bluuebunny/crossref_metadata_2025 huggingface dataset:
Growling from the gut: co-option of the gastric mill for acoustic communication in ghost crabs
Authors: Taylor Jennifer R. A. , deVries Maya S. , Elias Damian O.
Published: September 2019

Animal acoustic communication systems can be built upon co-opted structures that become specialized for sound production or morphological novelties. The ghost crab,Ocypode quadrata, evolved a novel stridulation apparatus on the claws that is used during agonistic interactions, but they also produce a rasping sound without their claw apparatus. We investigated the nature of these sounds and show thatO. quadrataadopted a unique and redundant mode of sound production by co-opting the gastric mill (grinding teeth of the foregut). Acoustic characteristics of the sound are consistent with stridulation and are produced by both male and female crabs during aggressive interactions. Laser Doppler vibrometry localized the source of maximum vibration to the gastric region and fluoroscopy showed movement of the gastric mill that coincided with stridulation. The lateral teeth of the gastric mill possess a series of comb-like structures that rub against the median tooth to produce stridulation with dominant frequencies below 2 kHz. This previously undescribed gastric stridulation can be modulated and provide a means of assessment during aggressive interactions, similar to the use of the claw stridulation apparatus. This functional redundancy of stridulation in crabs offers unique insights into the mechanisms of evolution of acoustic communication systems.
A phylogenomic framework for pelagiarian fishes (Acanthomorpha: Percomorpha) highlights mosaic radiation in the open ocean
Authors: Friedman Matt , Feilich Kara L. , Beckett Hermione T. , Alfaro Michael E. , Faircloth Brant C. , Černý David , Miya Masaki , Near Thomas J. , Harrington Richard C.
Published: September 2019

The fish clade Pelagiaria, which includes tunas as its most famous members, evolved remarkable morphological and ecological variety in a setting not generally considered conducive to diversification: the open ocean. Relationships within Pelagiaria have proven elusive due to short internodes subtending major lineages suggestive of rapid early divergences. Using a novel sequence dataset of over 1000 ultraconserved DNA elements (UCEs) for 94 of the 286 species of Pelagiaria (more than 70% of genera), we provide a time-calibrated phylogeny for this widely distributed clade. Some inferred relationships have clear precedents (e.g. the monophyly of ‘core’ Stromateoidei, and a clade comprising ‘Gempylidae’ and Trichiuridae), but others are unexpected despite strong support (e.g. Chiasmodontidae +Tetragonurus). Relaxed molecular clock analysis using node-based fossil calibrations estimates a latest Cretaceous origin for Pelagiaria, with crown-group families restricted to the Cenozoic. Estimated mean speciation rates decline from the origin of the group in the latest Cretaceous, although credible intervals for root and tip rates are broad and overlap in most cases, and there is higher-than-expected partitioning of body shape diversity (measured as fineness ratio) between clades concentrated during the Palaeocene–Eocene. By contrast, more direct measures of ecology show either no substantial deviation from a null model of diversification (diet) or patterns consistent with evolutionary constraint or high rates of recent change (depth habitat). Collectively, these results indicate a mosaic model of diversification. Pelagiarians show high morphological disparity and modest species richness compared to better-studied fish radiations in contrasting environments. However, this pattern is also apparent in other clades in open-ocean or deep-sea habitats, and suggests that comparative study of such groups might provide a more inclusive model of the evolution of diversity in fishes.
Paternal chronic folate supplementation induced the transgenerational inheritance of acquired developmental and metabolic changes in chickens
Authors: Wu Shengru , Guo Wei , Li Xinyi , Liu Yanli , Li Yulong , Lei Xinyu , Yao Junhu , Yang Xiaojun
Published: September 2019

Increasing evidence indicates that paternal diet can result in metabolic changes in offspring, but the definite mechanism remains unclear in birds. Here, we fed breeder cocks five different diets containing 0, 0.25, 1.25, 2.50 and 5.00 mg kg
−1
folate throughout life. Paternal folate supplementation (FS) was beneficial to the growth and organ development of broiler offspring. Most importantly, the lipid and glucose metabolism of breeder cocks and broiler offspring were affected by paternal FS, according to biochemical and metabolomic analyses. We further employed global analyses of hepatic and spermatozoal messenger RNA (mRNA), long non-coding RNA (lncRNA) and micro RNA (miRNA). Some key genes involved in the glycolysis or gluconeogenesis pathway and the PPAR signalling pathway, including
PEPCK
,
ANGPTL4
and
THRSP
, were regulated by differentially expressed hepatic and spermatozoal miRNAs and lncRNAs in breeder cocks and broiler offspring. Moreover, the expression of
ANGPTL4
could also be regulated by differentially expressed miRNAs and lncRNAs in spermatozoa via competitive endogenous RNA (ceRNA) mechanisms. Overall, this model suggests that paternal folate could transgenerationally regulate lipid and glucose metabolism in broiler offspring and the epigenetic transmission may involve altered spermatozoal miRNAs and lncRNAs.
Loss of olfaction in sea snakes provides new perspectives on the aquatic adaptation of amniotes
Authors: Kishida Takushi , Go Yasuhiro , Tatsumoto Shoji , Tatsumi Kaori , Kuraku Shigehiro , Toda Mamoru
Published: September 2019

