Probiotic Potential of Autochthonous Bacteria Isolated from the Gastrointestinal Tract of Four Freshwater Teleosts

In this study, a total of 121 bacterial strains were isolated from the gastrointestinal tract of four teleostean species, namely striped snakehead (Channa striatus), striped dwarf catfish (Mystus vittatus), orangefin labeo (Labeo calbasu) and mrigal carp (Cirrhinus mrigala), among which 8 isolates showed promising antibacterial activity against four potential fish pathogens, Aeromonas hydrophila, Aeromonas salmonicida, Aeromonas sobria and Pseudomonas fluorescens and were non-hemolytic. The isolates were further screened in response to fish bile tolerance and extracellular digestive enzyme activity. Two bacterial strains MVF1 and MVH7 showed highest tolerance and extracellular enzymes activities, and selected for further studies. Antagonistic activity of these two isolates was further confirmed by in vitro growth inhibition assay against four selected fish pathogens in liquid medium. Finally, these two bacterial strains MVF1 and MVH7 were selected as potential probiotic candidates and thus identification by partial 16S rRNA gene sequence analysis. The bacterial isolates MVF1 and MVH7 were identified as two strains of Bacillus sp.     

Electroporation-mediated RNA interference reveals a role of the multicopper oxidase 2 gene in dragonfly cuticular pigmentation

Dragonflies are colorful insects, and recent RNA sequencing studies have identified a number of candidate genes potentially involved in their color pattern formation and color vision. However, functional aspects of such genes have not been assessed due to the lack of molecular genetic tools applicable to dragonflies. We established an electroporation-mediated RNA interference (RNAi) procedure using the tiny dragonfly Nannophya pygmaea Rambur, 1842 (Odonata: Libellulidae) that targets the multicopper oxidase 2 gene (MCO2; also known as laccase2 gene) responsible for cuticular pigmentation in many insects. RNA sequencing of N. pygmaea and genomic survey of the dragonfly Ladona fulva identified four multicopper oxidase family genes: MCO1, MCO2, MCO3 and multicopper oxidase-related protein gene (MCORP). In N. pygmaea, MCO2 was specifically expressed around the cuticular pigmentation period, whereas MCO1 was constantly expressed. MCORP was expressed at adult stages, and MCO3 was scarcely expressed. When we applied in vivo electroporation, final instar larvae injected with MCO2 small interfering RNA became adults with patchy unpigmented regions. RNAi without in vivo electroporation did not affect cuticular pigmentation, suggesting that dragonflies do not show a systemic RNAi response. These results indicate that MCO2 is required for cuticular pigmentation across diverse insects, and highlight the usefulness of the electroporation-mediated RNAi method in dragonflies.     

Occurrence of two types of larvae of the Asian seaperch (<Emphasis Type="Italic">Lateolabrax</Emphasis>) in the estuaries of northern Vietnam

Lateolabrax sp. larvae were collected in the Tien Yen and Kalong estuaries of northern Vietnam, the southernmost locality for this genus distribution. Vietnamese Lateolabrax sp. larvae could be distinguished from those of L. japonicus by pigmentation patterns. Their morphological, meristic and pigmentation characters were closer to those of Chinese Lateolabrax than L. japonicus, so Vietnamese Lateolabrax is likely situated as a population of the Chinese one. Morphometric and pigmentation characters of larvae from the two estuaries differed, suggesting that Lateolabrax of northern Vietnam are diversified and consist of at least two different breeding stocks.     

Genetic Analysis of Anthocyanin Pigmentation of the Anthers and Culm in Common Wheat

Anthocyanin pigmentation of various organs develops during plant ontogeny in response to adverse and damaging abiotic and biotic stressors (environmental factors). Using the monosome method, the genes responsible for anther and culm anthocyanin pigmentation (Pan1 and Pc2, respectively) were localized to 7D chromosome in introgressive lines from crosses between common wheat Triticum aestivum L. and the species Triticum timopheevii Zhuk. Genetic analysis of ten common wheat genotypes using testers carrying genes Pan1, Pc1 and Pc2 showed that these genotypes contained Pan1 and Pc2 genes. Visual examination of plants from 70 and 76 varieties of respectively winter and spring common wheat revealed anthocyanin pigmentation of anthers and culms in 36 varieties. Pan1 and Pc2 genes were presumably introduced into common wheat from Aegilops tauschii (Eig.) Tzvel., a donor of the D genome.     

