scholarly journals Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus

2017 ◽  
Author(s):  
Yuki Yoshida ◽  
Georgios Koutsovoulos ◽  
Dominik R. Laetsch ◽  
Lewis Stevens ◽  
Sujai Kumar ◽  
...  
Keyword(s):  
Extreme Environments ◽  
Water Film ◽  
Animal Evolution ◽  
Genomic Changes ◽  
Velvet Worms ◽  
Rare Genomic Changes ◽  
Molecular Phylogenies ◽  
Drying Conditions ◽  
Hypsibius Dujardini

ABSTRACTTardigrada, a phylum of meiofaunal organisms, have been at the center of discussions of the evolution of Metazoa, the biology of survival in extreme environments, and the role of horizontal gene transfer in animal evolution. Tardigrada are placed as sisters to Arthropoda and Onychophora (velvet worms) in the superphylum Ecdysozoa by morphological analyses, but many molecular phylogenies fail to recover this relationship. This tension between molecular and morphological understanding may be very revealing of the mode and patterns of evolution of major groups. Similar to bdelloid rotifers, nematodes and other animals of the water film, limno-terrestrial tardigrades display extreme cryptobiotic abilities, including anhydrobiosis and cryobiosis. These extremophile behaviors challenge understanding of normal, aqueous physiology: how does a multicellular organism avoid lethal cellular collapse in the absence of liquid water? Meiofaunal species have been reported to have elevated levels of HGT events, but how important this is in evolution, and in particular in the evolution of extremophile physiology, is unclear. To address these questions, we resequenced and reassembled the genome of Hypsibius dujardini, a limno-terrestrial tardigrade that can undergo anhydrobiosis only after extensive pre-exposure to drying conditions, and compared it to the genome of Ramazzottius varieornatus, a related species with tolerance to rapid desiccation. The two species had contrasting gene expression responses to anhydrobiosis, with major transcriptional change in H. dujardini but limited regulation in R. varieornatus. We identified few horizontally transferred genes, but some of these were shown to be involved in entry into anhydrobiosis. Whole-genome molecular phylogenies supported a Tardigrada+Nematoda relationship over Tardigrada+Arthropoda, but rare genomic changes tended to support Tardigrada+Arthropoda.

scholarly journals Role of Polyphosphates in Microbial Adaptation to Extreme Environments

2008 ◽  
Vol 74 (19) ◽  
pp. 5867-5874 ◽  
Author(s):  
Manfredo J. Seufferheld ◽  
H�ctor M. Alvarez ◽  
Maria E. Farias
Keyword(s):  
Extreme Environments ◽  
Microbial Adaptation

scholarly journals Moisture Induced Degradation of Porous Low-k Materials

2006 ◽  
Vol 914 ◽  
Author(s):  
Mikhail Baklanov ◽  
David O'Dwyer ◽  
Adam M Urbanowicz ◽  
Quoc Toan Le ◽  
Steven Demuynck ◽  
...  
Keyword(s):  
Water Film ◽  
Internal Surface ◽  
Hydrophobic Surface ◽  
Adsorbed Water ◽  
Bulk Water ◽  
Oh Groups ◽  
Film Bulk ◽  
Low K

AbstractInteraction of moisture with porous low-k films is evaluated by using in situ ellipsometry setup. The adsorbed water amount is calculated from change of refractive index measured during the adsorption. Pristine low-k films reversibly adsorb 2 - 5% of water that reflects presence of constitutive hydrophilic centrums. Plasma and thermal treatments increase the number of hydrophilic centrums. Once the amount of these centrums has reached a certain critical value sufficient to form a continuous water film, bulk water condensation is observed. Change of properties during the water adsorption in the damaged films is not fully reversible. Each additional adsorption cycle increases the dielectric function of the film because of decreasing porosity, increasing skeleton density and shrinkage. The pressure corresponding to the bulk condensation allows us to calculate internal contact angle (internal surface energy) of low-k materials. The water molecules adsorbed on separate OH groups play the role of a catalyst that hydrolyses the siloxane bridges initially present on hydrophobic surface.

scholarly journals The role of semen and seminal plasma in inducing large-scale genomic changes in the female porcine peri-ovulatory tract