Marine amniotes, a polyphyletic group, provide an excellent opportunity for studying convergent evolution. Their sense of smell tends to degenerate, but this process has not been explored by comparing fully aquatic species with their amphibious relatives in an evolutionary context. Here, we sequenced the genomes of fully aquatic and amphibious sea snakes and identified repertoires of chemosensory receptor genes involved in olfaction. Snakes possess large numbers of theolfactory receptor(OR) genes and thetype-2 vomeronasal receptor(V2R) genes, and expression profiling in the olfactory tissues suggests that snakes use the ORs in the main olfactory system (MOS) and the V2Rs in the vomeronasal system (VNS). The number ofORgenes has decreased in sea snakes, and fully aquatic species lost MOS which is responsible for detecting airborne odours. By contrast, sea snakes including fully aquatic species retain a number ofV2Rgenes and a well-developed VNS for smelling underwater. This study suggests that the sense of smell also degenerated in sea snakes, particularly in fully aquatic species, but their residual olfactory capability is distinct from that of other fully aquatic amniotes. Amphibious species show an intermediate status between terrestrial and fully aquatic snakes, implying their importance in understanding the process of aquatic adaptation.
아로니아의 저장온도가 생리활성물질 및 항산화에 미치는 영향
Authors: Hwang Eun-Sun , Yeom Mi Sook
Published: September 2019

The fruit of aronia (Aronia melanocarpa, also called the “black chokeberry), which is rich in anthocyanin, polyphenol, and flavonoid content and possesses antioxidant, anticancerous, and anti-inflammatory properties. In this study, the influence of storage temperature and storage period on the phytochemical content and antioxidant activity of aronia was determined. The total polyphenol and flavonoid contents of aronia extract were found to be 308.48 μg gallic acid equivalent/g dry weight and 5.33 μg quercetin equivalent/g dry weight, respectively. HPLC analysis of aronia reveled four anthocyanin peaks corresponding to cyanidin-3-O-galactoside, cyanidin-3-O-glucoside, cyanidin-3-O-arabinose, and cyanidin-3-O-xylose and three polyphenol peaks corresponding to chlorogenic acid, vanillic acid, and rutin hydrate. Long-term storage at a refrigerated temperature (4℃) reduced the levels the levels of health promoting compounds. We found that the highest amounts of total polyphenols, flavonoids, and anthocyanins were retained in aronia samples stored at -80℃ followed by those stored at -20℃ and 4℃ samples. Furthermore, the samples stored at -80℃ showed the stronger antioxidant activities than those stored at other temperatures. Based on these findings, we concluded that freezing aronia at -80℃ can help preserve its antioxidant activity by maintaining high levels of anthocyanins and other bioactive compounds.
The effects of Allium hookeri on the physicochemical characteristics and storage of pork sausage
Authors: Lee Joo Hyung , Choi Seong Hee
Published: September 2019

The effects of Allium hookeri (AH) on the physicochemical properties and storage of pork sausage were examined. Sausages were prepared with different levels of AH (0.5 and 1%) and sodium nitrite (50, 100, and 150 ppm), and stored at 4℃ for four weeks. The addition of AH had little effect on the CIE color or texture value of the sausage. More than half of the added nitrite was removed during sausage preparation, and a further large reduction was observed during one week of storage. The TBARS content was observed to increase with storage, but lower increases were observed when more nitrite and AH were added. When stored for two or four weeks, the group with 100 ppm nitrite and 1% AH showed lower TBARS values than the group with only 150 ppm nitrite. The total microbial count after storage for four weeks was lower in sausage with 50 ppm nitrite and 1% AH than in sausage with only 100 ppm nitrite, and the sausage with 100 ppm nitrite and 1% AH exhibited the same microbial count as that with only 150 ppm nitrite. These results suggest that AH is a potential substitute for nitrite for use in sausage production by suppressing TBARS increases and inhibiting microbial growth during storage.
Nutritional components, phytochemicals and biological activities of Sibjeondaebohwan produced from balloon flower by high-temperature aging
Authors: Kim Su Cheol , Im Chae Youn , Hwang Chung Eun , Park Sang Won , Kang Min Cheol , Lee Dong-Hee , Cho Kye Man
Published: September 2019

In this study, general Sibjeondaebohwan (G-SDH) and high-temperature aged Sibjeondaebohwan (HTA-SDH) samples were prepared using ten herbal medicinal plants including balloon flower. The nutritional components (five nutrients, fatty acids, and free amino acids), phytochemicals (phenolic acids and flavonols), radical scavenging activities (DPPH, ABTS, and hydroxyl), digestive enzyme inhibitory activities (α-glucosidase and pancreatic lipase), and immune system activation of G-SDH and HTA-SDH were analyzed and compared. The contents of crude ash, fat, and protein, carbohydrate, total fatty acid, and total free amino acid of G-SDH were significantly higher than those of HTA-SDH. The major free amino acids and fatty acids in G-SDH were aspartic acid and oleic acid and those in HTA-SDH were glutamic acid and oleic acid. Compared to G-SDH, higher concentrations of total polyphenols, total flavonoids, Mailliard reaction products, total phenolic acids and total flavonols of HTA-SDH were estimated. After high-temperature aging, the total phenolic and flavonol contents increased from 272.03 to 303.31 μg/g and 310.71 to 372.58 μg/g, respectively. The DPPH, ABTS, and hydroxyl radical scavenging activities and the α-glucosidase, α-amylase, and pancreatic lipase inhibition activities in HTA-SDH were 85.65%, 89.93%, and 63.69%, and 61.06%, 34.21%, and 64.89%, respectively, which were considerably higher than those in the G-SDH. In addition, HTA-SDH showed the effect of controlling immune function.
Quality characteristics of spray-dried powders of Pueraria thunbergiana extracts with added forming agents
Authors: Kim Jung-Min , Youn Kwang-Sup
Published: September 2019

