates bone healing in a stable closed femoral fracture model in mice.

Calcium channel blockers (CCBs), which are widely used in the treatment of hypertension, have been shown to influence bone metabolism. However, there is little information on whether CCBs also influence the process of fracture healing. Therefore, the effect of the CCB amlodipine on bone healing was studied in a stable closed fracture model in mice using intramedullary screw fixation. Bone healing was investigated by radiology, biomechanics, histomorphometry and Western blot analysis 2 and 5 weeks after fracture healing. Animals were treated daily (post operatively) per os using a gavage with amlodipine low dose (1 mg/ kg body weight, n = 20), amlodipine high dose (3 mg/kg body weight, n = 20) or vehicle (NaCl) (control, n = 20) serving as a negative control. At 2 and 5 weeks, histomorphometric analysis revealed a significantly larger amount of bone tissue within the callus of amlodipine low-dose- and high-dose-treated animals when compared to controls. This was associated with a smaller amount of cartilaginous and fibrous tissue, indicating an acceleration of fracture healing. Biomechanics showed a slightly, but not significantly, higher bending stiffness in amlodipine low-dose- and high-dose-treated animals. Western blot analysis revealed a significantly increased expression of bone morphogenetic protein (BMP)-2 and vascular endothelial growth factor (VEGF). Moreover, the analysis showed a 5-fold higher expression of osteoprotegerin (OPG) and a 10-fold elevated expression of the receptor activator of NF-κB ligand (RANKL), indicating an increased bone turnover. These findings demonstrated that amlodipine accelerated fracture healing by stimulating bone formation, callus remodelling and osteoclast activity.

[Endovenous ablation versus open surgery for varicose veins : An attempt at an evaluation]. / Endochirurgie versus offene Chirurgie der Varikose : Versuch einer Wertung.

Open and endovenous surgery of varicose veins provides an excellent way to treat varicose veins. However, there are great differences in the how the techniques are performed. No matter which procedure is carried out, there are standards that should be observed. The state of the art of open venous surgery with radical crossectomy is well-known, but unfortunately is still not always performed correctly nowadays. The state of the art of endovenous surgery has unfortunately not yet been sufficiently documented, but should be based on open-surgical techniques. How the standard of both methods today is (or should be) is described in detail in this work. A recurrence definition which applies to both techniques, is set up.

Obesity does not affect the healing of femur fractures in mice.

Obesity is reported to be both protective and deleterious to bone. Lipotoxicity and inflammation might be responsible for bone loss through inhibition of osteoblasts and activation of osteoclasts. However, little is known whether obesity affects the process of fracture healing. Therefore, we studied the effect of high fat diet-induced (HFD) obesity on callus formation and bone remodelling in a closed femur fracture model in mice. Thirty-one mice were fed a diet containing 60kJ% fat (HFD) for a total of 20 weeks before fracture and during the entire postoperative observation period. Control mice (n=31) received a standard diet containing 10kJ% fat. Healing was analyzed using micro-CT, biomechanical, histomorphometrical, immunohistochemical, serum and protein biochemical analysis at 2 and 4 weeks after fracture. HFD-fed mice showed a higher body weight and increased serum concentrations of leptin and interleukin-6 compared to controls. Within the callus tissue Western blot analyses revealed a higher expression of transcription factor peroxisome proliferator-activated receptor y (PPARy) and a reduced expression of runt-related transcription factor 2 (RUNX2) and bone morphogenetic protein (BMP)-4. However, obesity did not affect the expression of BMP-2 and did not influence the receptor activator of nuclear factor κB (RANK)/RANK ligand/osteoprotegerin (OPG) pathway during fracture healing. Although the bones of HFD-fed animals showed an increased number of adipocytes within the bone marrow, HFD did not increase callus adiposity. In addition, radiological and histomorphometric analysis could also not detect significant differences in bone formation between HFD-fed animals and controls. Accordingly, HFD did not affect bending stiffness after 2 and 4 weeks of healing. These findings indicate that obesity does not affect femur fracture healing in mice.

Draft Genome Sequence of Xylella fastidiosa subsp. fastidiosa Strain Stag's Leap.

