Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Burnout among surgeons before and during the SARS-CoV-2 pandemic: an international survey

Background: SARS-CoV-2 pandemic has had many significant impacts within the surgical realm, and surgeons have been obligated to reconsider almost every aspect of daily clinical practice. Methods: This is a cross-sectional study reported in compliance with the CHERRIES guidelines and conducted through an online platform from June 14th to July 15th, 2020. The primary outcome was the burden of burnout during the pandemic indicated by the validated Shirom-Melamed Burnout Measure. Results: Nine hundred fifty-four surgeons completed the survey. The median length of practice was 10 years; 78.2% included were male with a median age of 37 years old, 39.5% were consultants, 68.9% were general surgeons, and 55.7% were affiliated with an academic institution. Overall, there was a significant increase in the mean burnout score during the pandemic; longer years of practice and older age were significantly associated with less burnout. There were significant reductions in the median number of outpatient visits, operated cases, on-call hours, emergency visits, and research work, so, 48.2% of respondents felt that the training resources were insufficient. The majority (81.3%) of respondents reported that their hospitals were included in the management of COVID-19, 66.5% felt their roles had been minimized; 41% were asked to assist in non-surgical medical practices, and 37.6% of respondents were included in COVID-19 management. Conclusions: There was a significant burnout among trainees. Almost all aspects of clinical and research activities were affected with a significant reduction in the volume of research, outpatient clinic visits, surgical procedures, on-call hours, and emergency cases hindering the training. Trial registration: The study was registered on clicaltrials.gov "NCT04433286" on 16/06/2020

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Summary Background Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. Methods We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung’s disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. Findings We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung’s disease) from 264 hospitals (89 in high-income countries, 166 in middleincome countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in lowincome countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. Interpretation Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between lowincome, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

Investigation of the Anticancer Effect of &alpha;-Aminophosphonates and Arylidine Derivatives of 3-Acetyl-1-aminoquinolin-2(1H)-one on the DMBA Model of Breast Cancer in Albino Rats with In Silico Prediction of Their Thymidylate Synthase Inhibitory Effect

Breast cancer is a major cause of death in women worldwide. In this study, 60 female rats were classified into 6 groups; negative control, &alpha;-aminophosphonates, arylidine derivatives of 3-acetyl-1-aminoquinolin-2(1H)-one, DMBA, DMBA &amp; &alpha;-aminophosphonates, and DMBA &amp; arylidine derivatives of 3-acetyl-1-aminoquinolin-2(1H)-one. New &alpha;-aminophosphonates and arylidine derivatives of 3-acetyl-1-aminoquinolin-2(1H)-one were synthesized and elucidated by different spectroscopic and elemental analysis. Histopathological examination showed marked proliferation of cancer cells in the DMBA group. Treatment with &alpha;-aminophosphonates mainly decreased tumor mass. Bcl2 expression increased in DMBA-administered rats and then declined in the treated groups, mostly with &alpha;-aminophosphonates. The level of CA15-3 markedly declined in DMBA groups treated with &alpha;-aminophosphonates and arylidine derivatives of 3-acetyl-1-aminoquinolin-2(1H)-one. Gene expression of GST-P, PCNA, PDK, and PIK3CA decreased in the DMBA group treated with &alpha;-aminophosphonates and arylidine derivatives of 3-acetyl-1-aminoquinolin-2(1H)-one, whereas PIK3R1 and BAX increased in the DMBA group treated with &alpha;-aminophosphonates and arylidine derivatives of 3-acetyl-1-aminoquinolin-2(1H)-one. The molecular docking postulated that the investigated compounds can inhibt the Thymidylate synthase TM due to high hydrophobicity charachter

Potential Impacts of Clove Essential Oil Nanoemulsion as Bio Fungicides against <i>Neoscytalidium</i> Blight Disease of <i>Carum carvi</i> L.

Fungal plant diseases are considered one of the most destructive diseases for plants. In this current study, Neoscytalidium dimidiatum as a fungal plant pathogen was isolated from an infected Carum carvi L. plant (C. carvi) for the first time and controlled it using clove essential oil nanoemulsion (CEONE). This fungal plant pathogen was identified morphologically and genetically, then deposited in the gene bank under accession number OQ338188. CEONE was prepared and characterized using DLS, Zeta potential, and TEM analysis. The characterization results illustrated that the size of CEONE was lower than 100 nm, which was confirmed by TEM, which appeared spherical in shape. Results revealed that CEONE has promising antifungal activity towards N. dimidiatum, where inhibition percentages of CEONE at concentrations of 5000, 3000, and 1000 ppm were 82.2%, 53.3%, and 25.5%, respectively. At the pot level, N. dimidiatum was highly virulent on C. carvi, and CEONE and CEO were highly effective against N. dimidiatum blight disease, with 71.42% and 57.14% protection, respectively. Moreover, results revealed that there was a vast improvement in root length, plant height, and leaves. Additionally, the application of CEONE and CEO induced plant resistance by modifying proline, phenol, hydrogen peroxide, malondialdehyde, and antioxidant enzymes. In conclusion, N. dimidiatum was highly virulent on C. carvi but can be effectively reduced by CEONE through the eco-friendly method

Inhibition of Aspergillus flavus Growth and Aflatoxin Production in Zea mays L. Using Endophytic Aspergillus fumigatus