This study was designed to investigate the quality characteristics of spray-dried powders from Pueraria thunbergiana extract with added forming agents (β-cyclodextrin (CD), dextrin (DE=10 and DE=20), and gum arabic (GA); 20% of each forming agent was added). The moisture contents of the powders were not affected by the addition of forming agents. Highest the total sugar content was observed in the spray-dried powder with DE=10. The color intensities (a*, b* values) were higher in the spray-dried powders than those in the freeze-dried powders. The water absortion index of the powder with DE=10 was the lowest among the powders with added forming agents. The water solubility indexes of the spray-dried powders were higher than those of the freeze-dried powders. Lowest dynamic angle was observed for the spray-dried powder with GA. The polyphenol and flavonoid contents in the spray-dried powders were significantly higher than those of freeze-dried powders, and the highest DPPH radical scavenging ability was found in the spray-dried powder with added GA (1mg/mL). SOD-like activity was not affected by the addition of forming agents. The activity of alcohol dehydrogenase (ADH) increased significantly in the presence of CD, but that of aldehyde dehydrogenase (ALDH) was not affected by the forming agent. Based on these results, the spray-dried powder with CD affected the desired quality characteristics and was found to be suitable for applications in food industry.
Quality characteristics of Cheonggukjang by mixed culture of biogenic amine producing- and degrading-bacteria
Authors: Lim Eun-Seo , Lee Eun-Woo
Published: September 2019

The objective of this study was to evaluate biogenic amine (BA) formation and degradation abilities of Bacillus strain and lactic acid bacteria (LAB) isolated from meju and doenjang and to determine the microbiological and physicochemical qualities of Cheonggukjang prepared by mixed culture of these strains. Accumulation of cadaverine (421.7 ± 11.0 mg/L) and histamine (628.7 ± 24.1 mg/L) was assessed in the culture media of Bacillus subtilis MJ226 that displayed lysine and histidine decarboxylase activities. No ability to form cadaverine, histamine, putrescine, tryptamine, and tyramine by Lactobacillus acidophilus D11, L. acidophilus D38, Lactobacillus sakei D44, Lactobacillus plantarum D70, which exhibited high BA degradation ability. The amino nitrogen and free amino acid contents were significantly (p<0.05) increased in Cheonggukjang prepared by the mixed culture of LAB (L. sakei D44, L. plantarum D70, or L. pentosus D74) and B. subtilis MJ226, whereas the ammonia nitrogen and BA (cadaverine and histamine) contents were significantly (p<0.05) decreased. Consequently, it was confirmed that BA formation in Cheonggukjang prepared by starter culture of B. subtilis was effectively inhibited by the certain strains of LAB having BA-degrading ability.
Alleviation of atopic dermatitis-related indications of the Lonicera japonica aqueous fraction produced by solid-state fermentation
Authors: Yoo Chi-yeol , Son Hyeong-U , Kim Jong-Myung , Lee Sang-Han
Published: September 2019

In the process of screening the extracts of various medicinal herbs exhibiting with potent anti-atopic activity, we first confirmed the effect of the anti-atopic activity of the aqueous fraction of Lonicera japonica stem extract (afLj) ontained by the solid fermentation process by Phellinus baumii was identified to show anti-atopic activity for the first time. Further animal experiments revealed that the antioxidative activity of afLj had decreased, while the anti-atopic activity was increased compared to control. Moreover, treatment with afLj significantly decreased the infiltration of immune cells into inflammatory sites to 32% level observed with the control treatment in a DNFB-induced mouse model (NT). In particular, afLj dramatically decreased the number of eosinophils by afLj than those compared to Lj. The overall decrease in antioxidant activity and lack of significant differences in the β-hexosaminidase activity of afLj imply that the activity possessed by Lj itself was converted into an anti-atopic active substance through biotransformation during solid fermentation. Overall, these results suggest that the potential of afLj will be possible to use as a new functional biomaterial or functional food ingredient related with anti-atopic benefits.
Solubilization of polysaccharides and functional components of ginger (Zingiber officinale Rosc.) using ethanol and enzyme
Authors: Nam Dong-Geon , Kim Mina , Im Pereum , Choe Jeong-Sook , Choi Ae-Jin
Published: September 2019

