bluuebunny/crossref_metadata_2025_split huggingface dataset:
Depolymerized lamins link nuclear envelope breakdown to mitotic transcriptional quiescence
Authors: Ikegami Kohta , Secchia Stefano , Lieb Jason D. , Moskowitz Ivan P. 
Published: May 2018

ABSTRACTThe nuclear envelope, a defining feature of eukaryotic cells, restricts DNA-dependent processes including gene transcription to the nucleus. The nuclear lamina is an integral component of the animal nuclear envelope, composed of polymers of nuclear lamin proteins1,2. Upon mitosis, the nuclear lamina disassembles, the nuclear envelope breaks down, and transcription becomes quiescent3,4. We report here a direct molecular link between nuclear lamina disassembly and mitotic transcriptional quiescence. We found that, at the G2 cell-cycle phase immediately preceding mitosis, nuclear lamin A/C (LMNA) became phosphorylated at Ser22 and depolymerized from the nuclear lamina. Depolymerized LMNA accumulated in the nuclear interior and physically associated with active cis-regulatory elements genome-wide. Depolymerized LMNA-associated sites were overrepresented near genes repressed by LMNA, suggesting that depolymerized LMNA participates in transcriptional repression at G2. Consistently, depolymerized LMNA-target genes underwent a steep expression decline from S to G2/M. Furthermore, LMNA deletion caused inappropriate RNA Polymerase II (Pol II) accumulation downstream of Pol II pause sites at promoters and enhancers genome-wide, leading to inappropriate and excessive transcriptional elongation. A subset of depolymerized LMNA-target genes were upregulated in fibroblasts of patients with Hutchinson-Gilford progeria, a premature aging disorder caused by LMNA mutations5, raising the possibility that defects in depolymerized LMNA-mediated mitotic transcriptional quiescence contribute to progeria pathogenesis. These observations support a model in which depolymerized LMNA targets active regulatory elements to promote RNA Pol II pausing preceding mitosis, coupling nuclear envelope breakdown to mitotic transcriptional quiescence.
Microbial Community Structure and Diversity of Shrimp Paste at Different Fermentation Stages
Authors: Dai Lingying , Wang Limei , Sun Jiang , Zheng Lixue , Qi Bin 
Published: May 2018

AbstractHigh-throughput sequencing was used to reveal the highly diverse bacterial populations in shrimp paste at different fermentation stages. We studied three stages of fermentation and obtained 448,916 reads. Using this approach, we revealed the presence of 30 phyla, 55 classes, 86 orders, 206 families and 695 genera of bacteria in the shrimp paste. Shrimp paste in fermentation metaphase had a more diverse microbiota than that in fermentation prophase and fermentation anaphase. Diversity appeared greatest in fermentation anaphase. The four dominant phyla were Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. The most common genera were Psychrobacter, Halomonas, Bacillus, Alteribacillus, and Lactococcus. Their content varied at different stages of fermentation. All the microbiome presented a variety of changes in the microbial diversity of shrimp paste.ImportanceMost research on the microbial diversity of shrimp paste has focused on the shrimp culture environment, or the chemical composition and sensory attributes of the paste. Little research has been conducted on the microbial diversity and composition of shrimp paste. The relationship between microbes and the flavor and quality of shrimp paste has thus been unknown. We therefore analyzed the microbial composition and variation of shrimp paste at different stages of fermentation. The dominant bacteria in fermentation prophase, metaphase, and anaphase were identified. Our preliminary findings give some insight into which microbes contribute to the flavor of shrimp paste and suggest how to improve its flavor. In addition, our findings are relevant to optimizing the production of shrimp paste and guaranteeing its quality and safety.
The Metabolic Capability and Phylogenetic Diversity of Mono Lake During a Bloom of the Eukaryotic Phototroph Picocystis strain ML
Authors: Stamps Blake W. , Nunn Heather S. , Petryshyn Victoria A. , Oremland Ronald S. , Miller Laurence G. , Rosen Michael R. , Bauer Kohen W. , Thompson Katharine J. , Tookmanian Elise M. , Waldeck Anna R. , Lloyd Sean J. , Johnson Hope A. , Stevenson Bradley S. , Berelson William M. , Corsetti Frank A. , Spear John R. 
Published: May 2018

