U7 snRNAs： A Computational Survey

U7 small nuclear RNA (snRNA) sequences have been described only for a handful of animal species in the past. Here we describe a computational search for func- tional U7 snRNA genes throughout vertebrates including the upstream sequence elements characteristic for snRNAs transcribed by polymerase Ⅱ. Based on the results of this search, we discuss the high variability of U7 snRNAs in both se- quence and structure, and report on an attempt to find U7 snRNA sequences in basal deuterostomes and non-drosophilids insect genomes based on a combination of sequence, structure, and promoter features. Due to the extremely short se- quence and the high variability in both sequence and structure, no unambiguous candidates were found. These results cast doubt on putative U7 homologs in even more distant organisms that are reported in the most recent release of the Rfam database.     

Demography of an alpine population of Savannah Sparrows

ABSTRACT.   Although Savannah Sparrows ( Passerculus sandwichensis ) have been well studied across their North American range, few data are available for populations that breed in high-elevation habitats. We collected data over six years on the demography of a population of Savannah Sparrows ( P. s. anthinus ) breeding in alpine tundra and sub-alpine meadows in northern British Columbia, Canada. The mean duration of the breeding season at our site was 45.5 d, and pairs produced a maximum of one brood per season. Clutch sizes varied annually (mean = 4.37, range = 3.90 – 4.71 eggs). Nest fate also varied among years (range = 33 – 92%) due to variation in abiotic (weather) and biotic (predators) conditions. Uncorrected return rates of banded birds were 68% for adults and 17% for juveniles ( N = 22 and 102, respectively). However, when resighting probability was taken into account, apparent annual survival was 75% for adults and 34% for juveniles. Compared to populations at lower elevations, Savannah Sparrows in our study had shorter breeding seasons, fewer broods per season, larger clutches, and higher adult and juvenile return rates. Our results suggest that Savannah Sparrows that breed in high-elevation habitats have adopted a low fecundity, high survival life history strategy that enables their persistence in these challenging environments.     

Acetylation of alpha MSH and beta-endorphin by rat neurointermediate pituitary secretory granule-associated acetyltransferase

ACTH(1-8) and ACTH(9-13)NH2 were used as potential enzyme inhibitors to begin examining the relationship between the acetylation of ACTH- and beta-endorphin-related peptides. ACTH(1-8) was a potent inhibitor of the acetylation of both ACTH- and beta-endorphin-related peptides, whereas ACTH(9-13)NH2 was an effective inhibitor only of the acetylation of ACTH-related substrates. This inhibition pattern indicated that there may be an unusual interaction between some ACTH- and beta-endorphin-related peptides as substrates for the acetyltransferase. Utilizing HPLC to separate ACTH- and beta-endorphin-related peptides present in the same reaction mixture, ACTH(1-14) and beta-endorphin(1-27) at Km and saturating concentrations were used as substrates to examine the ability of one peptide substrate to affect the acetylation of the other. It was observed that the acetylation of ACTH(1-14), even at Km concentration, was relatively unaffected by the presence of beta-endorphin(1-27). However, the acetylation of beta-endorphin(1-27) was significantly reduced by the presence of ACTH(1-14). This preferential acetylation of ACTH-related peptides over the acetylation of beta-endorphin-related peptides might have physiological importance under some conditions.     

Alkanetriols in psilotophyte cutins

The covalently bonded components of the stem cutin of Psilotum include 16-hydroxyhexadecanoic acid and substantial amounts of hexadecane-1,8,16-triol. While of generally similar composition, leaf cutin of Tmesipteris contains a mixture of hexadecanetriol isomers. The findings suggest that psilotophyte cutins evolved in a different manner from those of other land plants.     

