Abstract: Working with biodiversity data is a computationally intensive process. Numerous applications and services provide options to deal with sequencing and taxonomy data. Professional statistics software are also available to analyze these type of data. However, in-between the two processes there is a huge need to curate biodiversity sample files. Curation involves creating summed abundance values for chosen taxonomy ranks, excluding certain taxa from analysis, and finally merging and downsampling data files. Very few tools, if any, offer a solution to this problem, thus we present Taxamat, a simple data management application that allows for curation of biodiversity data files before they can be imported to other statistics software. Taxamat is a downloadable application for automated curation of biodiversity data featuring taxonomic classification, taxon filtering, sample merging, and downsampling. Input and output files are compatible with most widely used programs. Taxamat is available on the web at http://www.taxamat.com either as a single executable or as an installable package for Microsoft Windows platforms.
Keywords: biodiversity, data management, taxonomy, diversity indices
Abstract: Introduction: During mammalian brain development, neural activity leads to maturation of glutamatergic innervations to locus coeruleus. In this study, fast excitatory postsynaptic currents mediated by N-methyl-Daspartate (NMDA) receptors were evaluated to investigate the maturation of excitatory postsynaptic currents in locus coeruleus (LC) neurons. Methods: NMDA receptor-mediated synaptic currents in LC neurons were evaluated using whole-cell voltage-clamp recording during the primary postnatal weeks. This technique was used to calculate the optimum holding potential for NMDA receptor-mediated currents and the best frequency for detecting spontaneous excitatory postsynaptic currents (sEPSC). Results: The optimum holding potential for detecting NMDA receptor-mediated currents was þ 40 to þ 50 mV in LC neurons. The frequency, amplitude, rise time, and decay time constant of synaptic responses depended on the age of the animal and increased during postnatal maturation. Conclusion: These findings suggest that most nascent glutamatergic synapses express functional NMDA receptors in the postnatal coerulear neurons, and that the activities of the neurons in this region demonstrate an age-dependent variation.
Keywords: locus coeruleus, NMDA receptor, spontaneous activity, postnatal development, excitatory postsynaptic currents, patch clamp
Abstract: Social isolation damages the nervous system by weakening the antioxidant system and leading to behavioral disorders. Fennel (Foeniculum vulgare Mill.) is an herbal plant that has antioxidant and neuroprotective properties. The objective of this study was to evaluate the effect of fennel methanol extract and its major component trans-anethole on spatial learning and memory, anxiety and depression in male rats exposed to social isolation stress. Rats were divided into six groups of Control (C), Fennel (F), trans-Anethole (A), Isolation, Isolation-F and Isolation-A. The rats were kept in the cage alone for 30 days to induce isolation. Fennel extract (150 mg/kg) and trans-anethole (80 mg/kg) were also gavaged during this period. At the end of the course, spatial learning and memory, anxiety and depression were measured by Morris water maze (MWM), elevated plus maze (EPM) and forced swimming test (FST), respectively. Learning and memory were impaired in isolated rats. Swimming time and distance to reach the hidden platform in these animals increased compared with controls (P < 0.05). In the EPM test, the percentage of open arm entries and open arm time also decreased significantly in the Isolation group (P < 0.01). The immobilization time in FST also increased significantly in these animals compared with the Control group (P < 0.001). Fennel and trans-anethole were both able to eliminate these changes in isolated rats. It is concluded that fennel and its major component, trans-anethole are suitable candidates for the prevention and treatment of stress-induced neurological disorders.
