Mutation patterns of amino acid tandem repeats in the human proteome

Background: Amino acid tandem repeats are found in nearly one-fifth of human proteins. Abnormal expansion of these regions is associated with several human disorders. To gain further insight into the mutational mechanisms that operate in this type of sequence, we have analyzed a large number of mutation variants derived from human expressed sequence tags (ESTs).Results: We identified 137 polymorphic variants in 115 different amino acid tandem repeats. Of these, 77 contained amino acid substitutions and 60 contained gaps (expansions or contractions of the repeat unit). The analysis showed that at least about 21% of the repeats might be polymorphic in humans. We compared the mutations found in different types of amino acid repeats and in adjacent regions. Overall, repeats showed a five-fold increase in the number of gap mutations compared to adjacent regions, reflecting the action of slippage within the repetitive structures. Gap and substitution mutations were very differently distributed between different amino acid repeat types. Among repeats containing gap variants we identified several disease and candidate disease genes.Conclusion: This is the first report at a genome-wide scale of the types of mutations occurring in the amino acid repeat component of the human proteome. We show that the mutational dynamics of different amino acid repeat types are very diverse. We provide a list of loci with highly variable repeat structures, some of which may be potentially involved in disease.

Comparative analysis of amino acid repeats in rodents and humans

Amino acid tandem repeats, also called homopolymeric tracts, are extremely abundant in eukaryotic proteins. To gain insight into the genome-wide evolution of these regions in mammals, we analyzed the repeat content in a large data set of rat-mouse-human orthologs. Our results show that human proteins contain more amino acid repeats than rodent proteins and that trinucleotide repeats are also more abundant in human coding sequences. Using the human species as an outgroup, we were able to address differences in repeat loss and repeat gain in the rat and mouse lineages. In this data set, mouse proteins contain substantially more repeats than rat proteins, which can be at least partly attributed to a higher repeat loss in the rat lineage. The data are consistent with a role for trinucleotide slippage in the generation of novel amino acid repeats. We confirm the previously observed functional bias of proteins with repeats, with overrepresentation of transcription factors and DNA-binding proteins. We show that genes encoding amino acid repeats tend to have an unusually high GC content, and that differences in coding GC content among orthologs are directly related to the presence/absence of repeats. We propose that the different GC content isochore structure in rodents and humans may result in an increased amino acid repeat prevalence in the human lineage.

Dissecting the role of low-complexity regions in the evolution of vertebrate proteins

Low-complexity regions (LCRs) in proteins are tracts that are highly enriched in one or a few aminoacids. Given their high abundance, and their capacity to expand in relatively short periods of time through replication slippage, they can greatly contribute to increase protein sequence space and generate novel protein functions. However, little is known about the global impact of LCRs on protein evolution. We have traced back the evolutionary history of 2,802 LCRs from a large set of homologous protein families from H.sapiens, M.musculus, G.gallus, D.rerio and C.intestinalis. Transcriptional factors and other regulatory functions are overrepresented in proteins containing LCRs. We have found that the gain of novel LCRs is frequently associated with repeat expansion whereas the loss of LCRs is more often due to accumulation of amino acid substitutions as opposed to deletions. This dichotomy results in net protein sequence gain over time. We have detected a significant increase in the rate of accumulation of novel LCRs in the ancestral Amniota and mammalian branches, and a reduction in the chicken branch. Alanine and/or glycine-rich LCRs are overrepresented in recently emerged LCR sets from all branches, suggesting that their expansion is better tolerated than for other LCR types. LCRs enriched in positively charged amino acids show the contrary pattern, indicating an important effect of purifying selection in their maintenance. We have performed the first large-scale study on the evolutionary dynamics of LCRs in protein families. The study has shown that the composition of an LCR is an important determinant of its evolutionary pattern.

Laparoscopic Gastric Banding Outcomes Do Not Depend on Device or Technique. Long-Term Results of a Prospective Randomized Study Comparing the Lapband® and the SAGB®.

BACKGROUND: Gastric banding still represents one of the most widely used bariatric procedures. It provides acceptable weight loss in many patients, but has frequent long-term complications. Because different types of bands may lead to different results, we designed a randomized study to compare the Lapband® with the SAGB®. We hereby report on the long-term results. METHODS: Between December 1998 and June 2002, 180 morbidly obese patients were randomized between Lapband® or SAGB®. Weight loss, long-term morbidity, and need for reoperation were evaluated. RESULTS: Long-term weight loss did not differ between the two bands. Patients who maintained their band had an acceptable long-term weight loss of between 50 and 60 % EBMIL. In both groups, about half the patients developed long-term complications, with about 50 % requiring major redo surgery. There was no difference in the overall rates of long-term complications or failures between the two groups, but patients who had a Lapband® were significantly more prone to develop band slippage/pouch dilatation (13.3 versus 0 %, p < 0,001). CONCLUSIONS: Although in the absence of complication, gastric banding leads to acceptable weight loss; the long-term complication and major reoperation rates are very high independently from the type of band used or on the operative technique. Gastric banding leads to relatively poor overall long-term results and therefore should not be considered the procedure of choice for the treatment of morbid obesity. Patients should be informed of the limited overall weight loss and the very high complication rates.

