No evidence for phylosymbiosis in western chipmunk species

Phylosymbiosis refers to a congruent pattern between the similarity of microbiomes of different species and the branching pattern of the host phylogeny. Phylosymbiosis has been detected in a variety of vertebrate and invertebrate hosts, but has only been assessed in geographically isolated populations. We tested for phylosymbiosis in eight (sub)species of western chipmunks with overlapping ranges and ecological niches; we used a nuclear (Acrosin) and a mitochondrial (CYTB) phylogenetic marker because there are many instances of mitochondrial introgression in chipmunks. We predicted that similarity among microbiomes increases with: (1) increasing host mitochondrial relatedness, (2) increasing host nuclear genome relatedness and (3) decreasing geographic distance among hosts. We did not find statistical evidence supporting phylosymbiosis in western chipmunks. Furthermore, in contrast to studies of other mammalian microbiomes, similarity of chipmunk microbiomes is not predominantly determined by host species. Sampling site explained most variation in microbiome composition, indicating an important role of local environment in shaping microbiomes. Fecal microbiomes of chipmunks were dominated by Bacteroidetes (72.2%), followed by Firmicutes (24.5%), which is one of the highest abundances of Bacteroidetes detected in wild mammals. Future work will need to elucidate the effects of habitat, ecology and host genomics on chipmunk microbiomes.

The complete mitochondrial genome of Sasakia funebris (Leech) (Lepidoptera: Nymphalidae) and comparison with other Apaturinae insects

Sasakia funebris, a member of the lepidopteran family, Nymphalidae (superfamily Papilionoidea) is a rare species and is found only in some areas of South China. In this study, the 15,233 bp long complete mitochondrial genome of S. funebris was determined, and harbors the gene arrangement identical to all other sequenced lepidopteran insects. The nucleotide composition of the genome is highly A+T biased, accounting for 81.2%. All protein-coding genes (PCGs) start with typical ATN codons, except for COI which begins with the CGA codon. All tRNAs have a typical clover-leaf secondary structure, except for tRNASer(AGN), the dihydrouridine (DHU) arm of which forms a simple loop. The S. funebris A+T-rich region of 370 bp contains several features common to the Lepidoptera insects, including the motif ATAGA followed by a 19 bp poly-T stretch, and two tandem repeats consisting of 18 bp repeat units and 14 bp repeat units. The phylogenetic analyses of Apaturinae based on mitogenome sequences showed: (S. funebris+Sasakia charonda)+(Apatura metis+Apatura ilia). This result is consistent with the morphological classification.

Prevalence and diversity of Plasmodium and Haemoproteus parasites in the globally-threatened Aquatic Warbler Acrocephalus paludicola

The diversity and prevalence of malaria parasites of the genera Plasmodium and Haemoproteus were determined in the globally-threatened Aquatic Warbler Acrocephalus paludicola. Birds were sampled during migration in Portugal and at the wintering quarters in Senegal and parasites were detected using molecular methods. Only three generalist parasite lineages (Plasmodium) were found. There were no significant differences in the prevalence of parasites between sexes in Europe, but adults had higher prevalence than first-year birds, and birds in Europe had higher prevalence than those captured in Africa. When comparing with other Acrocephalus species and taking sample size into account, Aquatic Warblers had the lowest prevalence and, together with another threatened species, the Seychelles Warbler Acrocephalus sechellensis, the lowest diversity of malaria parasites. We hypothesize that the low diversity of parasites and absence of specialist lineages of Aquatic Warblers are caused by its small population size and fragmented distribution. Furthermore, Aquatic Warblers' extreme habitat specialization may decrease their exposure to malaria parasites, but other explanations such as high mortality (which would constraint the sampling of infected birds) or, in contrast, very efficient immunological system in clearing the infections cannot be ruled out. This study contributes to explain variation in prevalence and diversity of malaria parasites among hosts.

Genetic characterization and phylogenetic study of Indonesian indigenous catfish based on mitochondrial cytochrome B gene

Aims

This study aimed to determine the genetic characterization and phylogenetic structure of Indonesian indigenous catfish using cytochrome B (Cyt B) sequences.

Materials and Methods

The genomes of 26 catfishes caught from nine rivers from nine different geographical locations around Indonesia were analyzed. The tissue isolation method was used to isolate the total genome of the fishes. Furthermore, polymerase chain reaction was done to amplify the mtDNA Cyt B using the CytBF and CytBR primers. Following sequencing, the analysis of genetic variation and the phylogenetic relationship was performed using MEGA version X software.

