Management and analysis of high-throughput sequence data for infectious animal diseases.

Advances in technology and decreasing costs have accelerated the use of high-throughput sequencing (HTS) for both diagnosis and characterisation of infectious animal diseases. High-throughput sequencing offers several advantages over previous techniques, including rapid turnaround times and the ability to resolve single nucleotide changes among samples, both of which are important for epidemiological investigations of outbreaks. However, due to the plethora of genetic data being routinely generated, the storage and analysis of these data are proving challenging in their own right. In this article, the authors provide insight into the aspects of data management and analysis that should be considered before adopting HTS for routine animal health diagnostics. These elements fall largely into three interrelated categories: data storage, data analysis and quality assurance. Each has numerous complexities and may need to be adapted as HTS evolves. Making appropriate strategic decisions about bioinformatic sequence analysis early on in project development will help to avert major issues in the long term.

Les avancées technologiques dans le domaine du séquençage à haut débit (SHD) et la diminution des coûts liés à cette technique en ont accéléré l'utilisation à des fins de diagnostic et de caractérisation des maladies animales infectieuses. Le séquençage à haut débit offre plusieurs avantages par rapport aux techniques antérieures, en particulier la rapidité de son exécution et une résolution de l'ordre d'un seul changement de nucléotide parmi plusieurs échantillons, ce qui présente un grand intérêt lors des enquêtes épidémiologiques sur les foyers. Néanmoins, la pléthore de données génétiques générées en routine par le SHD devient un véritable problème en termes de stockage et d'analyse de ces données. Les auteurs apportent un éclairage sur les aspects de la gestion et de l'analyse des données qu'il convient de prendre en compte avant d'adopter le SHD pour le diagnostic de routine en santé animale. Ces éléments relèvent de trois catégories étroitement reliées : le stockage de données, l'analyse de données et l'assurance qualité. Chacun de ces aspects présente de nombreuses complexités et nécessitera sans doute d'être adapté à mesure que le SHD évolue. Lorsqu'elles sont prises dès la phase initiale d'un projet, des décisions stratégiques appropriées en matière d'analyse bio-informatique de séquences peuvent contribuer à éviter des problèmes majeurs sur le long terme.

Los avances tecnológicos y la reducción de los costos han acelerado el uso de la secuenciación de alto rendimiento (SAR) con fines de diagnóstico y caracterización de enfermedades animales infecciosas. La secuenciación de alto rendimiento presenta varias ventajas en comparación con otras técnicas anteriores, en particular ciclos más rápidos y una resolución que permite detectar diferencias de un solo nucleótido entre las muestras, aspectos ambos de gran importancia para el estudio epidemiológico de brotes infecciosos. Sin embargo, debido al sinnúmero de datos genéticos que constantemente se generan, no es de extrañar que esté resultando problemático almacenar y analizar los datos obtenidos. Los autores arrojan luz sobre los aspectos de la gestión y el análisis de datos que conviene tener en cuenta antes de aplicar la SAR a las labores sistemáticas de diagnóstico en sanidad animal. Estos elementos corresponden a grandes líneas a tres categorías relacionadas entre sí: el almacenamiento de datos; el análisis de datos; y la garantía de calidad. Cada una de ellas presenta multitud de complicaciones y exige un proceso permanente de adaptación a medida que la técnica de secuenciación va evolucionando. El hecho de adoptar las buenas decisiones estratégicas sobre el análisis bioinformático de secuencias en los primeros momentos de la concepción de un proyecto ayudará a evitar importantes problemas a largo plazo.

EAN consensus statement for management of patients with neurological diseases during the COVID-19 pandemic.

BACKGROUND AND PURPOSE: The recent SARS-CoV-2 pandemic has posed multiple challenges to the practice of clinical neurology including recognition of emerging neurological complications and management of coexistent neurological diseases. In a fast-evolving pandemic, evidence-based studies are lacking in many areas. This paper presents European Academy of Neurology (EAN) expert consensus statements to guide neurologists caring for patients with COVID-19. METHODS: A refined Delphi methodology was applied. In round 1, statements were provided by EAN scientific panels (SPs). In round 2, these statements were circulated to SP members not involved in writing them, asking for agreement/disagreement. Items with agreement >70% were retained for round 3, in which SP co-chairs rated importance on a five-point Likert scale. Results were graded by importance and reported as consensus statements. RESULTS: In round one, 70 statements were provided by 23 SPs. In round two, 259/1061 SP member responses were received. Fifty-nine statements obtained >70% agreement and were retained. In round three, responses were received from 55 co-chairs of 29 SPs. Whilst general recommendations related to prevention of COVID-19 transmission had high levels of agreement and importance, opinion was more varied concerning statements related to therapy. CONCLUSION: This is the first structured consensus statement on good clinical practice in patients with neurological disease during the COVID-19 pandemic that provides immediate guidance for neurologists. In this fast-evolving pandemic, a rapid response using refined Delphi methodology is possible, but guidance may be subject to change as further evidence emerges.

