Detection and Molecular Characterization of Grapevine Virus A in Jordan

In a study on grapevines in Jordan conducted between 2002 and 2003, grapevine virus A (GVA) was detected in all areas where grapevines were planted. DAS-ELISA analysis of samples from symptomatic trees found that 16.1% of samples were infected with GVA. Using a GVA- specific primer pair (H587/C995), a portion of the coat protein gene of the virus was amplified by IC-RT-PCR and RT-PCR, using leaf extracts and RNA extracted from infected grapevines respectively. After cloning and sequencing the coat protein gene of the Jordanian isolate of GVA (GVA-Jo), the sequence of the amplified product was compared with sequences of other GVA isolates from different countries

A permeability-increasing drug synergizes with bacterial efux pump inhibitors and restores susceptibility to antibiotics in multi-drug resistant Pseudomonas aeruginosa strains

Resistance to antibiotics poses a major global threat according to the World Health Organization. Restoring the activity of existing drugs is an attractive alternative to address this challenge. One of the most efficient mechanisms of bacterial resistance involves the expression of efflux pump systems capable of expelling antibiotics from the cell. Although there are efflux pump inhibitors (EPIs) available, these molecules are toxic for humans. We hypothesized that permeability-increasing antimicrobial peptides (AMPs) could lower the amount of EPI necessary to sensitize bacteria to antibiotics that are efflux substrates. To test this hypothesis, we measured the ability of polymyxin B nonapeptide (PMBN), to synergize with antibiotics in the presence of EPIs. Assays were performed using planktonic and biofilm-forming cells of Pseudomonas aeruginosa strains overexpressing the MexAB-OprM efflux system. Synergy between PMBN and EPIs boosted azithromycin activity by a factor of 2,133 and sensitized P. aeruginosa to all tested antibiotics. This reduced several orders of magnitude the amount of inhibitor needed for antibiotic sensitization. The selected antibiotic-EPI-PMBN combination caused a 10 million-fold reduction in the viability of biofilm forming cells. We proved that AMPs can synergize with EPIs and that this phenomenon can be exploited to sensitize bacteria to antibiotics

Dhvar5-chitosan nanogels and their potential to improve antibiotics activity

Infection is one of the main causes of orthopedic implants failure, with antibiotic-resistant bacteria playing a crucial role in this outcome. In this work, antimicrobial nanogels were developed to be applied in situ as implant coating to prevent orthopedic-device-related infections. To that regard, a broad-spectrum antimicrobial peptide, Dhvar5, was grafted onto chitosan via thiol-norbornene "photoclick" chemistry. Dhvar5-chitosan nanogels (Dhvar5-NG) were then produced using a microfluidic system. Dhvar5-NG (1010 nanogels (NG)/mL) with a Dhvar5 concentration of 6 μg/mL reduced the burden of the most critical bacteria in orthopedic infections - methicillin-resistant Staphylococcus aureus (MRSA) - after 24 h in medium supplemented with human plasma proteins. Transmission electron microscopy showed that Dhvar5-NG killed bacteria by membrane disruption and cytoplasm release. No signs of cytotoxicity against a pre-osteoblast cell line were verified upon incubation with Dhvar5-NG. To further explore therapeutic alternatives, the potential synergistic effect of Dhvar5-NG with antibiotics was evaluated against MRSA. Dhvar5-NG at a sub-minimal inhibitory concentration (109 NG/mL) demonstrated synergistic effect with oxacillin (4-fold reduction: from 2 to 0.5 μg/mL) and piperacillin (2-fold reduction: from 2 to 1 μg/mL). This work supports the use of Dhvar5-NG as adjuvant of antibiotics to the prevention of orthopedic devices-related infections.The authors B. Costa, P.M. Alves and D. R. Fonseca would like to thank the Portuguese Foundation for Science and Technology (FCT) (Refs. SFRH/BD/147027/2019, SFRH/BD/145471/2019 and SFRH/BD/146890/2019), FCT/MCTES (Ref. CEECIND/01921/2017). C. Monteiro Thanks FCT by her contract-program (art. 23 of Law no. 57/2016 & 57/2017). Paula Gomes thanks FCT/MCTES for financial support to the LAQV-REQUIMTE Research Unit (UIDB/50006/2020; DOI 10.54499/UIDB/50006/2020) through national funds. A. Gomes thanks FCT/MCTES for Junior Researcher Contract 2022.08044.CEECIND/CP1724/CT0004 (DOI:10.54499/2022.08044.CEECIND/CP1724/CT0004). M.C.L. Martins also acknowledges FCT (LA/P/0070/2020) and MOBILIsE Project, which has received funding from the European Union’’s Horizon 2020 research and innovation program under grant agreement no. 951723

