Temporally robust occupancy frequency distributions in riverine metacommunities explained by local biodiversity regulation

Aim

The mechanisms determining the distribution of the number of sites species occupy, the occupancy frequency distribution (OFD), remain incompletely understood despite decades of research. To explore the dominant mechanisms responsible for the shape and temporal dynamics of empirical OFD, we develop a simple patch occupancy framework with intrinsically regulated local richness and fit the model to a highly replicated dataset describing macroinvertebrate, macrophyte and diatom occupancy.

Location

England.

Time period

Up to $30$ years between 1990 and 2020.

Major taxa studied

Macroinvertebrates, macrophytes and diatoms.

Methods

We study the OFD in a highly replicated dataset of freshwater metacommunities in England across time. We consider temporal change in species richness, composition, and in the shape of the OFD. Goodness-of-fit of the steady state of a simple patch occupancy model—which predicts a log-series OFD—to the empirical observations is assessed. Additionally, we test the capacity of the model to predict metacommunity-scale processes.

Results

Our model provides a consistently good fit to empirical OFDs. It can additionally be used to predict metacommunity-scale species turnover.

Main conclusions

Our results support the view that metacommunity structure reflects a dynamic steady state controlled by local limits to coexistence.     

A lost opportunity for science: journals promote data sharing in metabolomics but do not enforce it

Introduction

Data sharing is being increasingly required by journals and has been heralded as a solution to the ‘replication crisis’.

Objectives

(i) Review data sharing policies of journals publishing the most metabolomics papers associated with open data and (ii) compare these journals’ policies to those that publish the most metabolomics papers.

Methods

A PubMed search was used to identify metabolomics papers. Metabolomics data repositories were manually searched for linked publications.

Results

Journals that support data sharing are not necessarily those with the most papers associated to open metabolomics data.

Conclusion

Further efforts are required to improve data sharing in metabolomics.

     

Optimization of fecal sample preparation for untargeted LC-HRMS based metabolomics

Introduction

Collecting feces is easy. It offers direct outcome to endogenous and microbial metabolites.

Objectives

In a context of lack of consensus about fecal sample preparation, especially in animal species, we developed a robust protocol allowing untargeted LC-HRMS fingerprinting.

Methods

The conditions of extraction (quantity, preparation, solvents, dilutions) were investigated in bovine feces.

Results

A rapid and simple protocol involving feces extraction with methanol (1/3, M/V) followed by centrifugation and a step filtration (10 kDa) was developed.

Conclusion

The workflow generated repeatable and informative fingerprints for robust metabolome characterization.

     

Metabolic response of porcine colon explants to in vitro infection by <Emphasis Type="Italic">Brachyspira hyodysenteriae</Emphasis>: a leap into disease pathophysiology

Introduction

Swine dysentery caused by Brachyspira hyodysenteriae is a production limiting disease in pig farming. Currently antimicrobial therapy is the only treatment and control method available.

Objective

The aim of this study was to characterize the metabolic response of porcine colon explants to infection by B. hyodysenteriae.

Methods

Porcine colon explants exposed to B. hyodysenteriae were analyzed for histopathological, metabolic and pro-inflammatory gene expression changes.

Results

Significant epithelial necrosis, increased levels of l-citrulline and IL-1α were observed on explants infected with B. hyodysenteriae.

Conclusions

The spirochete induces necrosis in vitro likely through an inflammatory process mediated by IL-1α and NO.

     

Does AMH Reflect Follicle Number Similarly in Women with and without PCOS?

Context

Increased Anti-Mullerian Hormone in polycystic ovary syndrome, may be due to overactive follicles rather than reflect antral follicle count.

Objective

Does Anti-Mullerian Hormone reflect antral follicle count similarly in women with or without polycystic ovary syndrome or polycystic ovarian morphology?

Design

Cross-sectional, case-control.

Setting

Women who delivered preterm in 1999–2006. For each index woman, a woman with a term delivery was identified.

Patients

Participation rate was 69%. Between 2006–2008, 262 women were included, and diagnosed to have polycystic ovary syndrome, polycystic ovarian morphology or to be normal controls.

Intervention(s)

Blood tests, a clinical examination and vaginal ultrasound.

Main Outcome Measure(s)

Anti-Mullerian Hormone / antral follicle count -ratio, SHBG, androstenedione and insulin, to test potential influence on the Anti-Mullerian Hormone / antral follicle count -ratio.

Results

Mean Anti-Mullerian Hormone / antral follicle count ratio in women with polycystic ovary syndrome or polycystic ovarian morphology was similar to that of the controls (polycystic ovary syndrome: 1,2 p = 0,10 polycystic ovarian morphology: 1,2, p = 0,27 Controls 1,3). Anti-Mullerian Hormone showed a positive linear correlation to antral follicle count in all groups. Multivariate analysis did not change the results.