ABSTRACTAlgal blooms in lakes are often associated with anthropogenic eutrophication; however, they can occur naturally. In Spring of 2016 Mono Lake, a hyperalkaline lake in California, was near the height of a rare bloom of the algae Picocystis strain ML and at the apex of a multi-year long drought. These conditions presented a unique sampling opportunity to investigate microbiological dynamics during an intense natural bloom. We conducted a comprehensive molecular analysis along a depth transect near the center of the lake from surface to 25 m depth during June 2016. Across sampled depths, rRNA gene sequencing revealed that Picocystis associated chloroplast were found at 40-50 % relative abundance, greater than values recorded previously. Despite the presence of the photosynthetic oxygenic algal genus Picocystis, oxygen declined below detectible limits below 15 m depth, corresponding with an increase in microorganisms known to be anaerobic. In contrast to previously sampled years, metagenomic and metatranscriptomic data suggested a loss of sulfate reducing microorganisms throughout the lake’s water column. Gene transcripts associated with Photosystem I and II were expressed at both 2 m and 25 m, suggesting that limited oxygen production may occur at extremely low light levels at depth within the lake. Oxygenic photosynthesis under low light conditions, in the absence of potential grazing by the brine shrimp Artemia, may allow for a cryptic redox cycle to occur in an otherwise anoxic setting at depth in the lake with the following effects: enhanced productivity, reduced grazing pressure on Picocystis, and an exacerbation of bloom.IMPORTANCEMono Lake, California provides habitat to a unique ecological community that is heavily stressed due to recent human water diversions and a period of extended drought. To date, no baseline information exists about Mono Lake to understand how the microbial community responds to drought, bloom, and what genetic functions are lost in the water column. While previously identified anaerobic members of the microbial community disappear from the water column during drought and bloom, sediment samples suggest these microorganisms seek refuge at lake bottom or in the subsurface. Thus, the sediments may represent a type of seed bank which could restore the microbial community as a bloom subsides. Our work also sheds light on the activity of the halotolerant algae Picocystis strain ML during a bloom at Mono Lake, its ability to potentially produce oxygen via photosynthesis even under extreme low-light conditions, and how the remainder of the microbial community responds.
In vitro characterization of multidrug-resistant influenza A(H1N1)pdm09 viruses carrying a dual amino acid substitution associated with reduced susceptibility to neuraminidase inhibitors
Authors: Takashita Emi , Fujisaki Seiichiro , Yokoyama Masaru , Shirakura Masayuki , Nakamura Kazuya , Kuwahara Tomoko , Kishida Noriko , Sato Hironori , Doi Ikuko , Sato Yuji , Takao Shinichi , Shimazu Yukie , Shimomura Takeshi , Ito Takuo , Watanabe Shinji , Odagiri Takato ,   The Influenza Virus Surveillance Group of Japan
Published: May 2018

AbstractWe detected influenza A(H1N1)pdm09 viruses carrying dual H275Y/I223R, H275Y/I223K, or H275Y/G147R substitutions in their neuraminidase protein, respectively. These viruses showed cross-resistance to oseltamivir and peramivir and reduced susceptibility to zanamivir. The H275Y/G147R virus retained its replication capability at least in vitro, but the H275Y/I223R and H275Y/I223K viruses did not.
Characterization of influenza B virus variants with reduced neuraminidase inhibitor susceptibility
Authors: Farrukee R , Zarebski AE , McCaw JM , Bloom JD , Reading PC , Hurt AC 
Published: May 2018

AbstractTreatment options for influenza B virus infections are limited to neuraminidase inhibitors (NAIs) which block the neuraminidase (NA) glycoprotein on the virion surface. The development of NAI resistance would therefore result in a loss of antiviral treatment options for influenza B infections. This study characterized two contemporary influenza B viruses with known resistance-conferring NA amino acid substitutions, D197N and H273Y, detected during routine surveillance. The D197N and H273Y variants were characterizedin vitroby assessing NA enzyme activity and affinity, as well as replication in cell culture compared to NAI-sensitive wild-type viruses.In vivostudies were also performed in ferrets to assess the replication and transmissibility of each variant. Mathematical models were used to analyse within-host and between-host fitness of variants relative to wild-type viruses. The data revealed that the H273Y variant had similar NA enzyme function relative to its wild-type but had slightly reduced replication and transmission efficiencyin vivo. The D197N variant had impaired NA enzyme function but there was no evidence of reduction in replication or transmission efficiency in ferrets. Our data suggest that the influenza B variant with H273Y NA substitution had a more notable reduction in fitness compared to wild-type viruses than the influenza B variant with the D197N NA substitution. Although a D197N variant is yet to become widespread, it is the most commonly detected NAI-resistant influenza B virus in surveillance studies. Our results highlight the need to carefully monitor circulating viruses for the spread of influenza B viruses with the D197N NA substitution.
Transdermal, but not oral mucosa exposure, causes sublethal leptospirosis in mice
Authors: Nair Nisha , Gomes-Solecki Maria 
Published: May 2018

