Hasil untuk "Biotechnology"

Seung-U Son, Ki Rim Hong, Kwang-Soon Shin

This study was designed to investigate the immunostimulatory and anticancer efficacies of pectic polysaccharides from ginseng leaves treated using the high-pressure extraction method (HPEM). The isolation of polysaccharides using HPEM resulted in 1.35-fold higher polysaccharide yields than those obtained using the commonly used hot water extraction method. In addition, component sugar analysis of ginseng-leaf-derived polysaccharides (GLHP) showed the presence of nine different types of monosaccharides, including galacturonic acid, galactose, rhamnose, and arabinose, which are characteristic of pectic polysaccharides. In addition, GLHP effectively induced activation of the complement system, and macrophages stimulated with GLHP showed enhanced production of cytokines such as IL-6, IL-12, and TNF-α. Intravenous (i.v.) and oral administration (p.o.) of GLHP significantly increased the cancer-cell-killing ability of spleen-derived NK cells. In a lung-cancer-bearing mouse model using Colon26-M3.1 carcinoma, prophylactic i.v. and p.o. GLHP potently inhibited 95.2% and 33.5% of lung cancer, respectively. Furthermore, GLHP showed significant anticancer effects, even in mice with NK cell dysfunction, via the anti-asialo GM1 antibody. These effects may be related to the cancer-cell-killing effects of cytotoxic T lymphocytes (CTL). Therefore, GLHP, a polysaccharide isolated from ginseng leaves using HPEM, has a potent anticancer effect, and these effects are closely related to the stimulation of various immune factors.

Maali Alabdulhafith, Abduljabbar S. Ba Mahel, Nagwan Abdel Samee et al.

Quality of life is greatly affected by chronic wounds. It requires more intensive care than acute wounds. Schedule follow-up appointments with their doctor to track healing. Good wound treatment promotes healing and fewer problems. Wound care requires precise and reliable wound measurement to optimize patient treatment and outcomes according to evidence-based best practices. Images are used to objectively assess wound state by quantifying key healing parameters. Nevertheless, the robust segmentation of wound images is complex because of the high diversity of wound types and imaging conditions. This study proposes and evaluates a novel hybrid model developed for wound segmentation in medical images. The model combines advanced deep learning techniques with traditional image processing methods to improve the accuracy and reliability of wound segmentation. The main objective is to overcome the limitations of existing segmentation methods (UNet) by leveraging the combined advantages of both paradigms. In our investigation, we introduced a hybrid model architecture, wherein a ResNet34 is utilized as the encoder, and a UNet is employed as the decoder. The combination of ResNet34’s deep representation learning and UNet’s efficient feature extraction yields notable benefits. The architectural design successfully integrated high-level and low-level features, enabling the generation of segmentation maps with high precision and accuracy. Following the implementation of our model to the actual data, we were able to determine the following values for the Intersection over Union (IOU), Dice score, and accuracy: 0.973, 0.986, and 0.9736, respectively. According to the achieved results, the proposed method is more precise and accurate than the current state-of-the-art.

Arju Hossain, Asif Ahsan, Imran Hasan et al.

Purpose Ultraviolet radiation causes skin cancer, but the exact mechanism by which it occurs and the most effective methods of intervention to prevent it are yet unknown. For this purpose, our study will use bioinformatics and systems biology approaches to discover potential biomarkers of skin cancer for early diagnosis and prevention of disease with applicable clinical treatments. Methods This study compared gene expression and protein levels in ultraviolet-mediated cultured keratinocytes and adjacent normal skin tissue using RNA sequencing data from the National Center for Biotechnology Information-Gene Expression Omnibus (NCBI-GEO) database. Then, pathway analysis was employed with a selection of hub genes from the protein-protein interaction (PPI) network and the survival and expression profiles. Finally, potential clinical biomarkers were validated by receiver operating characteristic (ROC) curve analysis. Results We identified 32 shared differentially expressed genes (DEGs) by analyzing three different subsets of the GSE85443 dataset. Skin cancer development is related to the control of several DEGs through cyclin-dependent protein serine/threonine kinase activity, cell cycle regulation, and activation of the NIMA kinase pathways. The cytoHubba plugin in Cytoscape identified 12 hub genes from PPI; among these 3 DEGs, namely, AURKA, CDK4 , and PLK1 were significantly associated with survival ( P  < 0.05) and highly expressed in skin cancer tissues. For validation purposes, ROC curve analysis indicated two biomarkers: AURKA (area under the curve (AUC) value = 0.8) and PLK1 (AUC value = 0.7), which were in an acceptable range. Conclusions Further translational research, including clinical experiments, teratogenicity tests, and in-vitro or in-vivo studies, will be performed to evaluate the expression of these identified biomarkers regarding the prognosis of skin cancer patients.

