Transkingdom Networks: A Systems Biology Approach to Identify Causal Members of Host-Microbiota Interactions

Improvements in sequencing technologies and reduced experimental costs have resulted in a vast number of studies generating high-throughput data. Although the number of methods to analyze these "omics" data has also increased, computational complexity and lack of documentation hinder researchers from analyzing their high-throughput data to its true potential. In this chapter we detail our data-driven, transkingdom network (TransNet) analysis protocol to integrate and interrogate multi-omics data. This systems biology approach has allowed us to successfully identify important causal relationships between different taxonomic kingdoms (e.g. mammals and microbes) using diverse types of data

Antimicrobial resistance of Campylobacter isolates from small scale and backyard chicken in Kenya

Background Thermophilic Campylobacter species are a major cause of bacterial foodborne diarrhoea in humans worldwide. Poultry and their products are the predominant source for human campylobacteriosis. Resistance of Campylobacter to antibiotics is increasing worldwide, but little is known about the antibiotic resistance in Campylobacter isolated from chicken in Kenya. In this study, 35 suspected Campylobacter strains isolated from faeces and cloacal swabs of chicken were tested for their susceptibility to seven antibiotics using a broth microdilution assay and molecular biological investigations. Results Overall, DNA of thermophilic Campylobacter was identified in 53 samples by PCR (34 C. jejuni, 18 C. coli and one mix of both species) but only 35 Campylobacter isolates (31 C. jejuni and 4 C. coli) could be re-cultivated after transportation to Germany. Isolates were tested for their susceptibility to antibiotics using a broth microdilution assay. Additionally, molecular biological detection of antibiotic resistance genes was carried out. C. jejuni isolates showed a high rate of resistance to nalidixic acid, tetracycline and ciprofloxacin of 77.4, 71.0 and 71.0 %, respectively. Low resistance (25.8 %) was detected for gentamicin and chloramphenicol. Multidrug resistance in C. jejuni could be detected in 19 (61.3 %) isolates. Resistance pattern of C. coli isolates was comparable. Resistance to ciprofloxacin was confirmed by MAMA–PCR and PCR–RFLP in all phenotypically resistant isolates. The tet(O) gene was detected only in 54.5 % of tetracycline resistant C. jejuni isolates. The tet(A) gene, which is also responsible for tetracycline resistance, was found in 90.3 % of C. jejuni and in all C. coli isolates. Thirteen phenotypically erythromycin-resistant isolates could not be characterised by using PCR–RFLP and MAMA–PCR. Conclusions To the best of our knowledge, this study is the first report about resistance to antibiotics in thermophilic Campylobacter originating from chicken in Kenya. Campylobacter spp. show a high level of resistance to ciprofloxacin, nalidixic acid and tetracycline but also a remarkable one to chloramphenicol and gentamicin and they are multidrug resistant. Resistance to antibiotics is a global public health concern. In Kenya, resistance surveillance needs further attention in the future. Efforts to establish at least a National Laboratory with facilities for performing phenotypic and genotypic characterization of thermophilic Campylobacter is highly recommended

Simultaneous genotyping of multiple polymorphisms in human serotonin transporter gene and detection of novel allelic variants

The serotonin transporter, called SLC6A4, SERT or 5-HTT, modulates neurotransmission by removal of serotonin from the synapse of serotonergic neurons, facilitating serotonin reuptake into the presynaptic terminus. Selective serotonin reuptake inhibitors block the action of the serotonin transporter and are used to treat depression and other neuropsychiatric disorders. Three polymorphisms in the 5-HTT gene have been implicated in treatment response and neuropsychiatric disorders. A 44-bp promoter ins/del polymorphism (5-HTTLPR) produces primarily long and/or short alleles due to either 14 (short) or 16 (long) repeats of variably conserved 20–23 bp units. Also implicated, a 17–18 bp variable number tandem repeat found in intron2 (StIn2) is expressed as triallelic content with 9, 10, or 12 repeats (StIn2.9, StIn2.10 or StIn2.12). Finally, a single nucleotide polymorphism rs25531 located within the promoter polymorphic-linked region alters the function of the long promoter allele. We developed a PCR-based fragment analysis assay, which is analyzed on an ABI sequencer, whereby we are able to detect all three genotypes simultaneously. Using this technique, we identified novel sequences, which demonstrate promoter repeat regions containing (1) a 17 repeat with rs25531 A/G polymorphism, (2) two with 18-repeat units, (3) one with 20-repeat units and (4) a 24-repeat sequence. The novel repeats were confirmed by direct sequencing of gel-purified amplicons

