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We analyzed phytoplankton assemblages’ variations in oligo-mesotrophic Shchuchie and Burabay lakes using traditional morphological and next-generation sequencing (NGS) approaches. The total phytoplankton biodiversity and abundance estimated by both microscopy and NGS were significantly higher in Lake Burabay than in Lake Shchuchie. NGS of 16S and 18S rRNA amplicons adequately identify phytoplankton taxa only on the genera level, while species composition obtained by microscopic examination was significantly larger. The limitations of NGS analysis could be related to insufficient coverage of freshwater lakes phytoplankton by existing databases, short algal sequences available from current instrumentation, and high homology of chloroplast genes in eukaryotic cells. However, utilization of NGS, together with microscopy allowed us to perform a complete taxonomic characterization of phytoplankton lake communities including picocyanobacteria, often overlooked by traditional microscopy. We demonstrate the high potential of an integrated morphological and molecular approach in understanding the processes of organization in aquatic ecosystem assemblages.

Background/aim Analysis of the characteristics of influenza virus in imported cases in Guangxi province of China. Materials and methods Throat swabs of imported cases with influenza-like symptoms were detected by real-time PCR from July 2016 to December 2019. Results 1292 laboratory detections of influenza were reported in 3974 influenza-like cases, of which 71.67% (926) were influenza A. The ratio of test positive was 32.82%. The proportion of detections of influenza B was 28.33% (366). A total of 70.51% of the cases mostly came from Vietnam (911). A total of 86.76% (1121) of the cases were imported from Dongxing Port, Nanning Airport, and Pingxiang Port. There was no statistical difference in all age groups. At the same time, 3 of the untyped A-type specimens were sequenced by next- generation sequencing. Among them, the sequences of 2 specimens from Vietnam had high homology with the influenza strain H3N2 in Hong Kong in 2017. The specimen sequence from Thailand is highly homologous to the influenza pandemic strain H1N1 in Brisbane, Australia in 2018. Conclusion Imported influenza cases in Guangxi have occurred throughout the year, with higher numbers in winter and spring. The cases mostly came from Vietnam with influenza A. Relevant measures should be taken to control the further spread of the virus.

Norovirus, the leading cause of non-bacterial acute gastroenteritis (AGE) worldwide, is constantly mutating. Continuous monitoring of the evolution of epidemic genotypes and emergence of novel genotypes is, therefore, necessary. This study determined the prevalence and clinical characteristics of norovirus strains in AGE in Guangzhou, China in 2019/2020 season. This study included children aged 2–60 months diagnosed with AGE in Guangzhou Women and Children Hospital, from August 2019 to January 2020. Norovirus was detected by real-time polymerase chain reaction and clinical data were obtained. Genotyping and phylogenetic analyses were performed with partial gene sequence fragments located within the open reading frames 1 and 2. During the study period, 168 children (61.3% males) were confirmed as norovirus infectious AGE. The main symptoms were diarrhoea and vomiting and 38 patients (22.6%) had seizures. Norovirus was mainly prevalent in October and November, and GII.4 Sydney[P31] was the major genotype circulating in Guangzhou. The phylogenetic tree showed that the Guangzhou strains had high homology with the strains circulating in 2017–2019 worldwide. GII.4 Sydney was the main prevalent norovirus genotype in Guangzhou from August 2019 to January 2020, which had more severe diarrhoea than those of other genotypes. These findings provide a valuable reference for the prevention, control, and treatment of norovirus in the future.

Single-domain antibodies (sdAbs), the autonomous variable domains of camelid and shark heavy-chain antibodies, have many desirable properties as components of biologic drugs. However, their sequences may increase the risk of immunogenicity and antidrug antibody (ADA) development in humans, and thus, sdAbs are routinely humanized during development. Here, we review and summarize the available evidence regarding the factors governing immunogenicity of sdAbs and our current state of knowledge of strategies to mitigate immunogenicity risks by humanization. While several sdAb properties, including high homology of camelid VH Hs with human IGHV3 gene products, favor low immunogenicity in humans, epitopes absent in the human repertoire including the exposed VH :VL interface may be intrinsically immunogenic. While most clinical trials have demonstrated minimal sdAb immunogenicity, two notable exceptions (the tetrameric DR5-specific VH H TAS266 and the TNFR1-specific VH GSK1995057) illustrate that special caution must be taken in identifying preexisting ADAs against highly potent sdAbs. Nonhuman sequence alone does not adequately explain sdAb immunogenicity, as some camelid VH Hs are nonimmunogenic while some fully human VH s elicit ADAs. The presence of preexisting ADAs directed against the exposed C-termini of some sdAbs in a significant proportion of individuals awaits a molecular explanation. Whether sdAb humanization reduces or promotes immunogenicity remains unclear: reduction of nonhuman sequence content at the expense of introducing low-level aggregation in humanized variants may be counterproductive. Further work will establish thresholds for VH H and VNAR humanization to maximize human sequence content while avoiding loss of binding affinity and/or immunogenicity resulting from aggregation or decreased stability.

