Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes.

Marine sedimentary ancient DNA (sedaDNA) is increasingly used to study past ocean ecosystems, however, studies have been severely limited by the very low amounts of DNA preserved in the subseafloor, and the lack of bioinformatic tools to authenticate sedaDNA in metagenomic data. We applied a hybridisation capture 'baits' technique to target marine eukaryote sedaDNA (specifically, phyto- and zooplankton, 'Planktonbaits1'; and harmful algal bloom taxa, 'HABbaits1'), which resulted in up to 4- and 9-fold increases, respectively, in the relative abundance of eukaryotes compared to shotgun sequencing. We further used the bioinformatic tool 'HOPS' to authenticate the sedaDNA component, establishing a new proxy to assess sedaDNA authenticity, "% eukaryote sedaDNA damage", that is positively correlated with subseafloor depth. We used this proxy to report the first-ever DNA damage profiles from a marine phytoplankton species, the ubiquitous coccolithophore Emiliania huxleyi. Our approach opens new avenues for the detailed investigation of long-term change and evolution of marine eukaryotes over geological timescales.

Combined effects of HIV and obesity on the gastrointestinal microbiome of young men who have sex with men.

OBJECTIVES: The prevalence of obesity is rising among people living with HIV, which may synergistically increase inflammation and the risk of associated diseases. Disruption of gut bacterial communities may be one of the key drivers of this inflammation; however, the combined effects of HIV and obesity on the microbiome have not been explored. METHODS: This study included 381 men who have sex with men. Thirty-nine were HIV-positive and obese (H+O+), 143 were HIV-positive and nonobese, 64 were HIV-negative and obese, and 135 were HIV-negative and nonobese. Microbiome composition was assessed by targeted sequencing of the V4 region of the 16S ribosomal RNA (rRNA) gene using rectal swab samples. Inverse probability of treatment-weighted marginal structural models were used to investigate differences in microbial composition between groups while controlling for numerous clinical and behavioural confounders. RESULTS: Significant variability in microbial composition was explained by the combination of HIV and obesity, over and above each condition alone (R2 for the marginal contribution of the H+/O+ group = 0.008; P = 0.001). H+O+ participants had the highest ratios of Prevotella to Bacteroides, a pro-inflammatory enterotype that has been described in HIV infection and obesity independently. H+O+ participants had lower levels of Bacteroides and Veillonella than all other groups, suggesting a synergistic effect of HIV and obesity on these genera. CONCLUSIONS: Our findings support the hypothesis that HIV and obesity act together to disrupt gut microbial communities, which may help explain higher levels of generalized inflammation among people living with both HIV and obesity.

Urogenital symptoms in mitochondrial disease: overlooked and undertreated.

BACKGROUND AND PURPOSE: Bowel symptoms are well documented in mitochondrial disease. However, data concerning other pelvic organs is limited. A large case-control study has therefore been undertaken to determine the presence of lower urinary tract symptoms (LUTS) and sexual dysfunction in adults with genetically confirmed mitochondrial disease. METHODS: Adults with genetically confirmed mitochondrial disease and control subjects were recruited from a specialist mitochondrial clinic. The presence and severity of LUTS and their impact on quality of life, in addition to sexual dysfunction and bowel symptoms, were captured using four validated questionnaires. Subgroup analysis was undertaken in patients harbouring the m.3243A>G MT-TL1 mitochondrial DNA mutation. A subset of patients underwent urodynamic studies to further characterize their LUTS. RESULTS: Data from 58 patients and 19 controls (gender and age matched) were collected. Adults with mitochondrial disease had significantly more overactive bladder (81.5% vs. 56.3%, P = 0.039) and low stream (34.5% vs. 5.3%, P = 0.013) urinary symptoms than controls. Urodynamic studies in 10 patients confirmed that bladder storage symptoms predominate. Despite high rates of LUTS, none of the patient group was receiving treatment. Female patients and those harbouring the m.3243A>G MT-TL1 mutation experienced significantly more sexual dysfunction than controls (53.1% vs. 11.1%, P = 0.026, and 66.7% vs. 26.3%, P = 0.011, respectively). CONCLUSIONS: Lower urinary tract symptoms are common but undertreated in adult mitochondrial disease, and female patients and those harbouring the m.3243A>G MT-TL1 mutation experience sexual dysfunction. Given their impact on quality of life, screening for and treating LUTS and sexual dysfunction in adults with mitochondrial disease are strongly recommended.

Multi-phase volcanic resurfacing at Loki Patera on Io.

