Chromosome Mediated Fluoroquinolone and Extended Spectrum Beta-lactamase Resistant Genes in E. coli of Poultry Origin in Ekiti State

Background: One health approach aimed at solving global health crisis links human, animal, and environmental health. This inclusive strategy has contributed to antibiotic classification in both human and animal medicine. Aims: The aims of this research work are to determine the phylogenetic relationship of E. coli isolated from poultry and waste sources. The presence of chromosome mediated fluoroquinolone and extended spectrum beta-lactamase resistant genes will also be detected in the isolates. Study Design: Experimental design. Methodology: Data on farming attitudes of poultry farmers were collected using a questionnaire. E. coli was isolated from fresh poultry droppings and waste disposal sites using eosine methylene blue agar. The antibiotic sensitivity profile of the isolates was determined using the modified Kirby Bauer disc diffusion method. Phenotypic expression of fluoroquinolone (qnrS) and beta-lactamase (blaCMY) resistant traits were further detected using Polymerase Chain Reaction. The 16S rRNA gene sequencing was carried out followed by sequence alignment of E. coli genes with those from GenBank sources to determine the molecular identity of the isolates. Spearman’s correlation coefficient (rs) was run to determine the relationship between antibiotic treatment and resistant profile of the isolates. The phylogenetic relationship of the isolates was determined using Bio edit and Mega 6 software. Results: Organic poultry farming was practiced by small-scaled, peasant farmers who raised free range birds while antibiotics were widely used on farms that adopted intensive mode of farming. The percentage occurrence of E. coli from waste disposal sources was lesser than that from fresh poultry droppings. Highest percentage of antibiotic resistance to the fluoroquinolones was found while the carbapenemase recorded the lowest. Statistical analysis shows that antibiotic treatment in poultry and resistant profile of isolates to antibiotics are directly related. The percentage similarity of gene sequence with those from Gene Data Bank (≥99.29%) validates the identity of the isolates as E. coli. About, 60% of the sampled population had the qnrS gene with a band size of approximately 322 base pair. Besides, 40% of the sampled isolates possessed the blaCMY gene with a band size of approximately 460 base pair. Both genes co-existed in the chromosome of 15% of the sampled isolates sourced from poultry droppings and waste sources. Phylogenetic classification links the origin of isolates from waste disposal sources to poultry production sites. Besides, variant strains of multiple antibiotic resistant E. coli from poultry with antibiotic treatment were more diverse compared to those obtained from birds raised without antibiotics. Conclusion: The qnrS and blaCMY genes found in multiple antibiotic resistant E. coli mediated resistance to critically important antibiotics. The co-existence of these genes in variants strains of E. coli occupying different phylogenetic clusters suggests that antibiotics were widely used on the birds. Antibiotic treatment regimen in poultry may be responsible for the expression of antibiotic resistant genes found in the chromosome of the variant strains of E. coli.

Testing the Relationship between Bursty Star Formation and Size Fluctuations of Local Dwarf Galaxies

Stellar feedback in dwarf galaxies plays a critical role in regulating star formation via galaxy-scale winds. Recent hydrodynamical zoom-in simulations of dwarf galaxies predict that the periodic outward flow of gas can change the gravitational potential sufficiently to cause radial migration of stars. To test the effect of bursty star formation on stellar migration, we examine star formation observables and sizes of 86 local dwarf galaxies. We find a correlation between the R-band half-light radius (R e ) and far-UV luminosity (L FUV) for stellar masses below 108 M ⊙ and a weak correlation between the R e and Hα luminosity (L Hα ). We produce mock observations of eight low-mass galaxies from the FIRE-2 cosmological simulations and measure the similarity of the time sequences of R e and a number of star formation indicators with different timescales. Major episodes of R e time sequence align very well with the major episodes of star formation, with a delay of ∼50 Myr. This correlation decreases toward star formation rate indicators of shorter timescales such that R e is weakly correlated with L FUV (10–100 Myr timescale) and is completely uncorrelated with L Hα (a few Myr timescale), in agreement with the observations. Our findings based on FIRE-2 suggest that the R-band size of a galaxy reacts to star formation variations on a ∼50 Myr timescale. With the advent of a new generation of large space telescopes (e.g., JWST), this effect can be examined explicitly in galaxies at higher redshifts, where bursty star formation is more prominent.

