Comparative analysis of multiple consensus genomes of the same strain of Marek's disease virus reveals intrastrain variation.

Current strategies to understand the molecular basis of Marek's disease virus (MDV) virulence primarily consist of cataloging divergent nucleotides between strains with different phenotypes. However, most comparative genomic studies of MDV rely on previously published consensus genomes despite the confirmed existence of MDV strains as mixed viral populations. To assess the reliability of interstrain genomic comparisons relying on published consensus genomes of MDV, we obtained two additional consensus genomes of vaccine strain CVI988 (Rispens) and two additional consensus genomes of the very virulent strain Md5 by sequencing viral stocks and cultured field isolates. In conjunction with the published genomes of CVI988 and Md5, this allowed us to perform three-way comparisons between multiple consensus genomes of the same strain. We found that consensus genomes of CVI988 can vary in as many as 236 positions involving 13 open reading frames (ORFs). By contrast, we found that Md5 genomes varied only in 11 positions involving a single ORF. Notably, we were able to identify 3 single-nucleotide polymorphisms (SNPs) in the unique long region and 16 SNPs in the unique short (US) region of CVI988GenBank.BAC that were not present in either CVI988Pirbright.lab or CVI988USDA.PA.field. Recombination analyses of field strains previously described as natural recombinants of CVI988 yielded no evidence of crossover events in the US region when either CVI988Pirbright.lab or CVI988USDA.PA.field were used to represent CVI988 instead of CVI988GenBank.BAC. We were also able to confirm that both CVI988 and Md5 populations were mixed, exhibiting a total of 29 and 27 high-confidence minor variant positions, respectively. However, we did not find any evidence of minor variants in the positions corresponding to the 19 SNPs in the unique regions of CVI988GenBank.BAC. Taken together, our findings suggest that continued reliance on the same published consensus genome of CVI988 may have led to an overestimation of genomic divergence between CVI988 and virulent strains and that multiple consensus genomes per strain may be necessary to ensure the accuracy of interstrain genomic comparisons.

Comparative Analysis of Multiple Consensus Genomes of the Same Strain of Marek's Disease Virus Reveals Intrastrain Variation.

Current strategies to understand the molecular basis of Marek's disease virus (MDV) virulence primarily consist of cataloguing divergent nucleotides between strains with different phenotypes. However, each MDV strain is typically represented by a single consensus genome despite the confirmed existence of mixed viral populations. To assess the reliability of single-consensus interstrain genomic comparisons, we obtained two additional consensus genomes of vaccine strain CVI988 (Rispens) and two additional consensus genomes of the very virulent strain Md5 by sequencing viral stocks and cultured field isolates. In conjunction with the published genomes of CVI988 and Md5, this allowed us to perform 3-way comparisons between consensus genomes of the same strain. We found that consensus genomes of CVI988 can vary in as many as 236 positions involving 13 open reading frames (ORFs). In contrast, we found that Md5 genomes varied only in 11 positions involving a single ORF. Phylogenomic analyses showed all three Md5 consensus genomes clustered closely together, while also showing that CVI988 GenBank.BAC diverged from CVI988 Pirbright.lab and CVI988 USDA.PA.field . Comparison of CVI988 consensus genomes revealed 19 SNPs in the unique regions of CVI988 GenBank.BAC that were not present in either CVI988 Pirbright.lab or CVI988 USDA.PA.field . Finally, we evaluated the genomic heterogeneity of CVI988 and Md5 populations by identifying positions with >2% read support for alternative alleles in two ultra-deeply sequenced samples. We were able to confirm that both populations of CVI988 and Md5 were mixed, exhibiting a total of 29 and 27 high-confidence minor variant positions, respectively. We did not find any evidence of minor variants in the positions corresponding to the 19 SNPs in the unique regions of CVI988 GenBank.BAC . Taken together, our findings confirm that consensus genomes of the same strain of MDV can vary and suggest that multiple consensus genomes per strain are needed in order to maximize the accuracy of interstrain genomic comparisons.

Relationship between TLR-2 level and clinical or radiological severity on patients with tuberculosis spondylitis in Dr. Wahidin Sudirohusodo hospital Makassar.

Spinal tuberculosis or TB spondylitis is one of the most common types of extra pulmonary tuberculosis, which is about 15% of all cases. It causes severe morbidity, neurological deficits, and severe deformities in the patients. The growth of Mycobacterium tuberculosis in culture specimens obtained from infected tissue is the single gold standard diagnostic test for spinal TB. Toll-like receptor (TLR) is one of the important receptors in the first-line defence system against microbes. TLR-2 and TLR-4 are known to be associated with tuberculosis infection. Based on this background, the researchers were interested in examining the relationship between TLR-2 levels and the clinical and radiological severity of TB spondylitis patients. A cross-sectional study was conducted with patients diagnosed with tuberculosis spondylitis at Dr Wahidin Sudirohusodo Makassar. Patients diagnosed with TB spondylitis confirmed by blood tests, GeneExpert, and magnetic resonance imaging without prior treatment were included. Data analysis were conducted by using descriptive analysis and one-way ANOVA for bivariate analysis. The mean value of TLR2 levels in TB spondylitis patients was 9.1 g/dL. TLR2 levels in paraesthesia were significantly higher than normal (P < .05). Similar trend were analyzed on the motor neurologic status with TLR2 levels in paraparesis were significantly higher than those in normal (P < .05). There is a significant relationship between the TLR2 levels in TB spondylitis and their impaired motor and sensory function. Spinal destruction has been shown to provide significant relationship with TLR2 value in spondylitis TB.

