Differentially methylated genes involved in reproduction and ploidy levels in recent diploidized and tetraploidized Eragrostis curvula genotypes.

Epigenetics studies changes in gene activity without changes in the DNA sequence. Methylation is an epigenetic mechanism important in many pathways, such as biotic and abiotic stresses, cell division, and reproduction. Eragrostis curvula is a grass species reproducing by apomixis, a clonal reproduction by seeds. This work employed the MCSeEd technique to identify deferentially methylated positions, regions, and genes in the CG, CHG, and CHH contexts in E. curvula genotypes with similar genomic backgrounds but with different reproductive modes and ploidy levels. In this way, we focused the analysis on the cvs. Tanganyika INTA (4x, apomictic), Victoria (2x, sexual), and Bahiense (4x, apomictic). Victoria was obtained from the diploidization of Tanganyika INTA, while Bahiense was produced from the tetraploidization of Victoria. This study showed that polyploid/apomictic genotypes had more differentially methylated positions and regions than the diploid sexual ones. Interestingly, it was possible to observe fewer differentially methylated positions and regions in CG than in the other contexts, meaning CG methylation is conserved across the genotypes regardless of the ploidy level and reproductive mode. In the comparisons between sexual and apomictic genotypes, we identified differentially methylated genes involved in the reproductive pathways, specifically in meiosis, cell division, and fertilization. Another interesting observation was that several differentially methylated genes between the diploid and the original tetraploid genotype recovered their methylation status after tetraploidization, suggesting that methylation is an important mechanism involved in reproduction and ploidy changes.

Identification of genomic regions associated with total and progressive sperm motility in Italian Holstein bulls.

Sperm motility is directly related to the ability of sperm to move through the female reproductive tract to reach the ovum. Sperm motility is a complex trait that is influenced by environmental and genetic factors and is associated with male fertility, oocyte penetration rate, and reproductive success of cattle. In this study we carried out a GWAS in Italian Holstein bulls to identify candidate regions and genes associated with variations in progressive and total motility (PM and TM, respectively). After quality control, the final data set consisted of 5,960 records from 949 bulls having semen collected in 10 artificial insemination stations and genotyped at 412,737 SNPs (call rate >95%; minor allele frequency >5%). (Co)variance components were estimated using single trait mixed models, and associations between SNPs and phenotypes were assessed using a genomic BLUP approach. Ten windows that explained the greatest percentage of genetic variance were located on Bos taurus autosomes 1, 2, 4, 6, 7, 23, and 26 for TM and Bos taurus autosomes 1, 2, 4, 6, 8, 16, 23, and 26 for PM. A total of 150 genes for TM and 72 genes for PM were identified within these genomic regions. Gene Ontology enrichment analyses identified significant Gene Ontology terms involved with energy homeostasis, membrane functions, sperm-egg interactions, protection against oxidative stress, olfactory receptors, and immune system. There was significant enrichment of quantitative trait loci for fertility, calving ease, immune response, feed intake, and carcass weight within the candidate windows. These results contribute to understanding the architecture of the genetic control of sperm motility and may aid in the development of strategies to identify subfertile bulls and improve reproductive success.

Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe.

European populations display low genetic differentiation as the result of long-term blending of their ancient founding ancestries. However, it is unclear how the combination of ancient ancestries related to early foragers, Neolithic farmers, and Bronze Age nomadic pastoralists can explain the distribution of genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the continental diversity, but have been systematically understudied. Here, we characterize the ancestry profiles of Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe, and the rest of the world. Italian genomes capture several ancient signatures, including a non-steppe contribution derived ultimately from the Caucasus. Differences in ancestry composition, as the result of migration and admixture, have generated in Italy the largest degree of population structure detected so far in the continent, as well as shaping the amount of Neanderthal DNA in modern-day populations.

Validation of Polymer-Based Screen-Printed Textile Electrodes for Surface EMG Detection.

