Clear Clustering Research Articles

Population-based prevalence of cranial autonomic symptoms in migraine and proposed diagnostic appendix criteria.

Migraine with cranial autonomic symptoms is well described in the literature, but its prevalence in previous studies varies enormously. A precise estimate of the prevalence in a population-based material is important because migraine with cranial autonomic symptoms might represent an endophenotype, in which genetic and pathophysiological features differ from those without cranial autonomic features. The aim of the present study, therefore, was to estimate the prevalence in a big population-based sample using both questionnaire-based diagnosis (N = 12,620) and interview-based diagnosis (N = 302). We validate questionnaire-based diagnosis of migraine with cranial autonomic symptoms and develop the first diagnostic criteria for future research of this possible endophenotype. The Danish Blood Donor Study included 127,802 persons who all received a migraine diagnostic questionnaire. Participants who had answered the diagnostic questionnaire constituted the Danish Migraine Population Cohort (N = 62,677) of whom 12,620 had migraine. The diagnostic migraine questionnaire included questions about the following cranial autonomic symptoms: Facial/forehead sweating, lacrimation, ptosis, conjunctival injection, rhinorrhea, nasal congestion, and miosis. Validation was performed by a follow-up semi-structured, purpose-built interview of 302 participants with migraine, where detailed questions were asked to ascertain the validity of the symptoms. The questionnaire-based prevalences of one, respectively two cranial autonomic symptoms were 57% and 31%. The semi-structured interview-based prevalences of one, respectively two symptoms were 44% and 22%. The most common symptoms were facial/forehead sweating (39%) and lacrimation (24%). The specificity of the questionnaire was 80% and the sensitivity was 68%. Correlation analysis showed a weak correlation between symptoms ranging from 0.07 - 0.41, and no clear clustering of symptoms was detected. We suggest the first diagnostic appendix criteria for genetic and epidemiological studies and tighter criteria for clinical and pathophysiological studies. We encourage further studies of severity and consistency of symptoms. Migraine with cranial autonomic symptoms is prevalent in the general population. Suggested diagnostic appendix criteria are important for future studies of this possible migraine endophenotype.

The effect of sickle cell genotype on the pharmacokinetic properties of artemether-lumefantrine in Tanzanian children

Since there are inconsistent data relating to the effect of haemoglobinopathies on disposition of artemisinin antimalarial combination therapy, and none in sickle cell trait (SCT) or sickle cell disease (SCD), the aim of this study was to characterize the pharmacokinetic properties of artemether-lumefantrine (ARM-LUM) in children with SCD/SCT. Thirty-eight Tanzanian children aged 5–10 years with normal (haemoglobin AA; n = 12), heterozygous (haemoglobin AS; n = 14) or homozygous (haemoglobin SS; n = 12) sickle genotypes received six ARM-LUM doses (1.7 mg/kg plus 10 mg/kg, respectively) over 3 days. Sparse venous and mixed-capillary dried blood spot (DBS) samples were taken over 42 days. Plasma and DBS ARM and LUM, and their active metabolites dihydroartemisinin (DHA) and desbutyl-lumefantrine (DBL), were assayed using validated liquid chromatography-mass spectrometry. Multi-compartmental pharmacokinetic models were developed using a population approach. Plasma but not DBS concentrations of ARM/DHA were assessable. The majority (85%) of the 15 measurable values were within 95% prediction intervals from a published population pharmacokinetic ARM/DHA model in Papua New Guinean children of similar age without SCD/SCT who had uncomplicated malaria, and there was no clear sickle genotype clustering. Plasma (n = 38) and corrected DBS (n = 222) LUM concentrations were analysed using a two-compartment model. The median [inter-quartile range] LUM AUC0–∞ was 607,296 [426,480–860,773] μg.h/L, within the range in published studies involving different populations, age-groups and malaria status. DBS and plasma DBL concentrations correlated poorly and were not modelled. These data support use of the conventional ARM-LUM treatment regimen for uncomplicated malaria in children with SCT/SCD.

Relationship between gene expression networks and muscle contractile physiology differences in Anolis lizards.

