Y chromosome sequence and epigenomic reconstruction across human populations

Recent advances in long-read sequencing technologies have allowed the generation and curation of more complete genome assemblies, enabling the analysis of traditionally neglected chromosomes, such as the human Y chromosome (chrY). Native DNA was sequenced on a MinION Oxford Nanopore Technologies sequencing device to generate genome assemblies for seven major chrY human haplogroups. We analyzed and compared the chrY enrichment of sequencing data obtained using two different selective sequencing approaches: adaptive sampling and flow cytometry chromosome sorting. We show that adaptive sampling can produce data to create assemblies comparable to chromosome sorting while being a less expensive and time-consuming technique. We also assessed haplogroup-specific structural variants, which would be otherwise difficult to study using short-read sequencing data only. Finally, we took advantage of this technology to detect and profile epigenetic modifications among the considered haplogroups. Altogether, we provide a framework to study complex genomic regions with a simple, fast, and affordable methodology that could be applied to larger population genomics datasets.

Antimicrobial effect of Moringa oleifera seed powder against Vibrio cholerae isolated from the rearing water of shrimp (Penaeus vannamei) postlarvae

Shrimp farming has experienced rising costs as a result of disease outbreaks associated with Vibrio spp. Suitable strategies for disease prevention and control are therefore urgently needed. This study aimed to evaluate the antimicrobial effect of Moringa oleifera seed powder against Vibrio cholerae in the rearing water of Pacific white shrimp (Penaeus vannamei) postlarvae. In vitro assays included the determination of minimum inhibitory concentration (MIC) of M. oleifera seed powder against V. cholerae, whereas in vivo assays included the effect of M. oleifera seed powder on bacterial load and water quality parameters in the rearing tanks, as well as its effect on shrimp postlarvae survival. M. oleifera seed powder inhibited the growth of V. cholerae with MIC values of 62·5 µg ml^-1 . Moreover, seawater pH of treated tanks (8·66) was significantly lower (P < 0·01) than pH of the control tanks (9·02), whereas the visibility of treated tanks (37·08 cm) was significantly higher (P < 0·01) as compared to control tanks (35·37 cm). Likewise, V. cholerae load was significantly reduced (P < 0·01) from 4·7 × 10⁴ to 3·1 × 10³  CFU per ml in tanks treated with M. oleifera seed powder. Altogether, this study demonstrates the antimicrobial activity of M. oleifera against V. cholerae in shrimp culture.

Differential iron management in monocotyledon and dicotyledon plants from the Río Tinto basin

The study of plants adapted to an extreme environment with a high concentration of iron such as Río Tinto allowed the study of important elements for the development and control of plant growth including their localization, management, and storage. The absorption, transport, and accumulation of iron were studied in different species of dicotyledons (Sarcocornia pruinosa, Salicornia patula, Arthrocnemum macrostachyum, and Halogeton sativus of the Chenopodiaceae family) and monocotyledons (Imperata cylindrica, Cynodon dactylon, and Panicum repens from the Poaceae family), all obtained from the Río Tinto banks in different sample collection campaigns. The results clearly show that phytoferritin is not observed in the chloroplast of monocotyledons, an important difference from what is observed in dicotyledons. The presence of plastids with a high concentration of iron in the sieve tubes of monocotyledons strongly suggests their possible role in the transport and accumulation of iron in these plants.

Flow Sorting Enrichment and Nanopore Sequencing of Chromosome 1 From a Chinese Individual

Sorting of individual chromosomes by Flow Cytometry (flow-sorting) is an enrichment method to potentially simplify genome assembly by isolating chromosomes from the context of the genome. We have recently developed a workflow to sequence native, unamplified DNA and applied it to the smallest human chromosome, the Y chromosome. Here, we modify improve upon that workflow to increase DNA recovery from chromosome sorting as well as sequencing yield. We apply it to sequence and assemble the largest human chromosome - chromosome 1 - of a Chinese individual using a single Oxford Nanopore MinION flow cell. We generate a selective and highly continuous assembly whose continuity reaches into the order of magnitude of the human reference GRCh38. We then use this assembly to call candidate structural variants against the reference and find 685 putative novel SV candidates. We propose this workflow as a potential solution to assemble structurally complex chromosomes, or the study of very large plant or animal genomes that might challenge traditional assembly strategies.