Relative contribution of various chronic diseases and multi-morbidity to potential disability among Dutch elderly

BACKGROUND: The amount of time spent living with disease greatly influences elderly people’s wellbeing, disability and healthcare costs, but differs by disease, age and sex. METHODS: We assessed how various single and combined diseases differentially affect life years spent living with disease in Dutch elderly men and women (65+) over their remaining life course. Multistate life table calculations were applied to age and sex-specific disease prevalence, incidence and death rates for the Netherlands in 2007. We distinguished congestive heart failure, coronary heart disease (CHD), breast and prostate cancer, colon cancer, lung cancer, diabetes, COPD, stroke, dementia and osteoarthritis. RESULTS: Across ages 65, 70, 75, 80 and 85, CHD caused the most time spent living with disease for Dutch men (from 7.6 years at age 65 to 3.7 years at age 85) and osteoarthritis for Dutch women (from 11.7 years at age 65 to 4. 8 years at age 85). Of the various co-occurrences of disease, the combination of diabetes and osteoarthritis led to the most time spent living with disease, for both men (from 11.2 years at age 65 to 4.9 -years at age 85) and women (from 14.2 years at age 65 to 6.0 years at age 85). CONCLUSIONS: Specific single and multi-morbid diseases affect men and women differently at different phases in the life course in terms of the time spent living with disease, and consequently, their potential disability. Timely sex and age-specific interventions targeting prevention of the single and combined diseases identified could reduce healthcare costs and increase wellbeing in elderly people

Towards an understanding of the information and support needs of surgical adolescent idiopathic scoliosis patients: a qualitative analysis

<p>Abstract</p> <p>Background</p> <p>Informed decision making for adolescents and families considering surgery for scoliosis requires essential information, including expected outcomes with or without treatment and the associated risks and benefits of treatment. Ideally families should also receive support in response to their individual concerns. The aim of this study was to identify health-specific needs for online information and support for patients with adolescent idiopathic scoliosis who have had or anticipate having spinal surgery.</p> <p>Methods</p> <p>Focus group methodology was chosen as the primary method of data collection to encourage shared understandings, as well as permit expression of specific, individual views. Participants were considered eligible to participate if they had either experienced or were anticipating surgery for adolescent idiopathic scoliosis within 12 months, were between the ages of 10 and 18 years of age, and were English-speaking.</p> <p>Results</p> <p>Two focus groups consisting of 8 adolescents (1 male, 7 female) and subsequent individual interviews with 3 adolescents (1 male, 2 female) yielded a range of participant concerns, in order of prominence: (1) recovery at home; (2) recovery in hospital; (3) post-surgical appearance; (4) emotional impact of surgery and coping; (5) intrusion of surgery and recovery of daily activities; (6) impact of surgery on school, peer relationships and other social interactions; (7) decision-making about surgery; (8) being in the operating room and; (9) future worries.</p> <p>Conclusion</p> <p>In conclusion, adolescents welcomed the possibility of an accessible, youth-focused website with comprehensive and accurate information that would include the opportunity for health professional-moderated, online peer support.</p

Protein C anticoagulant system—anti-inflammatory effects

Activated protein C (APC) plays active roles in preventing progression of a number of disease processes. These include thrombosis due to its direct anticoagulant activity which is likely augmented by its cytoprotective activity, thereby limiting exposure of procoagulant cellular membrane surfaces on cells. Beyond that, the pathway signals the cells to prevent apoptosis, to dampen inflammation, to increase endothelial barrier function, and to selectively downregulate some genes implicated in disease progression. Most of these functions are manifested to APC binding to endothelial protein C receptor (EPCR) allowing PAR1 activation, but activation of other PARS is also implicated in some cases. In addition to EPCR orchestrating these changes, CD11b is also capable of supporting APC signaling. Selective control of these pathways offers potential in new therapeutic approaches to disease

