bluuebunny/crossref_metadata_2025 huggingface dataset:
Stool sampling and DNA isolation kits affect DNA quality and bacterial composition following 16S rRNA gene sequencing using MiSeq Illumina platform
Authors: Videnska Petra , Smerkova Kristyna , Zwinsova Barbora , Popovici Vlad , Micenkova Lenka , Sedlar Karel , Budinska Eva
Published: September 2019

Many studies correlate changes in human gut microbiome with the onset of various diseases, mostly by 16S rRNA gene sequencing. Setting up the optimal sampling and DNA isolation procedures is crucial for robustness and reproducibility of the results. We performed a systematic comparison of several sampling and DNA isolation kits, quantified their effect on bacterial gDNA quality and the bacterial composition estimates at all taxonomic levels. Sixteen volunteers tested three sampling kits. All samples were consequently processed by two DNA isolation kits. We found that the choice of both stool sampling and DNA isolation kits have an effect on bacterial composition with respect to Gram-positivity, however the isolation kit had a stronger effect than the sampling kit. The proportion of bacteria affected by isolation and sampling kits was larger at higher taxa levels compared to lower taxa levels. The PowerLyzer PowerSoil DNA Isolation Kit outperformed the QIAamp DNA Stool Mini Kit mainly due to better lysis of Gram-positive bacteria while keeping the values of all the other assessed parameters within a reasonable range. The presented effects need to be taken into account when comparing results across multiple studies or computing ratios between Gram-positive and Gram-negative bacteria.
Prenatal Exposure to Environmentally-Relevant Contaminants Perturbs Male Reproductive Parameters Across Multiple Generations that are Partially Protected by Folic Acid Supplementation
Authors: Lessard Maryse , Herst Pauline M. , Charest Phanie L. , Navarro Pauline , Joly-Beauparlant Charles , Droit Arnaud , Kimmins Sarah , Trasler Jacquetta , Benoit-Biancamano Marie-Odile , MacFarlane Amanda J. , Dalvai Mathieu , Bailey Janice L.
Published: September 2019

The paternal environment is thought to influence sperm quality and future progeny may also be impacted. We hypothesized that prenatal exposure to environmentally-relevant contaminants impairs male reproduction, altering embryo gene expression over multiple generations. Folic acid (FA) can improve sperm quality and pregnancy outcomes, thus we further hypothesized that FA mitigates the contaminants. Sprague-Dawley F0 female rats treated with persistent organic pollutants (POPs) or corn oil and fed basal or supplemented FA diets, then used to yield four generations of litters. Only F0 females received POPs and/or FA treatments. In utero POPs exposure altered sperm parameters in F1, which were partly rescued by FA supplementation. Paternal exposure to POPs reduced sperm quality in F2 males, and the fertility of F3 males was modified by both POPs and FA. Ancestral FA supplementation improved sperm parameters of F4 males, while the POPs effect diminished. Intriguingly, F3 males had the poorest pregnancy outcomes and generated the embryos with the most significantly differentially expressed genes. Early-life exposure to POPs harms male reproduction across multiple generations. FA supplementation partly mitigated the impact of POPs. The two-cell embryo transcriptome is susceptible to paternal environment and could be the foundation for later pregnancy outcomes.
Dual-probe molecular MRI for the in vivo characterization of atherosclerosis in a mouse model: Simultaneous assessment of plaque inflammation and extracellular-matrix remodeling
Authors: Reimann Carolin , Brangsch Julia , Kaufmann Jan O. , Adams Lisa C. , Onthank David C. , Thöne-Reineke Christa , Robinson Simon P. , Hamm Bernd , Botnar Rene M. , Makowski Marcus R.
Published: September 2019

Molecular MRI is a promising in-vivo modality to detect and quantify morphological and molecular vessel-wall changes in atherosclerosis. The combination of different molecular biomarkers may improve the risk stratification of patients. This study aimed to investigate the feasibility of simultaneous visualization and quantification of plaque-burden and inflammatory activity by dual-probe molecular MRI in a mouse-model of progressive atherosclerosis and in response-to-therapy. Homozygous apolipoprotein E knockout mice (ApoE−/−) were fed a high-fat-diet (HFD) for up to four-months prior to MRI of the brachiocephalic-artery. To assess response-to-therapy, a statin was administered for the same duration. MR imaging was performed before and after administration of an elastin-specific gadolinium-based and a macrophage-specific iron-oxide-based probe. Following in-vivo MRI, samples were analyzed using histology, immunohistochemistry, inductively-coupled-mass-spectrometry and laser-inductively-coupled-mass-spectrometry. In atherosclerotic-plaques, intraplaque expression of elastic-fibers and inflammatory activity were not directly linked. While the elastin-specific probe demonstrated the highest accumulation in advanced atherosclerotic-plaques after four-months of HFD, the iron-oxide-based probe showed highest accumulation in early atherosclerotic-plaques after two-months of HFD. In-vivo measurements for the elastin and iron-oxide-probe were in good agreement with ex-vivo histopathology (Elastica-van-Giesson stain: y = 298.2 + 5.8, R2 = 0.83, p < 0.05; Perls‘ Prussian-blue-stain: y = 834.1 + 0.67, R2 = 0.88, p < 0.05). Contrast-to-noise-ratio (CNR) measurements of the elastin probe were in good agreement with ICP-MS (y = 0.11x-11.3, R² = 0.73, p < 0.05). Late stage atherosclerotic-plaques displayed the strongest increase in both CNR and gadolinium concentration (p < 0.05). The gadolinium probe did not affect the visualization of the iron-oxide-probe and vice versa. This study demonstrates the feasibility of simultaneous assessment of plaque-burden and inflammatory activity by dual-probe molecular MRI of progressive atherosclerosis. The in-vivo detection and quantification of different MR biomarkers in a single scan could be useful to improve characterization of atherosclerotic-lesions.
Association study identified biologically relevant receptor genes with synergistic functions in celiac disease
Authors: Banerjee Pratibha , Bhagavatula Sandilya , Sood Ajit , Midha Vandana , Thelma B. K. , Senapati Sabyasachi
Published: September 2019