Results

Cyt B gene sequencing attained a total of 1139 nucleotides encrypting 379 amino acids for all samples. The ClustalW alignment program using MEGA X software revealed 395 substituted nucleotides, which then translated into 63 amino acid variation sites among all 26 samples. No amino acids in catfish BB were different compared to catfish PM, MP, and KR2,3. Catfish MS had one modified amino acid; KR1 and KS had two different amino acids; BF had 38 different amino acids; EM had 31 different amino acids; and BSBJ had 26 different amino acids compared to catfish BB. The most significant alteration of amino acids was between catfish EM and BF (49 amino acids).

Conclusion

Indonesian catfish were divided into five clades based on the Cyt B gene. Samples KR and MP (Sumatra); MS and BB (Kalimantan); and PM (Java) were clustered with Hemibagrus nemurus and Hemibagrus wyckioides (Bagridae family). Samples from Kalimantan (KS) and one sample of KR (KR1) from Sumatra were clustered with Sperata seenghala and Hemibagrus spilopterus (Bagridae family). Samples from Java (BSBJ) were clustered with Pseudolais pleurotaenia (Pangasiidae family). Samples EM (Java) were together with Mystus cavasius (Bagridae family). Samples from West Papua were clustered with Potamosilurus latirostris (Ariidae family).

Rapid Full-Cycle Technique to Control Adulteration of Meat Products: Integration of Accelerated Sample Preparation, Recombinase Polymerase Amplification, and Test-Strip Detection

Verifying the authenticity of food products is essential due to the recent increase in counterfeit meat-containing food products. The existing methods of detection have a number of disadvantages. Therefore, simple, cheap, and sensitive methods for detecting various types of meat are required. In this study, we propose a rapid full-cycle technique to control the chicken or pig adulteration of meat products, including 3 min of crude DNA extraction, 20 min of recombinase polymerase amplification (RPA) at 39 °C, and 10 min of lateral flow assay (LFA) detection. The cytochrome B gene was used in the developed RPA-based test for chicken and pig identification. The selected primers provided specific RPA without DNA nuclease and an additional oligonucleotide probe. As a result, RPA-LFA, based on designed fluorescein- and biotin-labeled primers, detected up to 0.2 pg total DNA per μL, which provided up to 0.001% w/w identification of the target meat component in the composite meat. The RPA-LFA of the chicken and pig meat identification was successfully applied to processed meat products and to meat after heating. The results were confirmed by real-time PCR. Ultimately, the developed analysis is specific and enables the detection of pork and chicken impurities with high accuracy in raw and processed meat mixtures. The proposed rapid full-cycle technique could be adopted for the authentication of other meat products.

The Mitochondrial Epigenome: An Unexplored Avenue to Explain Unexplained Myopathies?

Mutations in either mitochondrial DNA (mtDNA) or nuclear genes that encode mitochondrial proteins may lead to dysfunctional mitochondria, giving rise to mitochondrial diseases. Some mitochondrial myopathies, however, present without a known underlying cause. Interestingly, methylation of mtDNA has been associated with various clinical pathologies. The present study set out to assess whether mtDNA methylation could explain impaired mitochondrial function in patients diagnosed with myopathy without known underlying genetic mutations. Enhanced mtDNA methylation was indicated by pyrosequencing for muscle biopsies of 14 myopathy patients compared to four healthy controls, at selected cytosines in the Cytochrome B (CYTB) gene, but not within the displacement loop (D-loop) region. The mtDNA methylation patterns of the four healthy muscle biopsies were highly consistent and showed intriguing tissue-specific differences at particular cytosines with control skin fibroblasts cultured in vitro. Within individual myopathy patients, the overall mtDNA methylation pattern correlated well between muscle and skin fibroblasts. Despite this correlation, a pilot analysis of four myopathy and five healthy fibroblast samples did not reveal a disease-associated difference in mtDNA methylation. We did, however, detect increased expression of solute carrier family 25A26 (SLC25A26), encoding the importer of S-adenosylmethionine, together with enhanced mtDNA copy numbers in myopathy fibroblasts compared to healthy controls. To confirm that pyrosequencing indeed reflected DNA methylation and not bisulfite accessibility, mass spectrometry was employed. Although no myopathy-related differences in total amount of methylated cytosines were detected at this stage, a significant contribution of contaminating nuclear DNA (nDNA) was revealed, and steps to improve enrichment for mtDNA are reported. In conclusion, in this explorative study we show that analyzing the mitochondrial genome beyond its sequence opens novel avenues to identify potential molecular biomarkers assisting in the diagnosis of unexplained myopathies.

