Signature Domain Research Articles

Ferroelectric Organic-Inorganic Hybrid Ammonium Halogenobismuthate(III) for Piezoelectric Energy Harvesting.

Halogenobismuthate(III) compounds are of recent interest because of their low toxicity and distinct electrical properties. The utility of these materials as ferroelectrics for piezoelectric energy harvesters is still in its early stages. Herein, we report a hybrid ammonium halogenobismuthate(III) [BPBrDMA]2·[BiBr5], crystallizing in a ferroelectrically active polar noncentrosymmetric Pna21 space group. Its noncentrosymmetric structure was confirmed by the detection of the second harmonic generation response. The ferroelectric P-E hysteresis loop measurements on the thin film sample of [BPBrDMA]2·[BiBr5] gave a saturation polarization (Ps) of 5.72 μC cm-2. The piezoresponse force microscopy analysis confirmed its ferroelectric and piezoelectric nature, showing characteristic domain structures and signature hysteresis and butterfly loops. The piezoelectric energy harvesting attributes of [BPBrDMA]2·[BiBr5] were further probed on its polylactic acid (PLA) composites. The 15 wt % [BPBrDMA]2·[BiBr5]-PLA polymer composite resulted in a high output voltage of 26.2 V and power density of 15.47 μW cm-2. The energy harvested from this device was further utilized for charging a 10 μF capacitor within 3 min.

Identification and expression profiles of Tubby‑like proteins coding genes in walnut (Juglans regia L.) in response to stress and hormone treatments

Tubby-like proteins (TLPs) constitute a diverse multigene family found across a broad range of eukaryotic organisms, from single-celled to multicellular eukaryotes. Despite their importance, the existence of TLPs in walnuts (Juglans regia L.) has not been reported until now. In this study, we identified 12 members of the JrTLP gene family in the walnut genome, revealing a pattern of gene replication events. Notably, all JrTLPs exhibited a split gene structure, containing two to eight introns, and these genes could be divided into five distinct categories based on their evolutionary relationships. The majority of TLP proteins possess two signature domains: the F-box and Tubby domains. Subcellular localization prediction and experiments confirmed that JrTLP2 was located in the nucleus and membrane. Expression profiling revealed that multiple JrTLPs respond to a range of stimuli, including pathogen infection, hormonal treatment (such as auxin, ABA, MeJA, and GA), and abiotic stress conditions such as cold, heat, and salt. This study represents the first comprehensive identification of the walnut TLP family, providing valuable insights into the function and regulation of TLP in walnut and laying the foundation for future functional dissection, particularly in the context of stress tolerance.

Ecology shapes the genomic and biosynthetic diversification of Streptomyces bacteria from insectivorous bats.

Streptomyces are prolific producers of secondary metabolites from which many clinically useful compounds have been derived. They inhabit diverse habitats but have rarely been reported in vertebrates. Here, we aim to determine to what extent the ecological source (bat host species and cave sites) influence the genomic and biosynthetic diversity of Streptomyces bacteria. We analysed draft genomes of 132 Streptomyces isolates sampled from 11 species of insectivorous bats from six cave sites in Arizona and New Mexico, USA. We delineated 55 species based on the genome-wide average nucleotide identity and core genome phylogenetic tree. Streptomyces isolates that colonize the same bat species or inhabit the same site exhibit greater overall genomic similarity than they do with Streptomyces from other bat species or sites. However, when considering biosynthetic gene clusters (BGCs) alone, BGC distribution is not structured by the ecological or geographical source of the Streptomyces that carry them. Each genome carried between 19-65 BGCs (median=42.5) and varied even among members of the same Streptomyces species. Nine major classes of BGCs were detected in ten of the 11 bat species and in all sites: terpene, non-ribosomal peptide synthetase, polyketide synthase, siderophore, RiPP-like, butyrolactone, lanthipeptide, ectoine, melanin. Finally, Streptomyces genomes carry multiple hybrid BGCs consisting of signature domains from two to seven distinct BGC classes. Taken together, our results bring critical insights to understanding Streptomyces-bat ecology and BGC diversity that may contribute to bat health and in augmenting current efforts in natural product discovery, especially from underexplored or overlooked environments.

Role of mucin 2 gene for growth in Anas platyrhynchos: a novel report.

