Evidences for a role of two Y-specific genes in sex determination in Populus deltoides

AbstractAlmost all plants in the genus Populus are dioecious (i.e. trees are either male or female), but it is unknown whether dioecy evolved in a common ancestor or independently in different subgenera. Here, we sequence the small peritelomeric X- and Y-linked regions of P. deltoides chromosome XIX. Two genes are present only in the Y-linked region. One is a duplication of a non-Y-linked, female-specifically expressed response regulator, which produces siRNAs that block this gene’s expression, repressing femaleness. The other is an LTR/Gypsy transposable element family member, which generates long non-coding RNAs. Overexpression of this gene in A. thaliana promotes androecium development. We also find both genes in the sex-determining region of P. simonii, a different poplar subgenus, which suggests that they are both stable components of poplar sex-determining systems. By contrast, only the duplicated response regulator gene is present in the sex-linked regions of P. davidiana and P. tremula. Therefore, findings in our study suggest dioecy may have evolved independently in different poplar subgenera.

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A universal stress protein in Mycobacterium smegmatis sequesters the cAMP-regulated lysine acyltransferase and is essential for biofilm formation

Journal of Biological Chemistry ◽

10.1074/jbc.ra119.011373 ◽

2019 ◽

Vol 295 (6) ◽

pp. 1500-1516 ◽

Cited By ~ 2

Author(s):

Sintu Samanta ◽

Priyanka Biswas ◽

Arka Banerjee ◽

Avipsa Bose ◽

Nida Siddiqui ◽

...

Keyword(s):

Stress Responses ◽

Mycobacterium Smegmatis ◽

Biofilm Formation ◽

Stress Proteins ◽

Response Regulator ◽

Stress Protein ◽

Colony Morphology ◽

Regulator Gene ◽

Its Gene

Universal stress proteins (USPs) are present in many bacteria, and their expression is enhanced under various environmental stresses. We have previously identified a USP in Mycobacterium smegmatis that is a product of the msmeg_4207 gene and is a substrate for a cAMP-regulated protein lysine acyltransferase (KATms; MSMEG_5458). Here, we explored the role of this USP (USP4207) in M. smegmatis and found that its gene is present in an operon that also contains genes predicted to encode a putative tripartite tricarboxylate transporter (TTT). Transcription of the TTT-usp4207 operon was induced in the presence of citrate and tartrate, perhaps by the activity of a divergent histidine kinase-response regulator gene pair. A usp4207-deleted strain had rough colony morphology and reduced biofilm formation compared with the WT strain; however, both normal colony morphology and biofilm formation were restored in a Δusp4207Δkatms strain. We identified several proteins whose acetylation was lost in the Δkatms strain, and whose transcript levels increased in M. smegmatis biofilms along with that of USP4207, suggesting that USP4207 insulates KATms from its other substrates in the cell. We propose that USP4207 sequesters KATms from diverse substrates whose activities are down-regulated by acylation but are required for biofilm formation, thus providing a defined role for this USP in mycobacterial physiology and stress responses.

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Evolutionary insights into Mariner-like elements in Apis species

10.1101/2020.04.15.035063 ◽

2020 ◽

Author(s):

Kakeru Yokoi ◽

Kiyoshi Kimura ◽

Hidemasa Bono

Keyword(s):

