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2.
Database (Oxford) ; 20232023 03 30.
Article in English | MEDLINE | ID: mdl-36999559

ABSTRACT

There is an urgent need for high-quality biodiversity data in the context of rapid environmental change. Nowhere is this need more urgent than in the deep ocean, with the possibility of seabed mining moving from exploration to exploitation, but where vast knowledge gaps persist. Regions of the seabed beyond national jurisdiction, managed by the International Seabed Authority (ISA), are undergoing intensive mining exploration, including the Clarion-Clipperton Zone (CCZ) in the Central Pacific. In 2019, the ISA launched its database 'DeepData', publishing environmental (including biological) data. Here, we explore how DeepData could support biological research and environmental policy development in the CCZ (and wider ocean regions) and whether data are findable, accessible, interoperable and reusable (FAIR). Given the direct connection of DeepData with the regulator of a rapidly developing potential industry, this review is particularly timely. We found evidence of extensive duplication of datasets; an absence of unique record identifiers and significant taxonomic data-quality issues, compromising FAIRness of the data. The publication of DeepData records on the OBIS ISA node in 2021 has led to large-scale improvements in data quality and accessibility. However, limitations in the usage of identifiers and issues with taxonomic information were also evident in datasets published on the node, stemming from mismapping of data from the ISA environmental data template to the data standard Darwin Core prior to data harvesting by OBIS. While notable data-quality issues remain, these changes signal a rapid evolution for the database and significant movement towards integrating with global systems, through the usage of data standards and publication on the global data aggregator OBIS. This is exactly what has been needed for biological datasets held by the ISA. We provide recommendations for the future development of the database to support this evolution towards FAIR. Database URL https://data.isa.org.jm/isa/map.


Subject(s)
Biodiversity , United Nations , Oceans and Seas
3.
Clin Epigenetics ; 13(1): 21, 2021 01 28.
Article in English | MEDLINE | ID: mdl-33509276

ABSTRACT

BACKGROUND: Acute leukemia is an epigenetically heterogeneous disease. The intensity of treatment is currently guided by cytogenetic and molecular genetic risk classifications; however these incompletely predict outcomes, requiring additional information for more accurate outcome predictions. We aimed to identify potential prognostic implications of epigenetic modification of histone proteins, with a focus on H3K4 and H3K27 methylation marks in relation to mutations in chromatin, splicing and transcriptional regulators in adult-onset acute lymphoblastic and myeloid leukemia. RESULTS: Histone 3 lysine 4 di- and trimethylation (H3K4me2, H3K4me3) and lysine 27 trimethylation (H3K27me3) mark expression was evaluated in 241 acute myeloid leukemia (AML), 114 B-cell acute lymphoblastic leukemia (B-ALL) and 14T-cell ALL (T-ALL) patient samples at time of diagnosis using reverse phase protein array. Expression levels of the marks were significantly lower in AML than in B and T-ALL in both bone marrow and peripheral blood, as well as compared to normal CD34+ cells. In AML, greater loss of H3K27me3 was associated with increased proliferative potential and shorter overall survival in the whole patient population, as well as in subsets with DNA methylation mutations. To study the prognostic impact of H3K27me3 in the context of cytogenetic aberrations and mutations, multivariate analysis was performed and identified lower H3K27me3 level as an independent unfavorable prognostic factor in all, as well as in TP53 mutated patients. AML with decreased H3K27me3 demonstrated an upregulated anti-apoptotic phenotype. In ALL, the relative quantity of histone methylation expression correlated with response to tyrosine kinase inhibitor in patients who carried the Philadelphia cytogenetic aberration and prior smoking behavior. CONCLUSION: This study shows that proteomic profiling of epigenetic modifications has clinical implications in acute leukemia and supports the idea that epigenetic patterns contribute to a more accurate picture of the leukemic state that complements cytogenetic and molecular genetic subgrouping. A combination of these variables may offer more accurate outcome prediction and we suggest that histone methylation mark measurement at time of diagnosis might be a suitable method to improve patient outcome prediction and subsequent treatment intensity stratification in selected subgroups.