Conclusions

We confirmed the positive correlation between AMH and follicle count. Anti-Mullerian Hormone seems to be a reliable predictor of antral follicle count, independent of polycystic ovary syndrome diagnosis or ovarian morphology.     

Inbreeding as a cause for deafness: Dadhkai study

BACKGROUND:

We report on the higher prevalence of deaf-mutes from a village in Jammu and Kashmir State of India.

MATERIALS AND METHODS:

A cross-sectional study among 79 deaf mutes using pedigree analysis, audiometry, imaging and molecular analysis.

RESULTS:

A high rate of hereditary deafness with 79 individuals diagnosed to be suffering from non-syndrome deafness in a total population of 2452 individuals residing in the village.

INTERPRETATION:

Flourishing of intermarriages led to a population with high prevalence of deafness     

A methodology for elucidating regulatory mechanisms leading to changes in lipid profiles

Introduction

It is difficult to elucidate the metabolic and regulatory factors causing lipidome perturbations.

Objectives

This work simplifies this process.

Methods

A method has been developed to query an online holistic lipid metabolic network (of 7923 metabolites) to extract the pathways that connect the input list of lipids.

Results

The output enables pathway visualisation and the querying of other databases to identify potential regulators. When used to a study a plasma lipidome dataset of polycystic ovary syndrome, 14 enzymes were identified, of which 3 are linked to ELAVL1—an mRNA stabiliser.

Conclusion

This method provides a simplified approach to identifying potential regulators causing lipid-profile perturbations.

     

Quantitative analysis of tetrahydrofolate metabolites from <Emphasis Type="Italic">clostridium autoethanogenum</Emphasis>

Introduction

Quantification of tetrahydrofolates (THFs), important metabolites in the Wood–Ljungdahl pathway (WLP) of acetogens, is challenging given their sensitivity to oxygen.

Objective

To develop a simple anaerobic protocol to enable reliable THFs quantification from bioreactors.

Methods

Anaerobic cultures were mixed with anaerobic acetonitrile for extraction. Targeted LC–MS/MS was used for quantification.

Results

Tetrahydrofolates can only be quantified if sampled anaerobically. THF levels showed a strong correlation to acetyl-CoA, the end product of the WLP.

Conclusion

Our method is useful for relative quantification of THFs across different growth conditions. Absolute quantification of THFs requires the use of labelled standards.

     

Outcome of Assisted Reproductive Technology (ART) and Subsequent Self-Reported Life Satisfaction

Objective

To compare life satisfaction between women with successful or unsuccessful outcome after assisted reproductive treatment (ART) by taking into account the time since the last ART.

Design

Cohort study.

Setting

Tertiary hospital.

Patients

A total of 987 consecutive women who had undergone ART during 1996–2007 were invited and altogether 505 women participated in the study.

Interventions

A postal enquiry with a life satisfaction scale.

Main Outcome Measure

Self-reported life satisfaction in respect to the time since the last ART.

Results

In general, women who achieved a live birth after ART had a significantly higher life satisfaction than those who had unsuccessful ART, especially when compared in the first three years. The difference disappeared in the time period of 6–9 years after ART. The unsuccessfully treated women who had a child by some other means before or after the unsuccessful ART had comparable life satisfaction with successfully treated women even earlier.

Conclusions

Even if unsuccessful ART outcome is associated with subsequent lower level of life satisfaction, it does not seem to threaten the long-term wellbeing.     

Extraction of natural products from bark of <Emphasis Type="Italic">Betula pendula</Emphasis> using ionic liquids

Introduction

Aqueous–methanol mixtures have successfully been applied to extract a broad range of metabolites from plant tissue. However, a certain amount of material remains insoluble.

Objectives

To enlarge the metabolic compendium, two ionic liquids were selected to extract the methanol insoluble part of trunk from Betula pendula.

Methods

The extracted compounds were analyzed by LC/MS and GC/MS.

Results

The results show that 1-butyl-3-methylimidazolium acetate (IL-Ac) predominantly resulted in fatty acids, whereas 1-ethyl-3-methylimidazolium tosylate (IL-Tos) mostly yielded phenolic structures. Interestingly, bark yielded more ionic liquid soluble metabolites compared to interior wood.

Conclusion

From this one can conclude that the application of ionic liquids may expand the metabolic snapshot.

     

Recombination in human leukocyte antigen region in two Asian Indian families

BACKGROUND:

Recombination (crossing over) may generate novel haplotypes that can be beneficial to a population against recently introduced pathogens. It may lead to the generation of new alleles.

SETTINGS AND DESIGN:

A prospective study at a tertiary care centre.

AIM:

To report two rare cases of crossing over in HLA region.

