Strategies to determine the biological function of microRNAs

MicroRNAs (miRNAs) are regulators of gene expression that control many biological processes in development, differentiation, growth and metabolism. Their expression levels, small size, abundance of repetitive copies in the genome and mode of action pose unique challenges in studies elucidating the function of miRNAs. New technologies for identification, expression profiling and target gene validation, as well as manipulation of miRNA expression in vivo, will facilitate the study of their contribution to biological processes and disease. Such information will be crucial to exploit the emerging knowledge of miRNAs for the development of new human therapeutic applications.

Integrative analysis of RUNX1 downstream pathways and target genes

BACKGROUND: The RUNX1 transcription factor gene is frequently mutated in sporadic myeloid and lymphoid leukemia through translocation, point mutation or amplification. It is also responsible for a familial platelet disorder with predisposition to acute myeloid leukemia (FPD-AML). The disruption of the largely unknown biological pathways controlled by RUNX1 is likely to be responsible for the development of leukemia. We have used multiple microarray platforms and bioinformatic techniques to help identify these biological pathways to aid in the understanding of why RUNX1 mutations lead to leukemia. RESULTS: Here we report genes regulated either directly or indirectly by RUNX1 based on the study of gene expression profiles generated from 3 different human and mouse platforms. The platforms used were global gene expression profiling of: 1) cell lines with RUNX1 mutations from FPD-AML patients, 2) over-expression of RUNX1 and CBFbeta, and 3) Runx1 knockout mouse embryos using either cDNA or Affymetrix microarrays. We observe that our datasets (lists of differentially expressed genes) significantly correlate with published microarray data from sporadic AML patients with mutations in either RUNX1 or its cofactor, CBFbeta. A number of biological processes were identified among the differentially expressed genes and functional assays suggest that heterozygous RUNX1 point mutations in patients with FPD-AML impair cell proliferation, microtubule dynamics and possibly genetic stability. In addition, analysis of the regulatory regions of the differentially expressed genes has for the first time systematically identified numerous potential novel RUNX1 target genes. CONCLUSION: This work is the first large-scale study attempting to identify the genetic networks regulated by RUNX1, a master regulator in the development of the hematopoietic system and leukemia. The biological pathways and target genes controlled by RUNX1 will have considerable importance in disease progression in both familial and sporadic leukemia as well as therapeutic implications.

Monitoring thrombin generation by electrochemistry: development of an amperometric biosensor screening test for plasma and whole blood

BACKGROUND: Complete investigation of thrombophilic or hemorrhagic clinical presentations is a time-, apparatus-, and cost-intensive process. Sensitive screening tests for characterizing the overall function of the hemostatic system, or defined parts of it, would be very useful. For this purpose, we are developing an electrochemical biosensor system that allows measurement of thrombin generation in whole blood as well as in plasma. METHODS: The measuring system consists of a single-use electrochemical sensor in the shape of a strip and a measuring unit connected to a personal computer, recording the electrical signal. Blood is added to a specific reagent mixture immobilized in dry form on the strip, including a coagulation activator (e.g., tissue factor or silica) and an electrogenic substrate specific to thrombin. RESULTS: Increasing thrombin concentrations gave standard curves with progressively increasing maximal current and decreasing time to reach the peak. Because the measurement was unaffected by color or turbidity, any type of blood sample could be analyzed: platelet-poor plasma, platelet-rich plasma, and whole blood. The test strips with the predried reagents were stable when stored for several months before testing. Analysis of the combined results obtained with different activators allowed discrimination between defects of the extrinsic, intrinsic, and common coagulation pathways. Activated protein C (APC) predried on the strips allowed identification of APC-resistance in plasma and whole blood samples. CONCLUSIONS: The biosensor system provides a new method for assessing thrombin generation in plasma or whole blood samples as small as 10 microL. The assay is easy to use, thus allowing it to be performed in a point-of-care setting.