The international European Academy of Neurology survey on neurological symptoms in patients with COVID-19 infection.

BACKGROUND AND PURPOSE: Although the main clinical features of COVID-19 infection are pulmonary, several associated neurological signs, symptoms and diseases are emerging. The incidence and characteristics of neurological complications are unclear. For this reason, the European Academy of Neurology (EAN) core COVID-19 Task Force initiated a survey on neurological symptoms observed in patients with COVID-19 infection. METHODS: A 17-question online survey was made available on the EAN website and distributed to EAN members and other worldwide physicians starting on 9 April 2020. RESULTS: By 27 April 2020, proper data were collected from 2343 responders (out of 4199), of whom 82.0% were neurologists, mostly from Europe. Most responders (74.7%) consulted patients with COVID-19 mainly in emergency rooms and in COVID-19 units. The majority (67.0%) had evaluated fewer than 10 patients with neurological manifestations of COVID-19 (neuro COVID-19). The most frequently reported neurological findings were headache (61.9%), myalgia (50.4%), anosmia (49.2%), ageusia (39.8%), impaired consciousness (29.3%) and psychomotor agitation (26.7%). Encephalopathy and acute cerebrovascular disorders were reported at 21.0%. Neurological manifestations were generally interpreted as being possibly related to COVID-19; they were most commonly recognized in patients with multiple general symptoms and occurred at any time during infection. CONCLUSION: Neurologists are currently and actively involved in the management of neurological issues related to the COVID-19 pandemic. This survey justifies setting up a prospective registry to better capture the prevalence of patients with neuro COVID-19, neurological disease characteristics and the contribution of neurological manifestations to outcome.

Changes in fermentation and animal performance during recovery from classical diet-induced milk fat depression using corn with differing rates of starch degradability.

Diet-induced milk fat depression (MFD) is a multifactorial disorder that can be triggered by a variety of conditions. Feeding high amounts of starch and unsaturated fatty acids has been shown to reduce milk fat yield and composition, as well as alter ruminal biohydrogenation patterns. However, little is known about how starch degradability in the rumen influences recovery from diet-induced MFD and if production of milk fat-inhibiting isomers will persist following an episode of MFD. The objective of this study was to evaluate production performance and ruminal fermentation in cows recovering from MFD when corn with a low or high starch degradability is fed. Six ruminally fistulated Holstein cows were used in a crossover design with 2 periods. During each period, MFD was induced for 10 d by feeding a diet with low fiber, high starch, and high unsaturated fatty acid. The polyunsaturated fatty acid concentration of the diet during the induction phase was modified primarily through inclusion of soybean oil. Following induction, cows were switched to either a high degradable starch recovery diet (HDS) or a low degradable starch recovery diet (LDS) for 18 d. The 7-h starch degradability was 66.5% for LDS and 87.8% for HDS. Milk was collected every 3 d for component and fatty acid analysis. On d 0, 4, 7, 10, 16, 22, and 28 of each period, ruminal pH and rumen fluid were collected every 2 h. Milk fat yield and composition was reduced during MFD induction and progressively increased by day in both HDS and LDS during recovery. Dry matter intake was similar among treatments and increased steadily over time during recovery. Preformed fatty acids were greater for HDS-fed animals, and de novo fatty acid in milk fat was greater for LDS-fed animals. Milk trans-10 C18:1 tended to be greater for HDS, and trans-10,cis-12 conjugated linoleic acid was significantly greater for HDS. cis-9,trans-11 conjugated linoleic acid was not affected by starch degradability during recovery. Total volatile fatty acids, butyrate, and valerate tended to differ or differed with recovery treatment, but ruminal pH and ammonia concentration were unaffected. The HDS diet responded similarly to the LDS diet during recovery with regard to milk fat percentage, but milk and fat yield tended to consistently be lower in HDS. When considering approaches to ameliorate diet-induced MFD, the degradability of the starch within rations should be evaluated. Although animal performance was similar, some trans fatty acid isomers were persistent in the milk through the recovery phase with HDS-fed animals, suggesting that milk fat synthesis might be potentially inhibited and biohydrogenation pathways modified in the rumen following an episode of MFD.