Effectiveness and Safety of the Switch from Remicade® to CT-P13 in Patients with Inflammatory Bowel Disease

BACKGROUND AND AIMS

To evaluate the clinical outcomes in patients with IBD after switching from Remicade® to CT-P13 in comparison with patients who maintain Remicade®.

METHODS

Patients under Remicade® who were in clinical remission with standard dosage at study entry were included. The 'switch cohort' [SC] comprised patients who made the switch from Remicade® to CT-P13, and the 'non-switch' cohort [NC] patients remained under Remicade®.

RESULTS

A total of 476 patients were included: 199 [42%] in the SC and 277 [58%] in the NC. The median follow-up was 18 months in the SC and 23 months in the NC [p < 0.01]. Twenty-four out of 277 patients relapsed in the NC; the incidence of relapse was 5% per patient-year. The cumulative incidence of relapse was 2% at 6 months and 10% at 24 months in this group. Thirty-eight out of 199 patients relapsed in the SC; the incidence rate of relapse was 14% per patient-year. The cumulative incidence of relapse was 5% at 6 months and 28% at 24 months. In the multivariate analysis, the switch to CT-P13 was associated with a higher risk of relapse (HR = 3.5, 95% confidence interval [CI] = 2-6). Thirteen percent of patients had adverse events in the NC, compared with 6% in the SC [p < 0.05].

CONCLUSIONS

Switching from Remicade® to CT-P13 might be associated with a higher risk of clinical relapse, although this fact was not supported in our study by an increase in objective markers of inflammation. The nocebo effect might have influenced this result. Switching from Remicade® to CT-P13 was safe.

Laboratorio: Reconocimiento de los elementos del embrión de pollo y su empleo en virología

El embrión de pollo es uno de los medios de cultivo más favorables para el aislamiento de algunos virus. Los huevos embrionados pueden ser inoculados por varias vías y su elección depende del virus que se quiera estudiar.

Sitagliptin improved glucose assimilation in detriment of fatty-acid utilization in experimental type-II diabetes: role of GLP-1 isoforms in Glut4 receptor trafficking

BACKGROUND

The distribution of glucose and fatty-acid transporters in the heart is crucial for energy consecution and myocardial function. In this sense, the glucagon-like peptide-1 (GLP-1) enhancer, sitagliptin, improves glucose homeostasis but it could also trigger direct cardioprotective actions, including regulation of energy substrate utilization.

METHODS

Type-II diabetic GK (Goto-Kakizaki), sitagliptin-treated GK (10 mg/kg/day) and wistar rats (n = 10, each) underwent echocardiographic evaluation, and positron emission tomography scanning for [¹⁸F]-2-fluoro-2-deoxy-D-glucose (¹⁸FDG). Hearts and plasma were isolated for biochemical approaches. Cultured cardiomyocytes were examined for receptor distribution after incretin stimulation in high fatty acid or high glucose media.

RESULTS

Untreated GK rats exhibited hyperglycemia, hyperlipidemia, insulin resistance, and plasma GLP-1 reduction. Moreover, GK myocardium decreased ¹⁸FDG assimilation and diastolic dysfunction. However, sitagliptin improved hyperglycemia, insulin resistance, and GLP-1 levels, and additionally, enhanced ¹⁸FDG uptake and diastolic function. Sitagliptin also stimulated the sarcolemmal translocation of the glucose transporter-4 (Glut4), in detriment of the fatty acyl translocase (FAT)/CD36. In fact, Glut4 mRNA expression and sarcolemmal translocation were also increased after GLP-1 stimulation in high-fatty acid incubated cardiomyocytes. PI3K/Akt and AMPKα were involved in this response. Intriguingly, the GLP-1 degradation metabolite, GLP-1(9-36), showed similar effects.

CONCLUSIONS

Besides of its anti-hyperglycemic effect, sitagliptin-enhanced GLP-1 may ameliorate diastolic dysfunction in type-II diabetes by shifting fatty acid to glucose utilization in the cardiomyocyte, and thus, improving cardiac efficiency and reducing lipolysis.