Molecular Correlation between Larval, Deutonymph and Adult Stages of the Water Mite Arrenurus (Micruracarus) Novus

The systematics of many groups of organisms has been based on the adult stage. Morphological transformations that occur during development from the embryonic to the adult stage make it difficult (or impossible) to identify a juvenile (larval) stage in some species. Hydrachnidia (Acari, Actinotrichida, which inhabit mainly continental waters) are characterized by three main active stages—larval, deutonymph and adult—with intermediate dormant stages. Deutonymphs and adults may be identified through diagnostic morphological characters. Larvae that have not been tracked directly from a gravid female are difficult to identify to the species level. In this work, we compared the morphology of five water mite larvae and obtained the molecular sequences of that found on a pupa of the common mosquito Culex (Culex) pipiens with the sequences of 51 adults diagnosed as Arrenurus species and identified the undescribed larvae as Arrenurus(Micruracarus) novus. Further corroborating this finding, adult A. novus was found thriving in the same mosquito habitat. We established the identity of adult and deutonymph A. novus by morphology and by correlating COI and cytB sequences of the water mites at the larval, deutonymph and adult (both male and female) life stages in a particular case of ‘reverse taxonomy’. In addition, we constructed the Arrenuridae phylogeny based on mitochondrial DNA, which supports the idea that three Arrenurus subgenera are ‘natural’: Arrenurus, Megaluracarus and Micruracarus, and the somewhat arbitrary distinction of the species assigned to the subgenus Truncaturus.

A new fast real-time PCR method for the identification of three sibling Apodemus species (A. sylvaticus, A. flavicollis, and A. alpicola) in Italy

The identification of field mice Apodemus flavicollis, Apodemus sylvaticus, and Apodemus alpicola represents a challenge for field scientists due to their highly overlapping morphological traits and habitats. Here, we propose a new fast real-time PCR method to discriminate the three species by species-specific TaqMan assays. Primers and probes were designed based on the alignment of 54 cyt-b partial sequences from 25 different European countries retrieved from GenBank. TaqMan assays were then tested on 133 samples from three different areas of Italy. Real-time PCR analysis showed 92 samples classified as A. flavicollis, 13 as A. sylvaticus, and 28 as A. alpicola. We did not observe any double amplification and DNA sequencing confirmed species assignment obtained by the TaqMan assays. The method is implementable on different matrices (ear tissues, tail, and blood). It can be used on dead specimens or on alive animals with minimally invasive sampling, and given the high sensitivity, the assay may be also suitable for degraded or low-DNA samples. The method proved to work well to discriminate between the species analyzed. Furthermore, it gives clear results (amplified or not) and it does not require any postamplification handling of PCR product, reducing the time needed for the analyses and the risk of carryover contamination. It therefore represents a valuable tool for field ecologists, conservationists, and epidemiologists.

Mitochondrial Genome-Encoded Long Noncoding RNA Cytochrome B and Mitochondrial Dysfunction in Diabetic Retinopathy

Aims: Mitochondrial dysfunction is closely associated with the development of diabetic complications. In diabetic retinopathy, electron transport chain is compromised and mitochondrial DNA (mtDNA) is damaged, downregulating transcription of mtDNA-encoded cytochrome B (CYTB) and its antisense long noncoding RNA, long noncoding RNA cytochrome B (LncCytB). Our goal was to investigate the role of LncCytB in the regulation of CYTB and mitochondrial function in diabetic retinopathy. Methods: Using human retinal endothelial cells, genetically manipulated for LncCytB (overexpression or silencing), the effect of high glucose (20 mM d-glucose) on LncCytB-CYTB interactions (by chromatin isolation by RNA purification), CYTB gene expression (by real-time quantitative polymerase chain reaction), complex III activity, mitochondrial free radicals, and oxygen consumption rate (OCR, by Seahorse XF analyzer) was investigated. Key results were confirmed in the retinal microvessels from streptozotocin-induced diabetic mice. Results: High glucose decreased LncCytB-CYTB interactions, and while LncCytB overexpression ameliorated glucose-induced decrease in CYTB gene transcripts, complex III activity and OCR and increase in mitochondrial reactive oxygen species, LncCytB-siRNA further attenuated CYTB gene transcription, complex III activity, and OCR. Similar decrease in LncCytB-CYTB interactions and CYTB transcription was observed in diabetic mice. Furthermore, maintenance of mitochondrial homeostasis by overexpressing superoxide dismutase or sirtuin 1 in mice ameliorated diabetes-induced decrease in LncCytB-CYTB interactions and CYTB gene transcripts, and also improved complex III activity and mitochondrial respiration. Innovation and Conclusion: LncCytB downregulation in hyperglycemic milieu downregulates CYTB transcription, which inhibits complex III activity and compromises mitochondrial stability and OCR. Thus, preventing LncCytB downregulation in diabetes has potential of inhibiting the development of diabetic retinopathy, possibly via maintaining mitochondrial respiration. Antioxid. Redox Signal. 39, 817-828.

