Protocol for high throughput 3D drug screening of patient derived melanoma and renal cell carcinoma

High Throughput Screening (HTS) with 3D cell models is possible thanks to the recent progress and development in 3D cell culture technologies. Results from multiple studies have demonstrated different drug responses between 2D and 3D cell culture. It is now widely accepted that 3D cell models more accurately represent the physiologic conditions of tumors over 2D cell models. However, there is still a need for more accurate tests that are scalable and better imitate the complex conditions in living tissues. Here, we describe ultrahigh throughput 3D methods of drug response profiling in patient derived primary tumors including melanoma as well as renal cell carcinoma that were tested against the NCI oncologic set of FDA approved drugs. We also tested their autologous patient derived cancer associated fibroblasts, varied the in-vitro conditions using matrix vs matrix free methods and completed this in both 3D vs 2D rendered cancer cells. The result indicates a heterologous response to the drugs based on their genetic background, but not on their maintenance condition. Here, we present the methods and supporting results of the HTS efforts using these 3D of organoids derived from patients. This demonstrated the possibility of using patient derived 3D cells for HTS and expands on our screening capabilities for testing other types of cancer using clinically approved anti-cancer agents to find drugs for potential off label use.

FLECS technology for high-throughput screening of hypercontractile cellular phenotypes in fibrosis: A function-first approach to anti-fibrotic drug discovery

The pivotal role of myofibroblast contractility in the pathophysiology of fibrosis is widely recognized, yet HTS approaches are not available to quantify this critically important function in drug discovery. We developed, validated, and scaled-up a HTS platform that quantifies contractile function of primary human lung myofibroblasts upon treatment with pro-fibrotic TGF-β1. With the fully automated assay we screened a library of 40,000 novel small molecules in under 80 h of total assay run-time. We identified 42 hit compounds that inhibited the TGF-β1-induced contractile phenotype of myofibroblasts, and enriched for 19 that specifically target myofibroblasts but not phenotypically related smooth muscle cells. Selected hits were validated in an ex vivo lung tissue models for their inhibitory effects on fibrotic gene upregulation by TGF-β1. Our results demonstrate that integrating a functional contraction test into the drug screening process is key to identify compounds with targeted and diverse activity as potential anti-fibrotic agents.

Epidemiological and Genetic Analyses of Schizophrenia and Breast Cancer

BACKGROUND AND HYPOTHESIS

While the phenotypic association between schizophrenia and breast cancer has been observed, the underlying intrinsic link is not adequately understood. We aim to conduct a comprehensive interrogation on both phenotypic and genetic relationships between schizophrenia and breast cancer.

STUDY DESIGN

We first used data from UK Biobank to evaluate a phenotypic association and performed an updated meta-analysis incorporating existing cohort studies. We then leveraged genomic data to explore the shared genetic architecture through a genome-wide cross-trait design.

STUDY RESULTS

Incorporating results of our observational analysis, meta-analysis of cohort studies suggested a significantly increased incidence of breast cancer among women with schizophrenia (RR = 1.30, 95% CIs = 1.14-1.48). A positive genomic correlation between schizophrenia and overall breast cancer was observed (rg = 0.12, P = 1.80 × 10-10), consistent across ER+ (rg  = 0.10, P = 5.74 × 10-7) and ER- subtypes (rg = 0.09, P = .003). This was further corroborated by four local signals. Cross-trait meta-analysis identified 23 pleiotropic loci between schizophrenia and breast cancer, including five novel loci. Gene-based analysis revealed 27 shared genes. Mendelian randomization demonstrated a significantly increased risk of overall breast cancer (OR = 1.07, P = 4.81 × 10-10) for genetically predisposed schizophrenia, which remained robust in subgroup analysis (ER+: OR = 1.10, P = 7.26 × 10-12; ER-: OR = 1.08, P = 3.50 × 10-6). No mediation effect and reverse causality was found.

CONCLUSIONS

Our study demonstrates an intrinsic link underlying schizophrenia and breast cancer, which may inform tailored screening and management of breast cancer in schizophrenia.

Prevalence of extended-spectrum beta-lactamase and molecular detection of blaTEM, blaSHV, and blaCTX-M genotypes among gram-negative Bacilli isolates from hospital acquired infections in pediatrics, one institutional study

BACKGROUND

Gram-negative bacilli represents an important pathogen in hospital-acquired infections (HAIs) worldwide. The emergence of antibiotic resistance in these pathogens warrants attention for the proper management of infections. Extended-spectrum beta-lactamase (ESBL) resistance represents a major therapeutic problem in infections due to Gram-negative bacilli. The present study aimed to study the extended-spectrum beta-lactamase genes blaTEM, blaSHV, and blaCTX-M by multiplex polymerase reaction in isolated Gram-negative bacilli from HAIs in pediatric patients.

METHODS

The study included one hundred-five isolates of Gram-negative bacilli from pediatric patients with different types of HAIs. The isolates were subjected to full microbiological identification, antibiotics susceptibility by disc diffusion method, the phenotypic study of ESBL, and the genetic study of ESBL genes by multiplex PCR.

RESULTS

Fifty isolates of Gram-Negative bacilli showed ESBL activity by a phenotypic study by double disc diffusion method (50/105). All ESBL producers' isolates were positive by PCR for ESBL genes. The most frequent gene was blaTEM (64%), followed by blaSHV (30%) and CTX-M (22%). Mixed genes were found in 4 isolates (8%) for blaTEM and blaSHV, blaTEM and CTX-M. There was a significant association between PCR for ESBL genes and phenotypic ESBL detection (P = 0.001). There was significant detection of ESBL genes in E. coli (28%), followed by Enterobacter spp. (26%), Klebsiella spp. (24%), Serratia (14%), Pseudomonas spp. (6%) and Proteus (2%), P = 0.01. There Seventy percent of isolates positive for ESBL production had an insignificant association between MDR and PCR for ESBL genes (P = 0.23).

CONCLUSION

The present study highlights the prevalence of ESBL activity among clinical isolates of Gram-negative bacilli isolated from hospital-acquired infections in pediatric patients. The most common gene responsible for this activity was blaTEM gee followed by blaSHV and blaCTX-M. There was a high prevalence of multiple antibiotic resistance among isolates with ESBL activity. The finding of the present study denotes the importance of screening extended beta-lactamase among Gram-negative bacilli associated with HAIs in pediatric patients.

Lysobacter changpingensis sp. nov., a novel species of the genus Lysobacter isolated from a rhizosphere soil of strawberry in China

In the present work, we characterized in detail strain CM-3-T8T, which was isolated from the rhizosphere soil of strawberries in Beijing, China, in order to elucidate its taxonomic position. Cells of strain CM-3-T8T were Gram-negative, non-spore-forming, aerobic, short rod. Growth occurred at 25-37 °C, pH 5.0-10.0, and in the presence of 0-8% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CM-3-T8T formed a stable clade with Lysobacter soli DCY21T and Lysobacter panacisoli CJ29T, with the 16S rRNA gene sequence similarities of 98.91% and 98.50%. The average nucleotide identity and digital DNA-DNA hybridization values between strain SG-8 T and the two reference type strains listed above were 76.3%, 79.6%, and 34.3%, 27%, respectively. The DNA G + C content was 68.4% (mol/mol). The major cellular fatty acids were comprised of C15:0 iso (36.15%), C17:0 iso (8.40%), and C11:0 iso 3OH (8.28%). The major quinone system was ubiquinone Q-8. The major polar lipids were phosphatidylethanolamine (PE), phosphatidylethanolamine (PME), diphosphatidylglycerol (DPG), and aminophospholipid (APL). On the basis of phenotypic, genotypic, and phylogenetic evidence, strain CM-3-T8T (= ACCC 61714 T = JCM 34576 T) represents a new species within the genus Lysobacter, for which the name Lysobacter changpingensis sp. nov. is proposed.