ABSTRACTThe goal of this study was to determine the timing ofLeptospiradissemination after infection using natural physiologic routes and its correlation with signs and symptoms of leptospirosis. Groups of C3H-HeJ mice were sub-lethally infected through exposure of a dermis wound and the oral mucosa toL. interrogansserovar Copenhageni, and compared to mice infected via standard laboratory practice of intraperitoneal inoculation. We found that transdermal infection leads to delayed bacterial dissemination in blood and urine when compared to intraperitoneal infection using the same infectious dose, and that the overlapping presence ofL. interrogansin both fluids was twice as long as the standard intraperitoneal infection. Furthermore, dissemination ofL. interrogansand disease did not occur in mice infected with the same dose ofL. interrogansvia the oral mucosa. Over the course of these studies we also observed that the timing of exit ofLeptospirafrom blood and establishment of colonization of the kidney in the second week of infection correlated well with weight loss, but not with hypothermia. Thus, a non-invasive sign of leptospirosis such as weigh loss can be used to monitor bacterial dissemination and disease stage in mice. Our findings underline the importance of precise determination of windows of pathogen dissemination in biological fluids and how the route of infection affects the progression of disease. These studies could help focus the development of better treatment strategies and new technologies for diagnostic use.
New guidelines for DNA methylome studies regarding 5-hydroxymethylcytosine for understanding transcriptional regulation
Authors: Li Le , Gao Yuwei , Wu Qiong , Cheng Alfred S. L. , Yip Kevin Y. 
Published: May 2018

AbstractMany DNA methylome profiling methods cannot distinguish between 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Since 5mC typically acts as a repressive mark whereas 5hmC is an intermediate form during active demethylation, the inability to separate their signals could lead to incorrect interpretation of the data. Meanwhile, many analysis pipelines quantify methylation level by the count or ratio of methylated reads, but the proportion of discordant reads (PDR) has recently been proposed to be a better indicator of gene expression level. Is the amount of extra information contained in 5hmC signals and PDR worth the additional experimental and computational costs? Here we combine whole-genome bisulfite sequencing (WGBS) and oxidative WGBS (oxWGBS) data in normal human lung and liver tissues and their paired tumors to investigate the quantitative relationships between gene expression and signals of the two forms of DNA methylation at promoters, transcript bodies, and immediate downstream regions. We find that 5mC and 5hmC signals correlate with gene expression in the same direction in most samples, but considering both types of signals increases the accuracy of expression levels inferred from methylation data by a median of 18.2% as compared to having only standard WGBS data, showing that the two forms of methylation provide complementary information about gene expression. In addition, differential analysis between matched tumor and normal pairs is particularly affected by the superposition of 5mC and 5hmC signals in WGBS data, with at least 25-40% of the differentially methylated regions (DMRs) identified from 5mC signals not detected from WGBS data. We do not find PDR to be more informative about expression levels than ratio of methylated reads, and integrating the two types of methylation features only improves the accuracy of inferred expression levels by at most 9.8%. Our results also confirm previous finding that methylation signals at transcript bodies are more indicative of gene expression levels than promoter methylation signals, and further show that in addition to the first exon, methylation signals at the last exon and internal introns also contain non-redundant information about gene expression. Overall, our study provides concrete data for evaluating the cost effectiveness of some experimental and analysis options in the study of DNA methylation in normal and cancer samples.
Commensal bacteria act as a broad genetic buffer in Drosophila during chronic under-nutrition
Authors: Ma Dali , Bou-Sleiman Maroun , Joncour Pauline , Indelicato Claire-Emmanuelle , Frochaux Michael , Braman Virginie , Litovchenko Maria , Storelli Gilles , Deplancke Bart , Leulier François 
Published: May 2018

