bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid sulfur cycling in sediments from the Peruvian oxygen minimum zone featuring simultaneous sulfate reduction and sulfide oxidation
Authors: Treude Tina , Hamdan Leila J. , Lemieux Sydnie , Dale Andrew W. , Sommer Stefan 
Published: May 2021

AbstractBacterial sulfate reduction (SR) is often determined by radiotracer techniques using 35S‐labeled sulfate. In environments featuring simultaneous sulfide oxidation, SR can be underestimated due to re‐oxidation of 35S‐sulfide. Recycling of 35S‐tracer is expected to be high in sediment with low concentrations of pore‐water sulfide and high abundance of giant filamentous sulfur‐oxidizing bacteria (GFSOB). Here, we applied a sulfide‐spiking method, originally developed for water samples, to sediments along a shelf‐slope transect (72, 128, 243, 752 m water depth) traversing the Peruvian oxygen minimum zone. Sediment spiked with unlabeled sulfide prior to 35S‐sulfate injection to prevent radiotracer recycling was compared to unspiked sediment. At stations characterized by low natural sulfide and abundant GFSOB (128 and 243 m), the method revealed 1–3 times higher SR rates in spiked sediment. Spiking had no effect on SR in sediment with high natural sulfide despite presence of GFSOB (72 m). Bioturbated sediment devoid of GFSOB (752 m) showed elevated SR in spiked samples, likely from artificial introduction of sulfidic conditions. Sulfide oxidation rates at the 128 and 243 m station, derived from the difference in SR between spiked and unspiked sediment, approximated rates of dissimilatory nitrate reduction to ammonium by GFSOB. Gross SR contributed considerably to benthic dissolved inorganic carbon fluxes at the three shallowest station, confirming that SR is an important process for benthic carbon respirations within the oxygen minimum zone. We recommend to further explore the spiking method to capture SR in sediment featuring low sulfide concentrations and high sulfur cycling by GFSOB.
Longitudinal patterns and linkages in benthic fine particulate organic matter composition, respiration, and nutrient uptake
Authors: Hood James M. , Collis Lyndsie M. , Schade John D. , Stark Rebecca A. , Finlay Jacques C. 
Published: May 2021

AbstractLongitudinal changes in the structure and function of river ecosystems have long been recognized, yet our understanding of how such patterns shape elemental cycles remains limited. In particular, while benthic fine particulate organic matter (POM, 0.7–1000 μm) may control many stream nutrient cycles, less is known about longitudinal patterns or controls of benthic POM‐associated nutrient uptake. We conducted a survey of benthic POM‐associated respiration and nutrient uptake as well as microbial biomass (bacteria and algae) and benthic POM composition in four size classes (0.7–53 μm, 53–106 μm, 106–250 μm, and 250–1000 μm) in six streams in the forested South Fork Eel River watershed (California), encompassing a longitudinal gradient in light availability and primary production. Benthic POM at downstream sites was composed of smaller particles with lower organic matter content that were richer in nitrogen and autotrophic material. Areal respiration and nutrient uptake rates increased 11‐ to 67‐fold with stream size. While microbial activity rates did not increase with stream size, benthic POM‐associated microbial biomass increased 20‐fold with stream size, and closely tracked a 15‐fold increase in light availability, and primary production. Thus, microbial biomass, not activity, determined longitudinal patterns in benthic POM‐associated areal nutrient uptake and respiration rates. We attribute longitudinal patterns in microbial biomass to increases in light availability and primary production. Our findings help clarify the role of local (primary production) and upstream processes in shaping ecosystem structure and function.
Magnesium depletion extends fission yeast lifespan via general amino acid control activation
Authors: Ohtsuka Hokuto , Kobayashi Mikuto , Shimasaki Takafumi , Sato Teppei , Akanuma Genki , Kitaura Yasuyuki , Otsubo Yoko , Yamashita Akira , Aiba Hirofumi 
Published: May 2021