Keywords: Fennel (Foeniculum vulgare Mill.), trans-anethole, memory, anxiety, depression, social isolation
Abstract: The physiology of baroreceptors and chemoreceptors present in large blood vessels of the heart is well known in the regulation of cardiorespiratory functions. Since large blood vessels and peripheral blood vessels are of the same mesodermal origin, therefore, involvement of the latter in the regulation of cardiorespiratory system is expected. The role of perivascular nerves in mediating cardiorespiratory alterations produced after intraarterial injection of a nociceptive agent (bradykinin) was examined in urethane-anesthetized male rats. Respiratory frequency, blood pressure, and heart rate were recorded for 30 min after the retrograde injection of bradykinin/saline into the femoral artery. In addition, paw edema was determined and water content was expressed as percentage of wet weight. Injection of bradykinin produced immediate tachypneic, hypotensive and bradycardiac responses of shorter latency (5–8 s) favoring the neural mechanisms involved in it. Injection of equi-volume of saline did not produce any responses and served as time-matched control. Paw edema was observed in the ipsilateral hind limb. Pretreatment with diclofenac sodium significantly attenuated the bradykinin- induced responses and also blocked the paw edema. Ipsilateral femoral and sciatic nerve sectioning attenuated bradykinin-induced responses significantly, indicating the origin of responses from the local vascular bed. Administration of bradykinin in the segment of an artery produced reflex cardiorespiratory changes by stimulating the perivascular nociceptors involving prostaglandins. This is a novel study exhibiting the role of peripheral blood vessels in the regulation of the cardiorespiratory system.
Keywords: nociceptive agent, bradykinin, diclofenac sodium, vasosensory afferents, perivascular nerve, femoral and sciatic denervation, VR1 receptors
Abstract: Numerous studies indicate that smoking during pregnancy exerts harmful effects on fetal brain development. The aim of this study was to determine the influence of maternal smoking during pregnancy on the early physical and neurobehavioral development of newborn rats. Wistar rats were subjected to whole-body smoke exposure for 2 3 40 min daily from the day of mating until day of delivery. For this treatment, a manual closed-chamber smoking system and 4 research cigarettes per occasion were used. After delivery the offspring were tested daily for somatic growth, maturation of facial characteristics and neurobehavioral development until three weeks of age. Motor coordination tests were performed at 3 and 4 weeks of age. We found that prenatal cigarette smoke exposure did not alter weight gain or motor coordination. Critical physical reflexes indicative of neurobehavioral development (eyelid reflex, ear unfolding) appeared significantly later in pups prenatally exposed to smoke as compared to the control group. Prenatal smoke exposure also resulted in a delayed appearance of reflexes indicating neural maturity, including hind limb grasping and forelimb placing reflexes. In conclusion, clinically relevant prenatal exposure to cigarette smoke results in slightly altered neurobehavioral development in rat pups. These findings suggest that chronic exposure of pregnant mothers to cigarette smoke (including passive smoking) results in persisting alterations in the developing brain, which may have long-lasting consequences supporting the concept of developmental origins of health and disease (DoHAD).
Keywords: prenatal, smoking during pregnancy, tobacco, neurobehavioral development, rat
Abstract: Purpose: Betanin is a betacyanin with antioxidant and anti-inflammatory activities whose effects were investigated in a nonalcoholic steatohepatitis (NASH) model. Main methods: Ninety-six male naval medical research institute (NMRI) mice were divided into eight groups (n 5 12) including normal control, high fat diet (HFD), Sham, and positive control treated with trans-chalcone. Three experimental groups were treated with 5 mg/kg, 10 mg/kg or 20 mg/kg betanin, and a betanin protective group was also defined. Results: Four weeks of HFD treatment resulted in steatohepatitis with associated fibrosis. Significant increase was observed in serum levels of triglycerides (TG), total cholesterol (TC), glucose, insulin, leptin, liver enzymes, malondialdehyde (MDA), furthermore insulin resistance and (sterol regulatory element-binding protein-1c) SREBP-1c were detected. Levels of high-density lipoprotein cholesterol (HDL-C), adiponectin, superoxide dismutase (SOD), catalase (CAT), and PPAR-a (peroxisome proliferator-activated receptor-a) considerably decreased. Treatment by betanin, particularly the 20 mg/kg dosage, attenuated these changes. Conclusion: Betanin is a potential treating agent of steatohepatitis and works through up-regulation of PPAR-a, down-regulation of SREBP-1c, modification of adipokine levels and modulation of lipid profile.
