Genes

24 pages, 2390 KiB

Open AccessArticle

Genome-Guided Analysis of Clostridium ultunense and Comparative Genomics Reveal Different Strategies for Acetate Oxidation and Energy Conservation in Syntrophic Acetate-Oxidising Bacteria

by Shahid Manzoor, Anna Schnürer, Erik Bongcam-Rudloff and Bettina Müller

Genes 2018, 9(4), 225; https://doi.org/10.3390/genes9040225 - 23 Apr 2018

Cited by 26 | Viewed by 6259

Abstract

Syntrophic acetate oxidation operates close to the thermodynamic equilibrium and very little is known about the participating organisms and their metabolism. Clostridium ultunense is one of the most abundant syntrophic acetate-oxidising bacteria (SAOB) that are found in engineered biogas processes operating with high [...] Read more.

Syntrophic acetate oxidation operates close to the thermodynamic equilibrium and very little is known about the participating organisms and their metabolism. Clostridium ultunense is one of the most abundant syntrophic acetate-oxidising bacteria (SAOB) that are found in engineered biogas processes operating with high ammonia concentrations. It has been proven to oxidise acetate in cooperation with hydrogenotrophic methanogens. There is evidence that the Wood-Ljungdahl (WL) pathway plays an important role in acetate oxidation. In this study, we analysed the physiological and metabolic capacities of C. ultunense strain Esp and strain BS^T on genome scale and conducted a comparative study of all the known characterised SAOB, namely Syntrophaceticus schinkii, Thermacetogenium phaeum, Tepidanaerobacter acetatoxydans, and Pseudothermotoga lettingae. The results clearly indicated physiological robustness to be beneficial for anaerobic digestion environments and revealed unexpected metabolic diversity with respect to acetate oxidation and energy conservation systems. Unlike S. schinkii and Th. phaeum, C. ultunense clearly does not employ the oxidative WL pathway for acetate oxidation, as its genome (and that of P. lettingae) lack important key genes. In both of those species, a proton motive force is likely formed by chemical protons involving putative electron-bifurcating [Fe-Fe] hydrogenases rather than proton pumps. No genes encoding a respiratory Ech (energy-converting hydrogenase), as involved in energy conservation in Th. phaeum and S. schinkii, were identified in C. ultunense and P. lettingae. Moreover, two respiratory complexes sharing similarities to the proton-translocating ferredoxin:NAD⁺ oxidoreductase (Rnf) and the Na⁺ pumping NADH:quinone hydrogenase (NQR) were predicted. These might form a respiratory chain that is involved in the reduction of electron acceptors rather than protons. However, involvement of these complexes in acetate oxidation in C. ultunense and P. lettingae needs further study. This genome-based comparison provides a solid platform for future meta-proteomics and meta-transcriptomics studies and for metabolic engineering, control, and monitoring of SAOB. Full article

(This article belongs to the Special Issue Microbial Metabolic Engineering)

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16 pages, 9644 KiB

Open AccessArticle

Genome Wide Identification, Evolutionary, and Expression Analysis of VQ Genes from Two Pyrus Species

by Yunpeng Cao, Dandan Meng, Muhammad Abdullah, Qing Jin, Yi Lin and Yongping Cai

Genes 2018, 9(4), 224; https://doi.org/10.3390/genes9040224 - 23 Apr 2018

Cited by 17 | Viewed by 4687

Abstract

The VQ motif-containing gene, a member of the plant-specific genes, is involved in the plant developmental process and various stress responses. The VQ motif-containing gene family has been studied in several plants, such as rice (Oryza sativa), maize (Zea mays [...] Read more.

The VQ motif-containing gene, a member of the plant-specific genes, is involved in the plant developmental process and various stress responses. The VQ motif-containing gene family has been studied in several plants, such as rice (Oryza sativa), maize (Zea mays), and Arabidopsis (Arabidopsis thaliana). However, no systematic study has been performed in Pyrus species, which have important economic value. In our study, we identified 41 and 28 VQ motif-containing genes in Pyrus bretschneideri and Pyrus communis, respectively. Phylogenetic trees were calculated using A. thaliana and O. sativa VQ motif-containing genes as a template, allowing us to categorize these genes into nine subfamilies. Thirty-two and eight paralogous of VQ motif-containing genes were found in P. bretschneideri and P. communis, respectively, showing that the VQ motif-containing genes had a more remarkable expansion in P. bretschneideri than in P. communis. A total of 31 orthologous pairs were identified from the P. bretschneideri and P. communis VQ motif-containing genes. Additionally, among the paralogs, we found that these duplication gene pairs probably derived from segmental duplication/whole-genome duplication (WGD) events in the genomes of P. bretschneideri and P. communis, respectively. The gene expression profiles in both P. bretschneideri and P. communis fruits suggested functional redundancy for some orthologous gene pairs derived from a common ancestry, and sub-functionalization or neo-functionalization for some of them. Our study provided the first systematic evolutionary analysis of the VQ motif-containing genes in Pyrus, and highlighted the diversification and duplication of VQ motif-containing genes in both P. bretschneideri and P. communis. Full article

(This article belongs to the Section Plant Genetics and Genomics)

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15 pages, 2496 KiB

Open AccessArticle

Divergent Roles of RPA Homologs of the Model Archaeon Halobacterium salinarum in Survival of DNA Damage

by Jessica J. Evans, Patrick E. Gygli, Julienne McCaskill and Linda C. DeVeaux

Genes 2018, 9(4), 223; https://doi.org/10.3390/genes9040223 - 20 Apr 2018

Cited by 5 | Viewed by 4906

Abstract

The haloarchaea are unusual in possessing genes for multiple homologs to the ubiquitous single-stranded DNA binding protein (SSB or replication protein A, RPA) found in all three domains of life. Halobacterium salinarum contains five homologs: two are eukaryotic in organization, two are prokaryotic [...] Read more.

The haloarchaea are unusual in possessing genes for multiple homologs to the ubiquitous single-stranded DNA binding protein (SSB or replication protein A, RPA) found in all three domains of life. Halobacterium salinarum contains five homologs: two are eukaryotic in organization, two are prokaryotic and are encoded on the minichromosomes, and one is uniquely euryarchaeal. Radiation-resistant mutants previously isolated show upregulation of one of the eukaryotic-type RPA genes. Here, we have created deletions in the five RPA operons. These deletion mutants were exposed to DNA-damaging conditions: ionizing radiation, UV radiation, and mitomycin C. Deletion of the euryarchaeal homolog, although not lethal as in Haloferax volcanii, causes severe sensitivity to all of these agents. Deletion of the other RPA/SSB homologs imparts a variable sensitivity to these DNA-damaging agents, suggesting that the different RPA homologs have specialized roles depending on the type of genomic insult encountered. Full article

(This article belongs to the Special Issue Genetics and Genomics of Extremophiles)

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1 pages, 195 KiB

Open AccessErratum

Erratum: Jimena Soledad Cadona, et al.; Pathogenicity Islands Distribution in Non-O157 Shiga Toxin-Producing Escherichia coli (STEC). Genes 2018, 9, 81

by Jimena Soledad Cadona, Ana Victoria Bustamante, Juliana González and Andrea Mariel Sanso

Genes 2018, 9(4), 222; https://doi.org/10.3390/genes9040222 - 20 Apr 2018

Viewed by 3083

Abstract

We wish to make the following correction to the paper by Soledad-Cadona et al.[...] Full article

(This article belongs to the Special Issue Genetics and Genomics of Foodborne Pathogens)

14 pages, 5752 KiB

Open AccessArticle

Genome-Wide Analyses of Calcium Sensors Reveal Their Involvement in Drought Stress Response and Storage Roots Deterioration after Harvest in Cassava

by Wei Hu, Yan Yan, Weiwei Tie, Zehong Ding, Chunlai Wu, Xupo Ding, Wenquan Wang, Zhiqiang Xia, Jianchun Guo and Ming Peng

Genes 2018, 9(4), 221; https://doi.org/10.3390/genes9040221 - 19 Apr 2018

Cited by 8 | Viewed by 4481

Abstract

Calcium (Ca²⁺) plays a crucial role in plant development and responses to environmental stimuli. Currently, calmodulins (CaMs), calmodulin-like proteins (CMLs), and calcineurin B-like proteins (CBLs), such as Ca²⁺ sensors, are not well understood in cassava (Manihot esculenta Crantz), an [...] Read more.