AbstractNutrients including glucose, nitrogen, sulfur, zinc, and iron are involved in the regulation of chronological lifespan (CLS) of yeast, which serves as a model of the lifespan of differentiated cells of higher organisms. Herein, we show that magnesium (Mg2+) depletion extends CLS of the fission yeast Schizosaccharomyces pombe through a mechanism involving the Ecl1 gene family. We discovered that ecl1+ expression, which extends CLS, responds to Mg2+ depletion. Therefore, we investigated the underlying intracellular responses. In amino acid auxotrophic strains, Mg2+ depletion robustly induces ecl1+ expression through the activation of the general amino acid control (GAAC) pathway—the equivalent of the amino acid response of mammals. Polysome analysis indicated that the expression of Ecl1 family genes was required for regulating ribosome amount when cells were starved, suggesting that Ecl1 family gene products control the abundance of ribosomes, which contributes to longevity through the activation of the evolutionarily conserved GAAC pathway. The present study extends our understanding of the cellular response to Mg2+ depletion and its influence on the mechanism controlling longevity.
Differences in the intestinal microbiota between insecticide‐resistant and ‐sensitive Aedes albopictus based on full‐length 16S rRNA sequencing
Authors: Wang Haiyang , Zhang Chongxing , Cheng Peng , Wang Yang , Liu Hongmei , Wang Haifang , Wang Huaiwei , Gong Maoqing 
Published: May 2021

AbstractThe intestinal symbiotic bacteria of Aedes albopictus play a potential role in host resistance to insecticides. In this study, we sequenced the full‐length of 16S rRNA and analyzed the differences in the intestinal microbiota between deltamethrin‐resistant and ‐sensitive Ae. albopictus. Symbiotic bacteria were cultured and analyzed using six types of culture media in aerobic and anaerobic environments. We found significant differences in the diversity and abundance of the intestinal microbiota of the two strains of Ae. albopictus. The symbiotic bacteria cultured in vitro were found to be mainly facultative anaerobes. The cultured bacteria such as Serratia oryzae and Acinetobacter junii may function to promote the development of insecticide resistance. This work indicates that intestinal bacteria may contribute to the enhancement of insecticide resistance of Ae. albopictus It also highlights the analytical advantage of full‐length 16S rRNA sequencing to study the intestinal microbiota of mosquitoes.
Comparative analysis of the intestinal bacterial communities in mud crab Scylla serrata in South India
Authors: Apine Elina , Rai Praveen , Mani Madhu K. , Subramanian Vikram , Karunasagar Indrani , Godhe Anna , Turner Lucy M. 
Published: May 2021

AbstractLittle is known about the functions of the crustacean gut microbiome, but environmental parameters and habitat are known to affect the composition of the intestinal microbiome, which may in turn affect the physiological status of the host. The mud crab Scylla serrata is an economically important species, and is wild‐caught, and farmed across the Indo‐Pacific region. In this study, we compared the composition of the gut microbiome (in terms of gut microbial species richness and abundance) of S. serrata collected from wild sites, and farms, from the east and west coast of India, and also tested the effects of the environment on the composition. The water temperature had a statistically significant effect on gut microbiome composition, with microbial biodiversity decreasing with increasing water temperature. This could have negative effects on both wild and farmed mud crabs under future climate change conditions, although further research into the effects of temperature on gut microbiomes is required. By comparison, salinity, crab mass and carapace width, geographical location as well as whether they were farmed or wild‐caught crabs did not have a significant impact on gut microbiome composition. The results indicate that farming does not significantly alter the composition of the gut microbiome when compared to wild‐caught crabs.
The genome sequence of hairy root Rhizobium rhizogenes strain LBA9402: Bioinformatics analysis suggests the presence of a new opine system in the agropine Ri plasmid
Authors: Hooykaas Marjolein J. G. , Hooykaas Paul J. J. 
Published: May 2021

AbstractWe report here the complete genome sequence of the Rhizobium rhizogenes (formerly Agrobacterium rhizogenes) strain LBA9402 (NCPPB1855rifR), a pathogenic strain causing hairy root disease. To assemble a complete genome, we obtained short reads from Illumina sequencing and long reads from Oxford Nanopore Technology sequencing. The genome consists of a 3,958,212 bp chromosome, a 2,005,144 bp chromid (secondary chromosome) and a 252,168 bp Ri plasmid (pRi1855), respectively. The primary chromosome was very similar to that of the avirulent biocontrol strain K84, but the chromid showed a 724 kbp deletion accompanied by a large 1.8 Mbp inversion revealing the dynamic nature of these secondary chromosomes. The sequence of the agropine Ri plasmid was compared to other types of Ri and Ti plasmids. Thus, we identified the genes responsible for agropine catabolism, but also a unique segment adjacent to the TL region that has the signature of a new opine catabolic gene cluster including the three genes that encode the three subunits of an opine dehydrogenase. Our sequence analysis also revealed a novel gene at the very right end of the TL‐DNA, which is unique for the agropine Ri plasmid. The protein encoded by this gene was most related to the succinamopine synthases of chrysopine and agropine Ti plasmids and thus may be involved in the synthesis of the unknown opine that can be degraded by the adjacent catabolic cluster. The available sequence will facilitate the use of R. rhizogenes and especially LBA9402 in both the laboratory and for biotechnological purposes.
Gut dysbiosis and clinical phases of pancolitis in patients with ulcerative colitis
Authors: Maldonado‐Arriaga Brenda , Sandoval‐Jiménez Sergio , Rodríguez‐Silverio Juan , Lizeth Alcaráz‐Estrada Sofía , Cortés‐Espinosa Tomás , Pérez‐Cabeza de Vaca Rebeca , Licona‐Cassani Cuauhtémoc , Gámez‐Valdez July Stephany , Shaw Jonathan , Mondragón‐Terán Paul , Hernández‐Cortez Cecilia , Suárez‐Cuenca Juan Antonio , Castro‐Escarpulli Graciela 
Published: May 2021