The objectives of this study were to increase the contents of functional ingredients and water soluble polysaccharides obtained from ginger extracts using ethanol and enzymes and to determine the applicability in pilot-scale production for the food industry. The processing of ethanol-treated extract (step I) depended on the extraction methods and time period of extraction. The enzyme-treated extract (step II) was processed with or without pH adjustment. The water soluble index (WSI) and total polyphenol (TP) content of the enzyme-treated extract (B) without pH adjustment decreased by 5.1% and 0.85%, respectively, as compared with that of the pH-adjusted extract (A). For the ethanol-treated extract processed by the reflux method, WSI of 9.59%, TP content of 4.75%, total flavonoid (TF) content of 1.38%, and total gingerol/shogaol content of 6.50% were obtained. The total gingerol/shogaol content was higher by 3.6 times than those obtained from the extract processed by the stirring method. As the reflux extraction time increased, WSI and the TP, TF, total gingerol/shogaol contents increased significantly. Therefore, the optimum condition for processing the ethanol extract involved refluxing for 2 h at 83℃ unadjusting the optimum pH. The variability of analysis of the parameters depending on different extraction scales was confirmed to be within ±7%. The ethanol and enzyme based approach described in this study would be beneficial to food industries for developing functional products and materials from ginger.
Comparison of primary and secondary metabolite compositions and antioxidant effects of specific soybean cultivars
Authors: Hwang Chung Eun , Kim Su Cheul , Lee Jin Hwan , Lee Dong-Hee , Cho Kye Man
Published: September 2019

The metabolite composition and antioxidant activity of the Saedanbaek, Jinyang, and Wooram soybean cultivars were evaluated. The moisture, crude ash, protein, fat, and carbohydrate contents in these soybean cultivars varied in the range 7.9-9.8 mg/g, 4.8-4.9 mg/g, 35.9-47.5 mg/g, 14.2-16.5 mg/g, and 21.4-35.0 mg/g, respectively. The crude protein content was found to be the highest 47.5 mg/g in the Saedanbaek soybean. The contents of saturated fatty acids such as palmitic acid, arachidic acid, behenic acid, and lignoceric acid were 1391.1, 490.8, 37.5, 44.9, and 16.6 mg/100 g, respectively, and were the highest in the Jinyang soybean. The unsaturated fatty acids (linoleic acid, oleic acid, and α-linolenic acid) were estimated to be 8258.0, 2896.8, and 906.5 mg/100 g, respectively, in the Saedanbaek, Jinyang, and Wooram soybeans. The highest total amino acid content (44598.54 mg/100 g) was found in the Saedanbaek soybean, and this was almost 2 and 1.6 folds higher than those in the Jinyang (21,525.93 mg/100 g) and Wooram (26,250.63 mg/100 g) soybeans. The highest glycosides, malonylglycosides, and aglycone contents (836.46 μg/g, 2,975.86 μg/g, and 231.60 μg/g, respectively) were found in the Wooram soybean.
Determination of aroma profiles of coffee cultivated in Goheung, Korea by gas chromatography–ion mobility spectrometry
Authors: Moon Sang Yoon , Baek Seung Yeon , Kim Mee Ree
Published: September 2019

In this study, we investigated the aroma characteristics of Goheung coffee in Jeonnam, which was firstly tested and cultivated as a special crop in Korea, using GC-IMS electronic nose. As a result of principal component analysis of the aroma pattern detected by electronic nose, the aroma of Goheung coffee was distinguished from five foreign species of origin (Colombia, Guatemala, Ethiopia, Brazil, India). Of the volatile compounds in Korea's Goheung coffee, the nine components that showed high sensitivity were not found in other foreign coffee. The unique fragrance composition of coffee from Goheung in Korea was observed, and the fragrance components of buttery, oily, caramel-like 1-heptene, 2-methyl- and 1-propanol, which have strongly fruity and floral aroma, were strongly detected in ethiopia coffee, and strongly detected in Guatemala. Sweet and fruity components such as 2-pentanone and isopropyl tert-butyl ether and components such as amine and pyridine with negative aroma characteristics such as sour, putrid, bitter, and fishy were found to be the lowest in the five foreign coffees. From these results, the aroma characteristics of Korean Goheung coffee are expected to a good response to domestic consumers.
Physicochemical characteristics and antioxidant activities of solvent fractions from ethanol extract of Wasabia koreana Nakai leaf
Authors: Kang Da Young , Hitayezu Emmanuel , Han In Hye , Kim Ji Su , Jo Young Min , Kang Yoon-Han
Published: September 2019

This study was conducted to investigate the physicochemical properties and antioxidant activity of the solvent fractions obtained from 80% ethanol extracts of Wasabia koreana Nakai leaves. From the ethanol extracts, hexane, chloroform, ethyl acetate, and n-butanol fractions were sequentially extracted and collected, and further used for the investigation. The highest yield was obtained in the water fraction and its pH was 4.25. The total polyphenol, total flavonoid and total pectin contents in the ethyl acetate fraction were 56.24 mgGAE/g, 97.29 mgNE/g and 108.8 mg/g, respectively. This indicated that the extraction yields of the phenolic compounds and pectin in the solvent fractions obtained from the Wasabi leaves and petiole were significantly different. Analysis of the taste components of the ethyl acetate and water fractions was carried out using an electronic tongue sensor. A negative concentration-dependent population for the ethyl acetate fraction and a positive population for the water fraction, corresponding to DF1 (83.96%) in the discriminant function analysis (DFA) plot, were confirmed from the analysis. In the ethyl acetate fraction, the IC50 values ​​of 1,1-diphenyl-2-picrylhydrazyl(DPPH) radical scavenging activity and 2,2’-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid(ABTS) radical scavenging activity were 899.88 ppm and 276.63 ppm, respectively. Therefore, the ethanol extracts and fractions from Wasabia koreana Nakai leaf have low utilization, which will be beneficial for the development of high value-added products via improvement in the taste components and antioxidant activity.
The relationship between misfolding avoidance hypothesis and protein evolutionary rates in the light of empirical evidence
Authors: Usmanova Dinara R. , Plata Germán , Vitkup Dennis
Published: September 2019