Muscles facilitate most animal behavior, from eating to fleeing. However, to generate the variation in behavior necessary for survival, different muscles must perform differently; for instance, sprinting requires multiple rapid muscle contractions, whereas biting may require fewer contractions but greater force. Here, we use a transcriptomic approach to identify genes associated with variation in muscle contractile physiology among different muscles from the same individual. We measured differential gene expression between a leg and jaw muscle of Anolis lizards known to differ in muscle contractile physiology and performance. For each individual, one muscle was used to measure muscle contractile physiology, including contractile velocity (Vmax and V40), specific tension, power ratio, and twitch time, whereas the contralateral muscle was used to extract RNA for transcriptomic sequencing. Using the transcriptomic data, we found clear clustering of muscle type. Expression of genes clustered in gene ontology (GO) terms related to muscle contraction and extracellular matrix was, on average, negatively correlated with Vmax and slower twitch times but positively correlated to power ratio and V40. Conversely, genes related to the GO terms related to aerobic respiration were downregulated in muscles with higher power ratio and V40, and over-expressed as twitch time decreased. Determining the molecular mechanisms that underlie variation in muscle contractile physiology can begin to explain how organisms are able to optimize behavior under variable conditions. Future studies pursuing the effects of differential gene expression across muscle types in different environments might inform researchers about how differences develop across species, populations, and individuals varying in ecological history.

Genomic diversity of Bacillus anthracis in endemic settings: novel approaches and data

Anthrax, caused by the spore-forming bacterium Bacillus anthracis, remains endemic in many developing countries where it has significant impacts on the health and livelihoods of livestock-keeping communities. While the global genomic diversity of B. anthracisis is well characterised, few studies have quantified its diversity in endemic settings at more local scales, where this information could be critical for elucidating transmission dynamics and guiding control efforts. We collected samples from 526 anthrax-suspected animal carcasses between 2016 and 2018 in the Ngorongoro Conservation Area in northern Tanzania. Seventy five percent were confirmed positive through qPCR, suggesting that anthrax is responsible for a large proportion of sudden deaths in livestock in this area. A subset of positive samples were cultured for whole genome sequencing (n = 73), including multiple isolates from individual carcasses. All sequenced isolates belonged to the Ancient A lineage of B. anthracis, a common strain in southeastern Africa. No clear spatial clustering was observed, possibly reflecting extensive animal movement related to local nomadic practices. Moreover, high levels of within-host diversity were observed which suggests that cases commonly result from simultaneous infection with multiple strains. Additionally, we trialed a targeted sequence capture approach on 93 samples. This was successful in recovering >80% of the chromosomal genome at > 15X coverage from 60% of samples tested, thus representing a valuable tool for culture-free sequencing of this high-risk bacterium. Our work paves the way for integrating genomic data for B. anthracis into epidemiological studies and monitoring of control programs in endemic areas worldwide.

Genetic diversity of Iranian populations of Pyrenophora graminea, the causal agent of leaf stripe disease on barley

AbstractLeaf stripe disease caused by Pyrenophora graminea is an economically significant disease of cultivated barley worldwide, including Iran. Considering economic impact of this disease on barley industry in Iran, in this study genetic diversity of P. graminea populations mainly collected from barley (229 isolates) in different regions of East Azerbaijan Province was examined using ISSR and RAPD molecular markers. The average polymorphic information content (PIC) values for ISSR and RAPD were 0.28 in both markers, and a significant correlation was observed between ISSR and RAPD data (r = .78, p < .05). No clear clustering was found within P. graminea populations in relation to their geographical origins. Applying the unweighted pair group method with arithmetic mean (UPGMA) procedure and principal coordinates analysis (PCoA) revealed no obvious clustering of isolates based on geographic region. Totally, gene diversity of 0.2 was noticed among P. graminea isolates. High level of genetic differentiation (PhiPT = 0.257; p ≤ .001), with 74% of the genetic variation occurring within populations and 26% occurring among populations, indicated the existence of population differentiation. In addition, a moderate amount of gene flow (Nm = 1.1985) was found between populations. Information obtained from this study may be beneficial to design and improve management strategies such as breeding resistant barley varieties to leaf stripe disease.