Factors associated with long-term weight-loss maintenance following bariatric surgery in adolescents with severe obesity.

BACKGROUND/OBJECTIVES: Bariatric surgery produces robust weight loss, however, factors associated with long-term weight-loss maintenance among adolescents undergoing Roux-en-Y gastric bypass surgery are unknown. SUBJECTS/METHODS: Fifty adolescents (mean±s.d. age and body mass index (BMI)=17.1±1.7 years and 59±11 kg m-2) underwent Roux-en-Y gastric bypass surgery, had follow-up visits at 1 year and at a visit between 5 and 12 years following surgery (Follow-up of Adolescent Bariatric Surgery at 5 Plus years (FABS-5+) visit; mean±s.d. 8.1±1.6 years). A non-surgical comparison group (n=30; mean±s.d. age and BMI=15.3±1.7 years and BMI=52±8 kg m-2) was recruited to compare weight trajectories over time. Questionnaires (health-related and eating behaviors, health responsibility, impact of weight on quality of life (QOL), international physical activity questionnaire and dietary habits via surgery guidelines) were administered at the FABS-5+ visit. Post hoc, participants were split into two groups: long-term weight-loss maintainers (n=23; baseline BMI=58.2 kg m-2; 1-year BMI=35.8 kg m-2; FABS-5+ BMI=34.9 kg m-2) and re-gainers (n=27; baseline BMI=59.8 kg m-2; 1-year BMI=36.8 kg m-2; FABS-5+ BMI=48.0 kg m-2) to compare factors which might contribute to differences. Data were analyzed using generalized estimating equations adjusted for age, sex, baseline BMI, baseline diabetes status and length of follow-up. RESULTS: The BMI of the surgical group declined from baseline to 1 year (-38.5±6.9%), which, despite some regain, was largely maintained until FABS-5+ (-29.6±13.9% change). The BMI of the comparison group increased from baseline to the FABS-5+ visit (+10.3±20.6%). When the surgical group was split into maintainers and re-gainers, no differences in weight-related and eating behaviors, health responsibility, physical activity/inactivity, or dietary habits were observed between groups. However, at FABS-5+, maintainers had greater overall QOL scores than re-gainers (87.5±10.5 vs 65.4±20.2, P<0.001) and in each QOL sub-domain (P<0.01 all). CONCLUSIONS: Long-term weight outcomes for those who underwent weight-loss surgery were superior to those who did not undergo surgical treatment. While no behavioral factors were identified as predictors of success in long-term weight-loss maintenance, greater QOL was strongly associated with maintenance of weight loss among adolescents who underwent Roux-en-Y gastric bypass surgery surgery.

Short communication: Field study to investigate the associations between herd-level risk factors for milk fat depression and bulk tank milk fat percent in dairy herds feeding monensin.

Fat is the most variable milk component, and maintaining milk fat continues to be a challenge on commercial dairy farms. Our objectives were to establish associations between herd-level risk factors for milk fat depression and bulk tank milk fat content in commercial dairy herds feeding monensin. Seventy-nine Holstein commercial dairy herds in the northeast and Upper Midwest United States were enrolled in an observational study. Data were collected on herd characteristics, total mixed ration (TMR) samples, all component silage samples, and bulk tank milk samples. The unconditional univariable association of each explanatory variable and bulk tank milk fat percentage was evaluated using simple linear regression and multivariable regression models. Milk fat content of trans-10 C18:1 had an exponentially negative relationship to herd milk fat percentage. In general, milk fat content of fatty acids synthesized de novo in the mammary gland were positively related to herd milk fat, and the content of several trans-C18:1 fatty acids, which would be products of alternate pathways of ruminal biohydrogenation, were negatively related to herd milk fat. Variables related to TMR composition did not have univariable relationships with herd milk fat percentage. Herds that had >49.8% of the TMR particles on the middle screen of the Penn State particle separator had higher milk fat percentage than those with ≤49.8%, and herds with >54.0% of TMR particles in the bottom pan had lower milk fat percentage than herds with ≤54.0%. Dietary content of monounsaturated fatty acids (C16:1 and C18:1) had negative relationships with herd milk fat percentage; however, no single diet component accounted for more than 11% of the variation in herd-level milk fat percentage. Univariable monensin dose was not associated with herd milk fat percentage. The relative lack of significant univariate relationships with herd-level milk fat suggests many factors contribute to milk fat content, and herds experiencing low milk fat will need to examine many potential risk factors when working to troubleshoot this challenge.