Hoda A. Ahmed, R. Elhossini, M. Aglan et al.

Background: Spondyloepimetaphyseal dysplasias (SEMD) are a large group of skeletal disorders represented by abnormalities of vertebrae in addition to epiphyseal and metaphyseal areas of bones. Several genes have been identified underlying different forms. ACAN gene mutations were found to cause Aggrecan-related bone disorders (spondyloepimetaphyseal dysplasias,spondyloepiphyseal dysplasias, familial osteochondritis dissecans and short stature syndromes). This study aims to find the disease causing variant in Egyptian patient with SEMD using whole exome sequencing. Methods: Whole-exome sequencing was performed for an Egyptian male patient who presented with short stature, clinical and radiological features suggestive of unclassified SEMD. Results: The study identified a novel de novo heterozygous ACAN gene variant (c.7378G>A; p.Gly2460Arg) in G3 domain. Mutations in ACAN gene have been more commonly associated with short stature than SEMD. The phenotype of our patient was intermediate in severity between spondyloepiphyseal dysplasia presentation; Kimberley type(SEDK) and Spondyloepimetaphyseal dysplasias Aggrecan (SEMDAG) Conclusions: Whole exome sequencing revealed a novel de novo ACAN gene variant in patient with SEDK. The clinical and skeletal phenotype of our patient was much severe than those reported originally and showed more metaphyseal involvement. To the best of our knowledge, two previous studies reported a heterozygous variant in ACAN with spondyloepiphyseal dysplasia presentation; Kimberley type.

Hailun Jiang, Li Zeng, Xueqi Dong et al.

Geng G. Tian, Jing Li, Ji Wu

Zhuang Liu, Menglong Zhao, Han Wang et al.

Abstract Contrast-enhanced MR angiography (MRA) is a critical technique for vascular imaging. Nevertheless, the efficacy of MRA is often limited by the low rate of relaxation, short blood-circulation time, and metal ion-released potential long-term toxicity of clinical available Gd-based contrast agents. In this work, we report a facile and efficient strategy to achieve Gd-chelated organic nanoparticles with high relaxivity for T 1 -weighted MRA imaging. The Gd-chelated PEG-TCPP nanoparticles (GPT NPs) have been engineered composite structured consisting of Gd-chelated TCPP and PEG. The spherical structure of TCPP offers more chemical sites for Gd3+ coordination to improve the relaxivity and avoid leakage of the Gd3+ ions. The synthesized GPT NPs exhibit a high relaxation rate of 35.76 mM− 1 s− 1 at 3.0 T, which is higher than the rates for most reported MR contrast agents. Therefore, GPT NPs can be used for MRA with much stronger vascular signals, longer circulation time, and high-resolution arterial vascular visualization than those using clinical MR contrast agents at the same dose. This work may make the T 1 MRI contrast agents for high-resolution angiography possible and offer a new candidate for preclinical and clinical applications of MR vascular imaging and vascular disease diagnosis. Graphical Abstract

