Synonymous codon usage pattern among the S,M, and L segments in Crimean-congo hemorrhagic fever virus

Crimean-Congo hemorrhagic fever (CCHF) virus is one among the major zoonosis viral diseases that use the Hyalomma ticks as their transmission vector to cause viral infection to the human and mammalian community. The fatality of infectious is high across the world especially in Africa, Asia, Middle East, and Europe. This study regarding codon usage bias of S, M, and L segments of the CCHF virus pertaining to the host Homo sapiens, reveals in-depth information about the evolutionary characteristics of CCHFV. Relative Synonymous Codon Usage (RSCU), Effective number of codons (ENC) were calculated, to determine the codon usage pattern in each segment. Correlation analysis between Codon adaptation index (CAI), GRAVY (Hydrophobicity), AROMO (Aromaticity), and nucleotide composition revealed bias in the codon usage pattern. There was no strong codon bias found among any segments of the CCHF virus, indicating both the factors i.e., natural selection and mutational pressure shapes the codon usage bias.     

The approximate entropy of the electromyographic signals of tremor correlates with the osmotic fragility of human erythrocytes

Background  

The main problem of tremor is the damage caused to the quality of the life of patients, especially those at more advanced ages. There is not a consensus yet about the origins of this disorder, but it can be examined in the correlations between the biological signs of aging and the tremor characteristics.     

Measurements in potassium-supplemented athletes during and after hypokinetic and ambulatory conditions

Hypokinesia (diminished movement) induces significant potassium (K) changes; however, little is known about K deposition and deficiency during hypokinesia (HK). Using K supplements during and after HK, the aim was to establish body K deposition and K deficiency during HK. Studies were done during the pre-HK period of 30 d, HK period of 364 d, and post-HK period of 30 d. Forty male trained athletes aged 24.9 ± 8.0 y were chosen as subjects. They were equally divided into four groups: unsupplemented active control subjects (UACS), unsupplemented hypokinetic subjects (UHKS), supplemented active control subjects (SACS), and supplemented hypokinetic subjects (SHKS). Hypokinetic subjects were limited to an average walking distance of 0.7 km/d. Control subjects ran an average distance of 11.6 km/d. The SHKS and SACS groups took 95.0 mg elemental K/kg body weight daily. Fecal K excretion, urinary sodium (Na) and K excretion, plasma K and Na levels, plasma renin activity (PRA), plasma aldosterone (PA), food and fluid intake, and physical characteristics were measured. During HK, fecal K loss, urinary K and Na loss, and plasma K, Na, PRA, and PA levels increased significantly (p ≤ 0.05), whereas during the initial days of post-HK, the levels of the measured parameters decreased significantly (p ≤ 0.05) in the SHKS and UHKS groups as compared with the SACS and UACS groups, respectively. During HK, body weight, body fat, peak oxygen uptake, food and fluid intake decreased significantly (p ≤ 0.05), whereas during the initial days of post-HK period remained significantly (p ≤ 0.05) depressed and fluid intake increased in SHKS and UHKS groups when compared with the SACS and UACS groups, respectively. However, during HK and post-HK plasma, urinary, and fecal K changed significantly (p ≤ 0.05) more in the SHKS group than in the UHKS group. The deposition of K was significantly (p ≤ 0.05) lower and K deficiency much higher in the SHKS group than in the UHKS group. Fecal K loss, urinary K and Na loss, plasma K, Na, PRA, and PA levels, body weight, body fat, peak oxygen uptake, and food and fluid intake did not change significantly in the SACS and UACS when compared with their baseline control values. It was shown that plasma K concentration and urinary and fecal K excretion increased during HK and decreased significantly (p ≤ 0.05) during post-HK. post-HK. Oral K supplements did not influence plasma or fecal and urinary K either during HK or post-HK. It was concluded that the low plasma K level and fecal and urinary K loss during post-HK may indicate the presence of K deficiency, and increased K in plasma, urine, and feces during HK and in the presence of K deficiency may suggest the body’s inability to retain K during HK.     