MATERIALS AND METHODS:

Tissue-typing was done by sequence specific primers (SSP) for DR locus and by both SSP and serology for Class I which was reconfirmed on fresh samples.

RESULTS:

In one patient crossing over had taken place in the region of A locus resulting in inheritance of A*01 instead of expected A*11. In second family crossing over had taken place in region of DRB1 locus and the sibling inherited DRB1*08 instead of DRB1*10.

CONCLUSIONS:

Possibility of recombination must be considered when interpreting implausible tissue-typing results of families worked up for BMT.     

NMRProcFlow: a graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics

Introduction

Concerning NMR-based metabolomics, 1D spectra processing often requires an expert eye for disentangling the intertwined peaks.

Objectives

The objective of NMRProcFlow is to assist the expert in this task in the best way without requirement of programming skills.

Methods

NMRProcFlow was developed to be a graphical and interactive 1D NMR (¹H & ¹³C) spectra processing tool.

Results

NMRProcFlow (http://nmrprocflow.org), dedicated to metabolic fingerprinting and targeted metabolomics, covers all spectra processing steps including baseline correction, chemical shift calibration and alignment.

Conclusion

Biologists and NMR spectroscopists can easily interact and develop synergies by visualizing the NMR spectra along with their corresponding experimental-factor levels, thus setting a bridge between experimental design and subsequent statistical analyses.

     

Esophagitis in a high H. pylori prevalence area: severe disease is rare but concomitant peptic ulcer is frequent

Background

Few data are available on the prevalence of erosive and severe esophagitis in Western countries.

Objective

To retrospectively determine the prevalence and the factors predicting erosive esophagitis and severe esophagitis in a large series of endoscopies in Spain.

Design

Retrospective observational study. A multivariate analysis was performed to determine variables predicting severe esophagitis.

Setting

Databases of 29 Spanish endoscopy units.

Patients

Patients submitted to a diagnostic endoscopy during the year 2005.

Interventions

Retrospective review of the databases.

Main Outcome Measurements

Esophagitis severity (graded according to the Los Angeles classification) and associated endoscopic findings.

Results

Esophagitis was observed in 8.7% of the 93,699 endoscopies reviewed. Severe esophagitis (LA grade C or D) accounted for 22.5% of cases of the disease and was found in 1.9% of all endoscopies. Incidences of esophagitis and those of severe esophagitis were 86.2 and 18.7 cases per 100,000 inhabitants per year respectively. Male sex (OR 1.89) and advanced age (OR 4.2 for patients in the fourth age quartile) were the only variables associated with severe esophagitis. Associated peptic ulcer was present in 8.8% of cases.

Limitations

Retrospective study, no data on individual proton pump inhibitors use.

Conclusions

Severe esophagitis is an infrequent finding in Spain. It occurs predominantly in males and in older individuals. Peptic ulcer disease is frequently associated with erosive esophagitis.     

Cost-Effectiveness of a Community Pharmacist-Led Sleep Apnea Screening Program – A Markov Model

Background

Despite the high prevalence and major public health ramifications, obstructive sleep apnea syndrome (OSAS) remains underdiagnosed. In many developed countries, because community pharmacists (CP) are easily accessible, they have been developing additional clinical services that integrate the services of and collaborate with other healthcare providers (general practitioners (GPs), nurses, etc.). Alternative strategies for primary care screening programs for OSAS involving the CP are discussed.

Objective

To estimate the quality of life, costs, and cost-effectiveness of three screening strategies among patients who are at risk of having moderate to severe OSAS in primary care.

Design

Markov decision model.

Data Sources

Published data.

Target Population

Hypothetical cohort of 50-year-old male patients with symptoms highly evocative of OSAS.

Time Horizon

The 5 years after initial evaluation for OSAS.

Perspective

Societal.

Interventions

Screening strategy with CP (CP-GP collaboration), screening strategy without CP (GP alone) and no screening.

Outcomes measures

Quality of life, survival and costs for each screening strategy.

Results of base-case analysis

Under almost all modeled conditions, the involvement of CPs in OSAS screening was cost effective. The maximal incremental cost for “screening strategy with CP” was about 455€ per QALY gained.

Results of sensitivity analysis

Our results were robust but primarily sensitive to the treatment costs by continuous positive airway pressure, and the costs of untreated OSAS. The probabilistic sensitivity analysis showed that the “screening strategy with CP” was dominant in 80% of cases. It was more effective and less costly in 47% of cases, and within the cost-effective range (maximum incremental cost effectiveness ratio at €6186.67/QALY) in 33% of cases.

Conclusions

CP involvement in OSAS screening is a cost-effective strategy. This proposal is consistent with the trend in Europe and the United States to extend the practices and responsibilities of the pharmacist in primary care.     