Mapping of <Emphasis Type="BoldItalic">Id</Emphasis> locus for dermal shank melanin in a Chinese indigenous chicken breed

The dermal shank pigmentation, one of the defining traits of chicken breeds, is caused by an abnormal deposition of melanin in the dermis of the shank. The abnormal deposition is controlled by the sex-linked inhibitor of dermal melanin (Id). In this study, we aim to locate the gene responsible for the dermal shank pigmentation in chickens by an association analysis and a differential expression analysis. Based on our results, 72 single-nucleotide polymorphisms (SNPs) located in Z chromosome (chrZ): 71–73 Mb (galGal3) were selected to further explore their relationships with the dermal shank pigmentation in pure lines of 96 Gushi hens and 96 Gushi hens with a yellow shank skin colour. The results of the association analysis showed that the SNPs located in chrZ: 72.58–72.99 Mb (galGal3) (chrZ: 79.02–79.44 Mb (galGal4)) are significantly associated with the dermal shank pigmentation. Based on the results of our previous studies and the present association analysis, the zinc-finger protein 608 (ZNF608), GRAM domain containing 3 (GRAMD3), aldehyde dehydrogenase 7 family member A1 (ALDH7A1), fem-1 homologue C (FEM1C), beta-1,4-galactosyltransferase 1 (B4GALT1) and versican (VCAN) genes were selected for the differential expression analysis. The gene expression profiles showed that the expression of GRAMD3 gene in the dermis tissues of the shank was significantly (\(P= 0.010738 < 0.05\)) higher in 350-day-old Gushi chickens characterized by the dermal shank pigmentation than in one-day-old Gushi chickens. The dermal shank pigmentation was not present in the one-day-old Gushi chickens. Additionally, the results of the association analysis and the expression analysis showed that GRAMD3 could be the most likely candidate gene for the Id locus. However, we did not detect a mutation, i.e. significantly associated with this trait within GRAMD3. Therefore, we concluded that the variations located in the flanking region of GRAMD3 led to the abnormal expression of GRAMD3, which requires further study.     

Small mammals as sentinels of antimicrobial-resistant staphylococci

A total of 39 coagulase-negative staphylococci and seven Staphylococcus aureus strains were isolated from small mammal feces, i.e., the striped field mouse (Apodemus agrarius) and the yellow-necked mouse (A. flavicollis) in two sampling areas, deciduous forest and karst plains. MALDI-TOF analysis revealed five species of coagulase-negative staphylococci: S. sciuri, S. hominis, S. warneri, S. haemolyticus, and S. xylosus. All strains were susceptible to tetracycline, linezolid, vancomycin, and teicoplanin. Three MRSA strains with the mecA gene were detected. The beta-lactamase gene blaZ was detected in ampicillin-resistant staphylococci and in the high-level resistant strains (oxacillin over 2 mg/L) mecA gene. The mecC gene was not detected by PCR. Erythromycin-resistant staphylococci harbored the ermC gene and/or the efflux gene msrA. There were no detectable dfr genes in trimethoprim-resistant staphylococci and the rifampicin-resistant strains were without mutation in the rpoB gene. In summary, wild small mammals may serve as sentinels of mecA-positive S. aureus with erythromycin resistance genes ermC and efflux msrA. Small mammals appear to be useful indicators of antibiotic resistance.     

Epigenetic regulation of <Emphasis Type="Italic">MdMYB1</Emphasis> is associated with paper bagging-induced red pigmentation of apples

Main conclusion

Paper-bagging treatment can transform non-transcribed MdMYB1 - 2 and MdMYB1 - 3 alleles into transcribed alleles through epigenetic regulations, resulting in the red pigmentation of a normally non-red apple cultivar ‘Mutsu.’ Anthocyanin biosynthesis in apples is regulated by MdMYB1/A/10, an R2R3-Type MYB gene. ‘Mutsu,’ a triploid apple cultivar harboring non-transcribed MdMYB1-2 and MdMYB1-3 alleles, retains green skin color under field conditions. However, it can show red/pink pigmentation under natural or artificial ultraviolet-B (UV-B) light exposure after paper-bagging and bag removal treatment. In the present study, we found that in ‘Mutsu,’ paper bagging-induced red pigmentation was due to the activation of non-transcribed MdMYB1-2/-3 alleles, which triggered the expression of downstream anthocyanin biosynthesis genes in a UV-B-dependent manner. By monitoring the epigenetic changes during UV-B-induced pigmentation, no significant differences in DNA methylation and histone modifications in the 5′ upstream region of MdMYB1-2/-3 were recorded between the UV-B-treated fruit skin (red) and the fruit skin treated only by white light (green). In contrast, bag treatment lowered the DNA methylation in this region of MdMYB1-2/-3 alleles. Similarly, higher levels of histone H3 acetylation and trimethylation of H3 tail at lysine 4, and lower level of trimethylation of H3 tail at lysine 27 were observed in the 5′ upstream region of MdMYB1-2/-3 in the skin of the fruit immediately after bag removal. These results suggest that bagging treatment can induce epigenetic changes, facilitating the binding of trans factor(s) to MdMYB1-2/-3 alleles, resulting in the activation of these MYBs after bag removal.