In recent years, the variety of textile electrodes developed for electrophysiological signal detection has increased rapidly. Among the applications that could benefit from this advancement, those based on surface electromyography (sEMG) are particularly relevant in rehabilitation, training, and muscle function assessment. In this work, we validate the performance of polymer-based screen-printed textile electrodes for sEMG signal detection. We obtained these electrodes by depositing poly-3,4-ethylenedioxythiophene doped with poly(styrene sulfonate) (PEDOT:PSS) onto cotton fabric, and then selectively changing the physical properties of the textile substrate. The manufacturing costs are low and this process meets the requirements of textile-industry production lines. The validation of these electrodes was based on their functional and electrical characteristics, assessed for two different electrode sizes and three skin-interface conditions (dry, solid hydrogel, or saline solution), and compared to those of conventional disposable gelled electrodes. Results show high similarity in terms of noise amplitude and electrode-skin impedance between the conventional and textile electrodes with the addition of solid hydrogel or saline solution. Furthermore, we compared the shape of the electrically induced sEMG, as detected by conventional and textile electrodes from tibialis anterior. The comparison yielded an [Formula: see text] value higher than 97% for all measurement conditions. Preliminary tests in dynamic conditions (walking) revealed the exploitability of the proposed electrode technology with saline application for the monitoring of sEMG for up to 35 min of activity. These results suggest that the proposed screen-printed textile electrodes may be an effective alternative to the conventional gelled electrodes for sEMG acquisition, thereby providing new opportunities in clinical and wellness fields.

Whole Mitogenomes Reveal the History of Swamp Buffalo: Initially Shaped by Glacial Periods and Eventually Modelled by Domestication.

The newly sequenced mitochondrial genomes of 107 Asian swamp buffalo (Bubalus bubalis carabensis) allowed the reconstruction of the matrilineal divergence since ~900 Kya. Phylogenetic trees and Bayesian skyline plots suggest a role of the glacial periods in the demographic history of swamp buffalo. The ancestral swamp-buffalo mitogenome is dated ~232 ± 35 Kya. Two major macro-lineages diverged during the 2nd Pleistocene Glacial Period (~200-130 Kya), but most (~99%) of the current matrilines derive from only two ancestors (SA1'2 and SB) that lived around the Last Glacial Maximum (~26-19 Kya). During the late Holocene optimum (11-6 Kya) lineages differentiated further, and at least eight matrilines (SA1, SA2, SB1a, SB1b, SB2a, SB2b, SB3 and SB4) were domesticated around 7-3 Kya. Haplotype distributions support an initial domestication process in Southeast Asia, while subsequent captures of wild females probably introduced some additional rare lineages (SA3, SC, SD and SE). Dispersal of domestic buffaloes created local population bottlenecks and founder events that further differentiated haplogroup distributions. A lack of maternal gene flow between neighboring populations apparently maintained the strong phylogeography of the swamp buffalo matrilines, which is the more remarkable because of an almost complete absence of phenotypic differentiation.

Textile Organic Electrochemical Transistors as a Platform for Wearable Biosensors.

The development of wearable chemical sensors is receiving a great deal of attention in view of non-invasive and continuous monitoring of physiological parameters in healthcare applications. This paper describes the development of a fully textile, wearable chemical sensor based on an organic electrochemical transistor (OECT) entirely made of conductive polymer (PEDOT:PSS). The active polymer patterns are deposited into the fabric by screen printing processes, thus allowing the device to actually "disappear" into it. We demonstrate the reliability of the proposed textile OECTs as a platform for developing chemical sensors capable to detect in real-time various redox active molecules (adrenaline, dopamine and ascorbic acid), by assessing their performance in two different experimental contexts: i) ideal operation conditions (i.e. totally dipped in an electrolyte solution); ii) real-life operation conditions (i.e. by sequentially adding few drops of electrolyte solution onto only one side of the textile sensor). The OECTs response has also been measured in artificial sweat, assessing how these sensors can be reliably used for the detection of biomarkers in body fluids. Finally, the very low operating potentials (<1 V) and absorbed power (~10-4 W) make the here described textile OECTs very appealing for portable and wearable applications.

A performance evaluation of three membrane bioreactor systems: aerobic, anaerobic, and attached-growth.