Subject(s)
Histones/metabolism , Leukemia, Myeloid, Acute/genetics , Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics , Age of Onset , Aged , Antigens, CD34/metabolism , Case-Control Studies , Chromosome Aberrations/statistics & numerical data , DNA Methylation , Epigenomics , Female , Gene Expression Regulation, Leukemic/genetics , Histone Code/genetics , Histones/genetics , Humans , Jumonji Domain-Containing Histone Demethylases/genetics , Leukemia, Myeloid, Acute/blood , Leukemia, Myeloid, Acute/pathology , Male , Middle Aged , Mutation , Precursor Cell Lymphoblastic Leukemia-Lymphoma/blood , Precursor Cell Lymphoblastic Leukemia-Lymphoma/pathology , Prognosis , Protein Array Analysis/methods , Proteomics , Survival Rate , Transcription Factors/genetics
4.
Sci Total Environ ; 672: 815-833, 2019 Jul 01.
Article in English | MEDLINE | ID: mdl-30978544

ABSTRACT

Spatial variation in landscape attributes can account for much of the variability in water quality relative to land use on its own. Such variation results from the coupling between the dominant processes governing water quality, namely hydrological, redox, and weathering and gradients in key landscape attributes, such as topography, geology, and soil drainage. Despite the importance of 'process-attribute' gradients (PAG), few water quality models explicitly account for their influence. Here a processes-based water quality modelling framework is presented that more completely accounts for the role of landscape variability over water quality - Process-Attribute Mapping (PoAM). Critically, hydrochemical measures form the basis for the identification and mapping of effective landscape attributes, producing PAG maps that attempt to replicate the natural landscape gradients governing each dominant process. Application to the province of Southland (31,824 km2), New Zealand, utilised 12 existing geospatial datasets and a total of 28,626 surface water, groundwater, spring, soil water, and precipitation analyses to guide the identification and mapping of 11 individual PAG. The ability of PAGs to replicate regional hydrological, redox, and weathering gradients was assessed on the accuracy with which the hydrochemical indicators of each dominant process (e.g. hydrological tracers, redox indicators) were estimated across 93 long-term surface water monitoring sites (cross-validated R2 values of 0.75-0.95). Given hydrochemical evidence that PAGs replicate actual landscape gradients governing the dominant processes, they were combined with a land use intensity layer and used to estimate steady-state surface water quality. Cross-validated R2 values ranged between 0.81 and 0.92 for median total nitrogen, total oxidised nitrogen, total phosphorus and dissolved reactive phosphorus. Models of particulate species E. coli and total suspended sediment, although reasonable (R2 0.72-0.73), were less accurate, suggesting finer-grained land use, landscape attribute, and/or flow normalised measures are required to improve estimation.

5.
Leukemia ; 31(12): 2568-2576, 2017 12.
Article in English | MEDLINE | ID: mdl-28484265

ABSTRACT

While outcomes for children with T-cell acute lymphoblastic leukemia (T-ALL) have improved dramatically, survival rates for patients with relapsed/refractory disease remain dismal. Prior studies indicate that glucocorticoid (GC) resistance is more common than resistance to other chemotherapies at relapse. In addition, failure to clear peripheral blasts during a prednisone prophase correlates with an elevated risk of relapse in newly diagnosed patients. Here we show that intrinsic GC resistance is present at diagnosis in early thymic precursor (ETP) T-ALLs as well as in a subset of non-ETP T-ALLs. GC-resistant non-ETP T-ALLs are characterized by strong induction of JAK/STAT signaling in response to interleukin-7 (IL7) stimulation. Removing IL7 or inhibiting JAK/STAT signaling sensitizes these T-ALLs, and a subset of ETP T-ALLs, to GCs. The combination of the GC dexamethasone and the JAK1/2 inhibitor ruxolitinib altered the balance between pro- and anti-apoptotic factors in samples with IL7-dependent GC resistance, but not in samples with IL7-independent GC resistance. Together, these data suggest that the addition of ruxolitinib or other inhibitors of IL7 receptor/JAK/STAT signaling may enhance the efficacy of GCs in a biologically defined subset of T-ALL.


Subject(s)
Antineoplastic Agents/pharmacology , Drug Resistance, Neoplasm , Glucocorticoids/pharmacology , Interleukin-7/metabolism , Janus Kinases/metabolism , Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/metabolism , STAT Transcription Factors/metabolism , Signal Transduction/drug effects , Animals , Antineoplastic Agents/therapeutic use , Bcl-2-Like Protein 11/metabolism , Cell Line, Tumor , Dexamethasone/pharmacology , Disease Models, Animal , Humans , Janus Kinase Inhibitors/pharmacology , Mice , Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/drug therapy , Proto-Oncogene Proteins c-bcl-2/metabolism , Xenograft Model Antitumor Assays
6.
Pac Symp Biocomput ; 22: 485-496, 2017.
Article in English | MEDLINE | ID: mdl-27897000