Getachew Bantihun, Mulugeta Kebede

Abstract Background Pest control strategies almost entirely rely on chemical insecticides, which cause environmental problems such as biosphere deterioration and emergence of resistant pests. Bio-pesticide is an alternative approach, which uses organisms such as entomopathogenic fungi, Metarhizium anisopliae, to control pests. Screening such potential organism at a molecular level and understanding their gene regulation mechanism is an important approach to reduce emergence of pesticide resistance and worsening of the biosphere. Understanding promoter regions which play a pivotal role in gene regulation is crucial. In particular, identification of the promoter regions in M. anisopliae Strain ME1 remains poorly understood. To our knowledge, the mitogenome trn gene clusters of M. anisopliae Strain ME1 were not characterized. Here, we used machine learning approach to identify and characterize the promoter regions, regulatory elements, and CpG island densities of 15 protein coding genes of entomopathogenic fungi, M. anisolpliae Strain ME1. Results The current analysis revealed multiple transcription start sites (TSS) for all utilized sequences, except for promoter region genes of Pro-cob and Pro-nad5. With reference to the start codon (ATG), 85.3% of TSS was located above – 500 bp. Based on the standard predictive score at cut off value of 0.8a, the current study revealed 54.7% of predictive score greater than or equal from 0.9 promoter prediction score. Expectation maximization algorithm output identified five candidate motifs. Nonetheless, of all candidate motifs, MtrnI was revealed as the common promoter region motif with a value of 76.9% both in terms of size of binding sites and with an E value of 9.1E−054. Accordingly, we perceived that MtrnI serve as the binding site for tryptophan cluster with P value 0.0044 and C4 type zinc fingers functions as the binding site to regulate gene expression of M. anisopliae Strain ME1. The analysis revealed that mitogenome trn gene clusters of M. anisopliae Strain ME1 showed homologues evolutionary ancestor supported with a bootstrap value of 100%. Conclusion Identified common candidate motifs and binding transcription factors through in silico approach are likely expected to contribute for better understanding of gene expression and strain improvement of M. anisopliae Strain ME1 for its bio-pesticides role.

Shujie Wang, Defu Zhang, Chenggang Jiang et al.

<i>Streptococcus suis</i> causes disease in pigs and is implicated increasingly in human disease worldwide. Although most clinical cases are associated with serotype 2, infections by other serotypes have sometimes been reported. Here, we sequenced the genome of a multidrug-resistant <i>S. suis</i> serotype 28 (strain 11313) and a multidrug-resistant <i>S. suis</i> serotype 31 (strain 11LB5). Strain 11313 was apathogenic in mouse infection models, whereas strain 11LB5 displayed ganglion demyelination, meningeal thickening, congestion, mononuclear cell infiltration, massive proliferation of cortical glial cells, and bacteria (>10⁴ CFU/g) in the spinal cord and ganglia in mice. Furthermore, immunohistochemistry found that the heavily infiltrated glial cells were astrocytes. Strain 11313 harbored the resistance genes <i>ant(6)-Ia</i>, <i>erm(B)</i>, <i>optrA</i>, <i>tet(l)</i>, <i>tet(o)</i>, and strain 11LB5 harbored the resistance genes <i>ant(6)-Ia</i>, <i>erm(B)</i>, <i>tet(40)</i>, <i>tet(o/w/32/o)</i>, <i>aac(6′)-aph(2″)</i>. Mouse studies showed that strain 11LB5 exhibited a similar virulence to serotype 2 strain 700794, highlighting the need for surveillance of the other serotype <i>S. suis</i> isolates, in addition to serotype 2, in farms. This is the first report of the aminoglycoside resistance gene <i>ant(6)-Ia</i> in <i>S. suis</i> from animals. This suggests that <i>S. suis</i> might serve as an antibiotic resistance reservoir, which spreads the resistance gene <i>ant(6)-Ia</i> or <i>optrA</i> to other streptococcal pathogens on farms.

Phuoc Truong Nguyen, Santiago Garcia-Vallvé, Pere Puigbò

Early characterization of emerging viruses is essential to control their spread, such as the Zika Virus outbreak in 2014. Among other non-viral factors, host information is essential for the surveillance and control of virus spread. Flaviviruses (genus <i>Flavivirus</i>), akin to other viruses, are modulated by high mutation rates and selective forces to adapt their codon usage to that of their hosts. However, a major challenge is the identification of potential hosts for novel viruses. Usually, potential hosts of emerging zoonotic viruses are identified after several confirmed cases. This is inefficient for deterring future outbreaks. In this paper, we introduce an algorithm to identify the host range of a virus from its raw genome sequences. The proposed strategy relies on comparing codon usage frequencies across viruses and hosts, by means of a normalized Codon Adaptation Index (CAI). We have tested our algorithm on 94 flaviviruses and 16 potential hosts. This novel method is able to distinguish between arthropod and vertebrate hosts for several flaviviruses with high values of accuracy (virus group 91.9% and host type 86.1%) and specificity (virus group 94.9% and host type 79.6%), in comparison to empirical observations. Overall, this algorithm may be useful as a complementary tool to current phylogenetic methods in monitoring current and future viral outbreaks by understanding host–virus relationships.