Multi-replicon plasmids harboring the IncpA1763-KPC replicon together with other replicons are being increasingly reported among Enterobacteriaceae species. However, plasmids with single IncpA1763-KPC replicons are poorly studied as a different incompatibility (Inc) group, despite their rise in appearance in some strains. IncpA1763-KPC plasmids, pA1763-KPC, and p427113-2, from two clinical Klebsiella pneumoniae isolates were fully sequenced by high-throughput genome sequencing. Linear structural comparisons of IncpA1763-KPC backbone region were made between these two plasmids and six arbitrarily selected representative IncpA1763-KPC plasmids sequenced previously. A further detailed genomic comparison was carried out between plasmids pA1763-KPC, p427113-2, and pFB2.2, which show high homology across the backbone sequence to one another. Among all sequenced IncpA1763-KPC plasmids considered in this study, plasmids pA1763-KPC and p427113-2 showed the most complete IncpA1763-KPC backbones. These were composed of the IncpA1763-KPC replicon (repAIncpA1763-KPC and its iterons), the 5.6-kb IncpA1763-KPC -type maintenance region, the 27.7-kb IncFIIK -type maintenance region, and the 36.6-kb IncFIIK -type conjugal transfer regions. Compared with pA1763-KPC or p427113-2, the backbone regions of the other analyzed IncpA1763-KPC plasmids had gradually undergone different deletions or truncations, but shared small and core IncpA1763-KPC backbones including the IncpA1763-KPC replicon, IncpA1763-KPC -type maintenance region, and residual IncFIIK -type maintenance region. Accessory modules integrated into IncpA1763-KPC backbones included the multidrug-resistant module blaKPC-2 region in pA1763-KPC, the metal-resistance modules ars region together with ncr region in pFB2.2 and sil in pKPN-9a0d, the ISKpn14-to-IS26 region in p427113-2, and other non-resistance region in the respective plasmids. This detailed comparative genomics analysis of IncpA1763-KPC plasmids provides a deep insight into their diversification and evolution.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the ongoing pandemic of coronavirus disease 2019 (COVID-19), belongs to the betacoronavirus genus and shares high homology to the severe acute respiratory syndrome coronavirus (SARS-CoV) that emerged in 2003. These are highly transmissible and pathogenic viruses which very likely originated in bats. SARS-CoV-2 uses the same receptor, angiotensin-converting enzyme 2 (ACE2) as SARS-CoV, and spreads primarily through the respiratory tract. Although several trials for vaccine development are currently underway, investigations into the virology of SARS-CoV-2 to understand the fundamental biology of the infectious cycle and the associated immunopathology underlying the clinical manifestations of COVID-19 are crucial for identification and rational design of effective therapies. This review provides an overview of how SARS-CoV-2 infects and spreads within human hosts with specific emphasis on key aspects of its lifecycle, tropism and immunopathological features.

Growth differentiation factor 11 (GDF11) and myostatin (MSTN) are closely related TGFβ family members that are often believed to serve similar functions due to their high homology. However, genetic studies in animals provide clear evidence that they perform distinct roles. While the loss of Mstn leads to hypermuscularity, the deletion of Gdf11 results in abnormal skeletal patterning and organ development. The perinatal lethality of Gdf11-null mice, which contrasts with the long-term viability of Mstn-null mice, has led most research to focus on utilizing recombinant GDF11 proteins to investigate the postnatal functions of GDF11. However, the reported outcomes of the exogenous application of recombinant GDF11 proteins are controversial partly because of the different sources and qualities of recombinant GDF11 used and because recombinant GDF11 and MSTN proteins are nearly indistinguishable due to their similar structural and biochemical properties. Here, we analyze the similarities and differences between GDF11 and MSTN from an evolutionary point of view and summarize the current understanding of the biological processing, signaling, and physiological functions of GDF11 and MSTN. Finally, we discuss the potential use of recombinant GDF11 as a therapeutic option for a wide range of medical conditions and the possible adverse effects of GDF11 inhibition mediated by MSTN inhibitors., Growth factors: untangling twin proteins A growth factor protein called GDF11 has potential for rejuvenation of heart, brain, and muscle tissues, but first its relationship with a twin growth factor (MSTN) must be unraveled. Although GDF11 and MSTN are almost identical in amino acid sequence, MSTN controls growth of skeletal muscles, and GDF11 regulates bone and organ patterning. To untangle what differentiates these proteins, Yun-Sil Lee and Joonho Suh at Seoul National University, South Korea, reviewed their evolution and function. They report that GDF11 and MSTN are the result of duplication of an original gene and have evolved to perform different roles. They cover some of the beneficial effects reported with GDF11 supplementation, such as tissue rejuvenation and increased lifespan, but caution that negative effects have been reported. Further investigation may illuminate growth and development processes, and therapeutic potential.

Viral pseudoenzymes are represented by enzyme‐deficient homologs of glutamine amidotransferase (GAT), kinase, and superoxide dismutase that modulate the signaling output in immune defense, viral genome replication, and cell proliferation, respectively. Specifically, pseudo‐GAT cooperates with a cellular GAT to enable deamidation; pseudo‐SOD competes with cellular SODs for chaperoned‐copper to cripple dismutase activity; and pseudokinase pairs with viral and cellular kinases to balance the phosphorylation of key signaling molecules (e.g., BAF)., Pseudoenzymes are proteins that are evolutionarily related to active enzymes, but lack relevant catalytic activity. As obligate intracellular pathogens, viruses complete their life cycle fully dependent on the cellular supplies of macromolecule and energy. Traditionally, studies of viral proteins sharing high homology with host counterparts reveal insightful mechanisms by which host signaling pathways are delicately regulated. Recent investigations into the action of cellular pseudoenzymes elucidate diverse molecular means how enzymes are differentially controlled under various physiological conditions, hinting to the potential that pathogens may exploit these regulatory modalities. To date, there have been three types of viral pseudoenzymes reported and our understanding concerning their mechanism of regulation is rudimentary at best. However, it is clear that viral pseudoenzymes are emerging with surprising functions in infection and immunity, and we are only at the beginning to understand this new group of enzyme regulators. In this review, we will summarize current knowledge in viral pseudoenzymes and provide a perspective for future research.

Zebrafish is a well-established in vivo model that exhibit high homology with the development of human innate immunity while well-established human disease model in vivo for various human diseases as well as the drug safetyevaluation process. However, few optical imaging methods could effectively visualize the structure of adult zebrafish due to their limited penetration depth. In this paper, in vivo high-resolution and long-term characterization of human bone disease models based on zebrafish were achieved with optical coherence tomography (OCT). The capability of three-dimensional OCT imaging was also played important role in visualization of zebrafish bone disease model. This paper presents the construction of bone degradation and regeneration model and OCT imaging in vivo based on zebrafish.

Carbonic Anhydrases (CAs) are ubiquitous metalloenzymes involved in several disease conditions. There are 15 human CA (hCA) isoforms and their high homology represents a challenge for the discovery of potential drugs devoid of off-target side effects. For this reason, many synthetic and pharmacologic research efforts are underway to achieve the full pharmacological potential of CA modulators of activity. We report here a novel series of sulfanilamide derivatives containing heterocyclic carboxamide moieties which were evaluated as CA inhibitors against the physiological relevant isoforms hCA I, II, IX, and XII. Some of them showed selectivity toward isoform hCA II and hCA XII. Molecular docking was performed for some of these compounds on isoforms hCA II and XII to understand the possible interaction with the active site amino acid residues, which rationalized the reported inhibitory activity.