Overcoming Recruitment Challenges: A Pilot Study in Arab Americans

While diabetes prevalence and cardiovascular risk factors have been increasing among Arab populations worldwide, few studies of Arab Americans have been conducted because of the difficulty in recruiting Arab American participants. Cultural sensitivity and social awareness of different immigrant groups could ensure successful recruitment and retention in clinical studies. While the primary objective of our overall research project was to determine the prevalence of metabolic syndrome in Arab Americans, the focus of this article is to describe the methodology used to overcome challenges in recruiting and enrolling Arab Americans for a community-based study. We used novel methods, including open houses, religious-based venues, and engagement of community leaders, to encourage participation in this clinical and epidemiological study. A community-based approach involving community leaders and educators was useful in recruiting and encouraging participation in this study. As a result, we were able to collect clinical and anthropometric data from 136 Arab American men and women living in the Washington, DC, area and obtain information regarding their chronic diseases, mental health, and acculturation into U.S. culture and lifestyle. Our sampling methodology may serve as a model of a successful recruitment and enrollment strategy, and may assist other researchers to ensure sufficient power in future studies. Engagement of minority participants in clinical studies will enable the creation of targeted clinical intervention and prevention programs for underrepresented and understudied populations

Gene set enrichment analysis of microarray data from Pimephales promelas (Rafinesque), a non-mammalian model organism

<p>Abstract</p> <p>Background</p> <p>Methods for gene-class testing, such as Gene Set Enrichment Analysis (GSEA), incorporate biological knowledge into the analysis and interpretation of microarray data by comparing gene expression patterns to pathways, systems and emergent phenotypes. However, to use GSEA to its full capability with non-mammalian model organisms, a microarray platform must be annotated with human gene symbols. Doing so enables the ability to relate a model organism's gene expression, in response to a given treatment, to potential human health consequences of that treatment. We enhanced the annotation of a microarray platform from a non-mammalian model organism, and then used the GSEA approach in a reanalysis of a study examining the biological significance of acute and chronic methylmercury exposure on liver tissue of fathead minnow (<it>Pimephales promelas</it>). Using GSEA, we tested the hypothesis that fathead livers, in response to methylmercury exposure, would exhibit gene expression patterns similar to diseased human livers.</p> <p>Results</p> <p>We describe an enhanced annotation of the fathead minnow microarray platform with human gene symbols. This resource is now compatible with the GSEA approach for gene-class testing. We confirmed that GSEA, using this enhanced microarray platform, is able to recover results consistent with a previous analysis of fathead minnow exposure to methylmercury using standard analytical approaches. Using GSEA to compare fathead gene expression profiles to human phenotypes, we also found that fathead methylmercury-treated livers exhibited expression profiles that are homologous to human systems & pathways and results in damage that is similar to those of human liver damage associated with hepatocellular carcinoma and hepatitis B.</p> <p>Conclusions</p> <p>This study describes a powerful resource for enabling the use of non-mammalian model organisms in the study of human health significance. Results of microarray gene expression studies involving fathead minnow, typically used for aquatic ecological toxicology studies, can now be used to generate hypotheses regarding consequences of contaminants and other stressors on humans. The same approach can be used with other model organisms with microarray platforms annotated in a similar manner.</p

Musashi-2 controls cell fate, lineage bias, and TGF-β signaling in HSCs

Hematopoietic stem cells (HSCs) are maintained through the regulation of symmetric and asymmetric cell division. We report that conditional ablation of the RNA-binding protein Msi2 results in a failure of HSC maintenance and engraftment caused by a loss of quiescence and increased commitment divisions. Contrary to previous studies, we found that these phenotypes were independent of Numb. Global transcriptome profiling and RNA target analysis uncovered Msi2 interactions at multiple nodes within pathways that govern RNA translation, stem cell function, and TGF-β signaling. Msi2-null HSCs are insensitive to TGF-β–mediated expansion and have decreased signaling output, resulting in a loss of myeloid-restricted HSCs and myeloid reconstitution. Thus, Msi2 is an important regulator of the HSC translatome and balances HSC homeostasis and lineage bias

The correlation between immune subtypes and consensus molecular subtypes in colorectal cancer identifies novel tumour microenvironment profiles, with prognostic and therapeutic implications