Water sustainability is essential for meeting human needs for drinking water and sanitation in both developing and developed countries. Reuse, decentralization, and low energy consumption are key objectives to achieve sustainability in wastewater treatment. Consideration of these objectives has led to the development of new and tailored technologies in order to balance societal needs with the protection of natural systems. Membrane bioreactors (MBRs) are one such technology. In this investigation, a comparison of MBR performance is presented. Laboratory-scale submerged aerobic MBR (AMBR), anaerobic MBR (AnMBR), and attached-growth aerobic MBR (AtMBR) systems were evaluated for treating domestic wastewater under the same operating conditions. Long-term chemical oxygen demand (COD) and total organic carbon (TOC) monitoring showed greater than 80% removal in the three systems. The AnMBR system required three months of acclimation prior to steady operation, compared to one month for the aerobic systems. The AnMBR system exhibited a constant mixed liquor suspended solids concentration at an infinite solids retention time (i.e. no solids wasting), while the aerobic MBR systems produced approximately 0.25 g of biomass per gram of COD removed. This suggests a more economical solids management associated with the AnMBR system. Critical flux experiments were performed to evaluate fouling potential of the MBR systems. Results showed similar critical flux values between the AMBR and the AnMBR systems, while the AtMBR system showed relatively higher critical flux value. This result suggests a positive role of the attached-growth media in controlling membrane fouling in MBR systems.

Multiplex mtDNA coding region SNP assays for molecular dissection of haplogroups U/K and J/T.

Mitochondrial DNA (mtDNA) U/K and J/T are sister haplogroups within the superhaplogroup R. They are both common in Europe, with a combined overall frequency similar to the one reported for H, the most common European haplogroup (40-50%). In this study, we selected 159 Italian subjects, already ascribed to U/K and J/T by RFLP typing, and assigned each mtDNA to specific clades/subclades by investigating at least one diagnostic coding region SNP. For each sister haplogroup, one multiplex PCR and one SNaPshot minisequencing reaction were set up targeting 16 U/K and 7 J/T coding region SNPs. Each mtDNA sample was clearly assigned to a specific subclade, which could be further subdivided into several minor sub-branches according to peculiar HVS I/II motifs. Such a molecular dissection of haplogroups U/K and J/T could be extremely useful to reduce the overall analysis time and labor intensive sequencing procedures in high volume forensic casework, for example when it is important to rapidly exclude samples in order to restrict the number of suspects.

The complex and diversified mitochondrial gene pool of Berber populations.

The mitochondrial DNA variation of 295 Berber-speakers from Morocco (Asni, Bouhria and Figuig) and the Egyptian oasis of Siwa was evaluated by sequencing a portion of the control region (including HVS-I and part of HVS-II) and surveying haplogroup-specific coding region markers. Our findings show that the Berber mitochondrial pool is characterized by an overall high frequency of Western Eurasian haplogroups, a somehow lower frequency of sub-Saharan L lineages, and a significant (but differential) presence of North African haplogroups U6 and M1, thus occupying an intermediate position between European and sub-Saharan populations in PCA analysis. A clear and significant genetic differentiation between the Berbers from Maghreb and Egyptian Berbers was also observed. The first are related to European populations as shown by haplogroup H1 and V frequencies, whereas the latter share more affinities with East African and Nile Valley populations as indicated by the high frequency of M1 and the presence of L0a1, L3i, L4*, and L4b2 lineages. Moreover, haplogroup U6 was not observed in Siwa. We conclude that the origins and maternal diversity of Berber populations are old and complex, and these communities bear genetic characteristics resulting from various events of gene flow with surrounding and migrating populations.

Rare mtDNA variants in Leber hereditary optic neuropathy families with recurrence of myoclonus.