Evidence against a Late Heavy Bombardment event on Vesta

Impact events on planetary surfaces can leave significant volumes of melt, archived in planetary regoliths, which provide important information regarding the timing and nature of these events. For example, an observed ca. 3.9-4.1 Ga age cluster within lunar samples has been interpreted as indicative of a significant Solar System-wide event: the so-called “Late Heavy Bombardment”. Here, we report data from a laser ablation microprobe 40Ar/39Ar study of clasts within two unpaired howardite meteorites (NWA 1929 and Dho 485) to explore the impact history of their asteroid parent body – (4)Vesta. Laser microprobe dates for the howardites varied broadly between 3.5 to 4.5 Ga (NWA 1929) and 2.5 to 4.5 Ga (Dho 485), but show no clear cluster in ages at ca. 3.9-4.1 Ga. Consistent with previously reported U-Pb dates for HED meteorites, our data suggest an extended impact bombardment period on (4)Vesta as compared to the distribution of 40Ar/39Ar impactite dates for available samples from the Apollo and Luna sample archives. The impact history of Vesta revealed here highlights that current models of the impact flux in the inner Solar System based on the Late Heavy Bombardment hypothesis require refinement.

The healthy female microbiome across body sites: effect of hormonal contraceptives and the menstrual cycle.

STUDY QUESTIONHow does hormonal contraceptive use and menstrual cycle phase affect the female microbiome across different body sites?SUMMARY ANSWERThe menstrual cycle phase, but not hormonal contraceptive use, is associated with the vaginal and oral but not the gut microbiome composition in healthy young women.WHAT IS KNOWN ALREADYWomen with low vaginal levels of Lactobacillus crispatus are at increased risk of pre-term birth, fertility treatment failure, sexually transmitted infections and gynaecological cancers. Little is known about the effect of hormonal fluctuations on other body site’s microbiomes as well as the interplay between them.STUDY DESIGN, SIZE, DURATIONThis study includes a cohort of 160 healthy young Danish women using three different contraceptive regimens: non-hormonal methods (n = 54), combined oral contraceptive (COC, n = 52) or levonorgestrel intrauterine system (LNG-IUS, n = 54). Samples were collected from four body sites during the menstrual cycle (menses, follicular and luteal phases) at Copenhagen University Hospital, Rigshospitalet, Denmark.PARTICIPANTS/MATERIALS, SETTING, METHODSThe oral, vaginal, rectal and faecal microbiomes were characterized by shotgun sequencing. Microbial diversity and community distance measures were compared between study groups, menstrual phase timepoints and body sites. All participants answered an extensive questionnaire on current health, lifestyle and sex life. Confounding factors such as smoking, BMI and diet were analysed by PERMANOVA. Plasma oestradiol and progesterone levels are correlated with microbiome composition.MAIN RESULTS AND THE ROLE OF CHANCEThe use of COC and LNG-IUS was not associated with the microbiome composition or diversity. However, increased diversity in the vaginal microbiome was observed during menses, followed by a subsequent expansion of Lactobacillus spp. during the follicular and luteal phases which correlated with measured serum oestradiol levels (r = 0.11, P < 0.001). During menses, 89 women (58%) had a dysbiotic vaginal microbiome with <60% Lactobacillus spp. This declined to 49 (32%) in the follicular phase (P < 0.001) and 44 (29%) in the luteal phase (P < 0.001). During menses, bacterial richness and diversity in saliva reached its lowest point while no differences were observed in the faecal microbiome. The microbiome in different body sites was on average more similar within the same individual than between individuals, despite phase or hormonal treatment. Only the vagina presented a clear cluster structure with dominance of either L. crispatus, Lactobacillus iners, Gardnerella vaginalis or Prevotella spp.LARGE SCALE DATAThe microbiome samples analysed in this study were submitted to the European Nucleotide Archive under project number PRJEB37731, samples ERS4421369–ERS4422941.LIMITATIONS, REASONS FOR CAUTIONThe cohort is homogenous which limits extrapolation of the effects of ethnicity and socio-economic status on the microbiome. We only present three defined timepoints across the menstrual phase and miss potential important day to day fluctuations.WIDER IMPLICATIONS OF THE FINDINGSThe use of hormonal contraception did not significantly associate with the microbiome composition in the vagina, faeces, rectum or saliva in healthy young women. This is a welcome finding considering the widespread and prolonged use of these highly efficient contraceptive methods. The menstrual cycle is, however, a major confounding factor for the vaginal microbiome. As such, the time point in the menstrual cycle should be considered when analysing the microbiome of women of reproductive age, since stratifying by vaginal dysbiosis status during menstruation could be misleading. This is the first study to confirm by direct measurements of oestradiol, a correlation with the presence of L. crispatus, adding evidence of a possible hormonal mechanism for the maintenance of this desirable microbe.STUDY FUNDING/COMPETING INTEREST(S)This work was partly funded by the Ferring Pharmaceuticals through a research collaboration with The Centre for Translational Microbiome Research (CTMR) at the Karolinska Institutet (L.W.H., E.F., G.E. and I.S.-K.). Ferring Pharmaceuticals also funded the infrastructure to obtain the clinical samples at Copenhagen University Hospital ([#MiHSN01], M.C.K., Z.B., and H.S.N.). This work was also supported by funding from Rigshospitalet’s Research Funds ([#E-22614-01 and #E-22614-02] to M.C.K.) and Oda and Hans Svenningsen’s Foundation ([#F-22614-08] to H.S.N.). M.C.K., L.W.H., E.F., Z.B., G.E., L.E., I.S.-K. and H.S.N., are partially funded by Ferring Pharmaceuticals, which also provided funds for the collection and processing of the samples analysed in this study. H.S.N.’s research is further supported by Freya Biosciences and the BioInnovation Institute. H.S.N. has received honoraria from Ferring Pharmaceuticals, Merck A/S, Astra-Zeneca, Cook Medical and Ibsa Nordic. A.N.A. reports no competing interests.