Integration of phenotypic, qPCR and genome sequencing methodologies for the detection of antimicrobial resistance and virulence in clinical isolates of a tertiary hospital, India

The emergence of antimicrobial resistance (AMR) and virulence in clinical isolates is a significant public health concern. The rapid and accurate detection of these traits in clinical isolates is essential for effective infection control and treatment. We demonstrated the integration of multiple detection methodologies, including phenotypic testing, quantitative polymerase chain reaction (qPCR), and genome sequencing, to detect AMR and virulence in clinical isolates. One hundred sixty-two gram-negative bacterial clinical isolates were selected for this study from the Shri Vinoba Bhave Civil Hospital, Silvassa, a tertiary government hospital. Antimicrobial susceptibility was detected by determining the Minimum Inhibitory Concentration (MIC) using Vitek-2, whereas the combined disk (CD) method was used for phenotypic detection of carbapenemase activity. The highest sensitivity rates were obtained for antibiotics colistin 87.93%, amikacin 67.52%, tigecycline 63.39%, nitrofurantoin 60.87%, and gentamycin 56.08%. The most resistant antibiotics were ceftazidime (71.93%), ciprofloxacin (67.95%) and trimethoprim/sulfamethoxazole (65.56%). Approximately 46.91% (76) of all the isolates were MBL isolates. The qPCR results confirmed the presence of blaNDM-1 in 29.01% of the isolates. The blaNDM-1 harbouring isolates in descending order, were Acinetobacter, Enterobacter cloacae, and Klebsiella pneumoniae. Klebsiella and Acinetobacter isolates were extensively drug-resistant. Whole genome sequencing performed on one of the Klebsiella pneumoniae isolates revealed the presence of many virulence factors, which increased the pathogenicity of the clinical isolates. The results showed that antimicrobial resistance, including carbapenem resistance, blaNDM-1, and virulence factors, was highly prevalent among isolates from tertiary clinical hospitals. The integration of multiple detection methodologies can potentially improve the detection of AMR and virulence in clinical isolates, leading to better patient outcomes and a reduced spread of these essential traits.

Phenotypical characterization, and antibiotics susceptibility patterns of skin bacteria found in podoconiosis patients in the North West Region of Cameroon

BACKGROUND

Podoconiosis, a non-infectious disease originating from long-term exposure of bare feet to irritant red clay soil is a lifelong, disabling disease with no specific diagnostic tool, classified into 5 stages based on the severity of leg swelling (lymphoedema). Secondary bacterial infections have been suggested to cause acute dermatolymphangioadenitis (ADLA) attacks and drive disease progression. Although the North West Region of Cameroon has a proven history of podoconiosis endemicity, the bacterial composition of lymphoedema due to this condition has not been studied. Thus, this study investigated the leg bacterial diversity of patients who suffered from the lymphoedema and their susceptibility pattern to selected antibiotics.

METHODS

A cross-sectional study was carried out in which podoconiosis affected and non-lymphoedema individuals living in the same community were purposively selected. Samples were collected by swabbing the skin between the toes and around the anklebone, then cultured and sub-cultured on nutrient agar to obtain pure isolates. The cultured isolates were then morphologically and biochemically classified using microscopy and analytic profile index test kits, respectively. The disk diffusion technique was used to determine antibiotic susceptibility.

RESULTS

Thirty-three participants were recruited, and 249 bacterial isolates were characterized into 29 genera, 60 species; with 30 (50%) being gram positive rods, 19 (31.7%) gram positive cocci, and 11 (18.3%) gram negative rods. Thirteen gram positive rods, fifteen gram positive cocci, and eight gram negative rods of bacterial species were found only in podoconiosis individuals among which Cellulomonas spp / Microbacterium spp. (2.8%), Staphylococcus lentus (3.3%), and Burkholderia cepacia (4.0%) dominated. 90% (90%) of the bacterial isolates were sensitive to doxycycline, whereas ampicillin had a high level of intermediate resistance, and penicillin G had the greatest resistant profile.

CONCLUSION

Our findings show that 94 (37.8%) out of 249 described bacterial isolates were exclusively found in the legs of podoconiosis individuals, and their susceptibility pattern to antibiotics was similar to that of others.

Genetic and phenotypic assessments for the safety of probiotic Bacillus clausii 088AE

In this study, we report on whole genome sequence analysis of clinically documented, commercial probiotic Bacillus clausii 088AE and genome features contributing to probiotic properties. The whole genome sequence of B. clausii 088AE generated a single scaffold of 4,598,457 bp with 44.74 mol% G + C. This assembled genome sequence annotated by the RAST resulted in 4371 coding genes, 75 tRNAs, and 22 rRNAs. Gene ontology classification indicated 39.5% proteins with molecular function, 44.24% cellular component, and 16.25% proteins involved in biological processes. In taxonomic analysis, B. clausii 088AE shared 99% identity with B. clausii DSM 8716. The gene sequences related to safety and genome stability such as antibiotic resistance (840), virulence factors (706), biogenic amines (1), enterotoxin (0), emetic toxin (0), lanthipeptides (4), prophage (4) and clustered regularly interspaced short palindromic repeats (CRISPR) sequences (11), were identified and evaluated for safety and functions. The absence of functional prophage sequences and the presence of CRISPR indicated an advantage in genome stability. Moreover, the presence of genome features contributing to probiotic characteristics such as acid, and bile salt tolerance, adhesion to the gut mucosa, and environmental resistance ensure the strains survivability when consumed as a probiotic. In conclusion, the absence of risks associated with sequences/genes in the B. clausii 088AE genome and the presence of essential probiotic traits confirm the strain to be safe for use as a probiotic.

Protocol for 3D screening of lung cancer spheroids using natural products

Non-small cell lung cancer (NSCLC) is the most common type of lung cancer and accounts for ∼84% of all lung cancer cases. NSCLC remains one of the leading causes of cancer-associated death, with a 5-year survival rate less than 25%. This type of cancer begins with healthy cells that change and start growing out of control, leading to the formation of lesions or tumors. Understanding the dynamics of how the tumor microenvironment promotes cancer initiation and progression that leads to cancer metastasis is crucial to help identify new molecular therapies. 3D primary cell tumor models have received renewed recognition due to their ability to better mimic the complexity of in vivo tumors and as a potential bridge between traditional 2D culture and in vivo studies. Vast improvements in 3D cell culture technologies make them much more cost effective and efficient largely because of the use of a cell-repellent surfaces and a novel angle plate adaptor technology. To exploit this technology, we accessed the Natural Products Library (NPL) at UF Scripps, which consists of crude extracts, partially purified fractions, and pure natural products (NPs). NPs generally are not very well represented in most drug discovery libraries and thus provide new insights to discover leads that could potentially emerge as novel molecular therapies. Herein we describe how we combined these technologies for 3D screening in 1536 well format using a panel of ten NSCLC cells lines (5 wild type and 5 mutant) against ∼1280 selected members of the NPL. After further evaluation, the selected active hits were prioritized to be screened against all 10 NSCLC cell lines as concentration response curves to determine the efficacy and selectivity of the compounds between wild type and mutant 3D cell models. Here, we demonstrate the methods needed for automated 3D screening using microbial NPs, exemplified by crude extracts, partially purified fractions, and pure NPs, that may lead to future use targeting human cancer.

The relative effects of interspecific and intraspecific diversity on microplastic trapping in coastal biogenic habitats

Our understanding of how anthropogenic stressors such as climate change and plastic pollution interact with biodiversity is being widened to include diversity below the species level, i.e., intraspecific variation. The emerging appreciation of the key ecological importance of intraspecific diversity and its potential loss in the Anthropocene, further highlights the need to assess the relative importance of intraspecific versus interspecific diversity. One such issue is whether a species responds as a homogenous whole to plastic pollution. Using manipulative field transplant experiments and laboratory-controlled hydrodynamic simulations, we assessed the relative effects of intraspecific and interspecific diversity on microplastic trapping in coastal biogenic habitats dominated by two key bioengineers, the brown intertidal macroalgae Fucus vesiculosus and F. guiryi. At the individual level, northern morphotypes of F. guiryi trapped more microplastics than southern individuals, and F. vesiculosus trapped more microplastics than F. guiryi. Canopy density varied among species, however, leading to reversed patterns of microplastic accumulation, with F. guiryi canopies accumulating more microplastics than those of F. vesiculosus, while no differences were observed between the canopies of F. guiryi morphotypes. We emphasize the importance of assessing the effects of intraspecific variation which, along with other crucial factors such as canopy density, flow velocity and polymer composition, modulates the extent of microplastic accumulation in coastal biogenic habitats. Our findings indicate that a realistic estimation of plastic accumulation in biogenic habitats requires an understanding of within- and between-species traits at both the individual and population levels.

The proportion and phenotypic changes of CD4+CD25-Foxp3+ T cells in patients with untreated rheumatoid arthritis

OBJECTIVE

CD4⁺CD25⁺Foxp3⁺ regulatory T (Treg) cell-mediated immunosuppression is an essential mechanism of rheumatoid arthritis (RA). However, little is known regarding the specific role of CD4⁺CD25^-Foxp3⁺ Treg cells in RA. This study aimed to investigate the frequency of circulating CD4⁺CD25^-Foxp3⁺ Treg cells and their role in RA.