Management of 3 month old neglected talus neck fracture: A case report and review of literature.

Background: Talus fractures are extremely uncommon, accounting for approximately 1 % of foot and ankle fractures. The talar neck fracture has a high probability of damaging the anastomotic ring, which would interrupt blood circulation to talar body and cause serious issues with fracture healing and integrity. Due to insufficient radiological and clinical examination, approximately 39 % of midfoot and ankle fractures could be undiagnosed after initial evaluation. Talus fractures account for about half of these missed fractures. Anatomic reduction and advanced fixation methods can be performed in the management of neglected talus neck fracture for the purpose of improving functional outcome. Case report: A 30-year-old male patient presented with swelling and pain on the right foot while walking for three months. He had previously fallen about two meters from stairs three months back. Instead of going to the hospital, he received conventional massage therapy. Three months later, he came to us complaining of chronic, dull aching, swelling, and continuous pain when walking and standing. After radiology evaluation, the patient was diagnosed with neglected nonunion type III Hawkins fracture of the neck talus and managed by double incision approach, Iliac crest cancellous bone graft, open reduction and internal fixation (ORIF) with cannulated screw. He was able to return to full weight bearing and his previous activity without experiencing any pain after 14 months. Conclusion: Open reduction and internal fixation (ORIF) with Iliac crest cancellous bone graft is a reliable methods for neglected non-union type III Hawkins fracture of neck talus with great functional outcomes after 14 months of follow up.

Functional outcome of modified Jones procedure in patient with non-union Humerus and high radial nerve palsy: A case report.

Background: Middle to distal humeral fractures can cause high radial nerve palsy. A tendon transfer surgery can be performed to treat irreversible and longstanding radial nerve palsy in order to improve the lost hand function. Case report: A 39-year-old right-handed female office worker presented with deformity in her left arm and drop hand. She had a motorcycle accident a year before and was treated by a traditional bonesetter. The extension movements in her left wrist and fingers were restricted. We performed an ORIF with bone graft at her left nonunion humerus and also tendon transfer procedure to treat the high radial nerve palsy. We use the modified Jones procedure to attach the palmaris longus to the extensor pollicis longus. After that, we attached the flexor carpi radialis to extensor digitorum communis and extensor carpi radialis brevis with the Pulvertaft technique. After five months of follow up, the patient finally can extend her wrist and thumb. Conclusion: Modified Jones procedure is a viable option to treat high radial nerve palsy with great functional outcomes after 5 months of follow up.

Chronic Rupture of Achilles Tendon Caused by Haglund's Deformity: A Case Report.

A chronic Achilles tendon rupture is a tendon rupture occurring more than 4-6 weeks after a traumatic injury. Haglund's deformity, caused by bony abnormalities in the ankle (mostly due to osteophyte or bone spur), can cause chronic inflammation and degeneration of the Achilles tendon, eventually leading to rupture. This presents a challenge for clinicians who provide tendon repair procedures. We present a 69-year-old woman who had difficulty moving her left leg and had a deformity on the left leg compared to her right leg after falling nine months before but with pain starting three months before the accident. There was a seven-centimeter gap in the calcaneus with a positive Thompson test. The Haglund's deformity on the left calcaneus was visible on the ankle X-ray. The patient had a chronic total rupture of the left Achilles tendon, which was treated with a flexor hallucis longus (FHL) tendon transfer and resection of the deformity. One week after surgery, the patient's ability to walk and the shape of the left leg improved. This case report describes a chronic left Achilles tendon condition that was successfully repaired through tendon repair surgery using FHL tendon transfer and removal of Haglund's deformity.

The Surgical Procedure in Managing Peroneal Tendon Injury: A Case Series.

Introduction: Peroneal tendon injury is one of the pathological ankle conditions which causes pain and is frequently misdiagnosed as ankle sprain. There is a variety of peroneal tendon injuries, depending on the mechanism of injury. We report a series of three peroneal injuries in our institution. Case Presentation: All three of the patients presented with ankle pain and instability following injuries. There was a presence of peroneus quartus in one of the patients. Retromalleolar pain was revealed in all of the patients, in addition to instability. All of the three patients received open peroneal tendon repair with groove tubular deepening for the 1st patient. Following the surgery, the patients could partially weight-bear after 3-4 weeks. Full range of motion was restored 6 weeks after surgery. Discussion: The peroneal muscle functions as a dynamic stabilizer of the ankle, which is vital to control the dynamic stability of the lateral ankle. There is a variety of peroneal injuries ranging from split tear to chronic dislocation. The treatment for peroneal tendon subluxation can be conservative or surgical. There are several surgical techniques for peroneal tendon subluxation repair, such as: 1) direct repair of retinaculum; 2) retromalleolar groove deepening; 3) tendon graft reconstruction; 4) bone block procedure; 5) tendon rerouting procedure. Conclusion: Peroneal tendon injury should always be considered following inversion ankle trauma, especially in case of chronic lateral retromalleolar pain. Surgeries are often required after failure of conservative treatment which can cause impaired walking, decreased sports performance, or chronic pain and muscle strain.