ITALIC! Xylella fastidiosasubsp. ITALIC! fastidiosacauses Pierce's disease of grapevine. Presented here is the draft genome sequence of the Stag's Leap strain, previously used in pathogenicity/virulence assays to evaluate grapevine germplasm bearing Pierce's disease resistance and a phenotypic assessment of knockout mutants to determine gene function.

Effect of Stabilization on the Healing Process of Femur Fractures in Aged Mice.

BACKGROUND: The influence of mechanical stability on fracture healing has previously been studied in adult mice, but is poorly understood in aged animals. Therefore, we herein studied the effect of stabilization on the healing process of femur fractures in aged mice. METHODS: Twenty-four 18-month-old CD-1 mice were stabilized after midshaft fracture of the femur with an intramedullary screw. In another 24 18-month-old mice, the femur fractures were left unstabilized. Bone healing was studied by radiological, biomechanical, histomorphometric, and protein expression analyses. RESULTS: After 2 and 5 weeks of healing, the callus of nonstabilized fractures compared to stabilized fractures was significantly larger, containing a significantly smaller amount of osseous tissue and a higher amount of cartilaginous tissue. This was associated with a significantly lower biomechanical stiffness during the early phase of healing. However, during the late phase of fracture healing both nonstabilized and stabilized fractures showed a biomechanical stiffness of ∼40%. Of interest, Western blot analyses of callus tissue demonstrated that the expression of proteins related to angiogenesis, bone formation and remodeling, i.e. VEGF, CYR61, BMP-2, BMP-4, Col-2, Col-10, RANKL, OPG, did not differ between nonstabilized and stabilized fractures. CONCLUSION: Nonstabilized fractures in aged mice show delayed healing and remodeling. This is not caused by an altered protein expression in the callus but rather by the excessive interfragmentary movements.

Characterization of the healing process in non-stabilized and stabilized femur fractures in mice.

BACKGROUND: Although a variety of suitable fracture models for mice exist, in many studies bone healing was still analyzed without fracture stabilization. Because there is little information whether the healing of non-stabilized fractures differs from that of stabilized fractures, we herein studied the healing process of non-stabilized compared to stabilized femur fractures. MATERIALS AND METHODS: Twenty-one CD-1 mice were stabilized after midshaft fracture of the femur with an intramedullary screw allowing micromovements and endochondral healing. In another 22 mice the femur fractures were left unstabilized. Bone healing was studied by radiological, biomechanical, histomorphometric and protein expression analyses. RESULTS: Non-stabilized femur fractures revealed a significantly lower biomechanical stiffness compared to stabilized fractures. During the early phase of fracture healing non-stabilized fractures demonstrated a significantly lower amount of osseous tissue and a higher amount of cartilage tissue. During the late phase of fracture healing both non-stabilized and stabilized fractures showed almost 100 % osseous callus tissue. However, in stabilized fractures remodeling was almost completed with lamellar bone while non-stabilized fractures still showed large callus with great amounts of woven bone, indicating a delay in bone remodeling. Of interest, western blot analyses of callus tissue demonstrated in non-stabilized fractures a significantly reduced expression of vascular endothelial growth factor and a slightly lowered expression of bone morphogenetic protein-2 and collagen-10. CONCLUSION: Non-stabilized femur fractures in mice show a marked delay in bone healing compared to stabilized fractures. Therefore, non-stabilized fracture models may not be used to analyze the mechanisms of normal bone healing.

Endovenous laser ablation with and without high ligation compared to high ligation and stripping for treatment of great saphenous varicose veins: Results of a multicentre randomised controlled trial with up to 6 years follow-up.