ABSTRACT

Cancer metabolism differs remarkably from the metabolism of healthy surrounding tissues, and it is extremely heterogeneous across cancer types. While these metabolic differences provide promising avenues for cancer treatments, much work remains to be done in understanding how metabolism is rewired in malignant tissues. To that end, constraint-based models provide a powerful computational tool for the study of metabolism at the genome scale. To generate meaningful predictions, however, these generalized human models must first be tailored for specific cell or tissue sub-types. Here we first present two improved algorithms for (1) the generation of these context-specific metabolic models based on omics data, and (2) Monte-Carlo sampling of the metabolic model ux space. By applying these methods to generate and analyze context-specific metabolic models of diverse solid cancer cell line data, and primary leukemia pediatric patient biopsies, we demonstrate how the methodology presented in this study can generate insights into the rewiring differences across solid tumors and blood cancers.


Subject(s)
Models, Biological , Neoplasms/metabolism , Algorithms , Cell Line, Tumor , Child , Computational Biology , Humans , Leukemia/metabolism , Metabolic Networks and Pathways , Monte Carlo Method , Neoplasms/genetics , Proteomics
7.
Leukemia ; 31(6): 1314-1324, 2017 06.
Article in English | MEDLINE | ID: mdl-27872496

ABSTRACT

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy with a high incidence of relapse in pediatric ALL. Although most T-ALL patients exhibit activating mutations in NOTCH1, the cooperating genetic events required to accelerate the onset of leukemia and worsen disease progression are largely unknown. Here, we show that the gene encoding the transcription factor KLF4 is inactivated by DNA methylation in children with T-ALL. In mice, loss of KLF4 accelerated the development of NOTCH1-induced T-ALL by enhancing the G1-to-S transition in leukemic cells and promoting the expansion of leukemia-initiating cells. Mechanistically, KLF4 represses the gene encoding the kinase MAP2K7. Our results showed that in murine and pediatric T-ALL, loss of KLF4 leads to aberrant activation of MAP2K7 and of the downstream effectors JNK and ATF2. As a proof-of-concept for the development of a targeted therapy, administration of JNK inhibitors reduced the expansion of leukemia cells in cell-based and patient-derived xenograft models. Collectively, these data uncover a novel function for KLF4 in regulating the MAP2K7 pathway in T-ALL cells, which can be targeted to eradicate leukemia-initiating cells in T-ALL patients.


Subject(s)
Cell Proliferation/genetics , Kruppel-Like Transcription Factors/deficiency , MAP Kinase Kinase 7/metabolism , Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/pathology , Animals , Apoptosis , Child , Female , Humans , Kruppel-Like Factor 4 , MAP Kinase Kinase 7/genetics , Male , Mice , Mice, Inbred C57BL , Mice, Inbred NOD , Mice, Knockout , Mice, SCID , Mice, Transgenic , Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/genetics , Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/metabolism , Tumor Cells, Cultured
8.
Int J Obes (Lond) ; 37(9): 1192-7, 2013 Sep.
Article in English | MEDLINE | ID: mdl-23229737

ABSTRACT

OBJECTIVE: The roles that energy expenditure (EE) and nutrient oxidation play in a predisposition for weight gain in humans remains unclear. SUBJECTS: We measured EE and respiratory exchange ratio (RER) in non-obese obesity-prone (OP; n=22) and obesity-resistant (OR; n=30) men and women following a eucaloric (EU) diet and after 3 days of overfeeding (1.4 × basal energy). RESULTS: Twenty-four hour EE, adjusted for fat-free mass and sex, measured while consuming a EU diet was not different between OP and OR subjects (2367±80 vs 2285±98 kcals; P=0.53). Following overfeeding, EE increased in both OP and OR (OP: 2506±63.7, P<0.01; OR: 2386±99 kcals, P<0.05). Overfeeding resulted in an increase in 24-hour RER (OP: 0.857±0.01 to 0.893±0.01, P=0.01; OR: 0.852±0.01 to 0.886±0.01, P=0.005), with no difference between groups in either the EU or overfeeding conditions (P>0.05). Nighttime RER (∼10pm-6:30am) did not change with overfeeding in OR (0.823±0.02 vs 0.837±0.01, P=0.29), but increased significantly in OP subjects (0.798±0.15 to 0.839±0.15, P<0.05), suggesting that fat oxidation during the night was downregulated to a greater extent in OP subjects following a brief period of overfeeding, as compared with OR subjects who appeared to maintain their usual rate of fat oxidation. Protein oxidation increased significantly in both OP (P<0.001) and OR (P<0.01) with overfeeding, with no differences between OP and OR. CONCLUSION: These results support the idea that overfeeding a mixed diet results in increases in EE and RER, but these increases in EE and RER are likely not responsible for obesity resistance. Adaptive responses to overfeeding that occur during the night may have a role in opposing weight gain.