Lipid changes 8 years post gastric bypass in adolescents with severe obesity (FABS-5+ study).

OBJECTIVE: Severe obesity in adolescents is increasing and few effective treatments exist. Bariatric surgery is one option, but the extent to which surgery influences cardiovascular risk factors over time in youth is not clear. We hypothesized that Roux-en Y gastric bypass (RYGB) would be associated with sustained improvements in lipids over time (>5 years). PARTICIPANTS/METHODS: Youth who underwent RYGB from 2001 to 2007 were recruited for the Follow-up of Adolescent Bariatric Surgery-5+ (FABS-5+) in 2011-2014. Baseline body mass index (BMI) and lipids were abstracted from medical records. Follow-up data were obtained at a research visit. Analyses included paired t-tests to assess changes in BMI and lipids over time. General linear models were used to evaluate predictors of high-density lipoprotein (HDL) and non-HDL-cholesterol at follow-up. A non-operative group was recruited for comparison. RESULTS: Surgical participants (n=58) were a mean±s.d. age of 17±2 years at baseline and 25±2 years at long-term follow-up. Eighty-six percent were Caucasian and 64% were female. At long-term follow-up BMI decreased by 29% and all lipids (except total cholesterol) significantly improved (P<0.01). Female sex was a significant predictor of non-HDL-cholesterol level at 1 year, while change in BMI from 1 year to long-term follow-up was a significant predictor of non-HDL-cholesterol and HDL-cholesterol during the same interval (P<0.05). In the non-operative group, BMI increased by 8% and lipid parameters were unchanged. CONCLUSIONS: This is the longest and most complete follow-up of youth following RYGB. Weight loss maintenance over time was significantly associated with improvements in lipid profile over 5 years.

Contrasting patterns of population structure and gene flow facilitate exploration of connectivity in two widely distributed temperate octocorals.

Connectivity is an important component of metapopulation dynamics in marine systems and can influence population persistence, migration rates and conservation decisions associated with Marine Protected Areas (MPAs). In this study, we compared the genetic diversity, gene flow and population structure of two octocoral species, Eunicella verrucosa and Alcyonium digitatum, in the northeast Atlantic (ranging from the northwest of Ireland and the southern North Sea, to southern Portugal), using two panels of 13 and 8 microsatellite loci, respectively. Our results identified regional genetic structure in E. verrucosa partitioned between populations from southern Portugal, northwest Ireland and Britain/France; subsequent hierarchical analysis of population structure also indicated reduced gene flow between southwest Britain and northwest France. However, over a similar geographical area, A. digitatum showed little evidence of population structure, suggesting high gene flow and/or a large effective population size; indeed, the only significant genetic differentiation detected in A. digitatum occurred between North Sea samples and those from the English Channel/northeast Atlantic. In both species the vast majority of gene flow originated from sample sites within regions, with populations in southwest Britain being the predominant source of contemporary exogenous genetic variants for the populations studied. Overall, historical patterns of gene flow appeared more complex, though again southwest Britain appeared to be an important source of genetic variation for both species. Our findings have major conservation implications, particularly for E. verrucosa, a protected species in UK waters and listed by the IUCN as 'Vulnerable', and for the designation and management of European MPAs.

A 100-Year Review: Fat feeding of dairy cows.

Over 100 years, the Journal of Dairy Science has recorded incredible changes in the utilization of fat for dairy cattle. Fat has progressed from nothing more than a contaminant in some protein supplements to a valuable high-energy substitute for cereal grains, a valuable energy source in its own right, and a modifier of cellular metabolism that is under active investigation in the 21st century. Milestones in the use of fats for dairy cattle from 1917 to 2017 result from the combined efforts of noted scientists and industry personnel worldwide, with much of the research published in Journal of Dairy Science. We are humbled to have been asked to contribute to this historical collection of significant developments in fat research over the past 100 years. Our goal is not to detail all the work published as each development moved forward; rather, it is to point out when publication marked a significant change in thinking regarding use of fat supplements. This approach forced omission of critically important names and publications in many journals as ideas moved forward. However, we hope that a description of the major changes in fat feeding during the past 100 years will stimulate reflection on progress in fat research and encourage further perusal of details of significant events.