Yifat Brill-Karniely

Alina Kunicka-Styczyńska, Agnieszka Tyfa, Dariusz Laskowski et al.

Acidotermophilic bacteria <i>Alicyclobacillus acidoterrestris</i> is one of the main contaminants in the fruit industry forming biofilms which are difficult to remove from the production line by conventional methods. An alternative approach aims for the use of essential oils to prevent <i>Alicyclobacillus</i> biofilm development. The effect of clove essential oil on <i>A. acidoterrestris</i> biofilms on glass and polyvinyl chloride surfaces under static and agitated culture conditions was investigated by atomic force microscopy and the plate count method. The medium-flow and the type of technical surface significantly influenced <i>A. acidoterrestris</i> biofilm. The PVC was colonized in a greater extent comparing to glass. Clove essential oil in 0.05% (<i>v/v</i>) caused 25.1–65.0% reduction of biofilms on the technical surfaces along with substantial changes in their morphology by a decrease in the biofilm: height, surface roughness, and surface area difference. The oil also induced alteration in individual bacterial cells length and visible increase of their roughness. Clove essential oil seems to release EPS from biofilm and thus induce detachment of bacteria from the surface. Due to anti-<i>A. acidoterrestris</i> biofilm activity, the clove oil may be used in the juice industry to hinder a development of <i>A. acidoterrestris</i> biofilms on production surfaces.

Thomas K. Wood, Sooyeon Song

Procaryotes starve and face myriad stresses. The bulk population actively resists the stress, but a small population weathers the stress by entering a resting stage known as persistence. No mutations occur, and so persisters behave like wild-type cells upon removal of the stress and regrowth; hence, persisters are phenotypic variants. In contrast, resistant bacteria have mutations that allow cells to grow in the presence of antibiotics, and tolerant cells survive antibiotics better than actively-growing cells due to their slow growth (such as that of the stationary phase). In this review, we focus on the latest developments in studies related to the formation and resuscitation of persister cells and propose the guanosine pentaphosphate/tetraphosphate (henceforth ppGpp) ribosome dimerization persister (PRDP) model for entering and exiting the persister state.

Elena Biagi, Carlo Mengucci, Monica Barone et al.

The study of the microbiome in broiler chickens holds great promise for the development of strategies for health maintenance and performance improvement. Nutritional strategies aimed at modulating the microbiota—host relationship can improve chickens’ immunological status and metabolic fitness. Here, we present the results of a pilot trial aimed at analyzing the effects of a nutritional strategy involving vitamin B2 supplementation on the ileum, caeca and litter microbiota of Ross 308 broilers, as well as on the metabolic profile of the caecal content. Three groups of chickens were administered control diets and diets supplemented with two different dosages of vitamin B2. Ileum, caeca, and litter samples were obtained from subgroups of birds at three time points along the productive cycle. Sequencing of the 16S rRNA V3–V4 region and NMR metabolomics were used to explore microbiota composition and the concentration of metabolites of interest, including short-chain fatty acids. Vitamin B2 supplementation significantly modulated caeca microbiota, with the highest dosage being more effective in increasing the abundance of health-promoting bacterial groups, including <i>Bifidobacterium</i>, resulting in boosted production of butyrate, a well-known health-promoting metabolite, in the caeca environment.