Projecte d’ampliació i millores de l’explotació bovina de cria “CAN PEREAULET” de Bescanó

L’explotació ramadera a projectar és la “Can Pereaulet”, situada a la finca Can Pereaulet, situada al terme municipal de Bescanó, a la comarca del Gironès, manté una estructura d’àmbit familiar.L’objectiu d’aquest projecte és ampliar la capacitat de la granja Can Pereaulet per poder deslletar els vedells, millorar el benestar animal i la producció de vedells per a engreix a 600 vedells/any. La construcció de la nau permetrà una zona d’alimentació i descans totalment coberta, una zona d’exercici parcialment coberta i una sala de preparació i magatzem dels productes necessaris. De la granja actual s’utilitzarà una quadre per infermeria i la resta per diferents necessitats com ara, magatzem palla, garatge tractor

Soil compaction by machine traffic and least limiting water range related to soybean yield

The research aimed to evaluate machine traffic effect on soil compaction and the least limiting water range related to soybean cultivar yields, during two years, in a Haplustox soil. The six treatments were related to tractor (11 Mg weight) passes by the same place: T0, no compaction; and T1*, 1; T1, 1; T2, 2; T4, 4 and T6, 6. In the treatment T1*, the compaction occurred when soil was dried, in 2003/2004, and with a 4 Mg tractor in 2004/2005. Soybean yield was evaluated in relation to soil compaction during two agricultural years in completely randomized design (compaction levels); however, in the second year, there was a factorial scheme (compaction levels, with and without irrigation), with four replicates represented by 9 m² plots. In the first year, soybean [Glycine max (L.) Merr.] cultivar IAC Foscarim 31 was cultivated without irrigation; and in the second year, IAC Foscarim 31 and MG/BR 46 (Conquista) cultivars were cultivated with and without irrigation. Machine traffic causes compaction and reduces soybean yield for soil penetration resistance between 1.64 to 2.35 MPa, and bulk density between 1.50 to 1.53 Mg m-3. Soil bulk density from which soybean cultivar yields decrease is lower than the critical one reached at least limiting water range (LLWR =/ 0).

Long sequence duplications, repeats, and palindromes in HIV-1 gp120: length variation in V4 as the product of misalignment mechanism.

We have shown that indels in gp120 V4 are associated to the presence of duplicated and palindromic sequences, suggesting that they may be produced by strand-slippage misalignment mechanism. Indels in V4 involved region-specific duplications 9 to 15 bp long, and repeats of various lengths, associated to trinucleotides AAT. No duplications were found in V3 and C3. The frequency of palindromic sequences in individual genes was found to be significantly higher in gp120 (p < or = 3.00E-7), and significantly lower in Tat (p < or = 9.00E-7) than the average frequency calculated over the full genome. The finding of elements of misalignment in association with indels in V4 suggests that these mutations may occur in proviral DNA after integration of HIV into the host genome. It also implies that occurrence of large indels in gp120 is not random but is directed by the presence and distribution of elements of misalignment in the HIV genome.

Farm Safety is Important in Iowa, October 11, 2012

An IDPH Occupational Health and Safety Surveillance Program (OHSSP) analysis of Iowa’s work-related traumatic fatalities shows that transportation events accounted for 48 of 90 deaths in 2011. Agricultural activities were involved in 21 of the 48 transportation deaths (44%) and 32 of the 90 total fatalities (36%). Tractor and ATV (all-terrain vehicle) or UTV (utility vehicle) rollovers were responsible for 62% (13/21) of the farm or ag-related transportation deaths.

Nuevos neumáticos para tractores agrícolas

El neumático agrícola condiciona de forma determinante el rendimiento del tractor. Es necesario, por tanto, que el agricultar conozca las prestaciones de los neumáticos actuales. Ello le permitirá elegir el equipamiento más adecuado a sus necesidades.

Tractores especiales: viñeros y fruteros

A la hora de adquirir un tractor el viticultor y el fruticultor han de tener en cuenta sus necesidades, las características técnicas de la máquina y la utilidad de las innovaciones tecnológicas del mismo.