Short communication: Temporal effect of feeding potassium carbonate sesquihydrate on milk fat in lactating dairy cows fed a fat-depressing diet.

A lactation study with 10 multiparous dairy cows in early lactation, with an average of 64 days in milk (standard deviation=37), were used to evaluate how quickly milk fat concentration would change when potassium carbonate sesquihydrate was abruptly added to the diet. The experiment had 3 periods. In period 1 (d 0 to 7) all cows were fed the same basal (control) diet with 1.8% soy oil, dry basis; in period 2 (d 8 to 28) 5 cows received the control diet, whereas the other 5 cows received the control diet plus 0.59% of added K with K carbonate sesquihydrate; and in period 3 (d 29 to 42) all 10 cows received the control diet. The control diet was formulated for a dietary cation-anion difference (DCAD), calculated as Na + K - Cl - S, of 37.7mEq/100g of dry matter (DM), 1.74% of DM as K, and 5.7% long-chain fatty acids (DM%), which included 1.8% of DM as soybean oil. Period 1 was used as a covariate. In period 2, d 8 to 28, 5 cows remained on the control diet whereas 5 cows were fed with the control diet plus K carbonate sesquihydrate (DCAD+ diet; DCAD of 54.3mEq/100g DM and 2.33% of DM as K). After feeding the DCAD+ diet, we noted a difference in milk fat concentration from 3.9 to 4.3% within 72h. Over the 21d of period 2, the DCAD+ diet resulted in significantly greater milk fat percentage from 4.0 to 4.3%, lactose from 4.74 to 4.82%, and fat efficiency in the form of fat in milk divided by fat in DMI from 1.27 to 1.49, without affecting dry matter intake (DMI), milk protein concentration, solids-not fat concentration, 3.5% fat-corrected milk, and protein efficiency in the form of protein in milk divided by protein in DMI. In period 3 (d 29-42), all cows were again fed the control diet, resulting in a tendency for greater milk fat concentration, significantly greater lactose concentration, and fat efficiency in the form of fat in milk divided by fat in DMI for the cows having received the DCAD+ diet during period 2. In conclusion, the abrupt addition of K carbonate sesquihydrate resulted in a greater milk fat concentration and tended to maintain the greater concentration after cessation of K carbonate sesquihydrate feeding.

Changes in inflammation, oxidative stress and adipokines following bariatric surgery among adolescents with severe obesity.

BACKGROUND/OBJECTIVES: Inflammation, oxidative stress and dysregulation of adipokines are thought to be pathophysiological mechanisms linking obesity to the development of insulin resistance and atherosclerosis. In adults, bariatric surgery reduces inflammation and oxidative stress, and beneficially changes the levels of several adipokines, but little is known about the postsurgical changes among adolescents. SUBJECTS/METHODS: In two separate longitudinal cohorts we evaluated change from baseline of interleukin-6 (IL-6), tumor necrosis factor-alpha (TNF-α), monocyte chemo-attractant protein-1 (MCP-1), oxidized low-density lipoprotein cholesterol (oxLDL), adiponectin, leptin and resistin up to 12 months following elective laparoscopic Roux-en-Y gastric bypass (RYGB) or vertical sleeve gastrectomy (VSG) surgery in adolescents with severe obesity. RESULTS: In cohort 1, which consisted of 39 adolescents (mean age 16.5±1.6 years; 29 females) undergoing either RYGB or VSG, IL-6 (baseline: 2.3±3.4 pg ml(-1) vs 12 months: 0.8±0.6 pg ml(-1), P<0.01), leptin (baseline: 178±224 ng ml(-1) vs 12 months: 41.4±31.9 ng ml(-1), P<0.001) and oxLDL (baseline: 41.6±11.6 U l(-1) vs 12 months: 35.5±11.1 U l(-1), P=0.001) significantly decreased and adiponectin significantly increased (baseline: 5.4±2.4 µg ml(-1) vs 12 months: 13.5±8.9 µg ml(-1), P<0.001). In cohort 2, which consisted of 13 adolescents (mean age 16.5±1.6 years; 10 females) undergoing RYGB, results were similar: IL-6 (baseline: 1.7±0.9 pg ml(-1) vs 12 months: 0.4±0.9 pg ml(-1), P<0.05) and leptin (baseline: 92.9±31.3 ng ml(-1) vs 12 months: 37.3±33.4 ng ml(-1), P<0.001) significantly decreased and adiponectin significantly increased (baseline: 6.1±2.9 µg ml(-1) vs 12 months: 15.4±8.0 µg ml(-1), P<0.001). When the cohorts were combined to evaluate changes at 12 months, oxLDL also significantly decreased (baseline: 39.8±16.7 U l(-1) vs 12 months: 32.7±11.9 U l(-1), P=0.03). CONCLUSIONS: Bariatric surgery produced robust improvements in markers of inflammation, oxidative stress and several adipokines among adolescents with severe obesity, suggesting potential reductions in risk for type 2 diabetes and cardiovascular disease.