Isolation of Metallothionein (MT) Gene from Phytoremediation Agent, Eleusine indica

Belulang grass (Eleusine indica) is a plant in the Poaceae family that is commonly found in the coastal area of Dumai, Riau Province. Eleusine indica is characterized by narrow leaves, concave stems that can reach up to 95 cm high and strong roots. E. indica is known to be very tolerant of its environment, including the environment contaminated with heavy metals. The ability of E. indica as a phytoremediation agent in absorbing heavy metals has been widely known as the role of metallothionein (MT) protein. MT is believed to have a function in the metal metabolism and detoxification process through the metal chelating interaction between the cysteine amino acid residues. This unique function prompted the interest to isolate the MT gene from E. indica. This method involves the isolation of genomic DNA from E. indica followed by the process of amplification of the MT gene using specific primers, namely MTFS and MTRS by polymerase chain reaction (PCR) technology. The success of the MT gene isolation process from E. indica was evidenced by the presence of a single band size of around 172 bp via the visualization process on 1% agarose gel. Furthermore, the results of the PCR product are purified for the purpose of sequencing activity. The results of sequencing analysis of the 172 bp fragment showed 99.31% identical similarity with the complete metallothionein gene from E. indica (DQ082855.1) by using the BLASTN tool, NCBI website.

Fibropreventive and Antifibrotic Effects of Uncaria gambir on Rats with Pulmonary Fibrosis

Pulmonary fibrosis causes scar tissue formation that disrupts the functioning of the lungs. Uncaria gambir (Hunter) Roxb (hereafter gambir)—a plant native to West Sumatra in Indonesia—contains flavonoid (+)-catechin and has strong antioxidant activity, and it can be used to combat pulmonary fibrosis. This random in vivo experimental study analyzed the antifibrotic effect of gambir on the lungs of rats with bleomycin-induced fibrosis. The subjects were 10 groups of 10-week-old male rats weighing around 200–250 g. All groups were terminated at the end of the seventh week or on day 50. The lungs were cleaned, and tissues were taken to analyze inflammatory cell counts and TGF-β1 levels using bronchoalveolar lavage (BAL) with ELISA; type I collagen and tissue inhibitor of metalloproteinase 1 (TIMP-1) levels using immunohistochemistry (IHC); and activation of NF-κB using ELISA and Western blot assays. The most severe histopathological characteristic based on the modified Ashcroft score was in the bleomycin group (BG), whereas the mildest was in the 262 mg/kg of bodyweight antifibrotic gambir-dosed group (AF G262). The results showed a significant difference in the BAL inflammatory cell count (p = 0.017; p < 0.05). AF G262 differed most from the other antifibrotic groups in terms of the number of inflammatory cells (0.63), TGF-β1 levels (3.80), and NF-κB levels (0.48), followed by the 131 mg/kg of bodyweight antifibrotic gambir-dosed group (AF G131), which also differed most from other antifibrotic groups in terms of NF-κB (0.48), TIMP-1 (11.74), and collagen I (14.50) levels. Western blot analysis showed that the fibropreventive and antifibrotic groups had a specific band size of p65, whereas no specific band binding existed in the control group. This study concluded that the administration of AF G262 could improve fibrosis by lysing the extracellular matrix (ECM) in rat lungs.

