RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12.

RegulonDB is a database that contains the most comprehensive corpus of knowledge of the regulation of transcription initiation of Escherichia coli K-12, including data from both classical molecular biology and high-throughput methodologies. Here, we describe biological advances since our last NAR paper of 2019. We explain the changes to satisfy FAIR requirements. We also present a full reconstruction of the RegulonDB computational infrastructure, which has significantly improved data storage, retrieval and accessibility and thus supports a more intuitive and user-friendly experience. The integration of graphical tools provides clear visual representations of genetic regulation data, facilitating data interpretation and knowledge integration. RegulonDB version 12.0 can be accessed at https://regulondb.ccg.unam.mx.

Breast adipose tissue-derived extracellular vesicles from obese women alter tumor cell metabolism.

Breast adipose tissue is an important contributor to the obesity-breast cancer link. Extracellular vesicles (EVs) are nanosized particles containing selective cargo, such as miRNAs, that act locally or circulate to distant sites to modulate target cell functions. Here, we find that long-term education of breast cancer cells with EVs obtained from breast adipose tissue of women who are overweight or obese (O-EVs) results in increased proliferation. RNA-seq analysis of O-EV-educated cells demonstrates increased expression of genes involved in oxidative phosphorylation, such as ATP synthase and NADH: ubiquinone oxidoreductase. O-EVs increase respiratory complex protein expression, mitochondrial density, and mitochondrial respiration in tumor cells. The mitochondrial complex I inhibitor metformin reverses O-EV-induced cell proliferation. Several miRNAs-miR-155-5p, miR-10a-3p, and miR-30a-3p-which promote mitochondrial respiration and proliferation, are enriched in O-EVs relative to EVs from lean women. O-EV-induced proliferation and mitochondrial activity are associated with stimulation of the Akt/mTOR/P70S6K pathway, and are reversed upon silencing of P70S6K. This study reveals a new facet of the obesity-breast cancer link with human breast adipose tissue-derived EVs causing metabolic reprogramming of breast cancer cells.

Quality of hematology and clinical chemistry results in laboratory and zoo nonhuman primates: Effects of the preanalytical phase. A review.

Most errors in clinical pathology originate in the preanalytical phase, which includes all steps from the preparation of animals and equipment to the collection of the specimen and its management until analyzed. Blood is the most common specimen collected in nonhuman primates. Other specimens collected include urine, saliva, feces, and hair. The primary concern is the variability of blood hematology and biochemistry results due to sampling conditions with the effects of capture, restraint, and/or anesthesia. Housing and diet have fewer effects, with the exception of food restriction to reduce obesity. There has been less investigation regarding the impact of sampling conditions of nonblood specimens.

The microbiology of arabica and robusta coffee cherries: a comparative study of indigenous bacteria with presumptive impact on coffee quality.

Arabica and robusta are the two major coffee beans being sold worldwide. It is well recognized that coffee quality is influenced by their origin and the microbiological activities that drive their fermentation. However, in many coffee plantations, information about the natural diversity of bacteria that inhabit the arabica and robusta coffee cherries is limited. Here, we sampled arabica and robusta coffee cherries from Malang, East Java, Indonesia, then sequenced and analysed their bacterial composition. We found that: (a) arabica cherries contained bacteria with less diversity and abundance compared with robusta; (b) both coffee cherries were heavily populated by extremophiles, presumably dispersed from volcanic activities; (c) groups known to be involved in coffee fermentation such as lactic acid bacteria, acetic acid bacteria, Enterobacteria, and soil-associated bacteria were present in both arabica and robusta coffee cherries, and (d) arabica cherries were dominated by Leuconostoc pseudomesenteroides. These findings highlight that coffee cherry bacteria are highly diverse, the majority of which might come from the environment, with some potentially beneficial or detrimental to coffee quality. Knowledge of the natural microbial diversity of coffee cherries may be useful for the development of coffee fermentation technologies to yield coffee beans with consistent quality.

Breast adipose tissue-derived extracellular vesicles from women with obesity stimulate mitochondrial-induced dysregulated tumor cell metabolism.

