Investigating the Impact of Tillage and Crop Rotation on the Prevalence of phlD-Carrying Pseudomonas Potentially Involved in Disease Suppression

Winter oilseed rape (OSR) is becoming an increasingly popular crop in rotations as it provides a cash crop and reduces the incidence of take-all fungal disease (caused by Gaeumannomyces graminis) in subsequent wheat production. The exact mechanism of this inhibition of fungal pathogens is not fully understood; however, the selective recruitment of bacterial groups with the ability to suppress pathogen growth and reproduction is thought to play a role. Here we examine the effect of tillage practice on the proliferation of microbes that possess the phlD gene involved in the production of the antifungal compound 2,4-diacetylphloroglucinol (2,4-DAPG), in the rhizospheres of both winter oilseed rape and winter wheat grown in rotation over a two-year period. The results showed that conservation strip tillage led to a significantly greater phlD gene copy number, both in the soil and in the roots, of oilseed rape and wheat crops, whereas crop rotation of oilseed rape and wheat did not increase the phlD gene copy number in winter wheat.

At the nexus of ludology and narratology: Advances in reality-based story-driven games

Story-driven games are growing in popularity across a wide range of genres. However, the narrative potential of video games is still being debated, particularly in light of the so-called tension between gameplay and storytelling. This study proposes that rules and game mechanics perform narrative semiotic functions, offering a ludic grammar of interactive storytelling. Case studies of four representative games show through exploratory player action shaped by rules, the medium of video games can generate meanings that traditional media cannot, thereby better achieving their narrative goals.

Field scale biodegradation of total petroleum hydrocarbons and soil restoration by Ecopiles: microbiological analysis of the process

Ecopiling is a method for biodegradation of hydrocarbons in soils. It derives from Biopiles, but phytoremediation is added to biostimulation with nitrogen fertilization and bioaugmentation with local bacteria. We have constructed seven Ecopiles with soil heavily polluted with hydrocarbons in Carlow (Ireland). The aim of the study was to analyze changes in the microbial community during ecopiling. In the course of 18 months of remediation, total petroleum hydrocarbons values decreased in 99 and 88% on average for aliphatics and aromatics, respectively, indicating a successful biodegradation. Community analysis showed that bacterial alfa diversity (Shannon Index), increased with the degradation of hydrocarbons, starting at an average value of 7.59 and ending at an average value of 9.38. Beta-diversity analysis, was performed using Bray-Curtis distances and PCoA ordination, where the two first principal components (PCs) explain the 17 and 14% of the observed variance, respectively. The results show that samples tend to cluster by sampling time instead of by Ecopile. This pattern is supported by the hierarchical clustering analysis, where most samples from the same timepoint clustered together. We used DSeq2 to determine the differential abundance of bacterial populations in Ecopiles at the beginning and the end of the treatment. While TPHs degraders are more abundant at the start of the experiment, these populations are substituted by bacterial populations typical of clean soils by the end of the biodegradation process. Similar results are found for the fungal community, indicating that the microbial community follows a succession along the process. This succession starts with a TPH degraders or tolerant enriched community, and finish with a microbial community typical of clean soils.

