From data to QSP models: a pipeline for using Boolean networks for hypothesis inference and dynamic model building.

Quantitative Systems Pharmacology (QSP) models capture the physiological underpinnings driving the response to a drug and express those in a semi-mechanistic way, often involving ordinary differential equations (ODEs). The process of developing a QSP model generally starts with the definition of a set of reasonable hypotheses that would support a mechanistic interpretation of the expected response which are used to form a network of interacting elements. This is a hypothesis-driven and knowledge-driven approach, relying on prior information about the structure of the network. However, with recent advances in our ability to generate large datasets rapidly, often in a hypothesis-neutral manner, the opportunity emerges to explore data-driven approaches to establish the network topologies and models in a robust, repeatable manner. In this paper, we explore the possibility of developing complex network representations of physiological responses to pharmaceuticals using a logic-based analysis of available data and then convert the logic relations to dynamic ODE-based models. We discuss an integrated pipeline for converting data to QSP models. This pipeline includes using k-means clustering to binarize continuous data, inferring likely network relationships using a Best-Fit Extension method to create a Boolean network, and finally converting the Boolean network to a continuous ODE model. We utilized an existing QSP model for the dual-affinity re-targeting antibody flotetuzumab to demonstrate the robustness of the process. Key output variables from the QSP model were used to generate a continuous data set for use in the pipeline. This dataset was used to reconstruct a possible model. This reconstruction had no false-positive relationships, and the output of each of the species was similar to that of the original QSP model. This demonstrates the ability to accurately infer relationships in a hypothesis-neutral manner without prior knowledge of a system using this pipeline.

Observational cohort study of highly functioning community-dwelling older adults to assess their sarcopenic status, leisure physical activity, and quality of life over 12-months.

Background: The prevalence of sarcopenia varies depending on the cohort evaluated, and the diagnostic criteria used. Older adults with sarcopenia report lower quality of life than their non-sarcopenic peers. Leisure physical activity is reported to have a variable effect on sarcopenic status. Most studies to date, have been done in "vulnerable" populations, with fewer done on independent community-dwelling older adults. None have been done in an Alberta, Canada population. Objectives: To prospectively evaluate the sarcopenic status of independent community-dwelling older Albertan adults; whether this changed over 12-months; and any association with self-reported leisure activity or quality of life. Methods: Independent community-dwelling older adults were invited to participate in a 12-month observational study. Assessments were done at baseline, 6 and 12-months for physical function (TUG, SPPB, gait speed, Tinetti, grip strength), muscle mass (DXA, arm and calf circumference), body fat (skinfold, DXA), reported daily exercise (aerobic, resistance), quality of life (EQ5D), and laboratory parameters. European Working Group on Sarcopenia in Older People (EWGSOP) definitions of sarcopenic status were used. Results: All 50 participants (11 male), were independent of all basic activities of daily living at baseline, and most instrumental activities (some needed assistance with driving or finances). They had an average age of 75.8 (67-90) years, with average MMSE and MoCA cognitive scores of 28.1/30 (20-30) and 24.8/30 (14-30) respectively. Eight participants dropped out prior to their first DXA test. Of the remaining 42, 17 participants (5 male) fulfilled the EWGSOP revised criteria for probable, pre-sarcopenia, or sarcopenia, giving a rate of baseline total sarcopenia of 40.5% in this community-dwelling sample. The majority were pre-sarcopenic (28.6%), and sarcopenia was present only in 7.1%. The total sarcopenia group had a lower BMI (25.6 ± 5.1 versus 29 ± 5, p = 0.01), less body fat by skinfold measurement (36.4 ± 6.5 versus 39.3 ± 8.1, p = 0.01) and lower mid-calf (35.6 ± 3.2 versus 37.6 ± 3.4, p = 0.04) and mid-arm (29.1 ± 2.5 versus 31.9 ± 3.5, p = 0.02) circumferences when compared to their non-sarcopenic peers. After 12-months, 39 participants remained in the study. Of these, the sarcopenic status of 7 improved, 10 declined, with the remaining 56% not changing. There were no statistically significant differences in baseline laboratory parameters between the groups, including 25(OH)D status. But, of the status decliners, 40% had suboptimal 25(OH)D at baseline. Self-reported leisure activity (both total time and frequency) was not associated with sarcopenic status at 12-months. EuroQol -5D was not associated with sarcopenic status. Conclusions: The rate of sarcopenia was 7.1%, but the total rate of pre, probable and sarcopenia in this highly functioning, community-dwelling older adult cohort was 40.5%. In the majority (75%), there was either no change, or an improvement, in their sarcopenic status over 12-months. There was no association identified with self-reported leisure activity or quality of life in this cohort.