Evaluación de tres métodos para el arrastre de madera en rodales naturales de Pinus caribaea var. caribaea

El trabajo se realizó en rodales naturales de Pinus caribaea var. caribaea, ubicados en la unidad silvícola San Andrés, La Palma, provincia Pinar del Río. El objetivo de la investigación fue evaluar la eficiencia y los daños causados a la cubierta vegetal del suelo durante la operación de arrastre de madera. Se evaluaron tres métodos: 1 - el arrastre de fustes enteros con yuntas de bueyes hasta los patios de carga; 2 - el arrastre de fustes enteros con tractor hasta los patios de carga; 3 - el arrastre de fustes enteros con yuntas de bueyes hasta las pistas de arrastre y con tractor hasta los patios de carga. El método de arrastre de madera que consistió en la combinación del empleo de animales y de tractor resultó más eficiente y provocó menos alteraciones a la cubierta vegetal del suelo.

Evaluation of the surface erosion from different timber yarding methods in Honduras

Surface runoff and sediment production from different timber yarding practices, some using Best Management Practices (BMPs) recommended for Honduras, were monitored in experimental plots during the rainy seasons of two consecutive years in pine forest highlands of central Honduras. Different timber yarding systems were applied to pseudo-replicated plots during the rainy seasons of 1999 and 2000. In 1999, two treatments were studied: tractor yarding and skyline cable (a recommended BMP). In 2000, four treatments were evaluated: tractor skidding, skyline cable, animal skidding (another recommended BMP), and undisturbed forest (reference). During the rainy seasons of these years, surface runoff volumes and sediment yield were measured at five 1.5m x 10m erosion plots in each treated area. The results showed significant differences between traditional tractor yarding and the recommended skyline cable and animal skidding methods. Tractor yarding produced six to ten times more erosion during the rainy seasons than cable and animal yarding. The improved soil retention of cable and animal yarding was especially important during September when the highest rainfall occurred in this climate.

Efficiency of pneumatic and horizontal perforated disk meter mechanism in corn no-tillage seeders in soil with different mobilization reports

This work objectified to evaluate the efficiency of two meter mechanism of corn seeds when submitted to different forward speed and soil management system during the non-tillage seeding. It was used a factorial design in randomized blocks. The factors whose effects were examined were related to the seeders with pneumatic and horizontal disk meter mechanisms for the distribution of the seeds, to the set tractor-seeder forward speeds (4.4; 8.0 and 9.8 km h-1), and to the soil management system considering the corn no-tillage seeding over minimum tillage with chisel plow and the no-tillage system for the seeding of oat culture (Avena strigosa Schreb). It was verified that the forward speed didn't influence the initial and final stands of plants but it interfered in the regularity of longitudinal distribution of plants. The smallest speed provided the largest percentile of normal spacing between plants. The pneumatic meter mechanism presented better performance than the horizontal disk perforated in the longitudinal distribution of plants. About corn productivity aspect it's indifferent the recommendation of use for pneumatic and perforated horizontal disk meter mechanism of seeds.

Seeder-fertilizer machine: energetic demand as a function of vegetal covering handling and manure deposition shank depth in no-tillage system

The purpose of this work was evaluating the energetic demand of a seeder-fertilizer machine as a function of the type and handling of vegetal covering culture and of the fertilizer deposition shank depth. A Valtra BM100 tractor was used implemented to pull a high precision seeder-fertilizer machine with four ranks of seeding, spaced 0.9 m for maize culture. Experiment was conducted with design in randomized blocks in factorial plots, in the Laboratory of Machines and Agricultural Mechanization experimental area (LAMMA) of UNESP-Jaboticabal, using two covering cultures (black-mucuna and crotalaria), three handlings of this covering, two mechanical (straw crusher and roller knife) and one chemical (pulverization of herbicide), performed 120 days after seeding of covering cultures and three depths of fertilizer deposition shank, completing 18 treatments, with four repetitions, totaling 72 observations. Parameters of displacement speed, gliding, force on traction bar, peak force, power on pulling bar and fuel consumption were evaluated. It was possible to conclude that force on traction bar was less for depths of 0.11 and 0.14 m of fertilizer plough shank, the same occurring for peak force, power on traction bar and volumetric consumption. The specific consumption was lower at a depth of 0.17 m of fertilizer plough shank. Covering cultures and their handlings did not interfere in the performance of machines under inquiry.

Operational performance of the mechanized and semi-mechanized potato harvest

Potato is an important crop plant throughout the world. Harvesting is a fundamental step in its production system. Maybe, it is the most complex and expensive operation. Thus, the objective of this work was to compare the cost of the mechanized and semi-mechanized harvest, the operational capacity and the production losses during the potato harvest process. The work was accomplished in a commercial farming, cultivated under pivot system, in the municipal district of Perdizes - MG, Brazil. A completely randomized design with two treatments was used: mechanized and semi-mechanized harvest. The mechanized harvest used a self-propelled harvester. In the semi-automated harvest, a digger mounted on tractor was used and the potato was manually harvested. It was concluded that the cost of mechanized harvest was 49.03% lower than the cost of semi-mechanized harvest. On average, the harvester had a work for 23 workers in manual harvest. Mechanized harvest showed losses of 2.35% of potato yield, while the semi-mechanized harvest showed losses of 6.32%.