Receptors are essential mediators of cellular physiology, which facilitate molecular and cellular cross-talk with the environment. Nearly 20% of the all known celiac disease (CD) genes are receptors by function. We hypothesized that novel biologically relevant susceptibility receptor genes act in synergy in CD pathogenesis. We attempted to identify novel receptor genes in CD by re-analyzing published Illumina Immunochip dense genotype data for a north Indian and  a European (Dutch) cohort. North Indian dataset was screened for 269 known receptor genes. Association statistics for SNPs were considered with minor allele frequency >15% and association P ≤ 0.005 to attend desired study power. Identified markers were tested for cross-ethnic replication in a European CD dataset. Markers were analyzed in-silico to explain their functional significance in CD. Six novel SNPs from MOG (rs29231, p = 1.21e-11), GABBR1 (rs3025643, p = 1.60e-7), OR2H2 (rs1233388, p = 0.0002), ABCF1 (rs9262119, p = 0.0005), ADRA1A (rs10102024, p = 0.003), and ACVR2A (rs7560426, p = 0.004) were identified in north Indians, of which three genes namely, GABBR1 (rs3025643, p = 5.38e-8), OR2H2 (rs1233388, p = 3.29e-5) and ABCF1 (rs9262119, p = 0.0002) were replicated in Dutch. Tissue specific functional annotation, potential epigenetic regulation, co-expression, protein-protein interaction and pathway enrichment analyses indicated differential expression and synergistic function of key genes that could alter cellular homeostasis, ubiquitination mediated phagosome pathway and cellular protein processing to contribute for CD. At present multiple therapeutic compounds/drugs are available targeting GABBR1 and ADRA1A, which could be tested for their effectiveness against CD in controlled drug trials.
Conservation and novelty in the microRNA genomic landscape of hyperdiverse cichlid fishes
Authors: Xiong Peiwen , Schneider Ralf F. , Hulsey C. Darrin , Meyer Axel , Franchini Paolo
Published: September 2019

MicroRNAs (miRNAs) play crucial roles in the post-transcriptional control of messenger RNA (mRNA). These miRNA-mRNA regulatory networks are present in nearly all organisms and contribute to development, phenotypic divergence, and speciation. To examine the miRNA landscape of cichlid fishes, one of the most species-rich families of vertebrates, we profiled the expression of both miRNA and mRNA in a diverse set of cichlid lineages. Among these, we found that conserved miRNAs differ from recently arisen miRNAs (i.e. lineage specific) in average expression levels, number of target sites, sequence variability, and physical clustering patterns in the genome. Furthermore, conserved miRNA target sites tend to be enriched at the 5′ end of protein-coding gene 3′ UTRs. Consistent with the presumed regulatory role of miRNAs, we detected more negative correlations between the expression of miRNA-mRNA functional pairs than in random pairings. Finally, we provide evidence that novel miRNA targets sites are enriched in genes involved in protein synthesis pathways. Our results show how conserved and evolutionarily novel miRNAs differ in their contribution to the genomic landscape and highlight their particular evolutionary roles in the adaptive diversification of cichlids.
DeNeRD: high-throughput detection of neurons for brain-wide analysis with deep learning
Authors: Iqbal Asim , Sheikh Asfandyar , Karayannis Theofanis
Published: September 2019

Mapping the structure of the mammalian brain at cellular resolution is a challenging task and one that requires capturing key anatomical features at the appropriate level of analysis. Although neuroscientific methods have managed to provide significant insights at the micro and macro level, in order to obtain a whole-brain analysis at a cellular resolution requires a meso-scopic approach. A number of methods can be currently used to detect and count cells, with, nevertheless, significant limitations when analyzing data of high complexity. To overcome some of these constraints, we introduce a fully automated Artificial Intelligence (AI)-based method for whole-brain image processing to Detect Neurons in different brain Regions during Development (DeNeRD). We demonstrate a high performance of our deep neural network in detecting neurons labeled with different genetic markers in a range of imaging planes and imaging modalities.
Gene co-expression network analysis reveals key potential gene modules in utero-vaginal junction associated with duration of fertility trait of breeder hens
Authors: Gu Lantao , Jing Ruoxi , Gong Yanzhang , Yu Mei , Elokil Abdelmotaleb , Li Shijun
Published: September 2019

The number of days (DN) when hens lay fertile eggs as well as the number of fertile eggs (FN) were produced after a single artificial insemination (AI), including the two duration of fertility (DF) traits. Indeed, they are the key production performance that associates with the production cost of hatching egg when its determination the interval between successive artificial inseminations. However, the relevant genes response for regulating the DF has not been uncovered yet. Therefore, we performed a weighted gene co-expression network analysis (WGCNA) to investigate the insight into co-expression gene modules on DF process in hens. The total mRNA was extracted from the utero-vaginal junction (UVJ, with the sperm storage function in hen’s oviduct which is the biological basis for DF) of 20 hens with several levels of DF traits, and performed transcriptome sequences of mRNA. As a result, three co-expression gene modules were identified to be highly correlated with DF traits. Moreover, the expression changes of top 5 hub genes in each module with DF traits were further confirmed in other 20 hens by RT-PCR. These findings highlighted the co-expression modules and their affiliated genes as playing important roles in the regulation of DF traits.
GRK2 promotes growth of medulloblastoma cells and protects them from chemotherapy-induced apoptosis
Authors: Pathania Anup S. , Ren Xiuhai , Mahdi Min Y. , Shackleford Gregory M. , Erdreich-Epstein Anat
Published: September 2019