Phlebotomine (Diptera: Psychodidae) species and their blood meal sources in a new leishmaniasis focus in Los Montes de María, Bolívar, in northern Colombia

Introduction. El Alférez, a village in Los Montes de María (Bolívar, Colombia) and a macro-focus of leishmaniasis, recorded its first case in 2018, evidencing changes in the distribution and eco-epidemiology of the disease, although interactions between vectors and local fauna remain unknown. Objective. To evaluate the diversity of sandflies and their blood meal sources in the community of El Alférez in the municipality of El Carmen de Bolívar (Bolívar, Colombia). Materials and methods. In 2018, sandflies were collected using LED-based light traps in domestic, peridomestic, and sylvatic ecotopes and identified at the species level. Multiplex polymerase chain reaction targeting the mitochondrial cytochrome B gene was used to analyze blood from the digestive tract. Results. Lutzomyia evansi was the most abundant species (71.85%; n = 485/675), followed by Lu. panamensis, Lu. gomezi, Lu. trinidadensis, Lu. dubitans, Lu. abonnenci, and Lu.aclydifera. Twenty-five percent of the species had blood meals from Canis familiaris (36.00%; n = 9/25), Ovis aries (36.00%; n=9:/25), Bos taurus (24.00%; n = 6/25), Sus scrofa (20.00%; n = 5/25), and Homo sapiens (8.00%; n = 2/25). Lutzomyia evansi registered the highest feeding frequency (68.00%; n = 17/25), predominantly on a single (44.00%; n = 11/25) or multiple species (24.00%; n = 6/25). Conclusion. Results indicate a eclectic feeding behavior in Lu. evansi, implying potential reservoir hosts for Leishmania spp. and increasing transmission risk. This study is a first step towards understanding the diversity of mammalian blood sources used by sandflies, that may be crucial for vector identification and formulation of effective control measures.

Trimethylamine N-oxide induces pyroptosis in HTR8-S/Vneo cells through the ten-eleven translocation 2-cytochrome b-reactive oxygen species pathway

AIM

Pyroptosis is a type of programmed cell death characterized by pro-inflammatory activity and is an important factor in pre-eclampsia (PE). Trimethylamine N-oxide (TMAO) is a gut microbial metabolite closely associated with pyroptosis and PE. This study aims to investigate the role of TMAO in trophoblast cell pyroptosis and explore possible mechanisms.

METHODS

Western blot and qRT-polymerase chain reaction (PCR) were used to detect the expression levels of ten-eleven translocation 2 (TET2), cytochrome b (CYTB), pyroptosis-related molecules, and mitochondrial proteins. The level of mitochondrial reactive oxygen species (mtROS) was detected by fluorescent probe DCFH-DA. Immunofluorescence was used to measure the level of 5-hydroxymethylcytosine (5hmC). TET2 overexpression/silencing and CYTB overexpression/silencing lentiviruses were transfected into HTR8/SVneo cells, respectively. MitoTEMPO was used to reduce mtROS. TMAO levels in placental tissues were quantified by liquid chromatography-tandem mass spectrometry (LC-MS/MS), and representative extracted ion chromatograms were analyzed for retention times and peak areas. ELISA was used to further validate TMAO concentrations in placental tissues.

RESULTS

TMAO is capable of enhancing the expression of proteins related to pyroptosis (including NLRP3, GSDMD, GSDMD-N, Caspase-1) as well as inflammatory factors (such as IL-1β, IL-18) in HTR8-S/Vneo cells. Meanwhile, the positive rate of propidium iodide (PI), mtROS levels, and intracellular Ca2+ levels all increased. Electron microscopy results showed an increase in mitochondrial membrane pore numbers, abnormal mitochondrial morphology, and downregulation of the expression levels of mitochondrial proteins nuclear respiratory factor 1 (NRF1), NRF2, peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α), and NADH dehydrogenase subunit 2 (ND2). LC-MS/MS and ELISA analyses revealed significantly elevated TMAO levels in PE placental tissues compared to normal tissues, further supporting the role of TMAO accumulation in placental dysfunction associated with PE. Overexpression of CYTB inhibited TMAO-induced pyroptosis and mitochondrial dysfunction (MDF) in HTR8-S/Vneo cells, while silencing of CYTB promoted pyroptosis and MDF in HTR8-S/Vneo cells, but this condition could be partially reversed by MitoTEMPO. TMAO inhibited the expression of TET2 and CYTB and downregulated the level of 5hmc. The results of TET2 overexpression/knockout indicated that the expression of CYTB was regulated by TET2, and overexpression of TET2 alleviated TMAO-induced pyroptosis and MDF as well as the decrease in 5hmc levels in HTR8-S/Vneo cells, but this condition could be partially reversed by silencing CYTB.

CONCLUSION

In summary, these findings suggest that TMAO induces pyroptosis in HTR8/SVneo cells through the TET2-CYTB-mtROS pathway, contributing to mitochondrial dysfunction and inflammation. The significant elevation of TMAO levels in PE placental tissues further supports its role in the pathophysiology of PE. Targeting the TET2-CYTB-mtROS pathway may provide a novel therapeutic strategy for the treatment of PE.