Concurrent Risperidone Administration Attenuates the Development of Locomotor Sensitization Following Sub-Chronic Phencyclidine in Rats.

INTRODUCTION: In schizophrenia early treatment may prevent disorder onset, or at least minimize its impact, suggesting possible neuroprotective properties of antipsychotics. The present study investigates the effects of chronic treatment with the atypical antipsychotic, risperidone, on locomotor sensitization in the subchronic phencyclidine-treated rat. METHODS: Rats were treated with phencyclidine sub-chronically (2 mg/kg bi-daily for one week followed by a one-week wash-out period) or vehicle. Half of the phencyclidine group was concurrently treated with risperidone (0.5 mg/kg IP) twice daily for 15 days, beginning 3 days before the start of phencyclidine administration. 6 weeks after treatment all rats were injected with a phencyclidine-challenge (3.2 mg/kg) and immediately after their locomotor activity measured for 20 min. RESULTS: Co-administration of risperidone at the time of phencyclidine administration significantly reduced the phencyclidine-challenge locomotor effect administered 6 weeks later. DISCUSSION: These results demonstrate that concurrent risperidone is neuroprotective, and clearly suggests its functionality can be translated to a clinical setting for treating the so-called prodrome.

Changes in fermentation and biohydrogenation intermediates in continuous cultures fed low and high levels of fat with increasing rates of starch degradability.

Excessive levels of starch in diets for lactating dairy cattle is a known risk factor for milk fat depression, but little is known about how this risk is affected by differences in rates of starch degradability (Kd) in the rumen. The objective of this study was to compare accumulation of biohydrogenation intermediates causing milk fat depression, including conjugated linoleic acid (CLA), when corn with low or high Kd were fed to continuous cultures. Diets contained (dry matter basis) 50% forage (alfalfa pellets and grass hay) and 50% concentrate, with either no added fat (LF) or 3.3% added soybean oil (HF). Within both the LF and HF diets, 3 starch degradability treatments were obtained by varying the ratio of processed (heat and pressure treatments) and unprocessed corn sources, giving a total of 6 dietary treatments. Each diet was fed to dual-flow continuous fermenters 3 times a day at 0800, 1600, and 2400h. Diets were fed for four 10-d periods, with 7d for adaptation and 3d for sample collection. Orthogonal contrasts were used in the GLIMMIX procedure of SAS to test the effects of fat, starch degradability, and their interaction. Acetate and acetate:propionate were lower for HF than for LF but daily production of trans-10 18:1 and trans-10,cis-12 CLA were higher for HF than for LF. Increasing starch Kd from low to high increased culture pH, acetate, and valerate but decreased butyrate and isobutyrate. Changes in biohydrogenation intermediates (expressed as % of total isomers) from low to high starch Kd included reductions in trans-11 18:1 and cis-9,trans-11 CLA but increases in trans-10 18:1 and trans-10,cis-12 CLA. The results show that increasing the starch Kd in continuous cultures while holding starch level constant causes elevation of biohydrogenation intermediates linked to milk fat depression.

Associations of single nucleotide polymorphisms in the Pygo2 coding sequence with idiopathic oligospermia and azoospermia.