The mucin gene is expressed in the mucous membrane of the inner layer of the internal organs. Intestinalmucin 2 (MUC2), amajor gel-formingmucin, represents a primary barrier component of mucus layers. This is the first report on the role of mucin genes in growth traits in animals. In this study, we randomly studied Bengal ducks (Anas platyrhynchos) reared from day old to 10 weeks of age under an organized farm and studied the growth parameters as well as body weight and average daily body weight gain. We characterized the mucin gene for Bengal ducks and observed glycosylation and EGF1 (EGF-like domain signature) as important domains for growth traits in ducks. We observed a better expression profile for the mucin gene in high-growing ducks in comparison to that of low-growing ducks with real-time PCR. Hence, the mucin gene may be employed as a marker for growth traits.

REPercussions: how geminiviruses recruit host factors for replication.

Circular single-stranded DNA viruses of the family Geminiviridae encode replication-associated protein (Rep), which is a multifunctional protein involved in virus DNA replication, transcription of virus genes, and suppression of host defense responses. Geminivirus genomes are replicated through the interaction between virus Rep and several host proteins. The Rep also interacts with itself and the virus replication enhancer protein (REn), which is another essential component of the geminivirus replicase complex that interacts with host DNA polymerases α and δ. Recent studies revealed the structural and functional complexities of geminivirus Rep, which is believed to have evolved from plasmids containing a signature domain (HUH) for single-stranded DNA binding with nuclease activity. The Rep coding sequence encompasses the entire coding sequence for AC4, which is intricately embedded within it, and performs several overlapping functions like Rep, supporting virus infection. This review investigated the structural and functional diversity of the geminivirus Rep.

Establishment and characterization of a new class of adenylate cyclases (class VII ACs) in plants

Adenylate cyclase is the key enzyme in the synthesis of cAMP. Now, more and more plant genes which possessing AC function are being identified, but the classification of plant ACs has not yet been systematically studied and the relationship of plant ACs with other existing six classes ACs in animals and microorganisms is still unclear. In this study, we found that 7 of the 15 reported plant ACs with conserved CYTH-like_AC_Ⅳ-like domain were clustered into a group with high confidence (Group Ⅳ), while the other plant ACs were clustered into other three groups with no common domain. In addition, we also found that the Group Ⅳ plant ACs were grouped into an independent and specific class (Class VII), separated from the existing six classes of ACs. The Group Ⅳ plant ACs, compared to the existing six classes of ACs, own unique CYTH-like_AC_Ⅳ-like conserved domain and EXEXK signature motif, characteristic protein tertiary structures, specific subcellular localization and catalytic conditions. In view of the above, we regarded the Group Ⅳ plant ACs as the seventh class of AC (VII AC). This study does the systematic classification of plant ACs which could lay a foundation for further identification and study of the biological functions of the plant-specific VII ACs.

Recently evolved combination of unique sulfatase and amidase genes enables bacterial degradation of the wastewater micropollutant acesulfame worldwide.

Xenobiotics often challenge the principle of microbial infallibility. One example is acesulfame introduced in the 1980s as zero-calorie sweetener, which was recalcitrant in wastewater treatment plants until the early 2010s. Then, efficient removal has been reported with increasing frequency. By studying acesulfame metabolism in alphaproteobacterial degraders of the genera Bosea and Chelatococcus, we experimentally confirmed the previously postulated route of two subsequent hydrolysis steps via acetoacetamide-N-sulfonate (ANSA) to acetoacetate and sulfamate. Genome comparison of wildtype Bosea sp. 100-5 and an acesulfame degradation-defective mutant revealed the involvement of two plasmid-borne gene clusters. The acesulfame-hydrolyzing sulfatase is strictly manganese-dependent and belongs to the metallo beta-lactamase family. In all degraders analyzed, it is encoded on a highly conserved gene cluster embedded in a composite transposon. The ANSA amidase, on the other hand, is an amidase signature domain enzyme encoded in another gene cluster showing variable length among degrading strains. Transposition of the sulfatase gene cluster between chromosome and plasmid explains how the two catabolic gene clusters recently combined for the degradation of acesulfame. Searching available genomes and metagenomes for the two hydrolases and associated genes indicates that the acesulfame plasmid evolved and spread worldwide in short time. While the sulfatase is unprecedented and unique for acesulfame degraders, the amidase occurs in different genetic environments and likely evolved for the degradation of other substrates. Evolution of the acesulfame degradation pathway might have been supported by the presence of structurally related natural and anthropogenic compounds, such as aminoacyl sulfamate ribonucleotide or sulfonamide antibiotics.