G-protein coupled receptor kinase 2 (GRK2; ADRBK1, BARK1) is most known as a regulator of G-protein coupled receptors. However, GRK2 also has other functions. Medulloblastomas are the most common malignant brain cancers in children. GRK2 has not been implicated in medulloblastoma biology. Here we report that GRK2 knockdown slowed cell growth, diminished proliferation, and enhanced cisplatin- and etoposide-induced apoptosis in medulloblastoma cell lines UW228-2 and Daoy. Reciprocally, GRK2 overexpression attenuated apoptosis induced by these chemotherapy drugs. Cisplatin and etoposide increased phosphorylation of AKT (S473) and GRK2 knockdown mitigated this increase. Cisplatin and etoposide attenuated ERK phosphorylation, but GRK2 knockdown did not alter this effect. Wildtype GRK2 reversed the increase in cisplatin- and etoposide-induced apoptosis caused by GRK2 knockdown. GRK2-K220R (kinase dead) and GRK2-S670A (unphosphorylated, constitutively active) conferred protection from cisplatin that was similar to wildtype GRK2, suggesting that this protection may be mediated though a kinase-independent activity of GRK2. These data demonstrate that GRK2 contributes to proliferation and survival of these medulloblastoma cell lines and to their protection from cisplatin- and etoposide-induced apoptosis.
Percutaneous stereotactic image-guided microwave ablation for malignant liver lesions
Authors: Perrodin Stéphanie , Lachenmayer Anja , Maurer Martin , Kim-Fuchs Corina , Candinas Daniel , Banz Vanessa
Published: September 2019

Thermal ablation has proven beneficial for hepatocellular carcinoma and possibly for colorectal liver metastases, but data is lacking for other liver metastases. Computer-assisted navigation can increase ablation efficacy and broaden its indications. We present our experience with percutaneous stereotactic image-guided microwave ablation (SMWA) for non-colorectal liver metastases (NCRLM), in form of a retrospective study including all SMWA for NCRLM from 2015 to 2017. Indication for SMWA was determined at a multidisciplinary tumorboard. End-points include recurrence, overall and liver-specific disease progression and complications. Twenty-three patients underwent 25 interventions for 40 lesions, including 17 neuroendocrine tumor, nine breast cancer, four sarcoma, two non-small cell lung cancer, three duodenal adenocarcinoma, one esophageal adenocarcinoma, one pancreatic adenocarcinoma, one ampullary carcinoma, one prostate carcinoma, and one renal cell carcinoma metastases. Median follow-up was 15 months (2–32). Incomplete ablation rate was 2.5% (1/40), local recurrence rate 10% (4/40). Three patients (12%) had minor complications. Overall disease progression was 73.9% (17/23), median disease-free survival 7 months (0–26) and overall survival 18 months (2–39). SIMWA is feasible, safe and minimally invasive for NCRLM in selected patients. While it might offer an alternative to resection or palliative strategies, the oncological benefit needs to be evaluated in a larger patient cohort.
Spatial distribution of core monomers in acrylamide-based core-shell microgels with linear swelling behaviour
Authors: Cors Marian , Wrede Oliver , Wiehemeier Lars , Feoktystov Artem , Cousin Fabrice , Hellweg Thomas , Oberdisse Julian
Published: September 2019

The peculiar linear temperature-dependent swelling of core-shell microgels has been conjectured to be linked to the core-shell architecture combining materials of different transition temperatures. Here the structure of pNIPMAM-core and pNNPAM-shell microgels in water is studied as a function of temperature using small-angle neutron scattering with selective deuteration. Photon correlation spectroscopy is used to scrutinize the swelling behaviour of the colloidal particles and reveals linear swelling. Moreover, these experiments are also employed to check the influence of deuteration on swelling. Using a form-free multi-shell reverse Monte Carlo approach, the small-angle scattering data are converted into radial monomer density profiles. The comparison of ‘core-only’ particles consisting of identical cores to fully hydrogenated core-shell microgels, and finally to H-core/D-shell architectures unambiguously shows that core and shell monomers display gradient profiles with strong interpenetration, leading to cores embedded in shells which are bigger than their isolated ‘core-only’ precursor particles. This surprising result is further generalized to different core cross-linker contents, for temperature ranges encompassing both transitions. Our analysis demonstrates that the internal structure of pNIPMAM-core and pNNPAM-shell microgels is heterogeneous and strongly interpenetrated, presumably allowing only progressive core swelling at temperatures intermediate to both transition temperatures, thus promoting linear swelling behaviour.
Establishment of an Experimental Intracerebral Haemorrhage Model for Mass Effect Research using a Thermo-sensitive Hydrogel
Authors: Gong Yuhua , Gong Yuping , Hou Zongkun , Guo Tingwang , Deng Jia , Hao Shilei , Wang Bochu
Published: September 2019