For more than a decade the misfolding avoidance hypothesis (MAH) and related theories have dominated evolutionary discussions aimed at explaining the variance of molecular clock across cellular proteins. In this study we use various experimental data to further investigate the consistency of the MAH predictions with empirical evidence. We also critically discuss experimental results that motivated the MAH development and that are often viewed as evidence of its major contribution to constraining protein evolution. We demonstrate, in Escherichia coli and Homo sapiens, the lack of a substantial negative correlation between protein evolutionary rates and Gibbs free energies of unfolding, a direct measure of protein stability. We then analyze multiple new genome-scale datasets describing protein aggregation and interaction propensities, which are likely optimized in evolution to alleviate deleterious effects associated with toxic protein misfolding and misinteractions. Our results demonstrate that the propensity of proteins to aggregate, the fraction of charged amino acids, and protein stickiness do correlate with protein abundances. Nevertheless, across multiple organisms and datasets we do not observe substantial correlations between proteins aggregation- and stability-related properties and evolutionary rates. Therefore, diverse empirical data support the conclusion that the MAH and similar hypotheses are unlikely to play a major role in mediating a strong negative correlation between protein expression and molecular clock, and thus in explaining the variability of evolutionary rates across cellular proteins.

Significance statement

Evolutionary rates vary substantially across cellular proteins. Understanding the nature of molecular clock and its variability across proteins is a foundational question in molecular evolution. The popular and currently dominant theory to explain the molecular clock variability is the misfolding avoidance hypothesis (MAH). The role of the MAH is currently under active debate. In the manuscript we discuss how to appropriately test the MAH based on available empirical data, and then rigorously test the hypothesis using more than a dozen of new genome-wide datasets of protein stability and aggregation propensities. Our results suggest that the MAH is unlikely to play a major role in explaining the variability of molecular clock across proteins.
Expression of endoplasmic reticulum mannosyl-oligosaccharide α1, 2-mannosidase regulates tumorigenicity of prostate cancer cells
Authors: Toonstra Christian , Wang Xiangchun , Höti Naseruddin , Pan Jianbo , Zhang Hui
Published: September 2019

It has been previously demonstrated that glycogenes can function as important pleiotropic regulators of tumorigenesis. In this study, we investigated the function of endoplasmic reticulum mannosyl-oligosaccharide 1, 2-alpha-mannosidase (MAN1B1) on the behavior of prostate cancer cells and found that overexpression of MAN1B1 in androgen-independent PC3 cells reduced cellular migration. We extended the analysis to an androgen dependent cell line, LNCaP, and another androgen independent cell line, LNCaP-AI, observing a similar migratory phenotype. By using quantitative proteomics, we found the downregulation of vimentin expression when PC3 or LNCaP-AI cells with overexpressed MAN1B1. The current study suggests that MAN1B1 may regulate cellular migration and promote epithelial-to-mesenchymal transition (EMT) phenotype in prostate cancer cells.
Using null models to compare bacterial and microeukaryotic metacommunity assembly under shifting environmental conditions
Authors: Vass Máté , Székely Anna J. , Lindström Eva S. , Langenheder Silke
Published: September 2019

Temporal variations in microbial metacommunity structure and assembly processes in response to shifts in environmental conditions are poorly understood. Hence, we conducted a temporal field study by sampling rock pools in four-day intervals during a 5-week period that included strong changes in environmental conditions due to intensive rain. We characterized bacterial and microeukaryote communities by 16S and 18S rRNA gene sequencing, respectively. Using a suite of null-model approaches to assess dynamics in community assembly, we found that strong changes in environmental conditions induced small but significant temporal changes in assembly processes and triggered different responses in bacterial and microeukaryotic metacommunities, promoting distinct selection processes. Incidence-based approaches showed that the assemblies of both communities were mainly governed by stochastic processes. In contrast, abundance-based methods indicated the dominance of historical contingency and unmeasured factors in case of bacteria and microeukaryotes, respectively, which we distinguished from dispersal-related processes using additional tests. Taken together, our study highlights that community assembly processes are not static, and the relative importance of different assembly processes can vary under different conditions and between different microbial groups.
Single-cell atlas of the first intra-mammalian developmental stage of the human parasite Schistosoma mansoni
Authors: Diaz Soria Carmen Lidia , Lee Jayhun , Chong Tracy , Coghlan Avril , Tracey Alan , Young Matthew D , Andrews Tallulah , Hall Christopher , Ng Bee Ling , Rawlinson Kate , Doyle Stephen R. , Leonard Steven , Lu Zhigang , Bennett Hayley M , Rinaldi Gabriel , Newmark Phillip A. , Berriman Matthew
Published: September 2019