AbstractUlcerative colitis (UC) is a frequent type of inflammatory bowel disease, characterized by periods of remission and exacerbation. Gut dysbiosis may influence pathophysiology and clinical response in UC. The purpose of this study was to evaluate whether gut microbiota is related to the active and remission phases of pancolitis in patients with UC as well as in healthy participants. Fecal samples were obtained from 18 patients with UC and clinical‐endoscopic evidenced pancolitis (active phase n = 9 and remission phase n = 9), as well as 15 healthy participants. After fecal DNA extraction, the 16S rRNA gene was amplified and sequenced (Illumina MiSeq), operational taxonomic units were analyzed with the QIIME software. Gut microbiota composition revealed a higher abundance of the phyla Proteobacteria and Fusobacteria in active pancolitis, as compared with remission and healthy participants. Likewise, a marked abundance of the genus Bilophila and Fusobacteria were present in active pancolitis, whereas a higher abundance of Faecalibacterium characterized both remission and healthy participants. LEfSe analysis showed that the genus Roseburia and Faecalibacterium were enriched in remission pancolitis, and genera Bilophila and Fusobacterium were enriched in active pancolitis. The relative abundance of Fecalibacterium and Roseburia showed a higher correlation with fecal calprotectin, while Bilophila and Fusobacterium showed AUCs (area under the curve) of 0.917 and 0.988 for active vs. remission pancolitis. The results of our study highlight the relation of gut dysbiosis with clinically relevant phases of pancolitis in patients with UC. Particularly, Fecalibacterium, Roseburia, Bilophila, and Fusobacterium were identified as genera highly related to the different clinical phases of pancolitis.
Complete genome sequence of Photobacterium ganghwense C2.2: A new polyhydroxyalkanoate production candidate
Authors: Lascu Irina , Mereuță Ioana , Chiciudean Iulia , Hansen Hilde , Avramescu Sorin Marius , Tănase Ana‐Maria , Stoica Ileana 
Published: May 2021

AbstractPolyhydroxyalkanoates (PHAs) are biodegradable bioplastics that can be manufactured sustainably and represent a promising green alternative to petrochemical‐based plastics. Here, we describe the complete genome of a new marine PHA‐producing bacterium—Photobacterium ganghwense (strain C2.2), which we have isolated from the Black Sea seashore. This new isolate is psychrotolerant and accumulates PHA when glycerol is provided as the main carbon source. Transmission electron microscopy, specific staining with Nile Red visualized via epifluorescence microscopy and gas chromatography analysis confirmed the accumulation of PHA. This is the only PHA‐producing Photobacterium for which we now have a complete genome sequence, allowing us to investigate the pathways for PHA production and other secondary metabolite synthesis pathways. The de novo assembly genome, obtained using open‐source tools, comprises two chromosomes (3.5, 2 Mbp) and a megaplasmid (202 kbp). We identify the entire PHA synthesis gene cluster that encodes a class I PHA synthase, a phasin, a 3‐ketothiolase, and an acetoacetyl‐CoA reductase. No conventional PHA depolymerase was identified in strain C2.2, but a putative lipase with extracellular amorphous PHA depolymerase activity was annotated, suggesting that C2.2 is unable to degrade intracellular PHA. A complete pathway for the conversion of glycerol to acetyl‐CoA was annotated, in accordance with its ability to convert glycerol to PHA. Several secondary metabolite biosynthetic gene clusters and a low number of genes involved in antibiotic resistance and virulence were also identified, indicating the strain's suitability for biotechnological applications.
Short‐term exposure to synthetic flaxseed lignan LGM2605 alters gut microbiota in mice
Authors: Badger Reagan , Aho Ken , Serve Kinta 
Published: May 2021