Aspergillus flavus infection of vegetative tissues can affect the development and integrity of the plant and poses dangerous risks on human and animal health. Thus, safe and easily applied approaches are employed to inhibit A. flavus growth. To this end, the fungal endophyte, i.e., Aspergillus fumigatus, was used as a safe biocontrol agent to reduce the growth of A. flavus and its infection in maize seedlings. Interestingly, the safe endophytic A. fumigatus exhibited antifungal activity (e.g., 77% of growth inhibition) against A. flavus. It also reduced the creation of aflatoxins, particularly aflatoxin B1 (AFB1, 90.9%). At plant level, maize seedling growth, leaves and root anatomy and the changes in redox status were estimated. Infected seeds treated with A. fumigatus significantly improved the germination rate by 88.53%. The ultrastructure of the infected leaves showed severe disturbances in the internal structures, such as lack of differentiation in cells, cracking, and lysis in the cell wall and destruction in the nucleus semi-lysis of chloroplasts. Ultrastructure observations indicated that A. fumigatus treatment increased maize (leaf and root) cell wall thickness that consequentially reduced the invasion of the pathogenic A. flavus. It was also interesting that the infected seedlings recovered after being treated with A. fumigatus, as it was observed in growth characteristics and photosynthetic pigments. Moreover, infected maize plants showed increased oxidative stress (lipid peroxidation and H2O2), which was significantly mitigated by A. fumigatus treatment. This mitigation was at least partially explained by inducing the antioxidant defense system, i.e., increased phenols and proline levels (23.3 and 31.17%, respectively) and POD, PPO, SOD and CAT enzymes activity (29.50, 57.58, 32.14 and 29.52%, respectively). Overall, our study suggests that endophytic A. fumigatus treatment could be commercially used for the safe control of aflatoxins production and for inducing biotic stress tolerance of A. flavus-infected maize plants

Cellulosic Fiber Waste Feedstock for Bioethanol Production via Bioreactor-Dependent Fermentation

The bioconversion of environmental wastes into energy is gaining much interest in most developing and developed countries. The current study is concerned with the proper exploitation of some industrial wastes. Cellulosic fiber waste was selected as a raw material for producing bioethanol as an alternative energy source. A combination of physical, chemical, and enzymatic hydrolysis treatments was applied to maximize the concentration of glucose that could be fermented with yeast into bioethanol. The results showed that the maximum production of 13.9 mg/mL of glucose was achieved when 5% cellulosic fiber waste was treated with 40% HCl, autoclaved, and followed with enzymatic hydrolysis. Using SEM and FTIR analysis, the instrumental characterization of the waste fiber treatment confirmed the effectiveness of the degradation by turning the long threads of the fibers into small pieces, in addition to the appearance of new functional groups and peak shifting. A potent yeast strain isolated from rotten grapes was identified as Starmerella bacillaris STDF-G4 (accession number OP872748), which was used to ferment the obtained glucose units into bioethanol under optimized conditions. The maximum production of 3.16 mg/mL of bioethanol was recorded when 7% of the yeast strain was anaerobically incubated at 30 °C in a broth culture with the pH adjusted to 5. The optimized conditions were scaled up from flasks to a fermentation bioreactor to maximize the bioethanol concentration. The obtained data showed the ability of the yeast strain to produce 4.13 mg/mL of bioethanol after the first 6 h of incubation and double the amount after 36 h of incubation to reach 8.6 mg/mL, indicating the efficiency of the bioreactor in reducing the time and significantly increasing the product

Inhibition of **Aspergillus flavus** growth and aflatoxin production in **Zea mays L.** using endophytic **Aspergillus fumigatus**

Aspergillus flavus infection of vegetative tissues can affect the development and integrity of the plant and poses dangerous risks on human and animal health. Thus, safe and easily applied approaches are employed to inhibit A. flavus growth. To this end, the fungal endophyte, i.e., Aspergillus fumigatus, was used as a safe biocontrol agent to reduce the growth of A. flavus and its infection in maize seedlings. Interestingly, the safe endophytic A. fumigatus exhibited antifungal activity (e.g., 77% of growth inhibition) against A. flavus. It also reduced the creation of aflatoxins, particularly aflatoxin B(1) (AFB(1), 90.9%). At plant level, maize seedling growth, leaves and root anatomy and the changes in redox status were estimated. Infected seeds treated with A. fumigatus significantly improved the germination rate by 88.53%. The ultrastructure of the infected leaves showed severe disturbances in the internal structures, such as lack of differentiation in cells, cracking, and lysis in the cell wall and destruction in the nucleus semi-lysis of chloroplasts. Ultrastructure observations indicated that A. fumigatus treatment increased maize (leaf and root) cell wall thickness that consequentially reduced the invasion of the pathogenic A. flavus. It was also interesting that the infected seedlings recovered after being treated with A. fumigatus, as it was observed in growth characteristics and photosynthetic pigments. Moreover, infected maize plants showed increased oxidative stress (lipid peroxidation and H(2)O(2)), which was significantly mitigated by A. fumigatus treatment. This mitigation was at least partially explained by inducing the antioxidant defense system, i.e., increased phenols and proline levels (23.3 and 31.17%, respectively) and POD, PPO, SOD and CAT enzymes activity (29.50, 57.58, 32.14 and 29.52%, respectively). Overall, our study suggests that endophytic A. fumigatus treatment could be commercially used for the safe control of aflatoxins production and for inducing biotic stress tolerance of A. flavus-infected maize plants