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
M. Álvarez-Rodríguez ◽  
C. A. Martinez ◽  
D. Wright ◽  
H. Rodríguez-Martinez
Keyword(s):  
Seminal Plasma ◽  
Genital Tract ◽  
Large Scale ◽  
Enrichment Analysis ◽  
Estrogen Signaling ◽  
Cell Recognition ◽  
Genomic Changes ◽  
Expression Of Genes ◽  
Microarray Analyses

AbstractSemen modifies the expression of genes related to immune function along the porcine female internal genital tract. Whether other pathways are induced by the deposition of spermatozoa and/or seminal plasma (SP), is yet undocumented. Here, to determine their relative impact on the uterine and tubal transcriptomes, microarray analyses were performed on the endocervix, endometrium and endosalpinx collected from pre-ovulatory sows 24 h after either mating or artificial insemination (AI) with specific ejaculate fractions containing spermatozoa or sperm-free SP. After enrichment analysis, we found an overrepresentation of genes and pathways associated with sperm transport and binding, oxidative stress and cell-to-cell recognition, such as PI3K-Akt, FoxO signaling, glycosaminoglycan biosynthesis and cAMP-related transcripts, among others. Although semen (either after mating or AI) seemed to have the highest impact along the entire genital tract, our results demonstrate that the SP itself also modifies the transcriptome. The detected modifications of the molecular profiles of the pre/peri-ovulatory endometrium and endosalpinx suggest an interplay for the survival, transport and binding of spermatozoa through, for instance the up-regulation of the Estrogen signaling pathway associated with attachment and release from the oviductal reservoir.

scholarly journals The Mycobiota of the Deep Sea: What Omics Can Offer

Life ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 292
Author(s):  
Lluvia Vargas-Gastélum ◽  
Meritxell Riquelme
Keyword(s):  
Deep Sea ◽  
Fungal Diversity ◽  
High Salinity ◽  
Extreme Environments ◽  
Abiotic Conditions ◽  
Culture Independent ◽  
Sequencing Platforms ◽  
Generation Sequencing ◽  
Culture Dependent

The deep sea (>1000 m below sea level) represents one of the most extreme environments of the ocean. Despite exhibiting harsh abiotic conditions such as low temperatures, high hydrostatic pressure, high salinity concentrations, a low input of organic matter, and absence of light, the deep sea encompasses a great fungal diversity. For decades, most knowledge on the fungal diversity of the deep sea was obtained through culture-dependent techniques. More recently, with the latest advances of high-throughput next generation sequencing platforms, there has been a rapid increment in the number of studies using culture-independent techniques. This review brings into the spotlight the progress of the techniques used to assess the diversity and ecological role of the deep-sea mycobiota and provides an overview on how the omics technologies have contributed to gaining knowledge about fungi and their activity in poorly explored marine environments. Finally, current challenges and suggested coordinated efforts to overcome them are discussed.

scholarly journals Back to the Future: Portable Word Processors and the Electronic Health Record

2019 ◽  
Vol 34 (s1) ◽  
pp. s104-s105
Author(s):  
Alfredo Mori
Keyword(s):  
Electronic Health Record ◽  
Emergency Departments ◽  
Extreme Environments ◽  
Health Record ◽  
Physician Burnout ◽  
Software And Hardware ◽  
Electronic Health ◽  
Professional Writers ◽  
Word Processors

Introduction:The Electronic Health Record (EHR) is now the standard means for recording and maintaining medical notes in most emergency departments. The EHR is an independent cause of physician burnout, and maintenance of the EHR may occupy 30 to 50% of clinical time. There are software solutions available, but they are connected to fixed, expensive, distracting, and bright electronically powered computers. Scribes have been successfully trialed, but are also expensive and attached to computers on wheels. Portable digital word processors in the form of the AlphaSmart Neo is a redundant technology designed primarily for children with typing difficulties. It has recently enjoyed a resurgence in popularity among professional writers, journalists, and field researchers for the ultimate distraction-free writing experience. The Alphasmart Neo is cheap, nearly indestructible, intuitive, and requires almost no recharging. It is compatible with all software across Mac OS, Windows, and Linux. Notes are entered by the clinician or scribe, independently of computers, at the bedside, and uploaded to any software via USB cable.Aim:To describe the introduction and impact of the AlphaSmart Neo on the EHR in emergency departments across Australia.Methods:We will examine the role of the Alphasmart Neo in austere, low power, extreme environments with a demonstration on how to enter, maintain, and transfer an electronic health record independent of any computer or power source.Discussion:We believe the AlphaSmart Neo is an ideal, personalized, cheap, effective, and efficient hardware solution to entering notes independent of other software and hardware. It is distraction free at the patient’s bedside, resulting in better notes that the clinician enjoys writing.

