Application of Illumina next-generation sequencing to characterize the bacterial community of the Upper Mississippi River

AIMS

A next-generation, Illumina-based sequencing approach was used to characterize the bacterial community at ten sites along the Upper Mississippi River to evaluate shifts in the community potentially resulting from upstream inputs and land use changes. Furthermore, methodological parameters including filter size, sample volume and sample reproducibility were evaluated to determine the best sampling practices for community characterization.

METHODS AND RESULTS

Community structure and diversity in the river was determined using Illumina next-generation sequencing technology and the V6 hypervariable region of 16S rDNA. A total of 16,400 operational taxonomic units (OTUs) were observed (4594 ± 824 OTUs per sample). Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and Verrucomicrobia accounted for 93.6 ± 1.3% of all sequence reads, and 90.5 ± 2.5% belonged to OTUs shared among all sites (n = 552). Among nonshared sequence reads at each site, 33-49% were associated with potentially anthropogenic impacts upstream of the second sampling site. Alpha diversity decreased with distance from the pristine headwaters, while rainfall and pH were positively correlated with diversity. Replication and smaller filter pore sizes minimally influenced the characterization of community structure.

CONCLUSIONS

Shifts in community structure are related to changes in the relative abundance, rather than presence/absence of OTUs, suggesting a 'core bacterial community' is present throughout the Upper Mississippi River.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study is among the first to characterize a large riverine bacterial community using a next-generation-sequencing approach and demonstrates that upstream influences and potentially anthropogenic impacts can influence the presence and relative abundance of OTUs downstream resulting in significant variation in community structure.

Randomized comparison of prophylaxis and on-demand regimens with FEIBA NF in the treatment of haemophilia A and B with inhibitors

Factor replacement therapy for the treatment of moderate to severe haemophilia A and B can be complicated by the production of inhibitory alloantibodies to factor VIII (FVIII) or factor IX. Treatment with the nanofiltered anti-inhibitor coagulant complex, Factor Eight Inhibitor Bypassing Activity (FEIBA NF), is a key therapeutic option for controlling acute haemorrhages in patients with high-titre inhibitors or low-titre inhibitors refractory to replacement therapy. Given the high risk for morbidity and mortality in haemophilia patients with inhibitors to FVIII or FIX, we conducted this Phase 3 prospective study to evaluate whether prophylaxis with FEIBA NF is a safe and effective treatment option. Over a 1-year period, 17 subjects were treated prophylactically (85 ± 15 U kg⁻¹ every other day) while 19 subjects were treated on demand. The median (IQR) annualized bleeding rate (ABR) during prophylaxis was 7.9 (8.1), compared to 28.7 (32.3) during on-demand treatment, which amounts to a 72.5% reduction and a statistically significant difference in ABRs between arms (P = 0.0003). Three (17.6%) subjects (ITT) on prophylaxis experienced no bleeding episodes, whereas none treated on demand were bleeding episode-free. Total utilization of FEIBA NF for the treatment of bleeding episodes was significantly higher during on-demand therapy than prophylaxis (P = 0.0067). There were no differences in the rates of related adverse events between arms. This study demonstrates that FEIBA prophylaxis significantly reduces all types of bleeding compared with on-demand treatment, and the safety of prophylaxis is comparable to that of on-demand treatment.

Thermal inactivation of a single strain each of serotype O26:H11, O45:H2, O103:H2, O104:H4, O111:H⁻, O121:H19, O145:NM, and O157:H7 cells of Shiga toxin-producing Escherichia coli in wafers of ground beef

For each of two trials, freshly ground beef of variable fat content (higher: 70:30 %lean:%fat; lower: 93:7 %lean:%fat) was separately inoculated with ca. 7.0 log CFU/g of a single strain of Escherichia coli serotypes O26:H11, O45:H2, O103:H2, O104:H4, O111:H⁻, O121:H19, O145:NM, and O157:H7. Next, ca. 3-g samples of inoculated beef were transferred into sterile filter bags and then flattened (ca. 1.0 mm thick) and vacuum sealed. For each temperature and sampling time, three bags of the inoculated wafers of beef were submerged in a thermostatically controlled water bath and heated to an internal temperature of 54.4°C (130°F) for up to 90 min, to 60°C (140°F) for up to 4 min, or to 65.6°C (150°F) for up to 0.26 min. In lower fat wafers, D-values ranged from 13.5 to 23.6 min, 0.6 to 1.2 min, and 0.05 to 0.08 min at 54.4, 60.0, and 65.6°C, respectively. Heating higher fat wafers to 54.4, 60.0, and 65.6°C generated D-values of 18.7 to 32.6, 0.7 to 1.1, and 0.05 to 0.2 min, respectively. In addition, we observed reductions of ca. 0.7 to 6.7 log CFU/g at 54.4°C after 90 min, ca. 1.1 to 6.1 log CFU/g at 60.0°C after 4 min, and 0.8 to 5.8 log CFU/g at 65.6°C after 0.26 min. Thus, cooking times and temperatures effective for inactivating a serotype O157:H7 strain of E. coli in ground beef were equally effective against the seven non-O157:H7 Shiga toxin-producing strains investigated herein.