SummaryEukaryotic genomes encode several well-studied buffering mechanisms that robustly maintain invariant phenotypic outcome despite fluctuating environmental conditions. Here we show that the gut microbiota, represented by a single Drosophila facultative symbiont, Lactobacillus plantarum (LpWJL), acts also as a broad genetic buffer that masks the contribution of the cryptic genetic variations in the host under nutritional stress. During chronic under-nutrition, LpWJL consistently reduces variation in different host phenotypic traits and ensures robust organ patterning; LpWJL also decreases genotype-dependent expression variation, particularly for development-associated genes. We further demonstrate that LpWJL buffers via reactive oxygen species (ROS) signaling whose inhibition severely impairs microbiota-mediated phenotypic robustness. We thus identified an unexpected contribution of facultative symbionts to Drosophila fitness by assuring developmental robustness and phenotypic homogeneity in times of nutritional stress.
Pellino 1 Communicates Intercellular Signaling in Chronic Skin Inflammatory Microenvironment
Authors: Kim Suhyeon , Bae Seoyoon , Park Jihyun , Ha Geun-Hyoung , Hwang Kyungrim , Kim Hyun-Soo , Ji Jae-Hoon , Go Heounjeong , Lee Chang-Woo 
Published: May 2018

AbstractChronic skin inflammation including psoriasis is a multisystem disease, affecting more than 5% of the general population. Here we show that Pellino 1 (Peli1), a signal-responsive ubiquitin E3 ligase, is highly up-regulated in human psoriatic skin lesions and that increased Peli1 expression correlates with the immunopathogenesis of psoriasis-like chronic skin inflammatory disease. Interestingly, Peli1 directly interacts with interferon regulatory factor 4 (IRF4, a transcription factor that plays pivotal roles in proliferation and cytokine production) and induces lysine 63-mediated ubiquitination. Peli1-mediated IRF4 ubiquitination appears to be a common systemic signaling mechanism shared by lesional keratinocytes, dendritic cells, macrophages, and T cells, generating a feedback relationship between keratinocyte and Th17 cell responses. Conversely, inhibition of Peli1 interferes with IRF4 induction and attenuates immunopathogenic signaling in the psoriasis. In summary, Peli1-mediated ubiquitination is a common immunopathogenic intercellular signaling in psoriasis-like chronic skin inflammatory microenvironment. Thus, targeting Peli1 could be used as a potential strategy for psoriasis treatment.
Physiologically driven, altitude-adaptive model for the interpretation of pediatric oxygen saturation at altitudes above 2000 m a.s.l
Authors: Tüshaus Laura , Moreo Monica , Zhang Jia , Hartinger Stella Maria , Mäusezahl Daniel , Karlen Walter 
Published: May 2018

ABSTRACTMeasuring peripheral oxygen saturation (SpO2) with pulse oximeters at the point of care is widely established. However, since SpO2 is dependent on ambient atmospheric pressure, the distribution of SpO2 values in populations living above 2000 m a.s.l. is largely unknown. Here, we propose and evaluate a computer model to predict SpO2 values for pediatric permanent residents living between 0 and 4000 m a.s.l. Based on a sensitivity analysis of oxygen transport parameters, we created an altitude-adaptive SpO2 model that takes physiological adaptation of permanent residents into account. From this model, we derived an altitude-adaptive abnormal SpO2 threshold using patient parameters from literature. We compared the obtained model and threshold against a previously proposed threshold derived statistically from data and two empirical datasets independently recorded from Peruvian children living at altitudes up to 4100 m a.s.l. Our model followed the trends of empirical data, with the empirical data having a narrower healthy SpO2 range below 2000 m a.s.l., but the medians did never differ more than 2.29% across all altitudes. Our threshold estimated abnormal SpO2 in only 17 out of 5981 (0.3%) healthy recordings, whereas the statistical threshold returned 95 (1.6%) recordings outside the healthy range. The strength of our parametrised model is that it is rooted in physiology-derived equations and enables customisation. Furthermore, as it provides a reference SpO2, it could assist practitioners in interpreting SpO2 values for diagnosis, prognosis, and oxygen administration at higher altitudes.New & NoteworthyOur model describes the altitude-dependent decrease of SpO2 in healthy pediatric residents based on physiological equations and can be adapted based on measureable clinical parameters. The proposed altitude-specific abnormal SpO2 threshold might be more appropriate than rigid guidelines for administering oxygen that currently are only available for sea level patients. We see this as a starting point to discuss and adapt oxygen administration guidelines.
Humoral immune response to adenovirus induce tolerogenic bystander dendritic cells that promote generation of regulatory T cells
Authors: Phuong Tran Thi Thu , Eichholz Karsten , Amelio Patrizia , Moyer Crystal , Nemerow Glen R , Perreau Matthieu , Mennechet Franck JD , Kremer Eric J 
Published: May 2018