Calcium measurements in primates during and after hypokinesia in establishing calcium deficiency during prolonged hypokinesia

Hypokinesia (diminished movement) induces significant calcium (Ca) changes, but little is known about the effect of hypokinesia (HK) on Ca deficiency. Measuring Ca changes during and after HK the aim of this study was to determine Ca deficiency during prolonged HK. Studies were done on 12 male Macaca mulatta (rhesus monkeys) aged 3–5 yr (5.58–6.42 kg) during a 90-d pre-HK period, a 90-d HK period, and a 15-d post-HK period. Monkeys were equally divided into two groups: vivarium control monkeys (VCM) and hypokinetic monkeys (HKM). Hypokinetic monkeys were kept in small individual cages that restricted their movements in all directions without hindering food and water intakes. Urinary, fecal, and serum Ca, urinary and serum magnesium (Mg) and phosphate (P), serum intact parathyroid hormone (iPTH), and calcitonin (CT) concentration, body weight, food intake, fluid consumed and eliminated in urine were measured. During the HK period, fecal Ca loss, urinary Ca, P, and Mg excretion, fluid elimination, and serum P, Ca, and Mg concentration increased significantly (p≤0.01), whereas serum iPTH and CT concentration, food and fluid intakes, and body weight decreased significantly (p≤0.01) in the HKM group when compared with the VCM group. During the initial days of the post-HK period, serum Ca, Mg, and P concentration, fecal Ca loss, urinary Ca, Mg, and P excretion, and fluid elimination decreased significantly (p≤0.01), whereas fluid intake increased significantly (p≤0.01) in the HKM group when compared with the VCM group. Food intake, body weight, and serum iPTH and CT concentrations remained significantly (p≤0.01) depressed in the HKP group when compared with the VCM; however, they increased as the duration of the post-HK period increased. By contrast, the corresponding parameters remained stable in the VCM group when compared with the baseline control values. It was shown that fecal and urinary Ca loss and serum Ca concentration increases significantly during HK, whereas during post-HK fecal, urinary, and serum Ca decreases significantly. It was concluded that significant decrease of serum, urinary, and fecal Ca during post-HK may suggest the presence of Ca deficiency during prolonged HK.     

Long-term landscape changes in vegetation structure: fire management in the wetlands of KwaMbonambi,South Africa

In wetlands the effects of fire on vegetation dynamics are somewhat uncertain. A change detection analysis in the herbaceous wetlands of KwaMbonambi, South Africa, which were subject to frequent fires, revealed that in 1937 the study area comprised grassland (69%), herbaceous wetland (25%), indigenous swamp forest (4%) and tree plantations (1%). However, by 1970, tree plantations occupied 78% of the landscape and grasslands and herbaceous wetlands had declined to 9% and 6%, respectively, whereas indigenous swamp forest had increased to 6%. By 2009 tree plantations had been removed from the wetland areas. Despite this opportunity for herbaceous wetlands to recover their historical extent, they decreased to only 2%, mostly changing to indigenous swamp forest or to an herbaceous/fern (Stenochlaena tenuifolia)/woodland mosaic. Fire records showed suppression of fire to be an important contributing factor, particularly in wetlands that had been disturbed by tree plantations, although subsequently removed. A pilot burning experiment revealed that S. tenuifolia did not inhibit fire. It is therefore practicable to increase fire frequency to prevent the mosaic developing into forest. A conceptual model of the influence of fire regime on wetland vegetation type is presented and priorities for further research on wetlands and fire are recommended.     

Thalidomide attenuates nitric oxide mediated angiogenesis by blocking migration of endothelial cells

Background  

Thalidomide is an immunomodulatory agent, which arrests angiogenesis. The mechanism of anti-angiogenic activity of thalidomide is not fully understood. As nitric oxide is involved in angiogenesis, we speculate a cross-talk between thalidomide and nitric oxide signaling pathway to define angiogenesis. The aim of present study is to understand the mechanistic aspects of thalidomide-mediated attenuation of angiogenesis induced by nitric oxide at the cellular level.     