Keywords: betanin, nonalcoholic fatty liver disease (NAFLD), nonalcoholic steatohepatitis (NASH), peroxisome proliferatoractivated receptor-a (PPAR-a), insulin resistance
Abstract: Renal injury is reported to have a high mortality rate. Additionally, there are several limitations to current conventional treatments that are used to manage it. This study evaluated the protective effect of hesperidin against ischemia/reperfusion (I/R)-induced kidney injury in rats. Renal injury was induced by generating I/ R in kidney tissues. Rats were then treated with hesperidin at a dose of 10 or 20 mg/kg intravenously 1 day after surgery for a period of 14 days. The effect of hesperidin on renal function, serum mediators of inflammation, and levels of oxidative stress in renal tissues were observed in rat kidney tissues after I/Rinduced kidney injury. Moreover, protein expression and mRNA expression in kidney tissues were determined using Western blotting and RT-PCR. Hematoxylin and eosin (H&E) staining was done for histopathological observation of kidney tissues. The data suggest that the levels of blood urea nitrogen (BUN) and creatinine in the serum of hesperidin-treated rats were lower than in the I/R group. Treatment with hesperidin also ameliorated the altered level of inflammatory mediators and oxidative stress in I/Rinduced renal-injured rats. The expression of p-IkBa, caspase-3, NF-kB p65, Toll-like receptor 4 (TLR-4) protein, TLR-4 mRNA, and inducible nitric oxide synthase (iNOS) was significantly reduced in the renal tissues of hesperidin-treated rats. Histopathological findings also revealed that treatment with hesperidin attenuated the renal injury in I/R kidney-injured rats. In conclusion, our results suggest that hesperidin protects against renal injury induced by I/R by involving TLR-4/NF-kB/iNOS signaling.
Keywords: hesperidin, kidney injury, ischemia/reperfusion, oxidative stress, inflammation
Abstract: Pituitary adenylate cyclase activating polypeptide (PACAP) is involved in development and reproduction. We previously described elevated PACAP levels in the milk compared to the plasma, and the presence of its specific PAC1 receptor in the mammary gland. This study aimed to determine PACAP and vasoactive intestinal peptide (VIP) levels in female suckling lambs compared to ewe plasma and mammary gland, as well as their age-dependent alterations. mRNA expressions of PACAP, VIP, PAC1 receptor and brain-derived neurotrophic factor (BDNF) were quantified in the milk whey and mammary gland. PACAP38-like immunoreactivity (PACAP38-LI) was measured in plasma, milk whey and mammary gland by radioimmunoassay, VIP-LI by enzyme-linked immunoassay. PACAP38-LI was 5, 6 times higher in the milk compared to the plasma of lactating sheep. It significantly increased in the lamb plasma 1 h, but returned to basal level 2 h after suckling. However, VIP mRNA was not present in the mammary gland, we detected the VIP protein in the milk whey. BDNF mRNA significantly decreased with age to approximately 60% and 25% in the 3- and 10-year-old sheep respectively, compared to the 3- month-old lambs. No differences were found between mammary and jugular vein plasma PACAP and VIP concentrations, or during the daily cycle. We propose a rapid absorption of PACAP38 from the milk and/or its release in suckling lambs. PACAP accumulated in the milk might be synthesized in the mammary gland or secreted from the plasma of the mothers. PACAP is suggested to have differentiation/ proliferation promoting and immunomodulatory effects in the newborns and/or a local function in the mammary gland.
Keywords: PACAP, VIP, PAC1 receptor, BDNF, sheep, mammary gland, gene expression, development
Abstract: Purpose: We aimed to assess the etiological role of apoptotic genes Bcl-2 and Bax in the background of major obstetric and gynaecological diseases. Methods: Placental tissue samples were collected from 101 pregnancies with intrauterine growth restriction and 104 pregnancies with premature birth with 140 controll samples from term, eutrophic newborns. In addition, gene expression assessment of the genes Bax and Bcl-2 was performed in 101 uterine leiomyoma tissue samples at our disposal with 110 control cases. Gene expression levels were assessed by PCR method. Results: The expression of the Bcl-2 gene was decreased in placental samples with intrauterine growth restriction. Significant overexpression of the proapoptotic Bax gene was detected in samples from premature infants. Antiapoptotic Bcl-2 gene expression was found to be significantly increased in fibroid tissues. Conclusion: Apoptosis plays a crucial role in the development of the most common OB/GYN conditions. Decrease in the placental expression of the antiapoptotic gene Bcl-2 may upset the balance of programmed cell death.