Use of Integrated Malaria Management Reduces Malaria in Kenya

BACKGROUND: During an entomological survey in preparation for malaria control interventions in Mwea division, the number of malaria cases at the Kimbimbi sub-district hospital was in a steady decline. The underlying factors for this reduction were unknown and needed to be identified before any malaria intervention tools were deployed in the area. We therefore set out to investigate the potential factors that could have contributed to the decline of malaria cases in the hospital by analyzing the malaria control knowledge, attitudes and practices (KAP) that the residents in Mwea applied in an integrated fashion, also known as integrated malaria management (IMM). METHODS: Integrated Malaria Management was assessed among community members of Mwea division, central Kenya using KAP survey. The KAP study evaluated community members' malaria disease management practices at the home and hospitals, personal protection measures used at the household level and malaria transmission prevention methods relating to vector control. Concurrently, we also passively examined the prevalence of malaria parasite infection via outpatient admission records at the major referral hospital in the area. In addition we studied the mosquito vector population dynamics, the malaria sporozoite infection status and entomological inoculation rates (EIR) over an 8 month period in 6 villages to determine the risk of malaria transmission in the entire division. RESULTS: A total of 389 households in Mwea division were interviewed in the KAP study while 90 houses were surveyed in the entomological study. Ninety eight percent of the households knew about malaria disease while approximately 70% of households knew its symptoms and methods to manage it. Ninety seven percent of the interviewed households went to a health center for malaria diagnosis and treatment. Similarly a higher proportion (81%) used anti-malarial medicines bought from local pharmacies. Almost 90% of households reported owning and using an insecticide treated bed net and 81% reported buying the nets within the last 5 years. The community also used mosquito reduction measures including, in order of preference, environmental management (35%), mosquito repellent and smoke (31%) insecticide canister sprays (11%), and window and door screens (6%). These methods used by the community comprise an integrated malaria management (IMM) package. Over the last 4 years prior to this study, the malaria cases in the community hospital reduced from about 40% in 2000 to less than 10% by 2004 and by the year 2007 malaria cases decreased to zero. In addition, a one time cross-sectional malaria parasite survey detected no Plasmodium infection in 300 primary school children in the area. Mosquito vector populations were variable in the six villages but were generally lower in villages that did not engage in irrigation activities. The malaria risk as estimated by EIR remained low and varied by village and proximity to irrigation areas. The average EIR in the area was estimated at 0.011 infectious bites per person per day. CONCLUSIONS: The usage of a combination of malaria control tools in an integrated fashion by residents of Mwea division might have influenced the decreased malaria cases in the district hospital and in the school children. A vigorous campaign emphasizing IMM should be adopted and expanded in Mwea division and in other areas with different eco-epidemiological patterns of malaria transmission. With sustained implementation and support from community members integrated malaria management can reduce malaria significantly in affected communities in Africa

The Effect of Chronic Antipsychotic Drug on Hypothalamic Expression of Neural Nitric Oxide Synthase and Dopamine D2 Receptor in the Male Rat

Antipsychotic-induced sexual dysfunction is a common and serious clinical side effect. It has been demonstrated that both neuronal nitric oxide (nNOS) and dopamine D2 receptor (DRD2) in the medial preoptic area (MPOA) and the paraventricular nucleus (PVN) of the hypothalamus have important roles in the regulation of sexual behaviour. We investigated the influences of 21 days’ antipsychotic drug administration on expression of nNOS and DRD2 in the rat hypothalamus. Haloperidol (0.5 mg/kg/day i.p.) significantly decreased nNOS integrated optical density in a sub-nucleus of the MPOA, medial preoptic nucleus (MPN), and decreased the nNOS integrated optical density and cell density in another sub-nucleus of the MPOA, anterodorsal preoptic nucleus (ADP). Risperidone (0.25 mg/kg) inhibited the nNOS integrated optical density in the ADP. nNOS mRNA and protein in the MPOA but not the PVN was also significantly decreased by haloperidol. Haloperidol and risperidone increased DRD2 mRNA and protein expression in both the MPOA and the PVN. Quetiapine (20 mg/kg/day i.p.) did not influence the expression of nNOS and DRD2 in either the MPOA or the PVN. These findings indicate that hypothalamic nNOS and DRD2 are affected to different extents by chronic administration of risperidone and haloperidol, but are unaffected by quetiapine. These central effects might play a role in sexual dysfunction induced by certain antipsychotic drugs