Failures and complications in patients with birth defects restored with fixed dental prostheses and single crowns on teeth and/or implants

OBJECTIVES: To assess retrospectively, over at least 5 years, the incidences of technical and biological complications and failures in young adult patients with birth defects affecting the formation of teeth. MATERIAL AND METHODS: All insurance cases with a birth defect that had crowns and fixed dental prostheses (FDPs) inserted more than 5 years ago were contacted and asked to participate in a reexamination. RESULTS: The median age of the patients was 19.3 years (range 16.6-24.7 years) when prosthetic treatment was initiated. Over the median observation period of 15.7 years (range 7.4-24.9 years) and considering the treatment needs at the reexamination, 19 out of 33 patients (58%) with reconstructions on teeth remained free from all failures or complications. From the patients with FDPs and single unit crowns (SCs) on implants followed over a median observation period of 8 years (range 4.6-15.3 years), eight out of 17% or 47% needed a retreatment or repair at some point due to a failure or a complication. From the three groups of patients, the cases with amelogenesis/dentinogenesis imperfecta demonstrated the highest failure and complication rates. In the cases with cleft lip, alveolus and palate (CLAP) or hypodontia/oligodontia, 71% of the SCs and 73% of the FDPs on teeth (FDP T) remained complication free over a median observation period of about 16 years. Sixty-two percent of the SCs and 64% of the FDPs on implants remained complication free over 8 years. Complications occurred earlier with implant-supported reconstructions. CONCLUSIONS: Because healthy, pristine teeth can be left unprepared, implant-supported SCs and FDPs are the treatment choice in young adults with birth defects resulting in tooth agenesis and in whom the edentulous spaces cannot be closed by means of orthodontic therapy. However, the trend for earlier and more frequent complications with implant-supported reconstructions in young adults, expecting many years of function with the reconstructions, has to be weighed against the benefits of keeping teeth unprepared. In cases with CLAP in which anatomical conditions render implant placement difficult and in which teeth adjacent to the cleft require esthetic corrections, the conventional FDP T still remains the treatment of choice.

Cumulative costs for the prosthetic reconstructions and maintenance in young adult patients with birth defects affecting the formation of teeth

OBJECTIVES: To assess retrospectively the cumulative costs for the long-term oral rehabilitation of patients with birth defects affecting the development of teeth. METHODS: Patients with birth defects who had received fixed reconstructions on teeth and/or implants > or =5 years ago were asked to participate in a comprehensive clinical, radiographic and economic evaluation. RESULTS: From the 45 patients included, 18 were cases with a cleft lip and palate, five had amelogenesis/dentinogenesis imperfecta and 22 were cases with hypodontia/oligodontia. The initial costs for the first oral rehabilitation (before the age of 20) had been covered by the Swiss Insurance for Disability. The costs for the initial rehabilitation of the 45 cases amounted to 407,584 CHF (39% for laboratory fees). Linear regression analyses for the initial treatment costs per replaced tooth revealed the formula 731 CHF+(811 CHF x units) on teeth and 3369 CHF+(1183 CHF x units) for reconstructions on implants (P<.001). Fifty-eight percent of the patients with tooth-supported reconstructions remained free from failures/complications (median observation 15.7 years). Forty-seven percent of the patients with implant-supported reconstructions remained free from failures/complications (median observation 8 years). The long-term cumulative treatment costs for implant cases, however, were not statistically significantly different compared with cases reconstructed with tooth-supported fixed reconstructions. Twenty-seven percent of the initial treatment costs were needed to cover supportive periodontal therapy as well as the treatment of technical/biological complications and failures. CONCLUSION: Insurance companies should accept to cover implant-supported reconstructions because there is no need to prepare healthy teeth, fewer tooth units need to be replaced and the cumulative long-term costs seem to be similar compared with cases restored on teeth.

Soil Erosion and Conservation in Global Agriculture

About one-sixth of the world’s land area, that is, about one-third of the land used for agriculture, has been affected by soil degradation in the historic past. While most of this damage was caused by water and wind erosion, other forms of soil degradation are induced by biological, chemical, and physical processes. Since the 1950s, pressure on agricultural land has increased considerably owing to population growth and agricultural modernization. Small-scale farming is the largest occupation in the world, involving over 2.5 billion people, over 70% of whom live below the poverty line. Soil erosion, along with other environmental threats, particularly affects these farmers by diminishing yields that are primarily used for subsistence. Soil and water conservation measures have been developed and applied on many farms. Local and science-based innovations are available for most agroecological conditions and land management and farming types. Principles and measures developed for small-scale as well as modern agricultural systems have begun to show positive impacts in most regions of the world, particularly in wealthier states and modern systems. Much more emphasis still needs to be given to small-scale farming, which requires external support for investment in sustainable land management technologies as an indispensable and integral component of farm activities.