Effect of Batissa violacea celebensis Martens, 1897, Extract on β-Catenin Gene in Mice (Mus musculus) Induced by Azoxymethane and Dextran Sulfate Sodium using Polymerase Chain Reaction-restriction Fragment Length Polymorphism Method

BACKGROUND: At present, the β-catenin gene is a genetic change considered as the most important factor in the initiation and the progress of cancer. Bivalve extract contains steroid compounds that are thought to have an aphrodisiac and anti-inflammatory effect. The triterpenoid component detected in the crude bivalves extract is thought to have antitumor activity. AIM: This study aimed at knowing the effect of ethanol (EtOH) extract, ethyl acetate fraction, and the n-hexane fraction of pokea clam on β-catenin gene mutation in mice induced by azoxymethane (AOM) and dextran sulfate sodium (DSS) using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. METHODS: The testing of the effect of pokea clam extract was conducted on several treatment groups, namely, AOM/DSSinfected mice treated with EtOH extract, ethyl acetate fraction, and N-hexane fraction. The positive control and the negative control of the three treatment groups were done by giving the extract with a dosage of 0.25 mg/bb to mice for 14 days. RESULTS: Based on the result of β-catenin gene amplification using the PCR method and RFLP analysis, the EtOH extract and ethyl acetate fraction groups had the same band, namely, 56 bp and 12 bp, consecutively; meanwhile, the n-hexane fraction was marked by the band formation of 191 bp, 82 bp and 48 bp, 69 bp, 116 bp, 151 bp, 180 bp, and 234 bp. From the types of band and the band size that have been formed, it shows that they have the same formation and similarities in the positive and negative treatment characterized by the amplification that occurred in the band size of 227 bp, and the result of amplification from RFLP analysis showed the same band with the same band size, namely, 89 and 138 bp. CONCLUSION: Based on this, it can be concluded that N-hexane fraction affects β-catenin gene mutation at the first or second base at codon position 32 or 33, and the third base, namely, the bands of 82 and 145 bp that also characterize the effect of N-hexane on β-catenin gene mutation at the second or third base. It is supported by the sequencing method obtaining the homological percentage of 99.13%.

Group Composition and Social Structure of Red-Shanked Doucs (Pygathrix nemaeus) at Son Tra Nature Reserve, Vietnam

Multilevel societies, consisting of multiple one-male multi-female units, are relatively rare among primates, but are more widespread in the odd-nosed colobines than other taxa. Multilevel societies are found particularly in snub-nosed monkeys (<i>Rhinopithecus</i>)<i></i>and have been debated in studies of proboscis monkeys (<i>Proboscis</i>). While it has been suggested that douc langurs (<i>Pygathrix</i>) may also form multilevel societies, the limited data available make the details of their social organization unclear. We aimed to establish a more comprehensive picture of the social organization of red-shanked doucs (<i>Pygathrix nemaeus</i>) and to address the question of whether this species forms multilevel societies, specifically collections of multiple distinct one-male units hereafter termed “bands.” We collected 259 h of behavioral data at Son Tra Nature Reserve in Vietnam from February 2010 to May 2011. The mean band size was approximately 18 individuals. Bands were comprised of approximately 2.7 units, and each unit contained approximately 6.5 individuals. Units had an average sex ratio of 1.0:1.6. We observed fission and fusion behaviors which were not correlated with phenological or weather measures. Activity budget data showed that fission and fusion behaviors between units were positively correlated with activity. Both vocalizations and vigilance increased when units engaged in fission. Based on this evidence, <i>P. nemaeus</i> at Son Tra Nature Reserve appear to engage in daily fission-fusion activity which does not vary between seasons. Additionally, our data suggest that these primates may form multilevel societies made up of distinct units. However, future data including proximity pattern analyses are necessary for confirmation.