The Opioid Crisis: Prevalence and Markets of Opioids

The US opioid crisis came in three waves - prescription opioids, heroin, and illicitly manufactured fentanyls - Centers for Disease Control and Prevention Centers for Disease Control and Prevention resulting in the deaths of nearly 500,000 people from 1996 to 2019. In 2009, drug overdose deaths exceeded those involving automobiles. Opioid overdose deaths contributed to the decrease in life expectancy for Americans from 78.8 to 78.5 during 2014 to 2017. The overprescribing of a schedule II prescription opioid was escalated by pharmaceutical companies promoting a growing belief that pain was an undertreated condition. In 2012, the number of opioid prescriptions peaked at 255 million and deaths exceeded 11,000 per year. The typical prescription opioid abuser was white, male, and 45-55 years of age. The hardest-hit states were in Appalachia and the Northeast. When an abuse-resistant formulation was introduced for OxyContin, the most prevalent prescription opioid, users turned to heroin. From the early 1980s, a new pizza delivery style of Mexican trafficking in black tar heroin infiltrated many of the same states hit hardest by prescription opioids. Heroin overdose deaths reached 14,495 in 2017. As heroin abuse increased in states supplied with black tar heroin, fentanyl-contaminated white powder heroin began to appear in the Northeast. Fentanyl was quickly followed by fentanyl analogs. While heroin deaths continued to escalate through 2017, they were soon overshadowed by fentanyl overdose deaths. Finally, prescription opioid and heroin overdose deaths started to decline in 2017, though fentanyl deaths continued to increase. In late 2019, it appeared that restrictions on transportation and travel due to the COVID-19 pandemic had resulted in decreased availability of illicit drugs, but by 2020 drug abuse had escalated in many countries. Globally, heroin was the primary opioid of abuse and only a few countries - including Canada, Germany, Austria, and Belgium - have experienced a significant increase in prescription opioids. However, illicitly manufactured fentanyls are a growing problem in North America, Europe, Australia, and Asia.

Influence of food and lifestyle on the risk of developing inflammatory bowel disease

BACKGROUND

The Barwon area in Australia has one of the highest incidence rates of inflammatory bowel disease (IBD) and therefore is an ideal location to study the impact of environmental exposures on the disease's development.

AIM

To study these exposures prior to the development of IBD in a population-based cohort.

METHOD

One hundred and thirty-two incident cases (81 Crohn disease (CD) and 51 ulcerative colitis (UC)) from an IBD registry and 104 controls replied to the International Organization of Inflammatory Bowel Diseases environmental questionnaire. This included 87 questions about pre-illness exposures that included childhood illnesses, vaccinations, breastfeeding, house amenities, pets and swimming, diet and smoking.

RESULTS

The factors associated with CD included smoking (odds ratio (OR): 1.42, confidence interval (CI): 1-2.02, P = 0.029); childhood events, including tonsillectomy (OR: 1.74, CI: 1.15-2.6, P = 0.003) and chicken pox infection (OR: 3.89, CI: 1.61-9.4, P = 0.005) and pre-diagnosis intake of frequent fast food (OR: 2.26, CI: 1.76-4.33, P = 0.003). In UC, the risk factors included smoking (OR: 1.39, CI: 1.1-1.92, P = 0.026) and pre-diagnosis intake of frequent fast food (OR: 2.91, CI: 1.54-5.58, P < 0.001), and high caffeine intake was protective (OR: 0.51, 95% CI: 0.3-0.87, P = 0.002). Other protective exposures for UC included high fruit intake (OR: 0.59, CI: 0.4-0.88, P = 0.003) and having pets as a child (OR: 0.36, CI: 0.2-0.79, P = 0.001).

CONCLUSION

This first Australian population-based study of environmental risk factors confirms that smoking, childhood immunological events and dietary factors play a role in IBD development; while high caffeine intake and pet ownership offer a protective effect.

Does lymphopenia or macrocytosis reflect 6-thioguanine levels in patients with inflammatory bowel disease treated with azathioprine or 6-mercaptopurine?

BACKGROUND

The thiopurine drugs, 6-mercaptopurine and azathioprine, remain the mainstay of immunomodulator therapy for inflammatory bowel disease (IBD). Optimal management depends on achieving therapeutic levels of 6-thioguanine (6-TGN), but measuring thiopurine metabolites is associated with significant cost. Thiopurines cause lymphopenia and an increase in mean corpuscular volume (MCV). It is unclear whether any clinically useful correlation exists between 6-TGN levels and lymphocyte count or MCV.

AIMS

The aim of this study is to investigate the correlation between 6-TGN levels and lymphocyte count and MCV in thiopurine-treated patients with IBD.

METHODS

We analysed a prospectively acquired database of 67 patients with IBD treated with thiopurine therapy. The data were analysed looking at the relationship between 6-TGN levels and both lymphocyte count and MCV by using the Spearman's rank correlation coefficient.