The mechanical response of brain tissue closely relates to cerebral blood flow and brain diseases. During intracerebral haemorrhage (ICH), a mass effect occurs during the initial bleeding and results in significant tissue deformation. However, fewer studies have focused on the brain damage mechanisms and treatment approaches associated with mass effects compared to the secondary brain injuries after ICH, which may be a result of the absence of acceptable animal models mimicking a mass effect. Thus, a thermo-sensitive poly (N-isopropylacrylamide) (PNIPAM) hydrogel was synthesized and injected into the rat brain to establish an ICH model for mass effect research. The PNIPAM hydrogel or autologous blood was injected to establish an ICH animal model, and the space-occupying volumes, brain tissue elasticity, brain oedema, neuronal cell death, iron deposition and behavioural recovery were evaluated. The lower critical solution temperature of PNIPAM hydrogel was 32 °C, and the PNIPAM hydrogel had a rough surface with similar topography and pore structure to a blood clot. Furthermore, the ICH model animals who received an injection of PNIPAM and blood produced similar lesion volumes, elasticity changes and mechanically activated ion channel piezo-2 upregulation in brain tissue. Meanwhile, slight iron deposition, neuronal cell death and brain oedema were observed in the PNIPAM hydrogel model compared to the blood model. In addition, the PNIPAM hydrogel showed good biocompatibility and stability in vivo via subcutaneous implantation. Our findings show that PNIPAM hydrogel cerebral infusion can form a mass effect similar to haematoma and minimize the interference of blood, and the establishment of a mass effect ICH model is beneficial for understanding the mechanism of primary brain injury and the role of mass effects in secondary brain damage after ICH.
Comparison of the microbial composition of African fermented foods using amplicon sequencing
Authors: Diaz Maria , Kellingray Lee , Akinyemi Nwanneka , Adefiranye Oyetayo Olaoluwa , Olaonipekun Arinola B. , Bayili Geoffroy Romaric , Ibezim Jekwu , du Plessis Adriana Salomina , Houngbédji Marcel , Kamya Deus , Mukisa Ivan Muzira , Mulaw Guesh , Manthi Josiah Samuel , Onyango Chienjo William , Atter Amy , Agbemafle Evans , Annan Theophilus , Bernice Ackah Nina , Buys Elna M. , Joseph Hounhouigan D. , Muyanja Charles , Nakavuma Jesca , Odeny Damaris Achieng , Sawadogo-Lingani Hagretou , Tesfaye Tefera Anteneh , Amoa-Awua Wisdom , Obodai Mary , Mayer Melinda J. , Oguntoyinbo Folarin A. , Narbad Arjan
Published: September 2019

Fermented foods play a major role in the diet of people in Africa, where a wide variety of raw materials are fermented. Understanding the microbial populations of these products would help in the design of specific starter cultures to produce standardized and safer foods. In this study, the bacterial diversity of African fermented foods produced from several raw materials (cereals, milk, cassava, honey, palm sap, and locust beans) under different conditions (household, small commercial producers or laboratory) in 8 African countries was analysed by 16S rRNA gene amplicon sequencing during the Workshop “Analysis of the Microbiomes of Naturally Fermented Foods Training Course”. Results show that lactobacilli were less abundant in fermentations performed under laboratory conditions compared to artisanal or commercial fermentations. Excluding the samples produced under laboratory conditions, lactobacilli is one of the dominant groups in all the remaining samples. Genera within the order Lactobacillales dominated dairy, cereal and cassava fermentations. Genera within the order Lactobacillales, and genera Zymomonas and Bacillus were predominant in alcoholic beverages, whereas Bacillus and Lactobacillus were the dominant genera in the locust bean sample. The genus Zymomonas was reported for the first time in dairy, cereal, cassava and locust bean fermentations.
Transcriptional regulator ArcA mediates expression of oligopeptide transport systems both directly and indirectly in Shewanella oneidensis
Authors: Liang Huihui , Mao Yinting , Sun Yijuan , Gao Haichun
Published: September 2019

In γ-proteobacterial species, such asEscherichia coli, the Arc (anoxic redox control) two-component system plays a major role in mediating the metabolic transition from aerobiosis to anaerobiosis, and thus is crucial for anaerobic growth but dispensable for aerobic growth. InShewanella oneidensis, a bacterium renowned for respiratory versatility, Arc (SoArc) primarily affects aerobic growth. To date, how this occurs has remained largely unknown although the growth defect resulting from the loss of DNA-binding response regulatorSoArcA is tryptone-dependent. In this study, we demonstrated that the growth defect is in part linked to utilization of oligopeptides and di-tripeptides, and peptide uptake but not peptide degradation is significantly affected by theSoArcA loss. A systematic characterization of major small peptide uptake systems manifests that ABC peptide transporter Sap and four proton-dependent oligopeptide transporters (POTs) are responsible for transport of oligopeptides and di-tripeptides respectively. Among them, Sap and DtpA (one of POTs) are responsive to theSoarcAmutation but onlydtpAis under the direct control ofSoArcA. We further showed that both Sap and DtpA, when overproduced, improve growth of theSoarcAmutant. While the data firmly establish a link between transport of oligopeptides and di-tripeptides and theSoarcAmutation, other yet-unidentified factors are implicated in the growth defect resulting from theSoArcA loss.
The characteristics of drug information inquiries in an Ethiopian university hospital: A two-year observational study
Authors: Tefera Yonas Getaye , Gebresillassie Begashaw Melaku , Ayele Asnakew Achaw , Belay Yared Belete , Emiru Yohannes Kelifa
Published: September 2019