The Jovian moon Io hosts the most powerful persistently active volcano in the Solar System, Loki Patera. The interior of this volcanic, caldera-like feature is composed of a warm, dark floor covering 21,500 square kilometres surrounding a much cooler central 'island'. The temperature gradient seen across areas of the patera indicates a systematic resurfacing process, which has been seen to occur typically every one to three years since the 1980s. Analysis of past data has indicated that the resurfacing progressed around the patera in an anti-clockwise direction at a rate of one to two kilometres per day, and that it is caused either by episodic eruptions that emplace voluminous lava flows or by a cyclically overturning lava lake contained within the patera. However, spacecraft and telescope observations have been unable to map the emission from the entire patera floor at sufficient spatial resolution to establish the physical processes at play. Here we report temperature and lava cooling age maps of the entire patera floor at a spatial sampling of about two kilometres, derived from ground-based interferometric imaging of thermal emission from Loki Patera obtained on 8 March 2015 ut as the limb of Europa occulted Io. Our results indicate that Loki Patera is resurfaced by a multi-phase process in which two waves propagate and converge around the central island. The different velocities and start times of the waves indicate a non-uniformity in the lava gas content and/or crust bulk density across the patera.

Abdominal wall ectopic testis torsion mimicking a Spigelian hernia in an adult.

We report an unusual case of an ectopic testis identified in a 37-year-old man presenting with acute severe right iliac fossa pain and an irreducible mass. Initially diagnosed as a Spigelian hernia, computed tomography and ultrasonography identified the presence of an ectopic testis in the abdominal wall. Interparietal testicular ectopia is an extremely rare condition. We present and discuss the first case in the literature of an ectopic testis located between the internal and external oblique muscle layers of the anterior abdominal wall in an adult.

Accelerated exploration of multi-principal element alloys with solid solution phases.

Recent multi-principal element, high entropy alloy (HEA) development strategies vastly expand the number of candidate alloy systems, but also pose a new challenge--how to rapidly screen thousands of candidate alloy systems for targeted properties. Here we develop a new approach to rapidly assess structural metals by combining calculated phase diagrams with simple rules based on the phases present, their transformation temperatures and useful microstructures. We evaluate over 130,000 alloy systems, identifying promising compositions for more time-intensive experimental studies. We find the surprising result that solid solution alloys become less likely as the number of alloy elements increases. This contradicts the major premise of HEAs--that increased configurational entropy increases the stability of disordered solid solution phases. As the number of elements increases, the configurational entropy rises slowly while the probability of at least one pair of elements favouring formation of intermetallic compounds increases more rapidly, explaining this apparent contradiction.

Landscape hydrology. The hydrological legacy of deforestation on global wetlands.

Increased catchment erosion and nutrient loading are commonly recognized impacts of deforestation on global wetlands. In contrast, an increase in water availability in deforested catchments is well known in modern studies but is rarely considered when evaluating past human impacts. We used a Budyko water balance approach, a meta-analysis of global wetland response to deforestation, and paleoecological studies from Australasia to explore this issue. After complete deforestation, we demonstrated that water available to wetlands increases by up to 15% of annual precipitation. This can convert ephemeral swamps to permanent lakes or even create new wetlands. This effect is globally significant, with 9 to 12% of wetlands affected, including 20 to 40% of Ramsar wetlands, but is widely unrecognized because human impact studies rarely test for it.

Induction of cadBA in an Escherichia coli lysine auxotroph transformed with a cad-gfp transcriptional fusion.

CadBA functions as a part of overall Escherichia coli response to low extracellular pH. A gfpmut3 structural gene transcriptionally fused to the cadBA promoter (Pcad) was used as a reporter to monitor changes in intracellular lysine as a potential factor influencing cadBA induction. Different patterns of cadBA induction were observed in two E. coli strains with different lysine biosynthetic capabilities. In E. coli ZK126 (pJBA25-Pcad), a lysine prototroph, maximum levels of induction were detected 3 h after the transfer of bacterial cells under inducing conditions (pH 5.8; 3.4 microM extracellular lysine). The induction subsequently decreased until hour 7 after which no further change in expression was observed. However, in the lysine depleted strain E. coli ATCC 23812 (pJBA25-Pcad) which is an auxotroph for lysine, no decrease in cadBA expression was observed over time under the same induction conditions. Although no time dependent statistical differences in intracellular lysine were observed, bacterial cells depleted for no longer than 4 h (1.38 +/- 0.25 micromol lysine/g cell dry weight) exhibited more rapid induction of cadBA (after 3 h) and a lower maximum level of induction compared to cells with relatively lower intracellular lysine (approximately 1.08 micromol/g cell dry weight). For the latter, the detectable level of induction was delayed for 1 h but the maximum level of induction response was higher.