High Uniformity and Enhancement Au@AgNS 3D Substrates for the Diagnosis of Breast Cancer.

Breast cancer appears to be one of the leading causes of cancer-related morbidity and mortality for women worldwide. The accurate and rapid diagnosis of breast cancer is hence critical for the treatment and prognosis of patients. With the vibrational fingerprint information and high detection sensitivity, surface-enhanced Raman spectroscopy (SERS) has been extensively applied in biomedicine. Here, an optimized bimetallic nanosphere (Au@Ag NS) 3D substrate was fabricated for the aim of the diagnosis of breast cancer based on the SERS analysis of the extracellular metabolites. The unique stacking mode of 3D Au@Ag NSs provided multiple plasmonic hot spots according to the theoretical calculations of the electromagnetic field distribution. The low relative standard deviation (RSD = 2.7%) and high enhancement factor (EF = 1.42 × 105) proved the uniformity and high sensitivity. More importantly, the normal breast cells and breast cancer cells could be readily distinguished from the corresponding SERS spectra based on the extracellular metabolites. Furthermore, the clear clusters of SERS spectra from MCF-7 and MDA-MB-231 extracellular metabolites in the orthogonal partial least-squares discriminant analysis plot indicate the distinct metabolic fingerprint between breast cancer cells, which imply their potential clinical application in the diagnosis of breast cancer.

Agavin induces beneficial microbes in the shrimp microbiota under farming conditions