First assessment of the potential introduction by hunters of eastern cottontail rabbits (Sylvilagus floridanus) in Spain

Context Humans have introduced lagomorph species in areas outside their native ranges for their meat, fur or value as game species. Assessing the rate of success of lagomorph introductions is vital to address the ecological damage they may cause. Cases of failed lagomorph introductions in apparently suitable areas may also shed light on mechanisms that may deter invasion, which are useful in developing strategies for population control. In Spain, it has been suggested that hunters introduced the non-native eastern cottontail (Sylvilagus floridanus) to compensate for the recent drastic declines of the native European rabbit (Oryctolagus cuniculus). Aims Our main goals were to investigate (1) whether Sylvilagus rabbits have indeed been introduced by hunters across Spain, and (2) whether the species has become established in Spanish ecosystems. Methods We interviewed 311 hunters or naturalists across Spain. The questionnaires inquired about the characteristics of game management in each locality, including the frequency of rabbit restocking, and particularly whether Sylvilagus rabbits had been released in the surveyed localities. In addition, we sampled 192 rabbit populations (n=3974 individuals) across Spain by using molecular analysis to determine whether Sylvilagus rabbits were present in these areas. Key results Our interview results suggest that Sylvilagus rabbits may have been released in 6% of the 311 localities surveyed. However, molecular analyses failed to confirm their persistence, because all samples belonged to O. cuniculus. Conclusions We infer that Sylvilagus rabbits failed to establish themselves in Spain, although interviewees reported their introduction. Several reasons may explain the unsuccessful establishment of this species, such as a low propagule pressure, competition with native species, predation, inability to cope with local pathogens and unsuitable climatic conditions. Implications The risk of future introductions of non-native game species can be reduced through the implementation of stricter regulations of animal releases into the wild. Long-term monitoring networks should be developed to help identify non-native game species before they become established and spread to neighbouring areas, thereby preventing any ecological or economic impacts these species may cause.

Catalytic activity dependence on morphological properties of acidic ion-exchange resins for the simultaneous ETBE and TAEE liquid-phase synthesis

Resin acid capacity and specific volume of the swollen polymer are the key properties that determine its catalytic activity.

Screening for trisomies 21 and 18 in a Spanish public hospital: from the combined test to the cell-free DNA test

OBJECTIVE

To describe our experience in first-trimester screening for trisomies 21 and 18 firstly by the combined test alone and secondly by cell-free (cf) DNA testing contingent on the results from a previously performed combined test.

METHODS

Women with singleton pregnancies attending Torrejon University Hospital in Madrid, Spain, from November 2011 to January 2016, were screened for trisomy (T)21 and T18 by the combined test at 11-13 weeks. Before the introduction of cfDNA testing, women at high risk (>1 in 250) were offered invasive testing (IT) and from January 2015 they were offered cfDNA test as well as IT.

RESULTS

Combined test was performed in 6011 pregnancies. The risk was high in 202 (3.4%) cases. There was complete follow-up for 5507 (91.6%) pregnancies. Detection rate (DR) for T21 was 83.3% (15/18) and 100% (4/4) for T18. Additionally, 2/2 (100%) cases of T13 and 2/2 (100%) cases of triploidy were also detected. False positive rate (FPR) was 3.2% (174/5488). The introduction of this contingent model was followed by a 73% reduction on the IT rate in the high-risk group, from 76.3% to 20.8%.

CONCLUSION

Contingent screening for trisomies 21 and 18 by cfDNA testing at 11-13 weeks is feasible and has a lower IT rate than combined testing alone.

Two cases of overlap severe cutaneous adverse reactions to benznidazole treatment for asymptomatic Chagas disease in a nonendemic country

Chagas disease is a parasitosis endemic to South America. It is normally treated with benznidazole as first choice, which has been associated with numerous cutaneous reactions. However, very few benznidazole-associated severe cutaneous adverse reactions have been reported to date. The rise of Chagas disease in nonendemic countries represents a growing public health challenge. We report two patients who met the criteria for drug reaction with eosinophilia and systemic symptoms syndrome and Stevens-Johnson syndrome/toxic epidermal necrolysis according to the RegiSCAR scoring systems. They were thus deemed overlapping cases, with a lymphocyte transformation test positive for benznidazole. Both required intensive care unit admission and both survived. Considering the rising application of this drug for trypanosomiasis in immigrant populations, clinicians should be aware of this newly reported, potentially life-threatening risk.

