Mycobacteriophage Endolysins: Diverse and Modular Enzymes with Multiple Catalytic Activities

The mycobacterial cell wall presents significant challenges to mycobacteriophages – viruses that infect mycobacterial hosts – because of its unusual structure containing a mycolic acid-rich mycobacterial outer membrane attached to an arabinogalactan layer that is in turn linked to the peptidoglycan. Although little is known about how mycobacteriophages circumvent these barriers during the process of infection, destroying it for lysis at the end of their lytic cycles requires an unusual set of functions. These include Lysin B proteins that cleave the linkage of mycolic acids to the arabinogalactan layer, chaperones required for endolysin delivery to peptidoglycan, holins that regulate lysis timing, and the endolysins (Lysin As) that hydrolyze peptidoglycan. Because mycobacterial peptidoglycan contains atypical features including 3→3 interpeptide linkages, it is not surprising that the mycobacteriophage endolysins also have non-canonical features. We present here a bioinformatic dissection of these lysins and show that they are highly diverse and extensively modular, with an impressive number of domain organizations. Most contain three domains with a novel N-terminal predicted peptidase, a centrally located amidase, muramidase, or transglycosylase, and a C-terminal putative cell wall binding domain

MYCOBACTERIOPHAGE LYSINS: BIOINFORMATIC CHARACTERIZATION OF LYSIN A AND IDENTIFICATION OF THE FUNCTION OF LYSIN B IN INFECTION

Tuberculosis kills nearly 2 million people each year, and more than one-third of the world�s population is infected with the causative agent, Mycobacterium tuberculosis. Mycobacteriophages, or bacteriophages that infect Mycobacterium species including M. tuberculosis, are already being used as tools to study mycobacteria and diagnose tuberculosis. More than 60 mycobacteriophage genomes have been sequenced, revealing a vast genetic reservoir containing elements useful to the study and manipulation of mycobacteria. Mycobacteriophages also encode proteins capable of fast and efficient killing of the host cell. In most bacteriophages, lysis of the host cell to release progeny phage requires at minimum two proteins: a holin that mediates the timing of lysis and permeabilizes the cell membrane, and an endolysin (lysin) that degrades peptidoglycan. Accessory lysis proteins have also been discovered, often with functions specific to that phage�s host.Many lysins of phages infecting Gram-positive bacteria are proving to be potent antibacterials. Further, lysis proteins can provide insight into the properties and composition of the host cell wall. Given the complexity of the mycobacterial cell wall and its medical relevance in tuberculosis as an immunogenic barrier that complicates treatment, as well as the urgent need for new therapeutic options, the mycobacteriophage lysins clearly warrant further scientific investigation.This work focuses on the mycobacteriophage lysin LysA and the accessory lysis protein LysB. Bioinformatic characterizations show that LysA proteins posess a variety of domains arranged in modular organizations, reflecting extensive recombination within the mycobacteriophage population. In addition to known peptidoglycan-hydrolytic activities, novel cell wall-binding domains are identified, as well as several domains of unknown function found only in mycobacteriophages. LysB proteins are unique to mycobacteriophages and perform a singular role as mycolylarabinogalactan esterases that sever the connection between the mycobacterial outer membrane and the peptidoglycan cell wall complex to ensure efficient lysis and progeny phage release. There is also preliminary evidence of peptidoglycan hydrolytic ability, inducible cell lysis, and growth inhibition of Mycobacterium smegmatis by LysA and LysB proteins. These studies suggest that mycobacteriophage lysis proteins can be exploited as useful tools, both in the laboratory and clinical setting

Microbial biomass and nitrogen availability under the invasive plant species Lonicera japonica and native grasses in wetland soil

Invasive plants decrease aboveground biodiversity and suitable wildlife habitat. Wetlands are especially valuable ecosystems because they provide habitat, floodwater control, and function as filters for urban runoff. Wetland soils also act as sinks for nutrients. This characteristic reduces levels of excess nutrients often found in adjacent aquatic systems. The importance of soil functions in wetlands necessitates further investigation of the effects of invasive species on belowground nutrient pools. Approximately 75% of a small neighborhood wetland located in Fayetteville, Ark., has been invaded by Lonicera japonica. The effects of L. japonica and its replacement with native grasses on soil microbial biomass and nutrient pools were evaluated. Eight plots were established in April 2003. Four were left vegetated with the invasive species L. japonica while the other four were revegetated with transplants of five native grass species: Andropogon gerardii, Schizachyrium spp., Sorghastrum nutans, Panicum virgatum, and Tripsacum dactyloides. Soil samples were taken three times over the growing season, once prior to the removal of L. japonica and twice after transplanting occurred. Microbial biomass, soil carbon and nitrogen, Mehlich III- extractable phosphorus, pH, moisture content, and inorganic nitrogen were analyzed and significance was tested using a one-way ANOVA test (