RESULTS

Twenty-seven (40%) patients had therapeutic 6-TGN levels. Thirty-three (49%) patients had sub-therapeutic 6-TGN levels. A weak positive correlation between 6-TGN levels and lymphocyte count was demonstrated, but this was not statistically significant (Spearman's R = 0.14, P = 0.23). Spearman's rank correlation coefficient between 6-TGN levels and MCV was statistically significant (R = 0.42, P = 0.0005). MCV >101 fL excluded a subtherapeutic 6-TGN level with positive predictive value of 92%.

CONCLUSIONS

There is no specific lymphopenia that can be assumed to indicate a therapeutic 6-TGN level. The relationship between 6-TGN levels and MCV is likely to be clinically relevant. If MCV is elevated, 6-TGN is unlikely to be sub-therapeutic. MCV is a potential surrogate marker which can rule out sub-therapeutic thiopurine metabolites in patients with IBD treated with azathioprine or 6-mercaptopurine.

An in vitro screen employing human neonatal dendritic cells identifies distinct synergy between Toll-like receptor and C-type lectin receptor agonists (VAC10P.966)

Due to impairments in cell-mediated immunity, newborns are markedly susceptible to infection with intracellular pathogens. Impaired newborn immunity includes a reduced response to Toll-like Receptor agonists (TLRAs) by dendritic cells (DCs), placing them at risk for infection and limiting Th1-responses to many vaccines. Our hypothesis was that dual stimulation with TLRAs and C-type Lectin Receptor agonists (CLRAs) may overcome the reduced response of newborn DCs to common vaccine formulations. We screened TLRAs, CLRAs and their combinations for their ability to induce Th1-polarizing cytokine production from neonatal dendritic cells. Human adult- and cord blood monocyte-derived DCs (MoDCs) were generated in the presence of autologous plasma and stimulated for 18 hours. Cytokines and markers for cellular toxicity were measured to assess correlates of immunogenicity and reactogenicity. Dual activation of newborn DCs with a TLR8 agonist (R848) and a Mincle agonist (TDB) or with a TLR4 agonist (MPLA or GLA) and a Dectin-1 agonist (alkali-treated Zymosan) synergistically enhanced the production of the T-cell activating and -polarizing cytokines TNF-α, IL-12p70 and IL-1β. Our data suggest that targeting vaccinal antigens to the endocytic receptors Mincle or Dectin-1 is a powerful approach to induce Th1-mediated immunity in newborns. This study has the potential to inform development of novel adjuvanted neonatal vaccines and reduce infections in infants.

Genome sequence reveals that Pseudomonas fluorescens F113 possesses a large and diverse array of systems for rhizosphere function and host interaction

Background

Pseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR) isolated from the sugar-beet rhizosphere. This bacterium has been extensively studied as a model strain for genetic regulation of secondary metabolite production in P. fluorescens, as a candidate biocontrol agent against phytopathogens, and as a heterologous host for expression of genes with biotechnological application. The F113 genome sequence and annotation has been recently reported.

Results

Comparative analysis of 50 genome sequences of strains belonging to the P. fluorescens group has revealed the existence of five distinct subgroups. F113 belongs to subgroup I, which is mostly composed of strains classified as P. brassicacearum. The core genome of these five strains is highly conserved and represents approximately 76% of the protein-coding genes in any given genome. Despite this strong conservation, F113 also contains a large number of unique protein-coding genes that encode traits potentially involved in the rhizocompetence of this strain. These features include protein coding genes required for denitrification, diterpenoids catabolism, motility and chemotaxis, protein secretion and production of antimicrobial compounds and insect toxins.

Conclusions

The genome of P. fluorescens F113 is composed of numerous protein-coding genes, not usually found together in previously sequenced genomes, which are potentially decisive during the colonisation of the rhizosphere and/or interaction with other soil organisms. This includes genes encoding proteins involved in the production of a second flagellar apparatus, the use of abietic acid as a growth substrate, the complete denitrification pathway, the possible production of a macrolide antibiotic and the assembly of multiple protein secretion systems.