Subject(s)
Energy Intake , Energy Metabolism , Hyperphagia/metabolism , Obesity/metabolism , Overnutrition/metabolism , Weight Gain , Adult , Body Composition , Calorimetry, Indirect , Circadian Rhythm , Female , Humans , Hyperphagia/epidemiology , Hyperphagia/genetics , Male , Obesity/epidemiology , Obesity/genetics , Oxidation-Reduction , Thinness/metabolism , Time Factors , United States/epidemiology
9.
Pediatr Hematol Oncol ; 29(5): 415-23, 2012 Aug.
Article in English | MEDLINE | ID: mdl-22632168

ABSTRACT

Despite the favorable outcome of most pediatric patients with Hodgkin lymphoma (HL), there is rising concern about risks of carcinogenesis from both diagnostic and therapeutic radiation exposure for patients treated on study protocols. Although previous studies have investigated radiation exposure during treatment, radiation from post-treatment surveillance imaging may also increase the likelihood of secondary malignancies. All diagnostic imaging examinations involving ionizing radiation exposure performed for surveillance following completion of therapy were recorded for 99 consecutive pediatric patients diagnosed with HL from 2000 to 2010. Cumulative radiation dosage from these examinations and the frequency of relapse detection by these examinations were recorded. In the first 2 years following completion of therapy, patients in remission received a median of 11 examinations (range 0-26). Only 13 of 99 patients relapsed, 11 within 5 months of treatment completion. No relapse was detected by 1- or 2-view chest radiographs (n = 38 and 296, respectively), abdomen/pelvis computed tomography (CT) scans (n = 211), or positron emission tomography (PET) scans alone (n = 11). However, 10/391 (2.6%) of chest CT scans, 4/364 (1.1%) of neck CT scans, and 3/47 (6.4%) of PET/CT scans detected relapsed disease. Thus, only 17 scans (1.3%) detected relapse in a total of 1358 scans. Mean radiation dosages were 31.97 mSv for Stage 1, 37.76 mSv for Stage 2, 48.08 mSv for Stage 3, and 51.35 mSv for Stage 4 HL. Approximately 1% of surveillance imaging examinations identified relapsed disease. Given the very low rate of relapse detection by surveillance imaging stipulated by current protocols for pediatric HL patients, the financial burden of the tests themselves, the high cure rate, and risks of second malignancy from ionizing radiation exposure, modification of the surveillance strategy is recommended.


Subject(s)
Hodgkin Disease/diagnostic imaging , Positron-Emission Tomography/adverse effects , Radiation Dosage , Tomography, X-Ray Computed/adverse effects , Adolescent , Adult , Child , Child, Preschool , Female , Hodgkin Disease/therapy , Humans , Male , Positron-Emission Tomography/methods , Retrospective Studies , Tomography, X-Ray Computed/methods
10.
AJNR Am J Neuroradiol ; 33(9): 1825-31, 2012 Oct.
Article in English | MEDLINE | ID: mdl-22517278

ABSTRACT

BACKGROUND AND PURPOSE: Neurophysiological monitoring for neuroendovascular procedures typically involves EEG and SSEP monitoring via cutaneous electrodes. MEP monitoring has been used less frequently because, traditionally, this has required subdural electrode placement. With the advent of transcutaneous techniques, MEP monitoring use has increased. However, little has been published regarding the use of this technique in therapeutic neuroendovascular procedures. The purpose of this study was therefore to determine whether TcMEP monitoring is feasible and efficacious in therapeutic neuroendovascular procedures. MATERIALS AND METHODS: We retrospectively reviewed our data base of therapeutic neuroendovascular procedures performed with the use of TcMEP monitoring. We specifically determined the incidence of TcMEP changes compared with changes in either SSEP or EEG. We then correlated these changes to actual adverse neurologic events. RESULTS: Although TcMEP monitoring was technically successful in all of the 140 patients in which it was attempted, we observed significant changes in TcMEP signals in only 1 patient. This patient experienced changes involving all 3 monitoring modalities after intraprocedural aneurysm rupture. In contrast, changes in SSEP tracings alone were found in 9 patients. Of these, 2 patients were known to be moribund before their procedures and neither recovered. Among the remaining 7 patients, temporary SSEP changes tended to correlate with temporary neurologic deficits, while permanent changes were associated with permanent or long-lasting deficits. CONCLUSIONS: These results suggest that TcMEP monitoring is feasible in therapeutic neuroendovascular procedures. However, it appears that the addition of TcMEP monitoring provides no added benefit to SSEP and EEG monitoring alone.