Review of the apoptosis pathways in pancreatic cancer and the anti-apoptotic effects of the novel sea cucumber compound, Frondoside A.

Pancreatic cancer cells are resistant to the growth-inhibitory and apoptosis-inducing effects of conventional chemotherapeutic agents. There are multiple genetic and epigenetic events during the process of carcinogenesis that enable the cancer cells to avoid normal growth constraints and apoptosis. Investigation of the mechanisms involved has led to multiple strategies that encourage cell death and apoptosis to occur. The pathways involved are summarized in this review, together with some recently developed strategies to promote cell death in this cancer and with a particular focus on the frondoside A, a novel triterpenoid glycoside isolated from the Atlantic sea cucumber, Cucumaria frondosa. Frondoside A inhibited proliferation of AsPC-1 human pancreatic cancer cells in a concentration- and time-dependent manner, as measured by (3)H-thymidine incorporation and cell counting. In concert with inhibition of cell growth, frondoside A induced significant morphological changes consistent with apoptosis. Propidium iodide DNA staining showed an increase of sub-G0/G1 cell population of apoptotic cells induced by frondoside A. Frondoside A-induced apoptosis was confirmed by annexin V binding and TUNEL assay. Furthermore, western blotting showed a decrease in expression of Bcl-2 and Mcl-1, an increase in Bax expression, activation of caspases 3, 7, and 9, and an increase in the expression of the cyclin-dependent kinase inhibitor, p21. These findings show that frondoside A induced apoptosis in human pancreatic cancer cells through the mitochondrial pathway and activation of the caspase cascade. Finally, a very low concentration of frondoside A (10 mug/kg/day) inhibited growth of AsPC-1 xenografts in athymic mice. In conclusion, new chemotherapeutic agents are desperately needed for pancreatic cancer because of the poor responsiveness to currently available treatment options. Frondoside A has potent growth inhibitory effects on human pancreatic cancer cells, and the inhibition of proliferation is accompanied by marked apoptosis. Frondoside A may be valuable for the treatment or chemoprevention of this devastating disease.

Immunomodulatory properties of frondoside A, a major triterpene glycoside from the North Atlantic commercially harvested sea cucumber Cucumaria frondosa.

Frondoside A, a major triterpene glycoside from North Atlantic commercially harvested sea cucumber Cucumaria frondosa, possesses strong immunomodulatory properties in subtoxic doses. Frondoside A stimulates lysosomal activity of mouse macrophages in vivo at a maximal effective stimulatory dose of 0.2 microg per mouse and is maintained over 10 days. This glycoside also shows a 30% stimulation of lysosomal activity in mouse macrophages in vitro at concentrations of 0.1-0.38 microg/mL. Frondoside A enhances macrophage phagocytosis of the bacterium Staphylococcus aureus in vitro at a maximal effective concentration of 0.001 microg/mL. Frondoside A stimulates reactive oxygen species formation in macrophages in vitro at a maximal effective concentration of 0.001 microg/mL. Frondoside A stimulates an increase in the number of antibody plaque-forming cells (normally B-cells in spleen) in vivo with a maximal stimulatory effect at a concentration of 0.2 microg per mouse (stimulatory index, 1.86). Frondoside A has a weak effect upon immunoglobulin (Ig) M production after immunization with sheep erythrocytes in mice. Frondoside A does not stimulate Ig production in mice and does not significantly enhance the ovalbumin-stimulated IgM and IgG antibody levels in ovalbumin-immunized mice. Hence frondoside A is an immunostimulant of cell-based immunity including phagocytosis without a significant effect on amplification of humoral immune activity or adjuvant properties. Therefore, frondoside A may provide curative and/or preventive treatment options against diseases wherein a depleted immune status contributes to the pathological processes.

The influence of a fructooligosaccharide prebiotic combined with alfalfa molt diets on the gastrointestinal tract fermentation, Salmonella enteritidis infection, and intestinal shedding in laying hens.