Synthesis of ethyl hexyl ether over acidic ion-exchange resins for cleaner diesel fuel

Identifying the resin polymer zones where ethyl hexyl ether and by-products are preferentially formed in hexanol etherification with diethyl carbonate.

Proton pump inhibitors are associated with hypersensitivity reactions to drugs in hospitalized patients: a nested case-control in a retrospective cohort study

BACKGROUND

Previous research has shown that gastric acid suppression by antacid drugs can promote allergic reactions to acid-labile food proteins. No data are available about whether antacid drugs can promote drug hypersensitivity reactions. The most potent and longer lasting inhibition of gastric secretion is provided by proton pump inhibitors (PPIs). We hypothesized that gastric acid suppression by proton pump inhibitors could be causative of drug hypersensitivity reactions during hospitalization.

OBJECTIVE

To estimate the risk of developing drug hypersensitivity reactions during the hospitalization of patients treated with proton pump inhibitors, and other associated factors.

METHODS

A nested case-control in a retrospective cohort study of hospitalized patients from September 2008 to December 2010 (70 771 admissions) was conducted using the registry of cases of interconsultations to the Allergy Department (161 confirmed cases of drug hypersensitivity reactions). A total of 318 controls were matched by first drug suspected in the hypersensitivity reaction, time of admission, age, gender and hospitalization wards.

RESULTS

The relative risk of drug hypersensitivity reaction occurrence during hospitalization of patients treated with PPIs compared with those not treated in the period of study was significant (RR: 3.97; 95% CI: 1.97-8.29). After controlling for confounders in the nested case-control cohort, the use of PPIs persists as a predisposing factor (OR: 4.35; 95% CI: 2-9.45). Personal history of drug allergy and a long hospitalization time were other predisposing factors of drug hypersensitivity reactions (DHRs). The hazard that a DHR has occurred during PPI treatment was 3.7% per day. The hazard for immediate or accelerated reactions was 1.706 (P = 0.003) times that of delayed reactions.

CONCLUSION AND CLINICAL RELEVANCE

In hospitalized patients, the use of proton pump inhibitors was associated with a significant increase risk of drug hypersensitivity reactions along with a personal history of drug allergies and long hospitalization time.

Triplication of DYRK1A causes retinal structural and functional alterations in Down syndrome

Down syndrome (DS) results from the triplication of approximately 300 human chromosome 21 (Hsa21) genes and affects almost all body organs. Children with DS have defects in visual processing that may have a negative impact on their daily life and cognitive development. However, there is little known about the genes and pathogenesis underlying these defects. Here, we show morphometric in vivo data indicating that the neural retina is thicker in DS individuals than in the normal population. A similar thickening specifically affecting the inner part of the retina was also observed in a trisomic model of DS, the Ts65Dn mouse. Increased retinal size and cellularity in this model correlated with abnormal retinal function and resulted from an impaired caspase-9-mediated apoptosis during development. Moreover, we show that mice bearing only one additional copy of Dyrk1a have the same retinal phenotype as Ts65Dn mice and normalization of Dyrk1a gene copy number in Ts65Dn mice completely rescues both, morphological and functional phenotypes. Thus, triplication of Dyrk1a is necessary and sufficient to cause the retinal phenotype described in the trisomic model. Our data demonstrate for the first time the implication of DYRK1A overexpression in a developmental alteration of the central nervous system associated with DS, thereby providing insights into the aetiology of neurosensorial dysfunction in a complex disease.

