scholarly journals Biodiversity of Enterobacteriaceae on masin (fermented sauce) from Sumbawa, West Nusa Tenggara, Indonesia

2020 ◽  
Vol 21 (3) ◽  
Author(s):  
Baso Manguntungi ◽  
Dinar Saputri ◽  
Chairul Afgani ◽  
Apon Mustopa ◽  
Fatimah ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Pathogenic Bacteria ◽  
Bacterial Population ◽  
Dna Analysis ◽  
Phylogenetic Analyses ◽  
Sequencing Analysis ◽  
Nacl Concentration ◽  
Enterobacter Ludwigii ◽  
Flat Edge ◽  
Raw Shrimp

Abstract. Manguntungi B, Saputri DS, Afgani CA, Mustopa AZ, Fatimah, Kusmiran A. 2020. Biodiversity of Enterobacteriaceae on masin (fermented sauce) from Sumbawa, West Nusa Tenggara, Indonesia. Biodiversitas 21: 1001-1006. Masin is fermented sauce originating from Sumbawa, West Nusa Tenggara which is made from raw shrimp with the addition of tamarind, salt, and fingerroot (Boesenbergia pandurata) flower. The study aimed to determine the biodiversity of pathogenic bacteria, especially Enterobacteriaceae family in Masin. The methods used in this study were isolation of bacteria using MRS media with modified NaCl concentration (1-12%) and molecular identification by using PCR-RAPD (randomly amplified polymorphic DNA) analysis and 16S ribosomal RNA-based sequencing analysis. The characteristics of bacteria that were successfully isolated on media with various concentrations of salt were round, milky white, and formed a flat edge with convex elevation in each colony. The highest bacterial population was 29.65 x 106 CFU/g in MRS + NaCl 7% treatment. From 48 selected isolates that morphologically close to Enterobacteriaceae family, 5 isolates were chosen for sequencing analysis. Based on the phylogenetic analyses, isolate 01 had a close kinship with Leclercia adecarboxylata, isolate 11 had a close kinship with Citrobacter freundii, isolate 33 had a close kinship with Enterobacter cloacae, isolate 40 had a close kinship with Pantoea agglomerans and isolate 46 had a close kinship with Enterobacter ludwigii.

scholarly journals The Profile Analysis of Lactic Acid Bacteria (LAB) from Sumbawa White Honey and Its Potential Producing Antibacterial Compounds

2021 ◽  
Vol 18 (15) ◽  
Author(s):  
Baso MANGUNTUNGI ◽  
Apon Zaenal MUSTOPA ◽  
Lita MEILINA ◽  
Maritsa NURFATWA ◽  
Leggina Rezzy VANGGY ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Enterococcus Faecium ◽  
Pathogenic Bacteria ◽  
Profile Analysis ◽  
Positive Control ◽  
Sequencing Analysis ◽  
Accession Number ◽  
Enterobacter Ludwigii ◽  
Different Strains

Honey acts as an antibacterial without side effects, and also contains antiseptic substances which function to inhibit bacterial growth. This study aimed to isolate the Lactic Acid Bacteria (LAB) in Sumbawa white honey and the bioactive compounds produced as pathogenic antibacteria. The 1st stage in this study was the isolation of lactic acid bacteria (LAB) in Sumbawa white honey, then continued with a grading test, morphological test, catalase test, methyl red test, and the last test, namely the antimicrobial test against 5 pathogenic bacteria (Salmonellatyhposa, Staphylococcus aureus, Escherichia coli, Enterobacter ludwigii, and Leclerciaadecarboxylata). Data analysis was performed using the Analysis of variance (ANOVA) test at a confidence level of 0.05 with SPSS 24. Based on the results of sequencing analysis, it was found that the 5 selected isolates were Enterococcus faecium species. The Enterococcus faecium species obtained from the sequencing results had different strains. The accession numbers of the 5 Enterococcus faecium were: Isolate-03 with a percentage of 97.29 % (accession number: KU324920.1), Isolate-07 has a percent identity of 97.36 % (accession number: MF108201.1), Isolate-09 of 97.73 % (accession number: CP041261.3), Isolate-20 with a percentage of 96.40 % (accession number: MN511819.1), and Isolate-24 with a percentage of 98.61 % (accession number: KM495938.1). These isolates can inhibit the growth of all tested pathogenic bacteria treated with 100 % LAB metabolites and were not significantly different (p > 0.05) compared to a positive control (Ampicillin). HIGHLIGHTS Antibacterial compound of Lactic Acid Bacteria (LAB) from Sumbawa white honey Lactic acid bacteria isolation, characterization, and biosprosprection against pathogens Identified LAB by 16s rRNA sequencing gives five strains of Enterococcus faecium All identified LAB metabolites can inhibit all pathogens by similar inhibition percentage with Ampicillin GRAPHICAL ABSTRACT