Breast adipose tissue is an important contributor to the obesity-breast cancer link. Dysregulated cell metabolism is now an accepted hallmark of cancer. Extracellular vesicles (EVs) are nanosized particles containing selective cargo, such as miRNAs, that act locally or circulate to distant sites to modulate target cell functions. Here, we found that long-term education of breast cancer cells (MCF7, T47D) with EVs from breast adipose tissue of women who are overweight or obese (O-EVs) leads to sustained increased proliferative potential. RNA-Seq of O-EV-educated cells demonstrates increased expression of genes, such as ATP synthase and NADH: ubiquinone oxidoreductase, involved in oxidative phosphorylation. O-EVs increase respiratory complex protein expression, mitochondrial density, and mitochondrial respiration in tumor cells. Mitochondrial complex I inhibitor, metformin, reverses O-EV-induced cell proliferation. Several miRNAs, miR-155-5p, miR-10a-3p, and miR-30a-3p, which promote mitochondrial respiration and proliferation, are enriched in O-EVs relative to EVs from lean women. O-EV-induced proliferation and mitochondrial activity are associated with stimulation of the Akt/mTOR/P70S6K pathway, and are reversed upon silencing of P70S6K. This study reveals a new facet of the obesity-breast cancer link with human breast adipose tissue-derived EVs causing the metabolic reprogramming of ER+ breast cancer cells.

Improving the Quality of EDTA-treated Blood Specimens from Mice.

Nonterminal blood sampling in laboratory mice is a very common procedure. With the goal of improving animal welfare, different sampling sites and methods have been compared but have not achieved a consensus. Moreover, most of these studies overlooked the quality of blood specimens collected. The main preanalytical concern with EDTA-treated blood specimens for hematology analyses is platelet aggregation, which is known to cause analytical errors. Our objective was to find a nonterminal blood sampling method with minimal adverse effects on mice and few or no platelet aggregates. We tested and compared 2 collection sites, 4 sampling methods, and 3 antithrombotic drugs in 80 C57BL6/j male and female mice by evaluating platelet aggregates on blood smears and platelet, WBC, and RBC counts. In addition, the blood collection process was carefully evaluated, and adverse effects were recorded. Platelet aggregation was lower in specimens collected from the jugular vein than from the facial vein, with no effect of the sampling device or the presence of an antithrombotic additive. Highly aggregated specimens were significantly associated with lower platelet counts, whereas aggregation had no effect on WBC or RBC counts. Adverse events during sampling were significantly associated with more numerous platelet aggregates. The jugular vein is thus a satisfactory sampling site in mice in terms of both animal welfare and low platelet aggregation. Using antithrombotic agents appears to be unnecessary, whereas improving sampling conditions remains a key requirement to ensure the quality of EDTA-treated blood specimens from mice.

Temporal dynamics of insight in body dysmorphic disorder: An ecological momentary assessment study.

Individuals with body dysmorphic disorder (BDD) often lack insight into the nature of their perceived appearance flaws that are slight, if they exist at all. Despite the generally held assumption that insight fluctuates over time within individuals with BDD, its temporal instability and associated features remain unstudied. We examined insight as a multidimensional, contextually embedded, and dynamic factor using ecological momentary assessment (EMA), further assessing affect and self-esteem as potentially associated states. Thirty individuals with BDD and 30 mentally healthy controls (HCs) completed 6 days of EMA (M = 8.54 assessments per day, N = 3075 assessments in total). Multilevel analyses revealed substantial intraindividual fluctuations of insight dimensions (across 30 min to hours) that were more pronounced for individuals with BDD than for HCs. Poorer insight correlated with higher negative affect, lower positive affect, and lower self-esteem at concurrent time points in the BDD group. Considering all predictors at the same time point, poorer insight was characterized by lower self-esteem and, partly, negative affect in the BDD group. Across time, self-esteem and insight influenced each other reciprocally, with comparatively stronger effects for the prediction of poorer insight by previously lower self-esteem. These findings demonstrate that insight is a highly variable phenomenon in BDD, further suggesting a clinically and etiologically relevant link between self-esteem and insight in symptom maintenance. (PsycInfo Database Record (c) 2021 APA, all rights reserved).

Extracellular vesicle- and particle-mediated communication shapes innate and adaptive immune responses.

Intercellular communication among immune cells is vital for the coordination of proper immune responses. Extracellular vesicles and particles (EVPs) act as messengers in intercellular communication, with important consequences for target cell and organ physiology in both health and disease. Under normal physiological conditions, immune cell-derived EVPs participate in immune responses by regulating innate and adaptive immune responses. EVPs play a major role in antigen presentation and immune activation. On the other hand, immune cell-derived EVPs exert immunosuppressive and regulatory effects. Consequently, EVPs may contribute to pathological conditions, such as autoimmune and inflammatory diseases, graft rejection, and cancer progression and metastasis. Here, we provide an overview of the role of EVPs in immune homeostasis and pathophysiology, with a particular focus on their contribution to innate and adaptive immunity and their potential use for immunotherapies.