Exploring Signature‐Based Model Calibration for Streamflow Prediction in Ungauged Basins

AbstractCalibration of precipitation‐streamflow models to streamflow signatures is a promising approach for streamflow prediction in ungauged basins (PUB). The estimation of parameter and prediction uncertainty in this case is not trivial because: (a) calibration takes place in the signature domain, while predictions are required in the time domain, and (b) streamflow signatures are estimated (e.g., from donor catchments) rather than “observed” (computed from observed streamflow in the target catchment), and therefore particularly uncertain. This study investigates model calibration using estimated signatures in an Approximate Bayesian Computation framework. First, we construct a stochastic signature transfer model, based on seasonal flow duration curves. Second, we calibrate a precipitation‐streamflow model to the estimated signatures, accounting for their uncertainty. The proposed method is tested in six catchments of the Thur basin, Switzerland. Three data availability scenarios are considered: (a) concomitant scenario, where signatures are “observed,” (b) non‐concomitant scenario, where signatures are transferred from a different time period, and (c) regionalization scenario, where signatures are transferred from (neighboring) donor catchments. In this study, the switch from observed to regionalized signatures increases predictive streamflow uncertainty by 38% and worsens the (deterministic) fit to observations by 17% (in terms of Nash‐Sutcliffe efficiency). Despite this deterioration, posterior predictive uncertainty remains lower than prior predictive uncertainty generated using uniform priors over representative parameter ranges (“uncalibrated” model), which demonstrates the effectiveness of the proposed signature‐based calibration. More importantly, uncertainty is reliably estimated at the ungauged catchments, which represents a key advance in stochastic streamflow PUB.

CeGAL: Redefining a Widespread Fungal-Specific Transcription Factor Family Using an In Silico Error-Tracking Approach.

In fungi, the most abundant transcription factor (TF) class contains a fungal-specific 'GAL4-like' Zn2C6 DNA binding domain (DBD), while the second class contains another fungal-specific domain, known as 'fungal_trans' or middle homology domain (MHD), whose function remains largely uncharacterized. Remarkably, almost a third of MHD-containing TFs in public sequence databases apparently lack DNA binding activity, since they are not predicted to contain a DBD. Here, we reassess the domain organization of these 'MHD-only' proteins using an in silico error-tracking approach. In a large-scale analysis of ~17,000 MHD-only TF sequences present in all fungal phyla except Microsporidia and Cryptomycota, we show that the vast majority (>90%) result from genome annotation errors and we are able to predict a new DBD sequence for 14,261 of them. Most of these sequences correspond to a Zn2C6 domain (82%), with a small proportion of C2H2 domains (4%) found only in Dikarya. Our results contradict previous findings that the MHD-only TF are widespread in fungi. In contrast, we show that they are exceptional cases, and that the fungal-specific Zn2C6-MHD domain pair represents the canonical domain signature defining the most predominant fungal TF family. We call this family CeGAL, after the highly characterized members: Cep3, whose 3D structure is determined, and GAL4, a eukaryotic TF archetype. We believe that this will not only improve the annotation and classification of the Zn2C6 TF but will also provide critical guidance for future fungal gene regulatory network analyses.

In silico characterization of differentially expressed short-read nucleotide sequences identified in dieback stress-induced transcriptomic analysis reveals their role as antimicrobial peptides.

We investigated the in silico characterization of short-length nucleotide sequences that were differentially expressed in dieback stress-induced transcriptomic analysis. They displayed homology with C-terminal flanking peptides and defensins-like proteins, revealing their antimicrobial activity. Their predicted fingerprints displayed protein signatures related to antimicrobial peptides. These short-length RGAs have been shown to possess structural motifs such as APLT P-type ATPase, casein kinase II (CK2), protein kinase 3, protein kinase C (PKC), and N-glycosylation site that are the attributes of disease resistance genes. The prediction of arginine and lysine residues in active binding sites in ligand docking analysis prophesied them as antimicrobial peptides due to their strong relation with antimicrobial activity. The in silico structural-functional characterization has predicted their role in resistance against microbial pathogens. Moreover, the predicted antimicrobial peptide regions showed their homology with the signature domain of PR-5-like protein and AMP family Thaumatin.