The types of drug-related information request from patients and health professionals, the extent of inquiry and capability of existing drug information centers are seldom studied in Ethiopia. This study aimed to identify the types and potential areas of drug information inquiry at the Drug Information Center (DIC) of Gondar University specialized Hospital (GUSH), Ethiopia. An observational study was employed. The drug information query was collected by distributing the drug information queries in different hospital units through two batches of graduating undergraduate pharmacy students. Descriptive statistics used to describe, characterize and classify drug related queries. Binary logistic regression test was employed to identify predictor variables to type of drug information query. A total of 781 drug related queries were collected and 697 were included in the final analysis. Near to half (45.3%) of queries comes from the pharmacists followed by general practitioners (11.3%) and nurses (10.2%). Slightly greater than half of the queries (51.9%) were focused on therapeutic information. 39.6% of drug related queries related to infectious disease case scenarios, followed by cardiovascular cases in 21.3% of queries. More than half of (53.9%) and nearly one in five (19.4%) of the queries took 5 to 30 minutes and 30 minutes to 1 hour of literature searching to answer, respectively. Pharmacists (with odds ratio of 2.474(95% CI (1.373-4.458)) and patients (with odds ratio of 4.121(1.403–12.105)) ask patient-specific questions in their drug related queries higher than other group of health professionals. Pharmacists are the primary drug information users and frequent drug related information inquirers at the DIC. Most of the queries targeted therapeutic indications, adverse drug events, infectious or cardiovascular disease related requests. This is imperative that drug information services can assist the growing role of pharmacists in addressing the patient specific drug related needs.
MicroRNA-27a/b-3p and PPARG regulate SCAMP3 through a feed- forward loop during adipogenesis
Authors: Kulyté Agné , Kwok Kelvin Ho Man , de Hoon Michiel , Carninci Piero , Hayashizaki Yoshihide , Arner Peter , Arner Erik
Published: September 2019

MicroRNAs (miRNA) modulate gene expression through feed-back and forward loops. Previous studies identified miRNAs that regulate transcription factors, including Peroxisome Proliferator Activated Receptor Gamma (PPARG), in adipocytes, but whether they influence adipogenesis via such regulatory loops remain elusive. Here we predicted and validated a novel feed-forward loop regulating adipogenesis and involved miR-27a/b-3p, PPARG and Secretory Carrier Membrane Protein 3 (SCAMP3). In this loop, expression of both PPARG and SCAMP3 was independently suppressed by miR-27a/b-3p overexpression. Knockdown of PPARG downregulated SCAMP3 expression at the late phase of adipogenesis, whereas reduction of SCAMP3 mRNA levels increased PPARG expression at early phase in differentiation. The latter was accompanied with upregulation of adipocyte-enriched genes, including ADIPOQ and FABP4, suggesting an anti-adipogenic role for SCAMP3. PPARG and SCAMP3 exhibited opposite behaviors regarding correlations with clinical phenotypes, including body mass index, body fat mass, adipocyte size, lipolytic and lipogenic capacity, and secretion of pro-inflammatory cytokines. While adipose PPARG expression was associated with more favorable metabolic phenotypes, SCAMP3 expression was linked to increased fat mass and insulin resistance. Together, we identified a feed-forward loop through which miR-27a/b-3p, PPARG and SCAMP3 cooperatively fine tune the regulation of adipogenesis, which potentially may impact whole body metabolism.
Microbiome-Transcriptome Interactions Related to Severity of Respiratory Syncytial Virus Infection
Authors: Sonawane Abhijeet R. , Tian Liang , Chu Chin-Yi , Qiu Xing , Wang Lu , Holden-Wiltse Jeanne , Grier Alex , Gill Steven R. , Caserta Mary T. , Falsey Ann R. , Topham David J. , Walsh Edward E. , Mariani Thomas J. , Weiss Scott T. , Silverman Edwin K. , Glass Kimberly , Liu Yang-Yu
Published: September 2019

Respiratory syncytial virus (RSV) is a major cause of lower respiratory tract infections and hospital visits during infancy and childhood. Although risk factors for RSV infection have been identified, the role of microbial species in the respiratory tract is only partially known. We aimed to understand the impact of interactions between the nasal microbiome and host transcriptome on the severity and clinical outcomes of RSV infection. We used 16 S rRNA sequencing to characterize the nasal microbiome of infants with RSV infection. We used RNA sequencing to interrogate the transcriptome of CD4+ T cells obtained from the same set of infants. After dimension reduction through principal component (PC) analysis, we performed an integrative analysis to identify significant co-variation between microbial clade and gene expression PCs. We then employed LIONESS (Linear Interpolation to Obtain Network Estimates for Single Samples) to estimate the clade-gene association patterns for each infant. Our network-based integrative analysis identified several clade-gene associations significantly related to the severity of RSV infection. The microbial taxa with the highest loadings in the implicated clade PCs included Moraxella, Corynebacterium, Streptococcus, Haemophilus influenzae, and Staphylococcus. Interestingly, many of the genes with the highest loadings in the implicated gene PCs are encoded in mitochondrial DNA, while others are involved in the host immune response. This study on microbiome-transcriptome interactions provides insights into how the host immune system mounts a response against RSV and specific infectious agents in nasal microbiota.
Multifaceted Changes in Synaptic Composition and Astrocytic Involvement in a Mouse Model of Fragile X Syndrome
Authors: Simhal Anish K. , Zuo Yi , Perez Marc M. , Madison Daniel V. , Sapiro Guillermo , Micheva Kristina D.
Published: September 2019