OBJECTIVES: High ligation and stripping was compared to endovenous laser ablation for the therapy of great saphenous vein varicosity. Long-term efficacy was assessed in terms of avoidance of inguinal reflux and mechanisms of recurrence were investigated. DESIGN: Multicentre, randomised, three-arm, parallel trial. MATERIALS AND METHODS: A total of 449 patients were randomised into three different treatment groups: high ligation and stripping group (n = 159), endovenous laser ablation group (n = 142; 980 nm, 30 W continuous mode, bare fibre) or a combination of laser ablation with high ligation (endovenous laser ablation group/ high ligation group, n = 148). Patients were examined clinically and by duplex ultrasound once a year.The primary end point of this study is inguinal reflux at the saphenofemoral junction after 2 years. This paper presents secondary data on sonographically determined inguinal reflux and clinical recurrences in the treated area after up to 6 years of follow-up. RESULTS: Median time to follow-up was 4.0 years; the mean time follow-up 3.6 years. Follow-up rates were: 2 years 74%, 3 years 47%, 4 years 39%, 5 years 36% and 6 years 31%. Most reflux into the great saphenous vein appeared in the endovenous laser ablation group (after 6 years: high ligation/stripping versus endovenous laser ablation p = 0.0102; high ligation/endovenous laser ablation vs. endovenous laser ablation p < 0.0002). Furthermore, more refluxive side branches were also observed in the endovenous laser ablation group (after 6 years high ligation/stripping vs. endovenous laser ablation p = 0.0569; high ligation/endovenous laser ablation vs. endovenous laser ablation p = 0.0111). In terms of clinical recurrence during the 6 years post therapy, no significant differences between the three treatment groups were observed (p values from log-rank test: high ligation/stripping vs. endovenous laser ablation p = 0.5479; high ligation/stripping vs. high ligation/endovenous laser ablation p = 0.2324; high ligation/endovenous laser ablation vs. endovenous laser ablation p = 0.0848).The postoperative decline and later development in Class C (clinical etiological anatomical pathological) went parallel in all groups. CONCLUSIONS: Clinical recurrence appears with the same frequency in all three treatment groups, but the responsible pathological mechanisms seem to differ. Most reflux into the great saphenous vein and side branches appears after endovenous laser ablation, whereas more saphenofemoral junction-independent recurrences are seen after high ligation/stripping.

[Two-year results of a prospective randomised controlled multicenter trial to compare open operative therapy vs. endoluminal venous laser therapy with and without high ligation for the therapy of varicose greater saphenous veins]. / Zweijahresergebnisse einer prospektiv-randomisierten kontrollierten Multicenterstudie zum Vergleich der offen operativen Therapie vs. der lasergestützten endoluminalen Therapie mit und ohne Crossektomie zur Therapie der Varikose der V. saphena magna.

INTRODUCTION: Therapeutic options for the treatment of varicosis of the great saphenous vein (gsv) include endoluminal laser therapy, crossectomy/stripping and a combination of both. In this paper we present data for clinical and sonographic inguinal recurrencies up to two years post operation. MATERIAL AND METHODS: In an open multicentre, randomised three-arm trial, sonographic and clinical parameters were compared perioperatively, after 2, 6, 12 and 24 months between endoluminal venous laser therapy, high ligation and invaginating stripping and a combination of both (laser: 980 nm, continuous mode, 30 W, Biolitec®, Jena, Germany). Data of 449 patients were available for the perioperative and 2 months examination. 388 patients were followed up until 6, 380 patients for 12 and 332 patients for 24 months. We compared clinical recurrences, sonographic reflux findings, and reflux side branches in the inguinal region at the saphenofemoral junction. RESULTS: We found significantly more inguinal reflux and reflux side branches in the laser groups (p < 0.0001), however, there was no statistically significant relation between clinical recurrences and sonographic reflux. Over time, there were no intraindividual constant refluxes. Regarding the secondary endpoints oedema, lymphatic oedema, local disturbances of sensibility and irritations of the saphenous nerve, lymphatic oedema and irritations of the saphenous nerve were significantly more present in the two laser groups. After two years pain and restrictions in professional life were no longer relevant in all groups. DISCUSSION: Clinical recurrences developed both in the C/S and in the laser group but reflux into the gsv and into proximal side branches developed significantly more often in the laser group. In a long-term follow-up we have to investigate the importance of reflux side branches for the development of clinical recurrences to reveal differences between the three therapeutic strategies.

Endovenous laser ablation with and without high ligation compared with high ligation and stripping in the treatment of great saphenous varicose veins: initial results of a multicentre randomized controlled trial.