Risk Factors for Falls in Individuals With Lower Extremity Amputations During the Pre-Prosthetic Phase: A Retrospective Cohort Study

BACKGROUND: Falls in individuals with lower limb amputations (LLAs) pose significant health concerns. The literature is limited regarding falls during the preprosthetic phase of rehabilitation for persons with LLAs. OBJECTIVE: To determine the incidence of falls and identify factors associated with falls during the preprosthetic recovery phase. DESIGN: Retrospective chart audit. SETTING: Inpatient rehabilitation program. PARTICIPANTS: Four hundred forty individuals with LLAs (age ± SD = 61.93 ± 14.53 years, 73.18% male) who attended inpatient rehabilitation from 26 July 2011 to 21 August 2017. INTERVENTIONS: Not applicable. MAIN OUTCOME MEASUREMENTS: The number of self-reported falls was recorded from the time of surgery to admission for inpatient rehabilitation. Outcomes of interest were any fall (1+ fall) and recurrent falls (2+ falls). A retrospective chart audit was performed on consecutive admissions to an inpatient rehabilitation program. RESULTS: The incidence of falls was 8.37 per 1000 patient-days. Falls were sustained by 60.9% of the sample. Unilateral transtibial amputation was independently associated with an increased risk of recurrent falls (relative risk [RR] 1.59, 95% confidence interval [CI] 1.13-2.23, P = .008). Diabetes mellitus was independently associated with an increased risk of any fall (RR 1.18, 95% CI 1.01-.38, P = .03). Finally, bilateral transtibial amputation was independently associated with a reduced risk of any fall (RR 0.59, 95% CI 0.39-0.90, P = .014). CONCLUSIONS: Consistent with the current literature, diabetes mellitus and a unilateral transtibial amputation were risk factors for falling, whereas a bilateral transtibial amputation and increasing age presented new findings as factors associated with decreased falling. LEVEL OF EVIDENCE: III

Reliability of Three Landmarking Methods for Dual Inclinometry Measurements of Lumbar Flexion and Extension

Background To examine the intra and inter-rater reliability of lumbar flexion and extension measurements attained using three landmarking methods for dual inclinometry. Methods This was a repeated measures reliability study. Convenience sampling was used to obtain forty volunteer subjects. Two assessors measured a series of lumbar flexion and extension movements using the J-Tech™ dual inclinometer. Three different landmarking methods were used: 1) straight palpation of PSIS and L1, 2) palpation of PSIS and the site of the nearest 5 cm interval point closest to L1 and 3) location of PSIS and 15 cm cephalad. Upon landmarking, adhesive tape was used to mark landmarks and the inclinometer was placed on sites for three trials of flexion and extension. Tape was removed and landmarks were relocated by the same assessor (intra-rater) for an additional three trials; and this process was repeated by a second assessor (inter-rater). Reliability was determined using intra-class correlation coefficients. Results Reliability within a set of three repetitions was very high (ICCs \u3e 0.90); intra-rater reliability after relocating landmarks was high (ICCs \u3e 0.80); reliability between therapists was moderate to high (0.60 \u3e ICCs \u3c 0.76). Assessment of flexion and extension movements by straight palpation of bony landmarks as in the Straight palpation of PSIS and L1 method (ICC: Flexion 0.60; Extension 0.74) was found to be marginally less reliable than the other two landmarking measurement strategies (ICC: Flexion 0.66; Extension 0.76). Conclusion All three methods of land marking are reliable. We recommend the use of the PSIS to 15 cm cephalad method as used in the modified-modified Schobers test as it is the simplest to perform and aligns with current clinical practice