E. V. Melnikova, O. A. Rachinskaya, G. A. Trusov et al.

The manufacturer (developer) has to prepare a specification for each newly developed biomedical cell product (BCP) that has passed the stage of preclinical studies. The specification is included into the registration dossier when applying for marketing authorisation of a BCP. In accordance with the Order of the Ministry of Health of the Russian Federation No. 14n of 19 January 2017 «On approval of the specification format for a biomedical cell product» the specification should contain information about authenticity of the cell line used in the BCP, namely: morphological characteristics, expression of specific markers, expression of specific genes, expression of specific proteins, as well as markers of cell line stability. At present Russia has no practical experience in BCP quality evaluation. The aim of the study was to substantiate methodological approaches to authentication of cell lines used in BCPs as illustrated by quality evaluation of the DF-2 model cell line using test methods that allow for characterisation of the morphological, genetic, immunophenotypic, and cytogenetic profile of the cell line. Materials and methods: the study analysed the DF-2 cell line — human dermal fibroblasts (mesenchymal stem cells) obtained from the Institute of Cytology of the Russian Academy of Sciences (St. Petersburg). The following analytical test methods were used in the study: morphological analysis; flow cytometry for immunophenotyping of the DF-2 model cell line; short tandem repeats for creating an allelic profile of the model cell line; cytogenetic analysis — differential DAPI staining of metaphase chromosomes. Results: the paper summarises methodological approaches to identification testing of medicines containing living human cells (BCP analogues) currently used in international practice, and presents the results of authentication of the model cell line. Conclusions: methods used for BCP identification testing should ensure unambiguous authentication of the cell line according to its specification. The study performed helped to work out the procedure of authentication of a model cell line.

A.V. Nedoluzhko, F.S. Sharko, S.V. Tsygankova et al.

The vast majority of multicellular organisms coexist with bacterial symbionts that may play various roles during their life cycle. Parasitoid wasp Megaphragma amalphitanum (Hymenoptera: Trichogrammatidae) belongs to the smallest known insects whose size is comparable with some bacteria. Using 16S rRNA gene sequencing and Whole Genome Sequencing (WGS), we described microbiota diversity for this arthropod and its potential impact on their lifecycle. Metagenomic sequences were deposited to SRA database which is available at NCBI with accession number SRX2363723 and SRX2363724. We found that small body size and limited lifespan do not lead to a significant reduction of bacterial symbionts diversity. At the same time, we show here a specific feature of microbiota composition in M. amalphitanum – the absence of the Rickettsiaceae family representatives that are known to cause sex-ratio distortion in arthropods and well represented in other populations of parasitoid wasps.

Salah Sheweita, Basant Salama, Mostafa Hassan

Erectile dysfunction (ED) affected the lives of more than 300 million men worldwide. Erectile dysfunction drugs (EDD), known as phosphodiesterase inhibitors (PDEIs), have been used for treatment of ED. It has been shown that oxidative stress plays an important role in the progression of erectile dysfunction. Oxidative stress can be alleviated or decreased by antioxidant enzymes. Therefore, the present study aims at investigating the changes in the activity of antioxidant enzymes such as superoxide dismutase, catalase, and glutathione reductase as well as protein expression of glutathione peroxidase and glutathione S-transferase after treatment of male rats with a daily dose of sildenafil (1.48 mg/kg), tadalafil (0.285 mg/kg) and vardenafil (0.285 mg/kg) for three weeks. In addition, levels of reduced glutathione and malondialdyhyde (MDA) were assayed. The present study showed that sildenafil, vardenafil, and tadalafil treatments significantly decreased the levels of glutathione, MDA and the activity of glutathione reductase. In addition, vardenafil and sildenafil increased the activity of superoxide dismutase and catalase. Interestingly, western immunoblotting data showed that vardenafil induced the activity of glutathione peroxidase (GPX) and its protein expression, whereas tadalafil and sildenafil inhibited such enzyme activity and its protein expression. In addition, the protein expression of GST π isozyme was markedly reduced after treatment of rats with sildenafil. It is concluded that ED drugs induced the activities of both SOD and catalase which consequently decreased MDA level. Therefore, decrement in MDA levels could increase nitric oxide–cGMP level which in turn promotes the erection mechanism.

Okumura Kayo, Shimomura Yumi, Murayama Somay et al.