Magnetic resonance imaging anatomy of the normal equine larynx and pharynx

The purpose of the present study was to describe normal magnetic resonance (MR) imaging anatomy of the equine larynx and pharynx and to present the optimal protocol, sequences, and possible limitations of this examination technique. Using a 0.3 T unit, the laryngeal and pharyngeal regions was imaged in two horses. The protocol consisted of sagittal and transverse T2-weighted (T2w) fast spin echo, transverse T1-weighted (T1w) spin echo, and dorsal high-resolution T1w gradient echo (both pre- and postcontrast enhancement) sequences. Euthanasia was performed at the end of the imaging procedure. Macroscopic anatomy of the cadaver sections were compared with the MR images in transverse, midsagittal, and parasagittal planes. There was good differentiation of anatomic structures, including soft tissues. The laryngeal cartilages, hyoid apparatus, and upper airway muscle groups with their attachments could be clearly identified. However, it was not always possible to delineate individual muscles in each plane. Most useful were both T2w and T1w transverse sequences. Intravenous application of contrast medium was helpful to identify blood vessels. The MR images corresponded with the macroscopic anatomy of cadaver sections.

Intracellular localization of the BCL-2 family member BOK and functional implications

The pro-apoptotic BCL-2 family member BOK is widely expressed and resembles the multi-BH domain proteins BAX and BAK based on its amino acid sequence. The genomic region encoding BOK was reported to be frequently deleted in human cancer and it has therefore been hypothesized that BOK functions as a tumor suppressor. However, little is known about the molecular functions of BOK. We show that enforced expression of BOK activates the intrinsic (mitochondrial) apoptotic pathway in BAX/BAK-proficient cells but fails to kill cells lacking both BAX and BAK or sensitize them to cytotoxic insults. Interestingly, major portions of endogenous BOK are localized to and partially inserted into the membranes of the Golgi apparatus as well as the endoplasmic reticulum (ER) and associated membranes. The C-terminal transmembrane domain of BOK thereby constitutes a 'tail-anchor' specific for targeting to the Golgi and ER. Overexpression of full-length BOK causes early fragmentation of ER and Golgi compartments. A role for BOK on the Golgi apparatus and the ER is supported by an abnormal response of Bok-deficient cells to the Golgi/ER stressor brefeldin A. Based on these results, we propose that major functions of BOK are exerted at the Golgi and ER membranes and that BOK induces apoptosis in a manner dependent on BAX and BAK.

Health of farmed fish: its relation to fish welfare and its utility as welfare indicator

This brief review focuses on health and biological function as cornerstones of fish welfare. From the function-based point of view, good welfare is reflected in the ability of the animal to cope with infectious and non-infectious stressors, thereby maintaining homeostasis and good health, whereas stressful husbandry conditions and protracted suffering will lead to the loss of the coping ability and, thus, to impaired health. In the first part of the review, the physiological processes through which stressful husbandry conditions modulate health of farmed fish are examined. If fish are subjected to unfavourable husbandry conditions, the resulting disruption of internal homeostasis necessitates energy-demanding physiological adjustments (allostasis/acclimation). The ensuing energy drain leads to trade-offs with other energy-demanding processes such as the functioning of the primary epithelial barriers (gut, skin, gills) and the immune system. Understanding of the relation between husbandry conditions, allostatic responses and fish health provides the basis for the second theme developed in this review, the potential use of biological function and health parameters as operational welfare indicators (OWIs). Advantages of function- and health-related parameters are that they are relatively straightforward to recognize and to measure and are routinely monitored in most aquaculture units, thereby providing feasible tools to assess fish welfare under practical farming conditions. As the efforts to improve fish welfare and environmental sustainability lead to increasingly diverse solutions, in particular integrated production, it is imperative that we have objective OWIs to compare with other production forms, such as high-density aquaculture. However, to receive the necessary acceptance for legislation, more robust scientific backing of the health- and function-related OWIs is urgently needed.

