Genome-wide identification and evolution of ATP-binding cassette transporters in the ciliate Tetrahymena thermophila: A case of functional divergence in a multigene family

<p>Abstract</p> <p>Background</p> <p>In eukaryotes, ABC transporters that utilize the energy of ATP hydrolysis to expel cellular substrates into the environment are responsible for most of the efflux from cells. Many members of the superfamily of ABC transporters have been linked with resistance to multiple drugs or toxins. Owing to their medical and toxicological importance, members of the ABC superfamily have been studied in several model organisms and warrant examination in newly sequenced genomes.</p> <p>Results</p> <p>A total of 165 ABC transporter genes, constituting a highly expanded superfamily relative to its size in other eukaryotes, were identified in the macronuclear genome of the ciliate <it>Tetrahymena thermophila</it>. Based on ortholog comparisons, phylogenetic topologies and intron characterizations, each highly expanded ABC transporter family of <it>T</it>. <it>thermophila </it>was classified into several distinct groups, and hypotheses about their evolutionary relationships are presented. A comprehensive microarray analysis revealed divergent expression patterns among the members of the ABC transporter superfamily during different states of physiology and development. Many of the relatively recently formed duplicate pairs within individual ABC transporter families exhibit significantly different expression patterns. Further analysis showed that multiple mechanisms have led to functional divergence that is responsible for the preservation of duplicated genes.</p> <p>Conclusion</p> <p>Gene duplications have resulted in an extensive expansion of the superfamily of ABC transporters in the <it>Tetrahymena </it>genome, making it the largest example of its kind reported in any organism to date. Multiple independent duplications and subsequent divergence contributed to the formation of different families of ABC transporter genes. Many of the members within a gene family exhibit different expression patterns. The combination of gene duplication followed by both sequence divergence and acquisition of new patterns of expression likely plays a role in the adaptation of <it>Tetrahymen </it>a to its environment.</p

Comparative genomic analysis of NAC transcriptional factors to dissect the regulatory mechanisms for cell wall biosynthesis

BACKGROUND: NAC domain transcription factors are important transcriptional regulators involved in plant growth, development and stress responses. Recent studies have revealed several classes of NAC transcriptional factors crucial for controlling secondary cell wall biosynthesis. These transcriptional factors mainly include three classes, SND, NST and VND. Despite progress, most current analysis is carried out in the model plant Arabidopsis. Moreover, many downstream genes regulated by these transcriptional factors are still not clear. METHODS: In order to identify the key homologue genes across species and discover the network controlling cell wall biosynthesis, we carried out comparative genome analysis of NST, VND and SND genes across 19 higher plant species along with computational modelling of genes regulated or co-regulated with these transcriptional factors. RESULTS: The comparative genome analysis revealed that evolutionarily the secondary-wall-associated NAC domain transcription factors first appeared in Selaginella moellendorffii. In fact, among the three groups, only VND genes appeared in S. moellendorffii, which is evolutionarily earlier than the other two groups. The Arabidopsis and rice gene expression analysis showed specific patterns of the secondary cell wall-associated NAC genes (SND, NST and VND). Most of them were preferentially expressed in the stem, especially the second internodes. Furthermore, comprehensive co-regulatory network analysis revealed that the SND and MYB genes were co-regulated, which indicated the coordinative function of these transcriptional factors in modulating cell wall biosynthesis. In addition, the co-regulatory network analysis revealed many novel genes and pathways that could be involved in cell wall biosynthesis and its regulation. The gene ontology analysis also indicated that processes like carbohydrate synthesis, transport and stress response, are coordinately regulated toward cell wall biosynthesis. CONCLUSIONS: Overall, we provided a new insight into the evolution and the gene regulatory network of a subgroup of the NAC gene family controlling cell wall composition through bioinformatics data mining and bench validation. Our work might benefit to elucidate the possible molecular mechanism underlying the regulation network of secondary cell wall biosynthesis

Tracing the structural evolution of eukaryotic ATP binding cassette transporter superfamily