Understanding the molecular response of non-mammalian toll-like receptor 22 (TLR22) in amphibious air-breathing catfish, Clarias magur (Hamilton, 1822) to bacterial infection or ligand stimulation through molecular cloning and expression profiling

Toll-like receptor (TLR) 22 is a non-mammalian TLR, which is identified initially as a functional substitute of mammalian TLR3 in recognizing cell surface long dsRNA in teleosts. To understand the pathogen surveillance role played by TLR22 in an air-breathing catfish model the full-length cDNA of TLR22 was identified in Clarias magur and found to be consisted of 3597 nucleotides encoding for 966 amino acids. In the deduced amino acid sequence of C. magur TLR22 (CmTLR22) key signature domains such as one signal peptide, 13 LRRs, one transmembrane domain, one LRR_CT domain and an intracellular TIR domain could be identified. The CmTLR22 formed a separate cluster with other catfish TLR22 genes and situated within the TLR22 cluster in the phylogenetic analysis of teleost TLR groups. The CmTLR22 was constitutively expressed in all the 12 tested tissues of healthy C. magur juveniles with the highest transcript abundance in spleen followed by brain, intestine and head kidney. Following induction with the dsRNA viral analogue, poly (I:C), the level of expression of CmTLR22 was up-regulated in tissues such as kidney, spleen and gills. Whereas, in Aeromonas hydrophila-challenged C. magur, the expression levels of CmTLR22 was found to be up-regulated in gills, kidney and spleen, and down-regulated in liver. The findings of the current study suggest that the specific function of TLR22 is evolutionarily conserved in C. magur and might play a key role in mounting immune response by recognizing Gram-negative fish pathogen such as A. hydrophila and aquatic viruses in air-breathing amphibious catfishes.

Wireless Technology Identification Employing Dynamic Mode Decomposition Modeling

Significant growth in broadband wireless services, as well as ever-increasing demand on the spectrum caused by the Internet of Things (IoT) have overstretched limited available spectrum space for wireless services. Heterogeneous wireless networks (HetNets)—wherein multiple wireless technologies (e.g., Wi-Fi, Bluetooth, Zigbee, LTE, and GSM) coexist and share spectrum—are a promising solution for enhancing spectrum sharing. An essential element in developing coexistence protocols is correctly identifying wireless technologies anticipated to share spectrum and to shift users between available wireless technologies in an effort to optimize spectrum usage and minimize interference. For the coexistence research reported in this paper, we analyzed the performance of our developed novel algorithm based on dynamic mode decomposition (DMD) mathematical modeling to identify and differentiate among various wireless technologies. More specifically, our technique identified GSM and LTE signals in the cellular domain, IEEE802.11n, ac, and ax in the Wi-Fi domain, as well as Bluetooth and Zigbee. The proposed DMD-based technique identifies the time domain signature of a signal by capturing embedded periodic features transmitted within the signal. Performance and accuracy were tested and validated using an experimental dataset collected for various time series, and raw-power measurements of the targeted technologies. Results showed that the developed DMD-based algorithm can differentiate and classify individual and coexisting wireless signals with high accuracy —greater than 90% for most cases. Furthermore, only a short time— less than one second—is required for identifying a signal and enabling implementation in real-time practical networks. The advantage of the developed technique over comparable techniques is lower complexity (i.e., shorter processing and training time, no channel estimation, no time/frequency synchronization, and no need for long observation-time intervals).