Femoropopliteal in-stent restenosis: review and potential for drug based therapy

Endovascular treatment of symptomatic peripheral arterial disease in the femoropopliteal (FP) artery is fraught with high rates of restenosis. Success of the antiproliferative drug, paclitaxel, in the coronary arteries, has lead to the investigation of paclitaxel in the peripheral arteries to treat restenosis. This article reviews restenosis rates for the major treatment modalities used in the FP segment. Use of drug-elution for restenosis is also reviewed, including the use of drug-eluting balloons and drug-eluting stents.

Curcumin inhibits UV radiation-induced skin cancer in SKH-1 mice

OBJECTIVE

As skin cancer incidence increases, research has focused on novel chemopreventive agents that inhibit tumor formation. In prior experimentation, curcumin, a naturally occurring food substance and anticarcinogenic agent, inhibited cutaneous squamous cell carcinoma xenograft growth. We hypothesize curcumin will inhibit UVB radiation-induced skin cancer growth in mice, approximating a human chemopreventive model.

STUDY DESIGN

Randomized experimental animal and laboratory study.

SETTING

Louisiana State University Health Sciences Center-Shreveport, Louisiana.

SUBJECTS AND METHODS

SKH-1 mice were pretreated with oral or topical curcumin or oral or topical control (n = 11/group) for 14 days. Mice received UVB radiation 3 times weekly for 24 weeks or were not radiated. Number of tumors formed and time to tumor onset for each mouse were recorded through tumor harvest after week 24. Tumor multiplicity and time to tumor onset were compared.

RESULTS

Time to tumor onset was significantly shorter in control mice compared to mice receiving either oral (P = .025) or topical (P = .015) curcumin. A significant difference in the average number of tumors formed per mouse was seen, as fewer tumors were formed in the oral curcumin (P = .01) and topical curcumin (P = .01) groups, compared with respective controls. No significant difference in average number of tumors per mouse was seen between oral and topical curcumin (P = .56), suggesting that both routes were equally effective.

CONCLUSION

Curcumin appears to inhibit skin cancer formation and prolong time to tumor onset when administered by either an oral or topical route. These data suggest that curcumin may have chemopreventive potential against skin cancer, necessitating future experimentation with human subjects.

11Beta-hydroxylase deficiency and other syndromes of mineralocorticoid excess as a rare cause of endocrine hypertension

Hypertension represents a major public and global health problem, most of which likely can be improved by lifestyle changes including changing dietary habits with less consumption of processed and preserved foods, which generally contain higher amounts of salt than freshly prepared food items. Among causes for endocrine hypertension are syndromes of mineralocorticoid excess. This group of mostly monogenic and acquired disorders typically causes hypertension through activation of the mineralocorticoid receptor either directly or indirectly via hormonal mediators and from overactive amiloride-sensitive epithelial sodium channels located in the distal tubule and collecting ducts of the kidneys. Apart from primary aldosteronism, mineralocorticoid excess can be caused by congenital adrenal hyperplasia (CAH) due to mutations of the 11beta-hydroxylase and 17alpha-hydroxylase genes, by inactivating mutations of the glucocorticoid receptor gene (Chrousos syndrome), endogenous hypercortisolism (Cushing's syndrome), by mutations of the 11beta-hydroxysteroid dehydrogenase type 2 gene (apparent mineralocorticoid excess/AME) or licorice/carbenoxolone intake, mutations of the epithelial sodium channel genes (Liddle syndrome), mutations of the mineralocorticoid receptor gene (Geller syndrome), and by mutations in the WNK1, WNK4, KLHL3, CUL3 genes (pseudohypoaldosteronism type 2 or Gordon syndrome). Most of these conditions are treated by restricting dietary salt intake. However, some require special therapies including dexamethasone/hydrocortisone (CAH), spironolactone/eplerenone (AME), epithelial sodium channel inhibitors amiloride/triamterene (Liddle and Gordon syndrome), while in others spironolactone and MR antagonists may be contraindicated due to an abnormally structured MR (Geller syndrome). We here review the pathophysiology, diagnosis, and therapy of these rare conditions including the presentation of a patient with 11beta-hydroxylase deficiency.

Making decisions about delirium: a qualitative comparison of decision making between nurses working in palliative care, aged care, aged care psychiatry, and oncology

BACKGROUND

Delirium has a significant impact on nursing practice from diagnosis and management, with under-detection and variable management of delirium being international problems. This study aimed to explore nurses' assessment and management of delirium when caring for people with cancer, the elderly or older people requiring psychiatric care in the inpatient setting.