Extracellular vesicle and particle isolation from human and murine cell lines, tissues, and bodily fluids.

We developed a modified protocol, based on differential ultracentrifugation (dUC), to isolate extracellular vesicles and particles (specifically exomeres) (EVPs) from various human and murine sources, including cell lines, surgically resected tumors and adjacent tissues, and bodily fluids, such as blood, lymphatic fluid, and bile. The diversity of these samples requires robust and highly reproducible protocols and refined isolation technology, such as asymmetric-flow field-flow fractionation (AF4). Our isolation protocol allows for preparation of EVPs for various downstream applications, including proteomic profiling. For complete details on the use and execution of this protocol, please refer to Hoshino et al. (2020).

Cell-free DNA (cfDNA) and Exosome Profiling from a Year-Long Human Spaceflight Reveals Circulating Biomarkers.

Liquid biopsies based on cell-free DNA (cfDNA) or exosomes provide a noninvasive approach to monitor human health and disease but have not been utilized for astronauts. Here, we profile cfDNA characteristics, including fragment size, cellular deconvolution, and nucleosome positioning, in an astronaut during a year-long mission on the International Space Station, compared to his identical twin on Earth and healthy donors. We observed a significant increase in the proportion of cell-free mitochondrial DNA (cf-mtDNA) inflight, and analysis of post-flight exosomes in plasma revealed a 30-fold increase in circulating exosomes and patient-specific protein cargo (including brain-derived peptides) after the year-long mission. This longitudinal analysis of astronaut cfDNA during spaceflight and the exosome profiles highlights their utility for astronaut health monitoring, as well as cf-mtDNA levels as a potential biomarker for physiological stress or immune system responses related to microgravity, radiation exposure, and the other unique environmental conditions of spaceflight.

Recent Advances in Experimental Models of Breast Cancer Exosome Secretion, Characterization and Function.

Breast cancer (BC) is responsible for 15% of all the cancer deaths among women in the USA. The tumor microenvironment (TME) has the potential to act as a driver of breast cancer progression and metastasis. The TME is composed of stromal cells within an extracellular matrix and soluble cytokines, chemokines and extracellular vesicles and nanoparticles that actively influence cell behavior. Extracellular vesicles include exosomes, microvesicles and large oncosomes that orchestrate fundamental processes during tumor progression through direct interaction with target cells. Long before tumor cell spread to future metastatic sites, tumor-secreted exosomes enter the circulation and establish distant pre-metastatic niches, hospitable and permissive milieus for metastatic colonization. Emerging evidence suggests that breast cancer exosomes promote tumor progression and metastasis by inducing vascular leakiness, angiogenesis, invasion, immunomodulation and chemoresistance. Exosomes are found in almost all physiological fluids including plasma, urine, saliva, and breast milk, providing a valuable resource for the development of non-invasive cancer biomarkers. Here, we review work on the role of exosomes in breast cancer progression and metastasis, and describe the most recent advances in models of exosome secretion, isolation, characterization and functional analysis. We highlight the potential applications of plasma-derived exosomes as predictive biomarkers for breast cancer diagnosis, prognosis and therapy monitoring. We finally describe the therapeutic approaches of exosomes in breast cancer.

AXL Is a Driver of Stemness in Normal Mammary Gland and Breast Cancer.

The receptor tyrosine kinase AXL is associated with epithelial plasticity in several solid tumors including breast cancer and AXL-targeting agents are currently in clinical trials. We hypothesized that AXL is a driver of stemness traits in cancer by co-option of a regulatory function normally reserved for stem cells. AXL-expressing cells in human mammary epithelial ducts co-expressed markers associated with multipotency, and AXL inhibition abolished colony formation and self-maintenance activities while promoting terminal differentiation in vitro. Axl-null mice did not exhibit a strong developmental phenotype, but enrichment of Axl + cells was required for mouse mammary gland reconstitution upon transplantation, and Axl-null mice had reduced incidence of Wnt1-driven mammary tumors. An AXL-dependent gene signature is a feature of transcriptomes in basal breast cancers and reduced patient survival irrespective of subtype. Our interpretation is that AXL regulates access to epithelial plasticity programs in MaSCs and, when co-opted, maintains acquired stemness in breast cancer cells.

Extracellular Vesicle and Particle Biomarkers Define Multiple Human Cancers.