A preliminary model to avoid the overestimation of sample size in bioequivalence studies

Often the only available data in literature for sample size estimations in bioequivalence studies is intersubject variability, which tends to result in overestimation of sample size. In this paper, we proposed a preliminary model of intrasubject variability based on intersubject variability for Cmax and AUC data from randomized, crossovers, bioequivalence (BE) studies. From 93 Cmax and 121 AUC data from test-reference comparisons that fulfilled BE criteria, we calculated intersubject variability for the reference formulation and intrasubject variability from ANOVA. Lineal and exponential models (y=a(1-e-bx)) were fitted weighted by the inverse of the variance, to predict the intrasubject variability based on intersubject variability. To validate the model we calculated the coefficient of cross-validation of data from 30 new BE studies. The models fit very well (R2=0.997 and 0.990 for Cmax and AUC respectively) and the cross-validation correlation were 0.847 for Cmax and 0.572 for AUC. A preliminary model analyses allow us to estimate the intrasubject variability based on intersubject variability for sample size calculation purposes in BE studies. This approximation provides an opportunity for sample size reduction avoiding unnecessary exposure of healthy volunteers. Further modelling studies are desirable to confirm these results especially suggestions of the higher intersubject variability range.

Widespread exposure to Sarcoptes scabiei in wild European rabbits (Oryctolagus cuniculus) in Spain

Sarcoptic mange was recently described in the wild European rabbit (Oryctolagus cuniculus) in north-eastern Mediterranean Spain, the first such infection reported in this species anywhere in the world. This finding has created concern in conservationists and game managers given that an outbreak of mange after a translocation would have catastrophic consequences for naïve rabbit populations in other parts of Spain. A retrospective serosurvey using an 'in house' ELISA test based on the use of a recombinant antigen aimed at determining the rates of contact with Sarcoptes scabiei was carried out on sera from 966 rabbits collected between 1993 and 2010 in Spain. Antibodies were found in 13% of wild rabbits in 60% of the 53 areas surveyed, as well as in 16 of the 17 Spanish provinces and islands studied. Seropositive rabbits were found amongst the oldest samples analyzed and in all studied years. Antibodies were also detected in 36% of rabbits from the protected island of Dragonera, where rabbits have probably not been released since the 1970s. On Mallorca, where 89 rabbits were inspected for both lesions and antibodies, the prevalence of lesions (5.6%) was much lower than the seroprevalence (22.5%), indicating that rabbits often survive infection or that ELISA detects infected rabbits before they develop visible lesions. Seroprevalence was higher in areas with medium levels of rabbit abundance, no restocking and high rainfall. The results show that mange is widespread in rabbits and that the mite is not a recent introduction. Thus, sarcoptic mange could be considered as an enzootic disease in the wild rabbit and so prophylactic measures implemented during rabbit translocations are to be encouraged to avoid local outbreaks in naïve populations.

Prospective study on autoantibodies against apolipoprotein H (beta2GPI) in several clinical parameters from patients with terminal renal failure and functioning renal transplants

Renal transplantation is the best therapeutic option for patients with end-stage renal disease. However, long-term results have not been very encouraging because of patient deaths due to cardiovascular disease and chronic transplant nephropathy (CTN), which includes vascular damage similar to arteriosclerosis injury. Several autoantibodies have been related to vasculopathy in the transplant such as anti-beta2GPI IgA, IgG, and IgM autoantibodies. We analyzed the levels of these autoantibodies among a cohort of 176 transplant recipients and a control group of 80 healthy subjects using enzyme-linked immunosorbent assay (ELISA). We collected data concerning the cardiovascular status of the patients, such as age, sex, diabetes mellitus, biopsy-confirmed CTN, schemic cardiopathy, cholesterol, triglycerides, and renal status by Modification of Diet in Renal Disease (MDRD) clearance and proteinuria. We also selected other characteristics, including hepatitis C virus infection and systolic/diastolic arterial pressures. The proportion of patients with high levels of IgG and IgM anti-beta2GPI autoantibodies did not differ from that observed in the control group, whereas the difference became significant in the case of anti-beta2GPI IgA autoantibodies (19.88% vs 1%). These results for the presence of anti-beta2GPI IgA autoantibodies were related to clinical data through a multivariate analysis, where the only parameter influenced by the presence of these autoantibodies seemed to be proteinuria, which in most cases was due to CTN.

