| 51. |
- Abarenkov, Kessy, et al.
(författare)
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Protax-fungi: A web-based tool for probabilistic taxonomic placement of fungal internal transcribed spacer sequences
- 2018
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 220:2, s. 517-525
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Tidskriftsartikel (refereegranskat)abstract
- © 2018 New Phytologist Trust. Incompleteness of reference sequence databases and unresolved taxonomic relationships complicates taxonomic placement of fungal sequences. We developed Protax-fungi, a general tool for taxonomic placement of fungal internal transcribed spacer (ITS) sequences, and implemented it into the PlutoF platform of the UNITE database for molecular identification of fungi. With empirical data on root- and wood-associated fungi, Protax-fungi reliably identified (with at least 90% identification probability) the majority of sequences to the order level but only around one-fifth of them to the species level, reflecting the current limited coverage of the databases. Protax-fungi outperformed the Sintax and Rdb classifiers in terms of increased accuracy and decreased calibration error when applied to data on mock communities representing species groups with poor sequence database coverage. We applied Protax-fungi to examine the internal consistencies of the Index Fungorum and UNITE databases. This revealed inconsistencies in the taxonomy database as well as mislabelling and sequence quality problems in the reference database. The according improvements were implemented in both databases. Protax-fungi provides a robust tool for performing statistically reliable identifications of fungi in spite of the incompleteness of extant reference sequence databases and unresolved taxonomic relationships.
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| 52. |
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| 53. |
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| 54. |
- Abbas, Aamer, 1973, et al.
(författare)
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Chemical images of marine bio-active compounds by surface enhanced Raman spectroscopy and transposed orthogonal partial least squares (T-OPLS)
- 2012
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Ingår i: Analytica Chimica Acta. - : Elsevier BV. - 0003-2670 .- 1873-4324. ; 737, s. 37-44
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Tidskriftsartikel (refereegranskat)abstract
- Surface enhanced Raman spectroscopy combined with transposed Orthogonal Partial Least Squares (T-OPLS) was shown to produce chemical images of the natural antibacterial surface-active compound 1,1,3,3-tetrabromo-2-heptanone (TBH) on Bonnemaisonia hamifera. The use of gold colloids function-alised with the internal standard 4-mercapto-benzonitrile (MBN) made it possible to create images of the relative concentration of TBH over the surfaces. A gradient of TBH could be mapped over and in the close vicinity of the B. hamifera algal vesicles at the attomol/pixel level. T-OPLS produced a measure of the spectral correlation for each pixel of the hyperspectral images whilst not including spectral variation that was linearly independent of the target spectrum. In this paper we show the possibility to retrieve specific spectral information with a low magnitude in a complex matrix.
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| 55. |
- Abbas, Abdul-Karim, 1959, et al.
(författare)
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Emetine treatment masks initial LTP without affecting long-term stability.
- 2011
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Ingår i: Brain research. - : Elsevier BV. - 1872-6240 .- 0006-8993. ; 1426, s. 18-29
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Tidskriftsartikel (refereegranskat)abstract
- Applying emetine, a protein synthesis inhibitor, at 20-40μM for 90-120min prior to LTP induction in hippocampal slices from young rats (2-3weeks) and washing it out afterwards revealed a slowly developing potentiation that reached maximum after 20-30min, distinct from the LTP observed under normal conditions. Nevertheless, the later phase of this potentiation was similar to standard LTP as judged by experiments lasting up to 8h after induction. Emetine preapplication for 3h without subsequent washout resulted in a substantial decay of evoked responses. By comparison between test and control pathways, LTP could still be assessed in these experiments for up to 4-6h after induction and was found not to differ from normal, except for the slow onset. The NMDA-R blocker AP5 fully blocked LTP; however, with emetine pretreatment there was an initial depression of responses with a gradual recovery during 20-30min. This depression involved not only the field EPSP but also the presynaptic fiber volley. However, when using the protein synthesis inhibitors cycloheximide and anisomycin there was essentially no such depression. In conclusion, the present results support the idea that preexisting proteins are sufficient for inducing stable LTP. Moreover, emetine but not anisomycin or cycloheximide impairs presynaptic action potentials, leading to an apparent slow onset of LTP. The emetine-dependent effect could be due to a characteristic blocking spectrum of the drug, preferred targeting of presynaptic compartments or effects unrelated to protein synthesis.