Calcium (Ca²⁺) plays a crucial role in plant development and responses to environmental stimuli. Currently, calmodulins (CaMs), calmodulin-like proteins (CMLs), and calcineurin B-like proteins (CBLs), such as Ca²⁺ sensors, are not well understood in cassava (Manihot esculenta Crantz), an important tropical crop. In the present study, 8 CaMs, 48 CMLs, and 9 CBLs were genome-wide identified in cassava, which were divided into two, four, and four groups, respectively, based on evolutionary relationship, protein motif, and gene structure analyses. Transcriptomic analysis revealed the expression diversity of cassava CaMs-CMLs-CBLs in distinct tissues and in response to drought stress in different genotypes. Generally, cassava CaMs-CMLs-CBLs showed different expression profiles between cultivated varieties (Arg7 and SC124) and wild ancestor (W14) after drought treatment. In addition, numerous CaMs-CMLs-CBLs were significantly upregulated at 6 h, 12 h, and 48 h after harvest, suggesting their possible role during storage roots (SR) deterioration. Further interaction network and co-expression analyses suggested that a CBL-mediated interaction network was widely involved in SR deterioration. Taken together, this study provides new insights into CaMs-CMLs-CBLs-mediated drought adaption and SR deterioration at the transcription level in cassava, and identifies some candidates for the genetic improvement of cassava. Full article

(This article belongs to the Section Plant Genetics and Genomics)

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14 pages, 2700 KiB

Open AccessArticle

Full Mitogenomes in the Critically Endangered Kākāpō Reveal Major Post-Glacial and Anthropogenic Effects on Neutral Genetic Diversity

by Nicolas Dussex, Johanna Von Seth, Bruce C. Robertson and Love Dalén

Genes 2018, 9(4), 220; https://doi.org/10.3390/genes9040220 - 19 Apr 2018

Cited by 27 | Viewed by 8392

Abstract

Understanding how species respond to population declines is a central question in conservation and evolutionary biology. Population declines are often associated with loss of genetic diversity, inbreeding and accumulation of deleterious mutations, which can lead to a reduction in fitness and subsequently contribute [...] Read more.

Understanding how species respond to population declines is a central question in conservation and evolutionary biology. Population declines are often associated with loss of genetic diversity, inbreeding and accumulation of deleterious mutations, which can lead to a reduction in fitness and subsequently contribute to extinction. Using temporal approaches can help us understand the effects of population declines on genetic diversity in real time. Sequencing pre-decline as well as post-decline mitogenomes representing all the remaining mitochondrial diversity, we estimated the loss of genetic diversity in the critically endangered kākāpō (Strigops habroptilus). We detected a signal of population expansion coinciding with the end of the Pleistocene last glacial maximum (LGM). Also, we found some evidence for northern and southern lineages, supporting the hypothesis that the species may have been restricted to isolated northern and southern refugia during the LGM. We observed an important loss of neutral genetic diversity associated with European settlement in New Zealand but we could not exclude a population decline associated with Polynesian settlement in New Zealand. However, we did not find evidence for fixation of deleterious mutations. We argue that despite high pre-decline genetic diversity, a rapid and range-wide decline combined with the lek mating system, and life-history traits of kākāpō contributed to a rapid loss of genetic diversity following severe population declines. Full article

(This article belongs to the Special Issue Conservation Genetics and Genomics)

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15 pages, 1297 KiB

Open AccessArticle

Patchoulol Production with Metabolically Engineered Corynebacterium glutamicum

by Nadja A. Henke, Julian Wichmann, Thomas Baier, Jonas Frohwitter, Kyle J. Lauersen, Joe M. Risse, Petra Peters-Wendisch, Olaf Kruse and Volker F. Wendisch

Genes 2018, 9(4), 219; https://doi.org/10.3390/genes9040219 - 17 Apr 2018

Cited by 60 | Viewed by 9697

Abstract

Patchoulol is a sesquiterpene alcohol and an important natural product for the perfume industry. Corynebacterium glutamicum is the prominent host for the fermentative production of amino acids with an average annual production volume of ~6 million tons. Due to its robustness and well [...] Read more.

Patchoulol is a sesquiterpene alcohol and an important natural product for the perfume industry. Corynebacterium glutamicum is the prominent host for the fermentative production of amino acids with an average annual production volume of ~6 million tons. Due to its robustness and well established large-scale fermentation, C. glutamicum has been engineered for the production of a number of value-added compounds including terpenoids. Both C40 and C50 carotenoids, including the industrially relevant astaxanthin, and short-chain terpenes such as the sesquiterpene valencene can be produced with this organism. In this study, systematic metabolic engineering enabled construction of a patchoulol producing C. glutamicum strain by applying the following strategies: (i) construction of a farnesyl pyrophosphate-producing platform strain by combining genomic deletions with heterologous expression of ispA from Escherichia coli; (ii) prevention of carotenoid-like byproduct formation; (iii) overproduction of limiting enzymes from the 2-c-methyl-d-erythritol 4-phosphate (MEP)-pathway to increase precursor supply; and (iv) heterologous expression of the plant patchoulol synthase gene PcPS from Pogostemon cablin. Additionally, a proof of principle liter-scale fermentation with a two-phase organic overlay-culture medium system for terpenoid capture was performed. To the best of our knowledge, the patchoulol titers demonstrated here are the highest reported to date with up to 60 mg L⁻¹ and volumetric productivities of up to 18 mg L⁻¹ d⁻¹. Full article

(This article belongs to the Special Issue Microbial Metabolic Engineering)

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16 pages, 7330 KiB

Open AccessArticle

Genetic Evaluation of Natural Populations of the Endangered Conifer Thuja koraiensis Using Microsatellite Markers by Restriction-Associated DNA Sequencing

by Lu Hou, Yanhong Cui, Xiang Li, Wu Chen, Zhiyong Zhang, Xiaoming Pang and Yingyue Li

Genes 2018, 9(4), 218; https://doi.org/10.3390/genes9040218 - 17 Apr 2018

Cited by 9 | Viewed by 4859

Abstract

Thuja koraiensis Nakai is an endangered conifer of high economic and ecological value in Jilin Province, China. However, studies on its population structure and conservation genetics have been limited by the lack of genomic data. Here, 37,761 microsatellites (simple sequence repeat, SSR) were [...] Read more.