Molecular Variability of Yellow Mosaic Virus (YMV) of Blackgram in Southern India

Background: The yellow mosaic disease (YMD) creates a major hindrance and known to affect a number of grain leguminous crops in the Indian sub-continent. However, blackgram (Vigna mungo L.) is the most important grain legume crop which is affected widely by this disease. The disease is caused by a single stranded DNA containing begomovirus viz., Yellow mosaic virus (YMV) which is mainly transmitted through whitefly (Bemisia tabaci Genn.). Symptoms include severe patho-physiological alterations characterized by the presence of bright chlorotic yellow patches interspersed with green areas on leaf lamina. The present study was aimed to determine the variability among disease causing agents in six different geographical isolates representing four states viz. Andhra Pradesh, Karnataka, Odisha and Telangana states of southern India during the 2019 rabi season. Methods: The variability of YMV associated with YMD of blackgram was studied based on molecular characterization of partial DNA-A coat protein gene with subsequent nucleotide sequencing and phylogenetic tree construction. Result: The synthetic primers designed for the partial DNA-A segment forms a distinct viral gene specific PCR product. The band size corresponding to CP ~704 bp was obtained for MYMV, whereas CP ~500 bp gene band was obtained for MYMIV. Further, phylogenetic analysis based on partial DNA-A gene sequences of six isolates with other isolates from GenBank formed into two unique clusters viz., MYMV and MYMIV. Overall, our study confirming that the begomovirus causing YMD of blackgram in southern India is explored to be as strains of MYMV and MYMIV.

First report of sweet potato chlorotic stunt virus infecting sweet potatoes in Hungary

Sweet potato chlorotic stunt virus (SPCSV), a crinivirus in the family Closteroviridae, is a quarantine pest in Europe and one of the most economically important viruses of sweet potato (Ipomoea batatas (L.) Lam) crops globally. It forms synergies with other viruses in sweet potato, leading to yield loss of 30-100% (Qin et al., 2014). In summer 2020, 62 symptomatic and 38 symptomless sweet potato vines were randomly collected in farmers’ fields in the south (Ásotthalom, Szeged) and central (Galgahévíz) parts of Hungary and transplanted in an insect-proof greenhouse. Six of the plants expressed SPCSV-like symptoms, including stunting, vein clearing and leaf purpling (Suppl1). To check for common viruses of sweet potato (Suppl2), total RNA and DNA were extracted from leaves of each of the 100 plants using Trizolate reagent (UD-GenoMed, Debrecen, Hungary) and Zenogene kit (Zenon Bio, Szeged, Hungary), respectively. Primer pair Ch2N (Suppl2) was designed using Primer3 (v. 0.4.0) to amplify a 194 bp fragment of SPCSV RNA1. Presence of the RNA viruses was checked by qPCR using qPCRBIO SyGreen 1-step qPCR kit (PCR Biosystems, London, UK), while DNA viruses were checked by PCR using DreamTaq DNA Polymerase (Thermo Scientific, Vilnius, Lithuania), followed by 1% agarose gel electrophoresis. Four samples (labelled A5.1, A6.1, A6V9-1, A6V9-2) out of the 100 tested positive for SPCSV. Two of them (A6V9-1 and A6V9-2) were co-infected with SPCSV, a badnavirus sweet potato pakakuy virus (SPPV) and a potyvirus sweet potato virus 2 (SPV2), while the other two (A5.1 and A6.1) lacked SPV2. Plants infected with SPCSV, SPV2 and SPPV displayed more severe symptoms. To confirm the results, cDNA synthesized from the four SPCSV positive samples using RevertAid first strand cDNA synthesis kit (Thermo Scientific, Vilnius, Lithuania) underwent PCR (94oC 4 min, 94oC 1 min, 53oC 30 s, 72oC 70 s and 72oC 10 min for a total of 30 cycles) using primers CL43U and CL43L for the viral heat shock protein 70 gene (Maliogka et al., 2020). An expected band size of 486 bp was obtained in all cases. The amplicon from sample A6.1 was sequenced and found to be identical to SPCSV Guatemalan isolate GT:B3:08 (acc. JF699628). RNA1 and RNA2 complete sequences from sample A6.1 were obtained via PCR amplifications of cDNA using primers (Suppl2) designed (from acc. KC888966 for RNA1 and acc. KC888963 for RNA2) to amplify overlapping fragments of West African strain of SPCSV. QIAquick gel extraction kit (QIAGEN, Hilden, Germany) was used to purify the PCR fragments, which were then cloned into pGEM-T Easy Vector (Promega, Madison, USA) and sequenced using Sanger sequencing technique (Biomi, Gödöllő, Hungary). BLASTn search revealed that RNA1 of our isolate Hun_01 (acc. MW892835) had 99.63% sequence identity to SPCSV isolate su-17-10 (acc. MK802073), while RNA2 of Hun_01 (acc. MW892836) was 99.68% similar to SPCSV isolate min-17-1 (acc. MK802078) and isolate 24-1 (acc. MK802080). Phylogenetic analysis using MegAlign (v. 7.1.0, 44.1) showed a close relationship between our isolate and those isolated in China, suggesting that they may have a common origin (Suppl1). Severe stunting and leaf yellowing symptoms developed in I. setosa indicator plants grafted with SPCSV infected sweet potato scions. qPCR test for the virus confirmed its presence in the I. setosa leaves. To the best of our knowledge, this is the first report on the occurrence of SPCSV in Hungary and the third in Europe (Valverde et al. 2004; EPPO 2021).