METHODS

Sixty-one untreated RA patients and 40 healthy controls (HCs) were enrolled in this study. The proportion of CD4⁺CD25^-Foxp3⁺ T cells and CD4⁺CD25⁺Foxp3⁺ Tregs; the levels of CTLA4, GITR, Helios, and ICOS; and the production of IL-17A, IFN-γ, and IL-10 were assessed by flow cytometry. The correlation of CD4⁺CD25^-Foxp3⁺ T cells and CD4⁺CD25⁺Foxp3⁺ Tregs with the clinical indicators was conducted by Spearman correlation analysis.

RESULTS

The proportion of CD4⁺CD25^-Foxp3⁺ T cells was elevated in RA and positively correlated with disease activity. CD4⁺CD25^-Foxp3⁺ T cells expressed less Helios and produced more IFN-γ than conventional Tregs in RA. Additionally, the proportion of CD4⁺CD25^-Foxp3⁺ T cells was positively correlated with DAS28 score, IgG titer, and anti-CCP titer.

CONCLUSIONS

These data indicate that CD4⁺CD25^-Foxp3⁺ T cells in RA exhibit several different functional properties from conventional Tregs and are correlated with RA disease activity.

Antibiotic resistance patterns of carbapenemase-producing Enterobacterales in Mohammed VI University Hospital of Marrakech, Morocco

OBJECTIVES

The emergence and spread of Carbapenem-Resistant Enterobacterales (CRE) has become a growing concern for health services, internationally, nationally, and regionally. In Morocco, the situation is more worrisome as studies on CRE are scarce and/or scattered and/or outdated. As a result, we carried out the present study to determine and update CRE prevalence at Mohammed VI University Hospital of Marrakech, Morocco.

PATIENTS AND METHODS

A cross-sectional prospective study was carried out from March 2018 to March 2020 on 41161 clinical specimens of 23,469 patients suspected of bacterial infections. Enterobacterales strains were isolated following standard bacteriological procedures. Bacterial strains were identified using BD-Phoenix and MALDI-TOF-MS. Antibiotic susceptibility was determined for 14 antibiotics. Carbapenemase production and phenotypic detection were characterized using modified carbapenem inactivation phenotypic and immunochromatographic methods.

RESULTS

All in all, 484 Enterobaterales resistant to at least one carbapenem were recovered. The majority was isolated from the neonatal unit (14%), followed by the urology-nephrology (11%), and plastic surgery departments (10%). K. pneumoniae (n=232) was the most isolated, followed by E. cloacae (n=148), E. coli (n=56), and S. marcescens (n=17). Antibiotic susceptibility profile showed high rates of resistance to ciprofloxacin (75.21%), gentamicin (84.50%), and cotrimoxazole (88.42%). Out of 484 CRE positive cultures, 388 (80.16%) were Carbapenemase-positive. Out of the latter, 170 were metallo-beta-lactamase producers (NDM), 162 OXA-48-like, and 56 both.

CONCLUSION

These findings emphasize the urgent need for control precautions and strict measures to contain and mitigate this issue.

Isolation, discrimination, and molecular detection of Listeria species from slaughtered cattle in Namwala District, Zambia

BACKGROUND

The food industry is increasingly becoming more scrutinized, given the frequency and intensity with which zoonotic diseases are being reported. Pathogen tracking has become more applicable with regards food safety. It is in this regard that the present study was formulated to track Listeria species. in freshly slaughtered cattle carcasses by utilizing standard and molecular biological techniques.

METHODS

A cross-sectional study design was conducted from March to December 2020 with 200 samples being equally collected in the rainy and dry seasons. A total of 180 and 20 swabs were aseptically collected from carcasses and the environment respectively. Samples were first subjected to pre-enrichment in half-strength Fraser broth followed by enrichment in full strength Fraser broth and subsequent plating on Listeria agar. Listeria growth characteristics were identified up to species level based on their morphological and biochemical characteristics. Further, molecular detection and phylogenetic analysis was conducted. Quantitative proportionate survey data were analyzed using Stata Version 15 software to estimate crude prevalence taking into account complex design at abattoir level. Factors associated with contamination were characterized using logistic regression. Sequences were analyzed using, Genetyyx version 12 and phylogenetic Mega.

RESULTS

Of the 200 samples, 19 were positive for Listeria species identified as L.innocua 14/19 (73.7%) and L. monocytogenes 5/19 (26.3%). All isolates were from freshly slaughtered carcasses, and none from environment. Siginificant differences in contamination levels were observed based on season: rainy season yielded 14 (73.6%) whilst the dry season 5 (26.3%). The L. monocytogenes strains showed a high degree of homogeneity on phylogenetic analysis and clustered based on abattoir. Seasonality was identified as a major determinant influencing contamination based on the final logistic regression model.

CONCLUSION

This study found evidence of L. monocytogenes contamination on traditionally raised beef carcasses across various abattoirs surveyed. The failure to find Listeria contamination on the abattoir environment may to a greater extent intimate cattle carccases as primary sources of contamination. However, a more comprerehnsive study incorporating different geographical regions is needed to conclusively ascertain these present findings.

Lead identification using 3D models of pancreatic cancer

Recent technological advances have enabled 3D tissue culture models for fast and affordable HTS. We are no longer bound to 2D models for anti-cancer agent discovery, and it is clear that 3D tumor models provide more predictive data for translation of preclinical studies. In a previous study, we validated a microplate 3D spheroid-based technology for its compatibility with HTS automation. Small-scale screens using approved drugs have demonstrated that drug responses tend to differ between 2D and 3D cancer cell proliferation models. Here, we applied this 3D technology to the first ever large-scale screening effort completing HTS on over 150K molecules against primary pancreatic cancer cells. It is the first demonstration that a screening campaign of this magnitude using clinically relevant, ex-vivo 3D pancreatic tumor models established directly from biopsy, can be readily achieved in a fashion like traditional drug screen using 2D cell models. We identified four unique series of compounds with sub micromolar and even low nanomolar potency against a panel of patient derived pancreatic organoids. We also applied the 3D technology to test lead efficacy in autologous cancer associated fibroblasts and found a favorable profile for better efficacy in the cancer over wild type primary cells, an important milestone towards better leads. Importantly, the initial leads have been further validated in across multiple institutes with concordant outcomes. The work presented here represents the genesis of new small molecule leads found using 3D models of primary pancreas tumor cells.

Genotypic and phenotypic characterization of Escherichia coli isolated from indigenous individuals in Malaysia

Objectives

The occurrence of asymptomatic verocytotoxin (VT)-producing Escherichia coli (VTEC) infections among humans in recent years is posing a high risk to public health. Thus, the role of asymptomatic human carriers as a source of dissemination should not be underestimated. This study aimed to elucidate the phenotypic and genotypic characteristics of E. coli in the stool samples collected from indigenous individuals in Malaysia.

Materials and Methods

E. coli strains (n=108) were isolated from stool samples obtained from 41 indigenous individuals. All strains were subjected to Repetitive Extragenic Palindromic-Polymerase Chain Reaction (REP-PCR) typing and confirmation of VTEC variants. Non-duplicate strains were selected based on REP-PCR profiles and further subjected to antimicrobial susceptibility test (AST). The genotypic and phenotypic characteristics of the strains were then correlated with the demographic data of the subjects.

Results

A total of 66 REP-PCR profiles grouped in 53 clusters (F=85%) were obtained. Four genetically distinct strains were confirmed as VTEC (eaeA-positive). The predominant resistance was against ampicillin (34.2%), followed by trimethoprim-sulfamethoxazole (32.9%), ampicillin-sulbactam (5.5%), and ciprofloxacin (1.4%). All isolates were sensitive to amoxicillin-clavulanate, cefuroxime, ceftriaxone, imipenem, and meropenem.

Conclusion

Genetically diverse E. coli and VTEC strains were found to colonize the intestines of the indigenous populations. This study is important for the prospective surveillance of E. coli among the indigenous individuals in Malaysia, especially in asymptomatic VTEC infection and antimicrobial resistance phenomenon.

Morphological, transcriptomic and metabolomic analyses of Sophora davidii mutants for plant height

Sophora davidii is an important plant resource in the karst region of Southwest China, but S. davidii plant-height mutants are rarely reported. Therefore, we performed phenotypic, anatomic structural, transcriptomic and metabolomic analyses to study the mechanisms responsible for S. davidii plant-height mutants. Phenotypic and anatomical observations showed that compared to the wild type, the dwarf mutant displayed a significant decrease in plant height, while the tall mutant displayed a significant increase in plant height. The dwarf mutant cells were smaller and more densely arranged, while those of the wild type and the tall mutant were larger and loosely arranged. Transcriptomic analysis revealed that differentially expressed genes (DEGs) involved in cell wall biosynthesis, expansion, phytohormone biosynthesis, signal transduction pathways, flavonoid biosynthesis and phenylpropanoid biosynthesis were significantly enriched in the S. davidii plant-height mutants. Metabolomic analysis revealed 57 significantly differential metabolites screened from both the dwarf and tall mutants. A total of 8 significantly different flavonoid compounds were annotated to LIPID MAPS, and three metabolites (chlorogenic acid, kaempferol and scopoletin) were involved in phenylpropanoid biosynthesis and flavonoid biosynthesis. These results shed light on the molecular mechanisms of plant height in S. davidii mutants and provide insight for further molecular breeding programs.

