DNA Barcoding of Invasive Terrestrial Plant Species in India.

Invasive plants are known to cause biodiversity loss and pose a major risk to human health and environment. Identification of invasive plants and distinguishing them from native species has been relied on morphological examination. Stringent requirement of floral characters and decreasing number of expert taxonomists are making conventional morphology-based identification system tedious and resource-intensive. DNA barcoding may help in quick identification of invasive species if distinct sequence divergence pattern at various taxonomic levels is observed. The present work evaluates the utility of four molecular markers; rbcL, matK, their combination (rbcL + matK), and psbA-trnH for identification of 37 invasive plant species from India and also in distinguishing them from 97 native species. A psbA-trnH locus was found to be of restricted utility in this work as it was represented by the members of a single family. A hierarchical increase in K2P mean divergence across different taxonomic levels was found to be the maximum for matK alone followed by rbcL + matK and rbcL alone, respectively. NJ clustering analysis, however, confirmed the suitability of combined locus (rbcL + matK) over individual rbcL and matK as the DNA barcode. RbcL showed the lowest resolution power among the three markers studied. MatK exhibited much better performance compared to rbcL alone in identifying most of the species accurately although it failed to show monophyly of genus Dinebra. Two families; Asteraceae and Poaceae, remained polyphyletic in the trees constructed by all three markers. Combined locus (rbcL + matK) was found to be the most suitable marker as it raised the resolution power of both the markers and could identify more than 90% of genera correctly. Phylogenetic tree constructed by Maximum-Parsimony method using combined locus as a molecular marker exhibited the best resolution, thus, supporting the significance of two-locus combination of rbcL + matK for barcoding invasive plant species from India. Present study contributes to the global barcode data of invasive plant species by adding fifty-one new sequences to it. Effective barcoding of additional number of native as well as invasive plant species from India is possible using this dual locus if it is combined with one or more new molecular plastid markers. Expansion of barcode database with a focus on barcode performance optimisation to improve discrimination ability at species level can be undertaken in future.

Effect of dehydration on the inactivation of Listeria monocytogenes and Salmonella enterica on enoki and wood ear mushrooms.

Foodborne illness outbreaks in the U.S. associated with consumption of both fresh and dried specialty mushrooms have recently occurred. Dried wood ear mushrooms were implicated in a salmonellosis outbreak in 2020, while fresh enoki mushrooms were associated with two listeriosis outbreaks in 2020 and 2023. These specialty mushrooms are commercially available in both their fresh and dried states. Due to the short shelf life of mushrooms, dehydration is a common method used in both industry and by consumers to extend the shelf life and preserve quality. Therefore, the aim of this study was to evaluate the use of dehydration on the inactivation kinetics of both Listeria monocytogenes and Salmonella enterica on enoki and wood ear mushrooms. Fresh mushrooms were inoculated with four strain cocktails of either L. monocytogenes or S. enterica and dried at ambient conditions for 10 min. Following drying of the inoculum, mushrooms were placed into food dehydrators preheated to 70, 80, or 90°C and treated for up to 24 h. At treatment intervals, mushrooms were removed from the dehydrators for pathogen enumeration. Inactivation kinetics for both pathogens were modeled using the Weibull, log-linear with tail, and log-linear with shoulder models. Pathogen reductions of >4 log CFU/g were achieved on both enoki and wood ear mushrooms during dehydration at 90°C after only 2-4 h. At 70 and 80°C, log reductions of >4 log CFU/g were observed on wood ear mushrooms after 4-8 h. On enoki mushrooms, a tailing effect was observed with residual populations (>2 log CFU/g) of L. monocytogenes and S. enterica remaining even after 24 h of treatment at both 70 and 80°C. This study emphasizes the need for an individualized dehydration strategy for each mushroom type to ensure the effectiveness of dehydration as a process to reduce pathogen populations. Results of this study will aid in informing proper time and temperature combinations for dehydration of specialty mushrooms to ensure product safety.

COVID-19 progression towards ARDS: a genome wide study reveals host factors underlying critical COVID-19.