Performance of Envelope Demodulation for Bearing Damage Detection on CWRU Accelerometric Data: Kurtogram and Traditional Indicators vs. Targeted a Posteriori Band Indicators

Envelope demodulation of vibration signals is surely one of the most successful methods of analysis for highlighting diagnostic information of rolling element bearings incipient faults. From a mathematical perspective, the selection of a proper demodulation band can be regarded as an optimization problem involving a utility function to assess the demodulation performance in a particular band and a scheme to move within the search space of all the possible frequency bands {f, Δf} (center frequency and band size) towards the optimal one. In most of cases, kurtosis-based indices are used to select the proper demodulation band. Nevertheless, to overcome the lack of robustness to non-Gaussian noise, different utility functions can be found in the literature. One of these is the kurtosis of the unbiased autocorrelation of the squared envelope of the filtered signal found in the autogram. These heuristics are usually sufficient to highlight the defect spectral lines in the demodulated signal spectrum (i.e., usually the squared envelope spectrum (SES)), enabling bearings diagnostics. Nevertheless, it is not always the case. In this work, then, posteriori band indicators based on SES defect spectral lines are proposed to assess the general envelope demodulation performance and the goodness of traditional indicators. The Case Western Reserve University bearing dataset is used as a test case.

Microbial metagenomic approach uncovers the first rabbit haemorrhagic disease virus genome in Sub-Saharan Africa

Rabbit Haemorrhagic Disease (RHD) causes high morbidity and mortality in rabbits and hares. Here, we report the first genomic characterization of lagovirus GI.2 virus in domestic rabbits from sub-Saharan Africa. We used an unbiased microbial metagenomic Next Generation Sequencing (mNGS) approach to diagnose the pathogen causing the suspected outbreak of RHD in Ibadan, Nigeria. The liver, spleen, and lung samples of five rabbits from an outbreak in 2 farms were analyzed. The mNGS revealed one full and two partial RHDV2 genomes on both farms. Phylogenetic analysis showed close clustering with RHDV2 lineages from Europe (98.6% similarity with RHDV2 in the Netherlands, and 99.1 to 100% identity with RHDV2 in Germany), suggesting potential importation. Subsequently, all the samples were confirmed by RHDV virus-specific RT-PCR targeting the VP60 gene with the expected band size of 398 bp for the five rabbits sampled. Our findings highlight the need for increased genomic surveillance of RHDV2 to track its origin, understand its diversity and to inform public health policy in Nigeria, and Sub-Saharan Africa.