AbstractLGM2605 is a synthetic version of the naturally occurring flaxseed lignan secoisolariciresinol diglucoside (SDG), with known anti‐inflammatory and antioxidant properties; however, its effects on gut microbial composition have not previously been evaluated. In the present study, we sought to determine how the 10‐day oral administration of LGM2605 alters the gut microbiota of mice. Eight‐week‐old female C57BL/6 mice were treated with either LGM2605 or saline, administered daily via oral gavage over a 10‐day treatment period. Upon termination of treatment, mouse cecums (n = 31) were collected, and cecal DNA was isolated. 16S rRNA genes were sequenced and analyzed in Mothur to identify changes in gut microbial composition induced by LGM2605 treatment (v. saline control). We then assessed community composition, performed indicator taxa analysis, and measured alpha and beta diversity. Overall, LGM2605 significantly altered the gut microbiota of mice; we reported alterations in 3 bacterial phyla and 22 genera as a result of treatment. The study here identifies for the first time significant alterations in the gut microbiota of mice following oral administration of LGM2605, in general shifting toward a more anti‐inflammatory composition. These findings lay the foundation for future investigations utilizing LGM2605 to control gut dysbiosis and, by extension, systemic inflammation.
Dynamic changes occur in the DNA gut virome of female cynomolgus macaques during aging
Authors: Tan Xunmin , Chai Tingjia , Duan Jiajia , Wu Jing , Zhang Hanping , Li Yifan , Huang Yu , Hu Xi , Zheng Peng , Song Jinlin , Ji Ping , Jin Xin , Zhang Hongmei , Xie Peng 
Published: May 2021

AbstractAging is a critical factor affecting physical health and disease in mammals. Emerging evidence indicates that aging may affect the gut bacteriome in cynomolgus macaques, but little is known about whether or how the gut virome changes with age. Here, we compared the DNA gut viral composition of 16 female cynomolgus monkeys (Macaca fascicularis) at three life stages (young, adult, and old) using the shotgun metagenome sequencing method. We found that the DNA gut virome from these monkeys differed substantially among the three groups. The gut viruses were dominated by bacteriophages, the most abundant of which was the Caudovirales order (i.e., Siphoviridae, Myoviridae, and Podoviridae families). Additionally, the co‐occurrence analysis revealed that the age‐related bacteriophages were correlated in an extensive and complex manner with the main intestinal bacteria (i.e., Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria phyla). Furthermore, the age‐related DNA gut viral functions were enriched for genetic information processing, nucleotide, and folate metabolism. Our gut virome analysis provides new insight into how aging influences the gut virome of non‐human primates.
Discovery of KV1.3 ion channel inhibitors: Medicinal chemistry approaches and challenges
Authors: Gubič Špela , Hendrickx Louise A. , Toplak Žan , Sterle Maša , Peigneur Steve , Tomašič Tihomir , Pardo Luis A. , Tytgat Jan , Zega Anamarija , Mašič Lucija P. 
Published: May 2021

AbstractThe KV1.3 voltage‐gated potassium ion channel is involved in many physiological processes both at the plasma membrane and in the mitochondria, chiefly in the immune and nervous systems. Therapeutic targeting KV1.3 with specific peptides and small molecule inhibitors shows great potential for treating cancers and autoimmune diseases, such as multiple sclerosis, type I diabetes mellitus, psoriasis, contact dermatitis, rheumatoid arthritis, and myasthenia gravis. However, no KV1.3‐targeted compounds have been approved for therapeutic use to date. This review focuses on the presentation of approaches for discovering new KV1.3 peptide and small‐molecule inhibitors, and strategies to improve the selectivity of active compounds toward KV1.3. Selectivity of dalatazide (ShK‐186), a synthetic derivate of the sea anemone toxin ShK, was achieved by chemical modification and has successfully reached clinical trials as a potential therapeutic for treating autoimmune diseases. Other peptides and small‐molecule inhibitors are critically evaluated for their lead‐like characteristics and potential for progression into clinical development. Some small‐molecule inhibitors with well‐defined structure–activity relationships have been optimized for selective delivery to mitochondria, and these offer therapeutic potential for the treatment of cancers. This overview of KV1.3 inhibitors and methodologies is designed to provide a good starting point for drug discovery to identify novel effective KV1.3 modulators against this target in the future.
Costello syndrome with special cutaneous manifestations and HRAS G12D mutation: A case report and literature review
Authors: Qian Wen , Zhang Meijie , Huang Hequn , Chen Yihe , Park Gajin , Zeng Ni , Li Yueyue , Lu Qian , Luo Dan 
Published: May 2021