Deciphering microRNA code in pain and inflammation: lessons from bladder pain syndrome

MicroRNAs (miRNAs), a novel class of molecules regulating gene expression, have been hailed as modulators of many biological processes and disease states. Recent studies demonstrated an important role of miRNAs in the processes of inflammation and cancer, however, there are little data implicating miRNAs in peripheral pain. Bladder pain syndrome/interstitial cystitis (BPS/IC) is a clinical syndrome of pelvic pain and urinary urgency/frequency in the absence of a specific cause. BPS is a chronic inflammatory condition that might share some of the pathogenetic mechanisms with its common co-morbidities inflammatory bowel disease (IBD), asthma and autoimmune diseases. Using miRNA profiling in BPS and the information about validated miRNA targets, we delineated the signaling pathways activated in this and other inflammatory pain disorders. This review projects the miRNA profiling and functional data originating from the research in bladder cancer and immune-mediated diseases on the BPS-specific miRNAs with the aim to gain new insight into the pathogenesis of this enigmatic disorder, and highlighting the common regulatory mechanisms of pain and inflammation.

A quantitative phenytoin GC-MS method and it's validation for samples from human ex situ brain microdialysis, blood and saliva using solid-phase extraction

This study describes the development and validation of a gas chromatography-mass spectrometry (GC-MS) method to identify and quantitate phenytoin in brain microdialysate, saliva and blood from human samples. A solid-phase extraction (SPE) was performed with a nonpolar C8-SCX column. The eluate was evaporated with nitrogen (50°C) and derivatized with trimethylsulfonium hydroxide before GC-MS analysis. As the internal standard, 5-(p-methylphenyl)-5-phenylhydantoin was used. The MS was run in scan mode and the identification was made with three ion fragment masses. All peaks were identified with MassLib. Spiked phenytoin samples showed recovery after SPE of ≥94%. The calibration curve (phenytoin 50 to 1,200 ng/mL, n = 6, at six concentration levels) showed good linearity and correlation (r² > 0.998). The limit of detection was 15 ng/mL; the limit of quantification was 50 ng/mL. Dried extracted samples were stable within a 15% deviation range for ≥4 weeks at room temperature. The method met International Organization for Standardization standards and was able to detect and quantify phenytoin in different biological matrices and patient samples. The GC-MS method with SPE is specific, sensitive, robust and well reproducible, and is therefore an appropriate candidate for the pharmacokinetic assessment of phenytoin concentrations in different human biological samples.

Design, synthesis and pharmacological characterization of analogs of 2-aminoethyl diphenylborinate (2-APB), a known store-operated calcium channel blocker, for inhibition of TRPV6-mediated calcium transport

2-Aminoethyl diphenylborinate (2-APB) is a known modulator of the IP3 receptor, the calcium ATPase SERCA, the calcium release-activated calcium channel Orai and TRP channels. More recently, it was shown that 2-APB is an efficient inhibitor of the epithelial calcium channel TRPV6 which is overexpressed in prostate cancer. We have conducted a structure-activity relationship study of 2-APB congeners to understand their inhibitory mode of action on TRPV6. Whereas modifying the aminoethyl moiety did not significantly change TRPV6 inhibition, substitution of the phenyl rings of 2-APB did. Our data show that the diaryl borinate moiety is required for biological activity and that the substitution pattern of the aryl rings can influence TRPV6 versus SOCE inhibition. We have also discovered that 2-APB is hydrolyzed and transesterified within minutes in solution.