Molecular Characterization of a Type I Quantitative Factor V Deficiency in a Thrombosis Patient that Is “Pseudo Homozygous” for Activated Protein C Resistance

1997 ◽  
Vol 77 (02) ◽  
pp. 252-257 ◽  
Author(s):  
Joan F Guasch ◽  
Ruud P M Lensen ◽  
Rogier M Bertina
Keyword(s):  
Protein C ◽  
Dna Analysis ◽  
Activated Protein C ◽  
Type I ◽  
Factor V ◽  
Sequencing Analysis ◽  
Apc Resistance ◽  
Quantitative Factor ◽  
Factor V Deficiency ◽  
Fv Leiden

SummaryResistance to activated protein C (APC), which is associated with the FV Leiden mutation in the large majority of the cases, is the most common genetic risk factor for thrombosis. Several laboratory tests have been developed to detect the APC-resistance phenotype. The result of the APC-resistance test (APC-sensitivity ratio, APC-SR) usually correlates well with the FV Leiden genotype, but recently some discrepancies have been reported. Some thrombosis patients that are heterozygous for FV Leiden show an APC-SR usually found only in homozygotes for the defect. Some of those patients proved to be compound heterozygotes for the FV Leiden mutation and for a type I quantitative factor V deficiency. We have investigated a thrombosis patient characterized by an APC-SR that would predict homozygosity for FV Leiden. DNA analysis showed that he was heterozygous for the mutation. Sequencing analysis of genomic DNA revealed that the patient also is heterozygous for a G5509→A substitution in exon 16 of the factor V gene. This mutation interferes with the correct splicing of intron 16 and leads to the presence of a null allele, which corresponds to the “non-FV Leiden” allele. The conjunction of these two defects in the patient apparently leads to the same phenotype as observed in homozygotes for the FV Leiden mutation.

Phylogeny of hymenolepidids (Cestoda: Cyclophyllidea) from mammals: sequences of 18S rRNA and COI genes confirm major clades revealed by the 28S rRNA analyses

2021 ◽  
Vol 95 ◽  
Author(s):  
B. Neov ◽  
G.P. Vasileva ◽  
G. Radoslavov ◽  
P. Hristov ◽  
D.T.J. Littlewood ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
18S Rrna ◽  
Phylogenetic Analyses ◽  
The Other ◽  
Rrna Genes ◽  
Host Switching ◽  
28S Rrna ◽  
Mitochondrial Cytochrome ◽  
Rapid Radiation ◽  
18S Rrna Genes