Neural mechanisms of context-dependent processing of CO2 avoidance behavior in fruit flies

The fruit fly, Drosophila melanogaster, innately avoids even low levels of CO₂. CO₂ is part of the so-called Drosophila stress odor produced by stressed flies, but also a byproduct of fermenting fruit, a main food source, making the strong avoidance behavior somewhat surprising. Therefore, we addressed whether feeding states might influence the fly’s behavior and processing of CO₂. In a recent report, we showed that this innate behavior is differentially processed and modified according to the feeding state of the fly. Interestingly, we found that hungry flies require the function of the mushroom body, a higher brain center required for olfactory learning and memory, but thought to be dispensable for innate olfactory behaviors. In addition, we anatomically and functionally characterized a novel bilateral projection neuron connecting the CO₂ sensory input to the mushroom body. This neuron was essential for processing of CO₂ in the starved fly but not in the fed fly. In this Extra View article, we provide evidence for the potential involvement of the neuromodulator dopamine in state-dependent CO₂ avoidance behavior. Taken together, our work demonstrates that CO₂ avoidance behavior is mediated by alternative neural pathways in a context-dependent manner. Furthermore, it shows that the mushroom body is not only involved in processing of learned olfactory behavior, as previously suggested, but also in context-dependent innate olfaction.     

Calcium supplementation effect on calcium balance in endurance-trained athletes during prolonged hypokinesia and ambulatory conditions

Calcium (Ca) supplements may be used to normalize Ca-balance changes but little is known about the effect of Ca supplements on Ca balance during hypokinesia (decreased kilometers per day). The aim of this study was to evaluate the effect of daily intakes of Ca supplements on Ca balance during hypokinesia (HK). Studies were done during 30 d of a pre-HK period and during 364 d of a HK period. Forty male athletes aged 23–26 yr were chosen as subjects. They were divided equally into four groups: unsupplemented ambulatory control subjects (UACS), unsupplemented hypokinetic subjects (UHKS), supplemented hypokinetic subjects (SHKS), and supplemented ambulatory control subjects (SACS). The SHKS and UHKS groups were kept under an average running distance of 0.7 km/d. In the SHKS and SACS groups supplemented with 35.0 mg Ca lactate/kg body weight. Fecal Ca loss, urinary excretion of Ca and phosphate (P), serum concentrations of ionized calcium (Ca_I) total Ca, P, and Ca balance, intact parathyroid hormone (iPTH) and 1,25 dihydroxyvitamin D (1,25(OH)2D), anthropometric characteristics and peak oxygen uptake were measured. Fecal Ca excretion, urinary Ca and P excretion, serum Ca_I, total Ca, and P concentration, and negative Ca balanced increased significantly (p ≤ 0.01) in the SHKS and UHKS groups when compared with the SACS and UACS groups. Serum, urinary, and fecal Ca changes were much greater and appeared much faster in the SHKS group than in the UHKS group. Serum iPTH and 1,25 (OH)2 D, body weight, and peak oxygen uptake decreased significantly (p ≤ 0.01) in the SHKS and UHKS groups when compared with the SACS and UACS groups. In contrast, the corresponding parameters remained stable in the SACS and UACS groups when compared with the baseline control values. It was concluded that during prolonged HK, urinary and fecal Ca excretion and serum Ca concentration increased significantly despite the presence of a negative Ca balance; thus, Ca supplements cannot be used to normalize negative Ca balance during prolonged HK.     

High-depth sequencing of over 750 genes supports linear progression of primary tumors and metastases in most patients with liver-limited metastatic colorectal cancer

BackgroundColorectal cancer with metastases limited to the liver (liver-limited mCRC) is a distinct clinical subset characterized by possible cure with surgery. We performed high-depth sequencing of over 750 cancer-associated genes and copy number profiling in matched primary, metastasis and normal tissues to characterize genomic progression in 18 patients with liver-limited mCRC.ResultsHigh depth Illumina sequencing and use of three different variant callers enable comprehensive and accurate identification of somatic variants down to 2.5% variant allele frequency. We identify a median of 11 somatic single nucleotide variants (SNVs) per tumor. Across patients, a median of 79.3% of somatic SNVs present in the primary are present in the metastasis and 81.7% of all alterations present in the metastasis are present in the primary. Private alterations are found at lower allele frequencies; a different mutational signature characterized shared and private variants, suggesting distinct mutational processes. Using B-allele frequencies of heterozygous germline SNPs and copy number profiling, we find that broad regions of allelic imbalance and focal copy number changes, respectively, are generally shared between the primary tumor and metastasis.ConclusionsOur analyses point to high genomic concordance of primary tumor and metastasis, with a thick common trunk and smaller genomic branches in general support of the linear progression model in most patients with liver-limited mCRC. More extensive studies are warranted to further characterize genomic progression in this important clinical population.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0589-1) contains supplementary material, which is available to authorized users.