Subject(s)
Cerebrovascular Disorders/diagnosis , Cerebrovascular Disorders/surgery , Evoked Potentials, Motor , Monitoring, Intraoperative/methods , Neurosurgical Procedures/methods , Vascular Surgical Procedures/methods , Adolescent , Adult , Aged , Aged, 80 and over , Child , Feasibility Studies , Female , Humans , Male , Middle Aged , Treatment Outcome , Young Adult
11.
Leukemia ; 26(2): 271-9, 2012 Feb.
Article in English | MEDLINE | ID: mdl-21844871

ABSTRACT

Although the cure rate of newly diagnosed acute lymphoblastic leukemia (ALL) has improved over the past four decades, the outcome for patients who relapse remains poor. New therapies are needed for these patients. Our previous global gene expression analysis in a series of paired diagnosis-relapse pediatric patient samples revealed that the antiapoptotic gene survivin was consistently upregulated upon disease relapse. In this study, we demonstrate a link between survivin expression and drug resistance and test the efficacy of a novel antisense agent in promoting apoptosis when combined with chemotherapy. Gene-silencing experiments targeting survivin mRNA using either short-hairpin RNA (shRNA) or a locked antisense oligonucleotide (LNA-ON) specifically reduced gene expression and induced apoptosis in leukemia cell lines. When used in combination with chemotherapy, the survivin shRNA and LNA-ON potentiated the chemotherapeutic antileukemia effect. Moreover, in a mouse primary xenograft model of relapse ALL, the survivin LNA-ON decreased survivin expression in a subset of animals, and produced a statistically significant decrease in tumor progression. Taken together, these findings suggest that targeting endogenous levels of survivin mRNA by LNA-ON methods may augment the response to standard chemotherapy by sensitizing otherwise resistant tumor cells to chemotherapy.


Subject(s)
Antineoplastic Agents/therapeutic use , Gene Knockdown Techniques , Inhibitor of Apoptosis Proteins/genetics , Precursor Cell Lymphoblastic Leukemia-Lymphoma/drug therapy , Base Sequence , DNA Primers , Humans , Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics , Precursor Cell Lymphoblastic Leukemia-Lymphoma/pathology , Reverse Transcriptase Polymerase Chain Reaction , Survivin , Treatment Outcome
12.
J Hand Surg Eur Vol ; 32(3): 256-61, 2007 Jun.
Article in English | MEDLINE | ID: mdl-17335948

ABSTRACT

This study investigated the relationship between socioeconomic deprivation and the incidence, patterns of injury, process of care and outcome of hand trauma using data collected prospectively on 1234 injuries presented during six months. The Index of Multiple Deprivation 2004 was derived from census data and postcodes. Socioeconomic deprivation is significantly associated with hand trauma. The odds ratio for suffering hand injuries in the most deprived quintile is 1.6 (SE 0.09 95% CI 1.45, 1.83) compared to the least deprived quintile. This is most marked among older children and adults. Fractures, sprains and ligament injuries showed the strongest association with the degree of deprivation. Injuries related to sport were not associated with deprivation. Surgical time utilised is greater in more deprived patients and their self reported physical outcome is worse. Hand surgery units working in areas of high socioeconomic deprivation will have higher trauma workloads and unit costs. Social deprivation may also influence physical outcomes.


Subject(s)
Hand Injuries/epidemiology , Social Class , Adolescent , Adult , Age Factors , Child , England , Female , Humans , Incidence , Male , Middle Aged , Socioeconomic Factors
13.
Mar Pollut Bull ; 54(3): 253-65, 2007 Mar.
Article in English | MEDLINE | ID: mdl-17266994

ABSTRACT

This paper identifies and defines ecosystem goods and services provided by marine biodiversity. Case studies have been used to provide an insight into the practical issues associated with the assessment of marine ecosystem goods and services at specific locations. The aim of this research was to validate the definitions of goods and services, and to identify knowledge gaps and likely difficulties of quantifying the goods and services. A validated theoretical framework for the assessment of goods and services is detailed, and examples of the goods and services at a variety of case study areas are documented. These results will enable future assessments of marine ecosystem goods and services. It is concluded that the utilisation of this goods and services approach has the capacity to play a fundamental role in the Ecosystem Approach, by enabling the pressures and demands of society, the economy and the environment to be integrated into environmental management.