Mining and characterization of the PKS–NRPS hybrid for epicoccamide A: a mannosylated tetramate derivative from Epicoccum sp. CPCC 400996

BackgroundGenomic analysis indicated that the genomes of ascomycetes might carry dozens of biosynthetic gene clusters (BGCs), yet many clusters have remained enigmatic. The ascomycete genus Epicoccum, belonging to the family Didymellaceae, is ubiquitous that colonizes different types of substrates and is associated with phyllosphere or decaying vegetation. Species of this genus are prolific producers of bioactive substances. The epicoccamides, as biosynthetically distinct mannosylated tetramate, were first isolated in 2003 from Epicoccum sp. In this study, using a combination of genome mining, chemical identification, genetic deletion, and bioinformatic analysis, we identified the required BGC epi responsible for epicoccamide A biosynthesis in Epicoccum sp. CPCC 400996.ResultsThe unconventional biosynthetic gene cluster epi was obtained from an endophyte Epicoccum sp. CPCC 400996 through AntiSMASH-based genome mining. The cluster epi includes six putative open reading frames (epiA-epiF) altogether, in which the epiA encodes a tetramate-forming polyketide synthase and nonribosomal peptide synthetases (PKS−NRPS hybrid). Sequence alignments and bioinformatic analysis to other metabolic pathways of fungal tetramates, we proposed that the gene cluster epi could be involved in generating epicoccamides. Genetic knockout of epiA completely abolished the biosynthesis of epicoccamide A (1), thereby establishing the correlation between the BGC epi and biosynthesis of epicoccamide A. Bioinformatic adenylation domain signature analysis of EpiA and other fungal PKS-NRPSs (NRPs) indicated that the EpiA is l-alanine incorporating tetramates megasynthase. Furthermore, based on the molecular structures of epicoccamide A and deduced gene functions of the cluster epi, a hypothetic metabolic pathway for biosynthesizing compound 1 was proposed. The corresponding tetramates releasing during epicoccamide A biosynthesis was catalyzed through Dieckmann-type cyclization, in which the reductive (R) domain residing in terminal module of EpiA accomplished the conversion. These results unveiled the underlying mechanism of epicoccamides biosynthesis and these findings might provide opportunities for derivatization of epicoccamides or generation of new chemical entities.ConclusionGenome mining and genetic inactivation experiments unveiled a previously uncharacterized PKS − NRPS hybrid-based BGC epi responsible for the generation of epicoccamide A (1) in endophyte Epicoccum sp. CPCC 400996. In addition, based on the gene cluster data, a hypothetical biosynthetic pathway of epicoccamide A was proposed.

Molecular and kinetic properties of three acetylcholinesterases in the Varroa mite, Varroa destructor

The Varroa mite, Varroa destructor, poses one of the most serious threats to honey bees worldwide. Although coumaphos, an anticholinesterase pesticide, is widely used for varroa mite control, little information is available on the properties of Varroa mite acetylcholinesterases (VdAChEs). In this study, three putative VdAChEs were annotated and named VdAChE1, VdAChE2, and VdAChE3. All VdAChEs possessed most of the functionally important signature domains, suggesting that they are catalytically active. Phylogenetic analysis revealed that VdAChE1 was clustered into a clade containing most arthropod AChE1s, whereas VdAChE2 and VdAChE3 formed a unique clade with other arachnid AChEs. VdAChE1 was determined to be membrane-anchored, but both VdAChE2 and VdAChE3 are soluble, as judged by electrophoresis in conjunction with western blotting. Tissue-specific transcription profiling revealed that VdAChE1 was most predominantly expressed in the synganglion. In contrast, VdAChE2 was most predominantly expressed in the legs and cuticle. VdAChE3 showed negligible expression levels in all the tissues examined. In a kinetic analysis using recombinant VdAChEs, VdAChE1 exhibited the highest catalytic efficiency, followed by VdAChE2 and VdAChE3. Inhibition experiments revealed that VdAChE1 was most sensitive to all tested inhibitors. Taken together, VdAChE1 appears to be the major synaptic enzyme with a more toxicological relevance, whereas VdAChE2 is involved in other noncatalytic functions, including chemical defense against xenobiotics. Current findings contribute to a more detailed understanding of the evolutionary and functional traits of VdAChEs and to the design of novel anticholinesterase varroacides.