Thuja koraiensis Nakai is an endangered conifer of high economic and ecological value in Jilin Province, China. However, studies on its population structure and conservation genetics have been limited by the lack of genomic data. Here, 37,761 microsatellites (simple sequence repeat, SSR) were detected based on 875,792 de novo-assembled contigs using a restriction-associated DNA (RAD) approach. Among these SSRs, 300 were randomly selected to test for polymorphisms and 96 obtained loci were able to amplify a fragment of expected size. Twelve polymorphic SSR markers were developed to analyze the genetic diversity and population structure of three natural populations. High genetic diversity (mean N_A = 5.481, H_E = 0.548) and moderate population differentiation (pairwise F_st = 0.048–0.078, N_m = 2.940–4.958) were found in this species. Molecular variance analysis suggested that most of the variation (83%) existed within populations. Combining the results of STRUCTURE, principal coordinate, and neighbor-joining analysis, the 232 individuals were divided into three genetic clusters that generally correlated with their geographical distributions. Finally, appropriate conservation strategies were proposed to protect this species. This study provides genetic information for the natural resource conservation and utilization of T. koraiensis and will facilitate further studies of the evolution and phylogeography of the species. Full article

(This article belongs to the Section Plant Genetics and Genomics)

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17 pages, 6742 KiB

Open AccessArticle

The Effects on Parapatric Divergence of Linkage between Preference and Trait Loci versus Pleiotropy

by Maria R. Servedio and Reinhard Bürger

Genes 2018, 9(4), 217; https://doi.org/10.3390/genes9040217 - 17 Apr 2018

Cited by 11 | Viewed by 4299

Abstract

Attempts to uncover the genetic basis of female mating preferences and male signals involved in reproductive isolation have discovered intriguing cases in which loci contributing to these traits co-localize in their chromosomal positions. Such discoveries raise the question of whether alleles at certain [...] Read more.

Attempts to uncover the genetic basis of female mating preferences and male signals involved in reproductive isolation have discovered intriguing cases in which loci contributing to these traits co-localize in their chromosomal positions. Such discoveries raise the question of whether alleles at certain loci contribute pleiotropically to male and female components of premating reproductive isolation, versus whether these loci are merely tightly linked. Here we use population genetic models to assess the degree to which these alternatives affect both short term and equilibrium patterns of trait (signal) and preference divergence. We take advantage of the fact that in the case of secondary contact between populations exchanging migrants, patterns of divergence across the range of preference strengths differ markedly when preferences and traits are controlled by the same locus (the case of phenotype matching) versus when they are on separate chromosomes. We find that tight linkage between preference and trait loci can mimic the pleiotropic pattern for many generations (roughly the reciprocal of the recombination rate), but that any recombination ultimately results in equilibrium patterns of divergence far more similar to those found when preferences and traits are on separate chromosomes. In general, our finding that pleiotropy results in quite different long-term patterns from tight linkage highlights the importance of distinguishing between these possibilities in empirical systems. Full article

(This article belongs to the Special Issue Evolutionary Genetics of Reproductive Isolation)

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18 pages, 5744 KiB

Open AccessArticle

Accurate Classification of NF1 Gene Variants in 84 Italian Patients with Neurofibromatosis Type 1

by Alessandro Stella, Patrizia Lastella, Daria Carmela Loconte, Nenad Bukvic, Dora Varvara, Margherita Patruno, Rosanna Bagnulo, Rosaura Lovaglio, Nicola Bartolomeo, Gabriella Serio and Nicoletta Resta

Genes 2018, 9(4), 216; https://doi.org/10.3390/genes9040216 - 17 Apr 2018

Cited by 22 | Viewed by 6979

Abstract

Neurofibromatosis type 1 (NF1) is one of the most common autosomal dominant genetic diseases. It is caused by mutations in the NF1 gene encoding for the large protein, neurofibromin. Genetic testing of NF1 is cumbersome because 50% of cases are sporadic, and there [...] Read more.

Neurofibromatosis type 1 (NF1) is one of the most common autosomal dominant genetic diseases. It is caused by mutations in the NF1 gene encoding for the large protein, neurofibromin. Genetic testing of NF1 is cumbersome because 50% of cases are sporadic, and there are no mutation hot spots. In addition, the most recognizable NF1 clinical features—café-au-lait (CALs) spots and axillary and/or inguinal freckling—appear early in childhood but are rather non-specific. Thus, the identification of causative variants is extremely important for early diagnosis, especially in paediatric patients. Here, we aimed to identify the underlying genetic defects in 72 index patients referred to our centre for NF1. Causative mutations were identified in 58 subjects, with 29 being novel changes. We evaluated missense and non-canonical splicing mutations with both protein and splicing prediction algorithms. The ratio of splicing mutations detected was higher than that reported in recent patients’ series and in the Human Gene Mutation Database (HGMD). After applying in silico predictive tools to 41 previously reported missense variants, we demonstrated that 46.3% of these putatively missense mutations were forecasted to alter splicing instead. Our data suggest that mutations affecting splicing can be frequently underscored if not analysed in depth. We confirm that hamartomas can be useful for diagnosing NF1 in children. Lisch nodules and cutaneous neurofibromas were more frequent in patients with frameshifting mutations. In conclusion, we demonstrated that comprehensive in silico analysis can be a highly specific method for predicting the nature of NF1 mutations and may help in assuring proper patient care. Full article

(This article belongs to the Section Human Genomics and Genetic Diseases)

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10 pages, 498 KiB

Open AccessEditorial

Special Issue Introduction: Inherited Retinal Disease: Novel Candidate Genes, Genotype–Phenotype Correlations, and Inheritance Models

by Frans P. M. Cremers, Camiel J. F. Boon, Kinga Bujakowska and Christina Zeitz

Genes 2018, 9(4), 215; https://doi.org/10.3390/genes9040215 - 16 Apr 2018

Cited by 62 | Viewed by 8401

Abstract

Inherited retinal diseases (IRDs) are genetically and clinically heterogeneous disorders.[...] Full article

(This article belongs to the Special Issue Inherited Retinal Disease: Novel Candidate Genes, Genotype–Phenotype Correlations and Inheritance Models)

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19 pages, 4320 KiB

Open AccessArticle

Identification of Major Rhizobacterial Taxa Affected by a Glyphosate-Tolerant Soybean Line via Shotgun Metagenomic Approach

by Gui-Hua Lu, Xiao-Mei Hua, Li Liang, Zhong-Ling Wen, Mei-Hang Du, Fan-Fan Meng, Yan-Jun Pang, Jin-Liang Qi, Cheng-Yi Tang and Yong-Hua Yang

Genes 2018, 9(4), 214; https://doi.org/10.3390/genes9040214 - 16 Apr 2018

Cited by 9 | Viewed by 6302

Abstract

The worldwide commercial cultivation of transgenic crops, including glyphosate-tolerant (GT) soybeans, has increased widely during the past 20 years. However, it is accompanied with a growing concern about potential effects of transgenic crops on the soil microbial communities, especially on rhizosphere bacterial communities. [...] Read more.