Gene expression of two shell colors in Meretrix petechialis were analyzed by sequence related amplified polymorphism-cDNA to screen the associated molecular markers. The two shell color genomes of M. petechialis were amplified using combinations of 30 primers; 11 pairs of primers showed differential fragments, and by recovery, cloning and sequencing, 18 different differential sequences were obtained. The sequencing results were analyzed by BlastX. Only one fragment shared high homology with memory-related protein-2 and TonB-dependent receptor was found that related to shell color. Sequence characterized amplified region primers were designed according to the difference sequences, and PCR amplification was performed in both 'yellow' and 'red' M. petechialis. Four pairs of differential primers were obtained. Using the population to verify the four markers (Me1-Em2, Me2-Em3, Me4-The Em11 and Me4-Em12), it was found that Me1-Em2 and Me2-Em3 were positive in the 'yellow' and Me4-The Em11 and Me4-Em12 were positive in the 'red' M. petechialis populations. All four markers can, therefore, be used as M. petechialis shell color related markers. This provides a theoretical basis for studying shell color regulation in M. petechialis, which may help to reveal the underlying molecular mechanisms more comprehensively.

Molecular marker is robust to precisely monitor the genetic stability of in vitro -banana plants. This study examined the genetic stability of 8 monthold banana plants of Soka variety derived from floral axis organogenesis using newly developed SSR markers. The results showed that the same qualitative and similar quantitative morphological characters of pseudostem, leaf and fruit were identified between mother plants and culture plants from floral axis regeneration. Both plants types were quite similar in number of tillers, brix percentage, fruit peel/mesocarp thickness and fruit length. Eleven out of 211 good quality of SSR loci showing high homology with important genes were selected for suitable PCR primers and produced unambiguous bands.The number of total bands was 323 for total SSR primers, in range of 20-60 per primer for total individual plants. Most culture plants showed identical with their mother plants, with very minor variation as reflected by genetic similarity coefficient range of 0.9-1.0. A high similar pattern on SSR to support morphological characters of mother plants and culture plants indicated a successful micropropagation using floral axis to encounter off-type clones.The floral axis organogenesis in this study is able to provide sufficient genetic materials of Soka for varietal registration and other applications.

Shewanella xiamenensis is an emerging pathogen causing intra-abdominal infection and intestinal colonization. Epidemiologic clues suggest its role as a potential food-borne zoonotic agent. To date, four genome sequences of S. xiamenensis have been made publicly available. All of them were isolated from water samples. In this study, we characterized the genome of a S. xiamenensis strain isolated from a giant grouper in Taiwan. The genome of S. xiamenensis ZYW1 is 4,827,717 bp in length and encodes 4,239 open reading frames. Its genomic sequence shares high homology with other S. xiamenensis strains. blaOXA-416 was identified. This is the first detection of S. xiamenensis in Taiwan. These genomic data and analyses contribute to our understanding of S. xiamenensis and may help to elucidate disease-causing mechanisms in future studies.

The insulin-like growth factor (IGF) pathway is essential for promoting growth and survival of virtually all tissues. It bears high homology to its related protein insulin, and as such, there is an interplay between these molecules with regard to their anabolic and metabolic functions. Skeletal muscle produces a significant proportion of IGF-1, and is highly responsive to its actions, including increased muscle mass and improved regenerative capacity. In this overview, the regulation of IGF-1 production, stability, and activity in skeletal muscle will be described. Second, the physiological significance of the forms of IGF-1 produced will be discussed. Last, the interaction of IGF-1 with other pathways will be addressed. © 2019 American Physiological Society. Compr Physiol 9:413-438, 2019.

BACE1 is an attractive target for disease-modifying treatment of Alzheimer's disease. BACE2, having high homology around the catalytic site, poses a critical challenge to identifying selective BACE1 inhibitors. Recent evidence indicated that BACE2 has various roles in peripheral tissues and the brain, and therefore, the chronic use of nonselective inhibitors may cause side effects derived from BACE2 inhibition. Crystallographic analysis of the nonselective inhibitor verubecestat identified explicit water molecules with different levels of free energy in the S2' pocket. Structure-based design targeting them enabled the identification of propynyl oxazine 3 with improved selectivity. Further optimization efforts led to the discovery of compound 6 with high selectivity. The cocrystal structures of 7, a close analogue of 6, bound to BACE1 and BACE2 confirmed that one of the explicit water molecules is displaced by the propynyl group, suggesting that the difference in the relative water displacement cost may contribute to the improved selectivity.

A revised structure of natural 14-mer cyclic depsipeptide MA026, isolated from Pseudomonas sp. RtlB026 in 2002 was established by physicochemical analysis with HPLC, MS/MS, and NMR and confirmed by total solid-phase synthesis. The revised structure differs from that previously reported in that two amino acid residues, assigned in error, have been replaced. Synthesized MA026 with the revised structure showed a tight junction (TJ) opening activity like that of the natural one in a cell-based TJ opening assay. Bioinformatic analysis of the putative MA026 biosynthetic gene cluster (BGC) of RtIB026 demonstrated that the stereochemistry of each amino acid residue in the revised structure can be reasonably explained. Phylogenetic analysis with xantholysin BGC indicates an exceptionally high homology (ca. 90 %) between xantholysin and MA026. The TJ opening activity of MA026 when binding to claudin-1 is a key to new avenues for transdermal administration of large hydrophilic biologics.

Marine bacteria of the genus Cobetia, which are promising sources of unique enzymes and secondary metabolites, were found to be complicatedly identified both by phenotypic indicators due to their ecophysiology diversity and 16S rRNA sequences because of their high homology. Therefore, searching for the additional methods for the species identification of Cobetia isolates is significant. The species-specific coding sequences for the enzymes of each functional category and different structural families were applied as additional molecular markers. The 13 closely related Cobetia isolates, collected in the Pacific Ocean from various habitats, were differentiated by the species-specific PCR patterns. An alkaline phosphatase PhoA seems to be a highly specific marker for C. amphilecti. However, the issue of C. amphilecti and C. litoralis, as well as C. marina and C. pacifica, belonging to the same or different species remains open.