Isolation of identical nitrilase genes from multiple bacterial strains and real-time PCR detection of the genes from soils provides evidence of horizontal gene transfer

Bacterial enzymes capable of nitrile hydrolysis have significant industrial potential. Microbacterium sp. AJ115, Rhodococcus erythropolis AJ270 and AJ300 were isolated from the same location in England and harbour identical nitrile hydratase/amidase gene clusters. Strain AJ270 has been well studied due to its nitrile hydratase and amidase activity. R. erythropolis ITCBP was isolated from Denmark and carries a very similar nitrile hydratase/amidase gene cluster. In this study, an identical nitrilase gene (nit1) was isolated from the four strains, and the nitrilase from strain AJ270 cloned and expressed in Escherichia coli. Analysis of the recombinant nitrilase has shown it to be functional with activity demonstrated towards phenylacetonitrile. A real-time PCR TaqMan assay was developed that allowed nit1 detection directly from soil enrichment cultures without DNA extraction, with nit1 detected in all samples tested. Real-time PCR screening of isolates from these soils resulted in the isolation of nit1 and also very similar nitrilase gene nit2 from a number of Burkholderia sp. The genes nit1 and nit2 have also been detected in many bacteria of different genera but are unstable in these isolates. It is likely that the genes were acquired by horizontal gene transfer and may be wide-spread in the environment.

A comparative analysis of cytokine responses, cell surface marker expression and MAPKs in DCs matured with LPS compared with a panel of TLR ligands

Dendritic cells (DCs) are professional antigen-presenting cells that play a vital role in shaping adaptive immunity. DC maturation begins when exogenous danger signals bind to the appropriate toll-like receptor (TLR) and initiate expression of cell surface markers and the secretion of cytokines. This process occurs through defined mitogen-activated protein kinase (MAPK) signalling pathways. Of the 13 known mammalian TLRs, lipopolysaccharide (LPS), which activates TLR4, is the most commonly used ligand for the maturation of DCs in vitro. This comprehensive study measures cytokine secretion and cell surface marker expression in murine bone-marrow-derived DCs following maturation with LPS compared to DCs matured with a panel of other TLR-ligands (zymosan A (TLR2/6), PGN (TLR2), poly(I:C) (TLR3), flagellin (TLR5) and CpG-ODN1826 (TLR9)). The role of MAPK signalling pathways in the maturation process was also examined. Results demonstrate that zymosan A and CpG induce comparable cytokine and cell surface marker profiles to LPS. The remaining ligands differed significantly for cytokine and CD40 expression, but not for CD80 and CD86 expression. While there were differences for MAPK signalling pathways for all ligands, the effect of the inhibitors were broadly similar. These findings broaden our knowledge of TLR ligand-matured DCs.

Objective cervical portio length measurements: consistency and efficacy of screening for a short cervix

OBJECTIVE

To determine the consistency of 4-quadrant cervical portio length measurements with an objective cervical measuring device and to identify patients who may benefit from transvaginal ultrasound.

STUDY DESIGN

Prenatal patients (12-34 weeks) derwent 4-quadrant cervical portio measurements and transvaginal ultrasound by different, blinded examiners. Cervical portio quadrant measures were analyzed by correlation analysis, and the predictive ability of cervical portio length measurements to identify short cervices with transvaginal ultrasound was assessed.

RESULTS

The right and left lateral cervical portio measurements were consistently available and correlated highly with each other. Cervical portio length had excellent sensitivity (88%), specificity (92%) and negative predictive value (99%) in identifying patients with a short cervix (< 30 mm) by transvaginal ultrasound.

CONCLUSION

Right and left lateral cervical portio length measurements are highly consistent and provide an effective screen for patients with short cervixes who may benefit from transvaginal ultrasound.