Abstract The aim of the study is to test a hypothesis for the phylogenetic relationships among mammalian hymenolepidid tapeworms, based on partial (D1–D3) nuclear 28S ribosomal RNA (rRNA) genes, by estimating new molecular phylogenies for the group based on partial mitochondrial cytochrome c oxidase I (COI) and nuclear 18S rRNA genes, as well as a combined analysis using all three genes. New sequences of COI and 18S rRNA genes were obtained for Coronacanthus integrus, C. magnihamatus, C. omissus, C. vassilevi, Ditestolepis diaphana, Lineolepis scutigera, Spasskylepis ovaluteri, Staphylocystis tiara, S. furcata, S. uncinata, Vaucherilepis trichophorus and Neoskrjabinolepis sp. The phylogenetic analyses confirmed the major clades identified by Haukisalmi et al. (Zoologica Scripta 39: 631–641, 2010): Ditestolepis clade, Hymenolepis clade, Rodentolepis clade and Arostrilepis clade. While the Ditestolepis clade is associated with soricids, the structure of the other three clades suggests multiple evolutionary events of host switching between shrews and rodents. Two of the present analyses (18S rRNA and COI genes) show that the basal relationships of the four mammalian clades are branching at the same polytomy with several hymenolepidids from birds (both terrestrial and aquatic). This may indicate a rapid radiation of the group, with multiple events of colonizations of mammalian hosts by avian parasites.

scholarly journals Molecular Identification of Trypanosoma evansi Isolated from Arabian Camels (Camelus dromedarius) in Riyadh and Al-Qassim, Saudi Arabia

Animals ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 1149
Author(s):  
Dina M. Metwally ◽  
Isra M. Al-Turaiki ◽  
Najwa Altwaijry ◽  
Samia Q. Alghamdi ◽  
Abdullah D. Alanazi
Keyword(s):  
Saudi Arabia ◽  
Infection Rate ◽  
Ribosomal Rna ◽  
Phylogenetic Analyses ◽  
Trypanosoma Evansi ◽  
Camelus Dromedarius ◽  
18S Ribosomal Rna ◽  
18S Ribosomal Rna Gene ◽  
Polymerase Chain ◽  
Pcr Targeting

We analyzed the blood from 400 one-humped camels, Camelus dromedarius (C. dromedarius), in Riyadh and Al-Qassim, Saudi Arabia to determine if they were infected with the parasite Trypanosoma spp. Polymerase chain reaction (PCR) targeting the internal transcribed spacer 1 (ITS1) gene was used to detect the prevalence of Trypanosoma spp. in the camels. Trypanosoma evansi (T. evansi) was detected in 79 of 200 camels in Riyadh, an infection rate of 39.5%, and in 92 of 200 camels in Al-Qassim, an infection rate of 46%. Sequence and phylogenetic analyses revealed that the isolated T. evansi was closely related to the T. evansi that was detected in C. dromedarius in Egypt and the T. evansi strain B15.1 18S ribosomal RNA gene identified from buffalo in Thailand. A BLAST search revealed that the sequences are also similar to those of T. evansi from beef cattle in Thailand and to T. brucei B8/18 18S ribosomal RNA from pigs in Nigeria.

scholarly journals Characterization, Comparative Analysis and Phylogenetic Implications of Mitogenomes of Fulgoridae (Hemiptera: Fulgoromorpha)

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1185
Author(s):  
Wenqian Wang ◽  
Huan Zhang ◽  
Jérôme Constant ◽  
Charles R. Bartlett ◽  
Daozheng Qin
Keyword(s):  
Control Region ◽  
Ribosomal Rna ◽  
Phylogenetic Analyses ◽  
Start Codon ◽  
Rrna Genes ◽  
Rich Region ◽  
Protein Coding ◽  
Phylogenetic Implications ◽  
Rna Genes ◽  
Unpaired Base

