Outliers involving the Poly(A) effect among highly-expressed genes in microarrays

BACKGROUND: The Poly(A) effect is a cross-hybridization artifact in which poly(T)-containing molecules, which are produced by the reverse transcription of a poly(A)(+ )RNA mixture, bind promiscuously to the poly(A) stretches of the DNA in microarray spots. It is customary to attempt to block such hybridization by adding poly(A) to the hybridization solution. This note describes an experiment intended to evaluate circumstances under which the blocking procedure may not have been successful. RESULTS: The experiment involves a spot-by-spot comparison between the hybridization signals obtained by hybridizing a microarray to: (1) end-labeled oligo(dT), versus, (2) cDNA prepared from muscle tissue. We found that the blocking appears to be successful for the vast majority of microarray spots, as evidenced by the weakness of the correlation between signals (1) and (2). However, we found that for microarray spots having oligo(dT) hybridization levels greater than a certain threshold, the blocking might be ineffective or incomplete, as evidenced by an exceptionally strong signal (2) whenever signal (1) is greater than the threshold. CONCLUSION: The PolyA effect may be more subtle than simply a hybridization signal that is proportional to the PolyA content of each microarray spot. It may instead be present only in spots that hybridize oligo(dT) greater than some threshold level. The strong signal generated at these "outlier" spots by cDNA probes might be due to the formation of hybridization heteropolymers

Quantifying the relative contribution of ante- and post-mortem factors to the variability in beef texture

This study aims to investigate the relative contribution of ante- and post-mortem factors to the final quality of beef. In all, 112 steers (four breed-crosses) were arranged in a 2 3 2 3 2 factorial experimental including production system, growth implant and b-adrenergic agonist strategies. Carcasses were suspended by the Achilles tendon or the aitch bone and meat was aged for 2/6/13/21/27 days (longissimus muscle) or 2/27 days (semimembranosus muscle). Meat quality traits related to beef texture were measured. Statistical analyses were developed including ante- and post-mortem factors and their relative contribution to the variability observed for each measured trait was calculated. The main factor responsible for the variability in sarcomere length was the suspension method (91.1%), which also influenced drip-loss (44.3%). Increasing the percentage of British breeds increased (P , 0.05) the intramuscular fat content in longissimus muscle, but only when implants were not used. Thus, the breed-cross, implant strategy and their interaction were responsible for .58% of the variability in this trait. The variability in instrumental and sensory tenderness was mainly affected by post-mortem factors (carcass suspension, ageing time and their interaction), explaining generally , 70% of the variability in these traits. Breed-cross was the second most important effect ( ,15%) when carcass suspension was not considered in the model, but still ageing time was responsible for a much larger proportion of the variability in tenderness (.45%). In conclusion, post-mortem handling of the carcasses may be much more effective in controlling beef tenderness than pre-mortem strategies

Recent and future trends in synthetic greenhouse gas radiative forcing

Atmospheric measurements show that emissions of hydrofluorocarbons (HFCs) and hydrochlorofluorocarbons are now the primary drivers of the positive growth in synthetic greenhouse gas (SGHG) radiative forcing. We infer recent SGHG emissions and examine the impact of future emissions scenarios, with a particular focus on proposals to reduce HFC use under the Montreal Protocol. If these proposals are implemented, overall SGHG radiative forcing could peak at around 355 mW m[superscript −2] in 2020, before declining by approximately 26% by 2050, despite continued growth of fully fluorinated greenhouse gas emissions. Compared to “no HFC policy” projections, this amounts to a reduction in radiative forcing of between 50 and 240 mW m[superscript −2] by 2050 or a cumulative emissions saving equivalent to 0.5 to 2.8 years of CO2 emissions at current levels. However, more complete reporting of global HFC emissions is required, as less than half of global emissions are currently accounted for.Natural Environment Research Council (Great Britain) (Advanced Research Fellowship NE/I021365/1)United States. National Aeronautics and Space Administration (Upper Atmospheric Research Program Grant NNX11AF17G)United States. National Oceanic and Atmospheric Administratio

Extended ageing time and temperature effects on quality of sub-primal cuts of boxed beef