The worldwide commercial cultivation of transgenic crops, including glyphosate-tolerant (GT) soybeans, has increased widely during the past 20 years. However, it is accompanied with a growing concern about potential effects of transgenic crops on the soil microbial communities, especially on rhizosphere bacterial communities. Our previous study found that the GT soybean line NZL06-698 (N698) significantly affected rhizosphere bacteria, including some unidentified taxa, through 16S rRNA gene (16S rDNA) V4 region amplicon deep sequencing via Illumina MiSeq. In this study, we performed 16S rDNA V5–V7 region amplicon deep sequencing via Illumina MiSeq and shotgun metagenomic approaches to identify those major taxa. Results of these processes revealed that the species richness and evenness increased in the rhizosphere bacterial communities of N698, the beta diversity of the rhizosphere bacterial communities of N698 was affected, and that certain dominant bacterial phyla and genera were related to N698 compared with its control cultivar Mengdou12. Consistent with our previous findings, this study showed that N698 affects the rhizosphere bacterial communities. In specific, N698 negatively affects Rahnella, Janthinobacterium, Stenotrophomonas, Sphingomonas and Luteibacter while positively affecting Arthrobacter, Bradyrhizobium, Ramlibacter and Nitrospira. Full article

(This article belongs to the Special Issue Emerging Applications for Next Generation Sequencing)

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9 pages, 591 KiB

Open AccessArticle

Genome Sequence of the Freshwater Yangtze Finless Porpoise

by Yuan Yuan, Peijun Zhang, Kun Wang, Mingzhong Liu, Jing Li, Jinsong Zheng, Ding Wang, Wenjie Xu, Mingli Lin, Lijun Dong, Chenglong Zhu, Qiang Qiu and Songhai Li

Genes 2018, 9(4), 213; https://doi.org/10.3390/genes9040213 - 16 Apr 2018

Cited by 15 | Viewed by 7039

Abstract

The Yangtze finless porpoise (Neophocaena asiaeorientalis ssp. asiaeorientalis) is a subspecies of the narrow-ridged finless porpoise (N. asiaeorientalis). In total, 714.28 gigabases (Gb) of raw reads were generated by whole-genome sequencing of the Yangtze finless porpoise, using an Illumina [...] Read more.

The Yangtze finless porpoise (Neophocaena asiaeorientalis ssp. asiaeorientalis) is a subspecies of the narrow-ridged finless porpoise (N. asiaeorientalis). In total, 714.28 gigabases (Gb) of raw reads were generated by whole-genome sequencing of the Yangtze finless porpoise, using an Illumina HiSeq 2000 platform. After filtering the low-quality and duplicated reads, we assembled a draft genome of 2.22 Gb, with contig N50 and scaffold N50 values of 46.69 kilobases (kb) and 1.71 megabases (Mb), respectively. We identified 887.63 Mb of repetitive sequences and predicted 18,479 protein-coding genes in the assembled genome. The phylogenetic tree showed a relationship between the Yangtze finless porpoise and the Yangtze River dolphin, which diverged approximately 20.84 million years ago. In comparisons with the genomes of 10 other mammals, we detected 44 species-specific gene families, 164 expanded gene families, and 313 positively selected genes in the Yangtze finless porpoise genome. The assembled genome sequence and underlying sequence data are available at the National Center for Biotechnology Information under BioProject accession number PRJNA433603. Full article

(This article belongs to the Special Issue Conservation Genetics and Genomics)

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15 pages, 31469 KiB

Open AccessArticle

Transcriptomic Analysis of Flower Bud Differentiation in Magnolia sinostellata

by Lijie Fan, Mengqian Chen, Bin Dong, Ninghang Wang, Qin Yu, Xingli Wang, Lingjuan Xuan, Yaling Wang, Shouzhou Zhang and Yamei Shen

Genes 2018, 9(4), 212; https://doi.org/10.3390/genes9040212 - 16 Apr 2018

Cited by 32 | Viewed by 8132

Abstract

Magnolias are widely cultivated for their beautiful flowers, but despite their popularity, the molecular mechanisms regulating flower bud differentiation have not been elucidated. Here, we used paraffin sections and RNA-seq to study the process of flower bud differentiation in Magnolia sinostellata. Flower [...] Read more.

Magnolias are widely cultivated for their beautiful flowers, but despite their popularity, the molecular mechanisms regulating flower bud differentiation have not been elucidated. Here, we used paraffin sections and RNA-seq to study the process of flower bud differentiation in Magnolia sinostellata. Flower bud development occurred between 28 April and 30 May 2017 and was divided into five stages: undifferentiated, early flower bud differentiation, petal primordium differentiation, stamen primordium differentiation, and pistil primordium differentiation. A total of 52,441 expressed genes were identified, of which 11,592 were significantly differentially expressed in the five bud development stages. Of these, 82 genes were involved in the flowering. In addition, MADS-box and AP2 family genes play critical roles in the formation of flower organs and 20 differentially expressed genes associated with flower bud differentiation were identified in M. sinostellata. A qRT-PCR analysis verified that the MADS-box and AP2 family genes were expressed at high levels during flower bud differentiation. Consequently, this study provides a theoretical basis for the genetic regulation of flowering in M. sinostellata, which lays a foundation for further research into flowering genes and may facilitate the development of new cultivars. Full article

(This article belongs to the Section Plant Genetics and Genomics)

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17 pages, 2405 KiB

Open AccessReview

Chromatin Architectural Changes during Cellular Senescence and Aging

by Luyang Sun, Ruofan Yu and Weiwei Dang

Genes 2018, 9(4), 211; https://doi.org/10.3390/genes9040211 - 16 Apr 2018

Cited by 52 | Viewed by 11502

Abstract

Chromatin 3D structure is highly dynamic and associated with many biological processes, such as cell cycle progression, cellular differentiation, cell fate reprogramming, cancer development, cellular senescence, and aging. Recently, by using chromosome conformation capture technologies, tremendous findings have been reported about the dynamics [...] Read more.

Chromatin 3D structure is highly dynamic and associated with many biological processes, such as cell cycle progression, cellular differentiation, cell fate reprogramming, cancer development, cellular senescence, and aging. Recently, by using chromosome conformation capture technologies, tremendous findings have been reported about the dynamics of genome architecture, their associated proteins, and the underlying mechanisms involved in regulating chromatin spatial organization and gene expression. Cellular senescence and aging, which involve multiple cellular and molecular functional declines, also undergo significant chromatin structural changes, including alternations of heterochromatin and disruption of higher-order chromatin structure. In this review, we summarize recent findings related to genome architecture, factors regulating chromatin spatial organization, and how they change during cellular senescence and aging. Full article

(This article belongs to the Special Issue The Epigenetics of Aging and Longevity)

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11 pages, 3930 KiB

Open AccessReview

Quorum Sensing and Quorum Quenching in Agrobacterium: A “Go/No Go System”?

by Yves Dessaux and Denis Faure

Genes 2018, 9(4), 210; https://doi.org/10.3390/genes9040210 - 16 Apr 2018

Cited by 30 | Viewed by 7289

Abstract

The pathogen Agrobacterium induces gall formation on a wide range of dicotyledonous plants. In this bacteria, most pathogenicity determinants are borne on the tumour inducing (Ti) plasmid. The conjugative transfer of this plasmid between agrobacteria is regulated by quorum sensing (QS). However, processes [...] Read more.