<p>Abstract</p> <p>Background</p> <p><it>Streptococcus pyogenes</it> (GAS) harbors several superantigens (SAgs) in the prophage region of its genome, although <it>speG</it> and <it>smez</it> are not located in this region. The diversity of SAgs is thought to arise during horizontal transfer, but their evolutionary pathways have not yet been determined. We recently completed sequencing the entire genome of <it>S. dysgalactiae</it> subsp. <it>equisimilis</it> (SDSE), the closest relative of GAS. Although <it>speG</it> is the only SAg gene of SDSE, <it>speG</it> was present in only 50% of clinical SDSE strains and <it>smez</it> in none. In this study, we analyzed the evolutionary paths of streptococcal and staphylococcal SAgs.</p> <p>Results</p> <p>We compared the sequences of the 12–60 kb <it>speG</it> regions of nine SDSE strains, five <it>speG</it>⁺ and four <it>speG</it>^<it>–</it>. We found that the synteny of this region was highly conserved, whether or not the <it>speG</it> gene was present. Synteny analyses based on genome-wide comparisons of GAS and SDSE indicated that <it>speG</it> is the direct descendant of a common ancestor of streptococcal SAgs, whereas <it>smez</it> was deleted from SDSE after SDSE and GAS split from a common ancestor. Cumulative nucleotide skew analysis of SDSE genomes suggested that <it>speG</it> was located outside segments of steeper slopes than the stable region in the genome, whereas the region flanking <it>smez</it> was unstable, as expected from the results of GAS. We also detected a previously undescribed staphylococcal SAg gene, <it>selW</it>, and a staphylococcal SAg -like gene, <it>ssl</it>, in the core genomes of all <it>Staphylococcus aureus</it> strains sequenced. Amino acid substitution analyses, based on dN/dS window analysis of the products encoded by <it>speG</it>, <it>selW</it> and <it>ssl</it> suggested that all three genes have been subjected to strong positive selection. Evolutionary analysis based on the Bayesian Markov chain Monte Carlo method showed that each clade included at least one direct descendant.</p> <p>Conclusions</p> <p>Our findings reveal a plausible model for the comprehensive evolutionary pathway of streptococcal and staphylococcal SAgs.</p>

Drasko Boko, Ivana Weygand-Durasevic, Sonja Lesjak

Methanogenic archaea possess unusual seryl-tRNA synthetases (SerRS), evolutionarily distinct from the SerRSs found in other archaea, eucaryotes and bacteria. Our recent X-ray structural analysis of Methanosarcina barkeri SerRS revealed an idiosyncratic N-terminal domain and catalytic zinc ion in the active site. To shed further light on substrate discrimination by methanogenic-type SerRS, we set up to explore in vivo the interaction of methanogenic-type SerRSs with their cognate tRNAs in Escherichia coli or Saccharomyces cerevisiae. The expression of various methanogenic-type SerRSs was toxic for E. coli, resulting in the synthesis of erroneous proteins, as revealed by β-galactosidase stability assay. Although SerRSs from methanogenic archaea recognize tRNAsSer from all three domains of life in vitro, the toxicity presumably precluded the complementation of endogenous SerRS function in both, E. coli and S. cerevisiae. However, despite the observed toxicity, coexpression of methanogenic-type SerRS with its cognate tRNA suppressed bacterial amber mutation.

Waugh Robbie, Feuillet Catherine, Choulet Frédéric et al.

<p>Abstract</p> <p>Background</p> <p>Because of its size, allohexaploid nature and high repeat content, the wheat genome has always been perceived as too complex for efficient molecular studies. We recently constructed the first physical map of a wheat chromosome (3B). However gene mapping is still laborious in wheat because of high redundancy between the three homoeologous genomes. In contrast, in the closely related diploid species, barley, numerous gene-based markers have been developed. This study aims at combining the unique genomic resources developed in wheat and barley to decipher the organisation of gene space on wheat chromosome 3B.</p> <p>Results</p> <p>Three dimensional pools of the minimal tiling path of wheat chromosome 3B physical map were hybridised to a barley Agilent 15K expression microarray. This led to the fine mapping of 738 barley orthologous genes on wheat chromosome 3B. In addition, comparative analyses revealed that 68% of the genes identified were syntenic between the wheat chromosome 3B and barley chromosome 3 H and 59% between wheat chromosome 3B and rice chromosome 1, together with some wheat-specific rearrangements. Finally, it indicated an increasing gradient of gene density from the centromere to the telomeres positively correlated with the number of genes clustered in islands on wheat chromosome 3B.</p> <p>Conclusion</p> <p>Our study shows that novel structural genomics resources now available in wheat and barley can be combined efficiently to overcome specific problems of genetic anchoring of physical contigs in wheat and to perform high-resolution comparative analyses with rice for deciphering the organisation of the wheat gene space.</p>