Potential mechanisms of endogenous retroviral-mediated genomic instability in human cancer.

Malignancy results from a complex combination of genetic and epigenetic changes, the full effects of which are still largely unknown. Here we summarize current knowledge of the origin, retrotranspositional activity, epigenetic state, and transcription of human endogenous retroviruses (HERVs), and then discuss the potential effects of their deregulation in cancer. Evidence suggests that cancer-associated epigenetic changes most likely underlie potential HERV-mediated effects on genome and transcriptome instability and may play a role in malignancy. Despite our currently limited understanding of the importance of HERVs or other transposable elements in cancer development, we believe that the emerging era of high-throughput sequencing of cancer genomes, epigenomes, and transcriptomes will provide unprecedented opportunities to investigate these roles in the future.

Assessing the Impact of Factors that Influence the Ketogenic Response to Varying Doses of Medium Chain Triglyceride (MCT) Oil.

Objectives, Design, Setting: The ketogenic effect of medium chain triglyceride (MCT) oil offers potential for Alzheimer's disease prevention and treatment. Limited literature suggests a linear B-hyroxybutyrate (BHB) response to increasing MCT doses. This pharmacokinetic study evaluates factors affecting BHB response in three subject groups. PARTICIPANTS: Healthy subjects without cognitive deficits <65years, similarly healthy subjects >=65years, and those with Alzheimer's Disease were assessed. INTERVENTION: Different doses (0g,14g, 28g, 42g) of MCT oil (99.3% C8:0) were administered, followed by fasting during the study period. MEASUREMENTS: BHB measured by finger prick sampling hourly for 5 hours after ingestion. Each subject attended four different days for each ascending dose. Data was also collected on body composition, BMI, waist/hip ratio, grip strength, gait speed, nutrient content of pre-study breakfast and side effects. RESULTS: Twenty-five participants: eight healthy; average age of 44yr (25-61), nine healthy; 79yr (65-90) and eight with AD; 78.6yr (57-86) respectively. Compiled data showed the expected linear dose response relationship. No group differences, with baseline corrected area under the blood vs. time curve (r2=0.98) and maximum concentrations (r2=0.97). However, there was notable individual variability in maximum BHB response (42g dose: 0.4 -2.1mM), and time to reach maximum BHB response both, within and between individuals. Variability was unrelated to age, sex, sarcopenic or AD status. Visceral fat, BMI, waist/hip ratio and pretest meal CHO and protein content all affected the BHB response (p<0.001). CONCLUSION: There was a large inter-individual variability, with phenotype effects identified. This highlights challenges in interpreting clinical responses to MCT intake.

Expression of different members of the Ly-49 gene family defines distinct natural killer cell subsets and cell adhesion properties.

The murine Ly-49 antigen belongs to a family of type II transmembrane molecules containing lectin-like domains. The original member of this family, Ly-49A, has been demonstrated to be expressed by a subpopulation of natural killer (NK) cells, bind certain class I major histocompatibility complexes (MHC), and act as a negative regulator of lytic activity. The expression patterns and functional activities of the other Ly-49s, however, is unknown. We extended the study of this family by isolating cDNAs encoding two new Ly-49 molecules. The reactivity of these and previously identified Ly-49 molecules with NK antibodies was tested in a COS cell expression system. YE1/32 and YE1/48 bound Ly-49A specifically, and 5E6 reacted only with Ly-49C. Three-color flow cytometric analysis demonstrated Ly-49A and Ly-49C expression defines complex, but distinct subsets within NK1.1+ cells. Some NK1.1-CD3+ as well as NK1.1-CD3- cells expressing Ly-49A or C were also detected. Analysis of MHC congenic strains of mice demonstrated that YE1/32+ and YE1/48+ NK cells are not deleted, as has been shown with the Ly-49A mAb A1. Furthermore, COS cells transfected with Ly-49A bound H-2d and H-2k cell lines, whereas Ly-49C transfectants bound H-2d, H-2k, H-2b, and H-2s. The antibodies 5E6 and 34-1-2S (anti-class I MHC) inhibited the binding of Ly-49C to an H-2s cell line. These results imply that the NK cell antigens Ly-49A and C bind to different repertoires of class I MHC molecules.