Pediatric High Risk Leukemia — Molecular Insights

Acute leukemia comprises of 31% of all cancers in children making it the most common childhood malignancy. Significant strides have been made in treatment, partly through risk stratification and intensified therapy. A number of subtypes remain at high risk for relapse and poor outcome, despite current therapies. Here we describe risk stratification and molecular diagnosis used to identify high risk leukemias and guide treatment. Specific cytogenetic alterations that contribute to high risk B and T cell acute lymphoblastic leukemia (ALL), as well as infant leukemia are discussed. Particular attention is given to genetic alterations in IKZF1, CRLF2, and JAK, that have been identified by whole genome sequencing and recently associated with Ph-like ALL. Ongoing studies of disease mechanisms and challenges in developing pre-clinical patient-derived xenograft models to evaluate therapies are discussed

Assessment and restoration of a neighborhood wetland invaded by exotic plant species

The University of Arkansas Crop, Soil, and Environmental Sciences (CSES) Club adopted a local wetland in the spring of 2002 through the Fayetteville Parks and Recreation Department. This project has allowed students to interact with local community and governmental organizations as well as other academic departments within the university. Students have gained valuable laboratory and field experience through characterizing hydric soils, identifying bird and plant species, and analyzing water quality, soil nutrients, and microbial biomass. Under the main goal of restoring the wetland, the club has outlined both short and long-term objectives including soil and water assessments; removal of two invasive species—Lonicera japonica and Festuca arundinacea; revegetation of native species to provide wildlife habitat and forage; establishment of trails and educational signs; and community outreach. To facilitate removal of the invasive species, the club is experimenting with manual removal, implementing physical barriers to prevent plant photosynthesis, and working with city officials to obtain permission for selective use of herbicides. The adoption of the wetland has provided a catalyst for the CSES Club to organize, rebuild itself, and achieve its goals

Iodine supplementation for women during the preconception, pregnancy and postpartum period