Oxytocin-Associated Rupture of an Unscarred Uterus in a Primigravida

BACKGROUND

Intrapartum rupture of the unscarred uterus is an uncommon event, usually associated with such risk factors as grand multiparity, malpresentation, history of gestational trophoblastic disease, or instrumented delivery. Rupture during first pregnancy is extremely rare.

CASE

A 30-year-old primigravid woman was admitted for labor augmentation with oxytocin at 40.5 weeks of gestation. The oxytocin infusion rate was increased during the first and second stages of labor despite contractions occurring at a rate of 4-5 per 10 minutes. The uterus ruptured during second stage. Despite emergency cesarean delivery, the baby had evidence of severe asphyxia.

CONCLUSION

This case of uterine rupture in a primigravida with no prior uterine surgery and a structurally normal uterus underscores the importance of careful contraction monitoring and judicious control of oxytocin infusion rates.

Targeted mid-trimester ultrasound examination: how does fetal anatomic visualization depend upon the duration of the scan?

OBJECTIVE

To determine the relationship between visualization of key fetal anatomic structures during mid-trimester ultrasound examination with gestational age and duration of examination.

METHODS

One hundred ultrasound examinations at 16-22 weeks' gestation were reviewed to determine the times at which key fetal anatomic features were seen. Scans were terminated at 30 min or when a comprehensive anatomic survey was complete. Exclusion criteria included multiple gestation, maternal weight>77 kg, abdominal wall scarring, and suspected fetal anomalies.

RESULTS

Visualization of cranial anatomy including lips, face, midline, ventricles, choroid plexus, and cerebellum was achieved in 98% of patients within 30 min. The corresponding figures for spine, cardiac screening (four-chamber, aortic, and pulmonary outflow views) and for abdominal anatomy (stomach, kidneys, bladder, ventral wall, and three-vessel cord) were 91%, 91%, and 99%, respectively. A complete anatomic survey including each of the above elements was obtained by 10, 15, 20, 25, and 30 min in 8%, 31%, 53%, 72% and 81% of the subjects. Rates of complete anatomic surveys within 30 min improved by gestational age interval, from 20/30 (67%) at 16-18 weeks, to 36/44 (82%) at 18-20 weeks, and 25/26 (96%) at 20-22 weeks; this rise was primarily due to improvements in visualization of the spine and heart.

CONCLUSIONS

A comprehensive anatomical survey can be completed in 10 min or less in a minority of patients. For each 5-min time increment up to 30 min, the rate of complete surveys improves. Rates of completed anatomic surveys rise with gestational age.

BphK shows dechlorination activity against 4-chlorobenzoate, an end product of bph-promoted degradation of PCBs

A bphK gene encoding glutathione S-transferase (GST) activity is located in the bph operon in Burkholderia sp. strain LB400 but its role in polychlorinated biphenyl (PCB) metabolism is unknown. This gene was over-expressed in Escherichia coli and an in vivo assay based on growth of E. coli containing GST activity was used to identify potential novel substrates for this enzyme. Using this assay, 4-chlorobenzoate (4-CBA) was identified as a substrate for the BphK enzyme. High pressure liquid chromatography analysis and chloride ion detection showed removal of 4-CBA and an equivalent increase of chloride in cell extracts when incubated with this enzyme. These results would indicate that this BphK enzyme has dechlorination activity in relation to 4-CBA and may have a role in protection of other Bph enzymes against certain chlorinated metabolites of PCB degradation.

Additive antiviral effects of lamivudine and alpha-interferon in chronic hepatitis B infection

alpha-Interferon has limited efficacy against chronic hepatitis B virus (HBV) infection. Nucleoside analogues may confer greater benefits, however, it is likely that combination therapies will be required for effective control of this infection. We investigated the antiviral effect of lamivudine and interferon therapy in eight patients with high HBV-DNA levels. Six patients received lamivudine/interferon combination therapy followed, after a 6-month drug-free period, with lamivudine monotherapy. Mean HBV viral load (copies/ml) reduction was significantly greater after 4 months of combination therapy (4.3 x 10(3)) compared to an equivalent period of lamivudine monotherapy (2.9 x 10(2)) (P=0.03). Two patients were given 6 months of lamivudine/interferon combination therapy followed immediately by lamivudine monotherapy. Cessation of interferon in these patients led to a rapid 1-2 log10 increase in HBV viral load. These findings suggest that alpha-interferon has a direct antiviral effect on chronic HBV infection, which may be additive to, or synergistic with lamivudine.