Genome-wide identification and expression analysis of CRK gene family in chili pepper (Capsicum annuum L.) in response to Colletotrichum truncatum infection

ABSTRACT The cysteine-rich receptor-like kinases (CRKs) belong to the plant receptor-like kinases family and have multitudinous roles, including stress responses. However, information on CRKs in chili pepper (Capsicum annuum L.) plants is limited. In this study, a total of 22 C. annuum CRKs (CaCRKs) have been identified in the chili genome. All the identified CaCRKs were mapped onto different chili chromosomes. The gene duplication analysis revealed that five gene pairs had the Ka/Ks ratio greater than one, suggesting the positive selection of CaCRKs in chili. Phylogenetic analysis grouped the CaCRKs into four groups alongside other plant CRKs. The structural characterization of the CaCRKs revealed that all of them carry the signature domains and motifs. The gene ontology analysis predicted their major potential functions to be stress response and protein kinase activity. The expression analysis the CaCRKs in two contrasting chili varieties under Colletotrichum truncatum infection added valuable insights into their involvement in chili-C. truncatum interactions. The comparison of expression dynamics suggested that CaCRK13 could be a potential candidate gene in regulating chili defense against anthracnose pathogen. Moreover, the results of this study will help to get insights into the chili CRKs and their involvement in chili defense response against C. truncatum.

Structural mechanism of protein recognition by the FW domain of autophagy receptor Nbr1

Neighbor of BRCA1 (Nbr1) is a conserved autophagy receptor that provides cargo selectivity to autophagy. The four-tryptophan (FW) domain is a signature domain of Nbr1, but its exact function remains unclear. Here, we show that Nbr1 from the filamentous fungus Chaetomium thermophilum uses its FW domain to bind the α-mannosidase Ams1, a cargo of selective autophagy in both budding yeast and fission yeast, and delivers Ams1 to the vacuole by conventional autophagy in heterologous fission yeast. The structure of the Ams1-FW complex was determined at 2.2 Å resolution by cryo-electron microscopy. The FW domain adopts an immunoglobulin-like β-sandwich structure and recognizes the quaternary structure of the Ams1 tetramer. Notably, the N-terminal di-glycine of Ams1 is specifically recognized by a conserved pocket of the FW domain. The FW domain becomes degenerated in fission yeast Nbr1, which binds Ams1 with a ZZ domain instead. Our findings illustrate the protein binding mode of the FW domain and reveal the versatility of Nbr1-mediated cargo recognition.

The Histone Acetyltransferase HpGCN5 Involved in the Regulation of Abiotic Stress Responses and Astaxanthin Accumulation in Haematococcus pluvialis.

The histone acetyltransferases (HATs), together with histone deacetylases, regulate the gene transcription related to various biological processes, including stress responses in eukaryotes. This study found a member of HATs (HpGCN5) from a transcriptome of the economically important microalgae Haematococcus pluvialis. Its expression pattern responding to multiple abiotic stresses and its correlation with transcription factors and genes involved in triacylglycerols and astaxanthin biosynthesis under stress conditions were evaluated, aiming to discover its potential biological function. The isolated HpGCN5 was 1,712 bp in length encoding 415 amino acids. The signature domains of Acetyltransf_1 and BROMO were presented, as the GCN5 gene from Arabidopsis and Saccharomyces cerevisiae, confirming that HpGCN5 belongs to the GCN5 subfamily of the GNAT superfamily. The phylogenetic analysis revealed that HpGCN5 is grouped with GNAT genes from algae and is closer to that from higher plants, compared with yeast, animal, fungus, and bacteria. It was predicted that HpGCN5 is composed of 10 exons and contains multiple stress-related cis-elements in the promoter region, revealing its potential role in stress regulation. Real-time quantitative PCR revealed that HpGCN5 responds to high light and high salt stresses in similar behavior, evidenced by their down-regulation exposing to stresses. Differently, HpGCN5 expression was significantly induced by SA and Nitrogen-depletion stresses at the early stage but was dropped back after then. The correlation network analysis suggested that HpGCN5 has a strong correlation with major genes and a transcription factor involved in astaxanthin biosynthesis. Besides, the correlation was only found between HpGCN5 and a few genes involved in triacylglycerols biosynthesis. Therefore, this study proposed that HpGCN5 might play a role in the regulation of astaxanthin biosynthesis. This study firstly examined the role of HATs in stress regulation and results will enrich our understanding of the role of HATs in microalgae.