Tuberculosis with discordant drug resistance patterns- A diagnostic dilemma

Programmatic management of drug-resistant tuberculosis (PMDT) guidelines in India specify the use of cartridge based nucleic acid amplification test (CBNAAT) and Line probe assay (LPA) for early diagnosis of drug-resistant Tuberculosis. However, discrepancy among these genotypic tests (CBNAAT and LPA) or with the phenotypic DST in real practice poses a clinical dilemma. The usual solutions are to rely on methods with short turnaround times like CBNAAT and LPA to start an initial regimen. The culture and DST results, that are typically available after at least a few weeks, are used to modify the regimen if required. This practice is based on the fact that culture and DST based sensitivity patterns are considered the gold standard for diagnosing and drug resistance. DNA sequencing by pyrosequencing, Sanger sequencing and next generation sequencing (NGS) are being evaluated; their future availability may help in early clarifications in discordant drug resistance patterns. Such tests are costly and have limited availability, however, in view of immense benefit to detect TB Drug-resistant phenotypes, national guidelines plan to scale up their use in national and well-performing intermediate TB reference laboratories.

Phenotypic and genetic parameters of productive traits in Rahmani and Romanov sheep and crossbreds

Data of 651 lambs (68 Romanov, 49 Rahmani, 151 [♀1/2 Rahmani X ♂1/2 Romanov) and 383 (♀3/4 Rahmani and 1/4♂ Romanov]) were collected from Mehalet Mousa Farm, belonging to Animal Production Research Institute from the period of 2009 to 2016 to estimate phenotypic and genetic parameters. The traits studied were birth weight (BW), body weight at four week (BW4), body weight at eight weeks (BW8) and body weight at twelve weeks (BW12) or weaning weight. Least squares analysis of variance shows significance of the effects of breed groups, gender of lambs, birth type; month of birth and year of birth on all traits studied. Rahmani lambs had heavier BW, BW4, BW8 and BW12 while Romanov lambs had the lowest ones. The first generation (♀1/2 Rhamani X ♂1/2 Romanov) had heavier body weights than Romanov and the second generation (♀3/4 Rahmani X ♂1/4 Roamnov). Gender of lambs had highly significant effect on body weights. Males were significantly (p < 0.01) heavier than females for all traits studied. Least square means of BW, BW4, BW8 and BW12 for single lambs were 2.69, 10.43, 13.53 and 16.10 kg, respectively. Least square means of BW, BW4, BW8 and BW12 for twin lambs were 2.50, 9.37, 12.5 and 15.16 kg, respectively, while least square means of BW, BW4, BW8 and BW12 for triple lambs were 2.09, 7.86, 10.83 and 13.67 kg, respectively. Estimates of direct heritability measured by single trait animal model were 0.14, 0.23, 0.25 and 0.26 for BW, BW4, BW8 and BW12, respectively, and the corresponding measured by multi trait animal model were 0.17, 0.24, 0.32 and 0.36 for the same traits, respectively. All genetic and phenotypic correlations among different traits studied are positive and significant.

Comparison of virulence-related determinants between the ST59-t437 and ST239-t030 genotypes of methicillin-resistant Staphylococcus aureus

Background

Methicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen for human infection. Hospital-acquired (HA) and community-acquired (CA) MRSA infections are serious clinical problems worldwide. In this study, we selected typical HA-MRSA strain and CA-MRSA isolates from our previous research and compared their phenotypic and pathogenic abilities both in vitro and in vivo.

Results

ST59-t437-SCCmecIVa (YNSA7) and ST59-t437-SCCmecVb (YNSA53) belonged to two prevalent subclones of CA-MRSA, while ST239-t030-SCCmecIII (YNSA163) was an HA-MRSA epidemic clone in Southwest China. ST59-t437 strains demonstrated faster growth ability, higher survival rate resistance to human blood, and more toxin secretion levels and cytotoxicity than ST239-t030. The virulence and regulatory genes of hld, psm-α, RNAIII, agrA, and crtN were highly expressed on CA-MRSA isolates, especially the ST59-t437-SCCmecIVa subclone. However, the ST239-t030 strain had the strongest adhesion and biofilm ability among these MRSA bacteria. Animal experiments revealed the most serious lethal effect on BALB/c mice caused by the YNSA7 strain infection. The survival rates of BALB/c mice infected with the three MRSA strains were 16.7, 50.0 and 100.0% for YNSA7, YNSA53 and YNSA163, respectively. Histopathological analyses of infected animals indicated that the lungs were the most seriously damaged organs, especially for ST59-t437 MRSA. Severe inflammatory reactions, tissue destruction, and massive exudation of inflammatory mediators and cells could be identified in ST59-t437 strain-infected animals.

Conclusions

In general, ST59-t437 strains showed higher pathogenic ability than the ST239-t030 isolate, while ST239-t030 MRSA revealed the features prevalent in hospital settings, specifically for adhesion and biofilm ability.

cruzi infection

The complexity and multifactorial characteristics of Chagas disease pathogenesis hampers the establishment of appropriate experimental/epidemiological sets, and therefore, still represents one of the most challenging fields for novel insights and discovery. In this context, we used a set of attributes including phenotypic, functional and serological markers of immune response as candidates to decode the genotype-specific immune response of experimental T. cruzi infection. In this investigation, we have characterized in C57BL/6 J mice, the early (parasitemia peak) and late (post-parasitemia peak) aspects of the immune response elicited by T. cruzi strains representative of TcI, TcII or TcVI. The results demonstrated earlier parasitemia peak for TcII/Y strain followed by TcVI/CL-Brener and TcI/Colombiana strains. A panoramic overview of phenotypic and functional features of the TCD4⁺, TCD8⁺ and B-cells from splenocytes demonstrated that mice infected with TcI/Colombiana strain exhibited at early stages of infection low levels of most cytokine⁺ cells with a slight increase at late stages of infection. Conversely, mice infected with TcII/Y strain presented an early massive increase of cytokine⁺ cells, which decreases at late stages. The TcVI/CL-Brener strain showed an intermediate profile at early stages of infection with a slight increase later on at post-peak of parasitemia. The panoramic analysis of immunological connectivity demonstrated that early after infection, the TcI/Colombiana strain trigger immunological network characterized by a small number of connectivity, selectively amongst cytokines that further shade towards the late stages of infection. In contrast, the TcII/Y strain elicited in more imbricate networks early after infection, comprising a robust number of interactions between pro-inflammatory mediators, regulatory cytokines and activation markers that also decrease at late infection. On the other hand, the infection with TcVI/CL-Brener strain demonstrated an intermediate profile with connectivity axes more stable at early and late stages of infection. The analysis of IgG2a reactivity to AMA, TRYPO and EPI antigens revealed that at early stages of infection, the genotype-specific reactivity to AMA, TRYPO and EPI to distinguish was higher for TcI/Colombiana as compared to TcII/Y and TcVI/CL while, at late stages of infection, higher reactivity to AMA was observed in mice infected with TcVI/CL and TcII/Y strains. The novel systems biology approaches and the use of a flow cytometry platform demonstrated that distinct T. cruzi genotypes influenced in the phenotypic and functional features of the host immune response and the genotype-specific serological reactivity during early and late stages of experimental T. cruzi infection.

Phenotypic and Genotypic Antibiotic Resistant diarrheagenic Escherichia coli pathotypes isolated from Children with Diarrhea in Nairobi City, Kenya

Background

The marked genome plasticity of diarrheagenic Escherichia coli promotes emergence of pathotypes displaying unique phenotypic and genotypic resistance. This study examined phenotypic and genotypic antibiotic resistant diarrheagenic Escherichia coli pathotypes among children in Nairobi City, Kenya.

Methods

In a cross-sectional study, diarrheagenic Escherichia coli pathotypes were isolated from stool samples and their phenotypic and genotypic resistance against eight antimicrobial agents assayed.

Results

Diarrheagenic Escherichia coli was detected in 136(36.4%) children. Most of diarrheagenic Escherichia coli that were resistant to ampicillin, ceftriaxone, streptomycin, gentamycin, ciprofloxacin, chloramphenicol, erythromycin and tetracycline, harbored citm, bla CMY, aadA1, aac(3)-IV, qnr, catA, ere(A) and tet(A) corresponding resistant genes.