Schizophrenia is a severe disorder characterized by positive, negative and cognitive symptoms, which are still not fully understood. The development of efficient antipsychotics requires animal models of a strong validity, therefore the aims of the article were to summarize the construct, face and predictive validity of schizophrenia models based on rodents and zebrafish, to compare the advantages and disadvantages of these models, and to propose future directions in schizophrenia modeling and indicate when it is reasonable to combine these models. The advantages of rodent models stem primarily from the high homology between rodent and human physiology, neurochemistry, brain morphology and circuitry. The advantages of zebrafish models stem in the high fecundity, fast development and transparency of the embryo. Disadvantages of both models originate in behavioral repertoires not allowing specific symptoms to be modeled, even when the models are combined. Especially modeling the verbal component of certain positive, negative and cognitive symptoms is currently impossible.

The C1q-domain-containing (C1qDC) proteins are a family of proteins characterized by a globular C1q (gC1q) domain in their C-terminus which hold the potential function in the shell formation as shell matrix proteins. In this study, a C1qDC protein was identified and characterized in pearl oyster (Pinctada fucata martensii) (PmC1qDC) to explore its function in nacre formation. The PmC1qDC-deduced protein sequence carried a typical globular C1q (gC1q) domain that possessed the typical 10-stranded β-sandwich fold with a jelly-roll topology common to all C1qDC family members and shared high homology with other gC1q domains. Homologous analysis of PmC1qDC presented it contained conserved secondary structure and Phe135, Phe155, Tyr166, Phe173, Tyr181, Phe183, and Phe256 amino acid residues. Expression pattern analysis showed that PmC1qDC expressed in all the detected tissues and exhibited a significantly higher expression level in nacre formation-associated tissues. After the shell notching, the expression level of PmC1qDC showed significantly up-regulation after 12 h in the central zone of mantle (MC). PmC1qDC expression significantly decreased in the MC after RNA interference (RNAi). Furthermore, disordered crystals with evident rough surface and irregular crystal tablets were observed in the nacre after RNAi. Results suggested that PmC1qDC affects the shell nacre formation, which is significant to improve the pearl production of pearl oyster.

The processing of grapes for the manufacture of juices and wines, generates large quantities of by-products rich in metabolites with antioxidant, antimicrobial, anti-inflammatory and cicatrizing activities. The high homology between human enzymes and snake venoms makes the latter valuable laboratory tools for the study of pathophysiological processes. Proteases and phospholipases A2 act in processes related to hemostasis and inflammatory response. Thus, in this work, dried pomace obtained from grape (Isabel, Niagara, Bordô, BRS Violeta and Blend cultivars) processing were evaluated on phospholipase, proteolytic, hemolytic and thrombolytic activities induced by snakes venoms and the content of phenolic compounds and minerals was evaluated. The dried pomace exerted inhibitory and potentiating actions in all analyzed activities. The enzymatic modulators present in the evaluated dried pomace have potential for therapeutic use, although their broad characterization is still necessary, in order to define adequate amounts and formulations to obtain efficacy and safety in their use.

The purpose of this study was to investigate the distribution and specify the transmission and cross-contamination of Clostridium perfringens (C. perfringens) in the beef slaughtering and butchering process. The prevalence of 21.2% (150/708) yielded 208 isolates of C. perfringens, including 80.8% type A and 19.2% type D, 0.4% (3/708) samples carried both type A and D strains, and 72.5% type D isolates carried both cpe and atyp.cpb2 genes. C. perfringens were identified through the whole slaughtering process but no type F (cpe and cpa isolates) was found. 69 isolates were further analyzed and classified into 28 PFGE genotypes and clade I contained 94.2% isolates and 24 PFGE genotypes, which showed the genetic diversity and epidemic correlation. Our study traced C. perfringens contamination along the handling processes and showed a gradually ascending contamination rate during the whole process, revealing widespread cross-contamination from the feces and hides of slaughtered cattle to the carcass in the slaughtering workshop, so as from tools and personnel to meat of the cutting workshops. Strains from different slaughterhouses (regions) have high homology, and type A is the predominant toxinotype. It is necessary to monitor and control several key points of cross-contamination during slaughtering process to reduce a risk of C. perfringens infection.

Due to the observed increase of consumption of lupine-fortified food products and the high homology of lupine protein to other legumes, occurrence of new lupine allergy cases can increase significantly. Therefore, the aim of this study was to compare the seeds of 18 new Polish lupine breeding lines for immunoreactivity in relation to the sera of the patients sensitized to cross-reacting allergens, i.e. to soybeans and peanuts, using the western blot method. Antibodies present in the sera obtained from two adult outpatients cross-reacted with the studied extracts and made it possible to indicate six lines with decreased expression of Lup an 1 (high molecular weight subunit of β-conglutin): Mandelup, Mirela, Pulawski Rozowy Wczesny, Ignis, 25-65-M-4-1 and Stadoliszczenskij L-610 lines. Two more lines (Schmalblaettrige Schwerzplatzen and Rammiespielyj) are probably also less immunoreactive, due to the decreased content of alkaline subunit of α-conglutin—Lup an 2. The highest variability in immunoreactivity of proteins in question was noted for peptides with molecular weights ~ 20, 23, 28, 33, 38, 39, 43, 49, 50 and 63 kDa. Unfortunately, different patterns of immunoreactivity of the seeds obtained from various cultivation sites was noted for some lines. The correlation between the total protein content and reduced immunoreactivity of the tested lines was not confirmed. Thus, the lines with decreased immunoreactivity could be considered material for future crossing the narrow-leafed lupine lines to obtain varieties intended for food production.

Pollen food syndrome (PFS) is a highly prevalent condition causing mild oropharyngeal reactions to plant foods due to recognition by pollen-specific antibodies. It is most frequent in adults, but it can also occur in children. This review aims to establish the pitfalls of diagnosis and the nutritional consequences, and whether individuals with PFS require an individualised dietary and nutritional management strategy. The diagnosis of PFS can be made through history alone but is greatly enhanced by undertaking component-resolved diagnostic (CRD) tests to individual allergens in birch pollen and relevant foods. Management of PFS requires dietary avoidance of trigger foods, but often, many foods have to be avoided, which can affect quality of life and nutritional intake. Not all symptoms are mild, especially if concentrated forms of allergen are taken, which may occur more frequently with the increased emphasis of the health benefits of fruits and vegetables. Oral food challenge (OFC) and, in the future, novel immunotherapy may minimise necessary avoidance. Due to the high homology of the allergens involved, multiple allergy tests can result in mass exclusion of antioxidant-rich fruits and vegetables, which are important nutritional contributors to the diet. Thus, those with PFS should receive individual dietary counselling to prevent deficiency diseases, especially expectant mothers, children and those who are avoiding multiple foods.