Recognition of class I major histocompatibility complex molecules by Ly-49: specificities and domain interactions.

Ly-49 is a family type II transmembrane proteins encoded by a gene cluster on murine chromosome 6. One member of this family, Ly-49A, is expressed by a natural killer (NK) cell subset, binds to class I major histocompatibility complex (MHC) molecules, and blocks the killing of target cells bearing the appropriate H-2 antigens. Here we show that another member of this family which is expressed by an NK cell subset, Ly-49C, recognizes H-2b and H-2d structures which are distinct from and overlapping with those recognized by Ly-49A. Interactions between Ly-49A and C and their class I ligands are entirely blocked by the antibodies 5E6, YE1/48, YE1/32, and A1, all of which were found to recognize epitopes contained within the carbohydrate recognition domain (CRD). However, cell-cell binding assays revealed that class I binding specificity is conferred by a combination of sequences within both the CRD and a 19-amino acid adjacent region. We also investigated the question of whether Ly-49A and C form dimers on cells which express both receptors. When coexpressed on COS cells, sequential immunoprecipitation demonstrated that these receptors pair exclusively as homodimers, with no evidence for heterodimeric structures. These observations provide insight into both the biochemical nature of the Ly-49 family as well as the receptor functions of Ly-49C on NK cells.

Heterogeneity among Ly-49C natural killer (NK) cells: characterization of highly related receptors with differing functions and expression patterns.

Ly-49C is a member of the polymorphic family of murine NK cell inhibitory receptors. The 5E6 antibody that defines a subset of NK cells responsible for the rejection of parental H-2d bone marrow by F1 mice has been shown previously to react with Ly-49C. Here, the 5E6 antibody was found to detect two Ly-49C-related molecules in B6 mice. Two cDNA clones were isolated from B6 NK cells, one identical to previously reported Ly-49CB6 and the other a novel cDNA. The deduced amino acid sequence of the latter differs from that of Ly-49CBALB at only 4 residues, whereas the previously reported Ly-49CB6 differs at 22 residues. Flow cytometric analyses of COS cells transfected with the two cDNAs showed that the 5E6 antibody binds to both Ly-49 molecules, while another anti-Ly-49C antibody, 4LO3311, binds to the newly described Ly-49C but not the previously reported Ly-49CB6. Two-color flow cytometric analysis detected 5E6+4LO3311- as well as 5E6+4LO3311+ subsets of NK cells from B6, but not BALB/c, mice. The level of Ly-49C expression on B6 NK cells detected by the 4LO3311 antibody was substantially lower than that on BALB/c NK cells. Binding specificity of the novel Ly-49CB6 was indistinguishable from that of Ly-49CBALB, whereas no binding was detectable with previously reported Ly-49CB6. These results demonstrate that the newly described Ly-49CB6, not the previously reported Ly-49CB6, is the probable B6 allelic form of Ly-49C. The previously reported Ly-49CB6 must be encoded by a separate gene and should be renamed Ly-49I. The implication of these results with respect to the role of Ly-49C in hybrid resistance is discussed.

Pharmacokinetics and metabolism of (R,R)-methoxyfenoterol in rat.