AbstractBackgroundCostello syndrome (CS, OMIM 218040) is a rare congenital disorder caused by mutations in HRAS. Previous studies reported that approximately 80% of patients with CS share the same pathogenic variant in HRAS gene in c.34G> A (p.G12S). Here, we report a CS patient with c.34G> A (p.G12D) variant in HRAS gene and she presented with special manifestation.Methods and ResultsWe describe a 31‐year‐old female patient who presented with distinctive facial appearance, intellectual disability, dental abnormalities, hyperkeratosis of palmer and planter, loose skin at birth, papillomata on the face and nipples. The whole‐exome sequencing (WES) technology provided by Haotian Biotechnology (China) confirmed p.G12D variant in HRAS gene. To elucidate the typical features of CS with p.G12D variant, we further reviewed these previously reported cases and found that patients with G12D variant died within three months after birth due to multiple organ failure. They had the typical facial characteristics, failure to thrive, skin and cardiac abnormalities, and gene testing confirmed the diagnosis of CS.ConclusionTo the best of our knowledge, this is the first article to report a patient with a p.G12D variant that had special but mild manifestation. Moreover, this report and literature review casts new light on the clinical features of p.G12D variant.
Reconstruction of an infected midshaft radius and ulna nonunion using a free vascularized fibula and medial femoral condyle flap
Authors: Willemot Laurent , Stewart David , Lawson Richard 
Published: May 2021

AbstractConventional grafts do not perform well in the treatment of large diaphyseal bone defects. Forearm nonunions are especially challenging due to complex biomechanical and kinematic demands. Free bone flaps may yield more predictable bony restoration in these cases, while keeping morbidity acceptable to the patient. We aim to illustrate one combination of flaps which can be used in these conditions. This article reports on a 23 year old patient with an 8 cm diaphyseal nonunion of the radius and a similar 7 cm defect of the ulna after infection of fracture fixation hardware. The radius was treated with a free fibular flap (FFF) and the ulna with a medial femoral condyle (MFC) flap in a staged procedure after initial debridement. The patient was followed up for 6 months without significant complications. Both flaps healed within 3 months, yet the MFC demonstrated faster bony incorporation. We attributed this to the spongious nature of the MFC flap compared to the thick cortical FFF. This case report hopes to illustrate one type of flap combination for extensive forearm bone defects. The selection and approach minimizes donor site morbidity to a single limb and possibly hastens bony union of the forearm.
γ‐Oryzanol Improves Exercise Endurance and Muscle Strength by Upregulating PPARδ and ERRγ Activity in Aged Mice
Authors: Ahn Jisong , Son Hyo Jeong , Seo Hyo Deok , Ha Tae Youl , Ahn Jiyun , Lee Hyunjung , Shin Seung Ho , Jung Chang Hwa , Jang Young Jin 
Published: May 2021

Scopeγ‐Oryzanol, a well‐known antioxidant, has been used by body builders and athletes to boost strength and increase muscle gain, without major side effects. However, the effect of γ‐Oryzanol on sarcopenia and the underlying molecular mechanism is poorly understood.ResultsAged mice fed with the γ‐Oryzanol diet do not show significant changes in muscle weight, but show increased running endurance as well as improved grip strength. The expression and activity of PPARδ and ERRγ are increased in skeletal muscle of γ‐Oryzanol supplemented mice. γ‐Oryzanol upregulates oxidative muscle fibers by MEF2 transcription factor, and PGC‐1α and ERRα expressions. Fatty acid oxidation related genes and mitochondria biogenesis are upregulated by γ‐Oryzanol. In addition, γ‐Oryzanol inhibits TGF‐β‐Smad‐NADPH oxidase 4 pathway and inflammatory cytokines such as TNF‐α, IL‐1β, IL‐6, and p65 NF‐κB subunit, which cause skeletal muscle weakness. Collectively, γ‐Oryzanol attenuates muscle weakness pathway and increases oxidative capacity by increasing PPARδ and ERRγ activity, which contributes to enhance strength and improve oxidative capacity in muscles, consequently enhancing exercise capacity in aged mice. Particularly, γ‐Oryzanol directly binds to PPARδ.ConclusionsThese are the first findings showing that γ‐Oryzanol enhances skeletal muscle function in aged mice by regulating PPARδ and ERRγ activity without muscle gain.