scholarly journals The Essential Role of “Minor” Phyla in Molecular Studies of Animal Evolution

1998 ◽  
Vol 38 (6) ◽  
pp. 907-917 ◽  
Author(s):  
JAMES R. GAREY ◽  
ANDREAS SCHMIDT-RHAESA
Keyword(s):  
Essential Role ◽  
Animal Evolution ◽  
Molecular Studies

scholarly journals Tales of the ER-Golgi Frontier: Drosophila-Centric Considerations on Tango1 Function

2021 ◽  
Vol 8 ◽  
Author(s):  
Zhi Feng ◽  
Ke Yang ◽  
José C. Pastor-Pareja
Keyword(s):  
Secretory Pathway ◽  
Transmembrane Protein ◽  
Vesicular Transport ◽  
Fruit Fly ◽  
Evolutionary Perspective ◽  
Animal Evolution ◽  
Golgi Transport ◽  
Er Exit Sites ◽  
Related Proteins

In the secretory pathway, the transfer of cargo from the ER to the Golgi involves dozens of proteins that localize at specific regions of the ER called ER exit sites (ERES), where cargos are concentrated preceding vesicular transport to the Golgi. Despite many years of research, we are missing crucial details of how this highly dynamic ER-Golgi interface is defined, maintained and functions. Mechanisms allowing secretion of large cargos such as the very abundant collagens are also poorly understood. In this context, Tango1, discovered in the fruit fly Drosophila and widely conserved in animal evolution, has received a lot of attention in recent years. Tango1, an ERES-localized transmembrane protein, is the single fly member of the MIA/cTAGE family, consisting in humans of TANGO1 and at least 14 different related proteins. After its discovery in flies, a specific role of human TANGO1 in mediating secretion of collagens was reported. However, multiple studies in Drosophila have demonstrated that Tango1 is required for secretion of all cargos. At all ERES, through self-interaction and interactions with other proteins, Tango1 aids ERES maintenance and tethering of post-ER membranes. In this review, we discuss discoveries on Drosophila Tango1 and put them in relation with research on human MIA/cTAGE proteins. In doing so, we aim to offer an integrated view of Tango1 function and the nature of ER-Golgi transport from an evolutionary perspective.

scholarly journals The nucleosome DNA entry-exit site is important for transcription termination and prevention of pervasive transcription

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
A Elizabeth Hildreth ◽  
Mitchell A Ellison ◽  
Alex M Francette ◽  
Julia M Seraly ◽  
Lauren M Lotka ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Nucleosome Occupancy ◽  
Transcription Termination ◽  
Antisense Transcription ◽  
Exit Site ◽  
Genomic Changes ◽  
Sense Strand ◽  
Native Sequence

Compared to other stages in the RNA polymerase II transcription cycle, the role of chromatin in transcription termination is poorly understood. We performed a genetic screen in Saccharomyces cerevisiae to identify histone mutants that exhibit transcriptional readthrough of terminators. Amino acid substitutions identified by the screen map to the nucleosome DNA entry-exit site. The strongest H3 mutants revealed widespread genomic changes, including increased sense-strand transcription upstream and downstream of genes, increased antisense transcription overlapping gene bodies, and reduced nucleosome occupancy particularly at the 3’ ends of genes. Replacement of the native sequence downstream of a gene with a sequence that increases nucleosome occupancy in vivo reduced readthrough transcription and suppressed the effect of a DNA entry-exit site substitution. Our results suggest that nucleosomes can facilitate termination by serving as a barrier to transcription and highlight the importance of the DNA entry-exit site in broadly maintaining the integrity of the transcriptome.

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