The complete mitogenomes of nine fulgorid species were sequenced and annotated to explore their mitogenome diversity and the phylogenetics of Fulgoridae. All species are from China and belong to five genera: Dichoptera Spinola, 1839 (Dichoptera sp.); Neoalcathous Wang and Huang, 1989 (Neoalcathous huangshanana Wang and Huang, 1989); Limois Stål, 1863 (Limois sp.); Penthicodes Blanchard, 1840 (Penthicodes atomaria (Weber, 1801), Penthicodes caja (Walker, 1851), Penthicodes variegata (Guérin-Méneville, 1829)); Pyrops Spinola, 1839 (Pyrops clavatus (Westwood, 1839), Pyrops lathburii (Kirby, 1818), Pyrops spinolae (Westwood, 1842)). The nine mitogenomes were 15,803 to 16,510 bp in length with 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and a control region (A + T-rich region). Combined with previously reported fulgorid mitogenomes, all PCGs initiate with either the standard start codon of ATN or the nonstandard GTG. The TAA codon was used for termination more often than the TAG codon and the incomplete T codon. The nad1 and nad4 genes varied in length within the same genus. A high percentage of F residues were found in the nad4 and nad5 genes of all fulgorid mitogenomes. The DHU stem of trnV was absent in the mitogenomes of all fulgorids sequenced except Dichoptera sp. Moreover, in most fulgorid mitogenomes, the trnL2, trnR, and trnT genes had an unpaired base in the aminoacyl stem and trnS1 had an unpaired base in the anticodon stem. The similar tandem repeat regions of the control region were found in the same genus. Phylogenetic analyses were conducted based on 13 PCGs and two rRNA genes from 53 species of Fulgoroidea and seven outgroups. The Bayesian inference and maximum likelihood trees had a similar topological structure. The major results show that Fulgoroidea was divided into two groups: Delphacidae and ((Achilidae + (Lophopidae + (Issidae + (Flatidae + Ricaniidae)))) + Fulgoridae). Furthermore, the monophyly of Fulgoridae was robustly supported, and Aphaeninae was divided into Aphaenini and Pyropsini, which includes Neoalcathous, Pyrops, Datua Schmidt, 1911, and Saiva Distant, 1906. The genus Limois is recovered in the Aphaeninae, and the Limoisini needs further confirmation; Dichoptera sp. was the earliest branch in the Fulgoridae.

scholarly journals Three redescriptions in Tintinnopsis (Protista: Ciliophora: Tintinnina) from coastal waters of China, with cytology and phylogenetic analyses based on ribosomal RNA genes

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Yang Bai ◽  
Rui Wang ◽  
Wen Song ◽  
Lifang Li ◽  
Luciana F. Santoferrara ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Coastal Waters ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Middle Portion ◽  
Closely Related Species ◽  
Molecular Information ◽  
Ciliary Tuft ◽  
Rna Genes ◽  
Rrna Sequences

Abstract Background The taxonomy of tintinnine ciliates is vastly unresolved because it has traditionally been based on the lorica (a secreted shell) and it has only recently incorporated cytological and molecular information. Tintinnopsis, the most speciose tintinnine genus, is also the most problematic: it is known to be non-monophyletic, but it cannot be revised until more of its species are studied with modern methods. Results Here, T. hemispiralis Yin, 1956, T. kiaochowensis Yin, 1956, and T. uruguayensis Balech, 1948, from coastal waters of China, were studied. Lorica and cell features were morphometrically investigated in living and protargol-stained specimens, and sequences of three ribosomal RNA (rRNA) loci were phylogenetically analyzed. The three species show a complex ciliary pattern (with ventral, dorsal, and posterior kineties and right, left, and lateral ciliary fields), but differ in lorica morphology, details of the somatic ciliature and rRNA gene sequences. Tintinnopsis hemispiralis is further distinguished by a ciliary tuft (a ribbon of very long cilia originated from the middle portion of the ventral kinety and extending out of the lorica) and multiple macronuclear nodules. Both T. kiaochowensis and T. uruguayensis have two macronuclear nodules, but differ in the number of somatic kineties and the position of the posterior kinety. Two neotypes are fixed for T. hemispiralis and T. kiaochowensis to stabilize the species names objectively, mainly because of the previous unavailability of type materials. By phylogenetic analysis and comparison with closely-related species, we infer that the ciliary tuft and details such as the commencement of the rightmost kinety in the lateral ciliary field are synapomorphies that may help clarify the systematics of Tintinnopsis-like taxa. Conclusion The redescriptions of three poorly known Tintinnopsis species, namely T. hemispiralis, T. kiaochowensis, and T. uruguayensis firstly revealed their ciliary patterns and rRNA sequences. This study expands knowledge and database of tintinnines and helps in identifying potential synapomorphies for future taxonomic rearrangements.