Discovery and optimization of selective liver X receptor β (LXRβ) agonists are challenging due to the high homology of LXRα and LXRβ in the ligand-binding domain. There is only one different residue (Val versus Ile) at the ligand-binding pocket of LXRs. With machine learning methods, we identified pan LXR agonists with a novel scaffold (spiro[pyrrolidine-3,3′-oxindole]). Then, we figured out the mechanism of LXR isoform selectivity from co-crystal structures. Based on the mechanism and the new scaffold, LXRβ selective agonists were designed and synthesized. This led to the discovery of LXRβ agonists 4-7rr, 4–13 and 4-13rr with IC50 values ranging from 1.78 to 6.36 μM against glioblastoma in vitro. Treatment with 50 mg/kg/day of 4-13 for 15 days significantly reduced tumor growth using an in vivo xenograft glioblastoma model.

microRNAs (miRNAs) have been a class of promising disease diagnostic biomarkers and therapeutic targets for their important biological functions. However, because of the high homology, interference from precursors (pri-miRNA, pre-miRNA), as well as limitations in the current assay technologies, it poses high demand and challenge for a specific, efficient, and economic miRNA assay method. Here, we propose a new miRNA detection method based on a label-free probe and a small organic dye with sequence dependence, realizing the sequence-specific and colorimetric detection of target miRNA. What is pleasantly surprising, only one enzyme is enough to propel the whole miRNA assay process, greatly simplifying the reaction component and detection process. Together with PCR amplification for the high enough sensitivity and three checks for specificity control, a detection limit of 5 fM was obtained and even one mutation could be discriminated visually. Overall, the new method makes much progress in convenience and economy of PCR-based miRNA assay method so that miRNA assay is going to be more friendly and affordable.

The subtype H9N2 avian influenza virus greatly threatens the Chinese poultry industry, even with annual vaccination. Waterfowl can be asymptomatically infected with the H9N2 virus. In this study, three H9N2 virus strains, designated A/Goose/Jiangsu/YZ527/2011 (H9N2, Gs/JS/YZ527/11), A/Goose/Jiangsu/SQ119/2012 (H9N2, Gs/JS/SQ119/12), and A/Goose/Jiangsu/JD564/2012 (H9N2, Gs/JS/JD564/12), were isolated from domestic geese. Molecular characterization of the three isolates showed that the Gs/JS/YZ527/11 virus is a double-reassortant virus, combining genes of A/Quail/Hong Kong/G1/97 (H9N2, G1/97)-like and A/Chicken/Shanghai/F/98 (H9N2, F/98)-like; the Gs/JS/SQ119/12 virus is a triple-reassortant virus combining genes of G1/97-like, F/98-like, and A/Duck/Shantou/163/2004 (H9N2, ST/163/04)-like. The sequences of Gs/JS/JD564/12 share high homology with those of the F/98 virus, except for the neuraminidase gene, whereas the internal genes of Gs/JS/YZ527/11 and Gs/JS/SQ119/12 are closely related to those of the H7N9 viruses. An infectivity analysis of the three isolates showed that Gs/JS/SQ119/12 and Gs/JS/YZ527/11 replicated well, with seroconversion, in geese and chickens, the Gs/JS/JD564/12 did not infect well in geese or chickens, and the F/98 virus only infected chickens, with seroconversion. Emergence of these new reassortant H9N2 avian influenza viruses indicates that these viruses can infect both chicken and goose and can produce different types of lesions in each species.

A 50-year-old Chinese woman with a history of weakness and paroxysmal seizures of the left limb presented to our hospital with a ten-day history of neck pain. Imaging showed that there was a mass in the frontal lobe of her brain. On resection of the mass, a motile worm was identified. Morphological observation and molecular analysis of the mitochondrial COX1 and 28S rRNA genes of the worm extracted from the brain identified the causative agent as Spirometra mansoni. Homology search of the polymerase chain reaction (PCR)-amplified products from the case was conducted against gene fragments from local wild frogs. High homology was found between them, showing her likely exposure was frog consumption.

The concept of "Neurovascular Unit" (NVU) was put forward, so that the research goal of Central Nervous System (CNS) diseases gradually transitioned from a single neuron to the structural and functional integrity of the NVU. Zebrafish has the advantages of high homology with human genes, strong reproductive capacity and visualization of neural circuits, so it has become an emerging model organism for NVU research and has been applied to a variety of CNS diseases. Based on CNKI (https://www.cnki.net/) and PubMed (https://pubmed.ncbi.nlm.nih.gov/about/) databases, the author of this article sorted out the relevant literature, analyzed the construction of a zebrafish model of various CNS diseases，and the use of diagrams showed the application of zebrafish in the NVU, revealed its relationship, which would provide new methods and references for the treatment and research of CNS diseases.

Carbonic Anhydrases (CAs) are pharmaceutically relevant targets for the treatment of several disease conditions. The ubiquitous localization of these enzymes and the high homology shared by the different isoforms represent substantial impediments for the discovery of potential drugs devoid of off-target side effects. As a consequence, substantial efforts are still needed to allow for the full realization of the pharmacological potential of CA modulators. In this contribution, starting from our previous studies, we describe the synthesis of a set of new bicyclic tetrahydroindazoles featuring a secondary sulfonamide. Biological evaluation of the inhibitory activity against the hCA I, II, IV, and IX isoforms allowed drawing a structure-activity relationship profile that was rationalized through theoretical studies. This allowed dissecting the new molecules into the single portions influencing the zinc chelation properties and the selectivity profile thereby offering a new platform for the discovery of new isotype selective CA inhibitors. Carbonic Anhydrases (CAs) are pharmaceutically relevant targets for the treatment of several disease conditions. The ubiquitous localization of these enzymes and the high homology shared by the different isoforms represent substantial impediments for the discovery of potential drugs devoid of off-target side effects. As a consequence, substantial efforts are still needed to allow for the full realization of the pharmacological potential of CA modulators. In this contribution, starting from our previous studies, we describe the synthesis of a set of new bicyclic tetrahydroindazoles featuring a secondary sulfonamide. Biological evaluation of the inhibitory activity against the hCA I, II, IV, and IX isoforms allowed drawing a structure-activity relationship profile that was rationalized through theoretical studies. This allowed dissecting the new molecules into the single portions influencing the zinc chelation properties and the selectivity profile thereby offering a new platform for the discovery of new isotype selective CA inhibitors.