Over 250 million people suffer from schistosomiasis, a tropical disease caused by parasitic flatworms known as schistosomes. Humans become infected by free-swimming, water-borne larvae, which penetrate the skin. The earliest intra-mammalian stage, called the schistosomulum, undergoes a series of developmental transitions. These changes are critical for the parasite to adapt to its new environment as it navigates through host tissues to reach its niche, where it will grow to reproductive maturity. Unravelling the mechanisms that drive intra-mammalian development requires knowledge of the spatial organisation and transcriptional dynamics of different cell types that comprise the schistomulum body. To fill these important knowledge gaps, we performed single-cell RNA sequencing on two-day old schistosomula of Schistosoma mansoni. We identified likely gene expression profiles for muscle, nervous system, tegument, parenchymal/primordial gut cells, and stem cells. In addition, we validated cell markers for all these clusters by in situ hybridisation in schistosomula and adult parasites. Taken together, this study provides a comprehensive cell-type atlas for the early intra-mammalian stage of this devastating metazoan parasite.
Using a residency index to estimate the economic value of saltmarsh provisioning services for commercially important fish species
Authors: McCormick Hannah A. , Salguero-Gómez Roberto , Mills Morena , Davis Katrina
Published: September 2019

Every year, 100 hectares of saltmarsh in the United Kingdom are lost due to sea level rise. The remaining areas are threatened by land conversion, agricultural activities, and climate change. There are important economic consequences to saltmarsh loss, as saltmarsh provides valuable ecosystem services including flood protection, carbon sequestration, and nursery habitat for commercially fished species. Quantifying the economic value of these ecosystem services can help target policies for saltmarsh restoration, or ‘managed realignment’, of new saltmarsh areas. In this study, we quantify the economic value of saltmarsh as a habitat for commercially fished species by developing a residency index. The residency index weights the relative importance of saltmarsh along a species’ lifecycle by explicitly incorporating the target species’ life histories and the estimated proportion of time it spends in saltmarsh at juvenile and adult life stages. Using this index, we estimate the value of saltmarsh to UK commercial fisheries landings. We find that UK saltmarsh contributes annually between 16.7% and 18.2% of total UK commercial landings for European seabass (Dicentrarchus labrax), European plaice (Pleuronectes platessa), and Common sole (Solea solea). Our findings highlight the importance of saltmarsh protection and restoration. Furthermore, our approach provides a general framework that integrates population ecology methods and economic analyses to assess the value of saltmarsh and other coastal habitats for fisheries worldwide.
Integrated clonal analysis reveals circulating tumor DNA in urine and plasma of glioma patients
Authors: Mouliere Florent , Heider Katrin , Smith Christopher G. , Su Jing , Thompson Mareike , Morris James , Wan Jonathan C.M. , Chandrananda Dineika , Hadfield James , Grezlak Marta , Hudecova Irena , Cooper Wendy , Gale Davina , Eldridge Matt , Watts Colin , Brindle Kevin , Rosenfeld Nitzan , Mair Richard
Published: September 2019

Glioma-derived cell-free tumor DNA is challenging to detect using standard liquid biopsy techniques as its levels in body fluids are very low, similar to those in patients with early stage carcinomas. By sequencing cell-free DNA across thousands of clonal and private mutations identified individually in each patient’s tumor we detected tumor-derived DNA in plasma (10/12, 83%) and urine samples (8/11, 72%) from the majority (7/8, 87.5%) of glioma patients tested.

One Sentence Summary

Circulating tumor DNA can be detected in the majority of plasma and urine samples from primary brain tumor patients using sequencing guided by mutations detected in multi-region tumor biopsies.
High-sensitivity monitoring of ctDNA by patient-specific sequencing panels and integration of variant reads
Authors: Wan Jonathan C. M. , Heider Katrin , Gale Davina , Murphy Suzanne , Fisher Eyal , Morris James , Mouliere Florent , Chandrananda Dineika , Marshall Andrea , Gill Andrew B. , Chan Pui Ying , Barker Emily , Young Gemma , Cooper Wendy N. , Hudecova Irena , Marass Francesco , Bignell Graham R. , Alifrangis Constantine , Middleton Mark R. , Gallagher Ferdia A. , Parkinson Christine , Durrani Amer , McDermott Ultan , Smith Christopher G. , Massie Charles , Corrie Pippa G. , Rosenfeld Nitzan
Published: September 2019

Circulating tumor-derived DNA (ctDNA) can be used to monitor cancer dynamics noninvasively. Patients with small tumors have few copies of ctDNA in plasma, resulting in limited sensitivity to detect low-volume or residual disease. We show that sampling limitations can be overcome and sensitivity for ctDNA detection can be improved by massively parallel sequencing when hundreds to thousands of mutations are identified by tumor genotyping. We describe the INtegration of VAriant Reads (INVAR) analysis pipeline, which combines patient-specific mutation lists with both custom error-suppression methods and signal enrichment based on biological features of ctDNA. In this framework, the sensitivity can be estimated independently for each sample based on the number of informative reads, which is the product of the number of mutations analyzed and the average depth of unique sequencing reads. We applied INVAR to deep sequencing data generated by custom hybrid-capture panels, and showed that when ~106 informative reads were obtained INVAR allowed detection of tumor-derived DNA fractions to parts per million (ppm). In serial samples from patients with advanced melanoma on treatment, we detected ctDNA when imaging confirmed tumor volume of ~1cm3. In patients with resected early-stage melanoma, ctDNA was detected in 40% of patients who later relapsed, with higher rates of detection when more informative reads were obtained. We further demonstrated that INVAR can be generalized and allows improved detection of ctDNA from whole-exome and low-depth whole-genome sequencing data.
Does body position before and during blood sampling influence the athlete biological passport variables?
Authors: Tiffany Astolfi , Olaf Schumacher Yorck , von Roten Fabienne Crettaz , Martial Saugy , Raphael Faiss
Published: September 2019