Seroepidemiology of Toxoplasma gondii infection in human adults from three rural communities in Durango State, Mexico

There is scarce information concerning the epidemiology of Toxoplasma gondii infection in people of rural Mexico. Anti-T. gondii immunoglobulin (Ig)G and IgM antibodies were sought in 462 adult inhabitants from 3 rural communities of Durango, Mexico, using enzyme-linked immunoassays. In total, 110 (23.8%) of 463 persons had IgG anti-T. gondii antibodies. Ten (2.2%) of them also had IgM anti-T. gondii antibodies. Prevalences of T. gondii IgG antibodies in the 3 communities varied from 14.8 to 35.8%. The highest prevalence of infection was observed in participants older than 70 yr and in those with good housing conditions. Toxoplasma gondii infection was significantly associated with consumption of squirrel (adjusted odds ratio [OR] = 4.22; 95% confidence interval [CI] = 1.11-16.05) and turkey meat (adjusted OR = 4.58; 95% CI = 1.14-18.44). This is the first epidemiological study of T. gondii prevalence in rural Mexico.

Relative binding affinity of novel steroids to androgen receptors in hamster prostate

The in vivo and in vitro antiandrogenic activity of four aromatic esters 10a-10d, one aliphatic ester 10e based on the pregna-4,16-diene-6, 20-dione structure and two aromatic 17c, 17d and two aliphatic valeroyloxy esters 17a, 17b based on the more saturated 4-pregnene-6,20-dione skeleton was examined. The biological activity of steroids 9, 10a-10e and 17a-17d, was determined using prostate glands from gonadectomized adult male golden hamsters. In the in vitro studies, the relative binding affinity of these steroids to cytoplasmic androgen receptor (AR) of hamster prostate was determined from, the corresponding IC50 values obtained from the competitive binding plots. The standards dihydrotestosterone (DHT) and cyproterone (CA) acetate used have displaced [3H]DHT from the AR with an IC50 value of 3.2 and 4.4 nM respectively. All steroidal compounds synthesized in this study showed a binding affinity for the androgen receptor, present in the cytosol from prostate hamster; compounds 10a-10c showed the highest affinities for this receptor. The in vivo experiments showed that all steroidal derivatives were subcutaneously active, since they decreased the weight of the prostate gland in gonadectomized hamsters treated with DHT, and are antagonists for the androgen receptor since they block the DHT-induced prostate weight gain. The derivatives having the more conjugated 4,16-pregnadiene-6, 20-dione system (10a-10c) exhibited a higher antiandrogenic activity than the corresponding steroids (17a-17d) based on the more saturated 4-pregnene-6,20-dione system.

Evaluation of the pathogenicity and transmissibility of a chilean isolate of porcine reproductive and respiratory syndrome virus

The objective of this study was to determine clinical features, shedding and transmission of a Chilean Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) strain upon experimental inoculation of 4-week-old pigs. Six groups of five animals each were used. The G1 (donor) group was inoculated with PRRSV, maintained in an isolation unit for 35 days, and sampled daily to determine shedding in mucosal secretions and faeces, viraemia and seroconversion. An uninfected control group (G6) was equally maintained and sampled under strict isolation. Four other groups (G2 to G5) were exposed to PRRSV via direct contact with G1 for 5-day periods in a staggered manner, throughout the 35-day period, and were later placed in an independent isolation unit to monitor infection status for 7 days. All the animals in G1 and G6 were killed at 35 days post-inoculation (dpi) and the contact groups at 12 days post-contact (dpc). Samples were obtained from diverse organs for histopathological, immunohistochemical (IHC) and virological analysis. No clinical symptoms were evident in any group, except for a transient fever observed in G1. Histopathologically, all the animals of G1 had interstitial pneumonia, although scarce PRRSV-positive cells were detected in the lung using IHC. PRRSV-positive cells (IHC) were detected in the lymphoid tissue of all animals in infected groups, but especially in G3 and G4. Viraemia was detected in G1 (3-35 dpi) and in the all contact groups (5-12 dpc). Likewise, ranging from 3 to 19 dpi, PRRSV was detected in at least one animal from the tonsils and lungs in all infected groups, in nasal and ocular secretions, saliva or faeces. These results indicate that the donor group excreted infectious PRRSV and was able to transmit the infection to susceptible pigs. The critical shedding period was 7-19 dpi, during which, most likely, transmission took place.