OBJECTIVES: To compare reflux recurrences at the saphenofemoral junction after endovenous laser ablation (EVLA) with or without high ligation with high ligation and stripping (HL/ST) of the great saphenous vein (GSV) in patients with varicosity of the GSV. Design Multicentre, randomized, three-arm, parallel trial. Material and Methods Patients with varicosity of the GSV were randomized to one of three groups: HL/ST, laser ablation (980 nm) or a combination of laser ablation with high ligation (EVLA/HL). Patients were examined clinically and by ultrasound pre- and postoperatively and after two months. The primary endpoint of this ongoing study is the inguinal venous reflux (IVR) in the proximal section of the GSV after two years. We present data after two months. Secondary endpoints include postoperative ecchymosis, pain or discomfort, saphenous syndrome. Groups were compared by chi-squared test. RESULTS: A total of 449 patients were randomized; mean age 48 years and 71.2% were women. Postoperative ecchymosis developed among 69.2% in the HL/ST group, in 50.4% of the EVLA group and in 50.3% of the EVLA/HL group (P = 0.0007). Postoperative pain after one day occurred in 32.7% in the HL/ST group. Discomfort occurred after surgery in 37.3% in the EVLA group, and in 50.0% in the EVLA/HL group (P = 0.0069). Early postoperative nervus saphenous syndrome developed in 0.6% in the HL/ST group, in 3.7% in the EVLA group and in 6.1% in the EVLA/HL group (P = 0.0341). After two months, IVR persisted in 38 cases (8.5%) in the laser group, in 10 (2.2%) in the EVLA/HL group and none in the HL/ST group (P = 0.6800). CONCLUSIONS: After two months IVR was more often seen in both EVLA groups compared with the HL/ST group. There were significantly more postoperative ecchymosis in the HL/ST. Postoperative pain occurred significantly more often in the EVLA/HL group. Peri- and postoperative data showed significant differences between the three groups. For definitive results concerning the primary endpoint of IVR the later follow-up has to be waited for.

[High ligation and vein stripping. The classic procedure]. / Crossektomie und Strippingoperation. Der Klassiker.

The guidelines of the Society for Vascular Surgery and the American Venous Forum for management of patients with varicose veins recommend at level 1B endovenous thermal ablation for treatment of saphenous incompetence. High ligation and stripping is recommended only at level 2B. Consequently today most of the surgical procedures in the US are done endoluminally. The situation in Germany is different. The vast majority of the over 300,000 procedures done annually for varicose veins are surgical. In specialized centers in Germany, post-operative failures after high ligation are uncommon. Improper operative approaches seem likely in many of the randomized controlled trials (RCT). After proper high ligation, the results are very good.

Pantoprazole, a proton pump inhibitor, delays fracture healing in mice.

Proton pump inhibitors (PPIs), which are widely used in the treatment of dyspeptic problems, have been shown to reduce osteoclast activity. There is no information, however, on whether PPIs affect fracture healing. We therefore studied the effect of the PPI pantoprazole on callus formation and biomechanics during fracture repair. Bone healing was analyzed in a murine fracture model using radiological, biomechanical, histomorphometric, and protein biochemical analyses at 2 and 5 weeks after fracture. Twenty-one mice received 100 mg/kg body weight pantoprazole i.p. daily. Controls (n = 21) received equivalent amounts of vehicle. In pantoprazole-treated animals biomechanical analysis revealed a significantly reduced bending stiffness at 5 weeks after fracture compared to controls. This was associated with a significantly lower amount of bony tissue within the callus and higher amounts of cartilaginous and fibrous tissue. Western blot analysis showed reduced expression of the bone formation markers bone morphogenetic protein (BMP)-2, BMP-4, and cysteine-rich protein (CYR61). In addition, significantly lower expression of proliferating cell nuclear antigen indicated reduced cell proliferation after pantoprazole treatment. Of interest, the reduced expression of bone formation markers was associated with a significantly diminished expression of RANKL, indicating osteoclast inhibition. Pantoprazole delays fracture healing by affecting both bone formation and bone remodeling.

Residual stumps associated with inguinal varicose vein recurrences: a multicenter study.