Prebiotics and probiotics have shown a number of beneficial impacts preventing diseases in cultured shrimps. Complex soluble carbohydrates are considered ideal for fostering microbiota biodiversity by fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPS). Here we evaluated the growth performance and microbiota composition of the white shrimp Litopenaeus vannamei after dietary intervention using agavin as a FODMAP prebiotic under farming conditions. Adult L. vannamei were raised at a shrimp farm and the effect of agavin supplemented at 2% (AG2) or 10% (AG10) levels were compared to an agavin-free basal diet (BD). After 28 days-trial, the feed conversion ratio, total feed ingested, and protein efficiency ratio was significantly improved on animals fed with AG2. At the same time, no effect on growth performance was observed in AG10. Surprisingly, after sequencing the V3–V4 regions of the 16S rRNA gene a higher microbial richness and diversity in the hepatopancreas and intestine was found only in those animals receiving the AG10 diet, while those receiving the AG2 diet had a decreased richness and diversity, both diets compared to the BD. The beta diversity analysis showed a clear significant microbiota clustering by agavin diets only in the hepatopancreas, suggesting that agavin supplementation had a more substantial deterministic effect on the microbiota of hepatopancreas than on the intestine. We analyzed the literature to search beneficial microbes for shrimp’s health and found sequences for 42 species in our 16S data, being significantly increased Lactobacillus pentosus, Pseudomonas putida and Pseudomonas synxantha in the hepatopancreas of the AG10 and Rodopseudomonas palustris and Streptococcus thermophiles th1435 in the hepatopancreas of the AG2, both compared to BD. Interestingly, when we analyzed the abundance of 42 beneficial microbes as a single microbial community "meta-community," found an increase in their abundance as agavin concentration increases in the hepatopancreas. In addition, we also sequenced the DNA of agavin and found 9 of the 42 beneficial microbes. From those, Lactobacillus lactis and Lactobacillus delbrueckii were found in shrimps fed with agavin (both AG2 and AG10), and Lysinibacillus fusiformis in AG10 and they were absent the BD diet, suggesting these three species could be introduced with the agavin to the diet. Our work provides evidence that agavin supplementation is associated with an increase of beneficial microbes for the shrimp microbiota at farming conditions. Our study provides the first evidence that a shrimp prebiotic may selectively modify the microbiota in an organ-dependent effect.

Prenatal Supplementation in Beef Cattle and Its Effects on Plasma Metabolome of Dams and Calves.

This study investigated the effect of different prenatal nutrition on the plasma metabolome of Nellore dams and their offspring. For that purpose, three nutritional treatments were used in 126 cows during pregnancy: NP—(control) only mineral supplementation; PP—protein-energy supplementation in the final third; and FP—protein-energy supplementation during the entire pregnancy. Targeted metabolomics were analyzed in plasma at the beginning of pregnancy and in pre-delivery of cows (n = 27) as well as in calves (n = 27, 30 ± 9.6 days of age). Data were analyzed by the analysis of variance, partial least squares discriminant analysis, and the principal component analysis (PCA). The PCA showed a clear clustering in the periods investigated only in cows (early gestation and pre-delivery). We found significant metabolites in both supervised analyses (p < 0.05 and VIP score > 1) for cows (Taurine, Glutamic acid, Histidine, and PC aa C42:2) and for calves (Carnosine, Alanine, and PC aa C26:0). The enrichment analysis revealed biological processes (p < 0.1) common among cows and calves (histidine metabolism and beta-alanine metabolism), which may be indicative of transgenerational epigenetic changes. In general, fetal programming affected mainly the metabolism of amino acids.

Bacterial Communities in the Feces of Laboratory Reared Gampsocleis gratiosa (Orthoptera: Tettigoniidae) across Different Developmental Stages and Sexes.

Simple SummaryMany insects host a diverse gut microbial community, ranging from pathogenic to obligate mutualistic organisms. Little is known about the bacteria associated with katydids. Gampsocleis gratiosa (Orthoptera, Tettigoniidae) is an economically important singing pet in China. In the present study, the bacterial communities of the laboratory-reared G. gratiosa feces were characterized using Illumina sequencing of the 16S rDNA V3-V4 region.We used Illumina sequencing of the 16S rDNA V3-V4 region to identify the bacterial community in laboratory-reared G. gratiosa feces across different developmental stages (1st–7th instar nymph day 0, and 0-, 7-, 14-, and 21-day adult) and sexes. In total, 14,480,559 high-quality reads were clustered into 2982 species-level operational taxonomic units (OTUs), with an average of 481.197 (±137.366) OTUs per sample. These OTUs were assigned into 25 phyla, 42 classes, 60 orders, 116 families, 241 genera, and some unclassified groups. Only 21 core OTUs were shared by all samples. The most representative phylum was Proteobacteria, followed by Firmicutes, Bacteroidetes, and Acidobacteria. At the genus level, Kluyvera (387 OTUs), Obesumbacterium (339 OTUs), Buttiauxella (296 OTUs), Lactobacillus (286 OTUs), and Hafnia (152 OTUs) were dominant bacteria. The early-instar nymphs harbored a similar bacterial community with other developmental stages, which contain higher species diversity. Both principal coordinate analysis (PCoA) and non-metric multidimensional scaling analysis (NMDS) failed to provide a clear clustering based on the developmental stages and sexes. Overall, we assume that G. gratiosa transmits bacteria vertically by eating contaminated eggshells, and both developmental stages and sexes had no significant effect on the fecal bacterial community.