Phylogenetic Analysis ◽

Transposable Element ◽

Related Species ◽

Horizontal Transfer ◽

The Other ◽

Closely Related Species ◽

Sequences Analysis ◽

Almost All

AbstractBackgroundMariner and mariner-like elements (MLEs) are distributed in various species and their sequences are highly diverse. In previous reports, a few transposable element in the genomes of Apis species mainly consist of mariner and MLE. For further insight of Apis MLEs, detailed classifications of Apis MLE and sequences analysis of long MLEs, which may potentially encode the transposase, are needed.ResultsMuch more MLEs were detected in A. mellifera genome compared to other Apis species genomes. They were classified into 31 Drosophila MLE classes. In this classification, almost all of MLEs were classified into the three classes belonging to mellifera subfamilies, suggesting that Apis MLEs which exist thorough Apis species derived from single MLE belonging to mellifera subfamily. Phylogenetic analysis using MLEs in the three classes showed that there two types of clusters, of which one consist of multiple Apis species MLEs, and others of only A. mellifera MLEs. Long MLEs analysis showed that only one long MLE encoding complete transposase was found in all Apis genome except for A. mellifera genome, and the MLE and multiple MLEs similar to it were found in A. mellifera genome. The analysis also showed that other several long MLEs encoding complete transposase were found only in A. mellifera genome.ConclusionsAlmost all of Apis MLEs are mellifera subfamilies. Of these MLEs, one types of them settled in Apis species and burst in A. mellifera genome. The other one of MLEs invaded into A. mellifera genome by horizontal transfer and exploded in A. mellifera genome. This is the first example of the finer aspects of MLE evolution among closely related species.

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The Domestic Sources of Grand Strategy

10.1093/oxfordhb/9780198840299.013.13 ◽

2021 ◽

pp. 238-255

Author(s):

Jonathan D. Caverley

Keyword(s):

International Relations ◽

International System ◽

The Other ◽

Grand Strategy ◽

Economic Relations ◽

International Economic Relations ◽

Strategic Role ◽

Domestic Sources ◽

Almost All

Over the past decades of American-dominated International Relations, research on domestic sources of grand strategy has largely coalesced around the liberal ends of democracy and free trade. Given increasing Sino-American competition, this chapter predicts a turn to a more robust International Relations research program on the role that domestic ideas and material factors play in shaping grand strategy. This research will focus as much on the means of grand strategy as the ends. Much work already examines how democracy (and nondemocracy) can drive grand strategy, and important states in contemporary international politics differ on this front. On the other hand, almost all the major powers in the international system remain quite liberal in their international economic relations—the other concern of research on domestic influences on grand strategy. This chapter delves further into the grand-strategic role of regime type and the form of capitalism practiced within the state. It then suggests two additional under-researched domestic-level factors—militarism and nationalism—that will shape grand strategy in the coming years.

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A Review on the Role of Small Nucleolar RNA Host Gene 6 Long Non-coding RNAs in the Carcinogenic Processes

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.741684 ◽

2021 ◽

Vol 9 ◽

Author(s):

Soudeh Ghafouri-Fard ◽

Tayyebeh Khoshbakht ◽

Mohammad Taheri ◽

Seyedpouzhia Shojaei

Keyword(s):

Splice Variants ◽

Cell Types ◽

Host Gene ◽

Small Nucleolar Rna ◽

Non Coding Rnas ◽

Almost All ◽

Nucleolar Rna ◽

Tgf Β1

Being located on 17q25.1, small nucleolar RNA host gene 6 (SNHG16) is a member of SNHG family of long non-coding RNAs (lncRNA) with 4 exons and 13 splice variants. This lncRNA serves as a sponge for a variety of miRNAs, namely miR-520a-3p, miR-4500, miR-146a miR-16–5p, miR-98, let-7a-5p, hsa-miR-93, miR-17-5p, miR-186, miR-302a-3p, miR-605-3p, miR-140-5p, miR-195, let-7b-5p, miR-16, miR-340, miR-1301, miR-205, miR-488, miR-1285-3p, miR-146a-5p, and miR-124-3p. This lncRNA can affect activity of TGF-β1/SMAD5, mTOR, NF-κB, Wnt, RAS/RAF/MEK/ERK and PI3K/AKT pathways. Almost all studies have reported oncogenic effect of SNHG16 in diverse cell types. Here, we explain the results of studies about the oncogenic role of SNHG16 according to three distinct sets of evidence, i.e., in vitro, animal, and clinical evidence.

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The role of host miRNAs on Mycobacterium tuberculosis

ExRNA ◽

10.1186/s41544-019-0040-y ◽

2019 ◽

Vol 1 (1) ◽

Cited By ~ 2

Author(s):

Ava Behrouzi ◽

Marjan Alimohammadi ◽

Amir Hossein Nafari ◽

Mohammad Hadi Yousefi ◽

Farhad Riazi Rad ◽

...