Fragile X Syndrome (FXS), a common inheritable form of intellectual disability, is known to alter neocortical circuits. However, its impact on the diverse synapse types comprising these circuits, or on the involvement of astrocytes, is not well known. We used immunofluorescent array tomography to quantify different synaptic populations and their association with astrocytes in layers 1 through 4 of the adult somatosensory cortex of a FXS mouse model, the FMR1 knockout mouse. The collected multi-channel data contained approximately 1.6 million synapses which were analyzed using a probabilistic synapse detector. Our study reveals complex, synapse-type and layer specific changes in the neocortical circuitry of FMR1 knockout mice. We report an increase of small glutamatergic VGluT1 synapses in layer 4 accompanied by a decrease in large VGluT1 synapses in layers 1 and 4. VGluT2 synapses show a rather consistent decrease in density in layers 1 and 2/3. In all layers, we observe the loss of large inhibitory synapses. Lastly, astrocytic association of excitatory synapses decreases. The ability to dissect the circuit deficits by synapse type and astrocytic involvement will be crucial for understanding how these changes affect circuit function, and ultimately defining targets for therapeutic intervention.
Circulating exosomes may identify biomarkers for cows at risk for metabolic dysfunction
Authors: Almughlliq Fatema B. , Koh Yong Q. , Peiris Hassendrini N. , Vaswani Kanchan , Holland Olivia , Meier Susanne , Roche John R. , Burke Chris R. , Crookenden Mallory A. , Arachchige Buddhika J. , Reed Sarah , Mitchell Murray D.
Published: September 2019

Disease susceptibility of dairy cows is greatest during the transition from pregnancy to lactation. Circulating exosomes may provide biomarkers to detect at-risk cows to enhance health and productivity. From 490 cows, animals at high- (n = 20) or low-risk (n = 20) of transition-related diseases were identified using plasma non-esterified fatty acid and β-hydroxybutyrate concentrations and liver triacylglyceride concentrations during the two weeks post-calving. We isolated circulating exosomes from plasma of dairy cows at low-risk (LR-EXO) and high-risk (HR-EXO), and analyzed their proteome profiles to determine markers for metabolic dysfunction. We evaluated the effects of these exosomes on eicosanoid pathway expression by bovine endometrial stromal (bCSC) and epithelial (bEEL) cells. HR-EXO had significantly lower yield of circulating exosomes compared with LR-EXO, and unique proteins were identified in HR-EXO and LR-EXO. Exposure to LR-EXO or HR-EXO differentially regulated eicosanoid gene expression and production in bCSC and bEEL cells. In bCSC, LR-EXO exposure increased PGE2 and PGD2 production, whereas HR-EXO exposure increased PTGS2 gene expression. In bEEL, HR-EXO exposure caused a decrease in PGE2, PGF2α, PGD2, PGFM and TXB2 production. The unique presence of serpin A3-7, coiled-coil domain containing 88A and inhibin/activin β A chain in HR-EXO, indicates potential biomarkers for cows at-risk for metabolic diseases. Our results are in line with the health status of the cow indicating a potential diagnostic role for exosomes in enhancing cows’ health and fertility.
Analysis of the circadian transcriptome of the Antarctic krill Euphausia superba
Authors: Biscontin Alberto , Martini Paolo , Costa Rodolfo , Kramer Achim , Meyer Bettina , Kawaguchi So , Teschke Mathias , De Pittà Cristiano
Published: September 2019

Antarctic krill (Euphausia superba) is a high latitude pelagic organism which plays a central role in the Southern Ocean ecosystem. E. superba shows daily and seasonal rhythms in physiology and behaviour, which are synchronized with the environmental cycles of its habitat. Recently, the main components of the krill circadian machinery have been identified and characterized. However, the exact mechanisms through which the endogenous timing system operates the control and regulation of the overt rhythms remains only partially understood. Here we investigate the involvement of the circadian clock in the temporal orchestration of gene expression by using a newly developed version of a krill microarray platform. The analysis of transcriptome data from krill exposed to both light-dark cycles (LD 18:6) and constant darkness (DD), has led to the identification of 1,564 putative clock-controlled genes. A remarkably large proportion of such genes, including several clock components (clock, period, cry2, vrille, and slimb), show oscillatory expression patterns in DD, with a periodicity shorter than 24 hours. Energy-storage pathways appear to be regulated by the endogenous clock in accordance with their ecological relevance in daily energy managing and overwintering. Our results provide the first representation of the krill circadian transcriptome under laboratory, free-running conditions.
A rabbit model for assessing symblepharon after alkali burn of the superior conjunctival sac
Authors: Kang Yanwei , Li Shaowei , Liu Chang , Liu Mintian , Shi Shuai , Xu Man , He Jingliang , Zhang Tao
Published: September 2019

Symblepharon due to chemical burns affects ocular surface health, and there are currently no satisfactory treatments. To improve our understanding of symblepharon, an appropriate animal model is urgently needed. We established a rabbit model of superior conjunctival sac alkaline burn to evaluate symblepharon severity. Alkali burns were induced in rabbits by contacting the superior conjunctival sac with 2 N NaOH-soaked semicircle filter paper (10 mm diameter) for 60 s, 90 s or 120 s. Clinical and histological features were examined, symblepharon severity was evaluated via conjunctival sac depth (grade I - IV) and volume measurements (grade a-d) post-injury at 4 weeks. With increasing alkali burn duration, corneal perforation and symblepharon severity increased. The 60 s group manifested a sub-conjunctiva scar. The 90 s group featured localized adhesion. The 120 s group was characterized by extensive scar hyperplasia and adhesion. The rabbit model exhibited stable and reliable symblepharon following an alkali burn of the superior conjunctival sac. For further research, 90 s is a suitable duration for conjunctival sac burn. The volume measured using conjunctival sac casting was considered when developing a successful evaluation system for symblepharon severity.
Prolonged exposure to simulated microgravity diminishes dendritic cell immunogenicity
Authors: Tackett Nichole , Bradley Jillian H. , Moore Emily K. , Baker Stefanie H. , Minter Stephanie L. , DiGiacinto Brian , Arnold Jennifer P. , Gregg Randal K.
Published: September 2019