Male infertility is often associated with a decreased sperm count. The Pygo2 gene is expressed in the elongating spermatid during chromatin remodeling; thus impairment in PYGO2 function might lead to spermatogenic arrest, sperm count reduction, and subsequent infertility. The aim of this study was to identify mutations in Pygo2 that might lead to idiopathic oligospermia and azoospermia. DNA was isolated from venous blood from 77 men with normal fertility and 195 men with idiopathic oligospermia or azoospermia. Polymerase chain reaction-sequencing analysis was performed for the three Pygo2 coding regions. Non-synonymous single nucleotide polymorphisms (SNPs) were detected and analyzed using SIFT, Polyphen-2, and Mutation Taster softwares to identify possible changes in protein structure that could affect phenotype. Pygo2 sequencing was successful for 178 patients (30 with mild or moderate oligospermia, 57 with severe oligospermia, and 91 with azoospermia). Three previously reported non-synonymous SNPs were identified in patients with azoospermia or severe oligospermic but not in those with mild or moderate oligozoopermia or normozoospermia. SNPs rs61758740 (M141I) and rs141722381 (N240I) cause the replacement of one hydrophobic or hydrophilic amino acid, respectively, with another, and SNP rs61758741 (K261E) causes the replacement of a basic amino acid with an acidic one. The software predictions demonstrated that SNP rsl41722381 would likely result in disrupted tertiary protein structure and thus could be involved in disease pathogenesis. Overall, this study demonstrated that SNPs in the coding region of Pygo2 might be one of the causative factors in idiopathic oligospermia and azoospermia, resulting in male infertility.

Addition of potassium carbonate to continuous cultures of mixed ruminal bacteria shifts volatile fatty acids and daily production of biohydrogenation intermediates.

A recent study reported a 0.4 percentage unit increase in milk fat of lactating dairy cattle when dietary K was increased from 1.2 to 2% with potassium carbonate. Because milk fat yield has been associated with ruminal production of certain conjugated linoleic acid (CLA) isomers, 2 studies were conducted to determine if increasing potassium carbonate in the rumen would alter patterns of fermentation and biohydrogenation. In experiment 1, 5 dual-flow continuous fermenters were injected just before each feeding with a 10% (wt/wt) stock potassium carbonate solution to provide the equivalent of 1.1 (K1), 2.2 (K2), and 3.3 (K3) % of diet dry matter (DM) as added K. One of the remaining fermenters received no K (K0) and the last fermenter (NaOH) was injected with adequate NaOH stock solution (10%, wt/wt) to match the pH observed for the K3 treatment. For experiment 2, 6 dual-flow continuous fermenters were used to evaluate 6 treatments arranged in a 2 × 3 factorial to examine 2 levels of soybean oil (0 and 3.64% of diet DM) and added K at 0, 1.6, and 3.3% of diet DM. In both experiments, fermenters were fed 55 to 57 g of DM/d of a typical dairy diet consisting of 1:1 forage (10% alfalfa hay and 90% corn silage) to concentrate mix in 2 equal portions at 0800 and 1630 h, and fed the respective diets for 10-d periods. Potassium carbonate addition increased pH in both experiments. Acetate:propionate ratio and pH in experiment 1 increased linearly for K0 to K3. Acetate:propionate ratio was lower for NaOH compared with K3 but the pH was the same. The trans-11 18:1 and cis-9,trans-11 CLA production rates (mg/d) increased linearly from K0 to K3, but K3 and NaOH did not differ. Production of trans-10 18:1 decreased and that of trans-10,cis-12 tended to decrease from K0 to K3, but production of trans-10,cis-12 CLA remained high for NaOH. Addition of K to the cultures in experiment 2 decreased propionate and increased acetate and acetate:propionate ratio for the 0% fat diet but not for the 3.64% fat diet. Addition of K increased stearic acid and cis-9,trans-11 CLA but decreased daily production of trans-10 C18:1 and trans-10,cis-12 CLA. The results indicate that increasing potassium carbonate in the diet shifts both fermentation and biohydrogenation pathways toward higher milk fat percentage in dairy cows, but the effects are only explained in part by elevation of pH.

Invited review: palmitic and stearic acid metabolism in lactating dairy cows.

Energy is the most limiting nutritional component in diets for high-producing dairy cows. Palmitic (C16:0) and stearic (C18:0) acids have unique and specific functions in lactating dairy cows beyond a ubiquitous energy source. This review delineates their metabolism and usage in lactating dairy cows from diet to milk production. Palmitic acid is the fatty acid (FA) found in the greatest quantity in milk fat. Dietary sources of C16:0 generally increase milk fat yield and are used as an energy source for milk production and replenishing body weight loss during periods of negative energy balance. Stearic acid is the most abundant FA available to the dairy cow and is used to a greater extent for milk production and energy balance than C16:0. However, C18:0 is also intimately involved in milk fat production. Quantifying the transfer of each FA from diet into milk fat is complicated by de novo synthesis of C16:0 and desaturation of C18:0 to oleic acid in the mammary gland. In addition, incorporation of both FA into milk fat appears to be limited by the cow's requirement to maintain fluidity of milk, which requires a balance between saturated and unsaturated FA. Oleic acid is the second most abundant FA in milk fat and likely the main unsaturated FA involved in regulating fluidity of milk. Because the mammary gland can desaturate C18:0 to oleic acid, C18:0 appears to have a more prominent role in milk production than C16:0. To understand metabolism and utilization of these FA in lactating dairy cows, we reviewed production and milk fat synthesis studies. Additional and longer lactation studies on feeding both FA to lactating dairy cows are required to better delineate their roles in optimizing milk production and milk FA composition and yield.