scholarly journals Characterization, Phylogenetic Analyses, and Pathogenicity of Enterobacter cloacae on Rice Seedlings in Heilongjiang Province, China

Plant Disease ◽  
2020 ◽  
Vol 104 (6) ◽  
pp. 1601-1609
Author(s):  
Peng Cao ◽  
Chenxu Li ◽  
Kefei Tan ◽  
Chuanzeng Liu ◽  
Xi Xu ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Enterobacter Cloacae ◽  
Rrna Gene ◽  
Bacterial Disease ◽  
Heilongjiang Province ◽  
Rice Seedlings ◽  
Bacterial Strains ◽  
Gene Sequences

Rice is used as a staple food in different areas of world, especially in China. In recent years, rice seedlings have been affected seriously by symptoms resembling bacterial palea browning (BPB) in Heilongjiang Province. To isolate and identify the pathogenic bacteria responsible for the disease, 40 bacterial strains were isolated from diseased rice seedlings collected from the four major accumulative-temperature zones of rice fields cultivated in Heilongjiang Province, and these were identified as 13 species based on morphological characteristics and 16S ribosomal RNA (rRNA) gene sequences. Inoculation of all the isolates on healthy rice seedlings showed that the nine Enterobacter cloacae isolates were the pathogens causing typical symptoms of BPB, including yellowing to pale browning, stunting, withering, drying, and death. Moreover, the nine E. cloacae isolates could also cause symptoms of bacterial disease on the seedlings of soybean (Glycine max), maize (Zea mays L.), and tomato (Solanum lycopersicum). Phylogenetic analysis based on the 16S rRNA gene sequences and phenotypic and biochemical characteristics indicated that these nine pathogenic isolates were E. cloacae. In addition, analysis of the sequences of four housekeeping genes (rpoB, gyrB, infB, and atpD) from the selected strain SD4L also assigned the strain to E. cloacae. Therefore, E. cloacae is the pathogen causing disease of rice seedlings in Heilongjiang Province, which we propose to classify as a form of BPB. To the best of our knowledge, this is the first study to identify E. cloacae as a causal agent of BPB in rice.

scholarly journals The complete chloroplast genome sequences of five pinnate-leaved Primula species and phylogenetic analyses

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Wenbin Xu ◽  
Boshun Xia ◽  
Xinwei Li
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Analyses ◽  
Distinct Species ◽  
The Other ◽  
Trna Genes ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Noncoding Sequences ◽  
Chloroplast Genomes ◽  
Rna Genes

AbstractThe six pinnate-leaved species are a very particular group in the genus Primula. In the present paper, we sequenced, assembled and annotated the chloroplast genomes of five of them (P. cicutarrifolia, P. hubeiensis, P. jiugongshanensis, P. merrilliana, P. ranunculoides). The five chloroplast genomes ranged from ~ 150 to 152 kb, containing 113 genes (four ribosomal RNA genes, 29 tRNA genes and 80 protein-coding genes). The six pinnate-leaved species exhibited synteny of gene order and possessed similar IR boundary regions in chloroplast genomes. The gene accD was pseudogenized in P. filchnerae. In the chloroplast genomes of the six pinnate-leaved Primula species, SSRs, repeating sequences and divergence hotspots were identified; ycf1 and trnH-psbA were the most variable markers among CDSs and noncoding sequences, respectively. Phylogenetic analyses showed that the six Primula species were separated into two distant clades: one was formed by P. filchnerae and P. sinensis and the other clade was consisting of two subclades, one formed by P. hubeiensis and P. ranunculoides, the other by P. merrilliana, P. cicutarrifolia and P. jiugongshanensis. P. hubeiensis was closely related with P. ranunculoides and therefore it should be placed into Sect. Ranunculoides. P. cicutarrifolia did not group first with P. ranunculoides but with P. merrilliana, although the former two were once united in one species, our results supported the separation of P. ranunculoides from P. cicutarrifolia as one distinct species.