Immune dysfunction due to microgravity remains a hurdle in the next step of human space exploration. Dendritic cells (DC) represent a critical component of immunity, given their role in the detection of invaders and the subsequent task of activating T cells to respond and eliminate the threat. Upon encounter with microbes, DC undergo a process of maturation, whereby the cells upregulate the expression of surface proteins and secrete cytokines, both required for the optimal activation of CD4+ and CD8+ T cells. In this study, DC were cultured from 2–14 days in a rotary cell culture system, which generates a simulated microgravity (SMG) environment, and then the cells were assessed for maturation status and the capacity to activate T cells. Short-term culture (<72 h) of DC in SMG resulted in an increased expression of surface proteins associated with maturation and interleukin-6 production. Subsequently, the SMG exposed DC were superior to Static control DC at activating both CD4+ and CD8+ T cells as measured by interleukin-2 and interferon-γ production, respectively. However, long-term culture (4–14 d) of DC in SMG reduced the expression of maturation markers and the capacity to activate T cells as compared to Static DC controls.
Inhibition of the right dlPFC by theta burst stimulation does not alter sustainable decision-making
Authors: Langenbach Benedikt P. , Baumgartner Thomas , Cazzoli Dario , Müri René M. , Knoch Daria
Published: September 2019

Intergenerational sustainability is probably humankind’s most pressing challenge, exacerbated by the fact that the present generation has to incur costs in order to benefit future generations. However, people often fail to restrict their consumption, despite reporting strong pro-environmental attitudes. Recent theorising sees self-control processes as key component of sustainable decision-making and correlational studies support this view, yet causal evidence is lacking. Using TMS, we here disrupted an area known to be involved in self-control processes, the right dorsolateral prefrontal cortex (dlPFC), to provide causal evidence as to whether diminished self-control leads to less intergenerational sustainability. Participants then engaged in a behavioural economic paradigm to measure sustainable decision-making towards the next generation. This adequately powered study could not find an effect of inhibiting the right dlPFC on intergenerational sustainability. This result holds when controlling for a number of relevant covariates like gender, trait self-control, pro-environmental attitudes, or cortical thickness at the stimulation site. We seek to explain this result methodologically and theoretically, and speculate about other brain areas that could be more strongly related to intergenerational sustainability, e.g. the mentalising network.
Soil nitrogen dynamics during an oilseed rape (Brassica napus L.) growing cycle in a humid Mediterranean climate
Authors: Villar N. , Aranguren M. , Castellón A. , Besga G. , Aizpurua A.
Published: September 2019

Nitrogen budgets help explain the supply pattern of N from the soil to the crop. Through budgeting, an improvement of the N fertilization strategy can be achieved. The objective of the present study, which was carried out under humid Mediterranean climate conditions, was to assess the influence of N fertilization, temperature and soil humidity on soil N dynamics during a whole oilseed rape growing cycle. A field experiment was conducted with two treatments: without N (0 N) and with application of 180 kg N ha−1(180 N). Mineralization was calculated from N balances made throughout the growing cycle, all while taking into account measured N uptake by oilseed rape and N losses by leaching and N2O emissions. Nitrogen net mineralization was negative after fertilization, reaching –6.73 kg N ha−1, day−1, but total net mineralization over the year was similar for the 0 N and 180 N treatments (21 and 8 kg N ha−1, respectively). Temperatures over 5 °C were sufficient for initiating the mineralization processes. In the summer, when the soil water content was below the wilting point, immobilization took place; however, there is a risk of N leaching if rainfall occurs thereafter, mainly in the 180 N treatment.
Plasmon-coupled Charge Transfer in FSZA Core-shell Microspheres with High SERS Activity and Pesticide Detection
Authors: Han Donglai , Yao Jiacheng , Quan Yingnan , Gao Ming , Yang Jinghai
Published: September 2019

A commercial SERS substrate does not only require strong enhancement, but also can be reused and recycled in actual application. Herein, Fe3O4/SiO2/ZnO/Ag (FSZA) have been synthesised, which consisted of Fe3O4 core with strong magnetic field response and an intermediate SiO2 layer as an electronic barrier to keep the stability of magnetite particles and outer ZnO and Ag as the effective layers for detecting pollutants. The SERS enhancement factor (EF) of the FSZA was ~8.2 × 105. The enhancement mechanism of the FSZA core-shell microspheres were anatomized. The electromagnetic enhancement of surface deposited Ag, charge transfer, and molecular and exciton resonances act together to cause such high enhancement factors. For practical application, the FSZA core-shell microspheres were also used to detect thiram, moreover, which was collected and separated by an external magnetic field, and maintained the SERS activity without significant decline during multiple tests. So the good enhancement performance and magnetic recyclability make the FSZA core-shell microspheres a promising candidates for practical SERS detection applications.
ELTD1 facilitates glioma proliferation, migration and invasion by activating JAK/STAT3/HIF-1α signaling axis
Authors: Li Junjun , Shen Jianying , Wang Zhen , Xu Hao , Wang Qiangping , Chai Songshan , Fu Peng , Huang Tao , Anas Omarkhalil , Zhao Hongyang , Li Jinsong , Xiong Nanxiang
Published: September 2019