OBJECTIVE: To investigate the mechanisms underlying myoclonus in Leber hereditary optic neuropathy (LHON). METHODS: Five patients and one unaffected carrier from two Italian families bearing the homoplasmic 11778/ND4 and 3460/ND1 mutations underwent a uniform investigation including neurophysiologic studies, muscle biopsy, serum lactic acid after exercise, and muscle ((31)P) and cerebral ((1)H) magnetic resonance spectroscopy (MRS). Biochemical investigations on fibroblasts and complete mitochondrial DNA (mtDNA) sequences of both families were also performed. RESULTS: All six individuals had myoclonus. In spite of a normal EEG background and the absence of giant SEPs and C reflex, EEG-EMG back-averaging showed a preceding jerk-locked EEG potential, consistent with a cortical generator of the myoclonus. Specific comorbidities in the 11778/ND4 family included muscular cramps and psychiatric disorders, whereas features common to both families were migraine and cardiologic abnormalities. Signs of mitochondrial proliferation were seen in muscle biopsies and lactic acid elevation was observed in four of six patients. (31)P-MRS was abnormal in five of six patients and (1)H-MRS showed ventricular accumulation of lactic acid in three of six patients. Fibroblast ATP depletion was evident at 48 hours incubation with galactose in LHON/myoclonus patients. Sequence analysis revealed haplogroup T2 (11778/ND4 family) and U4a (3460/ND1 family) mtDNAs. A functional role for the non-synonymous 4136A>G/ND1, 9139G>A/ATPase6, and 15773G>A/cyt b variants was supported by amino acid conservation analysis. CONCLUSIONS: Myoclonus and other comorbidities characterized our Leber hereditary optic neuropathy (LHON) families. Functional investigations disclosed a bioenergetic impairment in all individuals. Our sequence analysis suggests that the LHON plus phenotype in our cases may relate to the synergic role of mtDNA variants.

Colony density influences invasive and filamentous growth in Saccharomyces cerevisiae.

The effect of colony density on the dimorphic switch was determined in natural strains of Saccharomyces cerevisiae. In some strains invasiveness and pseudohyphal (PH) growth were highly sensitive to colony density; moreover, strains constitutively able to invade the substrate with PH formation positively influenced the invasiveness but not the PH growth of a different strain less prone to the dimorphic switch.

The 13042G --> A/ND5 mutation in mtDNA is pathogenic and can be associated also with a prevalent ocular phenotype.

BACKGROUND: Overlapping phenotypes including LHON, MELAS, and Leigh syndrome have recently been associated with numerous mtDNA point mutations in the ND5 gene of complex I, now considered a mutational hot spot. OBJECTIVE: To identify the mtDNA defect in a family with a prevalent ocular phenotype, including LHON-like optic neuropathy, retinopathy, and cataract, but characterised also by strokes, early deaths, and miscarriages on the maternal line. RESULTS: Sequencing of the entire mitochondrial genome from the proband's muscle DNA identified the heteroplasmic 13042G-->A transition, which was previously described only once in a patient with a different mitochondrial disease. This mutation fulfils the major pathogenic criteria, inducing an amino acid change (A236T) at an invariant position in a highly conserved domain of the ND5 gene. Phosphorus magnetic resonance spectroscopy in the proband disclosed an in vivo brain and skeletal muscle energy metabolism deficit. CONCLUSIONS: These findings conclusively establish the pathogenic role of the 13042G-->A mutation and underscore its variable clinical expression.

Subtyping mtDNA haplogroup H by SNaPshot minisequencing and its application in forensic individual identification.

Sequence variation of the hypervariable segments (HVS) I/II of mitochondrial DNA (mtDNA) and the haplogroup affiliation were determined in a sample of 271 Italian subjects. This analysis showed that 42% of the individuals could be ascribed to H, the most frequent haplogroup in European Caucasian populations. This fraction was then screened for specific single nucleotide polymorphisms located in the coding region to identify H subclades H1-H15. We set up two multiplex polymerase chain reactions and specific SNaPshot assays to investigate the frequency distribution of these subgroups in our population sample and to examine their usefulness in discriminating among commonly shared HVS I/II sequences. This allowed the assignment of a large portion of the mtDNAs ( approximately 70%) to specific subhaplogroups, with H1 and H5 being the most represented. About two-thirds of the individuals sharing common HVS I/II sequences were subdivided and ascribed to specific H subhaplogroups with a significant reduction of the frequencies of the most common mtDNA haplotypes. Haplogroup H subtyping could thus be extremely useful in forensic identification when many samples have to be analysed and compared, avoiding excessive time-consuming and labor-intensive sequencing analysis.

The peopling of modern Bosnia-Herzegovina: Y-chromosome haplogroups in the three main ethnic groups.