The pathogen Agrobacterium induces gall formation on a wide range of dicotyledonous plants. In this bacteria, most pathogenicity determinants are borne on the tumour inducing (Ti) plasmid. The conjugative transfer of this plasmid between agrobacteria is regulated by quorum sensing (QS). However, processes involved in the disturbance of QS also occur in this bacteria under the molecular form of a protein, TraM, inhibiting the sensing of the QS signals, and two lactonases BlcC (AttM) and AiiB that degrade the acylhomoserine lactone (AHL) QS signal. In the model Agrobacterium fabrum strain C58, several data, once integrated, strongly suggest that the QS regulation may not be reacting only to cell concentration. Rather, these QS elements in association with the quorum quenching (QQ) activities may constitute an integrated and complex “go/no go system” that finely controls the biologically costly transfer of the Ti plasmid in response to multiple environmental cues. This decision mechanism permits the bacteria to sense whether it is in a gall or not, in a living or decaying tumor, in stressed plant tissues, etc. In this scheme, the role of the lactonases selected and maintained in the course of Ti plasmid and agrobacterial evolution appears to be pivotal. Full article

(This article belongs to the Special Issue Genetic Networks and Gene Regulation Mechanisms for Quorum Sensing and Quorum Quenching in Bacteria)

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26 pages, 47248 KiB

Open AccessArticle

A Novel G-Protein-Coupled Receptors Gene from Upland Cotton Enhances Salt Stress Tolerance in Transgenic Arabidopsis

by Pu Lu, Richard Odongo Magwanga, Hejun Lu, Joy Nyangasi Kirungu, Yangyang Wei, Qi Dong, Xingxing Wang, Xiaoyan Cai, Zhongli Zhou, Kunbo Wang and Fang Liu

Genes 2018, 9(4), 209; https://doi.org/10.3390/genes9040209 - 12 Apr 2018

Cited by 37 | Viewed by 6316

Abstract

Plants have developed a number of survival strategies which are significant for enhancing their adaptation to various biotic and abiotic stress factors. At the transcriptome level, G-protein-coupled receptors (GPCRs) are of great significance, enabling the plants to detect a wide range of endogenous [...] Read more.

Plants have developed a number of survival strategies which are significant for enhancing their adaptation to various biotic and abiotic stress factors. At the transcriptome level, G-protein-coupled receptors (GPCRs) are of great significance, enabling the plants to detect a wide range of endogenous and exogenous signals which are employed by the plants in regulating various responses in development and adaptation. In this research work, we carried out genome-wide analysis of target of Myb1 (TOM1), a member of the GPCR gene family. The functional role of TOM1 in salt stress tolerance was studied using a transgenic Arabidopsis plants over-expressing the gene. By the use of the functional domain PF06454, we obtained 16 TOM genes members in Gossypium hirsutum, 9 in Gossypium arboreum, and 11 in Gossypium raimondii. The genes had varying physiochemical properties, and it is significant to note that all the grand average of hydropathy (GRAVY) values were less than one, indicating that all are hydrophobic in nature. In all the genes analysed here, both the exonic and intronic regions were found. The expression level of Gh_A07G0747 (GhTOM) was significantly high in the transgenic lines as compared to the wild type; a similar trend in expression was observed in all the salt-related genes tested in this study. The study in epidermal cells confirmed the localization of the protein coded by the gene TOM1 in the plasma membrane. Analysis of anti-oxidant enzymes showed higher concentrations of antioxidants in transgenic lines and relatively lower levels of oxidant substances such as H₂O₂. The low malondialdehyde (MDA) level in transgenic lines indicated that the transgenic lines had relatively low level of oxidative damage compared to the wild types. The results obtained indicate that Gh_A07G0747 (GhTOM) can be a putative target gene for enhancing salt stress tolerance in plants and could be exploited in the future for the development of salt stress-tolerant cotton cultivars. Full article

(This article belongs to the Section Plant Genetics and Genomics)

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17 pages, 7271 KiB

Open AccessArticle

Identifying Patients with Atrioventricular Septal Defect in Down Syndrome Populations by Using Self-Normalizing Neural Networks and Feature Selection

by Xiaoyong Pan, Xiaohua Hu, Yu Hang Zhang, Kaiyan Feng, Shao Peng Wang, Lei Chen, Tao Huang and Yu Dong Cai

Genes 2018, 9(4), 208; https://doi.org/10.3390/genes9040208 - 12 Apr 2018

Cited by 36 | Viewed by 6827

Abstract

Atrioventricular septal defect (AVSD) is a clinically significant subtype of congenital heart disease (CHD) that severely influences the health of babies during birth and is associated with Down syndrome (DS). Thus, exploring the differences in functional genes in DS samples with and without [...] Read more.

Atrioventricular septal defect (AVSD) is a clinically significant subtype of congenital heart disease (CHD) that severely influences the health of babies during birth and is associated with Down syndrome (DS). Thus, exploring the differences in functional genes in DS samples with and without AVSD is a critical way to investigate the complex association between AVSD and DS. In this study, we present a computational method to distinguish DS patients with AVSD from those without AVSD using the newly proposed self-normalizing neural network (SNN). First, each patient was encoded by using the copy number of probes on chromosome 21. The encoded features were ranked by the reliable Monte Carlo feature selection (MCFS) method to obtain a ranked feature list. Based on this feature list, we used a two-stage incremental feature selection to construct two series of feature subsets and applied SNNs to build classifiers to identify optimal features. Results show that 2737 optimal features were obtained, and the corresponding optimal SNN classifier constructed on optimal features yielded a Matthew’s correlation coefficient (MCC) value of 0.748. For comparison, random forest was also used to build classifiers and uncover optimal features. This method received an optimal MCC value of 0.582 when top 132 features were utilized. Finally, we analyzed some key features derived from the optimal features in SNNs found in literature support to further reveal their essential roles. Full article

(This article belongs to the Special Issue Computational Approaches for Disease Gene Identification)

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15 pages, 2665 KiB

Open AccessReview

Gene Therapy for Chronic HBV—Can We Eliminate cccDNA?

by Kristie Bloom, Mohube Betty Maepa, Abdullah Ely and Patrick Arbuthnot

Genes 2018, 9(4), 207; https://doi.org/10.3390/genes9040207 - 12 Apr 2018

Cited by 64 | Viewed by 10098

Abstract

Chronic infection with the hepatitis B virus (HBV) is a global health concern and accounts for approximately 1 million deaths annually. Amongst other limitations of current anti-HBV treatment, failure to eliminate the viral covalently closed circular DNA (cccDNA) and emergence of resistance remain [...] Read more.

Chronic infection with the hepatitis B virus (HBV) is a global health concern and accounts for approximately 1 million deaths annually. Amongst other limitations of current anti-HBV treatment, failure to eliminate the viral covalently closed circular DNA (cccDNA) and emergence of resistance remain the most worrisome. Viral rebound from latent episomal cccDNA reservoirs occurs following cessation of therapy, patient non-compliance, or the development of escape mutants. Simultaneous viral co-infections, such as by HIV-1, further complicate therapeutic interventions. These challenges have prompted development of novel targeted hepatitis B therapies. Given the ease with which highly specific and potent nucleic acid therapeutics can be rationally designed, gene therapy has generated interest for antiviral application. Gene therapy strategies developed for HBV include gene silencing by harnessing RNA interference, transcriptional inhibition through epigenetic modification of target DNA, genome editing by designer nucleases, and immune modulation with cytokines. DNA-binding domains and effectors based on the zinc finger (ZF), transcription activator-like effector (TALE), and clustered regularly interspaced short palindromic repeat (CRISPR) systems are remarkably well suited to targeting episomal cccDNA. This review discusses recent developments and challenges facing the field of anti-HBV gene therapy, its potential curative significance and the progress towards clinical application. Full article

(This article belongs to the Special Issue Hepatitis B Virus Infection: An Update on Epidemiology, Diagnosis, Treatment and Prevention)

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22 pages, 6579 KiB

Open AccessArticle

Transcriptome Analysis of Two Rice Varieties Contrasting for Nitrogen Use Efficiency under Chronic N Starvation Reveals Differences in Chloroplast and Starch Metabolism-Related Genes

by Subodh Kumar Sinha, Amitha Mithra Sevanthi V., Saurabh Chaudhary, Punit Tyagi, Sureshkumar Venkadesan, Manju Rani and Pranab Kumar Mandal

Genes 2018, 9(4), 206; https://doi.org/10.3390/genes9040206 - 11 Apr 2018

Cited by 61 | Viewed by 8398

Abstract

The nitrogen use efficiency (NUE) of crop plants is limited and enhancing it in rice, a major cereal crop, would be beneficial for farmers and the environment alike. Here we report the genome-wide transcriptome analysis of two rice genotypes, IR 64 (IR64) and [...] Read more.

