Miracle-dz/UniFAR-FTUs huggingface dataset:
WHIRLY2 plays a key role in mitochondria morphology, dynamics, and functionality in Arabidopsis thaliana

Abstract WHIRLY2 is a single‐stranded DNA binding protein associated with mitochondrial nucleoids. In the why 2‐1 mutant of Arabidopsis thaliana, a major proportion of leaf mitochondria has an aberrant structure characterized by disorganized nucleoids, reduced abundance of cristae, and a low matrix density despite the fact that the macroscopic phenotype during vegetative growth is not different from wild type. These features coincide with an impairment of the functionality and dynamics of mitochondria that have been characterized in detail in wild‐type and why 2‐1 mutant cell cultures. In contrast to the development of the vegetative parts, seed germination is compromised in the why 2‐1 mutant. In line with that, the expression level of why 2 in seeds of wild‐type plants is higher than that of why 3, whereas in adult plant no difference is found. Intriguingly, in early stages of shoots development of the why 2‐1 mutant, although not in seeds, the expression level of why 3 is enhanced. These results suggest that WHIRLY3 is a potential candidate to compensate for the lack of WHIRLY2 in the why 2‐1 mutant. Such compensation is possible only if the two proteins are localized in the same organelle. Indeed, in organello protein transport experiments using intact mitochondria and chloroplasts revealed that WHIRLY3 can be dually targeted into both, chloroplasts and mitochondria. Together, these data indicate that the alterations of mitochondria nucleoids are tightly linked to alterations of mitochondria morphology and functionality. This is even more evident in those phases of plant life when mitochondrial activity is particularly high, such as seed germination. Moreover, our results indicate that the differential expression of why 2 and why 3 predetermines the functional replacement of WHIRLY2 by WHIRLY3, which is restricted though to the vegetative parts of the plant.
Has the term “conservation biology” had its day?

© The Ecological Society of America www.frontiersinecology. org Has the term “conservation biology” had its day? The “conservation biology” literature has increased tremendously in volume during the past two decades. Furthermore, the field has expanded in breadth to include various disciplines, reaching far beyond biological or ecological science. Consequently, is it time for a name change? Although the importance of social science disciplines within conservation biology has already been acknowledged in Soulé’s landmark paper (Soulé 1985), non-biological disciplines therein were largely neglected during the 1980s and 1990s. For example, the topics covered at the Society for Conservation Biology’s (SCB’s) first annual meeting, held in 1987, were almost entirely restricted to biology and land management (Ginsberg 1987). Since then, there is no doubt that conservation biology has – in practice – developed into a truly interdisciplinary subject (see eg Meine et al. [2006] for a historical account). Thus, the list of topic areas for SCB’s 2009 annual meeting included – in addition to more “traditional” conservation topics – environmental economics, politics and policy, anthropology, sociology, and psychology. A question that is increasingly being asked is whether the term “conservation biology” is appropriate in light of that conceptual expansion. We do not think so. In “conservation biology”, the word “conservation” is used as a noun adjunct modifying “biology”. Linguistically, this makes conservation biology a subdiscipline of biology, just like cell biology, freshwater biology, or invasion biology. Are there any alternative naming conventions that would capture the full contemporary span of this discipline? The term “conservation research”, which is already being used to some extent (eg Bhagabati 2007), would better acknowledge the field’s breadth. In cases where the ecological context may not be obvious, it may also be necessary to add qualifiers to distinguish the field from other disciplines that involve conserving things (eg architecture, art, or digital information). Here, terms such as “biodiversity conservation research” could be used. The term “conservation biology” is certainly appropriate as a name for the discipline addressing biological aspects of conservation. However, when referring to the wider interdisciplinary field that has developed over time, we argue that adopting a new terminology is warranted. This is an important step toward embracing the broad range of actors – from many disciplines – who are needed to save the world’s biodiversity. Jean-Michel Roberge, Grzegorz Mikusiński, and Hugh P Possingham Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden (Jean-Michel.Roberge @vfm.slu.se); Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences, Riddarhyttan, Sweden; The Ecology Centre, School of Integrative Biology, University of Queensland, St Lucia, Queensland, Australia
CRISPRi-mediated functional analysis of lung disease-associated loci at non-coding regions