     

The factors affecting the evolution of the anthocyanin biosynthesis pathway genes in monocot and dicot plant species

Background

The available data demonstrate that even in universal metabolic pathways, some species-specific regulatory features of structural genes are present. For instance, in the anthocyanin biosynthesis pathway (ABP), genes may be regulated by ABP-specific regulatory factors, and their expression levels may be strongly associated with anthocyanin pigmentation, or they may be expressed independently of pigmentation. A dataset of orthologous ABP genes (Chs, Chi, F3h, F3’h, Dfr, Ans) from monocot and dicot plant species that have distinct gene regulation patterns and different types of pollination was constructed to test whether these factors affect the evolution of the genes.

Results

Using a maximum likelihood approach, we demonstrated that although the whole set of the ABP genes is under purifying selection, with greater selection acting on the upstream genes than on the downstream genes, genes from distinct groups of plant species experienced different strengths of selective pressure. The selective pressure on the genes was higher in dicots than in monocots (F3h and further downstream genes) and in pollinator-dependent plants than in pollinator-independent species (Chi and further downstream genes), suggesting an important role of pollination type in the evolution of the anthocyanin biosynthesis gene network. Contrasting effects of the regulation patterns on evolution were detected for the F3h and Dfr genes, with greater selective pressure on the F3h gene in plant species where the gene expression was not strongly associated with pigmentation and greater selective pressure on Dfr in plant species where the gene expression was associated with pigmentation.

Conclusions

We demonstrated the effects of pollination type and patterns of regulation on the evolution of the ABP genes, but the evolution of some of the genes could not be explained in the framework of these factors, such as the weaker selective pressure acting on Chs in species that attract pollinators or the stronger selective pressure on F3h in plant species where the gene expression was not associated with pigmentation. The observations suggest that additional factors could affect the evolution of these genes. One such factor could be an effect of gene duplication with further division of functions among gene copies and relaxed selective pressure acting on them. Additional tests with an appropriate dataset combining data on duplicated gene sequences and their functions in the flavonoid biosynthesis pathway are required to test this hypothesis.

     

Exposure of Free-Ranging Wild Carnivores and Domestic Dogs to Canine Distemper Virus and Parvovirus in the Cerrado of Central Brazil

Human population growth around protected areas increases the contact between wild and domestic animals, promoting disease transmission between them. This study investigates the exposure of free-ranging wild carnivores and domestic dogs to canine distemper virus (CDV) and parvovirus in Emas National Park (ENP) in the Cerrado savanna of central Brazil. Serum samples were collected from 169 wild carnivores, including the maned wolf (Chrysocyon brachyurus), crab-eating fox (Cerdocyon thous), hoary fox (Pseudalopex vetulus), puma (Puma concolor), ocelot (Leopardus pardalis), pampas cat (Leopardus colocolo), jaguarundi (Herpailurus yagouaroundi), striped hog-nosed skunk (Conepatus semistriatus) and coati (Nasua nasua), and from 35 domestic dogs living on rural properties bordering ENP. Serological tests showed that 10.6% of wild carnivores (maned wolves, crab-eating foxes and ocelots) and 71.4% of domestic dogs were exposed to CDV, and 56.8% of wild carnivores, including all species sampled except coatis, and 57.1% of domestic dogs were exposed to parvovirus. This report is the first to indicate that the free-ranging pampas cat, jaguarundi and striped hog-nosed skunk are exposed to parvovirus. CDV and parvovirus deserve attention in ENP, and it is extremely important to monitor the health of carnivore populations and perform molecular diagnosis of the viruses to determine the possible involvement of the domestic dog in their transmission.     

Effect of coat color genes on the hair pigmentation morphology in the american mink (<Emphasis Type="Italic">Mustela vison</Emphasis> Schr. L.)

The morphological patterns of hair pigmentation (the size and shape of pigment granules and their distribution among layers) have been studied in four compound coat color forms of the American mink: moil-sapphire also known as violet (genotype m/m a/a p/p); moil-silver or sage (genotype m/m p/p); the color form determined by genotype m/+ a/a; and platinum leopard (S ^k /+ a/+ p/p). The hair pigmentation pattern specific for each coat color form and its difference from the standard coat color of the American mink (genotype +/+) has been determined. The possible mechanisms of the phenotypic expression of the nonallelic genes contributing to the described compound color forms are discussed.     