Keyword(s):

Immune Response ◽

Mycobacterium Tuberculosis ◽

Innate Immune Response ◽

Host Defense ◽

Pathogenic Bacteria ◽

Biological Pathways ◽

Innate Immune ◽

The Other ◽

Non Coding Rnas

Abstract MicroRNAs are non-coding RNAs, playing an important role in regulating many biological pathways, such as innate immune response against various infections. Different studies confirm that many miRNAs act as important regulators in developing a strategy for the survival of Mycobacterium tuberculosis in the host cell. On the other hand, an innate immune response is one of the important aspects of host defense against Mycobacterium. Considering the importance of miRNAs during tuberculosis infection, we focused on studies that performed on the role of various miRNAs related to pathogenic bacteria, M. tuberculosis in the host. Also, we have introduced important miRNAs that can be used as a biomarker for the detection of Mycobacterium.

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The Potential Role of Sulbactam and Cephalosporins Plus Daptomycin Against Daptomycin-Nonsusceptible VISA and H-VISA Isolates: An in Vitro Study

Antibiotics ◽

10.3390/antibiotics8040184 ◽

2019 ◽

Vol 8 (4) ◽

pp. 184 ◽

Cited By ~ 2

Author(s):

Lai ◽

Chen ◽

Lu ◽

Lin ◽

Chen ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Synergistic Effect ◽

Potential Role ◽

In Vitro Study ◽

Drug Combinations ◽

The Other ◽

In Vitro Activity ◽

Almost All

This study assesses the synergistic effect of the combination of cephalosporins and sulbactam with daptomycin against daptomycin-nonsusceptible, vancomycin-intermediate resistant Staphylococcus aureus (VISA) or heterogeneous vancomycin-intermediate S. aureus (h-VISA) isolates. The in vitro activity of daptomycin against daptomycin-nonsusceptible VISA/h-VISA isolates after adding cephalosporins with or without sulbactam was evaluated. The MIC of daptomycin against the VISA/h-VISA isolates was reduced after adding cephalosporins to daptomycin. Except for one VISA and two h-VISA isolates, the other VISA/h-VISA isolates became daptomycin-susceptible (MICs 1 mg/L). After adding sulbactam to each daptomycin/cephalosporin combination, the MIC of daptomycin against the VISA/h-VISA isolates decreased for 5 (33.3%), 6 (40.0%), 6 (40.0%), and 6 (40.0%) isolates with the cefazolin, cefmetazole, cefotaxime, and cefepime combinations, respectively. Synergism using the checkerboard method was noted in 100% of cefazolin and cefotaxime combinations and 87% and 80% of cefmetazole and cefepime combinations for all the VISA and h-VISA isolates. With the addition of sulbactam, synergism was noted in 100% of cefazolin, cefmetazole, and cefotaxime combinations and 93% of the cefepime combinations for all the VISA and h-VISA isolates. Almost all the FICs for the three-drug combinations were lower than those for the two-drug combinations. Using time-killing methods, a synergistic effect against five h-VISA isolates was observed. A synergistic effect of daptomycin, sulbactam, and each cephalosporin was observed for all VISA isolates. In conclusion, the activity of daptomycin against daptomycin-nonsusceptible VISA/h-VISA isolates can be enhanced by adding cephalosporins, and partially further promoted by sulbactam.

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Unleash multifunctional role of long noncoding RNAs biomarker panel in breast cancer: a predictor classification model

Epigenomics ◽

10.2217/epi-2019-0291 ◽

2020 ◽

Vol 12 (14) ◽

pp. 1215-1237

Author(s):

Eman A Toraih ◽

Aya El-Wazir ◽

Essam Al Ageeli ◽

Mohammad H Hussein ◽

Mohamed M Eltoukhy ◽

...