Oxidative remobilization of biogenic uranium(IV) precipitates: effects of iron(II) and pH.

The oxidative remobilization of uranium from biogenic U(IV) precipitates was investigated in bioreduced sediment suspensions in contact with atmospheric O2 with an emphasis on the influence of Fe(II) and pH on the rate and extent of U release from the solid to the aqueous phase. The sediment was collected from the U.S. Department of Energy Field Research Center (FRC) site at Oak Ridge, Tennessee. Biogenic U(IV) precipitates and bioreduced sediment were generated through anaerobic incubation with a dissimilatory metal reducing bacterium Shewanella putrefaciens strain CN32. The oxidative remobilization of freshly prepared and 1-yr aged biogenic U(IV) was conducted in 0.1 mol/L NaNO3 electrolyte with variable pH and Fe(II) concentrations. Biogenic U(IV)O2(s) was released into the aqueous phase with the highest rate and extent at pH 4 and 9, while the U remobilization was the lowest at circumneutral pH. Increasing Fe(II) significantly decreased U remobilization to the aqueous phase. From 70 to 100% of the U in the sediments used in all the tests was extractable at the experiment termination (41 d) with a bicarbonate solution (0.2 mol/L), indicating that biogenic U(IV) was oxidized regardless of Fe(II) concentration and pH. Sorption experiments and modeling calculations indicated that the inhibitive effect of Fe(II) on U(IV) oxidative remobilization was consistent with the Fe(III) oxide precipitation and U(VI) sorption to this secondary phase.

Influence of sediment bioreduction and reoxidation on uranium sorption.

The influence of sediment bioreduction and reoxidation on U(VI) sorption was studied using Fe(II) oxide-containing saprolite from the U.S. Department of Energy (DOE) Oak Ridge site. Bioreduced sediments were generated by anoxic incubation with a metal-reducing bacterium, Shewanella putrefaciens strain CN32, supplied with lactate as an electron donor. The reduced sediments were subsequently reoxidized by air contact. U(VI) sorption was studied in NaNO3-HCO3 electrolytes that were both closed and open to atmosphere and where pH, U(VI), and carbonate concentration were varied. Mössbauer spectroscopy and chemical analyses showed that 50% of the Fe(III)-oxides were reduced to Fe(II) that was sorbed to the sediment during incubation with CN32. However, this reduction and subsequent reoxidation of the sorbed Fe(II) had negligible influence on the rate and extent of U sorption or the extractability of sorbed U by 0.2 mol/L NaHCO3. Various results indicated that U(VI) surface complexation was the primary process responsible for uranyl sorption by the bioreduced and reoxidized sediments. A two-site, nonelectrostatic surface complexation model best described U(VI) adsorption under variable pH, carbonate, and U(VI) conditions. A ferrihydrite-based diffuse double layer model provided a better estimation of U(VI) adsorption without parameter adjustment than did a goethite-based model, even though a majority of the Fe(III)-oxides in the sediments were goethite. Our results highlight the complexity of the coupled U-Fe redox system and show that sorbed Fe(II) is not a universal reductant for U(VI) as commonly assumed.

Abnormal asymmetry in language association cortex in autism.

Autism is a neurodevelopmental disorder affecting cognitive, language, and social functioning. Although language and social communication abnormalities are characteristic, prior structural imaging studies have not examined language-related cortex in autistic and control subjects. Subjects included 16 boys with autism (aged 7-11 years), with nonverbal IQ greater than 80, and 15 age- and handedness-matched controls. Magnetic resonance brain images were segmented into gray and white matter; cerebral cortex was parcellated into 48 gyral-based divisions per hemisphere. Asymmetry was assessed a priori in language-related inferior lateral frontal and posterior superior temporal regions and assessed post hoc in all regions to determine specificity of asymmetry abnormalities. Boys with autism had significant asymmetry reversal in frontal language-related cortex: 27% larger on the right in autism and 17% larger on the left in controls. Only one additional region had significant asymmetry differences on post hoc analysis: posterior temporal fusiform gyrus (more left-sided in autism), whereas adjacent fusiform gyrus and temporooccipital inferior temporal gyrus both approached significance (more right-sided in autism). These inferior temporal regions are involved in visual face processing. In boys with autism, language and social/face processing-related regions displayed abnormal asymmetry. These structural abnormalities may relate to language and social disturbances observed in autism.