Subject(s)
Biodiversity , Conservation of Natural Resources/economics , Marine Biology/economics , Animals , Biodegradation, Environmental , Climate , Culture , Europe , Food , Food Chain , Gases , Humans , Oceans and Seas , Recreation
14.
J Hand Surg Eur Vol ; 32(2): 130-4, 2007 Apr.
Article in English | MEDLINE | ID: mdl-17234311

ABSTRACT

This study evaluated the flexor digitorum profundus quadriga effect by mimicking stiffness of one finger and observing its effect on the strengths of the other three fingers of the same hand. Thermoplastic wedges were used to simulate mild, moderate and severe stiffness of each finger and the individual strengths of each finger during power grip were measured using a digit-grip(TM) dynamometer in ten healthy adult volunteers. Middle, ring, and little fingers strength diminished significantly (P<0.05) when each of the other fingers, including the index, was stiffened. Index finger strength was largely unaffected by simulated stiffness of the other fingers. The degree of simulated stiffness influenced the strength of the other fingers, but there was considerable intersubject variability, suggesting that the significance of the quadriga effect varies between individuals. An anatomical basis for our findings is suggested.


Subject(s)
Hand Strength/physiology , Tendons/physiopathology , Adult , Female , Finger Joint/physiopathology , Humans , Male , Middle Aged , Muscle Strength Dynamometer , Tissue Adhesions/physiopathology
15.
Clin Pharmacol Ther ; 81(1): 42-9, 2007 Jan.
Article in English | MEDLINE | ID: mdl-17185998

ABSTRACT

Interindividual pharmacokinetic variability of the anticancer agent irinotecan is high. Life-threatening diarrhea is observed in up to 25% of patients receiving irinotecan and has been related with irinotecan pharmacokinetics and UGT1A1 genotype status. Here, we explore the association of ABCC2 (MRP2) polymorphisms and haplotypes with irinotecan disposition and diarrhea. A cohort of 167 Caucasian cancer patients who were previously assessed for irinotecan pharmacokinetics (90-min infusion given every 21 days), toxicity, and UGT1A1*28 genotype were genotyped for polymorphisms in ABCC2 using Pyrosequencing. Fifteen ABCC2 haplotypes were identified in the studied patients. The haplotype ABCC2*2 was associated with lower irinotecan clearance (28.3 versus 31.6 l/h; P=0.020). In patients who did not carry a UGT1A1*28 allele, a significant reduction of severe diarrhea was noted in patients with the ABCC2*2 haplotype (10 versus 44%; odds ratio, 0.15; 95% confidence interval, 0.04-0.61; P=0.005). This effect was not observed in patients with at least one UGT1A1*28 allele (32 versus 20%; odds ratio, 1.87; 95% confidence interval, 0.49-7.05; P=0.354). This study suggests that the presence of the ABCC2*2 haplotype is associated with less irinotecan-related diarrhea, maybe as a consequence of reduced hepatobiliary secretion of irinotecan. As the association was seen in patients not genetically predisposed at risk for diarrhea due to UGT1A1*28, confirmatory studies of the relationships of ABCC2 genotypes and irinotecan disposition and toxicity are warranted.


Subject(s)
Antineoplastic Agents, Phytogenic/adverse effects , Antineoplastic Agents, Phytogenic/pharmacokinetics , Camptothecin/analogs & derivatives , Diarrhea/chemically induced , Membrane Transport Proteins/genetics , Multidrug Resistance-Associated Proteins/genetics , Adult , Aged , Alleles , Antineoplastic Agents, Phytogenic/pharmacology , Camptothecin/adverse effects , Camptothecin/pharmacokinetics , Camptothecin/pharmacology , Female , Glucuronosyltransferase/genetics , Humans , Irinotecan , Male , Middle Aged , Multidrug Resistance-Associated Protein 2 , Polymorphism, Single Nucleotide
16.
Clin Pharmacol Ther ; 81(1): 76-82, 2007 Jan.
Article in English | MEDLINE | ID: mdl-17186002