Background Solid tumour growth is the consequence of a complex interplay between cancer cells and their microenvironment. Recently, a new global transcriptomic immune classification of solid tumours has identified six immune subtypes (ISs) (C1–C6). Our aim was to specifically characterise ISs in colorectal cancer (CRC) and assess their interplay with the consensus molecular subtypes (CMSs). Methods Clinical and molecular information, including CMSs and ISs, were obtained from The Cancer Genome Atlas (TCGA) (N = 625). Immune cell populations, differential gene expression and gene set enrichment analysis were performed to characterise ISs in the global CRC population by using CMSs. Results Only 5 ISs were identified in CRC, predominantly C1 wound healing (77%) and C2 IFN-γ dominant (17%). CMS1 showed the highest proportion of C2 (53%), whereas C1 was particularly dominant in CMS2 (91%). CMS3 had the highest representation of C3 inflammatory (7%) and C4 lymphocyte depleted ISs (4%), whereas all C6 TGF-β dominant cases belonged to CMS4 (2.3%). Prognostic relevance of ISs in CRC substantially differed from that reported for the global TCGA, and ISs had a greater ability to stratify the prognosis of CRC patients than CMS classification. C2 had higher densities of CD8, CD4 activated, follicular helper T cells, regulatory T cells and neutrophils and the highest M1/M2 polarisation. C2 had a heightened activation of pathways related to the immune system, apoptosis and DNA repair, mTOR signalling and oxidative phosphorylation, whereas C1 was more dependent of metabolic pathways. Conclusions The correlation of IS and CMS allows a more precise categorisation of patients with relevant clinical and biological implications, which may be valuable tools to improve tailored therapeutic interventions in CRC patients.This work was funded by projects DTS15/00157 , PI16/01827 and CIBER-ONC CB16/12/00442 from the Instituto de Salud Carlos III ( Ministry of Economy, Industry and Competitiveness, Spain ) and cofunded by the European Regional Development Fund (ERDF, European Union), and approved by the Ethics Committee or our Institution. BS is funded by AECC (Spain). MCR is funded by Instituto de Salud Carlos III and SEOM (Spain) CCP and BRC are funded by CAM (Programa de Empleo Juvenil (YEI)

Next station in microarray data analysis: GEPAS

The Gene Expression Profile Analysis Suite (GEPAS) has been running for more than four years. During this time it has evolved to keep pace with the new interests and trends in the still changing world of microarray data analysis. GEPAS has been designed to provide an intuitive although powerful web-based interface that offers diverse analysis options from the early step of preprocessing (normalization of Affymetrix and two-colour microarray experiments and other preprocessing options), to the final step of the functional annotation of the experiment (using Gene Ontology, pathways, PubMed abstracts etc.), and include different possibilities for clustering, gene selection, class prediction and array-comparative genomic hybridization management. GEPAS is extensively used by researchers of many countries and its records indicate an average usage rate of 400 experiments per day. The web-based pipeline for microarray gene expression data, GEPAS, is available at

Core Circadian Clock Genes Regulate Leukemia Stem Cells in AML

Leukemia stem cells (LSCs) have the capacity to self-renew and propagate disease upon serial transplantation in animal models, and elimination of this cell population is required for curative therapies. Here, we describe a series of pooled, in vivo RNAi screens to identify essential transcription factors (TFs) in a murine model of acute myeloid leukemia (AML) with genetically and phenotypically defined LSCs. These screens reveal the heterodimeric, circadian rhythm TFs Clock and Bmal1 as genes required for the growth of AML cells in vitro and in vivo. Disruption of canonical circadian pathway components produces anti-leukemic effects, including impaired proliferation, enhanced myeloid differentiation, and depletion of LSCs. We find that both normal and malignant hematopoietic cells harbor an intact clock with robust circadian oscillations, and genetic knockout models reveal a leukemia-specific dependence on the pathway. Our findings establish a role for the core circadian clock genes in AML.National Institutes of Health (U.S.) (Grant P01 CA066996)National Institutes of Health (U.S.) (Grant R01 HL082945)National Cancer Institute (U.S.) (Grant P30-CA14051

In vitro multiplication, antimicrobial, and insecticidal activity of Capparis spinosa L.

Caper (Capparis spinosa L.) is a medical plant grown in Jordan. Mass harvesting of caper plants from their origin environments caused a reduction of these germplasm. Therefore, an easy and consistent method for clonal proliferation and callus induction was established for this species. C. spinosa L. in vitro culture affected in MS medium provided by 0.5 mg/L BAP gave 5.9 microshoots/explant. Two months later MS medium supplemented with 2.0 mg/L NAA developed a maximum callus induction of 33.1 mm. Ex vitro, in vitro, and callus growth of C. spinosa L. using ethanolic and methanolic extracts were tested for their antimicrobial activity against different species of bacteria and fungi. Both ex-vitro and in vitro plants exhibited similar antimicrobial activity. Maximum ex vitro plant antibacterial activity was (23 mm ± 0.58 inhibition zone) against Staphylococcus epidermidi. In comparison, callus extracts gave the highest antibacterial activity against Bacillus cereus and Escherichia coli. Moreover, caper plant extracts showed different antifungal effects against the tested fungi species. Investigation of the data showed that ex-vitro extract exhibited maximum antifungal activity compared to in vitro plants. Additionally, exposed Bemisia tabaci 4th nymphal instar to C. spinosa L. extracts suffered mortality ranging from 2 to 28%.  In most instances, both ethanolic and methanolic extracts affected the survival of B. tabaci more than the control. The current study confirmed that C. spinosa L. has a wide range of antibacterial, antifungal, and insecticidal activity.