Molting is a natural process, which birds undergo to rejuvenate their reproductive organs. The US poultry egg production industry has used feed withdrawal to effectively induce molt; however, susceptibility of Salmonella Enteritidis has encouraged the development of alternative methods. Previous research conducted in our laboratory showed that alfalfa is effective at molt induction and provides equivalent postmolt production numbers and quality when compared with feed withdrawal. In the attempt to further increase the efficacy of alfalfa molt diet and decrease the chicken susceptibility to Salmonella Enteritidis during molt, fructooligosaccharide (FOS) was added to a combination of 90% alfalfa and 10% layer ration in 2 levels (0.750 and 0.375%). Ovary and liver colonization by Salmonella Enteritidis in 3 and 2 of the 4 trials, respectively, were reduced (P 0.05) the production of cecal total volatile fatty acids when compared with hens undergoing feed withdrawal. However, in all 3 alfalfa molt diets, the concentrations of lactic acid were greater (P 0.05) were observed among hens fed alfalfa combined with FOS and hens fed alfalfa/layer ration without FOS. Overall, given the similarities between hens fed 0.750% FOS (H) and 0.375% FOS (L), molt diets combined with the lower level of FOS should be sufficient.

In vitro fermentation response of laying hen cecal bacteria to combinations of fructooligosaccharide prebiotics with alfalfa or a layer ration.

The objective of this in vitro study was to evaluate the effects of combining a prebiotic with alfalfa on fermentation by laying hen cecal bacteria. Cecal contents from laying hens were diluted to a 1:3,000 concentration with an anaerobic dilution solution and added to serum tubes filled with ground alfalfa or a layer ration with or without fructooligosaccharide (FOS) prebiotic. Samples were processed in an anaerobic hood, pressurized by using a pressure manifold, and incubated at 37 degrees C. Volatile fatty acid (VFA) and lactic acid concentrations were quantified at 6 and 24 h of substrate fermentation. In this study, fermentation of alfalfa resulted in greater production of acetate, VFA, and lactic acid compared with the layer ration. Although with a relative inconsistency in data between trials, the amendment of FOS to both alfalfa and the layer ration appeared to further increase fermentation as demonstrated by overall higher propionate, butyrate, VFA, and lactic acid concentrations. The effect was more pronounced after 24 h of fermentation, implying time constraints for the optimal production of fermentation products in the chicken gastrointestinal tract. These data indicate that in vitro cecal fermentation can be enhanced by the addition of FOS.

Behavioral responses of laying hens to different alfalfa-layer ration combinations fed during molting.

Induced molting by feed withdrawal has been a common practice in the commercial layer industry and usually involves the removal of feed for a period of up to 14 d. However, this is a practice that is believed to adversely influence the welfare of the hens and there is a need to examine behavioral responses to alternative molt regimens. The behavioral patterns of hens on 90% alfalfa:10% layer ration, 80% alfalfa:20% layer ration, and 70% alfalfa:30% layer ration molt diets were compared with feed withdrawal (FW) hens, and fully fed (FF) hens. The White Leghorn laying hens were approximately 54 wk old and were placed in 3 identical climate-controlled rooms. The hens were individually housed in 2-tier wire battery cages and provided treatment rations and water ad libitum. Nonnutritive pecking, walking, drinking, feeder activity, preening, aggression, and head movement were quantified during two 10-min periods each day for 6 hens from each treatment. Over the 9-d treatment period, hens in the FW, 70% alfalfa:30% layer ration, and 80% alfalfa:20% layer ration groups spent significantly more time walking than hens in the 90% alfalfa:10% layer ration group. The FF and 70% alfalfa:30% layer ration hens spent half as much time preening, whereas the FW hens displayed nearly twice as much nonnutritive pecking when compared with other treatments. Most differences in head movements occurred at the beginning of the molt period, whereas during the last half of molt, alfalfa-fed hens exhibited feeder activity similar to FF hens, and all were significantly higher than that of FW hens. After some initial adjustment by the hens, consumption of alfalfa molt diets appeared to reduce nonnutritive pecking behavior, which is characteristically associated with FW hens.

Prediction of dislocation cores in aluminum from density functional theory.

The strain field of isolated screw and edge dislocation cores in aluminum are calculated using density-functional theory and a flexible boundary condition method. Nye tensor density contours and differential displacement fields are used to accurately bound Shockley partial separation distances. Our results of 5-7.5 A (screw) and 7.0-9.5 A (edge) eliminate uncertainties resulting from the wide range of previous results based on Peierls-Nabarro and atomistic methods. Favorable agreement of the predicted cores with limited experimental measurements demonstrates the need for quantum mechanical treatment of dislocation cores.

A cad-gfpmut3 plasmid construct in Escherichia coli for gene induction-based quantification of lysine in acid hydrolysates of feedstuffs.