The upregulation of ELTD1 ([epidermal growth factor (EGF), latrophilin and seven transmembrane domain-containing 1] on chromosome 1) in tumor cells has been reported in several types of cancer and correlates with poor cancer prognosis. However, the role of ELTD1 in glioma progression remains unknown. In this study, we examined ELTD1 expression levels in human glioma cell lines and in sixteen human gliomas of different grades. The molecular effects of ELTD1 in glioma cells were measured using quantitative polymerase chain reaction (qRT-PCR), Western blotting, Cell proliferation assays, Matrigel migration and invasion assays and brain orthotopic xenografts. We found that high expression levels of ELTD1 were positively associated with cancer progression and poor prognosis in human glioma. Mechanistically, ELTD1 activated the JAK/STAT3/HIF-1α signaling axis and p-STAT3 bound with HIF-1α. Taken together, our data provide a plausible mechanism for ELTD1-modulated glioma progression and suggest that ELTD1 may represent a potential therapeutic target in the prevention and therapy of glioma.
Direct conversion of fibroblasts into urothelial cells that may be recruited to regenerating mucosa of injured urinary bladder
Authors: Inoue Yuta , Kishida Tsunao , Kotani Shin-ichiro , Akiyoshi Mika , Taga Hideto , Seki Makoto , Ukimura Osamu , Mazda Osam
Published: September 2019

Urothelial cells play essential roles in protection of urine exudation and bacterial invasion at the urothelial mucosa, so that defect or damage of urothelial cells associated with urinary tract diseases may cause serious problems. If a sufficient number of functional urothelial cells are prepared in culture and transplanted into the damaged urothelial lesions, such technology may provide beneficial effects to patients with diseases of the urinary tract. Here we found that human adult dermal fibroblasts were converted into urothelial cells by transducing genes for four transcription factors, FOXA1, TP63, MYCL and KLF4 (FTLK). The directly converted urothelial cells (dUCs) formed cobblestone-like colonies and expressed urothelium-specific markers. dUCs were successfully expanded and enriched after serial passages using a specific medium that we optimized for the cells. The passaged dUCs showed similar genome-wide gene expression profiles to normal urothelial cells and had a barrier function. The FTLK-transduced fibroblasts were also converted into urothelial cells in vivo and recruited to the regenerating urothelial tissue after they were transplanted into the bladder of mice with interstitial cystitis. Our technology may provide a promising solution for a number of patients with urinary tract disorders.
Relationship between preoperative high intraocular pressure and retinal nerve fibre layer thinning after glaucoma surgery
Authors: Kim Woo-Jin , Kim Kyoung Nam , Sung Jae Yun , Kim Jung Yeul , Kim Chang-sik
Published: September 2019

Recent reports show varying results regarding peripapillary retinal nerve fibre layer (RNFL) thickness after intraocular pressure (IOP)-lowering glaucoma surgery. We hypothesised that different levels of the preoperative IOP influence RNFL thickness. A total of 60 patients (60 eyes) with glaucoma, who underwent glaucoma surgery and had a stable postoperative mean IOP < 22 mmHg, were enrolled. The RNFL thickness was measured using spectral domain optical coherence tomography, before and at 3–6 months after surgery. The preoperative peak IOP, 37.4 ± 10.8 mmHg, decreased to a postoperative mean IOP of 14.8 ± 3.5 mmHg (p < 0.001). The average RNFL thickness was significantly reduced from 75.6 ± 17.7 μm to 70.2 ± 15.8 μm (p < 0.001). In subgroup analyses, only patients with a preoperative peak IOP ≥ median value (37 mmHg) exhibited significant RNFL thinning (9.7 ± 6.6 μm, p < 0.001) associated with a higher preoperative peak IOP (r = 0.475, p = 0.008). The RNFL thinning was evident for a few months after glaucoma surgery in patients with a higher preoperative peak IOP, although the postoperative IOP was stable.
Concomitant screening of coronary artery disease and lung cancer with a new ultrafast-low-dose Computed Tomography protocol: A pilot randomised trial
Authors: Gaudio Carlo , Tanzilli Alessandra , Mei Mariachiara , Moretti Andrea , Barillà Francesco , Varveri Antonio , Paravati Vincenzo , Tanzilli Gaetano , Ciccaglioni Antonio , Strano Stefano , Pellegrini Massimo , Barillari Paolo , Pelliccia Francesco
Published: September 2019

We performed a pilot randomised study to assess the feasibility and radiation exposure of a new computed tomography (CT) protocol that allows screening of both coronary artery disease (CAD) and lung cancer. Current or former heavy smokers at high lung cancer risk with indication to cardiac CT for suspected or known CAD were randomised to undergo concomitant CT evaluation of either cardiac or thoracic area or cardiac CT only. Out of 129 subjects deemed eligible for the study, 110 agreed to participate and were randomised to simultaneous cardiac and lung CT (Gr.A; n = 55) or cardiac CT only (Gr.B; n = 55). The feasibility (i.e. adequate visualization of coronary artery segments) was noninferior with simultaneous cardiac and lung CT compared with the standard cardiac CT (870 of 889 segments [97%] in Gr.A vs 878/890 segments [99%] in Gr.B; mean difference 2.0% [90% confidence interval: −0.3% to 4.1%]). The safety (i.e. effective radiation dose) of the concomitant cardiac and lung CT protocol was noninferior to the standard cardiac CT (1.5 [95% confidence intervals: 1.2–1.7] vs. 1.4 [95% confidence intervals: 1.1–1.6] mSv; mean difference 0.1 mSv [90% confidence interval: −0.2 to 0.3 mSv]). In the two groups, a total of 25 significant (>70%) coronary stenoses were found at cardiac CT (9/55 cases of Gr.A vs 11/55 cases of Gr.B). Pulmonary nodules >2 mm were detected in 7 of the 55 Gr.A subjects. This pilot randomised study shows that concomitant CAD and lung cancer screening by means of a new CT protocol is both feasible and safe, thus allowing a comprehensive evaluation of both cardiac and thoracic regions during one CT scanning only. (ClinicalTrials.gov Identifier: NCT03727958).