The variation at 28 Y-chromosome biallelic markers was analysed in 256 males (90 Croats, 81 Serbs and 85 Bosniacs) from Bosnia-Herzegovina. An important shared feature between the three ethnic groups is the high frequency of the "Palaeolithic" European-specific haplogroup (Hg) I, a likely signature of a Balkan population re-expansion after the Last Glacial Maximum. This haplogroup is almost completely represented by the sub-haplogroup I-P37 whose frequency is, however, higher in the Croats (approximately 71%) than in Bosniacs (approximately 44%) and Serbs (approximately 31%). Other rather frequent haplogroups are E (approximately 15%) and J (approximately 7%), which are considered to have arrived from the Middle East in Neolithic and post-Neolithic times, and R-M17 (approximately 14%), which probably marked several arrivals, at different times, from eastern Eurasia. Hg E, almost exclusively represented by its subclade E-M78, is more common in the Serbs (approximately 20%) than in Bosniacs (approximately 13%) and Croats (approximately 9%), and Hg J, observed in only one Croat, encompasses approximately 9% of the Serbs and approximately 12% of the Bosniacs, where it shows its highest diversification. By contrast, Hg R-M17 displays similar frequencies in all three groups. On the whole, the three main groups of Bosnia-Herzegovina, in spite of some quantitative differences, share a large fraction of the same ancient gene pool distinctive for the Balkan area.

Osteonecrosis of the jaws in patients treated with bisphosphonates. Review of the literature and the Milan experience.

AIM: A series of 5 patients with osteonecrosis of the jaws possibly related to the use of bisphosphonates is presented. A brief review of the literature is also proposed. METHODS: A retrospective review of patients who received bisphosphonates and who developed osteonecrosis of the jaws following minor oral surgery was performed. RESULTS: In all 5 patients, a tooth extraction preceded the onset of osteonecrosis of the mandible. Patients were on chronic use of intravenous bisphosphonates. The presenting lesions was a nonhealing extraction socket and an exposed jawbone. Biopsy of the bone lesions showed no evidence of metastatic involvement. Antibiotic therapy, conservative debridement and, in some cases, bone sequestrectomy were performed. CONCLUSIONS: Osteonecrosis of the jaws appears to have a relationship with the use of bisphosphonates. It is important that medical oncologists and dentists become aware of this possible complication in order to perform minor oral surgery prior to starting bisphosphonates treatment.

Electrocardiographic pattern of Brugada syndrome disclosed by a febrile illness: clinical and therapeutic implications.

BACKGROUND: Recent studies have identified a direct link between the ionic mechanisms responsible for the electrocardiographic (ECG) pattern of the Brugada syndrome (BS) and the in vitro experimental temperature, pointing to the possibility that some BS patients may display the ECG phenotype only during a febrile state, being in this setting at risk of lethal arrhythmias. CASE REPORT: A 53-year-old man referred to the emergency room for abdominal pain and fever. The ECG showed dome-shaped ST-segment elevation in V1-V3, as in the typical BS. The personal and family history were unremarkable for syncope and sudden death and physical, laboratory and ultrasound examinations were negative. On day 3, at normal body temperature, the patient's ECG returned to normal and the ECG abnormalities were later reproduced with intravenous flecainide. The patient refused the implantation of a loop recorder and was discharged after 6 days. He has remained asymptomatic during 2 years of follow-up. CONCLUSIONS: The typical ECG phenotype of BS disclosed by a febrile illness confirms the in vitro experimental data that previously established a correlation between ECG pattern of BS and temperature variations. The clinical and therapeutic implications of these findings are discussed.

Stationary-phase mutations in proofreading exonuclease-deficient strains of the yeast Saccharomyces cerevisiae.

In order to understand the role of yeast polymerases in spontaneous mutagenesis in non-growing cells we have studied the effects of mutations that impair the 3'--> 5' exonuclease function of polymerases delta (pol3-01) and epsilon (pol2-4) on the spontaneous reversion frequency of the frameshift mutation his7-2 in cells starved for histidine. We showed that for each exonuclease-deficient mutant the rate of reversion per viable cell per day observed in stationary-phase cells remained constant up to the 9th day of starvation (while the number of viable cells dropped), and was very similar to that observed in the same mutants during the growth phase. These data suggest that both DNA polymerases are involved in the control of mutability in non-growing cells.