Heat shock temperature acclimation of normal secretory protein synthesis in barley aleurone cells

Exposure of barley (Hordeum vulgare L. cv. Himalaya) aleurone layers to 40°C for a period of 3 h results in the selective suppression of the synthesis and secretion of hydrolytic enzymes; other normal cellular protein synthesis continues during heat shock. This suppression is correlated with secretory protein mRNA destabilization and the dissociation of stacked ER lamellae during heat shock (Belanger et al. 1986, Proceedings of the National Academy of Sciences USA 83, pp. 1354–1358). In this report we examined the effect of exposure to extended periods of heat shock. If exposure to 40°C was continued for a period of 18 h, the synthesis of α-amylase, the predominant secreted hydrolase, resumed. This was accompanied by increased α-amylase mRNA levels and the reformation of ER lamellae. Though initial exposure (3 h) to 40°C reduced protein secretion to ～10% of that observed in aleurone cells maintained at 25°C, exposure for prolonged periods (16–20 h) permitted the resumption of protein secretion to ～66% of non-heat-shocked control levels. The resumption of normal secretory protein synthesis during prolonged exposure to 40°C was correlated with an increase in the incorporation of [¹⁴C]glycerol into phosphatidylcholine and an increase in the ratio of saturated to unsaturated fatty acids in lipids isolated from ER membrane preparations. Increased fatty acid saturation has been demonstrated to enhance thermostability in biological membranes, and such changes in membrane composition may be important to the recovery of secretory protein synthesis at the ER.     

Overproduction of d-xylose isomerase in Escherichia coli by cloning the d-xylose isomerase gene

The Escherichia coli d-xylose isomerase (d-xylose ketol-isomerase, EC 5.3.1.5) gene, xylA, has been cloned on various E. coli plasmids. However, it has been found that high levels of overproduction of the d-xylose isomerase, the protein product of the xylA gene, cannot be accomplished by cloning the intact gene on high copy-number plasmids alone. This is believed to be due to the fact that the expression of the gene through its natural promoter is highly regulated in E. coli. In order to overcome this, the xylA structural gene has been fused with other strong promoters such as tac and lac, resulting in the construction of a number of fused genes. Analysis of the E. coli transformants containing the fused genes, cloned on high copy-number plasmids, indicated that a 20-fold overproduction of the enzyme can now be obtained. It is expected that overproduction of the enzyme in E. coli can still be substantially improved through additional manipulation with recombinant DNA techniques.     

Enhancing Data Reliability in TOMAHAQ for Large‐Scale Protein Quantification

The analytical scale of most mass‐spectrometry‐based targeted proteomics assays is usually limited by assay performance and instrument utilization. A recently introduced method, called triggered by offset, multiplexed, accurate mass, high resolution, and absolute quantitation (TOMAHAQ), combines both peptide and sample multiplexing to simultaneously improve analytical scale and quantitative performance. In the present work, critical technical requirements and data analysis considerations for successful implementation of the TOMAHAQ technique based on the study of a total of 185 target peptides across over 200 clinical plasma samples are discussed. Importantly, it is observed that significant interference originate from the TMTzero reporter ion used for the synthetic trigger peptides. This interference is not expected because only TMT10plex reporter ions from the target peptides should be observed under typical TOMAHAQ conditions. In order to unlock the great promise of the technique for high throughput quantification, here a post‐acquisition data correction strategy to deconvolute the reporter ion superposition and recover reliable data is proposed.     

The results of a close follow-up of trainees to gain a good blood collection practice

BackgroundPhlebotomy is one of the most important steps in the preanalytical phase of a clinical laboratory process. In order to decrease phlebotomy errors, this specific procedure should be taught in detail by laboratory organizations. Our study aims to practice the training program on venous blood sampling and observe the close follow-up results.MethodsIn this observational study, 127 students who started their summer internship in Antalya Education and Research Hospital were given a one-day theoretical phlebotomy training in accordance with the Venous Blood Sampling Guidelines. After the theoretical training, phlebotomy applications of 10 students who were working in the field of out-patient blood sampling were observed both with and without their knowledge. A comprehensive checklist related to phlebotomy was created by the trainers in Antalya Education and Research Hospital and the observers answered each question as yes or no. For the statistical analysis, IBM SPSS Statistics 21.0 was used.ResultsAfter the theoretical education, the trainees were observed but no significant difference was found between the first and the second informed observations (p = 0.125). The students were observed three times more in the following week without their knowledge. There was a statistically significant difference between the first and the third unannounced observations (p=0.001).ConclusionsIn order to perform phlebotomy correctly, apart from theoretical education, a close follow-up is necessary too.