Conclusion

Antimicrobial-resistant genes are highly prevalent among phenotypic resistant ETEC pathotypes indicating a possibility of horizontal gene transfer in spreading antibiotic resistant genes among E. coli pathotypes.

Phenotypic and Genotypic Characterization of von Willebrand Factor Gene (Exon 18 and 20) in Saudi Healthy Individuals

Introduction:

Von Willebrand disease (VWD) is an autosomal congenital bleeding syndrome that was described as being the most widespread genetic condition among men. In Saudi Arabia, the genotyping of the VWF gene is necessary to establish a diagnosis procedure for VWD.

Aim:

The current research, however, attempted to evaluate the phenotypic-genotypic association of the Von Willebrand factor (exon 18 and 20) gene in healthy subjects to establish effective molecular diagnostic strategies.

Methods:

This was a cross-sectional retrospective included 100 healthy people who have been chosen from King Fahad University Hospital. Whole blood samples were collected from all individuals, as well as the laboratory analysis was done using automatic analyzers for; platelet count, ABO blood group and coagulation parameters. DNA Sanger sequencing has been used to sequestrate the full exons 18 and 20.

Results:

In exon 18 of healthy people, three unusual sequence variations (1 missense and 2 synonymous; rs775479826, rs1286572448 and rs369828268) compared to other recorded VWF variations (3 missense and 1 synonymous; c.2365A > G, c.2385T > C, c.2344C > T and c.2340C > G). But in exon 20 only 1 synonymous novel (rs113240752) 1 registered VWF variations in missense (c.2555G > A) were identified.

Conclusion:

The present variants found on those participates could be a realistic approach to detect mutation in the VWF gene to illustrating the relationship of phenotypic and genetic abnormalities variables may lead to determining the functional effect in mutations specific to the Saudi people that can be used to develop a diagnostic tool for VWD in KSA.

Revisiting HBV resistance to entecavir with a phenotypic approach

Treatment adaptation after hepatitis B virus (HBV) treatment failure relies on genotypic resistance testing. However, the results of such tests are not always consistent with treatment response. These discrepancies may be due to differences in resistance levels between isolates with the same genotypic resistance testing profiles. We explored this hypothesis by investigating six cases of entecavir treatment failure with an integrative strategy combining genotypic and phenotypic resistance testing, medical record review and therapeutic drug monitoring. Among isolates with genotypic reduced susceptibility to entecavir, one displayed a higher level of resistance to entecavir (mean fold change in entecavir IC₅₀ of 1 508 ± 531 vs. 318 ± 53, p = 0.008). This isolate harbored a substitution (rt250L) at a position reported to be associated with resistance (rt250V). Reversion to wild-type amino acid at this position partially restored susceptibility to entecavir, confirming that the rt250L mutation was responsible for the high level of resistance to entecavir. This is the first description of entecavir treatment failure associated with selection of the rt250L mutation without other entecavir resistance mutations. One isolate with genotypic resistance to entecavir, harboring the rt173L mutation, displayed a lower level of resistance than the other, harboring the rt202G mutation (mean fold change of 323 ± 124 vs. 6 036 ± 2 100, p = 0.20). These results suggest that isolates harboring the rt250L mutations should be considered resistant to entecavir, whereas isolates harboring the rt173L mutations should be considered to display reduced susceptibility to entecavir. An integrative approach to antiviral drug resistance in HBV would provide a more accurate assessment of entecavir treatment failures and help to improve the accuracy of genotypic testing algorithms.

Alternative therapy to manage otitis media caused by multidrug-resistant fungi

During the last few decades, the increase in the incidence of multidrug-resistant (MDR) fungal infections has become an emerging threat to public health. Therefore, it is important to illuminate the usage of alternative therapy to treat MDR fungal infection. This study was carried out to elucidate the usage of plant extract and essential oil, either alone or with other antifungal drugs to treat otitis media caused by MDR fungi. Medicinal plant is a safe and cheap source when compared with chemical antifungal drugs. Twenty-one fungal isolates out of 104 ear swabs from patients suffering from otitis media were characterized using both phenotypic and genotypic methods. The antibiogram typing was used to determine the MDR isolates. The sensitivity of MDR fungal isolates was tested against several plant extracts and essential oils, either alone or with other antifungal drugs. Thyme oil and clove extracts proved to have synergistic effects suggesting their use in the treatment of fungal infections, especially otitis media caused by MDR fungi. The ultrastructure of MDR fungal isolates exhibited a complete destruction post exposure to the used materials when observed under the transmission microscope (TEM). Thyme oil and clove extract were found to be the most effective agents against MDR fungal isolates and they constitute a promising tool for the management of fungal infection causing the otitis media.

Multifunctional compounds lithium chloride and methylene Blue attenuate the negative effects of diisopropylfluorophosphate on axonal transport in rat cortical neurons

Organophosphates (OPs) are valuable as pesticides in agriculture and for controlling deadly vector-borne illnesses; however, they are highly toxic and associated with many deleterious health effects in humans including long-term neurological impairments. Antidotal treatment regimens are available to combat the symptoms of acute OP toxicity, which result from the irreversible inhibition of acetylcholinesterase (AChE). However, there are no established treatments for the long-term neurological consequences of OP exposure. In addition to AChE, OPs can negatively affect multiple protein targets as well as biological processes such as axonal transport. Given the fundamental nature of axonal transport to neuronal health, we rationalized that this process might serve as a general focus area for novel therapeutic strategies against OP toxicity. In the studies described here, we employed a multi-target, phenotypic screening, and drug repurposing strategy for the evaluations of potential novel OP-treatments using a primary neuronal culture model and time-lapse live imaging microscopy. Two multi-target compounds, lithium chloride (LiCl) and methylene blue (MB), which are FDA-approved for other indications, were evaluated for their ability to prevent the negative effects of the OP, diisopropylfluorophosphate (DFP) on axonal transport. The results indicated that both LiCl and MB prevented DFP-induced impairments in anterograde and retrograde axonal transport velocities in a concentration dependent manner. While in vivo studies will be required to confirm our in vitro findings, these experiments support the potential of LiCl and MB as repurposed drugs for the treatment of the long-term neurological deficits associated with OP exposure (currently an unmet medical need).

Theileria annulata transformation altered cell surface molecules expression and endocytic function of monocyte-derived dendritic cells

Theileria annulata is a protozoan parasite transmitted by ticks to cattle. The most important processes of T. annulata are the infection and transformation of host monocytes, which promote cell division and generate a neoplastic phenotype. Dendritic cells play an important role in the development of adaptive immune responses against parasites and are traditionally classified into four types. One type of dendritic cell derived from afferent lymph was successfully transformed by T. annulata in vitro in a previous report. However, whether the monocyte-derived dendritic cells could be transformed and how the endocytic function is affected by T. annulata infection were not yet known. Bovine dendritic cells (DCs) derived from blood CD14⁺ monocytes were cocultured with T. annulata sporozoites in vitro. On day 15 post infection, rounded and continuously proliferating cells were observed. The effect of this transformation on cell phenotype was studied using immunostaining and flow cytometry. After transformation, the cells maintained the expression of the DC-specific marker CD11c, but it was downregulated as were the expression of CD11b, CD14 and CD86. In contrast, CD205, CD45 and MHC class Ⅱ molecules were upregulated in transformed cells. The levels of CD172a, CD21, CD40 and CD80 expression were very low in the transformed cells (<1 %). However, the transformed cells maintained high expression levels of MHC Ⅰ (>99 %). In addition, the normal and transformed DCs were cocultured with OVA-FITC antigen to compare the differences of the endocytic functions between these two types of cells. The results revealed that the endocytic functions of MoDCs were significantly inhibited after transformation by T. annulata.

Molecular Identification, Genotyping, Phenotyping, and Antifungal Susceptibilities of Medically Important Trichosporon, Apiotrichum, and Cutaneotrichosporon Species

Recently, Trichosporon taxonomy has been reevaluated and new genera of the Trichosporonaceae family have been described. Here, 26 clinical isolates were submitted for identification via sequencing of the intergenic space 1 (IGS1) region, genotyping, and investigation of virulence factors. Antifungal susceptibility was determined using the CLSI broth microdilution method for fluconazole (FLC), itraconazole (ITC), and amphotericin B (AMB). Of these, 24 isolates were identified, including 12 T. asahii, 4 T. inkin, 3 T. faecale, 1 T. coremiiforme, 1 T. japonicum, 2 Cutaneotrichosporon dermatis (formerly T. dermatis), and 1 Apiotrichum mycotoxinivorans (formerly T. mycotoxinivorans). Species-level identification of 2 isolates was not successful; they were described as Trichosporon sp. We observed optimal colonial development at 35-40 °C. Lipase was the major extracellular enzyme produced (100%); caseinase was not produced (0%). Biofilms were produced by all isolates (classified as low). High AMB minimum inhibitory concentration (MIC) was observed, with all strains resistant. Fluconazole was the most active drug among the antifungals tested. However, high MICs for FLC were observed in C. dermatis and A. mycotoxinivorans species, which also showed resistance to ITC and AMB. This study, conducted in the Northern region of Brazil, identified 5 Trichosporon species along with C. dermatis and A. mycotoxinivorans and demonstrated their pathogenic potential through their ability to produce important virulence factors. This may contribute to our understanding of the epidemiology and factors related to the pathogeneses of species in the Trichosporonaceae family.