Aim. Epidemiologic examination of the case of group HIV-1 infection based on data obtained by general diagnostics methods for confirmation of the investigation hypothesis of deliberate HIV infection during heterosexual intercourse. Materials and methods. Sera samples from 8 HIV infected patients (5 female and 3 male) from Veliky Novgorod sent for epidemiologic investigation were used. Determination was carried out based on 1285 nt sequence analysis of polymerase gene segment (pol). Results. The study allowed to identify HIV in clinical samples sent to the expertise and establish phylogenetic connections between virus isolates obtained from both target and control group patients. Analysis of the results allowed to isolate samples grouped in a separate cluster that indicates tight cordial connections between the vims isolates from clinical material of these patients. Patients of the target group were infected with HIV-1 isolate ofthe circulating recombinant form CRF03_AB from the same origin that is confirmed by high homology ofthe nucleotide sequences. Conclusion. Epidemiologic investigation of a group case of HIV-1 infection has determined that the infection of the women of the target group occurred from the same source. Phylogenetic analysis results indicate the presence of an epidemiologic connection within the examined group that confirms the HIV infection transmission and conclusions ofthe investigation. Use of molecular-phylogenetic analysis of data obtained by laboratory diagnostics methods of HIV resistance to antiretroviral preparations allows with anamnestic and investigation information (in the context of available evidence) to investigate cases of HIV infection.

Colletotrichum acutatum is known as the major causal agents of anthracnose disease of chilli pepper in Indonesia. This research was aimed to study genetic variability of C. acutatum in Java and Sumatera based on morphological and molecular characteristics and to evaluate pathogenicity of several isolates. Observation on morphological characteristics involved colour and growth of each colony as well as shape and size of conidia. Molecular identification was performed by DNA amplification using specific primer for C. acutatum, i.e. CaInt2/ITS4 followed by sequencing and nucleotide sequence analysis. Pathogenicity test for each isolate on Capsicum annuum and C. frutescens was conducted in the laboratory using detached chilli. Morphology variability was observed from 40 isolates of C. acutatum. Most of the isolates have white/beige colonies with fusiform conidia of 6.11–9.73 µm in length and 2.24­–2.73 µm in width. Pathogenicity of 3 C. acutatum isolates varies from moderate to high based on lesions size on infected chilli. Sequence analysis of 8 C. acutatum isolates indicated high homology among isolates from Java and Sumatera

Timely identification of pandemic influenza threats depends on monitoring for highly pathogenic avian influenza viruses. We isolated highly pathogenic avian influenza A(H5N6) virus clade 2.3.4.4, genotype G1.1, in samples from a bird in southwest Russia. The virus has high homology to human H5N6 influenza strains isolated from southeast China.

Cytochromes P450 (CYPs) play an important role in the metabolism of endogenic and xenobiotic substances, especially drugs. In addition, many CYPs may serve as targets for disease treatment. However, due to the presence of a common heme, the hydrophobicity of the CYP binding cavity, and the high homology within the binding pocket, most CYP inhibitors lack selectivity, which often leads to drug-drug interactions. Therefore, it is meaningful to develop highly selective CYP inhibitors. In this review, we summarize some of the strategies that have been used to develop highly selective CYP inhibitors, such as the weakening of the heme-binding group interaction, reduction of molecular lipophilicity and introduction of small structural changes within compounds.

Taxonomic studies of strain PAGU 1678T , an obligately anaerobic, gram-positive, spore-forming bacterium isolated from biobreeding rat feces, were performed. This strain has been demonstrated to have the ability to exacerbate pathosis in a mouse model of dextran sulfate sodium-induced ulcerative colitis. Phylogenetic analysis based on the 16S rRNA gene showed high homology with Paraclostridium bifermentans. To clarify the correct taxonomic position of strain PAGU 1678T , a comparative taxonomic study using P. bifermentans PAGU 2008T (═JCM 1386T ) and the closely related bacterial species P. benzoelyticum PAGU 2068T (═LMG 28745T ) was carried out. Despite the close similarity of 16S rRNA gene sequences, DNA-DNA hybridization between strain PAGU 1678T and P. bifermentans PAGU 2008T was 60.03% on average, average nucleotide identity was 96.17%, and it was shown to have different genomic sequences. Biochemically, strain PAGU 1678T could be differentiated from P. bifermentans PAGU 2008T by H2 S production. Furthermore, strain PAGU 1678T was characterized by the presence of two phospholipids with different polarity on polar lipid analysis. In addition, strain PAGU 1678T differed from P. bifermentans PAGU 2008T in findings on whole-cell protein analysis and matrix-assisted laser desorption/ionization-time of flight mass spectrometry. On the basis of these biochemical and genetic characteristics, a novel subspecies of P. bifermentans with the name Paraclostridium bifermentans subsp. muricolitidis subsp. nov. is here proposed, with PAGU 1678T (═CCUG 72489T ═NBRC 113386T ) as the type strain, which automatically creates P. bifermentans subsp. bifermentans subsp. nov. JCM 1386T (═ATCC 638T ═DSM 14991T ).

The severe acute respiratory syndrome coronavirus (SARS-CoV) first emerged in 2003, causing the SARS epidemic which resulted in a 10% fatality rate. The advancements in metagenomic techniques have allowed the identification of SARS-like coronaviruses (SL-CoVs) sequences that share high homology to the human SARS-CoV epidemic strains from wildlife bats, presenting concrete evidence that bats are the origin and natural reservoir of SARS-CoV. The application of reverse genetics further enabled that characterization of these bat CoVs and the prediction of their potential to cause disease in humans. The knowledge gained from such studies is valuable in the surveillance and preparation of a possible future outbreak caused by a spill-over of these bat SL-CoVs.