The nitrogen use efficiency (NUE) of crop plants is limited and enhancing it in rice, a major cereal crop, would be beneficial for farmers and the environment alike. Here we report the genome-wide transcriptome analysis of two rice genotypes, IR 64 (IR64) and Nagina 22 (N22) under optimal (+N) and chronic starvation (-N) of nitrogen (N) from 15-day-old root and shoot tissues. The two genotypes were found to be contrasting in their response to -N; IR64 root architecture and root dry weight remained almost equivalent to that under +N conditions, while N22 showed high foraging ability but a substantial reduction in biomass under -N. Similarly, the photosynthetic pigments showed a drastic reduction in N22 under low N, while IR64 was more resilient. Nitrate reductase showed significantly low specific activity under -N in both genotypes. Glutamate synthase (GOGAT) and citrate synthase CS activity were highly reduced in N22 but not in IR64. Transcriptome analysis of these genotypes revealed nearly double the number of genes to be differentially expressed (DEGs) in roots (1016) compared to shoots (571). The response of the two genotypes to N starvation was distinctly different reflecting their morphological/biochemical response with just two and eight common DEGs in the root and shoot tissues. There were a total of 385 nitrogen-responsive DEGs (106 in shoots and 279 in roots) between the two genotypes. Fifty-two of the 89 DEGs identified as specific to N22 root tissues were also found to be differentially expressed between the two genotypes under -N. Most of these DEGs belonged to starch and chloroplast metabolism, followed by membrane and signaling proteins. Physical mapping of DEGs revealed 95 DEGs in roots and 76 in shoots to be present in quantitative trait loci (QTL) known for NUE. Full article

(This article belongs to the Section Plant Genetics and Genomics)

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16 pages, 1705 KiB

Open AccessFeature PaperArticle

Portrait of Matrix Gene Expression in Candida glabrata Biofilms with Stress Induced by Different Drugs

by Célia F. Rodrigues and Mariana Henriques

Genes 2018, 9(4), 205; https://doi.org/10.3390/genes9040205 - 10 Apr 2018

Cited by 22 | Viewed by 4812

Abstract

(1) Background: Candida glabrata is one of the most significant Candida species associated with severe cases of candidiasis. Biofilm formation is an important feature, closely associated with antifungal resistance, involving alterations of gene expression or mutations, which can result in the failure of [...] Read more.

(1) Background: Candida glabrata is one of the most significant Candida species associated with severe cases of candidiasis. Biofilm formation is an important feature, closely associated with antifungal resistance, involving alterations of gene expression or mutations, which can result in the failure of antifungal treatments. Hence, the main goal of this work was to evaluate the role of a set of genes, associated with matrix production, in the resistance of C. glabrata biofilms to antifungal drugs. (2) Methods: the determination of the expression of BGL2, XOG1, FKS1, FKS2, GAS2, KNH1, UGP1, and MNN2 genes in 48-h biofilm’s cells of three C. glabrata strains was performed through quantitative real-time PCR (RT-qPCR), after contact with Fluconazole (Flu), Amphotericin B (AmB), Caspofungin (Csf), or Micafungin (Mcf). (3) Results: Mcf induced a general overexpression of the selected genes. It was verified that the genes related to the production of β-1,3-glucans (BGL2, XOG1, GAS2) had the highest expressions. (4) Conclusion: though β-1,6-glucans and mannans are an essential part of the cell and biofilm matrix, C. glabrata biofilm cells seem to contribute more to the replacement of β-1,3-glucans. Thus, these biopolymers seem to have a greater impact on the biofilm matrix composition and, consequently, a role in the biofilm resistance to antifungal drugs. Full article

(This article belongs to the Special Issue Fungal Pathogenesis in Humans: The Growing Threat)

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18 pages, 3710 KiB

Open AccessReview

Wnt Signaling in Thyroid Homeostasis and Carcinogenesis

by Kim A. Ely, Lindsay A. Bischoff and Vivian L. Weiss

Genes 2018, 9(4), 204; https://doi.org/10.3390/genes9040204 - 10 Apr 2018

Cited by 31 | Viewed by 6694

Abstract

The Wnt pathway is essential for stem cell maintenance, but little is known about its role in thyroid hormone signaling and thyroid stem cell survival and maintenance. In addition, the role of Wnt signaling in thyroid cancer progenitor cells is also unclear. Here, [...] Read more.

The Wnt pathway is essential for stem cell maintenance, but little is known about its role in thyroid hormone signaling and thyroid stem cell survival and maintenance. In addition, the role of Wnt signaling in thyroid cancer progenitor cells is also unclear. Here, we present emerging evidence for the role of Wnt signaling in somatic thyroid stem cell and thyroid cancer stem cell function. An improved understanding of the role of Wnt signaling in thyroid physiology and carcinogenesis is essential for improving both thyroid disease diagnostics and therapeutics. Full article

(This article belongs to the Special Issue Wnt Signaling in Stem Cells)

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17 pages, 3179 KiB

Open AccessArticle

The Brown Midrib Leaf (bml) Mutation in Rice (Oryza sativa L.) Causes Premature Leaf Senescence and the Induction of Defense Responses

by Delara Akhter, Ran Qin, Ujjal Kumar Nath, Md. Alamin, Xiaoli Jin and Chunhai Shi

Genes 2018, 9(4), 203; https://doi.org/10.3390/genes9040203 - 9 Apr 2018

Cited by 22 | Viewed by 6188

Abstract

Isolating and characterizing mutants with altered senescence phenotypes is one of the ways to understand the molecular basis of leaf aging. Using ethyl methane sulfonate mutagenesis, a new rice (Oryza sativa) mutant, brown midrib leaf (bml), was isolated from [...] Read more.

Isolating and characterizing mutants with altered senescence phenotypes is one of the ways to understand the molecular basis of leaf aging. Using ethyl methane sulfonate mutagenesis, a new rice (Oryza sativa) mutant, brown midrib leaf (bml), was isolated from the indica cultivar ‘Zhenong34’. The bml mutants had brown midribs in their leaves and initiated senescence prematurely, at the onset of heading. The mutants had abnormal cells with degraded chloroplasts and contained less chlorophyll compared to the wild type (WT). The bml mutant showed excessive accumulation of reactive oxygen species (ROS), increased activities of superoxide dismutase, catalase, and malondialdehyde, upregulation of senescence-induced STAY-GREEN genes and senescence-related transcription factors, and down regulation of photosynthesis-related genes. The levels of abscisic acid (ABA) and jasmonic acid (JA) were increased in bml with the upregulation of some ABA and JA biosynthetic genes. In pathogen response, bml demonstrated higher resistance against Xanthomonas oryzae pv. oryzae and upregulation of four pathogenesis-related genes compared to the WT. A genetic study confirmed that the bml trait was caused by a single recessive nuclear gene (BML). A map-based cloning using insertion/deletion markers confirmed that BML was located in the 57.32kb interval between the L5IS7 and L5IS11 markers on the short arm of chromosome 5. A sequence analysis of the candidate region identified a 1 bp substitution (G to A) in the 5′-UTR (+98) of bml. BML is a candidate gene associated with leaf senescence, ROS regulation, and disease response, also involved in hormone signaling in rice. Therefore, this gene might be useful in marker-assisted backcrossing/gene editing to improve rice cultivars. Full article