ABSTRACT

To explore retrospectively the relationships between paclitaxel pharmacokinetics and three known, non-synonymous single-nucleotide polymorphisms (SNPs) in SLCO1B3, the gene encoding organic anion transporting polypeptide (OATP)1B3. Accumulation of [(3)H]paclitaxel was studied in Xenopus laevis oocytes injected with cRNA of Oatp1b2, OATP1A2, OATP1B1, OATP1B3, OAT1, OAT3, OCT1, and NTCP. The 334T>G (Ser112Ala), 699G>A (Met233Ile), and 1564G>T (Gly522Cys) loci of SLCO1B3 were screened in 475 individuals from five ethnic groups and 90 European Caucasian cancer patients treated with paclitaxel. Only OATP1B3 was capable of transporting paclitaxel to a significant extent (P=0.003). The 334T>G and 699G>A SNPs were less common in the African-American and Ghanaian populations (P<0.000001). Paclitaxel pharmacokinetics were not associated with the studied SNPs or haplotypes (P>0.3). The studied SNPs in SLCO1B3 appear to play a limited role in the disposition of paclitaxel, although their clinical significance in other ethnic populations remains to be investigated.


Subject(s)
Antineoplastic Agents, Phytogenic/pharmacokinetics , Organic Anion Transporters, Sodium-Independent/genetics , Paclitaxel/pharmacokinetics , Racial Groups , Animals , Dose-Response Relationship, Drug , Female , Genotype , Humans , In Vitro Techniques , Oocytes , Polymorphism, Single Nucleotide , Retrospective Studies , Solute Carrier Organic Anion Transporter Family Member 1B3 , Xenopus laevis
17.
Plant Dis ; 91(3): 326, 2007 Mar.
Article in English | MEDLINE | ID: mdl-30780580

ABSTRACT

Characteristic Ascochyta blight lesions were observed on leaves and pods of wild pea (Pisum elatius Steven. ex M. Bieb.) growing at three sites in the Republic of Georgia during June and July of 2004. Site characteristics were 41°36.11'N, 44°31.34'E (elevation 919 m), 41°54.221'N, 44°05.667'E (elevation 744 m), and 41°44.907'N, 43°12.263'E (elevation 884 m). Lesions appeared similar to those induced by Ascochyta pisi Lib. on cultivated pea (P. sativum L.). Fungi were isolated by surface disinfesting small pieces of infected tissue in 95% EtOH for 10 s, 1% NaOCl for 1 min, and then in deionized sterile H20 for 1 min. Tissue pieces were placed on 3% water agar (WA) for 24 h under fluorescent lights with a 12-h photoperiod to induce sporulation. Single-conidial isolations were made by streaking conidia on 3% WA and picking germinated conidia 18 h later. Three fungi (isolates Georgia-6, -7, and -12) had colony morphology similar to that of A. pisi on V8 juice agar. Conidial suspensions (1 × 105 conidia/ml) of each isolate above were spray inoculated to runoff on three genotypes of 2-week-old P. elatius plants. Plants inoculated included PI lines 560055 and 513252 and W6 line 15006 from the USDA Western Region Plant Introduction Station, Pullman, WA with 11 replicate plants inoculated per isolate. Plants were incubated in a growth chamber for 48 h at 18°C and covered with a plastic cup to maintain high humidity. Characteristic Ascochyta blight lesions were apparent 7 days after inoculation. DNA was extracted from each isolate and 610 bp of the glyceraldehyde-3-phosphate-dehydrogenase gene (G3PD), 364 bp of chitin synthase 1, and 330 bp of the translation elongation factor 1-alpha gene were amplified with gpd-1 and gpd-2 primers (1), CHS-79 and CHS-354 primers (2), and EF1-728F and EF1-986R primers (2), respectively. Amplicons were direct sequenced on both strands, and BLAST searches of the NCBI nucleotide database with consensus G3PD, CHS, and EF sequences of isolates Georgia-6, -7, and -12 were performed. The closest match obtained for the G3PD sequences was A. pisi isolate ATCC 201617 (Accession No. DQ383963). G3PD sequences for Georgia-6, -7, and -12 were deposited in GenBank (Accession Nos. DQ383966 [Georgia-6 and -7] and DQ383963 [A. pisi isolate AP1 and Georgia-12]). Closest matches to CHS and EF sequences were A. pisi isolate ATCC 201618 (EF Accession No. DQ386494) and Didymella fabae isolate ATCC 96418 (CHS Accession No. DQ386481, EFAccession No. DQ386492), respectively. CHS sequences for Georgia-6, -7, and -12 were identical to each other and to A. fabae isolate AF1 and were deposited in GenBank (Accession No. DQ386481. EF sequences for Georgia-6, -7, and -12 were deposited in GenBank (Accession Nos. DQ386494 [Georgia-6 and A. pisi isolate AP2], DQ386495, and DQ386496, respectively. These results, coupled with the morphological identification and inoculation results, confirm the identity of the fungus as A. pisi. To our knowledge, this is the first report of Ascochyta blight of P. elatius in the Republic of Georgia. References: (1) M. L. Berbee et al. Mycologia 91:964. 1999. (2) I. Carbone and L. M. Kohn. Mycologia 91:553, 1999.