Maintenance of Genetic Diversity of Black Sea Bream despite Unmonitored and Large-Scale Hatchery Releases.

Simple SummaryStock enhancement aggressively replenishes depleted wild finfish populations. However, stock enhancement of black sea bream in Taiwan with complex genetic sources, especially when successful, maintains genetic diversity but dramatically changes the genetic structure within and among wild populations.Stock enhancement, used for replenishing depleted wild finfish populations, is an aggressive approach. Stock enhancement projects in Taiwan involve black sea bream (Acanthopagrus schlegelii), a major commercial species. During 2004–2015, even management agencies conducted stock enhancement projects, leading to numerous private releases that have not been recorded. Stock enhancement by a private hatchery without accurate genetic records may lead to a genetic structure change in wild populations. Using allele frequencies at nine microsatellite loci, we studied the genetic effects of stock enhancement in 19 samples collected from populations in the hatcheries and the wild. In 458 individuals from nine hatchery samples, most populations showed weak but significant genetic differences and complex clusters in structure analysis, indicating dramatic stock change within and among hatcheries. The 10 wild populations (n = 773) also had a complex genetic composition and were genetically different among sampling sites and times. However, a simple and clear cluster in structure analysis was found for only one sampling site, which had no release history. Thus, stock enhancement with complex genetic sources helps maintain genetic diversity but dramatically changes the genetic structure within and among wild populations, especially when stock enhancement is successful.

Calculating and comparing codon usage values in rare disease genes highlights codon clustering with disease-and tissue- specific hierarchy.

We designed a novel strategy to define codon usage bias (CUB) in 6 specific small cohorts of human genes. We calculated codon usage (CU) values in 29 non-disease-causing (NDC) and 31 disease-causing (DC) human genes which are highly expressed in 3 distinct tissues, kidney, muscle, and skin. We applied our strategy to the same selected genes annotated in 15 mammalian species. We obtained CUB hierarchical clusters for each gene cohort which showed tissue-specific and disease-specific CUB fingerprints. We showed that DC genes (especially those expressed in muscle) display a low CUB, well recognizable in codon hierarchical clustering. We defined the extremely biased codons as "zero codons" and found that their number is significantly higher in all DC genes, all tissues, and that this trend is conserved across mammals. Based on this calculation in different gene cohorts, we identified 5 codons which are more differentially used across genes and mammals, underlining that some genes have favorite synonymous codons in use. Since of the muscle genes clear clusters, and, among these, dystrophin gene surprisingly does not show any "zero codon" we adopted a novel approach to study CUB, we called "mapping-on-codons". We positioned 2828 dystrophin missense and nonsense pathogenic variations on their respective codon, highlighting that its frequency and occurrence is not dependent on the CU values. We conclude our strategy consents to identify a hierarchical clustering of CU values in a gene cohort-specific fingerprints, with recognizable trend across mammals. In DC muscle genes also a disease-related fingerprint can be observed, allowing discrimination between DC and NDC genes. We propose that using our strategy which studies CU in specific gene cohorts, as rare disease genes, and tissue specific genes, may provide novel information about the CUB role in human and medical genetics, with implications on synonymous variations interpretation and codon optimization algorithms.

The Importance of Dead Seagrass (Posidonia oceanica) Matte as a Biogeochemical Sink