(R,R)-fenoterol (Fen), a beta(2)-adrenoceptor agonist, is under clinical investigation in the treatment of congestive heart disease. The pharmacokinetics and metabolism of the 4-methoxyphenyl derivative of (R,R)-Fen, (R,R)-MFen, have been determined following intravenous and oral administration to the rat and compared with corresponding results obtained with (R,R)-Fen. Results from the study suggest that (R,R)-MFen can offer pharmacokinetic and metabolic advantages in comparison to an earlier (R,R)-Fen. The oral administration revealed that the net exposure of (R,R)-MFen was about three-fold higher than that of (R,R)-Fen (7.2 versus 2.3 min x nmol ml(-1)), while intravenous administration proved that the clearance was significantly reduced, 48 versus 146 ml min(-1) kg(-1), the T(1/2) was significantly longer, 152.9 versus 108.9 min, and the area under the curve (AUC) was significantly increased, 300 versus 119 min x nmol ml(-1). (R,R)-MFen was primarily cleared by glucuronidation associated with significant presystemic glucuronidation of the compound. After intravenous and oral administration of (R,R)-MFen, (R,R)-Fen and (R,R)-Fen-G were detected in the urine samples indicating that (R,R)-MFen was O-demethylated and subsequently conjugated to (R,R)-Fen-G. The total (R,R)-Fen and (R,R)-Fen-G as a percentage of the dose after intravenous administration was 3.6%, while after oral administration was 0.3%, indicating that only a small fraction of the drug escaped presystemic glucuronidation and was available for O-demethylation. The glucuronidation pattern was confirmed by the results from in vitro studies where incubation of (R,R)-MFen with rat hepatocytes produced (R,R)-MFen-G, (R,R)-Fen and (R,R)-Fen-G, while incubation with rat intestinal microsomes only resulted in the formation of (R,R)-MFen-G.

Reporting on outcome measures in pediatric chronic intestinal failure: A systematic review.

BACKGROUND & AIMS: Chronic intestinal failure (IF) in children is a rare and heterogeneous disease requiring treatment with parenteral nutrition. A uniform definition for chronic IF and standardized outcome measures to compare therapeutic trials in these children are lacking. Therefore, the aim of this study is to systematically assess how definitions and outcome measures are defined in therapeutic trials of children with chronic IF. METHODS: MEDLINE, EMBASE, and Cochrane Central Register of Controlled Trials (CENTRAL) databases were searched from inception till August 2018. No language restriction was used. RESULTS: A total of 1766 articles was found of which 70 studies fulfilled our inclusion criteria. 54 studies (76%) did not report any definition of IF. Of the 16 studies (23%) which reported a definition of IF, 7 different definitions were found. The two most frequently used definitions were: (1) the inability to absorb adequate nutrients to maintain body weight or normal growth and development (n = 5), and (2) the dependence upon parenteral nutrition to maintain minimal energy requirements for growth and development (n = 5). A total of 117 different outcomes were reported. The three most reported outcome measures were: mortality (n = 27), liver enzymes (alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase, and gamma-glutamyl trans peptidase) (n = 27), and growth (n = 23). Quality of reporting was considered fair to poor in most studies. CONCLUSION: There is a lack of reported definitions in studies concerning pediatric IF. Heterogeneity exists in outcome reporting in research concerning pediatric chronic IF. Therefore, we recommend the development of a core outcome set.

Keeping active endogenous retroviral-like elements in check: the epigenetic perspective.

Endogenous retrovirus-like elements, or ERVs, are an abundant component of all eukaryotic genomes. Their transcriptional and retrotranspositional activities have great potential for deleterious effects on gene expression. Consequences of such activity may include germline mutagenesis and cancerous transformation. As a result, mammalian genomes have evolved means of counteracting ERV transcription and mobilization. In this review, we discuss epigenetic mechanisms of ERV and LTR retrotransposon control during mouse development, focusing on involvement of DNA methylation, histone modifications, small RNAs and their interaction with one another. We also address relevance of research performed in the mouse system to human and challenges associated with studying repetitive families. (Part of a multi-author review).

Effects of branched chain amino acid supplementation on patient care outcomes in adults and children with liver cirrhosis: A systematic review.