Background Iodine is an essential nutrient required for the biosynthesis of thyroid hormones, which are responsible for regulating growth, development and metabolism. Iodine requirements increase substantially during pregnancy and breastfeeding. If requirements are not met during these periods, the production of thyroid hormones may decrease and be inadequate for maternal, fetal and infant needs. The provision of iodine supplements may help meet the increased iodine needs during pregnancy and the postpartum period and prevent or correct iodine deficiency and its consequences. Objectives To assess the benefits and harms of supplementation with iodine, alone or in combination with other vitamins and minerals, for women in the preconceptional, pregnancy or postpartum period on their and their children's outcomes. Search methods We searched Cochrane Pregnancy and Childbirth's Trials Register (14 November 2016), and the WHO International Clinical Trials Registry Platform (ICTRP) (17 November 2016), contacted experts in the field and searched the reference lists of retrieved studies and other relevant papers. Selection criteria Randomized and quasi‐randomized controlled trials with randomisation at either the individual or cluster level comparing injected or oral iodine supplementation (such as tablets, capsules, drops) during preconception, pregnancy or the postpartum period irrespective of iodine compound, dose, frequency or duration. Data collection and analysis Two review authors independently assessed trial eligibility, risk of bias, extracted data and conducted checks for accuracy. We used the GRADE approach to assess the quality of the evidence for primary outcomes. We anticipated high heterogeneity among trials, and we pooled trial results using random‐effects models and were cautious in our interpretation of the pooled results. Main results We included 14 studies and excluded 48 studies. We identified five ongoing or unpublished studies and two studies are awaiting classification. Eleven trials involving over 2700 women contributed data for the comparisons in this review (in three trials, the primary or secondary outcomes were not reported). Maternal primary outcomes Iodine supplementation decreased the likelihood of the adverse effect of postpartum hyperthyroidism by 68% (average risk ratio (RR) 0.32; 95% confidence interval (CI) 0.11 to 0.91, three trials in mild to moderate iodine deficiency settings, 543 women, no statistical heterogeneity, low‐quality evidence) and increased the likelihood of the adverse effect of digestive intolerance in pregnancy by 15 times (average RR 15.33; 95% CI 2.07 to 113.70, one trial in a mild‐deficiency setting, 76 women, very low‐quality evidence). There were no clear differences between groups for hypothyroidism in pregnancy or postpartum (pregnancy: average RR 1.90; 95% CI 0.57 to 6.38, one trial, 365 women, low‐quality evidence, and postpartum: average RR 0.44; 95% CI 0.06 to 3.42, three trials, 540 women, no statistical heterogeneity, low‐quality evidence), preterm birth (average RR 0.71; 95% CI 0.30 to 1.66, two trials, 376 women, statistical heterogeneity, low‐quality evidence) or the maternal adverse effects of elevated thyroid peroxidase antibodies (TPO‐ab) in pregnancy or postpartum (average RR 0.95; 95% CI 0.44 to 2.07, one trial, 359 women, low‐quality evidence, average RR 1.01; 95% CI 0.78 to 1.30, three trials, 397 women, no statistical heterogeneity, low‐quality evidence), or hyperthyroidism in pregnancy (average RR 1.90; 95% CI 0.57 to 6.38, one trial, 365 women, low‐quality evidence). All of the trials contributing data to these outcomes took place in settings with mild to moderate iodine deficiency. Infant/child primary outcomes Compared with those who did not receive iodine, those who received iodine supplements had a 34% lower likelihood of perinatal mortality, however this difference was not statistically significant (average RR 0.66; 95% CI 0.42 to 1.03, two trials, 457 assessments, low‐quality evidence). All of the perinatal deaths occurred in one trial conducted in a severely iodine‐deficient setting. There were no clear differences between groups for low birthweight (average RR 0.56; 95% CI 0.26 to 1.23, two trials, 377 infants, no statistical heterogeneity, low‐quality evidence), neonatal hypothyroidism/elevated thyroid‐stimulating hormone (TSH) (average RR 0.58; 95% CI 0.11 to 3.12, two trials, 260 infants, very low‐quality evidence) or the adverse effect of elevated neonatal thyroid peroxidase antibodies (TPO‐ab) (average RR 0.61; 95% CI 0.07 to 5.70, one trial, 108 infants, very low‐quality evidence). All of the trials contributing data to these outcomes took place in areas with mild to moderate iodine deficiency. No trials reported on hypothyroidism/elevated TSH or any adverse effect beyond the neonatal period. Authors' conclusions There were insufficient data to reach any meaningful conclusions on the benefits and harms of routine iodine supplementation in women before, during or after pregnancy. The available evidence suggested that iodine supplementation decreases the likelihood of postpartum hyperthyroidism and increases the likelihood of the adverse effect of digestive intolerance in pregnancy ‐ both considered potential adverse effects. We considered evidence for these outcomes low or very low quality, however, because of study design limitations and wide confidence intervals. In addition, due to the small number of trials and included women in our meta‐analyses, these findings must be interpreted with caution. There were no clear effects on other important maternal or child outcomes though these findings must also be interpreted cautiously due to limited data and low‐quality trials. Additionally, almost all of the evidence came from settings with mild or moderate iodine deficiency and therefore may not be applicable to settings with severe deficiency. More high‐quality randomised controlled trials are needed on iodine supplementation before, during and after pregnancy on maternal and infant/child outcomes. However, it may be unethical to compare iodine to placebo or no treatment in severe deficiency settings. Trials may also be unfeasible in settings where pregnant and lactating women commonly take prenatal supplements with iodine. Information is needed on optimal timing of initiation as well as supplementation regimen and dose. Future trials should consider the outcomes in this review and follow children beyond the neonatal period. Future trials should employ adequate sample sizes, assess potential adverse effects (including the nature and extent of digestive intolerance), and be reported in a way that allows assessment of risk of bias, full data extraction and analysis by the subgroups specified in this review

Viral forensic genomics reveals the relatedness of classic herpes simplex virus strains KOS, KOS63, and KOS79

Herpes simplex virus 1 (HSV-1) is a widespread global pathogen, of which the strain KOS is one of the most extensively studied. Previous sequence studies revealed that KOS does not cluster with other strains of North American geographic origin, but instead clustered with Asian strains. We sequenced a historical isolate of the original KOS strain, called KOS63, along with a separately isolated strain attributed to the same source individual, termed KOS79. Genomic analyses revealed that KOS63 closely resembled other recently sequenced isolates of KOS and was of Asian origin, but that KOS79 was a genetically unrelated strain that clustered in genetic distance analyses with HSV-1 strains of North American/European origin. These data suggest that the human source of KOS63 and KOS79 could have been infected with two genetically unrelated strains of disparate geographic origins. A PCR RFLP test was developed for rapid identification of these strains