The Athlete’s Biological Passport (ABP) is a tool for the indirect detection of blood doping. Current guidelines from the World Anti-Doping Agency (WADA) require a delay of 2 hours after any physical exercise and to be seated for 10 minutes prior to any blood sampling to obtain a valid measurement. Since body position prior to and during phlebotomy may influence the outcome, this study compared blood biomarker variations with changes in body position during blood sample collection. Ten successive venous blood samples from 38 subjects of 3 groups (elite cyclists, apnea divers and controls) in three situations (seated, after a 50 m walk, and supine) were collected and analyzed via flow cytometry. While reticulocytes percentage was unchanged in all conditions, haemoglobin concentration and hematocrit were stable after at least 10 min in a seated position. Due to shifts in plasma volume, the measures were significantly higher after changing posture for a short walk, but readjusted to previous levels after only 5 min. Supine position caused generally lower values after 10-30 min. The results support the current guidelines and additionally provide evidence to adjust the waiting time for blood sampling after short changes in posture.
Identification and quantification of meat product ingredients by whole-genome metagenomics (All-Food-Seq)
Authors: Hellmann Sören Lukas , Ripp Fabian , Bikar Sven-Ernö , Schmidt Bertil , Köppel René , Hankeln Thomas
Published: September 2019

Complex food matrices bear the risk of intentional or accidental admixture of non-declared species. Moreover, declared components can be present in false proportions, since expensive taxa might be exchanged for cheaper ones. We have previously reported that PCR-free metagenomic sequencing of total DNA extracted from sausage samples combined with bioinformatic analysis (termed All-Food-Seq, AFS), can be a valuable screening tool to identify the taxon composition of food ingredients. Here we illustrate this principle by analysing regional Doner kebap samples, which revealed unexpected and unlabelled poultry and plant components in three of five cases. In addition, we systematically apply AFS to a broad set of reference meat material of known composition (i.e. reference sausages) to evaluate quantification accuracy and potential limitations. We include a detailed analysis of the effect of different food matrices and the possibility of false-positive sequence read assignment to closely related species, and we compare AFS quantification results to quantitative real-time PCR (qPCR) and droplet digital PCR (ddPCR). AFS emerges as a potent PCR-free screening tool, which can detect multiple target species of different kingdoms of life within a single assay. Mathematical calibration accounting for pronounced matrix effects can significantly improves AFS quantification accuracy. In comparison, AFS performs better than classical qPCR, and is on par with ddPCR.
Massive analysis of 64’628 bacterial genomes to decipher a water reservoir and origin of mobile colistin resistance (mcr) gene variants: is there another role for this family of enzymes?
Authors: Khedher Mariem Ben , Baron Sophie Alexandra , Riziki Toilhata , Ruimy Raymond , Diene Seydina M. , Rolain Jean-Marc
Published: September 2019

Since 2015, new worrying colistin resistance mechanism, mediated by mcr-1 gene has been reported worldwide along with eight newly described variants (mcr-2 to mcr-9) but their source(s) and reservoir(s) remain largely unexplored. Here, we conducted a massive bioinformatic analysis of 64’628 downloaded bacterial genomes to investigate the reservoir and origin of these mcr variants. We identified a total of 6’651 significant positive hits (aa sequence coverage > 90 % and similarity >50%) with the nine MCR variants from these genomes that include 39 bacterial genera and more than 1050 species. Although these variants could be identified in bacteria from human and animal sources, we found plenty MCR variants in unsuspected bacteria from environmental origin, especially from water sources. The ubiquitous presence of mcr variants in bacteria from water likely suggests another role in the biosphere of these enzymes as an unknown defense system against natural antimicrobial peptides and/or bacteriophage predation.
When two cells are better than one: specialized stellate cells provide a privileged route for uniquely rapid water flux inDrosophilarenal tubule
Authors: Cabrero Pablo , Terhzaz Selim , Dornan Anthony J. , Ghimire Saurav , Holmes Heather L. , Turin Daniel R. , Romero Michael F. , Davies Shireen A. , Dow Julian A. T.
Published: September 2019

Insects are highly successful, in part through an excellent ability to osmoregulate. The renal (Malpighian) tubules can secrete fluid faster on a per-cell basis than any other epithelium, but the route for these remarkable water fluxes has not been established. InDrosophila melanogaster, we show that 4 members of the Major Intrinsic Protein family are expressed at very high level in the fly renal tissue; the aquaporins Drip and Prip, and the aquaglyceroporins Eglp2 and Eglp4. As predicted from their structure and by their transport function by expressing these proteins inXenopusoocytes, Drip, Prip and Eglp2 show significant and specific water permeability, whereas Eglp2 and Eglp4 show very high permeability to glycerol and urea. Knockdowns of any of these genes impacts tubule performance resulting in impaired hormone-induced fluid secretion. TheDrosophilatubule has two main secretory cell types: active cation-transporting principal cells with the aquaglyceroporins localize to opposite plasma membranes and small stellate cells, the site of the chloride shunt conductance, with these aquaporins localising to opposite plasma membranes. This suggests a model in which cations are pumped by the principal cells, causing chloride to follow through the stellate cells in order to balance the charge. As a consequence, osmotically obliged water follows through the stellate cells. Consistent with this model, fluorescently labelled dextran, anin vivomarker of membrane water permeability, is trapped in the basal infoldings of the stellate cells after kinin diuretic peptide stimulation, confirming that these cells provide the major route for transepithelial water flux. The spatial segregation of these components of epithelial water transport may help to explain the unique success of the higher insects.