BACKGROUND & AIMS: Malnutrition is highly prevalent in chronic liver disease (CLD) due to alterations in nutrient utilization, malabsorption and poor intake. Low serum concentrations of branched chain amino acids (BCAA) in the presence of elevated aromatic acid concentrations is commonly observed in adult and children with liver cirrhosis and is associated with malnutrition and other adverse patient outcomes. The efficacy of BCAA supplementation has not been well established in adults and children with CLD. The purpose of this review was to critically evaluate the literature regarding the impact of BCAA supplementation related to changes in body composition, muscle strength, liver biomarkers, medical and hepatic complications (hepatic encephalopathy (HE), ascites, edema) and patient care outcomes (event free survival, health related quality of life, length of hospitalization). METHODS: A total of 40 articles retrieved from PubMed or Web of Science databases (1989-2017) were included. RESULTS: BCAA supplementation may be beneficial in improving muscle strength, ascites and edema with potential clinically significant improvements in HE in adult liver patients. In children, limited data have shown that BCAA supplementation may exert favourable effects on weight, fat mass, fat free mass and serum albumin level. CONCLUSIONS: Heterogeneity of study findings attributed to variability in BCAA dose (total, relative proportions), duration, disease severity and lack of uniformity in tools used for assessing patient outcomes limit overall conclusions. Longitudinal studies examining the efficacy of BCAA supplementation as a therapeutic treatment of malnutrition in chronic liver disease is warranted.

Vitamin D status and risk for sarcopenia in youth with inflammatory bowel diseases.

Suboptimal vitamin D (vitD) status and reduced lean body mass are highly prevalent in pediatric inflammatory bowel diseases (IBD). The study objective was to determine sarcopenia prevalence and associations with vitD status in newly diagnosed pediatric IBD. Children with Crohn's disease (CD; n = 58) and ulcerative colitis (UC; n = 27) were included. Primary outcomes included body composition (total/regional/percent fat mass (FM), fat-free mass (FFM), skeletal muscle mass (SMM)), and vitD status (serum 25(OH)D). Sarcopenia was defined as SMM-z < -2. Additional variables measured included serum CRP, ESR, anthropometric, Pediatric Crohn's Disease Activity Index (PCDAI), and the Pediatric Ulcerative Colitis Disease Activity index (PUCAI). Sarcopenia and suboptimal 25(OH)D levels (< 50 nmol/l) were found in 23.5% (n = 20) and 52% (n = 44) of children, respectively. Younger children (< 13 years) with CD with suboptimal 25(OH)vitD (< 50 nmol/l) had the greatest frequency of sarcopenia (57.1%) (p = 0.004). Sarcopenia was prevalent in newly diagnosed, young children with CD with vitD deficiency.

Evolution of natural killer cell receptors: coexistence of functional Ly49 and KIR genes in baboons.

Natural killer (NK) cells represent an important first line of defense against viruses and malignancy [1]. NK cells express a variety of inhibitory and activating receptors that interact with classical major histocompatibility complex (MHC) class I molecules on potential target cells and determine the NK cell response [2-4]. Mouse NK receptors are encoded by the C-type lectin multigene family Ly49. However, in humans, a completely different family of receptors, the immunoglobulin-like killer inhibitory receptors (KIRs), performs the same function [2-4]. One Ly49-like gene, Ly49L, exists in humans but is incorrectly spliced and assumed to be nonfunctional [5, 6]. Mouse KIR-like genes have not been found, and evidence suggests that the primate KIRs amplified after rodents and primates diverged [7, 8]. Thus, two structurally dissimilar families, Ly49 and KIR, have evolved to play similar roles in mouse and human NK cells. This apparent example of functional convergent evolution raises several questions. It is unknown, for example, when the Ly49L gene became nonfunctional and if this event affected the functional evolution of the KIRs. The distribution of these gene families in different mammals is unstudied, and it is not known if any species uses both types of receptors. Here, we demonstrate that the Ly49L gene shows evidence of conservation in other mammals and that the human gene likely became nonfunctional 6-10 million years ago. Furthermore, we show that baboon lymphocytes express both full-length Ly49L transcripts and multiple KIR genes.

A phase I clinical and pharmacokinetic study of the multi-drug resistance protein-1 (MRP-1) inhibitor sulindac, in combination with epirubicin in patients with advanced cancer.