There is an unmet clinical need for improved tissue and liquid biopsy tools for cancer detection. We investigated the proteomic profile of extracellular vesicles and particles (EVPs) in 426 human samples from tissue explants (TEs), plasma, and other bodily fluids. Among traditional exosome markers, CD9, HSPA8, ALIX, and HSP90AB1 represent pan-EVP markers, while ACTB, MSN, and RAP1B are novel pan-EVP markers. To confirm that EVPs are ideal diagnostic tools, we analyzed proteomes of TE- (n = 151) and plasma-derived (n = 120) EVPs. Comparison of TE EVPs identified proteins (e.g., VCAN, TNC, and THBS2) that distinguish tumors from normal tissues with 90% sensitivity/94% specificity. Machine-learning classification of plasma-derived EVP cargo, including immunoglobulins, revealed 95% sensitivity/90% specificity in detecting cancer. Finally, we defined a panel of tumor-type-specific EVP proteins in TEs and plasma, which can classify tumors of unknown primary origin. Thus, EVP proteins can serve as reliable biomarkers for cancer detection and determining cancer type.

Testing the specificity of interpretation biases in women with eating disorder symptoms: An online experimental assessment.

OBJECTIVE: Cognitive biases, such as memory, attention, and interpretation bias, are thought to play a central role in the development and maintenance of eating disorders (EDs). The aim of the present study was to investigate whether the interpretation bias is ED-specific or can be generalized to comorbid disorder-related threats in women with high levels of ED symptoms. METHOD: In an online study, we measured interpretation bias using the modified Sentence Word Association Paradigm (SWAP), comparing women with (n = 39) and without (sub)threshold eating disorders (n = 56). We assessed endorsement and rejection rates as well as reaction times in response to a positive/neutral or a negative ED-specific, social anxiety-specific (SAD), or generalized anxiety-specific (GAD) interpretive word following an ambiguous sentence. RESULTS: In ambiguous situations, women with high ED symptoms selected more negative (p < .001) and fewer positive/neutral ED-related interpretations (p < .001). Negative interpretations were endorsed significantly faster (p < .001), while positive interpretations were rejected faster in this group (p < .001). These women also manifested negative SAD-specific interpretation bias patterns in reaction time measures. Nevertheless, ED severity was best predicted by the endorsement of negative ED-specific stimuli, whereas ED and SAD reaction time measures seemed to have a negligible effect. DISCUSSION: The results indicate that the interpretation bias might be ED-specific. The SWAP can be a useful tool for the further investigation of the etiological relevance of the interpretation bias as well as for the development of modification training interventions.

[Contribution of break up time in the diagnosis and the treatment of dry eye syndrome in tropic area: about 234 patients in Abidjan]. / Contribution du break up time au diagnostic et à la prise en charge du syndrome sec oculaire en milieu tropical : à propos de 234 yeux à Abidjan.

INTRODUCTION: Dry eye disease (DED) can be evaluated clinically by the tear film break up time (BUT). There is a discrepancy between symptoms in relationship with dry eye disease and objectives measures of BUT. So we tried to evaluate the reliability of BUT in the diagnosis and treatment of this disease in black African people. METHODS: We carried out a prospective study of 6 months where melanoderms adults presenting subjective symptoms of dry eye disease according a questionnaire of 7 items were included. Then the measure of BUT is performed after ocular instillation of fluorescein eyedrop. This measured is done by recording the time elapsed from the last complete palpebral blink to the appearance of the first dry spot. Patients with subjective symptoms and time of BUT lower than 10seconds were called concordants (suffering really of DED). The discrepant group was represented by a BUT upper than 10seconds despite the fact that these patients answered positively to the questionnaire. RESULTS: This survey included 234 patients and the average age was 49.1 years. Sex-ratio was 0.68 and we noticed predominance of BUT between 5 and 10seconds in 42.3% of cases. Subjective symptoms were strengthened clinically by a BUT lower to 10seconds in 149 patients. Therefore, the reliability of BUT as clinic tool for the diagnosis after symptoms in relationship with DED was 63.7%. In the group of concordants, women were more likely than men to experience symptoms of DED (P=0.0005). Age upper than 50 years and computer usage were risk factors of DED (P<0.01). DISCUSSION: Dry eye disease is a multifactorial affection of tear and ocular surface frequently seen in female and people using computer and older than 50. The reliability of BUT near to 65% is a reason to perform this test in our daily practice. CONCLUSION: Tear BUT is a reliable clinical test which must be performed systematically to assess the diagnosis of DED in black African people.