Bariatric surgery for adolescents.

Obesity is no longer just an adult disease. An increasing number of youth are overweight, defined as body mass index (BMI) at or greater than the 95th percentile for age (1). Between 2009 and 2010, 16.9% of children aged 2­19 yr were classified as overweight based on BMI (2), as compared with only 5% of children affected by obesity in 1976­1980 (3). This is a problem of enormous proportion from a public health standpoint, as without intervention these children will grow up to become overweight and obese adults. For an obese child, the risk of becoming an obese adult may be as high as 77%, compared with 7%for a child of healthy weight (4). Morbid obesity is a major risk factor for later complications such as cardiovascular disease, type 2 diabetes, obstructive sleep apnea (OSA), polycystic ovary syndrome (PCOS), and degenerative joint disease (4­10). Obesity is also an expensive problem: the US government spends $147 billion yearly on obesity-related healthcare costs (11). Thus, there is an urgent need to target obesity in the pediatric population, before the expensive and life-threatening consequences of obesity manifest. Unfortunately, the effectiveness of medical treatments for obesity is limited. Behaviorally based dietary and physical activity interventions offer little benefit for pediatric obesity, while pharmacologic therapy is also limited and carries low success rates and recidivism (12­14) (Table 1).

Targets for antibiotic and healthcare resource stewardship in inpatient community-acquired pneumonia: a comparison of management practices with National Guideline Recommendations.

PURPOSE: Community-acquired pneumonia (CAP) is the most common infection leading to hospitalization in the USA. The objective of this study was to evaluate management practices for inpatient CAP in relation to Infectious Diseases Society of America/American Thoracic Society (IDSA/ATS) guidelines to identify opportunities for antibiotic and health care resource stewardship. METHODS: This was a retrospective cohort study of adults hospitalized for CAP at a single institution from 15 April 2008 to 31 May 2009. RESULTS: Of the 209 patients with CAP who presented to Denver Health Medical Center during the study period and were hospitalized, 166 (79 %) and 43 (21 %) were admitted to a medical ward and the intensive care unit (ICU), respectively. Sixty-one (29 %) patients were candidates for outpatient therapy per IDSA/ATS guidance with a CURB-65 score of 0 or 1 and absence of hypoxemia. Sputum cultures were ordered for 110 specimens; however, an evaluable sample was obtained in only 49 (45 %) cases. Median time from antibiotic initiation to specimen collection was 11 [interquartile range (IQR) 6-19] h, and a potential pathogen was identified in only 18 (16 %) cultures. Blood cultures were routinely obtained for both non-ICU (81 %) and ICU (95 %) cases, but 15 of 36 (42 %) positive cultures were false-positive results. The most common antibiotic regimen was ceftriaxone + azithromycin (182, 87 % cases). Discordant with IDSA/ATS recommendations, oral step-down therapy consisted of a new antibiotic class in 120 (66 %), most commonly levofloxacin (101, 55 %). Treatment durations were typically longer than suggested with a median of 10 (IQR 8-12) days. CONCLUSIONS: In this cohort of patients hospitalized for CAP, management was frequently inconsistent with IDSA/ATS guideline recommendations, revealing potential targets to reduce unnecessary antibiotic and healthcare resource utilization.

Y chromosome sequence variation and the history of human populations.

Binary polymorphisms associated with the non-recombining region of the human Y chromosome (NRY) preserve the paternal genetic legacy of our species that has persisted to the present, permitting inference of human evolution, population affinity and demographic history. We used denaturing high-performance liquid chromatography (DHPLC; ref. 2) to identify 160 of the 166 bi-allelic and 1 tri-allelic site that formed a parsimonious genealogy of 116 haplotypes, several of which display distinct population affinities based on the analysis of 1062 globally representative individuals. A minority of contemporary East Africans and Khoisan represent the descendants of the most ancestral patrilineages of anatomically modern humans that left Africa between 35,000 and 89,000 years ago.