The ATP binding cassette (ABC) transporters superfamily is one of the largest classes of membrane proteins. The core of the ABC transporter protein is composed of transmembrane domains (TMDs) and nucleotide binding domains (NBD). Eukaryotes ABC transporters are classified into seven main families (ABCA to ABCG) based on sequence similarity and domain organizations. With different domain number and domain organizations, eukaryote ABC transporters show diverse structures: the single structure (NBD or TMD), the ABC2 structure (NBD-NBD), the half structure (TMD-NBD or NBD-TMD) and the full structure (TMD-NBD-TMD-NBD or NBD-TMD-NBD-TMD). However, studies on how various ABC transporter gene structures evolved is still absent. Therefore, in this study, we comprehensively investigated the structural evolution of eukaryotic ABC transporters. The seven eukaryote ABC transporter families (A to G) fell into three groups: A&G group, B,C&D group and E&F group. There were at least four times the number of NBD and TMD fusion events in the origin of the half structure transporter. Two fusion modes were found in the full and ABC2 structure origination. Based on these findings, we present a putative structural evolutionary path of eukaryote ABC transporters that will increase our understanding on their origin, divergence and function

Neoplasms of Central Nervous System: A Diagnostic Approach

Neoplasms of central nervous system accounts for approximately 1% of tumors of the human body, and they can be primary or secondary (metastatic), benign or malignant, and intra-axial or extra-axial. This chapter includes some most common brain and spinal cord tumors, like pituitary adenomas, meningiomas and gliomas, with their clinical, imaging, and histological characteristics for the diagnosis purpose, with additional treatment options and prognosis

Community health professionals’ dementia knowledge, attitudes and care approach: a cross-sectional survey in Changsha, China

© The Author(s). 2018 This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.Abstract Background Community health professionals play a significant role in dementia care. However, little is known about community health professionals’ capacity in dementia care, especially in low and middle-income countries. The aim of the present study was to assess community health professionals’ dementia knowledge, attitudes and care approach in China, a country with the largest population of people with dementia in the world and where community based dementia care services are much needed. Methods A cross-sectional survey was conducted. 450 health professionals were recruited into the study using random sampling from community health service centres in Changsha, China. Their knowledge, attitudes and care approach were assessed utilising the Chinese version of the Alzheimer’s Disease Knowledge Scale, Dementia Care Attitude Scale and Approach to Advanced Dementia Care Questionnaire respectively. Results A total of 390 participants returned the questionnaire (response rate 87%). Age, education, professional group and care experience were associated with knowledge scores, and overall dementia knowledge was poor. Attitudes were generally positive and influenced by age, professional group, gender and care experience. The experience of caring for people with dementia was positively associated with a person-centred care approach, although the participants tended not to use a person-centred care approach. A statistically significant association was found between knowledge and attitudes (r = 0.379, P < 0.001), and between attitudes and care approach (r = 0.143, P < 0.001). However, dementia knowledge has no relationship with a person-centred approach. Conclusions Community health professionals showed generally positive attitudes towards people with dementia. However, they demonstrated poor dementia knowledge and tended not to use a person-centred care approach. The results suggest that a multifaceted approach consisting of educational interventions for community health professionals, and policy and resource development to meet the demand for community dementia care services, is urgently needed in China

Observation of first-order quantum phase transitions and ferromagnetism in twisted double bilayer graphene

Twisted graphene multilayers are highly tunable flatband systems for developing new phases of matter. Thus far, while orbital ferromagnetism has been observed in valley polarized phases, the long-range orders of other correlated phases as well as the quantum phase transitions between different orders mostly remain unknown. Here, we report an observation of Coulomb interaction driven first-order quantum phase transitions and ferromagnetism in twisted double bilayer graphene (TDBG). At zero magnetic field, the transitions are revealed in a series of step-like abrupt resistance jumps with prominent hysteresis loop when either the displacement field (D) or the carrier density (n) is tuned across symmetry-breaking boundary near half filling, indicating a formation of ordered domains. It is worth noting that the good turnability and switching of these states gives a rise to a memory performance with a large on/off ratio. Moreover, when both spin and valley play the roles at finite magnetic field, we observe abundant first-order quantum phase transitions among normal metallic states from charge neutral point, orbital ferromagnetic states from quarter filling, and spin-polarized states from half filling. We interpret these first-order phase transitions in the picture of phase separations and spin domain percolations driven by multi-field tunable Coulomb interactions, in agreement with Lifshitz transition from Hartree-Fock calculations. The observed multi-filed tunable domain structure and its hysteresis resembles the characteristics of multiferroics, revealing intriguing magnetoelectric properties. Our result enriches the correlated phase diagram in TDBG for discovering novel exotic phases and quantum phase transitions, and it would benefit other twisted moir\'e systems as well

High-temperature modification of steel slag using composite modifier containing silicon calcium slag, fly ash, and reservoir sediment