We assessed the potential of dead seagrass Posidonia oceanica matte to act as a biogeochemical sink and provide a coherent archive of environmental change in a degraded area of the Mediterranean Sea (Augusta Bay, Italy). Change in sediment properties (dry bulk density, grain size), concentration of elements (Corg, Cinorg, N, Hg) and stable isotope ratios (δ13C, δ 15N) with sediment depth were measured in dead P. oceanica matte and unvegetated (bare) sediments in the polluted area, and an adjacent P. oceanica meadow. Principal Component Analysis (PCA) revealed a clear clustering by habitat, which explained 72% of variability in our samples and was driven mainly by the accumulation of N and Hg in finer sediments of the dead matte. Assessment of the temporal trends of Corg, N and Hg concentrations in the dead matte revealed changes in the accumulation of these elements over the last 120 years, with an increase following the onset of industrial activities 65 y BP (i.e., yr. 1950) that was sustained even after seagrass loss around 35 y BP. Despite a decrease in Hg concentrations in the early 1980s following the onset of pollution abatement, overall Hg levels were 2-fold higher in the local post-industrial period, with a Hg enrichment factor of 3.5 in the dead matte. Mean stocks of Corg, N and Hg in 25 cm thick sediment deposits (4.08 ± 2.10 kg Corg m-2, 0.14 ± 0.04 kg N m-2, 0.19 ± 0.04 g Hg m-2) and accumulation in the last 120 yr (35.3 ± 19.6 g Corg m-2 y-1, 1.2 ± 0.4 g N m-2 y-1, 0.0017 ± 0.0004 g Hg m-2 y-1) were higher in the dead matte than bare sediment or adjacent P. oceanica meadow. Our results indicate that dead P. oceanica matte maintained its potential as a biogeochemical sink and, like its living counterpart, dead matte can serve as an effective archive to allow for reconstructing environmental change in coastal areas of the Mediterranean where severe perturbations have led to P. oceanica loss. Appropriate management for contaminated areas should be prioritized to prevent release of pollutants and carbon from dead mattes.

Geographical and Seasonal Analysis of the Honeybee Microbiome

We previously showed that colonies of thriving and non-thriving honeybees co-located in a single geographically isolated apiary harboured strikingly different microbiomes when sampled at a single time point in the honey season. Here, we profiled the microbiome in returning forager bees from 10 to 12 hives in each of 6 apiaries across the southern half of Ireland, at early, middle, and late time points in the 2019 honey production season. Despite the wide range of geographical locations and forage available, apiary site was not the strongest determinant of the honeybee microbiome. However, there was clear clustering of the honeybee microbiome by time point across all apiaries, independent of which apiary was sampled. The clustering of microbiome by time was weaker although still significant in three of the apiaries, which may be connected to their geographic location and other external factors. The potential forage effect was strongest at the second timepoint (June–July) when the apiaries also displayed greatest difference in microbiome diversity. We identified bacteria in the forager bee microbiome that correlated with hive health as measured by counts of larvae, bees, and honey production. These findings support the hypothesis that the global honeybee microbiome and its constituent species support thriving hives.

Detection of Adulterations in Fruit Juices Using Machine Learning Methods over FT-IR Spectroscopic Data

Fruit juices are one of the most adulterated beverages, usually because of the addition of water, sugars, or less expensive fruit juices. This study presents a method based on Fourier transform infrared spectroscopy (FT-IR), in combination with machine learning methods, for the correct identification and quantification of adulterants in juices. Thus, three types of 100% squeezed juices (pineapple, orange, and apple) were evaluated and adulterated with grape juice at different percentages (5%, 10%, 15%, 20%, 30%, 40%, and 50%). The results of the exploratory data analysis revealed a clear clustering trend of the samples according to the type of juice analyzed. The supervised learning analysis, based on the development of models for the detection of adulteration, obtained significant results for all tested methods (i.e., support-vector machines or SVM), random forest or RF, and linear discriminant analysis or LDA) with an accuracy above 97% on the test set. Regarding quantification, the best results are obtained with the support vector regression and with partial least square regression showing an R2 greater than 0.99 and a root mean square error (RMSE) less than 1.4 for the test set.

Use of ATR-FTIR Spectroscopy and Chemometrics for the Variation of Active Components in Different Harvesting Periods of Lonicera japonica.

Lonicera japonica Thunb is a commonly used Chinese herbal medicine, which belongs to the family Caprifoliaceae. The active components varied greatly during bud development. Research on the variation of the main active components is significant for the timely harvesting and quality control of Lonicera japonica. In this study, the attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) combined with the chemometric method was performed to investigate the variability of different harvesting periods of Lonicera japonica. The preliminary characterization from ATR-FTIR fingerprints showed various characteristic absorption peaks of the main active components from the different harvesting times, such as flavonoids, organic acids, iridoids, and volatile oils. Additionally, principal component analysis (PCA) scatter plots showed that there was a clear clustering trend in the samples of the same harvesting period, and the samples of the different harvesting periods could be well distinguished. Finally, further analysis by the orthogonal partial least-squares discriminant analysis (OPLS-DA) showed that there were regular changes in flavonoids, phenolic acids, iridoids, and volatile oils in different harvesting periods. Therefore, ATR-FTIR, as a novel and convenient analytical method, could be applied to evaluate the quality of Lonicera japonica.