AIMS: To generate an inducible plasmid-borne cad-gfpmut3 transcriptional fusion and develop a method for quantification of total lysine. METHODS AND RESULTS: The cad-gfpmut3 transcriptional fusion was constructed by cloning the cad promoter (Pcad) upstream of a promotorless gfpmut3 located on a high-copy plasmid. The construct was electroporated into Escherichia coli ZK126 and the transformed strain was subsequently used to quantify lysine in feed ingredients. Lysine standard curves based on gene induction of the bacterial cells were used for estimating acid hydrolysate lysine concentrations in four feed ingredients. Except for sorghum, no substantial differences were observed when the data for lysine in soybean (2 x 49 +/- 0 x 37%), cottonseed (1 x 82 +/- 0 x 15%), and meat and bone meal (2 x 31 +/- 0 x 24%) generated by the newly developed construct were compared with previously published data. CONCLUSIONS: Using the cad-gfpmut3 fusion, feed derived lysine induction was measured easily and accurately, and could be a useful tool for the estimation of lysine in acid hydrolysates of feed ingredients. SIGNIFICANCE AND IMPACT OF THE STUDY: The described approach for lysine quantification in feed ingredients represents a cost- and time-efficient method offering rapid and accurate lysine quantification of multiple samples.

Episodic ataxia and hemiplegia caused by the 8993T->C mitochondrial DNA mutation.

The m.8993T-->C MTATP6 mutation of mitochondrial DNA (mtDNA) usually causes mitochondrial disease in childhood, but was recently described in a family with adult onset ataxia and polyneuropathy. Cytochrome c oxidase muscle histochemistry, which is the standard clinical investigation for mitochondrial disease in adults, is usually normal in patients with MTATP6 mutations. This raises the possibility that these cases have been missed in the past. We therefore studied 308 patients with unexplained ataxia and 96 patients with suspected Charcot-Marie-Tooth disease to determine whether the m.8993T-->C MTATP6 mutation is common in unexplained inherited ataxia and/or polyneuropathy. We identified a three-generation family with the m.8993T-->C mutation of mtDNA. One subject had episodic ataxia (EA) and transient hemipareses, broadening the phenotype. However, no further cases were identified in an additional cohort of 191 patients with suspected EA. In conclusion, m.8993T-->C MTATP6 should be considered in patients with unexplained ataxia, CMT or EA, but cases are uncommon.

Detection of methane and quantification of methanogenic archaea in faeces from young broiler chickens using real-time PCR.

AIMS: To detect the presence of methanogens in the faeces of broiler chicks during the first 2 weeks of age. METHODS AND RESULTS: Chicken faecal samples from 120 broiler chicks were incubated for methane gas formation and methanogenic archaea were analysed using real-time PCR. The copy number of the order Methanobacteriales 16S rDNA gene in chicken faeces when the broilers were 3-12 days of age, litter and house flies collected in the bird house ranged from 4.19 to 5.51 log(10) g(-1) wet weight. The number of positive methane culture tubes increased from 25% to 100% as the birds aged. CONCLUSIONS: Methanogens were successfully detected in faecal samples from 3- to 12-day-old broilers, as well as litter and house flies using real-time PCR. The copy number of methanogenic 16S rDNA gene in these samples was also similar to the number observed in litter and house flies. SIGNIFICANCE AND IMPACT OF THE STUDY: The same methanogens consistently appeared in chicken faeces a few days after birth. Detection of the methanogenic bacteria in litter and house flies implicated them as potential environmental sources for methanogen colonization in broiler chicks.

In vitro anaerobic incubation of Salmonella enterica serotype Typhimurium and laying hen cecal bacteria in poultry feed substrates and a fructooligosaccharide prebiotic.

The objective of this study was to investigate the effect of combining a prebiotic with poultry feeds on the growth of Salmonella enterica serotype Typhimurium (ST) in an in vitro cecal fermentation system. Cecal contents from three laying hens were pooled and diluted to a 1:3000 concentration in an anaerobic dilution solution. The cecal dilution was added to sterile test tubes filled with alfalfa and layer ration with and without fructooligosaccharide (FOS). Two controls containing cecal dilutions and anaerobic dilution solution were used. The samples were processed in the anaerobic hood and incubated at 37 degrees C. Samples were inoculated with Salmonella at 0 and 24h after in vitro cecal fermentation and plated at 0 and 24h after inoculation with ST. Plates were incubated for 24h and colony forming units (CFU) enumerated. The samples immediately inoculated with ST without prior cecal fermentation did not significantly lower ST counts 24h later. However, samples pre-incubated for 24h with cecal microflora prior to ST inoculation exhibited reduced ST CFU by approximately 2 logarithms, with the most dramatic decreases seen in alfalfa and layer ration combined with FOS. The addition of FOS to feed substrate diets in combination with cecal contents acted in a synergistic manner to decrease ST growth only after ST was introduced to 24h cecal incubations.