Pelagic molybdenum concentration anomalies and the impact of sediment resuspension on the molybdenum budget in two tidal systems of the North Sea

The seasonal dynamics of molybdenum (Mo) were studied in the water column of two tidal basins of the German Wadden Sea (Sylt-Rømø and Spiekeroog) between 2007 and 2011. In contrast to its conservative behaviour in the open ocean, both, losses of more than 50% of the usual concentration level of Mo in seawater and enrichments up to 20% were observed repeatedly in the water column of the study areas. During early summer, Mo removal by adsorption on algae-derived organic matter (e.g. after Phaeocystis blooms) is postulated to be a possible mechanism. Mo bound to organic aggregates is likely transferred to the surface sediment where microbial decomposition enriches Mo in the pore water. First δ98/95Mo data of the study area disclose residual Mo in the open water column being isotopically heavier than MOMo (Mean Ocean Molybdenum) during a negative Mo concentration anomaly, whereas suspended particulate matter shows distinctly lighter values. Based on field observations a Mo isotope enrichment factor of ε = −0.3‰ has been determined which was used to argue against sorption on metal oxide surfaces. It is suggested here that isotope fractionation is caused by biological activity and association to organic matter. Pelagic Mo concentration anomalies exceeding the theoretical salinity-based concentration level, on the other hand, cannot be explained by replenishment via North Sea waters alone and require a supply of excess Mo. Laboratory experiments with natural anoxic tidal flat sediments and modelled sediment displacement during storm events suggest fast and effective Mo release during the resuspension of anoxic sediments in oxic seawater as an important process for a recycling of sedimentary sulphide bound Mo into the water column.

The growing galectin network in colon cancer and clinical relevance of cytoplasmic galectin-3 reactivity

BACKGROUND/AIM Human lectins translate sugar-encoded signals of cell surface glycoconjugates into biological effects, and this is what is known for the adhesion/growth-regulatory galectins. In addition, the multifunctional members of this group can be intracellular, binding to distinct proteins. The presence of galectins and galectin reactivity were exemplarily studied in the present article. MATERIALS AND METHODS We combined immuno- and lectin histochemical monitoring in colon cancer on tissue arrays. RESULTS Intracellular presence of galectins-7 and -9 in colon cancer is detected, extending the previously known set of five expressed lectins this tumor type. The assumed significance of intracellular galectin presence, e.g. for an interplay with BCL2, β-catenin, oncogenic KRAS or synexin, is underscored by respective staining with labeled galectin-3. Statistical significance was obtained for galectin-3 staining with respect to tumor differentiation (p=0.0376), lymph node metastasis (p=0.0069) and lymphatic invasion (p=0.0156). Survival was correlated to staining, galectin-3 reactivity indicating a favorable prognosis (p=0.0183), albeit not as an independent marker. No correlation to KRAS/BRAF status was detected. CONCLUSION These results encourage further testing of labeled human galectins as probes and immunohistochemical fingerprinting instead of measuring single or few activities, in colon cancer and other tumor types.

The history of subaquatic volcanism recorded in the sediments of Lake Kivu

Subaquatic volcanic activity has been ongoing in Lake Kivu since the early Holocene and has a dynamic effect on the biological productivity in the surface water, and the preservation of carbonate in the deep anoxic water. Groundwater discharge into the lake’s deepwater propels the upward advection of the water column that ultimately supplies nutrients to the surface water for biological production. The amount of nutrients supplied from the deepwater can be increased suddenly by (1) a cold meteorological event that drives deep seasonal mixing resulting in increased nutrients from below and oxygen from above, or (2) subaquatic volcanic activity that induces a buoyant hydrothermal plume, which entrains nutrients from the deepwater and results in anoxia or suboxic conditions in the surface water. Previous sedimentological studies in Lake Kivu have hypothesized that regional climatic changes are responsible for sudden changes in the preservation of carbonates in the Main Basin. Here we reveal that sublacustrine volcanic events most likely induce the abrupt changes to the geochemistry in the sediment in Lake Kivu. An unprecedented look into the sediment stratigraphy and geochemistry from high-resolution seismic-reflection, and 15N-isotope analyses was conducted in the Main Basin. The results reveal that buoyant hydrothermal plumes caused by subaquatic volcanic activity are a possible trigger for increased biological productivity and organic matter preservation, and that ongoing hydrothermal activity increases the alkalinity in the deepwater, leading to carbonate preservation. The onset of carbonate preservation since the 1970s that is currently observed in the sediment could indicate that hydrothermal discharge has recently increased in the lake.