Gut microbiome modifications over time when removing in-feed antibiotics from the prophylaxis of post-weaning diarrhea in piglets.

Post-weaning diarrhea (PWD) in pigs has mainly an infectious basis and control strategies are centred on antibiotics added to the diet. Given concerns on the spread of multi-resistant bacteria, it is necessary to develop alternative prophylactic approaches to control PWD in piglets. The most promising alternative strategies are based on substances that act indirectly on the bacteria by stimulating the immune system or by improving gut health. The aim of this study was to evaluate the effect on the gut microbiota of feed supplemented with a mixture of essential oils (garlic and oregano) in weaning piglets, compared to traditional PWD management (in-feed antibiotics) and to a control group without any diet supplementation. The study involved 197 piglets from 18 litters in a single farm. The piglets were followed from birth to day 58 of age and were weaned at day 26. During the experimental period, the animals were monitored for weight and growth, average daily gain, morbidity and mortality. For the metataxonomics analysis, rectal samples were collected from 17 piglets from the three experimental groups at 4 different time-points (days 1, 12, 26 and 58). Results revealed that the gut microbiota in pre- and post-weaning piglets was dominated by the phyla Firmicutes (51%), Bacteroidetes (25%) and Proteobacteria (16%), which together make up for over 90% of the entire piglet core gut microbiota. The core microbiota comprised 10 taxa before weaning and 43 taxa after weaning, with 7 taxa overlapping between timepoints: two of them (Prevotella 9, p-value = 0.00095; Solobacterium p-value = 0.00821) were significantly more abundant after weaning. All alpha diversity indexes were significantly different between pre- and post-weaning, while only Shannon and Simpson diversity and equitability were significantly different between treatments. Based on the matrix of Bray-Curtis dissimilarities, samples showed clear clustering per timepoint (before and after weaning, p-value < 0.001) and between treatments by timepoint (p-value = 0.0086). The oil-diet group showed a consistently higher F:B ratio at all timepoints. These results show that the pig gut microbiota changes significantly with weaning, and suggest that the use of essential oils as feed supplementation to control PWD does not seem to alter sgnificantly the microbiota nor the growth parameters of piglets, however modifications of specific taxa may occur.

Karyotype characteristics and gene COI sequences of Chironomusbonus Shilova et Dzhvarsheishvili, 1974 (Diptera, Chironomidae) from the South Caucasus (Republic of Georgia, Paravani river).



LC-MS Analysis Revealed the Significantly Different Metabolic Profiles in Spent Culture Media of Human Embryos with Distinct Morphology, Karyotype and Implantation Outcomes.

In this study we evaluated possible differences in metabolomic profiles of spent embryo culture media (SECM) of human embryos with distinct morphology, karyotype, and implantation outcomes. A total of 153 samples from embryos of patients undergoing in vitro fertilization (IVF) programs were collected and analyzed by HPLC-MS. Metabolomic profiling and statistical analysis revealed clear clustering of day five SECM from embryos with different morphological classes and karyotype. Profiling of day five SECM from embryos with different implantation outcomes showed 241 significantly changed molecular ions in SECM of successfully implanted embryos. Separate analysis of paired SECM samples on days three and five revealed 46 and 29 molecular signatures respectively, significantly differing in culture media of embryos with a successful outcome. Pathway enrichment analysis suggests certain amino acids, vitamins, and lipid metabolic pathways to be crucial for embryo implantation. Differences between embryos with distinct implantation potential are detectable on the third and fifth day of cultivation that may allow the application of culture medium analysis in different transfer protocols for both fresh and cryopreserved embryos. A combination of traditional morphological criteria with metabolic profiling of SECM may increase implantation rates in assisted reproductive technology programs as well as improve our knowledge of the human embryo metabolism in the early stages of development.