Coinheritance of Chromosomes 3 and 11 in the Patients with Autosomal Recessive Polycythemia from Chuvachia

Inheritance of chromosomes 3 and 11 in the families with Chuvash autosomal recessive polycythemia and in control group with no disease symptoms was examined using polymorphic dinucleotide markers D3S1597 and D3S1263, mapped to region 3p25, and D11S4111, D11S4127, and D11S1356, mapped to region 11q23. All patients were homozygous for the C598T mutation in the VHL gene (3p25). The analysis showed that in 75% of the cases, chromosome 3 carrying C598T mutation was coinherited with certain chromosome 11, which differed from 50%, expected upon independent inheritance of each chromosome. In case of chromosome 3 without C598T mutation, this pattern was observed neither in healthy sibs form the families with autosomal recessive polycythemia (44%), nor in the control group (43%). These results suggest that in case of the C598T mutation in the VHL gene, chromosomal loci 3p25 and 11q23 are inherited not independently, compared to the inheritance of these loci in the absence of the mutation in healthy sibs from the affected families χ² = 16.14, p < 0.001), and also in the control family sample (χ² = 17.91, p < 0.001).     

Fungal Leukonychia and Melanonychia: a Review

Fungal leukonychia is a common condition in immunosuppressed patients; the most common clinical forms are white superficial and proximal white superficial onychomycosis. It is frequently associated with Trichophyton mentagrophytes var. interdigitale and with Trichophyton rubrum. The diagnosis can be easily made by direct examination and culture. Fungal melanonychia is the nail plate pigmentation caused by fungal infections. The most frequently isolated fungi is T. rubrum and melanized molds like Neoscytalidium dimidiatum. The main differential diagnosis is malignant melanoma, although other causes include subungueal hematomas, exogenous pigmentation, and bacterial infection. If homogeneous pigmentation in lines or structureless discoloration, and the absence of melanin inclusions are seen by dermoscopy, diagnosis must be complemented with KOH preparations and cultures.     

Heterozygosity for mutations affecting coat pigmentation in the American mink (<Emphasis Type="Italic">Neovison</Emphasis> vison) enhances structural stability of adrenal cortex under stress conditions

The results of the study of the effects of heterozygosity for mutations affecting coat pigmentation on the response to the environmental stress caused by extreme feeding conditions are provided. The animals with the following genotypes were taken into the study: homozygotes standard (+/+), hedlund white (h/h), and aleutian (a/a) and heterozygotes hedlund white (h/+) and aleutian (a/+). The animals homozygous for the aleutian mutation (a/a) showed a statistically lower growth rate than the animals of other genotypes both in the control and in the experiment (p < 0.05). Under the control conditions, the animals homozygous for both the wild type standard allele (+/+) and the mutant hedlund white (h/h) and aleutian (a/a) alleles showed the evident tendency for the zona fasciculata and zona reticularis of the adrenal cortex broadening compared to the experimental conditions. At the same time, in the animals heterozygous for the hedlund white (h/+) and the aleutian (a/+) mutations, a clear tendency for increasing size of the zona fasciculata and zona reticularis under the experimental conditions was observed. In the heterozygous animals, although we observed single destructive changes in the adrenal cortex under stress conditions, they were much less profound than in the homozygous ones. This may be related to the broader range of morphological adaptation in the heterozygotes, which gives them the possibility of more significant enlargement of the secreting zone to provide for its adequate functioning.     

A novel dominant rice male sterility mutant, <Emphasis Type="Italic">OsDMS-1</Emphasis>, simultaneously controlled by independent loci on chromosomes 1, 2, and 3

We found a rice dominant genetic male-sterile mutant OsDMS-1 from tissue culture-regenerated offspring of Zhonghua 11 (japonica rice). Compared to Zhonghua 11, OsDMS-1 mutant anthers were narrow and pale and incapable of pollen release although the glume opened normally. Approximately 81.4% of this mutant pollen was small and malformed and could not be stained by iodine treatment. A paraffin section assay showed delayed degradation of the OsDMS-1 mutant tapetum without starch accumulation in the mutant pollen, ultimately leading to pollen abortion. Classical genetic analysis indicated that only one dominant gene controlled the sterility in the OsDMS-1 mutant. However, molecular mapping suggested three loci simultaneously control male sterility in this mutant: OsDMS-1A (on chromosome 1), flanked by InDel markers C1D4 and C1D5, OsDMS-1B (on chromosome 2), flanked by InDel markers C2D3 and C2D10, and OsDMS-1C (on chromosome 3), flanked by InDel markers 0315 and C3D3. Molecular mapping disagreed with classical genetic analysis regarding the number of genes controlling the OsDMS-1 mutant, indicating a novel mechanism underlying sterility in OsDMS-1. We present two hypotheses to explain this novel inheritance behavior: one is described as Parent-Originated Loci Tying Inheritance (POLTI); while the alternate hypothesis is described as Loci Recombination Lethal (LRL).     