PURPOSE: It is unclear whether a residual sapheno-femoral stump left in place after stripping of the great saphenous vein can contribute to the formation of late inguinal varicose vein recurrence. In order to obtain information about the time course of recurrence development, patients with histologically proven residual stumps were recruited and asked about the interval between the initial operation and the first clinical signs of varicose vein recurrence. METHODS: A multi-centre study involving 7 centres was conducted amongst patients undergoing redo-surgery for inguinal varicose vein recurrences. The sapheno-femoral stumps resected during the redo-surgery were classified histologically. Patients with a proven long residual sapheno-femoral stump were asked to describe the first signs of varicose vein recurrence with the help of a standardised questionnaire. From these data the symptom-free interval, consisting of the time frame between the initial operation and the first signs of recurrence, was determined. RESULTS: In 279 legs of 251 patients a long residual sapheno-femoral stump was present. Most patients had experienced a symptom-free interval after the initial operation with a mean duration of 7.4 S.D. 5.5 years. Recurrent varicose veins became apparent after a mean time interval of 6.3 S.D. 5.3 years and congestion symptoms occurred after a mean interval of 8.5 S.D. 5.7 years. CONCLUSIONS: In patients with symptomatic groin recurrences, a long residual sapheno-femoral stump was found in about two thirds of cases. The first clinical signs of varicose vein recurrence can be expected 7-8 years after the initial treatment at the earliest. Long term follow up is required reliably to asses the outcome of treatment for varicose veins.

Effects of citrus and avocado irrigation and nitrogen-form soil amendment on host selection by adult Homalodisca vitripennis (Hemiptera: Cicadellidae).

Host plant water status is thought to influence dispersal of the xylophagous leafhopper Homalodisca vitripennis Germar, especially where plants are grown under high evaporative demand. Preference by adult H. vitripennis for plants grown under different water deficit and nitrogen form fertilization regimens was studied under laboratory conditions. Leafhopper abundance and ovipositional preference were studied on potted 'Washington navel' orange and 'Haas' avocado in cage choice tests, and feeding rate was estimated using excreta produced by insects confined on plants. A similar study compared responses to citrus treated with 1:1 and 26:1 ratios of fertigated nitrate-N to ammonium-N. The insects were more abundant, oviposited, and fed significantly more on surplus-irrigated plants than on plants under moderate continuous deficit irrigation except avocado feeding, which was nearly significant. Plants exposed to drought became less preferred after 3 and 7 d in avocado and citrus, respectively. Citrus xylem fluid tension at this point was estimated at 0.93 MPa. A corresponding pattern of decline in feeding rate was observed on citrus, but on avocado, feeding rate was low overall and not statistically different between treatments. No statistical differences in abundance, oviposition, or feeding were detected on citrus fertigated with 26:1 or 1:1 ratios of nitrate-N to ammonium-N. Feeding occurred diurnally on both plant species. Discussion is provided on the potential deployment of regulated deficit irrigation to manage H. vitripennis movement as part of a multitactic effort to minimize the risk of disease outbreaks from Xylella fastidiosa Wells et al. in southern California agriculture.

Substitution of conserved cysteine residues in wheat streak mosaic virus HC-Pro abolishes virus transmission by the wheat curl mite.

Substitutions in the amino-proximal region of wheat streak mosaic virus (WSMV) HC-Pro were evaluated for effects on transmission by the wheat curl mite (Aceria tosichella Keifer). Alanine substitution at cysteine residues 16, 46 and 49 abolished vector transmission. Although alanine substitution at Cys(20) had no effect, substitution with arginine reduced vector transmission efficiency. Random substitutions at other positions (Lys(7) to Asn, Asn(19) to Ile, and Arg(45) to Lys) did not affect vector transmission. These results suggest that a zinc-finger-like motif (His(13)-X2-Cys(16)-X29-Cys(46)-X2-Cys(49)) in WSMV HC-Pro is essential for vector transmission.

Surveillance of transcriptomes in basic military trainees with normal, febrile respiratory illness, and convalescent phenotypes.