18.
Med J Malaysia ; 61 Suppl A: 91-3, 2006 Feb.
Article in English | MEDLINE | ID: mdl-17042239

ABSTRACT

We report a case of a 55-year-old man who presented with a 6-month history of a fungating ulcer on the right hand at the site of a previously healed ulcer that had been present for 40 years. Histopathological examination of four-quadrant biopsy specimens showed a moderately differentiated squamous cell carcinoma (SCC). A transradiocarpal amputation with stump closure using radial flap was performed as it was not possible to achieve a functionally and cosmetically acceptable hand after a wide excision with 2 cm tumour-free margin. It is our intention to highlight this rare condition as reminder to consider this entity as a differential diagnosis of chronic non-healing skin ulcer.


Subject(s)
Carcinoma, Squamous Cell/diagnosis , Skin Neoplasms/diagnosis , Skin Ulcer/diagnosis , Acro-Osteolysis/diagnosis , Acro-Osteolysis/etiology , Acro-Osteolysis/surgery , Carcinoma, Squamous Cell/etiology , Carcinoma, Squamous Cell/surgery , Diagnosis, Differential , Hand/pathology , Humans , Male , Middle Aged , Risk Assessment , Risk Factors , Skin Neoplasms/etiology , Skin Neoplasms/surgery , Skin Ulcer/etiology , Skin Ulcer/surgery , Syndrome
19.
J Neuroendocrinol ; 18(5): 339-48, 2006 May.
Article in English | MEDLINE | ID: mdl-16629832

ABSTRACT

Siberian hamsters (Phodopus sungorus) undergo reproductive involution following exposure to short winter day lengths. Following approximately 20 weeks of exposure to short day (SD) lengths, hamsters become refractory to the inhibitory effects of SD, and reproductive competence is restored in anticipation of spring. The extent to which changes in gonadal steroid-dependent and -independent regulation of gonadotrophin secretion participate in this vernal reactivation of the gonads is not known. This experiment tested whether tonic and gonadotrophin-releasing hormone (GnRH)-stimulated regulation of lutenising hormone (LH) secretion differs between photoresponsive and photorefractory Siberian hamsters. Male hamsters born into long day (LD) lengths were castrated or subjected to a sham-castration surgery at 17 days of age, implanted s.c. with blank or testosterone-filled capsules, and housed in LD or SD thereafter. Baseline LH and LH responses to GnRH (200 ng/kg, s.c) were measured at 14 (photoresponsive) and 40 (photorefractory) weeks of age. Despite lower circulating testosterone concentrations in gonadally regressed SD hamsters on week 14, tonic LH concentrations were comparable among all groups of gonad-intact hamsters on weeks 14 and 40; however, week 14 SD hamsters exhibited significantly higher GnRH-stimulated LH responses. Tonic LH concentrations were indistinguishable among all groups of castrated hamsters bearing empty implants on week 14, but prolonged exposure to LD led to a decrease in resting LH, whereas prolonged exposure to SD resulted in an increase in LH. In castrated hamsters bearing testosterone implants, baseline LH concentrations were comparable in all groups, but GnRH treatment resulted in significantly higher LH concentrations in photorefractory (week 40, SD) hamsters relative to all other groups. The data suggest that the development of photorefractoriness in Siberian hamsters is characterised by enhanced gonadal hormone-independent stimulation of LH secretion, and diminished sensitivity to inhibitory negative-feedback effects of testosterone on LH secretion. Decreases in responsiveness of gonadotrophin secretion to gonadal hormone negative feedback may contribute to the process of photorefractoriness and assist in maintaining the growth of reproductive organs during the process of gonadal recrudescence.


Subject(s)
Gonadotropin-Releasing Hormone/physiology , Luteinizing Hormone/metabolism , Photoperiod , Seasons , Testis/physiology , Adaptation, Physiological/radiation effects , Animals , Cricetinae , Light , Male , Organ Size , Phodopus , Testis/anatomy & histology , Testosterone/physiology
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