[EN]Most of the information indicating ageing improves tenderness has been collected on the loin and rib-eye muscles over relatively short ageing times, assuming that all muscles will react similarly. In the present study, the effect of extended ageing times on instrumental texture (56 d) and sensory characteristics (42 d) of six different beef sub-primals [striploin (SL), inside round (IR), outside round (OR), eye of round (ER), blade eye (BE) and chuck tender (CT)] was studied. The effects of two ageing temperatures (1and 58C) were also compared. In general, ageing increased tenderness (P<0.05) of SL, BE, ER and CT sub-primals, although BE shear force increased after 42 d of ageing. On the other hand, ageing had no effect on IR tenderness (P<0.05) and resulted in a decrease in tenderness of OR (P<0.05) until day 35, with a later increase after 42 d of ageing. Increasing ageing temperature (58C) had limited effect on tenderness, but ageing time and temperature increases led to lower flavour and higher off-flavour intensity (P<0.05) of the studied sub-primals. These results suggest that cutspecific maximum ageing times and rigid adherence to temperature maximums would be of benefit to optimize postslaughter processes and meat quality[FRE]La plupart des données indiquant que le rassissement améliore la tendreté ont été recueillies sur les muscles de la longe et du faux-filet sur un temps relativement court, partant de l’hypothèse que les muscles réagissent tous de la même manière. Cette étude examine l’incidence d’un rassissement prolongé sur la texture (56 jours) et sur les propriétés organoleptiques (42 jours) de six coupes sous-primaires de boeuf [contre-filet (CF), intérieur de ronde (IR), extérieur de ronde (ER), noix de ronde (NR), noix de palette (NP) et bas de tendre (BT)]. Les auteurs ont aussi comparé l’effet de deux températures de rassissement (1et 58C). Dans l’ensemble, le rassissement accroît la tendreté (P<0,05) des morceaux CF, NP, NR et BT, bien que la résistance de la NP au cisaillement augmente après 42 jours. Parallèlement, le rassissement n’a aucune incidence sur la tendreté de l’IR (P<0,05) et diminue celle de l’ER (P<0,05) jusqu’au 35e jour, avant de l’amé liorer passé le 42e jour. Augmenter la température du rassissement (58C) a des effets restreints sur la tendreté , mais ajouteé à un rassissement plus long, la hausse de température atte´nue la saveur et intensifie l’arrière-goût (P<0,05) des pièces de viande examinées. Ces ré sultats laissent croire que l’établissement d’une dureé de rassissement adapteé au morceau et un strict respect de la température maximale optimiseraient les opérations suivant l’abattage et la qualité de la viande

Cattle Raiding, Cultural Survival, and Adaptability of East African Pastoralists

This is the published version. Also found here http://www.jstor.org/stable/359710

Withdrawal from Repeated Cocaine Alters Dopamine Transporter Protein Turnover in the Rat Striatum

ABSTRACT Several studies have shown that repeated cocaine administration, followed by withdrawal, alters dopamine transporter (DAT) levels in the rat. These changes must arise from changes in either transporter protein production or degradation, or both. Previously, our laboratory developed an approach to measure the synthesis rate, degradation rate constant, and half-life of DAT in the rat striatum and nucleus accumbens after administration of the irreversible dopamine transporter ligand, RTI-76 . These initial studies showed that: 1) the half-life of the transporter was between 2 and 3 days in these two brain regions; 2) pretreatment with dopamine D1 and D2 receptor agonists and antagonists over several days differentially altered DAT half-lives in the striatum and nucleus accumbens; and 3) pretreatment with cocaine for several days increased the half-life of DAT by decreasing the degradation rate constant in both brain regions. In the present study, we determined that repeated pretreatment (10 days) with 20 mg/kg cocaine (i.p.) and a subsequent withdrawal period (10 days) alters the dopamine transporter turnover in the rat striatum, but not in the nucleus accumbens. Cocaine pretreatment and withdrawal reduced the half-life of the transporter protein from 2.1 days to 0.94 day in the striatum, but did not alter the half-life of 2.2 days in the nucleus accumbens. The results indicate the complex and long-lasting effects of cocaine administration on cellular processes. The mechanism(s) of these effects remains to be elucidated

Synthesis of a novel series of Cu(I) complexes bearing alkylated 1,3,5-triaza-7-phosphaadamantane as homogeneous and carbon-supported catalysts for the synthesis of 1-and 2-substituted-1,2,3-triazoles