Keyword(s):

Breast Cancer ◽

Expression Patterns ◽

Noncoding Rnas ◽

The Other ◽

Classification Model ◽

Gene Expression Patterns ◽

Healthy Controls ◽

Reverse Transcription Pcr ◽

Non Coding Rnas

Aim: We aimed to explore the circulating expression profile of nine lncRNAs (MALAT1, HOTAIR, PVT1, H19, ROR, GAS5, ANRIL, BANCR, MIAT) in breast cancer (BC) patients relative to normal and risky individuals. Methods: Serum relative expressions of the specified long non-coding RNAs were quantified in 155 consecutive women, using quantitative reverse-transcription PCR. Random Forest (RF) and decision tree were also applied. Results: Significant MALAT1 upregulation and GAS5 downregulation could discriminate risky women from healthy controls. Overexpression of the other genes showed good diagnostic performances. Lower GAS5 levels were associated with metastasis and recurrence. RF model revealed a better performance when combining gene expression patterns with risk factors. Conclusion: The studied panel could be utilized as diagnostic/prognostic biomarkers in BC, providing promising epigenetic-based therapeutic targets.

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Long Non-Coding RNAs in Insects

Animals ◽

10.3390/ani11041118 ◽

2021 ◽

Vol 11 (4) ◽

pp. 1118

Author(s):

Chhavi Choudhary ◽

Shivasmi Sharma ◽

Keshav Kumar Meghwanshi ◽

Smit Patel ◽

Prachi Mehta ◽

...

Keyword(s):

Molecular Mechanisms ◽

Protein Translation ◽

Small Subset ◽

Biological Processes ◽

Insect Development ◽

Transfer Rnas ◽

Rna Molecules ◽

Non Coding Rnas ◽

Almost All

Only a small subset of all the transcribed RNAs are used as a template for protein translation, whereas RNA molecules that are not translated play a very important role as regulatory non-coding RNAs (ncRNAs). Besides traditionally known RNAs (ribosomal and transfer RNAs), ncRNAs also include small non-coding RNAs (sncRNAs) and long non-coding RNAs (lncRNAs). The lncRNAs, which were initially thought to be junk, have gained a great deal attention because of their regulatory roles in diverse biological processes in animals and plants. Insects are the most abundant and diverse group of animals on this planet. Recent studies have demonstrated the role of lncRNAs in almost all aspects of insect development, reproduction, and genetic plasticity. In this review, we describe the function and molecular mechanisms of the mode of action of different insect lncRNAs discovered up to date.

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The Role of Global and Local Landmarks in Virtual Environment Navigation

Presence Teleoperators & Virtual Environments ◽

10.1162/105474600566628 ◽

2000 ◽

Vol 9 (1) ◽

pp. 69-83 ◽

Cited By ~ 115

Author(s):

Sibylle D. Steck ◽

Hanspeter A. Mallot

Keyword(s):

Virtual Environment ◽

Visual Navigation ◽

Test Phase ◽

The Other ◽

Projection Screen ◽

Television Tower ◽

Almost All ◽

Global And Local ◽

Cue Conflict

In visual navigation, landmarks can be used in a number of different ways. In this paper, we investigate the role of global and local landmarks in virtual environment navigation. We performed an experiment in a virtual environment called “Hexatown”, consisting of a regular hexagonal grid of streets and junctions. Each junction was identified by the presence of distinct local landmarks (buildings, phone box, and so on). Additionally, compass information or a global frame of reference was provided by global landmarks (hilltop, television tower, and city skyline). According to participants' movement decisions, egomotion was simulated, and displayed on a 180 deg. projection screen. Participants learned the route back and forth between two local landmarks. In the test phase, individual junctions were approached and the participant's movement decision was recorded. We performed two experiments involving landmark changes after learning. In the first, we used conflicting cues by transposing landmarks. In the second experiment, we reduced either local or global landmark information. Results show that both local and global landmarks are used in wayfinding decisions. However, different participants rely on different strategies. In the first experiment (cue conflict) for example, some of the participants used only local landmarks while others relied exclusively on global landmarks. Other participants used local landmarks at one location and global landmarks at the other. When removing one landmark type in the second experiment, the other type could be used by almost all participants, indicating that information about the neglected landmark type was present in memory.

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