Steel slag (SS) is a kind of industrial solid waste, and its accumulation brings certain harm to the ecological environment. In order to promote the building material utilization of SS, high-temperature modification (HTM) of SS is performed using a composite modifier (CMSFR) containing silicon calcium slag (SCS), fly ash (FA), and reservoir sediment (RS). Then, the authors investigated the effect of CMSFR on the cementitious properties and volume soundness of SS mixture after HTM (SMHTM). After that, the mineral composition and microstructure of SMHTM were investigated through X-ray fluorescence analysis (XRF), X-ray diffraction (XRD), scanning electronic microscopy (SEM), energy dispersive spectrometry (EDS), and particle size analysis. It was found that the free CaO (f-CaO) content obviously decreased, and the cementitious properties improved in SMHTM. When the CMSFR content was 20% (SCS: FA: RS = 9:7:4), and the modification temperature (MT) was 1,250°C, the mass fraction of f-CaO in SMHTM dropped from 4.81% to 1.90%, down by 60.5%; the 28-day activity index of SMHTM increased to 85.4%, 14.3% higher than that of raw SS, which meets the technical requirement of Steel slag powder used for cement and concrete (GB/T 20491-2017): the activity index of grade I SS powder must be greater than or equal to 80%. As the mass fraction of CMSFR grew from 10% to 30%, new mineral phases formed in SMHTM, including diopside (CMS2), ceylonite (MgFe2O4), gehlenite (C2AS), tricalcium aluminate (C3A), and magnetite (Fe3O4). The HTM with CMSFR promotes the decomposition of RO phase (a continuous solid solution composed of divalent metal oxides like FeO, MgO, MnO, and CaO) in raw SS, turning the FeO in that phase into Fe3O4. The above results indicate that the SMHTM mixed with CMSFR can be applied harmless in cement and concrete, making low-energy fine grinding of SS a possibility

Room-temperature correlated states in twisted bilayer MoS2_2

Moir\'e superlattices have emerged as an exciting condensed-matter quantum simulator for exploring the exotic physics of strong electronic correlations. Notable progress has been witnessed, but such correlated states are achievable usually at low temperatures. Here, we report the transport evidences of room-temperature correlated electronic states and layer-hybridized SU(4) Hubbard model simulator in AB-stacked MoS$_2$ homo-bilayer moir\'e superlattices. Correlated insulating states at moir\'e band filling factors v = 1, 2, 3 are unambiguously established in twisted bilayer MoS$_2$. Remarkably, the correlated electronic states can persist up to a record-high critical temperature of over 285 K. The realization of room-temperature correlated states in twisted bilayer MoS$_2$ can be understood as the cooperation effects of the stacking-specific atomic reconstruction and the resonantly enhanced interlayer hybridization, which largely amplify the moir\'e superlattice effects on electronic correlations. Furthermore, extreme large non-linear Hall responses up to room-temperature are uncovered near correlated insulating states, demonstrating the quantum geometry of moir\'e flat conduction band.Comment: 13 pages, 3 figure

Transcriptome Analysis of the Model Protozoan, Tetrahymena thermophila, Using Deep RNA Sequencing

Background: The ciliated protozoan Tetrahymena thermophila is a well-studied single-celled eukaryote model organism for cellular and molecular biology. However, the lack of extensive T. thermophila cDNA libraries or a large expressed sequence tag (EST) database limited the quality of the original genome annotation. Methodology/Principal Findings: This RNA-seq study describes the first deep sequencing analysis of the T. thermophila transcriptome during the three major stages of the life cycle: growth, starvation and conjugation. Uniquely mapped reads covered more than 96 % of the 24,725 predicted gene models in the somatic genome. More than 1,000 new transcribed regions were identified. The great dynamic range of RNA-seq allowed detection of a nearly six order-of-magnitude range of measurable gene expression orchestrated by this cell. RNA-seq also allowed the first prediction of transcript untranslated regions (UTRs) and an updated (larger) size estimate of the T. thermophila transcriptome: 57 Mb, or about 55 % of the somatic genome. Our study identified nearly 1,500 alternative splicing (AS) events distributed over 5.2 % of T. thermophila genes. This percentage represents a two order-of-magnitude increase over previous EST-based estimates in Tetrahymena. Evidence of stage-specific regulation of alternative splicing was also obtained. Finally, our study allowed us to completely confirm about 26.8 % of the genes originally predicted by the gene finder, to correct coding sequence boundaries an