PURPOSE: Multi-drug resistance mediated by ATP-binding cassette trans-membrane protein pumps is an important cause of cancer treatment failure. Sulindac has been shown to be a competitive substrate for the clinically important resistance protein, multi-drug resistance protein-1 (MRP-1), and thus might enhance the anti-cancer activity of substrate chemotherapeutic agents, e.g. anthracyclines. METHODS: We conducted a dose-escalating, single arm, prospective, open label, non-randomised phase I trial of epirubicin (75 mg/m(2)) in combination with escalating oral doses of sulindac (0-800 mg) in patients with advanced cancer to identify an appropriate dose of sulindac to use in future resistance studies. Anthracycline and sulindac pharmacokinetics were studied in cycles 1 and 3. RESULTS: Seventeen patients (8 breast, 3 lung, 2 bowel, 1 melanoma, 1 renal, 1 ovarian and 1 of unknown primary origin, 16/17 having had prior chemotherapy) were enrolled. Eight patients received a full six cycles of treatment; 14 patients received three or more cycles. Dose-limiting toxicity was observed in two patients at 800 mg sulindac (1 renal impairment, 1 fatal haemoptysis in a patient with advanced lung cancer), and sulindac 600 mg was deemed to be the maximum tolerated dose. Sulindac had no effect on epirubicin pharmacokinetics. Among 15 patients with evaluable tumour, two partial responses were seen (malignant melanoma and breast cancer). Four others had prolonged stable disease. CONCLUSION: Epirubicin 75 mg/m(2) and sulindac 600 mg are the recommended doses for phase II studies for these agents in combination.

The coordinate replication of the human beta-globin gene domain reflects its transcriptional activity and nuclease hypersensitivity.

The temporal order of replication of DNA sequences in the chromosomal domain containing the human beta-globin gene cluster and its flanking sequences (140 kilobases) was measured and compared in two different human cell lines. In human erythroleukemia (K562) cells, in which embryonic and fetal globin genes are transcribed, all of the sequences we examined from the beta-globin domain replicated early during S phase, while in HeLa cells, in which globin genes are transcriptionally silent, these sequences replicated late during S. Potential sites of initiation of DNA replication within this domain were identified. The beta-globin gene domain was also found to differ with respect to the nuclease sensitivity of the chromatin in these two cell lines. In K562 cells, hypersensitive sites for endogenous nucleases and DNase I were present in the chromatin near the earliest-replicating segments in the beta-globin domain.

Clonal analysis of the late stages of erythroleukemia induced by two distinct strains of Friend leukemia virus.

We observed striking differences between the tumorigenic colony-forming cells present in the spleens of mice late after infection with the anemia-inducing strain of Friend leukemia virus (strain FV-A) and those present after infection with the polycythemia-inducing strain (strain FV-P). Cells within primary colonies derived from FV-A- and FV-P-transformed cells (CFU-FV-A and CFU-FV-P, respectively) contained hemoglobin and spectrin, indicating that the CFU-FV-A and CFU-FV-P were transformed erythroid progenitor cells. The proportion of cells containing hemoglobin was relatively high (> 25%) in newly isolated cell lines derived from CFU-FV-P colonies, whereas cell lines derived from CFU-FV-A colonies had only low levels (0 to 2%) of hemoglobin-containing cells. A high proportion of the cell lines derived from CFU-FV-A colonies responded to pure erythropoietin and accumulated spectrin and hemoglobin, whereas the cell lines derived from CFU-FV-P colonies did not. A cytogenetic analysis indicated that primary CFU-FV-P colony cells were diploid, whereas chromosomal aberrations were observed in the immediate progeny of CFU-FV-A. The presence of unique chromosomal markers in the majority of the cells within individual colonies derived from CFU-FV-A suggested that these colonies originated from single cells. Finally, leukemic progenitor cells transformed by strain FV-A appeared to have an extensive capacity to self-renew (i.e., form secondary colonies in methylcellulose), whereas a significant proportion of the corresponding cells transformed by strain FV-P did not. In addition, the self-renewal capacity of both CFU-FV-A and CFU-FV-P increased as the disease progressed. From these observations, we propose a model for the multistage nature of Friend disease; this model involves clonal evolution and expansion from a differentiating population with limited proliferative capacity to a population with a high capacity for self-renewal and proliferation.