Coliphages T7M and T3, Yersinia phage ϕYeO3-12, and Salmonella phage ϕSG-JL2 share high homology in genomic sequences. Simple sequence repeats (SSRs) are found in their genomes and variations of SSRs among these phages are observed. Analyses on regions of sequences in T7M and T3 genomes that are likely derived from phage recombination, as well as the counterparts in ϕYeO3-12 and ϕSG-JL2, have been discussed by Lin in “Simple sequence repeat variations expedite phage divergence: mechanisms of indels and gene mutations” [1]. These regions are referred to as recombinant regions. The focus here is on SSRs in the whole genome and regions of sequences outside the recombinant regions, referred to as non-recombinant regions. This article provides SSR counts, relative abundance, relative density, and GC contents in the complete genome and non-recombinant regions of these phages. SSR period sizes and motifs in the non-recombinant regions of phage genomes are plotted. Genomic sequence changes between T7M and T3 due to insertions, deletions, and substitutions are also illustrated. SSRs and nearby sequences of T7M in the non-recombinant regions are compared to the sequences of ϕYeO3-12 and ϕSG-JL2 in the corresponding positions. The sequence variations of SSRs due to vertical evolution are classified into four categories and tabulated: (1) insertion/deletion of SSR units, (2) expansion/contraction of SSRs without alteration of genome length, (3) changes of repeat motifs, and (4) generation/loss of repeats. Keywords: Simple sequence repeats, T7M, Bacteriophage genome, SSR variability classification

In this issue of Trends in Cardiovascular Medicine, Pyeritz [1] presents a concise review of the past and recent progress made in understanding the cause, pathogenesis, and clinical management of Marfan syndrome (MFS). From the time of its initial description in 1886, through key discoveries in the 1970s and 1990s, culminating in the initiation and completion of a series of mechanistically-based clinical trials in recent years, our understanding of the development and treatment of MFS has truly seen remarkable progress. While many questions remain about the molecular pathogenesis, and how to best manage the cardiovascular-related manifestations, as Pyeritz points out, life expectancy has steadily improved over the last 4 decades, approaching normal for most patients. Future efforts must continue to focus on defining the molecular and cellular response to fibrillin-1 (FBN-1) mutations, and how these basic mechanisms can be used for clinical advantage. A work by Dietz and Pyeritz [2] in the early 90s identified key mutations in the fibrillin-1 (FBN-1) gene that were associated with Marfan syndrome and its related disorders. Fibrillin-1 is a 350 kDa glycoprotein comprised of a series of epidermal growth factor-like motifs, many of which contain calcium-binding sequences, termed calcium-binding EGF (cbEGF) repeats [3]. These cbEGF modules are arranged in tandem, separated by cysteine-rich motifs (8-cys/TB) that have high homology to the family of latent transforming growth factor-beta (TGF-β) binding proteins (LTBPs) [3,4]. Fibrillin monomers self-assemble into macroaggregates forming the basic structures on which mature elastin fibers are synthesized from tropoelastin subunits. Accordingly, it was postulated that FBN-1 mutations within the aorta result in a weakened and disordered microfibril network connecting the elastic lamellae to the adjacent

Graphene oxide (GO) was introduced in the process of systematic evolution of ligands by exponential enrichment (SELEX) to screen ofloxacin-specific single-stranded DNA aptamers. Four sequences with high homology, ap1, ap3, ap4 and ap5 were picked out. Their secondary structures were simulated, and the dissociation constants (Kd) were measured, which were 251.3, 130.1, 159.1 and 304.4 nM, respectively. The specificity of the aptamers was also evaluated.

Made available in DSpace on 2020-12-12T02:11:59Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-07-01 Universidade Estadual Paulista Worldwide, Bartonella species are known to infect a wide range of mammalian and arthropod hosts, including humans. The current study aimed to investigate the prevalence of Bartonella spp. in synanthropic mammals captured in peri-urban areas from Central-Western and Southern Brazil and their ectoparasites. For this aim, 160 mammals belonging to four species, and 218 associated arthropods were sampled. DNA was extracted and subjected to different Bartonella screening assays. Additionally, blood samples from 48 small rodents were submitted to liquid BAPGM culture followed by qPCR assay and solid culture. Two out of 55 Rattus captured in Santa Catarina state were PCR-positive for Bartonella when targeting the nuoG, 16S, and ITS loci. Sequences showed high homology with Bartonella coopersplainsensis. Conversely, all 48 small rodents, 14 capybaras and 43 opossum DNA samples from animals trapped in Mato Grosso do Sul were Bartonella negative in the HRM real time PCR assays targeting the ITS locus and gltA gene. Additionally, all mammal-associated ectoparasites showed negativity results based on HRM real time PCR assays. The present study showed, for the first time, the occurrence of B. coopersplainsensis in Brazil, shedding some light on the distribution of rats-related Bartonella in South America. In addition, the majority of rodents and marsupials were negative for Bartonella spp. Since B. coopersplainsensis reservoirs - Rattus spp. - are widely dispersed around the globe, their zoonotic potential should be further investigated. Graduate Program of Agricultural and Livestock Microbiology Faculty of Agrarian and Veterinary Sciences (FCAV/UNESP) Department of Veterinary Pathology Faculty of Agrarian and Veterinary Sciences (FCAV/UNESP) Koret School of Veterinary Medicine The Robert H. Smith Faculty of Agriculture Food and Environment. The Hebrew University of Jerusalem Dom Bosco Catholic University Department of Veterinary Medicine University of Contestado Federal University of Mato Grosso do Sul Graduate Program of Agricultural and Livestock Microbiology Faculty of Agrarian and Veterinary Sciences (FCAV/UNESP) Department of Veterinary Pathology Faculty of Agrarian and Veterinary Sciences (FCAV/UNESP)

Yellow Spot Disease on Sweet Potato in Bogor, West JavaYellow spot symptom on sweet potato red cultivar was observed in Cikarawang and Leweung kolot area, Bogor regency. Symptomatic leaf samples gave positive reaction in serological detection by DIBA method using polyclonal antiserum for Potyvirus. DNA fragment of ± 700 bp in length was successfully amplified by RT-PCR using degenerate primer for cylindrical inclusion gene (CI) of Potyvirus. Further nucleotide sequence analysis indicated high homology to Sweet potato feathery mottle virus (SPFMV). The homology of SPFMV Cikarawang (Crkw) isolate ranging from 89–98% to several isolates from other countries with the highest homology to Japan and Spain isolates. SPFMV Crkw isolate was in the same cluster with the Japan and Spain isolates based on phylogenetic analysis of both nucleotide and amino acid sequences. This is the first report of SPFMV on sweet potato in Bogor, West Java, Indonesia.