(This article belongs to the Section Plant Genetics and Genomics)

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11 pages, 9390 KiB

Open AccessCommunication

In Silico Functional Networks Identified in Fish Nucleated Red Blood Cells by Means of Transcriptomic and Proteomic Profiling

by Sara Puente-Marin, Iván Nombela, Sergio Ciordia, María Carmen Mena, Verónica Chico, Julio Coll and María Del Mar Ortega-Villaizan

Genes 2018, 9(4), 202; https://doi.org/10.3390/genes9040202 - 9 Apr 2018

Cited by 33 | Viewed by 8698

Abstract

Nucleated red blood cells (RBCs) of fish have, in the last decade, been implicated in several immune-related functions, such as antiviral response, phagocytosis or cytokine-mediated signaling. RNA-sequencing (RNA-seq) and label-free shotgun proteomic analyses were carried out for in silico functional pathway profiling of [...] Read more.

Nucleated red blood cells (RBCs) of fish have, in the last decade, been implicated in several immune-related functions, such as antiviral response, phagocytosis or cytokine-mediated signaling. RNA-sequencing (RNA-seq) and label-free shotgun proteomic analyses were carried out for in silico functional pathway profiling of rainbow trout RBCs. For RNA-seq, a de novo assembly was conducted, in order to create a transcriptome database for RBCs. For proteome profiling, we developed a proteomic method that combined: (a) fractionation into cytosolic and membrane fractions, (b) hemoglobin removal of the cytosolic fraction, (c) protein digestion, and (d) a novel step with pH reversed-phase peptide fractionation and final Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometric (LC ESI-MS/MS) analysis of each fraction. Combined transcriptome- and proteome- sequencing data identified, in silico, novel and striking immune functional networks for rainbow trout nucleated RBCs, which are mainly linked to innate and adaptive immunity. Functional pathways related to regulation of hematopoietic cell differentiation, antigen presentation via major histocompatibility complex class II (MHCII), leukocyte differentiation and regulation of leukocyte activation were identified. These preliminary findings further implicate nucleated RBCs in immune function, such as antigen presentation and leukocyte activation. Full article

(This article belongs to the Section Technologies and Resources for Genetics)

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27 pages, 1551 KiB

Open AccessReview

Epigenetic Mechanisms Impacting Aging: A Focus on Histone Levels and Telomeres

by Shufei Song and F. Brad Johnson

Genes 2018, 9(4), 201; https://doi.org/10.3390/genes9040201 - 9 Apr 2018

Cited by 47 | Viewed by 10011

Abstract

Aging and age-related diseases pose some of the most significant and difficult challenges to modern society as well as to the scientific and medical communities. Biological aging is a complex, and, under normal circumstances, seemingly irreversible collection of processes that involves numerous underlying [...] Read more.

Aging and age-related diseases pose some of the most significant and difficult challenges to modern society as well as to the scientific and medical communities. Biological aging is a complex, and, under normal circumstances, seemingly irreversible collection of processes that involves numerous underlying mechanisms. Among these, chromatin-based processes have emerged as major regulators of cellular and organismal aging. These include DNA methylation, histone modifications, nucleosome positioning, and telomere regulation, including how these are influenced by environmental factors such as diet. Here we focus on two interconnected categories of chromatin-based mechanisms impacting aging: those involving changes in the levels of histones or in the functions of telomeres. Full article

(This article belongs to the Special Issue The Epigenetics of Aging and Longevity)

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14 pages, 16583 KiB

Open AccessArticle

A Possible Trifunctional β-Carotene Synthase Gene Identified in the Draft Genome of Aurantiochytrium sp. Strain KH105

by Hiroaki Iwasaka, Ryo Koyanagi, Ryota Satoh, Akiko Nagano, Kenshi Watanabe, Kanako Hisata, Noriyuki Satoh and Tsunehiro Aki

Genes 2018, 9(4), 200; https://doi.org/10.3390/genes9040200 - 9 Apr 2018

Cited by 33 | Viewed by 6200

Abstract

Labyrinthulomycetes have been regarded as a promising industrial source of xanthophylls, including astaxanthin and canthaxanthin, polyunsaturated fatty acids such as docosahexaenoic acid and docosapentaenoic acid, ω-3 oils, and terpenic hydrocarbons, such as sterols and squalene. A Thraustochytrid, Aurantiochytrium sp. KH105 produces carotenoids, including [...] Read more.

Labyrinthulomycetes have been regarded as a promising industrial source of xanthophylls, including astaxanthin and canthaxanthin, polyunsaturated fatty acids such as docosahexaenoic acid and docosapentaenoic acid, ω-3 oils, and terpenic hydrocarbons, such as sterols and squalene. A Thraustochytrid, Aurantiochytrium sp. KH105 produces carotenoids, including astaxanthin, with strong antioxidant activity. To gain genomic insights into this capacity, we decoded its 97-Mbp genome and characterized genes for enzymes involved in carotenoid biosynthesis. Interestingly, all carotenogenic genes, as well as other eukaryotic genes, appeared duplicated, suggesting that this strain is diploid. In addition, among the five genes involved in the pathway from geranylgeranyl pyrophosphate to astaxanthin, geranylgeranyl phytoene synthase (crtB), phytoene desaturase (crtI) and lycopene cyclase (crtY) were fused into single gene (crtIBY) with no internal stop codons. Functionality of the trifunctional enzyme, CrtIBY, to catalyze the reaction from geranylgeranyl diphosphate to β-carotene was confirmed using a yeast assay system and mass spectrometry. Furthermore, analyses of differential gene expression showed characteristic up-regulation of carotenoid biosynthetic genes during stationary and starvation phases under these culture conditions. This suggests genetic engineering events to promote more efficient production of carotenoids. We also showed an occurrence of crtIBY in other Thraustochytrid species. Full article

(This article belongs to the Special Issue Microbial Metabolic Engineering)

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15 pages, 25545 KiB

Open AccessArticle

Alteration of Hepatic Gene Expression along with the Inherited Phenotype of Acquired Fatty Liver in Chicken

by Yonghong Zhang, Zhen Liu, Ranran Liu, Jie Wang, Maiqing Zheng, Qinghe Li, Huanxian Cui, Guiping Zhao and Jie Wen

Genes 2018, 9(4), 199; https://doi.org/10.3390/genes9040199 - 8 Apr 2018

Cited by 35 | Viewed by 7385

Abstract

Fatty liver is a widespread disease in chickens that causes a decrease in egg production and even death. The characteristics of the inherited phenotype of acquired fatty liver and the molecular mechanisms underlying it, however, are largely unknown. In the current study, fatty [...] Read more.