METHODS

Participants in this qualitative study were nurses working in Australian public hospital inpatient dedicated units in palliative care, aged care (geriatrics), aged care (geriatric) psychiatry and oncology. Semi-structured interviews were used to explore nurses' views about specific areas of delirium assessment and management. Purposive sampling was used and interviews conducted until thematic saturation reached. A thematic content analysis was performed from a grounded theory perspective.

RESULTS

A total of 40 participants were included in the study. The analysis revealed four broad analytical themes: (1) superficial recognition and understanding of the operational definition of delirium or recognition of delirium as a syndrome; (2) nursing assessment: investigative versus a problem solving approach; (3) management: maintaining dignity and minimizing chaos; and (4) distress and the effect on others.

DISCUSSION

Nurses have limited knowledge of the features of delirium regardless of their specialty discipline. Delirium was uniformly identified as a highly distressing experience for patients, families and staff alike. The majority of nurses had a superficial understanding of delirium management, and adopted a task-orientated approach aimed at addressing the more noticeable problems. These findings have implications for both education and knowledge translation. Innovative approaches are needed to align health professional behaviours with best evidence delirium care.

Recurrent Laryngeal Neurofibroma Unrelated to NF Type 1

Objective: Although rare, neurofibromas arising from the recurrent laryngeal nerve in neurofibromatosis type I patients have been cited in the literature. However, recurrent laryngeal neurofibromas unrelated to this inherited disorder have not been reported. We describe a new entity of a recurrent laryngeal neurofibroma arising at the level of the glottis.

Method: A case report and literature review is presented. A patient with progressive dysphonia, dysphagia, and mild dyspnea was referred to our cancer center in November 2011 for assessment. Flexible laryngoscopy revealed right vocal cord paresis and a submucosal mass causing medial displacement of the right arytenoid.

Results: CT imaging revealed a well-defined, nonenhancing mass at the level of the posterior glottis. Transoral endoscopic surgical excision of the mass was performed. Pathology revealed a benign peripheral nerve sheath tumor consistent with a neurofibroma. The patient had resolution of his dyspnea and achieved significant improvement of his voice with a 6-week course of speech therapy, despite postoperative right vocal cord paralysis.

Conclusion: Isolated neurofibromas of the recurrent laryngeal nerve, without the appearance of other characteristic features of von Recklinhausen disease have not been reported. Although benign, early recognition and surgical excision of these lesions is necessary to prevent airway obstruction, dysphagia, and aspiration.

Curcumin Inhibits UV Radiation–Induced Skin Cancer In Vivo

Objective: As skin cancer incidence increases, research has focused on novel chemopreventive agents that inhibit tumor formation. In prior experimentation, curcumin, a naturally occurring food substance and anti-carcinogenic agent, inhibited cutaneous squamous cell carcinoma xenograft growth. We hypothesize curcumin will inhibit UVB-radiation–induced skin cancer growth in mice, approximating a human chemopreventive model.

Method: A randomized experimental animal and laboratory study is presented. SKH-1 mice were pre-treated with oral or topical curcumin, or oral or topical control (n = 22/group), for 14 days. Mice received UVB radiation 3 times weekly for 24 weeks or were not radiated. Tumor number, volume, and onset were compared.

Results: Time to tumor onset was significantly shorter in control mice compared to mice receiving either oral ( P = .025) or topical ( P = .015) curcumin. A significant difference in the average number of tumors formed per mouse was seen, as fewer tumors were formed in the oral curcumin ( P = .01) and topical curcumin ( P = .01) groups, compared with their respective controls. Once tumors formed, no significant difference in tumor volume was noted at 24 weeks.

Conclusion: Curcumin appears to inhibit skin cancer formation and prolong time to tumor onset when administered by either an oral or topical route. These data suggest that curcumin may have chemopreventive potential against skin cancer necessitating future experimentation with human subjects.

Dynamical hologram generation for high speed optical trapping of smart droplet microtools

This paper demonstrates spatially selective sampling of the plasma membrane by the implementation of time-multiplexed holographic optical tweezers for Smart Droplet Microtools (SDMs). High speed (>1000fps) dynamical hologram generation was computed on the graphics processing unit of a standard display card and controlled by a user friendly LabView interface. Time multiplexed binary holograms were displayed in real time and mirrored to a ferroelectric Spatial Light Modulator. SDMs were manufactured with both liquid cores (as previously described) and solid cores, which confer significant advantages in terms of stability, polydispersity and ease of use. These were coated with a number of detergents, the most successful based upon lipids doped with transfection reagents. In order to validate these, trapped SDMs were maneuvered up to the plasma membrane of giant vesicles containing Nile Red and human biliary epithelial (BE) colon cancer cells with green fluorescent labeled protein (GFP)-labeled CAAX (a motif belonging to the Ras protein). Bright field and fluorescence images showed that successful trapping and manipulation of multiple SDMs in x, y, z was achieved with success rates of 30-50% and that subsequent membrane-SDM interactions led to the uptake of Nile Red or GFP-CAAX into the SDM.