Rapid Susceptibility Testing Methods

With emerging antimicrobial resistance, rapid antimicrobial susceptibility testing (AST) is needed to provide early definitive therapeutic guidance to optimize patient outcome. Genotypic methods are fast, but can identify only a subset of known resistance elements. Phenotypic methods determine clinically predictive minimal inhibitory concentrations and include very sensitive optical and biophysical methods to detect changes in replication or physiology of pathogens in response to antibiotics. For the potential of rapid AST to be fully realized, results must be linked with robust decision support solutions that will implement therapeutic changes in real time.

Phenotypic and genotypic characteristics of Brucella isolates from the Republic of Kazakhstan

The purposes of this study were to determine phenotypic and genotypic characteristics of Brucella isolates from the Republic of Kazakhstan and to determine their biotype. The focus was laid on culture-morphological, biochemical, and biological properties of 59 Brucella isolates from primary cultures. Material was isolated from blood and tissue of serum-positive killed, dead diseased, or aborted domestic cattle from different regions of Kazakhstan where brucellosis is a common problem. Multiple-locus variable number tandem repeat analysis (MLVA) of all strains, isolated in different regions, has shown that Brucella isolates from the epizootic form two clusters. Based on the comparison with strains available in the MLVA database, B. abortus 0015/B is alike the B. abortus strains isolated from Italy and Portugal. B. melitensis 0016/B isolated from the Almaty region fits the third cluster and is alike the B. melitensis strains isolated from humans in Turkey, China, and Portugal. More than 90% of the overall B. abortus samples were isolated from the northern regions of the East and West Kazakhstan, while B. melitensis strains were registered in the southeast Kazakhstan. The most frequently recorded B. abortus biovar is biovar 3. The most frequently recorded B. melitensis biovars are biovars 1 and 3. SIGNIFICANCE AND IMPACT OF STUDY: These results contribute to a better understanding of the geographic pattern of Brucella infection in Kazakh cattle also important for developing the specific control measures. The results of current research can be used for creating a gene bank of Brucella strains circulating in Kazakhstan for producing diagnostic and therapeutic agents. The research material will be used to solve the problems of genetic characterization of Brucella species and to establish the phylogenetic relationships of strains.

Phenotypic and genotypic characterization of antibiotic-resistant in Escherichia coli isolates from patients with diarrhea

BACKGROUND AND OBJECTIVES

Escherichia coli is a common enteric pathogen of human and livevestock. Antibiotic resistance is the main concern of public health. The aim of this study was to detect this bacterium in stool samples of diarrheal patients and identify the phenotypic and genotypic characterizations of antibiotic-resistant isolates such as dfrA1, sul1, citm, tetA, qnr, aac(3)-IV in Shahrekord.

MATERIALS AND METHODS

Two hundred fifty diarrheal stool samples from patients were collected. Microbiological and biochemical examinations were done to detect E. coli. Phenotypic and genotypic antibiotic resistance of the isolates were determined using dick diffusion method and polymerase chain reaction (PCR), respectively.

RESULTS

Among 114 E. coli isolates, the least resistance was for gentamicin (0%) and the most resistance was for trimethoprim (79.8%). The resistance to sulfamethoxazole, ciprofloxacin, ampicillin, and tetracycline were 71.05%, 10.5%, 52.63%, and 3.5% respectively. The results of PCR assay revealed that 10 isolates contain sul1, 49 isolates harbor citm, 8 isolates tetA, 36 isolates dfrA1, 11 isolates qnr genes but there was no isolate with aac(3)-IV gene. In comparison between phenotypic and genotypic of the isolates revealed that citm, tetA, dfrA1, qnr, sul1, aac(3)-IV genes covered 42.98%, 7.01%, 31.57%, 9.64%, 8.7%, 0% of the antibiotic resistance, respectively.

CONCLUSION

Our results revealed that all isolates harbor one or more antibiotic resistance genes and that the PCR is a fast practical and appropriate method to determine the presence of antibiotic resistance genes.

Phenotypic and Molecular Survey of Metallo-beta-lactamase-producing Pseudomonas aeruginosa Isolated from Patients with Nosocomial and Non- Nosocomial Infections

BACKGROUND

Resistance to antimicrobial agents in Pseudomonas aeruginosa (P. aeruginosa) including carbapenems is a prominent problem in patients. The aim of this study is surveying Metallo-beta-lactamase (MBL)-producing P. aeruginosa isolated from patient specimens with nosocomial and non-nosocomial infections in Kurdistan province, Iran.

METHODS

In total, 146 Pseudomonas spp. were collected (December 2015 to August 2017). P. aeruginosa isolates were detected by phenotypic and polymerase chain reactions (PCR) of gyrB gene. Combination disk (CD) phenotypic test was used for the identification of MBL-producing strains and PCR was applied for identification of blaIMP and blaVIM genes in P. aeruginosa. Sensitivity and specificity of phenotypic tests were calculated as well. Fisher's exact test and logistic regression were used for data analysis (p≤0.05).

RESULTS

A total of 134 (91.78%) and 133 (91.09%) P. aeruginosa were detected using PCR and the phenotypic test, respectively. Fifty-six (41.79%) clinical isolates were isolated from patients with nosocomial infection. CD test proved that 67 out of 134 (50%) P. aeruginosa isolates were positive for MBL, of which 11 (8.20%) carried blaIMP gene. No significant relationship was found between MBL-producing P. aeruginosa and blaIMP genes; as well as between MBL-producing P. aeruginosa and blaIMP genes with age, sex, city of residence, inpatient/outpatient and specimen's type (p≥0.05).

CONCLUSION

Presence of MBL-producing P. aeruginosa strains and blaIMP genes were proved in this study; thus more precaution should be taken in the administration of carbapenem antibiotics to patients.

A phenotypic approach to the discovery of compounds that promote non-amyloidogenic processing of the amyloid precursor protein: Toward a new profile of indirect β-secretase inhibitors

Dysregulation of the Amyloid Precursor Protein (APP) processing leading to toxic species of amyloid β peptides (Aβ) is central to Alzheimer's disease (AD) etiology. Aβ peptides are produced by sequential cleavage of APP by β-secretase (BACE-1) and γ-secretase. Lysosomotropic agent, chloroquine (CQ), has been reported to inhibit Aβ peptide production. However, this effect is accompanied by an inhibition of lysosome-mediated degradation pathways. Following on from the promising activity of two series of APP metabolism modulators derived from CQ, we sought to develop new series of compounds that would retain the inhibitory effects on Aβ production without altering lysosome functions. Herein, we applied a ligand-based pharmacophore modeling approach coupled with de novo design that led to the discovery of a series of biaryl compounds. Structure-activity relationship studies revealed that minor modifications like replacing a piperidine moiety of compound 30 by a cyclohexyl (compound 31) allowed for the identification of compounds with the desired profile. Further studies have demonstrated that compounds 30 and 31 act through an indirect mechanism to inhibit β-secretase activity. This work shows that it is possible to dissociate the inhibitory effect on Aβ peptide secretion of CQ-derived compounds from the lysosome-mediated degradation effect, providing a new profile of indirect β-secretase inhibitors.

Intermediate Levels of Antibiotics May Increase Diversity of Colony Size Phenotype in Bacteria

Antibiotics select for resistant bacteria whose existence and emergence is more likely in populations with high phenotypic and genetic diversity. Identifying the mechanisms that generate this diversity can thus have clinical consequences for drug-resistant pathogens. We show here that intermediate levels of antibiotics are associated with higher levels of phenotypic diversity in size of colony forming units (cfus), within a single bacterial population. We examine experimentally thousands of populations of bacteria subjected to different disturbance levels that are created by varying antibiotic concentrations. Based on colony sizes, we find that intermediate levels of antibiotics always result in the highest phenotypic variation of this trait. This result is supported across bacterial densities and in the presence of three different antibiotics with two different mechanisms of action. Our results suggest intermediate levels of a stressor (as opposed to very low or very high levels) could affect the phenotypic diversity of a population, at least with regards to the single trait measured here. While this study is limited to a single phenotypic trait within a single species, the results suggest examining phenotypic and genetic variation created by disturbances and stressors could be a promising way to understand and limit variation in pathogens.