Scurvy in the tropics: Evidence for increasing non-adult micronutrient deficiency with the transition to agriculture in northern Vietnam

Objective

Scurvy in non-adults was assessed at the Pre-Neolithic site of Con Co Ngua and the Neolithic site of Man Bac in northern Vietnam to investigate nutritional stress during the agricultural transition in Mainland Southeast Asia (MSEA).

Materials

One hundred and four human skeletons under the age of 20 years old were assessed.

Methods

Lesions were recorded macroscopically and radiographically. Differential diagnosis using prior established paleopathological diagnostic criteria for scurvy was conducted.

Results

There was no clear evidence for scurvy at Con Co Ngua and a high burden of scurvy was present at Man Bac (>79% diagnosed with probable scurvy). Scurvy levels were high across all non-adult ages at Man Bac indicating significant burden throughout childhood and adolescence.

Conclusions

No scurvy at Con Co Ngua is consistent with widely available food sources at the peak of the Holocene thermal maximum. High levels of scurvy at Man Bac corresponds with decreased dietary diversity, high pathogen load, and increased population stress with the transition to agriculture around the time of the 4.2 ka desertification event.

Significance

This is the first systematic population-level non-adult investigation of specific nutritional disease in MSEA and demonstrates an increase in nutritional stress during the Neolithic transition in northern Vietnam.

Limitations

Subperiosteal new bone deposits can be due to normal growth in infants and young children, therefore, identification of scurvy in children under the age of 4 years needs to be considered critically.

Suggestions for Further Research

Further work in diagnosing specific nutritional disease in other non-adult cohorts throughout MSEA is required.     

Association of microsatellite instability and chronic obstructive pulmonary disorder in isocyanate-Exposed population of Bhopal

CONTEXT:

Survivors of the Bhopal gas disaster still suffer from various respiratory ailments. We examined the effects of exposures among a cross-section of current residents suffering from COPD by ISSR-PCR.

AIMS:

Molecular screening of the gas-affected population of Bhopal with COPD for microsatellite instability due to exposure of MIC.

SETTINGS AND DESIGN:

The isocyanate-exposed population of Bhopal city suffering from chronic obstructive pulmonary disorder.

MATERIALS AND METHODS:

Inter-(SSR) analysis was used to characterize microsatellite instability in 52 MIC victims of Bhopal, suffering from COPD using (CA)₈RG and (CA)₈R[Y-Q] primer.

STATISTICAL ANALYSIS USED:

Association analyses were performed using regression analysis.

RESULTS:

The study on the MIC-affected population in Bhopal showed weak association between microsatellite instability and age (r = + 0.37); exposure distance from site (r = −0.44); and smoking status(r = + 0.12); while regression analysis of the above parameters displayed supporting evidence.

CONCLUSIONS:

The high prevalence of smoking coupled with aging and poor living habits threatens, to further increase COPD incidences among this population, highlighting the need for enhanced screening efforts.     

Chilling slows anaerobic metabolism to improve anoxia tolerance of insects

Background

Insects are renowned for their ability to survive anoxia. Anoxia tolerance may be enhanced during chilling through metabolic suppression.

Aims

Here, the metabolomic response of insects to anoxia, both with and without chilling, for different durations (12–36 h) was examined to assess the potential cross-tolerance mechanisms.

Results

Chilling during anoxia (cold anoxia) significantly improved survival relative to anoxia at warmer temperatures. Reduced intermediate metabolites and increased lactic acid, indicating a switch to anaerobic metabolism, were characteristic of larvae in anoxia.

Conclusions

Anoxia tolerance was correlated survival improvements after cold anoxia were correlated with a reduction in anaerobic metabolism.

     

Human land use is comparable to climate as a driver of global plant occurrence and abundance across life forms

Aim

Historically, climate has been a dominant driver of global vegetation patterns. Recently, ecological understanding has been updated to acknowledge the influence of human land use (the dominant driver of biodiversity change) in shaping global vegetation patterns. We test whether Raunkiær's life form, a plant classification system designed to reflect climatic drivers, affects how plants respond to both land use and climate.

Location

Forty-one countries across six continents.

Time period

1990 to 2013.

Major taxa studied

Terrestrial plants.

Methods

Combining data from the biodiversity and land use database PREDICTS, and plant trait databases TRY and BIEN, we use generalized linear mixed models with weighted effects coding to test whether Raunkiær's life form affects plant response to land use and climate in over 4800 species at over 300 sites globally.

Results

We provide evidence that human land use is comparable to climate in influencing life form occurrence and that land use produces divergent outcomes across life forms.

Main conclusions

Combined with climatic suitability, land use acts as a filter contracting the realized niche of trees and expanding the realized niche of disturbance-tolerant species. Our results highlight the fundamental role of human activity in shaping species' distribution.