Funding Information: This research was funded by the Funda??o para a Ci?ncia e a Tecnologia (FCT), Portugal, project UIDB/00100/2020 of the Centro de Qu?mica Estrutural, FCT/MCTES (UIDB/50006/2020 and UIDP/50006/2020) from Associate Laboratory for Green Chemistry?LAQV, Scientific Employment Stimulus?Institutional Call (CEECINST/00102/2018) and by the RUDN University Strategic Academic Leadership Program. I.L.L. acknowledges the FCT through the CATSUS PhD Program (PD/BD 135555/2018). A.G.M. was funded by Instituto Superior T?cnico, Portugal through the project CO2usE-1801P.00867.1.01 (contract no. IST-ID/263/2019). Funding Information: Funding: This research was funded by the Fundação para a Ciência e a Tecnologia (FCT), Portugal, project UIDB/00100/2020 of the Centro de Química Estrutural, FCT/MCTES (UIDB/50006/2020 and UIDP/50006/2020) from Associate Laboratory for Green Chemistry—LAQV, Scientific Employment Stimulus—Institutional Call (CEECINST/00102/2018) and by the RUDN University Strategic Academic Leadership Program. I.L.L. acknowledges the FCT through the CATSUS PhD Program (PD/BD 135555/2018). A.G.M. was funded by Instituto Superior Técnico, Portugal through the project CO2usE-1801P.00867.1.01 (contract no. IST-ID/263/2019). Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.The N-alkylation of 1,3,5-triaza-7-phosphaadamantane (PTA) with ortho-, meta-and para-substituted nitrobenzyl bromide under mild conditions afforded three hydrophilic PTA ammonium salts, which were used to obtain a new set of seven water-soluble copper(I) complexes. The new compounds were fully characterized and their catalytic activity was investigated for the low power microwave assisted one-pot azide–alkyne cycloaddition reaction in homogeneous aqueous medium to obtain disubstituted 1,2,3-triazoles. The most active catalysts were immobilized on activated carbon (AC), multi-walled carbon nanotubes (CNT), as well as surface functionalized AC and CNT, with the most efficient support being the CNT treated with nitric acid and NaOH. In the presence of the immobilized catalyst, several 1,4-disubstituted-1,2,3-triazoles were obtained from the reaction of terminal alkynes, organic halides and sodium azide in moderate yields up to 80%. Furthermore, the catalyzed reaction of terminal alkynes, formaldehyde and sodium azide afforded 2-hydroxymethyl-2H-1,2,3-triazoles in high yields up to 99%. The immobilized catalyst can be recovered and recycled through simple workup steps and reused up to five consecutive cycles without a marked loss in activity. The described catalytic systems proceed with a broad substrate scope, under microwave irradiation in aqueous medium and according to “click rules”.publishersversionpublishe

The catalytic activity of carbon-supported Cu(I)-phosphine complexes for the microwave-assisted synthesis of 1,2,3-triazoles

This research was funded by Fundação para a Ciência e a Tecnologia (FCT), Portugal, through project UIDB/00100/2020 of the Centro de Química Estrutural. It was also funded by national funds though FCT, under the Scientific Employment Stimulus-Institutional Call (CEECINST/ 00102/2018). We also acknowledge the Associate Laboratory for Green Chemistry—LAQV financed by national funds from FCT/MCTES (UIDB/50006/2020 and UIDP/50006/2020). I.L.L. is grateful to the CATSUS Ph.D. Program for her grant (PD/BD 135555/2018). AGM is grateful to Instituto Superior Técnico, Portugal for his post-doctoral fellowship through the project CO2usE-1801P.00867.1.01 (Contract No. IST-ID/263/2019). It was also supported by the RUDN University Strategic Academic Leadership Program.A set of Cu(I) complexes with 3,7-diacetyl-1,3,7-triaza-5-phosphabicyclo-[3.3.1]nonane (DAPTA) phosphine ligands viz. [CuX(κP-DAPTA)3] (1: X = Br; 2: X = I) and [Cu(µ-X)((κP-DAPTA)2]2 (3: X = Br; 4: X = I) were immobilized on activated carbon (AC) and multi-walled carbon nanotubes (CNT), as well as on these materials after surface functionalization. The immobilized copper(I) complexes have shown favorable catalytic activity for the one-pot, microwave-assisted synthesis of 1,2,3-triazoles via the azide-alkyne cycloaddition reaction (CuAAC). The heterogenized systems with a copper loading of only 1.5-1.6% (w/w relative to carbon), established quantitative conversions after 15 min, at 80 °C, using 0.5 mol% of catalyst loading (relative to benzyl bromide). The most efficient supports concerning heterogenization were CNT treated with nitric acid and NaOH, and involving complexes 2 and 4 (in the same order, 2_CNT-ox-Na and 4_CNT-ox-Na). The immobilized catalysts can be recovered and recycled by simple workup and reused up to four consecutive cycles although with loss of activity.publishersversionpublishe