Selection of multiresistant hepatitis B virus during sequential nucleoside-analogue therapy

Hepatitis B virus (HBV) drug resistance to lamivudine is always accompanied by mutations in the viral polymerase gene at position 550, termed group 1 (M550V with L526M) or group 2 (M550I) mutations. The latter mutation has not been associated with famciclovir resistance. Thus, the addition of famciclovir to lamivudine therapy in persons with group 2 lamivudine resistance may lead to virus suppression. The effect of lamivudine/famciclovir combination therapy on HBV infection was monitored in 5 lamivudine-resistant patients by quantitative polymerase chain reaction and polymerase gene sequencing of serum virus. No patients treated with combination therapy had a decline in HBV load >1 log10. Continual evolution of the viral polymerase was detected in association with virologic resistance to both drugs. Cloning experiments identified the preexistence of these multidrug-resistant virus variants as minority species prior to addition of famciclovir therapy. HBV resistance to lamivudine monotherapy is associated with a complex mixture of variants that limit the efficacy of second-line nucleoside-analogue therapy. First-line potent combination therapy may reduce the emergence of HBV drug resistance.

Standard osteopathic manipulative treatment acutely improves gait performance in patients with Parkinson's disease

Patients with Parkinson's disease exhibit a variety of motor deficits which can ultimately result in complete disability. The primary objective of this study was to quantitatively evaluate the effect of osteopathic manipulative treatment (OMT) on the gait of patients with Parkinson's disease. Ten patients with idiopathic Parkinson's disease and a group of eight age-matched normal control subjects were subjected to an analysis of gait before and after a single session of an OMT protocol. A separate group of 10 patients with Parkinson's disease was given a sham-control procedure and tested in the same manner. In the treated group of patients with Parkinson's disease, statistically significant increases were observed in stride length, cadence, and the maximum velocities of upper and lower extremities after treatment. There were no significant differences observed in the control groups. The data demonstrate that a single session of an OMT protocol has an immediate impact on Parkinsonian gait. Osteopathic manipulation may be an effective physical treatment method in the management of movement deficits in patients with Parkinson's disease.

Nurse practitioners: meeting the ED's needs

Results of a descriptive analysis of emergency-department (ED) census data were used as a basis for initiating an innovative nurse practitioner (NP) position. In establishing the NP role, census levels, demographic considerations, legal considerations and scope of practice were considered.

The behavior of bacteria designed for biodegradation

Mineralization of organic molecules by microbes is essential for the carbon cycle to operate. The massive mobilization of compounds stored in natural resources, or the introduction of xenobiotics into the biosphere, leads to unidirectional fluxes, which result in the persistance of a number of chemicals in the biosphere, and thus constitute a source of pollution. Molecular biology offers the tools to optimize the biodegradative capacities of microorganisms, accelerate the evolution of "new" activities, and construct totally "new" pathways through the assemblage of catabolic segments from different microbes. Although the number of genetically engineered microbes (GEMs) for potential use in biodegradation is not large, these recombinant microbes function in microcosms according to their design. The survival and fate of recombinant microbes in different ecological niches under laboratory conditions is similar to what has been observed for the unmodified parental strains. rDNA, both on plasmids and on the host chromosome, is usually stably inherited by GEMs. The potential lateral transfer of rDNA from the GEMs to other microbes is significantly diminished, though not totally inhibited, when rDNA is incorporated on the host chromosome. The behavior and fate of GEMs can be predicted more accurately through the coupling of regulatory circuits that control the expression of catabolic pathways to killing genes, so that the GEMs survive in polluted environments, but die when the target chemical is eliminated.