Diversity and dynamics of lactic acid bacteria in <Emphasis Type="Italic">Atole agrio</Emphasis>, a traditional maize-based fermented beverage from South-Eastern Mexico,analysed by high throughput sequencing and culturing

The purpose of this work was to analyse the diversity and dynamics of lactic acid bacteria (LAB) throughout the fermentation process in Atole agrio, a traditional maize based food of Mexican origin. Samples of different fermentation times were analysed using culture-dependent and -independent approaches. Identification of LAB isolates revealed the presence of members of the genera Pediococcus, Weissella, Lactobacillus, Leuconostoc and Lactococcus, and the predominance of Pediococcus pentosaceus and Weissella confusa in liquid and solid batches, respectively. High-throughput sequencing (HTS) of the 16S rRNA gene confirmed the predominance of Lactobacillaceae and Leuconostocaceae at the beginning of the process. In liquid fermentation Acetobacteraceae dominate after 4 h as pH decreased. In contrast, Leuconostocaceae dominated the solid fermentation except at 12 h that were overgrown by Acetobacteraceae. Regarding LAB genera, Lactobacillus dominated the liquid fermentation except at 12 h when Weissella, Lactococcus and Streptococcus were the most abundant. In solid fermentation Weissella predominated all through the process. HTS determined that Lactobacillus plantarum and W. confusa dominated in the liquid and solid batches, respectively. Two oligotypes have been identified for L. plantarum and W. confusa populations, differing in a single nucleotide position each. Only one of the oligotypes was detected among the isolates obtained from each species, the biological significance of which remains unclear.     

Genetic control of different types of the aphid resistance in cereal crops

Inheritance of the two main types of the plant resistance to insects was investigated in the sorghum-greenbug (Schizaphis graminum Rond.) and wheat-bird cherry-oat aphid (Rhopalosiphon padi L.) interaction systems. The data obtained support the hypothesis that antixenosis (avoiding of the plant by the insect, given a choice) and antibiosis (adverse effect of the plant on the insect feeding on it) are pleiotropic manifestations of the same genes. This is confirmed by the following facts. (1) Identical patterns of segregation for antixenosis and antibiosis in different cases of sorghum resistance to the greenbug: monogenic control (gene Sgr4), digenic control (Sgr1, Sgr2 and Sgr7, Sgr8), and complementary action of the genes (Sgr9 and Sgr10). (2) Correlated changes in the levels of antibiosis and antixenosis during long-term reproduction of a greenbug clone on the resistant sorghum variety k-1206 (resistance controlled by one gene). (3) Simultaneous expression of antixenosis and antibiosis in F₃ wheat hybrid families to the bird cherry-oat aphid.     

Identification of <Emphasis Type="Italic">r</Emphasis> mutations conferring white flowers in the Japanese morning glory (<Emphasis Type="Italic">Ipomoea nil</Emphasis>)

The wild-type Japanese morning glory [Ipomoea nil (L.) Roth.] exhibits blue flowers with red stems, and spontaneous r mutants display white flowers with green stems. We have identified two r mutations, r1-1 and r1-2, that are caused by insertions of Tpn1-related DNA transposable elements, Tpn3 (5.6 kb) and Tpn6 (4.7 kb), respectively, into a unique intron of the CHS-D gene, which is responsible for flower and stem pigmentation. Both Tpn3 and Tpn6, which belong to the En/Spm or CACTA superfamily, are nonautonomous elements lacking transposase genes but containing unrelated cellular DNA segments including exons and introns. Interestingly, r1-2 contains an additional 4-bp insertion at the Tpn3 integration site in r1-1, presumably a footprint caused by the excision of Tpn3. The results strengthen the previous notion that Tpn1 and its relatives are major spontaneous mutagens for generating various floriculturally important traits in I. nil. Since I. nil has an extensive history of genetic studies, molecular identification of classical spontaneous mutations would also facilitate reinterpretation of the abundant classical genetic data available.