[Long-term clinical assessment of single-lead VDD electric stimulation]. / Valutazione clinica a lungo termine dell'elettrostimolazione VDD monocatetere.

BACKGROUND: During the last decade single lead VDD pacing has been progressively affirmed as an electrotherapy of choice in patients with advanced atrioventricular block without alterations of the sinus function. It combines the benefits of P-synchronous ventricular pacing with an easy implant procedure when compared to the conventional DDD approach. The aim of this study was to evaluate the validity of such an approach in a large population of patients, all implanted in a single center. METHODS: From 1987 up to now, 317 patients, all affected by advanced atrioventricular block and without sinus node dysfunction, were implanted in our center with a single lead VDD pacemaker. During follow-up the persistence of a proper atrioventricular synchronization was assessed and evaluated. RESULTS: The mean follow-up was 3.9 +/- 2.7 years/patient (range 6-138 months). The 94.6% of implanted systems maintained the normal VDD pacing function. Permanent reprogramming in VVI mode was necessary in 17 patients (5.36%); in 12 (3.78%) because of chronic atrial fibrillation and in 5 (1.63%) for loss of atrial sensing. The percentage of atrial synchronization was optimal (> 98%) and acceptable (> 95%) in 81% and 19% of patients, respectively. Episodes of paroxysmal atrial fibrillation occurred in 3 patients. Neither inhibition by myopotentials nor occurrence of sinus node disease was observed during follow-up. These results are in accordance with those reported by previous studies, performed on a smaller population or on a multicenter basis, and are comparable with the results reported for conventional DDD pacemaker. CONCLUSIONS: Our results confirm the high reliability of the single lead VDD pacing system concerning the long-term persistence of a proper atrioventricular synchronization. Data showed above enforce our opinion that this pacing approach should be considered the treatment of choice in patients with advanced atrioventricular block and preserved sinus node function.

Identification of viable myocardium by nitrate echocardiography after myocardial infarction: comparison with planar thallium reinjection scintigraphy.

BACKGROUND: The aim of this study was to validate a new diagnostic tool, nitrate echocardiography (NE), for the identification of viable noncontracting myocardium in patients with a history of prior myocardial infarction (MI). Nitroglycerin (NTG) may be useful for this purpose for its peculiar pharmacodynamic action and may represent an option other than dobutamine echocardiography for the detection of hibernating segments in the presence of severely reduced coronary reserve. METHODS: Twenty selected patients (pts) with an old MI were studied with NE and planar thallium scintigraphy with reinjection. NE was performed by administering i.v. NTG starting at 0.4 mcg/kg/minute with equal increments every five minutes up to 2 mcg/kg/minute or to early interruption of the test (decrease of systolic blood pressure > or = 20% or improvement of previously akinetic segments). Left ventricular wall motion was analyzed by dividing the left ventricle (LV) into 16 segments, and a wall motion score index (WMSI) was calculated. Thallium images were obtained at peak exercise, at four hours, and after reinjection. Myocardial viability was defined as an improvement in thallium uptake after reinjection in fixed defects. RESULTS: Basal echo demonstrated 74 akinetic segments; of these 21 (28%, 11 pts) showed improved contractility during NTG infusion at a mean dose of 0.87 +/-0.33 mcg/kg/minute. WMSI decreased from 1.69 +/- 0.29 to 1.46 +/- 0.31 (P = .001). The only hemodynamic response was a drop in systolic blood pressure (136 mmHg to 124; P = .02). Thallium studies showed 29 segments with a four-hour reversible defect and 79 segments with a four-hour fixed defect; of the latter, 14 regions demonstrated improvement in tracer uptake after reinjection (17.7%; 10 pts). Nine pts had a positive echo and thallium study, while 8 showed no improvement either during NE or after thallium reinjection. Two pts had a false-positive nitrate echocardiogram. Therefore, according to an echo/thallium study match, sensitivity, specificity, and accuracy are 90%, 80%, 85%, respectively. CONCLUSION: NE is a reliable and low-cost method for the detection of viable noncontracting myocardium in selected patients with CAD but needs further validation for widespread application.