CNS repurposing - Potential new uses for old drugs: Examples of screens for Alzheimer's disease, Parkinson's disease and spasticity

Drug repurposing is recently gaining increasing attention, not just from pharmaceutical companies but also from government agencies in an attempt to generate new medications to address increasing unmet medical needs in a cost effective and expedite manner. There are several approaches to identify novel indications for known drugs. Many are based on rational selection e.g. the known or a new mechanism of action of a drug. This review will focus rather on phenotypic or high content screening of compounds in models that are believed to be predictive of effectiveness of compounds irrespective of their mechanism of action. Three short cases studies of screens for Alzheimer's disease, Parkinson's disease and spasticity will be given as examples. This article is part of the Special Issue entitled 'Drug Repurposing: old molecules, new ways to fast track drug discovery and development for CNS disorders'.

The 2017 IUIS Phenotypic Classification for Primary Immunodeficiencies

Since the 1990s, the International Union of Immunological Societies (IUIS) PID expert committee (EC), now called Inborn Errors of Immunity Committee, has published every other year a classification of the inborn errors of immunity. This complete catalog serves as a reference for immunologists and researchers worldwide. However, it was unadapted for clinicians at the bedside. For those, the IUIS PID EC is now publishing a phenotypical classification since 2013, which proved to be more user-friendly. There are now 320 single-gene inborn errors of immunity underlying phenotypes as diverse as infection, malignancy, allergy, auto-immunity, and auto-inflammation. We herein propose the revised 2017 phenotypic classification, based on the accompanying 2017 IUIS Inborn Errors of Immunity Committee classification.

Etiologic classification of ischemic stroke: Where do we stand?

Despite major technological advances in ischemic stroke diagnostic techniques, our current understanding of stroke mechanisms and etiology continues to remain unclear in a significant percent of patients. As a result, several etiological ischemic stroke classifications have emerged during the last two decades but their reliability and validity is far from perfect and further world-wide research is needed in order to achieve the so much needed "standard reference language". An ideal ischemic stroke classification should both comprise all underlying pathologies that could potentially concur to an index event and emphasize the most likely etiological and pathophysiological mechanism. Currently available approaches to ischemic stroke classification are either phenotypic or causative in nature, a multitude of criteria being published by different authors. Phenotypic classifications are targeted towards describing the concurring underlying pathologies, without highlighting the most probable ischemic stroke etiology, while causative classifications focus on establishing the most likely cause, neglecting other associated diseases. A judicious use of this two different concepts might improve clinical research as well as daily clinical practice.

Differentiation and description of aromatic short grain rice landraces of eastern Indian state of Odisha based on qualitative phenotypic descriptors

Background

Speciality rice, in general, and aromatic rice in particular, possess enormous market potential for enhancing farm profits. However, systematic characterization of the diversity present in this natural wealth is a major pre requisite for using it in the breeding programs. This study reports qualitative phenotypic trait based characterization of 126 short grain aromatic rice genotypes, collected from different areas of the state of Odisha, India.

Results

Out of the 24 descriptors employed, highest variability (8 different types) was observed for lemma-palea colour with a genetic diversity index (He) of 0.696. The principal component analysis reveals that the tip colour of lemma, colour of awn and colour of stigma, cumulatively explain 74 % of the total variation. The Population STRUCTURE analysis classified the population into two subpopulations which were subdivided further into four distinct groups. The western and southern districts of Odisha are endowed with maximum diversity in comparison to eastern and northern districts and at district level comparisons, Koraput and Puri districts are rich with a genetic diversity values of 0.324 and 0.303 respectively. With this set of morphological qualitative traits, based on ‘phenoprinting’, a newly proposed bar coding system, unique fingerprints of each genotype can be effectively generated that can help in easy identification of these genotypes.

Conclusion

Though aromatic rices represent a tiny fraction of the total rice germplasm, a small collection of 126 land races did exhibit rich diversity for all the qualitative traits. For lemma-palea colour, eight different types were detected while for tip colour of lemma, six different types were recorded, suggesting the presence of rich variability in short grain aromatic rices that are conserved in this region. The proposed ‘phenoprinting’ can be an effective descriptor with the unique finger prints generated for each genotype and coupled with molecular (DNA) finger printing, we can discriminate and identify each and every aromatic short grain rice genotype. The proposed system not only help in conservation but also can confer IPR protection to these specialty rices.

Electronic supplementary material

The online version of this article (doi:10.1186/s12898-016-0086-8) contains supplementary material, which is available to authorized users.

Comparison of phenotypic and PCR methods for detection of carbapenemases production by Enterobacteriaceae

Dissemination of carbapenem resistance via Enterobacteriaceae, particularly among Klebsiella pneumoniae and Escherichia coli, is a major public health concern. Rapid methods for determining antimicrobial susceptibility are important to ensure adequate and appropriate use of antimicrobial agents and to limit the spread of these bacteria. In the current study, we compared the rapidity, sensitivity and specificity of traditional methods and molecular-based Xpert Carba-R PCR assay to identify sixty isolates, (26 E. coli and 34 K. pneumoniae). The specificity of MicroScan was 100% while sensitivity to ertapenem (ERT), imipenem (IMI), and meropenem (MER) was 93%, 68.9%, and 55.17%, respectively. For the modified Hodge test, the specificity was 96.77% and sensitivity was 89.65%. Although some results of phenotypic assays matched with the definite PCR identification, some results were misleading. Out of the 29 positive PCR samples, three samples of K. pneumoniae were negative for the MHT and one E. coli sample was MHT positive but negative for the PCR. Nine samples were positive for the PCR but were determined as carbapenem sensitive by MicroScan. While MicroScan and MHT requires several hours and multi-steps to obtain results, Xpert Carba-R PCR assay takes less than an hour. Therefore, we recommend using Gene xpert Carba-R assay for the optimal carbapenemnase detection with reducing material, manpower and cost. Also it is important to know the type of carbapenemase is present.

Tumour heterogeneity: principles and practical consequences

Two major reasons compel us to study tumour heterogeneity: firstly, it represents the basis of acquired therapy resistance, and secondly, it may be one of the major sources of the low level of reproducibility in clinical cancer research. The present review focuses on the heterogeneity of neoplastic disease, both within the primary tumour and between primary tumour and metastases. We discuss different levels of heterogeneity and the current understanding of the phenomenon, as well as imminent developments relevant for clinical research and diagnostic pathology. It is necessary to develop new tools to study heterogeneity and new biomarkers for heterogeneity. Established and new in situ methods will be very useful. In future studies, not only clonal heterogeneity needs to be addressed but also non-clonal phenotypic heterogeneity which might be important for therapy resistance. We also review heterogeneity established in major tumour types, in order to explore potential similarities that might help to define new strategies for targeted therapy.

Genetic polymorphisms analysis of CYP2D6 in the Uygur population

BACKGROUND

This study aimed to investigate genetic polymorphisms of CYP2D6 among healthy Uygur individuals. Genetic polymorphisms of CYP2D6 could greatly affect CYP2D6 activity and lead to differences among individuals in drug efficacy or side effects. To investigate genetic polymorphisms of CYP2D6 in the Uygur population, we directly sequenced the whole gene in 96 unrelated, healthy Uygur volunteers from the Xinjiang Uygur Autonomous Region and screened for genetic variants in the promoter, intron, exons, and 3'UTR.

RESULTS

We detected 62 genetic polymorphisms of CYP2D6, 16 of which were novel SNP with three novel non-synonymous mutations detected for the first time. The allelic frequencies of CYP2D6*1, *10, *39, and *48 were 0.542, 0.156, 0.068, 0.229, and 0.073, respectively. The frequency of CYP2D6*1/*10 which decreased CYP2D6 enzyme activity was 31.3 %.

CONCLUSIONS

Our results provided basic information about CYP2D6 polymorphisms, suggested that the enzymatic activities of CYP2D6 might be different within the Uygur ethnic group, and provide a basis for safer drug administration and better therapeutic treatment of Uygur individuals.

High-Throughput Cell Toxicity Assays

Understanding compound-driven cell toxicity is vitally important for all drug discovery approaches. With high-throughput screening (HTS) being the key strategy to find hit and lead compounds for drug discovery projects in the pharmaceutical industry [1], an understanding of the cell toxicity profile of hit molecules from HTS activities is fundamentally important. Recently, there has been a resurgence of interest in phenotypic drug discovery and these cell-based assays are now being run in HTS labs on ever increasing numbers of compounds. As the use of cell assays increases the ability to measure toxicity of compounds on a large scale becomes increasingly important to ensure that false hits are not progressed and that compounds do not carry forward a toxic liability that may cause them to fail at later stages of a project. Here we describe methods employed in the AstraZeneca HTS laboratory to carry out very large scale cell toxicity screening.