Coronavirus disease 2019 (COVID-19) is a viral infection produced by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus epidemic, which was declared a global pandemic in March 2020. The World Health Organization has recorded around 43.3 billion cases and 59.4 million casualties to date, posing a severe threat to global health. Severe COVID-19 indicates viral pneumonia caused by the SARS-CoV-2 infections, which can induce fatal consequences, including acute respiratory distress syndrome (ARDS). The purpose of this research is to better understand the COVID-19 and ARDS pathways, as well as to find targeted single nucleotide polymorphism. To accomplish this, we retrieved over 100 patients' samples from the Sequence Read Archive, National Center for Biotechnology Information. These sequences were processed through the Galaxy server next generation sequencing pipeline for variant analysis and then visualized in the Integrative Genomics Viewer, and performed statistical analysis using t-tests and Bonferroni correction, where six major genes were identified as DNAH7, CLUAP1, PPA2, PAPSS1, TLR4, and IFITM3. Furthermore, a complete understanding of the genomes of COVID-19-related ARDS will aid in the early identification and treatment of target proteins. Finally, the discovery of novel therapeutics based on discovered proteins can assist to slow the progression of ARDS and lower fatality rates.

Survival kinetics of Listeria monocytogenes and Salmonella enterica on dehydrated enoki and wood ear mushrooms during long-term storage.

Two specialty mushrooms have recently become novel vectors for foodborne outbreaks in the U.S.: fresh enoki and dried wood ear mushrooms were linked to a listeriosis and salmonellosis outbreak, respectively. The aim of this study was to evaluate the survival kinetics of Listeria monocytogenes and Salmonella enterica on dehydrated enoki and wood ear mushrooms during long-term storage. Following heat dehydration, mushrooms were inoculated with either L. monocytogenes or S. enterica, allowed to dry for 1 h, and then stored for up to 180 d at 25 °C and 33% relative humidity. Both pathogens were enumerated from the mushrooms at intervals during the storage period. Survival kinetics of both pathogens were modeled using both the Weibull and log-linear with tail models. After inoculation and 1 h drying, both pathogen populations decreased 2.26-2.49 log CFU/g on wood ear mushrooms; no decrease was observed on enoki. Both pathogens survived during storage on both mushroom types. On wood ear mushrooms, a 2-log decrease of both pathogens occurred during storage. On enoki mushrooms, 4-log decreases of both pathogens were modeled to occur after 127.50-156.60 d. The results of this study suggest that L. monocytogenes and S. enterica can persist on dehydrated specialty mushrooms during long-term storage.

Modeling the Fate of Listeria monocytogenes and Salmonella enterica on Fresh Whole and Chopped Wood Ear and Enoki Mushrooms.

Two recent foodborne illness outbreaks linked to specialty mushrooms have occurred in the United States, both representing novel pathogen-commodity pairings. Listeria monocytogenes and Salmonella enterica were linked to enoki and wood ear mushrooms, respectively. The aim of this study was therefore to examine the survival of both L. monocytogenes and S. enterica on raw whole and chopped enoki and wood ear mushrooms during storage at different temperatures. Fresh mushrooms were either left whole or chopped and subsequently inoculated with a cocktail of either S. enterica or rifampicin-resistant L. monocytogenes, resulting in an initial inoculation level of 3 log CFU/g. Mushroom samples were stored at 5, 10, or 25°C for up to 7 d. During storage, the population levels of S. enterica or L. monocytogenes on the mushrooms were enumerated. The primary Baranyi model was used to estimate the growth rates of both pathogens and the secondary Ratkowsky square root model was used to model the relationship between growth rates and temperature. Both L. monocytogenes and S. enterica survived on both mushroom types and preparations at all temperatures. No proliferation of either pathogen was observed on mushrooms stored at 5°C. At 10°C, moderate growth was observed for both pathogens on enoki mushrooms and for L. monocytogenes on wood ear mushrooms; no growth was observed for S. enterica on wood ear mushrooms. At 25°C, both pathogens proliferated on both mushroom types with growth rates ranging from 0.43 to 3.27 log CFU/g/d, resulting in 1 log CFU/g increases in only 0.31 d (7.44 h) to 2.32 d. Secondary models were generated for L. monocytogenes on whole wood ear mushrooms and S. enterica on whole enoki mushrooms with goodness-of-fit parameters of r2 = 0.9855/RMSE = 0.0479 and r2 = 0.9882/RMSE = 0.1417, respectively. Results from this study can aid in understanding the dynamics of L. monocytogenes and S. enterica on two types of specialty mushrooms.