Significance statement

The tiny insect renal (Malpighian) tubule can transport fluid at unparalleled speed, suggesting unique specialisations. Here we show that strategic allocation of Major Intrinsic Proteins (MIPs) to specific cells within the polarized tubule allow the separation of metabolically intense active cation transport from chloride and water conductance. This body plan is general to at least many higher insects, providing a clue to the unique success of the class Insecta.
Hippocampal place cells encode local surface texture boundaries
Authors: Wang Chia-Hsuan , Monaco Joseph D. , Knierim James J.
Published: September 2019

The cognitive map is often assumed to be a Euclidean map that isometrically represents the real world (i.e. the Euclidean distance between any two locations in the physical world should be preserved on the cognitive map). However, accumulating evidence suggests that environmental boundaries can distort the mental representations of a physical space. For example, the distance between two locations can be remembered as longer than the true physical distance if the locations are separated by a boundary. While this overestimation is observed under different experimental conditions, even when the boundary is formed by flat surface cues, its physiological basis is not well understood. We examined the neural representation of flat surface cue boundaries, and of the space segregated by these boundaries, by recording place cell activity from dorsal CA1 and CA3 while rats foraged on a circular track or square platform with inhomogeneous surface textures. About 40% of the place field edges concentrated near the surface cue boundaries on the circular track (significantly above the chance level 33%). Similarly, the place field edges were more prevalent near the boundaries on the platforms than expected by chance. In both 1-dimensional and 2-dimensional environments, the population vectors of place cell activity changed more abruptly with distance between locations that crossed cue boundaries than between locations within a bounded region. These results show that the locations of surface boundaries were evident as enhanced decorrelations of the neural representations of locations to either side of the boundaries. This enhancement might underlie the cognitive phenomenon of overestimation of distances across boundaries.
Gene activation and repression by the glucocorticoid receptor are mediated by sequestering Ep300 and two modes of chromatin binding
Authors: Portuguez Avital Sarusi , Grbesa Ivana , Tal Moran , Deitch Rachel , Raz Dana , Weismann Ran , Schwartz Michal , Loza Olga , Sung Myong-Hee , Kaplan Tommy , Hakim Ofir
Published: September 2019

The transcription factor glucocorticoid receptor (GR) is a key mediator of stress response and a broad range of physiological processes. How can GR rapidly activate the expression of some genes while repress others, remains an open question due to the challenge to associate GR binding sites (GBSs) to their distant gene targets. Mapping the full 3D scope of GR-responsive promoters using high-resolution 4C-seq unravelled spatial separation between chromatin interaction networks of GR-activated and repressed genes. Analysing GR binding sites and other regulatory loci in their functional 3D context revealed that GR sequesters the co-activator Ep300 from active non-GBS enhancers in both activated and repressed gene compartments. While this is sufficient for rapid gene repression, gene activation is countered by productive recruitment of Ep300 to GBS. Importantly, in GR-activated compartments Klf4 binding at non-GBS regulatory elements cluster in 3D with GBS and antagonizes GR activation. In addition, we revealed ROR and Rev-erb transcription factors as novel co-regulators for GR-mediated gene expression.
p53-induced apoptosis is specified by a translation program regulated by PCBP2 and DHX30
Authors: Rizzotto Dario , Zaccara Sara , Rossi Annalisa , Galbraith Matthew D. , Andrysik Zdenek , Pandey Ahwan , Sullivan Kelly D. , Quattrone Alessandro , Espinosa Joaquín M. , Dassi Erik , Inga Alberto
Published: September 2019

Activation of p53 by the small molecule Nutlin can result in a combination of cell cycle arrest and apoptosis. The relative strength of these events is difficult to predict by classical gene expression analysis, leaving uncertainty as to the therapeutic benefits of Nutlin. Here, we report a new translational control mechanism shaping p53-dependent apoptosis. Using polysome profiling, we establish Nutlin-induced apoptosis to be associated with the enhanced translation of mRNAs carrying multiple copies of a newly identified 3’UTR CG-rich motif mediating p53-dependent death (CGPD-motif). We identified PCBP2 and DHX30 as CGPD-motif interactors. We found that in cells undergoing persistent cell cycle arrest in response to Nutlin, CGPD-motif mRNAs are repressed by the PCBP2-dependent binding of DHX30 to the motif. Thus, upon DHX30 depletion in these cells, the translation of CGPD-motif mRNAs is increased, and the response to Nutlin shifts towards apoptosis. Instead, DHX30 inducible overexpression in SJSA1 cells, that undergo Nutlin-induced apoptosis, leads to decreased translation of CGPD-motif mRNAs. Overall, this work establishes the role of PCBP2-DHX30 in controlling the translation of CGPD-motif mRNAs and thus provide a new mechanism to modulate the induction of p53-dependent apoptosis.