Design and Implementation of High-Throughput Screening Assays

HTS remains at the core of the drug discovery process, and so it is critical to design and implement HTS assays in a comprehensive fashion involving scientists from the disciplines of biology, chemistry, engineering, and informatics. This requires careful consideration of many options and variables, starting with the choice of screening strategy and ending with the discovery of lead compounds. At every step in this process, there are decisions to be made that can greatly impact the outcome of the HTS effort, to the point of making it a success or a failure. Although specific guidelines should be established to ensure that the screening assay reaches an acceptable level of quality, many choices require pragmatism and the ability to compromise opposing forces.

Tracing of false negative results in phenotypic methods for identification of carbapenemase by Real-time PCR

BACKGROUND

Carbapenemase production causes multi antibiotics resistant in Gram-negative bacteria. A simple rapid and accurate phenotypic test for detection of Gram-negative carbapenemase-producing bacteria is useful for the treatment of infections. The aim of this study was to track the negative results in carbapenemase phenotypic test by Real-time PCR.

MATERIALS AND METHODS

In this study, 161 imipenem resistant Gram-negative bacteria were surveyed. Modified Hodge Test (MHT), boronic acid (BA), EDTA and dipicolinic acid were used for detection of Klebsiella pneumoniae carbapenemase (KPC) and metallo-beta-lactamase (MBLs). Different phenotypic methods and PCR confirmation followed by Real-time PCR for determination of phenotypic false-negative results were used.

RESULTS

Our results indicated that 85, 51 and 112 strains were MHT, BA and dipicolinic acid positive, respectively. No synergistic effect was observed between imipenem and EDTA. Sixty-nine strains were confirmed as carbapenemase-producers according to the results of molecular tests. All of the isolates carried the gene and expressed carbapenemase.

CONCLUSION

Comparison between the results of phenotypic and genotypic methods showed that the phenotypic methods could be used as the primary screening and the PCR remains as the gold standard for detection of carbapenemase positive strains.

Morphological and genetic diversity assessment of sesame (Sesamum indicum L.) accessions differing in origin

Sesame is an important ancient oilseed crop of high medicinal value. In the present study, 37 characters including both quantitative and qualitative traits of sixty genotypes were characterized following IPGRI morphological descriptors for sesame. Multivariate analysis was computed to distinguish the varieties into different groups. Though thirty six microsatellite markers including genomic and Est-SSR markers were initially selected, but, finally, the accessions were genotyped by eight polymorphic primers. Altogether, 27 alleles were detected among the 60 genotypes, with an average of 3.37 alleles per locus. The number of alleles ranged from 2 to 6 alleles. From data of microsatellite markers, dissimilarity coefficients between varieties were computed following Jaccard's coefficient method. Principal co-ordinate analysis was used to represent the varieties in bi-directional space. Dendrogram was constructed using NJ method based on dissimilarity matrix. Cluster analysis based on morphological and molecular marker classified sesame genotypes into two major groups. Mantel test showed an insignificant correlation between phenotypic and molecular marker information. The genotypes belonging to the same geographical area did not always occupy the same cluster. The results confirmed that both genetic and phenotypic diversity in a combined way could efficiently evaluate the variation present in different sesame accessions in any breeding program.

Phenotypic and Molecular Characterization of Extended-Spectrum β-Lactamase Produced by Escherichia coli, and Klebsiella pneumoniae Isolates in an Educational Hospital

Background:

Extended-spectrum beta-lactamases (ESBLs) are a group of enzymes that hydrolyze antibiotics, including those containing new cephalosporins, and they are found in a significant percentage of Escherichia coli and Klebsiellapneumoniae strains. With the widespread use of antibiotics, difficulties with infection therapy caused by drug resistant organisms, especially those that have acquired resistance to beta-lactams, such as broad-spectrum cephalosporins, have amplified the above-mentioned organisms.

Objectives:

This study was conducted to characterize ESBLs among E. coli and K. pneumonia isolates by molecular and phenotypic methods.

Materials and Methods:

Different strains of E. coli and K. pneumonia were collected from patients with urinary tract infections. The ESBL phenotype was determined by a double disk diffusion test (DDDT). In addition, polymerase chain reaction (PCR) analysis specific for β-lactamase genes of the TEM and SHV family was carried out. The PCR products were run on agarose and examined for DNA bands.

Results:

A total of 245 E. coli and 55 K. pneumonia strains were isolated from different samples. In total, 128 of the 300 isolates were confirmed as potential ESBLs producers as follows: 107 (43.67%) E. coli and 21 (38.18%) K. pneumonia. ESBLs genes were found in 24 isolates (18.75%): 21 E. coli and 3 K. pneumonia isolates. The TEM gene was present in 13 (12.14%) E. coli strains, but it was not detected in K. pneumonia. In addition, the SHV gene was present in 8 (7.47%) E. coli and 3 (14.28%) K. pneumonia isolates. Five (4.67%) of the E. coli isolates harbored both TEM and SHV genes. All isolates (100%) were susceptible to imipenem. The lowest rates of resistance to other antibiotics were observed for; piperacillin-tazobactam (6.25%), amikacin (12.5%) and gentamicin (14.84%). The rates of resistance to other antibiotics were as follow: nitrofurantoin (16.4%), nalidixic acid (23.43), co-trimoxazole (25%), cefepime (32%), ciprofloxacin (55.46%), ampicillin (69.53%), ceftazidime (100%), and cefotaxime (100%).

Conclusions:

The results of this study indicate the widespread prevalence of ESBLs and multiple antibiotic resistance in E. coli and K. pneumoniae. Therefore, beta-lactam antibiotics and beta-lactamase inhibitors or carbapenems should be prescribed based on an antibacterial susceptibility test.

Gender differences in obsessive-compulsive disorder: findings from a large Indian sample

AIM

Gender has been considered as one of the possible factors mediating phenotypic expression of obsessive-compulsive disorder (OCD). We examined gender differences in a large sample of subjects with OCD from India with respect to socio-demographic parameters, symptom characteristics, and comorbidity patterns.

METHODS

Consecutive patients (n=545) who consulted a specialty OCD clinic over 5 years at a large psychiatric hospital in India were evaluated.

RESULTS

Men (n=332) compared to women (n=213) with OCD had an earlier onset (p<0.001), higher frequency of sexual (p<0.001) and religious obsessions (p=0.001) pathological doubts (p<0.001) and checking (p<0.001) and repeating compulsions (p<0.001), and a greater tendency to have comorbid social phobia (p=0.006). Women compared to men were more likely to be married, had a higher frequency of fear of contamination (p=0.017), comorbid depression (p=0.014) and greater suicidal risk (p=0.003).

CONCLUSIONS

Our study provides further evidence for gender related differences in clinical features of obsessive-compulsive disorder. Our findings are only partly comparable with results from studies across the world possibly due to various biological and cultural factors mediating the phenotypic expression of OCD across the genders. There is a need to examine the biological basis for these gender differences.

Comparison of different phenotypic and genotypic methods for the detection of methicillin-resistant Staphylococcus aureus

Background:

Staphylococcus aureus is known as a powerful pathogen that causes various infections. Emergence of methicillin-resistant S. aureus (MSRA) is responsible for nosocomial and community-acquired infections worldwide.

Aims:

The present study aimed to evaluate the performance and ability of eight different phenotypic and genotypic methods for the detection of MSRA.

Materials and Methods:

A total of 186 S. aureus isolates were defined as methicillin-susceptible S. aureus (MSSA; 95) and MSRA (91) using polymerase chain reaction (PCR) as the gold standard. Susceptibility to methicillin was investigated using oxacillin, methicillin, cefotetan, cefoxitin, and cefmetazole disks, by oxacillin Adata Tab and strips. For all S. aureus isolates minimal inhibitory concentrations of oxacillin were determined using the broth microdilution method according to Clinical and Laboratory Standards Institute guidelines.

Results:

Among the diagnostic methods studied, broth microdilution and the cefoxitin disk had the highest specificity (98.9 and 94.7%), sensitivity (100 and 98.9%), and concordance with PCR results (98.9 and 93.6%). The cefotetan and cefmetazole disks had the lowest concordance with PCR results.

Conclusion:

Our results suggest that microdilution and cefoxitin disk methods have high sensitivities compared with other methods for detection of MSRA. The cefoxitin disk method may be preferred in clinical laboratories because it is easy to perform and does not require special equipment.