Serial Bone Density Changes in Women Undergoing Pelvic (Chemo) Radiation: Results From the PARCER Trial.

PURPOSE: Pelvic irradiation leads to substantial dose to the pelvic girdle. However, bone density loss as a function of radiation therapy dose and time has not been investigated. This study was undertaken to evaluate such a dose-response relationship. METHODS AND MATERIALS: Women undergoing pelvic radiation therapy for cervix cancer within a phase 3 trial were included. The study necessitated 2 computed tomography imaging sets acquired at least 12 months apart in patients with no evidence of relapse. All images were transferred to the treatment planning system to determine radiation dose and Hounsfield unit (HU). Across the entire lumbopelvic region (lumbar 1-5 [L1-5] vertebrae, pubic symphysis, femur, acetabulum, greater trochanter, and anterior-superior iliac spine) multiple regions were defined to measure radiation therapy dose and HU. Bone health was categorized as normal if >130 HU, osteopenic at 110 to 130 HU, and osteoporotic <110 HU at baseline and follow-up. Univariate analysis was performed to test the effect of various factors on HU. Further interaction among radiation therapy dose, time, and HU was assessed using a linear mixed model. RESULTS: Overall, 132 of 300 patients were eligible. The median age was 49 (42-56) years. With a prescription dose of 50 Gy, the L1 and L2 vertebrae received a median dose of 1.2 and 4 Gy, respectively, and L3-5 received 10 to 50 Gy. At 24 months, median HU loss at L4-5 was 45 HU (interquartile range, 34-77 HU). Out of the 132 patients, at baseline 96% had normal bone health. However, at the last follow-up, 3% of patients had normal bone health, 12% developed osteopenia, and 85% developed osteoporosis (P < .001). There were no patient- or treatment-related factors predicted for HU loss on univariate analysis. HU loss >60 to 70 was observed at >45 Gy at L5 vertebra (60-70 HU, P < .02) and >15 Gy at L4 vertebra (33 HU; P = .04). CONCLUSIONS: Dose-response relationship is observed between radiation dose and bone mineral density loss. Prospective studies are needed to corroborate these observations and design future interventions.

FIGO Classification 2018: Validation Study in Patients With Locally Advanced Cervix Cancer Treated With Chemoradiation.

PURPOSE: In 2018, the International Federation of Gynecology and Obstetrics (FIGO) proposed a new staging for cervical cancer. The present study was designed to reclassify patients with locally advanced cervix cancer and perform a comparative evaluation with FIGO 2009. METHODS AND MATERIALS: Patients with locally advanced cervical cancer (stage IB2-IVA) who had baseline cross-sectional imaging and received (chemo-) radiation and brachytherapy were included. Survival outcomes were analyzed according to FIGO 2009. Patients were then reclassified according to FIGO 2018, and TNM classification outcomes were analyzed. FIGO stage and known prognostic factors were included in univariate analysis, and multivariate analysis was performed to investigate the prognostic value of clinical stage. RESULTS: Six hundred thirty-two patients were included. Overall, 185 (29.3%) patients had pelvic adenopathy, and 51 (8.2%) had positive paraortic nodes. At a median follow-up of 33 months, 116 (18.3%) patients had recurrence. Three-year disease-free survival (DFS) according to FIGO 2009 for stage IB, IIA, IIB, IIIA, IIIB, and IVA was 86%, 91%, 76%, 57%, 65%, and 61%, respectively. The 3-year DFS after restaging according to FIGO 2018 for stage IB, IIA, IIB, IIIA, IIIB, IIIC1, IIIC2, and IVA was 100%, 93%, 84%, 53%, 77%, 74%, 61%, and 61%, respectively. Patients with clinically significant lymphadenopathy had inferior outcomes compared with node-negative patients (62.9% vs 77.8%; P = .002). Patients with ≥3 paraortic nodes had poorer DFS than patients with <3 paraortic lymphadenopathy (13.6% vs 56.3%; P = .001). Furthermore, patients with primary tumor volume >30 cm3 had worse 3-year DFS than those with primary tumor volume ≤30 cm3 (67.4% vs 78.5%; P = .002). CONCLUSIONS: FIGO 2018 modification is associated with heterogenous outcomes in node-positive patients that are affected by primary tumor and nodal volume. We propose a modification to the existing TNM staging system to allow more robust classification of outcomes.