Fatty liver is a widespread disease in chickens that causes a decrease in egg production and even death. The characteristics of the inherited phenotype of acquired fatty liver and the molecular mechanisms underlying it, however, are largely unknown. In the current study, fatty liver was induced in 3 breeds by a high-fat (HF) diet and a methionine choline-deficient (MCD) diet. The results showed that the dwarf Jingxing-Huang (JXH) chicken was more susceptible to fatty liver compared with the layer White Leghorns (WL) and local Beijing-You (BJY) breeds. In addition, it was found that the paternal fatty livers induced by HF diet in JXH chickens were inherited. Compared to birds without fatty liver in the control group, both offsprings and their sires with fatty livers in the paternal group exhibited altered hepatic gene expression profiles, including upregulation of several key genes involved in fatty acid metabolism, lipid metabolism and glucose metabolism (ACACA, FASN, SCD, ACSL5, FADS2, FABP1, APOA4 and ME1). This study uniquely revealed that acquired fatty liver in cocks can be inherited. The hepatic gene expression profiles were altered in chickens with the inherited phenotype of acquired paternal fatty liver and several genes could be candidate biomarkers. Full article

(This article belongs to the Section Animal Genetics and Genomics)

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16 pages, 6825 KiB

Open AccessArticle

Ancient DNA from Giant Panda (Ailuropoda melanoleuca) of South-Western China Reveals Genetic Diversity Loss during the Holocene

by Gui-Lian Sheng, Axel Barlow, Alan Cooper, Xin-Dong Hou, Xue-Ping Ji, Nina G. Jablonski, Bo-Jian Zhong, Hong Liu, Lawrence J. Flynn, Jun-Xia Yuan, Li-Rui Wang, Nikolas Basler, Michael V. Westbury, Michael Hofreiter and Xu-Long Lai

Genes 2018, 9(4), 198; https://doi.org/10.3390/genes9040198 - 6 Apr 2018

Cited by 16 | Viewed by 14515

Abstract

The giant panda was widely distributed in China and south-eastern Asia during the middle to late Pleistocene, prior to its habitat becoming rapidly reduced in the Holocene. While conservation reserves have been established and population numbers of the giant panda have recently increased, [...] Read more.

The giant panda was widely distributed in China and south-eastern Asia during the middle to late Pleistocene, prior to its habitat becoming rapidly reduced in the Holocene. While conservation reserves have been established and population numbers of the giant panda have recently increased, the interpretation of its genetic diversity remains controversial. Previous analyses, surprisingly, have indicated relatively high levels of genetic diversity raising issues concerning the efficiency and usefulness of reintroducing individuals from captive populations. However, due to a lack of DNA data from fossil specimens, it is unknown whether genetic diversity was even higher prior to the most recent population decline. We amplified complete cytb and 12s rRNA, partial 16s rRNA and ND1, and control region sequences from the mitochondrial genomes of two Holocene panda specimens. We estimated genetic diversity and population demography by analyzing the ancient mitochondrial DNA sequences alongside those from modern giant pandas, as well as from other members of the bear family (Ursidae). Phylogenetic analyses show that one of the ancient haplotypes is sister to all sampled modern pandas and the second ancient individual is nested among the modern haplotypes, suggesting that genetic diversity may indeed have been higher earlier during the Holocene. Bayesian skyline plot analysis supports this view and indicates a slight decline in female effective population size starting around 6000 years B.P., followed by a recovery around 2000 years ago. Therefore, while the genetic diversity of the giant panda has been affected by recent habitat contraction, it still harbors substantial genetic diversity. Moreover, while its still low population numbers require continued conservation efforts, there seem to be no immediate threats from the perspective of genetic evolutionary potential. Full article

(This article belongs to the Special Issue Novel and Neglected Areas of Ancient DNA Research)

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14 pages, 27552 KiB

Open AccessArticle

Transgenic Xenopus laevis Line for In Vivo Labeling of Nephrons within the Kidney

by Mark E. Corkins, Hannah L. Hanania, Vanja Krneta-Stankic, Bridget D. DeLay, Esther J. Pearl, Moonsup Lee, Hong Ji, Alan J. Davidson, Marko E. Horb and Rachel K. Miller

Genes 2018, 9(4), 197; https://doi.org/10.3390/genes9040197 - 6 Apr 2018

Cited by 12 | Viewed by 9716

Abstract

Xenopus laevis embryos are an established model for studying kidney development. The nephron structure and genetic pathways that regulate nephrogenesis are conserved between Xenopus and humans, allowing for the study of human disease-causing genes. Xenopus embryos are also amenable to large-scale screening, but [...] Read more.

Xenopus laevis embryos are an established model for studying kidney development. The nephron structure and genetic pathways that regulate nephrogenesis are conserved between Xenopus and humans, allowing for the study of human disease-causing genes. Xenopus embryos are also amenable to large-scale screening, but studies of kidney disease-related genes have been impeded because assessment of kidney development has largely been limited to examining fixed embryos. To overcome this problem, we have generated a transgenic line that labels the kidney. We characterize this cdh17:eGFP line, showing green fluorescent protein (GFP) expression in the pronephric and mesonephric kidneys and colocalization with known kidney markers. We also demonstrate the feasibility of live imaging of embryonic kidney development and the use of cdh17:eGFP as a kidney marker for secretion assays. Additionally, we develop a new methodology to isolate and identify kidney cells for primary culture. We also use morpholino knockdown of essential kidney development genes to establish that GFP expression enables observation of phenotypes, previously only described in fixed embryos. Taken together, this transgenic line will enable primary kidney cell culture and live imaging of pronephric and mesonephric kidney development. It will also provide a simple means for high-throughput screening of putative human kidney disease-causing genes. Full article

(This article belongs to the Special Issue DNA Variations in Evolution and Human Diseases)

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16 pages, 2013 KiB

Open AccessArticle

Identification of a WNT5A-Responsive Degradation Domain in the Kinesin Superfamily Protein KIF26B

by Edith P. Karuna, Shannon S. Choi, Michael K. Scales, Jennie Hum, Michael Cohen, Fernando A. Fierro and Hsin-Yi Henry Ho

Genes 2018, 9(4), 196; https://doi.org/10.3390/genes9040196 - 5 Apr 2018

Cited by 10 | Viewed by 6428

Abstract

Noncanonical WNT pathways function independently of the β-catenin transcriptional co-activator to regulate diverse morphogenetic and pathogenic processes. Recent studies showed that noncanonical WNTs, such as WNT5A, can signal the degradation of several downstream effectors, thereby modulating these effectors’ cellular activities. The protein domain(s) [...] Read more.

Noncanonical WNT pathways function independently of the β-catenin transcriptional co-activator to regulate diverse morphogenetic and pathogenic processes. Recent studies showed that noncanonical WNTs, such as WNT5A, can signal the degradation of several downstream effectors, thereby modulating these effectors’ cellular activities. The protein domain(s) that mediates the WNT5A-dependent degradation response, however, has not been identified. By coupling protein mutagenesis experiments with a flow cytometry-based degradation reporter assay, we have defined a protein domain in the kinesin superfamily protein KIF26B that is essential for WNT5A-dependent degradation. We found that a human disease-causing KIF26B mutation located at a conserved amino acid within this domain compromises the ability of WNT5A to induce KIF26B degradation. Using pharmacological perturbation, we further uncovered a role of glycogen synthase kinase 3 (GSK3) in WNT5A regulation of KIF26B degradation. Lastly, based on the identification of the WNT5A-responsive domain, we developed a new reporter system that allows for efficient profiling of WNT5A-KIF26B signaling activity in both somatic and stem cells. In conclusion, our study identifies a new protein domain that mediates WNT5A-dependent degradation of KIF26B and provides a new tool for functional characterization of noncanonical WNT5A signaling in cells. Full article

(This article belongs to the Special Issue Wnt Signaling in Stem Cells)

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