Phosphate-Rich Biomimetic Peptides Shed Light on High-Affinity Hyperphosphorylated Uranyl Binding Sites in Phosphoproteins.

Some phosphoproteins such as osteopontin (OPN) have been identified as high-affinity uranyl targets. However, the binding sites required for interaction with uranyl and therefore involved in its toxicity have not been identified in the whole protein. The biomimetic approach proposed here aimed to decipher the nature of these sites and should help to understand the role of the multiple phosphorylations in UO2 2+ binding. Two hyperphosphorylated cyclic peptides, pS168 and pS1368 containing up to four phosphoserine (pSer) residues over the ten amino acids present in the sequences, were synthesized with all reactions performed in the solid phase, including post-phosphorylation. These ß-sheet-structured peptides present four coordinating residues from four amino acid side chains pointing to the metal ion, either three pSer and one glutamate in pS168 or four pSer in pS1368 . Significantly, increasing the number of pSer residues up to four in the cyclodecapeptide scaffolds produced molecules with an affinity constant for UO2 2+ that is as large as that reported for osteopontin at physiological pH. The phosphate-rich pS1368 can thus be considered a relevant model of UO2 2+ coordination in this intrinsically disordered protein, which wraps around the metal ion to gather four phosphate groups in the UO2 2+ coordination sphere. These model hyperphosphorylated peptides are highly selective for UO2 2+ with respect to endogenous Ca2+ , which makes them good starting structures for selective UO2 2+ complexation.

[Selective laser trabeculoplasty in African blacks]. / Trabéculoplastie sélective chez le mélanoderme africain.

INTRODUCTION: The treatment of primary open angle glaucoma (POAG) is preferably medical. However, when medical therapy fails, alternative or complementary treatments may be considered. In this regard, selective laser trabeculoplasty is a widely popular procedural treatment whose accepted benefits have been very little studied in African blacks. The objective of this study was to assess the efficacy of selective laser trabeculoplasty on the reduction of intraocular pressure (IOP) in African blacks with POAG. METHODS: We conducted a retrospective study of black patients treated with selective laser trabeculoplasty between March 2010 and March 2011. All patients had POAG with trabecular meshwork accessible over 360°. The treatment protocol consisted of a 360°treatment in two sessions (180°/session) 15 days apart. Success was defined as decrease from the initial IOP≥3mm Hg without additional medications. RESULTS: We included 44 patients, corresponding to 82 eyes. The mean age of the patients was 55.94±11.66 years with extremes of 19 years and 76 years. The mean intraocular pressure before laser treatment (initial IOP) was 18.43±4.81mm Hg. After laser treatment, the mean pressure reduction was (i) 3.81mm Hg (20.67%) at 15 days ; (ii) 4.08mm Hg (22.14%) at 1 month; (iii) 4.45mm Hg (24.14%) at 3 months; and (iv) 4.95mm Hg (26.86%) at 6 months. The success rate after laser treatment was 67.60% at 15 days, 83.78% at 1 month, 72.09% at 3 months and 80.43% at 6 months. CONCLUSION: Selective laser trabeculoplasty is effective in African blacks. Its efficacy is comparable to that of a carbonic anhydrase inhibitor or even a prostaglandin. It could be a complementary or substitutive alternative to POAG medications in African blacks.

En garde! Redefinition of Nebela militaris (Arcellinida, Hyalospheniidae) and erection of Alabasta gen. nov.

Molecular data have considerably contributed to building the taxonomy of protists. Recently, the systematics of Hyalospheniidae (Amoebozoa; Tubulinea; Arcellinida) has been widely revised, with implications extending to ecological, biogeographical and evolutionary investigations. Certain taxa, however, still have an uncertain phylogenetic position, including the common and conspicuous species Nebela militaris. A phylogenetic reconstruction of the Hyalospheniidae using partial sequences of the mitochondrial Cytochrome Oxidase Subunit 1 (COI) gene shows that N. militaris does not belong to genus Nebela, but should be placed in its own genus. The morphological singularities (strongly curved pseudostome and a marked notch in lateral view) and phylogenetic placement of our isolates motivated the creation of a new genus: Alabasta gen. nov. Based on their morphology, we include in this genus Nebela kivuense and Nebela longicollis. We discuss the position of genus Alabasta within Hyalospheniidae, and the species that could integrate this new genus based on their morphological characteristics.