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| 56. |
- Abbas, Abdul-Karim, 1959
(författare)
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Evidence based medicine: a critical inquiry. Seminar Lecture
- 2010
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Ingår i: The 5th Annual Meeting of International Iraqi Medical Association, April 1-3, 2010, Sharjah, UAE.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Evidence-based medicine and practice (EBM/EBP) have since their inception in the early 1990s had widespread impact on the teaching and practice of medicine and health care. While the western societies are becoming more postmodernist, the medical system remains increasingly modernist in its outlook, this may make it increasingly irrelevant to the needs of a changing society. However, criticism is essentially a changing process of our realities. Hence, the prominence given to EBM can not be seen as a solely attempt to reassert modernism within the field, but as an improved paradigm reviewing itself in lights of challenges it faces. Relevant to my topic here is that the debate, which took sometimes, unfortunately, metaphorical and aggressive directions, has contributing effect on both the EBM and its critics moderating both methodologies and epistemes especially the introducing of other kinds of researches, than randomized controlled trails (RCT), systematic reviews or meta-analysis of RCTs, like user-led research and qualitative researches which focus on personal experience of both the patient and clinician. In the developing countries there are many challenges, whether technical, social or epistemological, facing practicing and using them. Although few Arab countries have recently developed either centers or associations for EBM, Iraq still lacks such kind of practice. Presenting an outlook of EMB from within the current intellectual debate and examining the environment and essential aspects of this debate between the EMB and its postmodernist critics might be helpful in not a merely dogmatic promotion of its practice nor a blind call for adopting and applying its guidelines and techniques but in enforcing the discussion and dialogue between the current disputable paradigms in the one hand and improve the possibilities and resources to use it as the “best” paradigm in medical practices and education. A conclusion has drawn on here that EBM paradigm does not only improve the decision-making in health services and provides a serious attempt to invent a new language that might reunite the Babel of doctors and patients, managers and consumers, but also it understands medical care in both the closed and open systems. Epistemological, methodological, ethical and social questions about the patient/subject are addressed here aiming to encourage the health and educational authorities in Iraq to take this paradigm seriously and introduce it in their future programs.
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| 57. |
- Abbas, Abdul-Karim, 1959
(författare)
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Evidence for constitutive protein synthesis in hippocampal LTP stabilization
- 2013
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Ingår i: Neuroscience. - : Elsevier BV. - 0306-4522. ; 246, s. 301-311
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Tidskriftsartikel (refereegranskat)abstract
- The notion that blockade of constitutive protein synthesis underlies the effect of protein synthesis inhibitors (PSIs) on long-term potentiation (LTP) stabilization was examined using the rat hippocampal CA3-CA1 synapse. Using a biochemical assay we found protein synthesis rate largely recovered 1h after wash-out of cycloheximide (CHX). Nonetheless, a 4-h CHX application followed by wash-out 1h prior to LTP resulted in a significant decrement of LTP stabilization. Wash-out initiated just prior to LTP, thus extending protein synthesis inhibition well into the post-LTP period, resulted in no further effect on LTP. However, short pre- and continuous post-tetanization application of PSIs failed to influence LTP persistence for up to 7h. Addition of hydrogen peroxide (H2O2) 5-25min following LTP induction resulted in parallel depression of potentiated and non-potentiated inputs, leaving LTP seemingly unaltered. However, in the presence of cyxloheximide the H2O2 application resulted in a significant reduction of LTP. In conclusion: LTP stabilization was impaired by pre-LTP application of protein synthesis inhibition but not by post-LTP application unless the slices were exposed to oxidative stress. We submit that these results favor the notion that constitutive rather than triggered protein synthesis is important for LTP stabilization.
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| 58. |
- Abbas, Abdul-Karim, 1959
(författare)
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Kainic Acid, NMDA and Bicuculline Induce Elevation in Concentrations of Glutathione and Amino Acids in Vivo: Biomarkers for Seizure Predisposition?
- 2015
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Ingår i: Journal of Behavioral and Brain Science. - : Scientific Research Publishing, Inc.. - 2160-5866 .- 2160-5874. ; 5:5, s. 163-172
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Tidskriftsartikel (refereegranskat)abstract
- The present study was carried out to investigate the effect of NMDA, bicuculline and kainic acid (KA) on the extracellular concentration of glutathione, phosphoethanolamine (PEA) and taurine in rat hippocampus in vivo. Rats were implanted with intrahippocampal microelectrodes perfused with free-glucose Krebs-Ringer solution and allowed to recover for about 2 h. After assaying baseline concentrations of amino acids, NMDA or bicuculline was administered intrahippocampally, whereas KA was given systemically. Either treatment resulted in significant high extracellular concentrations of glutathione, but only NMDA or KA resulted in high concentrations of PEA and taurine. Interestingly, the increase in glutathione concentration due to KA was followed by a delayed increase of glutamate and PEA. Our results demonstrated that increased efflux of glutathione, a common consequence of different neuroexcitotoxic agents, occurs in vivo. Given that the agents used in the present study were also convulsunts, the implication of the findings on seizure predisposition was also considered.