Gene expression profiles permit analysis of host immune response at the transcriptome level. We used the Pax gene Blood RNA (PAX) System and Affymetrix microarrays (HG-U133A&B) to survey profiles in basic military trainees and to classify them as healthy, febrile respiratory illness (FRI) without adenovirus, FRI with adenovirus, and convalescent from FRI with adenovirus. We assessed quality metrics of RNA processing for microarrays. Class prediction analysis discovered nested sets of transcripts that could categorize the phenotypes with optimized accuracy of 99% (nonfebrile vs febrile, P<0.0005), 87% (healthy vs convalescent, P=0.001), and 91% (febrile without vs with adenovirus, P<0.0005). The discovered set for classification of nonfebrile vs febrile patients consisted of 40 transcripts with functions related to interferon induced genes, complement cascades, and TNF and IL1 signaling. The set of seven transcripts for distinguishing healthy vs convalescent individuals included those associated with ribosomal structure, humoral immunity, and cell adhesion. The set of 10 transcripts for distinguishing FRI without vs with adenovirus had functions related to interferon induced genes, IL1 receptor accessory protein, and cell interactions. These results are the first in vivo demonstration of classification of infectious diseases via host signature transcripts and move us towards using the transcriptome in bio-surveillance.

Genetic and Phenotypic Variation of the Pepper golden mosaic virus Complex.

ABSTRACT Three isolates of the bipartite begomovirus Pepper golden mosaic virus (PepGMV) were characterized for genomic and biological properties. The complete nucleotide sequences of the DNA-A and DNA-B components were determined from infectious clones of PepGMV-Serrano (PepGMV-Ser), PepGMV-Mosaic (PepGMV-Mo), and PepGMV-Distortion (PepGMV-D). Nucleotide sequence identity among PepGMV components ranged from 91 to 96% for DNA-A and from 84 to 99% for DNA-B, with each PepGMV component most closely related to the corresponding component of Cabbage leaf curl virus (CaLCV). However, phylogenetic relationships among begomovirus components were incongruent because DNA-A of PepGMV and CaLCV share an inferred evolutionary history distinct from that of DNA-B. The cloned components of PepGMV-Ser, -Mo, and -D were infectious by biolistic inoculation to pepper but differed in symptom expression: PepGMV-Ser exhibited a bright golden mosaic, PepGMV-Mo produced a yellow-green mosaic, and PepGMV-D caused only a mild mosaic and foliar distortion followed by a "recovery" phenotype in which leaves developing after initial symptom expression appeared normal. Differences in symptoms also were observed on tomato, tobacco, and Datura stramonium. Progeny virus derived from clones of PepGMV-Ser and -Mo were transmitted from pepper to pepper by the B biotype of Bemisia tabaci; progeny virus derived from PepGMV-D clones was not transmissible by the B biotype. Reassortant genomes derived from heterologous DNA components of the three isolates were infectious in all possible pairwise combinations, with symptom phenotype in pepper determined by the DNA-B component. Collectively, these results indicate that the three virus isolates examined may be considered distinct strains of PepGMV that have the capacity to exchange genetic material.

Genome sequences of Agropyron mosaic virus and Hordeum mosaic virus support reciprocal monophyly of the genera Potyvirus and Rymovirus in the family Potyviridae.

Assignment of mite-transmitted species to the genus Rymovirus (family Potyviridae) has changed several times, and the status of the genus has been questioned. To address this issue, complete genome sequences of the rymoviruses Agropyron mosaic virus (AgMV) and Hordeum mosaic virus (HoMV) were determined. AgMV (9540 nucleotides) and HoMV (9463 nucleotides) each encode a single polyprotein with proteinase cleavage sites demarcating protein products characteristic of monopartite species of the family Potyviridae. Of the described species of Potyviridae, AgMV and HoMV are most closely related to each other (68.5% nucleotide and 71.6% amino acid sequence identity) and equidistant (about 53% nucleotide and about 49% amino acid sequence identity) from a third rymovirus, Ryegrass mosaic virus (RGMV). Phylogenetic analyses by neighbor joining, maximum parsimony, and Bayesian inference each grouped the three Rymovirus species in an exclusive clade distinct from a clade containing 34 species of the genus Potyvirus. Because AgMV, HoMV, and RGMV share a reciprocal monophyletic relationship with species of the genus Potyvirus and are divergent in sequence and type of vector, the genus Rymovirus should be retained as a taxonomic unit within the family Potyviridae.