scholarly journals Detection of potentially pathogenic bacteria from Ixodes ricinus carried by pets in Tuscany, Italy

2020 ◽  
Vol 7 (1) ◽  
pp. e000395
Author(s):  
Valentina Chisu ◽  
Cipriano Foxi ◽  
Gabriella Masu ◽  
Barbara D' Amaddio ◽  
Giovanna Masala
Keyword(s):  
Coxiella Burnetii ◽  
Pathogenic Bacteria ◽  
Bartonella Henselae ◽  
Companion Animals ◽  
Chlamydia Psittaci ◽  
Sequencing Analysis ◽  
Increased Risk ◽  
Domestic Environments ◽  
Preliminary Study ◽  
Potential Public Health

BackgroundTicks are vectors of disease-causing pathogens that pose a serious threat to animals and people. Dogs and cats are exposed to tick infestation in multiple ways and can easily transport infected ticks into domestic environments and potentially transfer them to people. Pet owners are at increased risk of picking up ticks from their pets and developing tickborne diseases. This study aims to detect the presence of pathogens of potential public health interest in ticks removed from cats and dogs in Tuscany, Italy.MethodsThe collected ticks were screened for the presence of protozoan (Theileria species and Babesia species) and bacterial (Rickettsia species, Anaplasma species, Ehrlichia species, Chlamydia species, Bartonella species and Coxiella burnetii) pathogens using PCR.ResultsPCR and sequencing analysis revealed that 3 per cent of the ticks were PCR-positive for the presence of Rickettsia helvetica DNA, 5 per cent of ticks were PCR-positive for Bartonella henselae DNA, and 46 per cent of ticks were PCR-positive for Chlamydia psittaci and Chlamydia abortus DNA. None of the examined ticks was PCR-positive for Theileria species, Babesia species, Anaplasma species, Ehrlichia canis or Coxiella burnetii DNA.ConclusionThe results of this preliminary study highlight the importance of monitoring companion animals as indicators to evaluate the health status of their owners. Preventive measures are necessary to limit the spread of zoonotic pathogens from companion animals to people within the home environment.

scholarly journals Survey and Diversity of Grapevine Pinot gris virus in Algeria and Comprehensive High-Throughput Small RNA Sequencing Analysis of Two Isolates from Vitis vinifera cv. Sabel Revealing High Viral Diversity

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1110
Author(s):  
Aleš Eichmeier ◽  
Eliška Peňázová ◽  
Jana Čechová ◽  
Akila Berraf-Tebbal
Keyword(s):  
Vitis Vinifera ◽  
Rna Sequencing ◽  
Small Rna ◽  
Phylogenetic Analyses ◽  
Small Rna Sequencing ◽  
Sequencing Analysis ◽  
Hop Stunt Viroid ◽  
Grapevine Virus B ◽  
Grapevine Pinot Gris Virus ◽  
Rupestris Stem Pitting

Grapevine Pinot gris virus (GPGV) is a putative causal agent of grapevine leaf mottling and deformation disease that has been reported worldwide throughout the grapevine-growing regions. Fifty-four grapevines collected from five Algerian grapevine-growing regions were tested for the presence of GPGV in phloem tissues. Eight of the tested grapevines were infected by GPGV. Viromes of two selected Vitis vinifera cv. Sabel grapevines infected by GPGV and showing virus-like symptoms were analyzed by small RNA sequencing. Phylogenetic analyses of the partial coding sequence (cds) of the RNA-dependent RNA polymerase (RdRp) domain showed that all Algerian GPGV isolates were grouped with some already-described asymptomatic isolates. This study provides the first survey of the occurrence of GPGV in Algeria. Moreover, Grapevine fleck virus, Grapevine rupestris stem pitting-associated virus, Grapevine virus B, Grapevine rupestris vein feathering virus, Hop stunt viroid and Grapevine yellow speckle viroid 1 were detected in Algeria for the first time.

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