AbstractFollowing repeated encounters with adenoviruses most of us develop robust humoral and cellular immune responses that are thought to act together to combat ongoing and subsequent infections. Yet in spite of robust immune responses, adenoviruses establish subclinical persistent infections that can last for decades. While adenovirus persistence pose minimal risk in B-cell compromised individuals, if T-cell immunity is severely compromised, reactivation of latent adenoviruses can be life threatening. This dichotomy led us to ask how anti-adenovirus antibodies influence adenovirus-specific T-cell immunity. Using primary human blood cells, transcriptome and secretome profiling, and pharmacological, biochemical, genetic, molecular, and cell biological approaches, we initially found that healthy adults harbor adenovirus-specific regulatory T cells (Tregs). As peripherally induced Tregsare generated by tolerogenic dendritic cells (DCs), we then addressed how tolerogenic DCs could be created. Here, we demonstrate that DCs that take up immunoglobulin-complexed (IC)-adenoviruses create an environment that causes bystander DCs to become tolerogenic. These adenovirus antigen-loaded tolerogenic DCs can drive naïve T cells to mature into adenovirus-specific Tregs. Our results may provide ways to improve antiviral therapy and/or pre-screening high-risk individuals undergoing immunosuppression.Author summaryWhile numerous studies have addressed the cellular and humoral response to primary virus encounters, relatively little is known about the interplay between persistent infections, neutralizing antibodies, antigen-presenting cells, and the T-cell response. Our studies suggests that if adenovirus–antibody complexes are taken up by professional antigen-presenting cells (dendritic cells), the DCs generate an environment that causes bystander dendritic cells to become tolerogenic. These tolerogenic dendritic cells favors the creation of adenovirus-specific regulatory T cells. While this pathway likely favors pathogen survival, there may be advantages for the host also.
Bidirectional alterations in antibiotics susceptibility in Staphylococcus aureus - Pseudomonas aeruginosa dual-species biofilm
Authors: Trizna Elena Y. , Yarullina Maria N. , Baidamshina Diana R. , Akhatova Farida S. , Rozhina Elvira V. , Fakhrullin Rawil F. , Khabibrakhmanova Alsu M. , Kurbangalieva Almira R. , Bogachev Mikhail I. , Kayumov Airat R. 
Published: May 2018

ABSTRACTWhile in biofilms bacteria are embedded into an extracellular matrix which forms inaccessible barrier for antimicrobials thereby drastically increasing the concentrations of antibiotics required for treatment. Here we show that the susceptibility of S. aureus and P. aeruginosa to antibiotics in mixed biofilms significantly differs from monoculture biofilms depending on both conditions and chosen antimicrobial agents. While S. aureus could completely avoid vancomycin, ampicillin and ceftriaxone by embedding into the biofilm of P. aeruginosa, the very same consortium was characterized by 10–fold increase in susceptibility to broad-spectrum antimicrobials like ciprofloxacin and aminoglycosides compared to monocultures. These data clearly indicate that efficient treatment of biofilm-associated mixed infections requires antimicrobials active against both pathogens, since the interbacterial antagonism would enhance the efficacy of treatment. Moreover, similar increase in antibiotics efficacy was observed when P. aeruginosa suspension was added to the mature S. aureus biofilm, compared to S. aureus monoculture, and vice versa. These findings open promising perspectives to increase the antimicrobial treatment efficacy of the wounds infected with nosocomial pathogens by the transplantation of the skin residential microflora.