Moleculer Characterization of Papaya ringspot virus type P on Cucumber in JavaInfection of Papaya ringspot virus (PRSV) on cucumber plants showing mosaic symptom was detected using specific antibody. Further investigation was conducted to determine molecular characters and status of PRSV infecting cucumber in Java. Infection of PRSV was detected from leaf samples collected from the field using dot immunobinding assay (DIBA). Disease frequency caused by PRSV infection reached 81.11%, 95.86%, 91.66%, and 92.3% in East Java, Central Java, Yogyakarta, and West Java, respectively. Characterization of PRSV isolates was conducted by reverse transcription polymerase chain reaction (RT-PCR) using specific primers for PRSV-P and PRSV-W, followed by cloning, and DNA sequencing. DNA fragment of 470 bp was successfully amplified using specific primers for PRSV-P from several samples from Nganjuk, Brebes, Kulon Progo, and Subang; but no amplification was achieved using specific primers for PRSV-W. Nucleotide and amino acid analysis showed high homology among PRSV-P isolates from Nganjuk, Brebes, Kulon Progo, and Subang, i.e. 98.6%-99.7% and 99.3%-100%, respectively. This is an indication of a low genetic variation among PRSV-P from Java. Further phylogenetic analysis indicated that PRSV-P isolate cucumber is in the same cluster with PRSV-P isolate papaya from Bali, Indonesia. This is the first report of PRSV-P infecting cucumber in Indonesia.

Interferon regulatory factor 9 (IRF9) is an integral transcription factor in mediating the type I interferon antiviral response, as part of the interferon-stimulated gene factor 3. However, the role of IRF9 in many important non-communicable diseases has just begun to emerge. The duality of IRF9’s role in conferring protection but at the same time exacerbates diseases is certainly puzzling. The regulation of IRF9 during these conditions is not well understood. The high homology of IRF9 DNA-binding domain to other IRFs, as well as the recently resolved IRF9 IRF-associated domain structure can provide the necessary insights for progressive inroads on understanding the regulatory mechanism of IRF9. This review sought to outline the structural basis of IRF9 that guides its regulation and interaction in antiviral immunity and other diseases.

Arthropod-borne flaviviruses are important human pathogens that cause a diverse range of clinical conditions, including severe hemorrhagic syndromes, neurological complications and congenital malformations. Consequently, there is an urgent need to develop safe and effective vaccines, a process requiring better understanding of the immunological mechanisms involved during infection. Decades of research suggest a paradoxical role of the immune response against flaviviruses: although the immune response is crucial for the control, clearance and prevention of infection, poor clinical outcomes are commonly associated with virus-specific immunity and immunopathogenesis. This relationship is further complicated by the high homology among viruses and the implication of cross-reactive immune responses in protection and pathogenesis. This Review examines the dual role of the adaptive immune response against flaviviruses, particularly emphasizing the most recent findings regarding cross-reactive T cell and antibody responses, and the effects that these concepts have on vaccine-development endeavors.

Noroviruses (NoVs) are the leading cause of acute viral gastroenteritis outbreaks. From June 2015 to March 2017, fifteen outbreaks of acute gastroenteritis (AGE) were reported to the Jinan Center for Disease Control and Prevention in China. To identify the circulating NoV genotypes associated with outbreaks in Jinan, China, 414 specimens from the 15 outbreaks were collected and analyzed for the causative viruses, and phylogenetic analysis was performed on the NoV-positive strains. The NoV detection rate was 57.5% (238/414), and a total of 14 outbreaks were caused by NoVs (eight by infection with genogroup II (GII), five by mixed infection with GI and GII, and one by mixed infection with GII and rotavirus (RoV)-A). A total of 75 NoV sequences were obtained from 13 NoV-positive outbreaks and classified into seven genotypes (38 GII.17, 13 GII.2, 4 GII.3, 4 GII.1, 10 GI.6, 5 GI.5 and 1 GI.3), while GII.4 was not identified. The most prevalent genotype changed yearly during the 2015-2017 period. Phylogenetic analysis demonstrated that these NoV genotypes had high homology with the strains circulating worldwide, especially strains from Asian countries and cities. Our study illustrated that multiple non-GII.4 NoV genotypes were prevalent in outbreaks of AGE in Jinan, China. Year-round surveillance of multiple NoV genotypes could help health authorities reduce the impact of NoV outbreaks on public health.

The Rhizopus strains in the Universitas Indonesia Culture Collection (UICC) were isolated from tempeh. Five strains of Rhizopus (UICC 26, UICC 36, UICC 39, UICC 55, UICC 121) were identified as R. arrhizus based on morphological and physiological characters. In the current taxonomy of Rhizopus, R. arrhizus is synonym of R. oryzae. The aim of this study was to re-identify five R. arrhizus strains by molecular approach based on internal transcribed spacers (ITS) regions of ribosomal DNA sequence data. The sequence homology search showed that strains UICC 36 and UICC 55 have very high homology (99.8%) to R. oryzae CBS 112.07T type strain, however the other three strains (UICC 26, UICC 39, and UICC 121) showed a lower homology (99.0-99.2%) to R. oryzae CBS 112.07T type strain. The phylogenetic tree showed that strains UICC 36 and UICC 55 were placed in a monophyletic group with R. oryzae CBS 112.07T type strain. The tree revealed that three strains (UICC 26, UICC 39, and UICC 121) were placed in a monophyletic group with R. delemar CBS 120.12T type strain. The phylogenetic tree showed that the group of R. delemar was phylogenetically very closely related with the group of R. oryzae. In this study, two strains (UICC 36 and UICC 55) were re-identified as R. oyzae (UICC 36 and UICC 55), and three strains (UICC 26, UICC 39, UICC 121) were re-identified as R. delemar. Morphological observation of all strains showed the characters corresponded to R. oryzae.