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| 59. |
- Abbas, Abdul-Karim, 1959, et al.
(författare)
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Long-term potentiation and insult conditioning in hippocampal slices from young rats: a role for protein synthesis under chemical stress?
- 2010
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Ingår i: The 10th Biennial Meeting of the Asia-Pacific Society for Neurochemistry (APSN), October 17-20, 2010, Phuket, Thailand.
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- We have previously demonstrated that in young rats (12-20-day-old) a sustained long-term potentiation (LTP) can still be induced under conditions of protein synthesis inhibition. It was therefore suggested that sufficient and necessary proteins were already available at the induction time to accomplish LTP maintenance for several hours. Against this background, we have questioned whether hippocampal slices subjected to certain insult conditions might be more sensitive to protein synthesis inhibitors. High K+ concentration has previously been reported to cause an amnesic effect in vivo as well as increasing protein turnover in vitro. We have here employed a K+ insult model under conditions when protein synthesis was inhibited. Recordings were obtained from hippocampal slices for up to 9 h, with or without a cocktail of protein synthesis inhibitors, containing cycloheximide (60 µM) and anisomycin (25 µM). High potassium (50 mM) was transiently applied (5-15 min) shortly after inducing LTP in one of two separate pathways stimulated alternatively. Additionally, an NMDA-receptor antagonist AP5 was supplied after LTP induction to minimize effects related to depolarization-induced glutamate release. Following elimination of all responses for about 30 min, both test and control responses partly recovered. The degree of remaining LTP, defined as test/control ratio, was reduced in both groups of slices (NMDA-independent depotentiation) but was significantly smaller in the drug-treated ones. We are also running an insult model based on oxidative stress, applying hydrogen peroxide (4-5 mM) before or after LTP induction; however, the results are still insufficient for a final conclusion. The potency of cycloheximide, anisomycin or cocktail of the drugs was verified by measurement of incorporation of [3H]-leucine into trichloracetic acid (TCA) precipitable macromolecules. Cycloheximide, anisomycin or cocktail, at concentrations used here caused 95%, 97% and 95% blocking effect, respectively. Our data confirm the idea that sufficient and necessary constitutive proteins are available in the young hippocampus to maintain LTP under conditions of protein synthesis inhibition. They also reveal that LTP in slices subjected to certain insult conditions early after the induction is sensitive to protein synthesis inhibition, probably due to increase in constitutive proteins turnover.
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| 60. |
- Abbas, Abdul-Karim, 1959, et al.
(författare)
-
Pharmacological characteristics of protein synthesis inhibitors by radioactive leucine incorporation in rat hippocampal slices: experimental evidence and pre-clinical implications
- 2011
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Ingår i: The 23rd Biennial Meeting of the International Society for Neurochemistry (ISN), August 28-September 1 2011, Athens, Greece.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Protein synthesis inhibitors (PSIs) constitute a major tool to validate the hypothesis of protein synthesis-dependent phase of synaptic plasticity and memory consolidation. However, several reports have showed inconsistent findings about the effect of these drugs on behavioral learning and synaptic plasticity. Testing the potencies of these drugs is hence crucial for validating such negative findings and in planning future studies. It is also necessary to examine the dose dependence, onset dynamics and reversibility, and possible effects on basal proteins. Here we used the labeled leucine as marker for the newly synthesized proteins. The fraction of leucine incorporation, following 50 min of pre-incubation, was compared between two groups of slices: a PSI-treated and a control group. Both anisomycin and cycloheximide revealed a dose-dependent but time-independent manner of inhibition reaching over 92% at concentrations well below those used in previous experiments which revealed effects on synaptic plasticity and learning. Surprisingly, washout of a “reversible” inhibitor, anisomycin was not followed by rapid reversibility of the action of the drug, the case that differs with cycloheximide. Interestingly, emetine revealed a time-dependent inhibition of protein synthesis, where levels above 80% needed drug pre-incubation for as long as 90 min. Since the duration of labeling relates to the half-life of the proteins, short-time labeling as used in this study will result in radioactivity incorporation into short-lived proteins and proteins that are synthesized in large quantities. We therefore studied the availability of newly synthesized proteins at 8-10 h following leucine incorporation. The results revealed virtually the same protein content as in slices retrieved for analysis immediately following the labeling period, indicating that the main pool of the newly synthesized proteins is of intracellular long-lived pool. This likely reflects a stable metabolic state of our prepared slices. These findings challenge current idea on the role of de novo protein synthesis in synaptic plasticity as well as brain changes underlying several neurological and psychiatric disorders.
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