Keywords: gene expression, placenta, apoptosis, intrauterine growth restriction, premature birth, uterine leiomyoma, Bcl-2, Bax
Abstract: Background: Thyroid cancer is the most common endocrine malignancy. Studies have observed an anticancer effect for vitamin D and found that polymorphisms of vitamin D receptors can influence the prevalence of various cancers. The present study investigated the serum level of vitamin D and FokI, BsmI and Tru9I polymorphisms of vitamin D receptors. Methods: Forty patients with medullary thyroid cancer and 40 healthy controls were investigated. The genomic DNA of the subjects was extracted using saturated salt/proteinase K and investigated by PCR sequencing. Serum levels of vitamin D were evaluated by ELISA. The results were analyzed in SPSS and GraphPad Prism 5 software. Results: The genotypic and allelic frequencies of FokI and BsmI polymorphisms showed no significant differences between test and control groups. For Tru9I polymorphism, Tt genotype and t allelic frequency in the test group were significantly different from those of the control group. Also, we found Tt genotype and t allelic frequency to be significantly associated with medullary thyroid cancer (MTC) type and the agressiveness of the disease. The average serum vitamin D level was 23.32 ng/mL and 18.95 ng/mL for patients and controls, respectively, and the difference between the two groups was statistically significant. Moreover, we found high serum vitamin D level to be associated with t allelic frequency. Conclusions: Unexpectedly, the mean serum vitamin D level of the test group was significantly higher than that of the control group. Tru9I polymorphism was found to be significantly correlated with the prevalence of medullary thyroid carcinoma.
Keywords: medullary thyroid carcinoma, vitamin D, vitamin D receptor, polymorphism
Abstract: Microvascular function has been assessed by determining the rhythmic oscillations in blood flow induced by the vasomotion of resistance vessels. Although laser-Doppler flowmetry (LDF) allows simple, noninvasive evaluation of this flow-motion in the cutaneous microcirculation, the temporal and spatial reproducibility of such assessments remains unclear. In the present study, we investigated cutaneous flow-motion in three consecutive years in eight skin regions using LDF in six healthy young volunteers. The characteristic flow-motion frequency was determined using fast-Fourier transformation. Additionally, in two years a more traditional measure of microvascular reactivity, postocclusive reactive hyperemia (PORH) was evoked in the forearm after transient brachial artery occlusion (1–2–3 min) induced by cuff inflation. Well-defined flow-motion was found in six regions showing significant differences in frequency: the highest flow-motion frequency was found in the frontal and temporal regions (8.0 ± 1.1 and 8.5 ± 1.0 cycles/min, cpm, respectively, mean ± SD) followed by the scapular, infraclavicular and coxal regions (7.5 ± 1.3; 6.7 ± 1.1 and 6.5 ± 1.2 cpm, respectively). The lowest, stable flow-motion was found in the posterior femoral region (5.5 ± 1.0 cpm), whereas flow-motion was detectable only sporadically in the limbs. The region-dependent flow-motion frequencies were very stable within individuals either between the body sides, or among the three measurements, only the infraclavicular region showed a small difference (114 ± 17%*, % of value in 1st year; *P < 0.05). However, PORH indices differed after 2–3 min occlusions significantly in consecutive years. We report that flow-motion frequencies determined from LDF signals show both region-specificity and excellent intra-individual temporal and spatial reproducibility suggesting their usefulness for non-invasive follow-up of microvascular reactivity.