Translocation of an erythroid-specific hypersensitive site in deletion-type hereditary persistence of fetal hemoglobin.

Hereditary persistence of fetal hemoglobin (HPFH) can involve large deletions which eliminate the 3' end of the beta-like globin gene cluster and more than 70 kilobases (kb) of flanking DNA. Blot hybridization revealed a DNase I-hypersensitive site extending from 1.1 to 1.4 kb downstream of the HPFH-1 3' deletion endpoint. The site was found in normal fetal and adult nucleated erythroid cells and in two erythroleukemia cell lines but not in nonerythroid cells and tissues. Simian virus 40 core enhancer-like sequences were found nonrandomly distributed within the boundaries of the site, which is contained in a fragment of known enhancer activity (E. A. Feingold and B. G. Forget, Blood, in press). A second hypersensitive site was found 0.5 kb upstream of the HPFH-1 3' deletion endpoint but was not erythroid specific. A third site, most prominent in fetal liver-derived erythroid cells, was found 1 kb upstream of the HPFH-2 deletion endpoint. As predicted by the locations of the deletion endpoints, the first two sites were translocated to within 12 kb of the A gamma gene in erythroid colonies derived from an HPFH-2 heterozygote and in hybrid mouse-human erythroid cells carrying the HPFH-2 deletion chromosome. Further analysis of this region showed that it was DNase I sensitive in erythroid and myeloid cells, indicating that it resides in an open chromatin domain. These observations suggest that alterations of chromatin structure flanking the fetal globin genes may contribute to abnormal gene regulation in deletion-type HPFH.

Novel functionalities of hybrid paper-polymer centrifugal devices for assay performance enhancement.

The presented work demonstrates novel functionalities of hybrid paper-polymer centrifugal devices for assay performance enhancement that leverage the advantages of both paper-based and centrifugal microfluidic platforms. The fluid flow is manipulated by balancing the capillary force of paper inserts with the centrifugal force generated by disc rotation to enhance the signal of a colorimetric lateral flow immunoassay for pathogenic E. coli. Low-cost centrifugation for pre-concentration of bacteria was demonstrated by sample sedimentation at high rotational speeds before supernatant removal by a paper insert via capillary force after deceleration. The live bacteria capture efficiency of the device was similar to a commercial centrifuge. This pre-concentrated sample when combined with gold nanoparticle immunoconjugate probes resulted in a detection limit that is 10× lower than a non-concentrated sample for a lateral flow immunoassay. Signal enhancement was also demonstrated through rotational speed variation to prevent the flow for on-device incubation and to reduce the flow rate, thus increasing the sample residence time for the improved capture of gold nanoparticle-bacteria complexes in an integrated paper microfluidic assay. Finally, multiple sequential steps including sample pre-concentration, filtration, incubation, target capture by an integrated paper microfluidic assay, silver enhancement and quenching, and index matching were completed within a single device. The detection limit was 105 colony forming units per ml, a 100× improvement over a similar paper-based lateral flow assay. The techniques utilize the advantages of paper-based microfluidic devices, while facilitating additional functionalities with a centrifugal microfluidic platform for detection performance enhancement in a low-cost, automated platform amenable to point-of-care environments.

Bacteria and cancer: cause, coincidence or cure? A review.

Research has found that certain bacteria are associated with human cancers. Their role, however, is still unclear. Convincing evidence links some species to carcinogenesis while others appear promising in the diagnosis, prevention or treatment of cancers. The complex relationship between bacteria and humans is demonstrated by Helicobacter pylori and Salmonella typhi infections. Research has shown that H. pylori can cause gastric cancer or MALT lymphoma in some individuals. In contrast, exposure to H. pylori appears to reduce the risk of esophageal cancer in others. Salmonella typhi infection has been associated with the development of gallbladder cancer; however S. typhi is a promising carrier of therapeutic agents for melanoma, colon and bladder cancers. Thus bacterial species and their roles in particular cancers appear to differ among different individuals. Many species, however, share an important characteristic: highly site-specific colonization. This critical factor may lead to the development of non-invasive diagnostic tests, innovative treatments and cancer vaccines.