Next generation sequencing and transcriptome analysis for identification of ARF and Aux/IAA in pointed gourd (Trichosanthes dioica Roxb.), a non-model plant

The Pointed gourd (Trichosanthes dioica Roxb.) belonging to the family Cucurbitaceae is a tropical perennial vegetable with an origin in the Indian subcontinent. There is a lack of genetic information for this commercially important cucurbit. A comprehensive transcriptome analysis of the T. dioica Roxb. ovary was carried out in this study. The BLAST-hits analysis of significantly annotated CDS of both samples revealed that pointed gourd is significantly related to cucumber (Cucumis sativus). A total of 10,996 annotated CDS was commonly identified in both samples. Notably, 1,859 CDS were found significantly down-regulated while 1,194 CDS were found up-regulated. 904 CDS of 1DBP and 971 CDS of 2DAF were identified to have SSRs. The auxin-dependent phenomenon in plant physiology, auxin signaling, is primarily regulated by transcription factors, such as ARF and Aux/IAA. The in-silico studies were carried out to identify the transcripts of ARFs and IAAs in T. dioica Roxb. A total of 48 ARF transcripts and 37 Aux/IAA transcripts were identified and named as TdARFs and TdIAAs, respectively. The peptides of TdARFs and TdIAAs are distributed in clusters to show similarity and evolutionary divergence. More than 70% of the peptide sequences derived from CDS of TdARFs and TdIAAs have their signature domains. The sub-cellular localization predicted that TdARF and TdIAA were found mainly in the nucleus. This study will pave the way further for elucidating the precise role of these transcription factors in auxin signaling and subsequent genetic manipulations for crop improvement. Additionally, the data sets gathered from whole transcriptome sequencing and analysis are useful resources for further studies regarding molecular genetics and functional genomics of T. dioica Roxb.

Molecular characterization, expression and functional analysis of large yellow croaker (Larimichthys crocea) peroxisome proliferator-activated receptor gamma

The peroxisome proliferator-activated receptor gamma (PPARγ) are nuclear receptors with distinct roles in energy metabolism and immunity. Although extensively studied in mammals, immunomodulatory roles of this molecule in teleost fish remain to be investigated. In this study, large yellow croaker (Larimichthys crocea) PPARγ (LcPPARγ) sequence was cloned, which encodes a polypeptide of 541 amino acids that include signature domains belonging to the nuclear receptor superfamily. Phylogenetically, LcPPARγ was most closely related to PPARγ derived from European sea bass (Dicentrarchus labrax). Quantitative analysis shown a ubiquitous expression of this molecule, with highest expression level detected in the intestine. The expression of LcPPARγ was decreased in the intestine, muscle, body kidney, spleen and head kidney-derived monocytes/macrophages (MO/MФs) over the course of Vibrio alginolyticus (V. alginolyticus) infection. In contrast, an up-regulation of LcPPARγ was observed in head kidney-derived MO/MФs following docosahexaenoic acid (DHA) treatment. This increase in LcPPARγ leads to an up-regulation of LcCD11b and LcCD18 and an enhancement of complement-mediated phagocytosis. Furthermore, cytokine secretions of V. alginolyticus-stimulated MO/MФs were modulated following LcPPARγ activations that up-regulated the expression of LcIL-10, while decreased the expression of LcIL-1β, LcTNF-α and LcTGF-β1. Overall, our results indicated that LcPPARγ plays a role in regulating functions of MO/MФs and likely contribute to MO/MФs polarization.

Investigation of Roles of TaTALE Genes during Development and Stress Response in Bread Wheat.

The three amino acid loop extension (TALE) genes of the homeobox superfamily are responsible for numerous biological functions in plants. Herein, we identified a total of 72 TaTALE genes in the allohexaploid genome of bread wheat (Triticum aestivum L.) and performed a comprehensive investigation for gene and protein structural properties, phylogeny, expression patterns, and multilevel gene regulations. The identified TaTALE proteins were further classified into two groups, TaBLHs and TaKNOXs, which were tightly clustered into the phylogeny. The negative Ka/Ks ratio of duplicated genes suggested purifying selection pressure with confined functional divergence. Various signature domains and motifs were found conserved in both groups of proteins. The occurrence of diverse cis-regulatory elements and modulated expression during various developmental stages and in the presence of abiotic (heat, drought, salt) and two different fungal stresses suggested their roles in development and stress response, as well. The interaction of TaTALEs with the miRNAs and other development-related homeobox proteins also suggested their roles in growth and development and stress response. The present study revealed several important aspects of TaTALEs that will be useful in further functional validation of these genes in future studies.