Keywords: vasomotion, postocclusive hyperemia, laser-Doppler flowmetry, cutaneous blood flow, microvascular reactivity
Abstract: Introduction: Left ventricular (LV) twist is considered an essential part of LV function due to oppositely directed LV basal and apical rotations. Several factors could play a role in determining LV rotational mechanics in normal circumstances. This study aimed to investigate the relationship between LV rotational mechanics and mitral annular (MA) size and function in healthy subjects. Methods: The study comprised 118 healthy adult volunteers (mean age: 31.5 ± 11.8 years, 50 males). All subjects had undergone complete two-dimensional (2D) Doppler echocardiography and three-dimensional speckle-tracking echocardiography (3DSTE) at the same time by the same echocardiography equipment. Results: The normal mean LV apical and basal rotations proved to be 9.57 ± 3.33 and -3.75 ± 1.988, respectively. LV apical rotation correlated with end-systolic MA diameter, area, perimeter, fractional area change, and fractional shortening, but did not correlate with any end-diastolic mitral annular morphologic parameters. The logistic regression model identified MA fractional area change as an independent predictor of ≤68 left ventricular apical rotation (P < 0.003). Conclusions: Correlations could be detected between apical LV rotation and end-systolic MA size and function, suggesting relationships between MA dimensions and function and LV rotational mechanics.
Keywords: healthy, left ventricular, rotation, mitral annulus, three-dimensional, speckle-tracking, echocardiography
Abstract: Purpose: High central blood pressure is more predictive of cardiovascular disease (CVD) versus high peripheral blood pressure. Measures of central pressures (CPs) include, central systolic blood pressure (CSBP) and central diastolic blood pressure. Measures of central pressures augmentation (CPsA) include augmentation pressure (AP) and the augmentation index @ 75 beats$min¯¹ (AIx@75). Increased sympathetic tone (ST) is also associated with CVD. The low to high frequency ratio (LF/HF) is often used to determine sympatho-vagal balance. Given the association between ST, CPs, CPsA and CVD there is a need to understand the association between these predictors of CVD. The aims of this study were to examine the association between the LF/HF ratio, CPs, and CPsA in men and women collectively and based on gender. Methods: We measured the LF/HF ratio, CSBP, AP, and AIx@75 in 102 participants (41F/61M). The LF/ HF ratio was determined via power spectral density analysis. CSBP, AP, and AIx@75 were determined via applanation tonometry. Results: The LF/HF ratio was inversely associated with AP (r 5 –0.26) and AIx @75 (r 5 –0.29) in the combined group of men and women. The LF/HF ratio was inversely associated with CSBP (r 5 –0.27), AP (r 5 –0.28), and AIx@75 (r 5 –0.32) in men, but not in women. Conclusion: There is an inverse association between the LF/HF ratio, AP, and AIx@75 in men and women combined. The association between the LF/HF ratio, CSBP, AP, and AIx@75, differs based on gender.
Keywords: sympatho-vagal balance, central systolic blood pressure, central diastolic blood pressure, augmentation pressure, augmentation index
Abstract: Exercise-induced stem cell activation is implicated in cardiovascular regeneration. However, ageing limits the capacity of cellular and molecular remodelling of the heart. It has been shown that exercise improves structure regeneration and function in the process of ageing. Aged male Wistar rats (n 5 24) were divided into three groups: Control (CO), High-intensity interval training (HIIT) (80–100% of the maximum speed), and continuous endurance training (CET) (60–70% of the maximum speed) groups. Training groups were trained for 6 weeks. The expression of the Nkx2.5 gene was determined by real-time (RT-PCRs) analysis. Immunohistochemical staining was performed to assess the C-kit positive cardiac progenitor and Ki67 positive cells. The mRNA level of Nkx2.5 was significantly increased in the CET and HIIT groups (P < 0.05). Also, cardiac progenitor cells positive for C-kit were increased in both the CET and HIIT groups (P < 0.05). Exercise training improved the ejection fraction and fractional shortening in both training groups (P < 0.05). This study indicated that training initiates the activation of cardiac progenitor cells, leading to the generation of new myocardial cells (R 5 0.737, P 5 0.001). It seems that C-kit positive cells in training groups showed an increase in the expression of some transcription factors (Nkx2.5 gene), representing an increased regenerative capacity of cardiomyocytes during the training period. These findings suggest that the endogenous regenerative capacity of the adult heart, mediated by cardiac stem cells, would be increased in response to exercise.
Keywords: cardiac stem cell, C-kit, Nkx2.5, exercise, ageing