Abstract Genome-wide association studies have identified lung disease-associated loci; however, the functions of such loci are not well understood in part because the majority of such loci are located at non-coding regions. Hi-C, ChIP-seq and eQTL data predict potential roles (e.g. enhancer) of such loci; however, they do not elucidate the molecular function. To determine whether these loci function as gene-regulatory regions, CRISPR interference (CRISPRi; CRISPR/dCas9-KRAB) has been recently used. Here, we applied CRISPRi along with Hi-C, ChIP-seq and eQTL to determine the functional roles of loci established as highly associated with asthma, cystic fibrosis (CF), chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF). Notably, Hi-C, ChIP-seq and eQTL predicted that non-coding regions located at chromosome 19q13 or chromosome 17q21 harboring single-nucleotide polymorphisms (SNPs) linked to asthma/CF/COPD and chromosome 11p15 harboring an SNP linked to IPF interact with nearby genes and function as enhancers; however, CRISPRi indicated that the regions with rs1800469, rs2241712, rs12603332 and rs35705950, but not others, regulate the expression of nearby genes (single or multiple genes). These data indicate that CRISPRi is useful to precisely determine the roles of non-coding regions harboring lung disease-associated loci as to whether they function as gene-regulatory regions at a genomic level.
Risk perception of heat related disorders on the workplaces: a survey among health and safety representatives from the autonomous province of Trento, Northeastern Italy

Summary Introduction This study will investigate knowledge, attitude and practices towards heat-related health issues in a sample of safety representatives from Northern Italy (H&SRs). Methods A cross-sectional questionnaire survey was conducted in 2016-2017 among 298 H&SR. Knowledge status was measured both in general but as well and focusing on first-aid issues. Assessment of risk perception included severity and frequency of heat-related events. Multivariate logistic regression analysis assessed individual and work-related characteristics associated with H&SRs’ risk perception. Results 258 questionnaires were retrieved (participation rate 86.6%; mean age 48.2 ± 8.4 years). Knowledge status was relatively good on technical/preventive issues (62.3% ± 16.8) and first aid measures (72.6% ± 27.2), but a large share of respondents ignored the risk from exertional heat stroke (35.9%), and for heat strokes elicited by non-environmental heat (e.g. machineries, use of protective equipment, etc. 47.9%). The majority of respondents acknowledged the high frequency of extreme events like heat waves (62.0%), but only 44.6% agreed on their potential health threat, with an unsatisfying cumulative risk perception score (55.4% ± 23.5). A specific first-aid formation course was reported by 49.2% of respondents, while 10.9% had any previous interaction with heat-related disorders. Specific countermeasures for heat waves had been put in place by parent company in 20.1% of cases. Eventually, higher educational achievements (mOR 2.239, 95% CI 1.184-4.233) and a better general knowledge status (mOR 1.703, 95% CI 1.073-2.979) were positive predictors for higher risk perception. Conclusions Although H&SRs exhibited a good understanding of heat-related health issues, stakeholders should improve the implementation of specific countermeasures on the workplaces.
Improved ADM Penetration Distance and Therapeutic Efficiency in a Rabbit VX2 Liver Cancer Model by Relaxin Infusion Combined with Transcatheter Chemoembolization Through Hepatic Artery

Purpose To evaluate the adriamycin (ADM) pervasion distance within tumor stroma after relaxin (RLX) infusion through tumor feeding artery and further investigate the therapeutic effects of RLX infusion combined with transcatheter chemoembolization (TACE) on the rabbit VX2 liver cancer, since the chemotherapy impaired due to limited drug distribution hindered by stiffened tumor stroma. Materials and Methods In the first part, rabbits received normal saline (NS), RLX or combined with TACE, and the penetration distance of ADM was measured by immunofluorescence and the matrix metalloproteinases (MMPs) were evaluated by gelatin substrate zymography in each group. In the second part, the rabbits received NS, TACE and RLX combined with TACE, respectively. The tumor growth rates, necrosis rates and intrahepatic metastasis were measured, and hematoxylin-eosin (HE), transferase-mediated dUTP-biotin nick end labelling (TUNEL) and Ki67 staining were conducted in each group. Results In the first part, the expression of MMP-9 was increased in groups treated by RLX compared with NS group, especially three days after RLX infusion (p=0.001). The ADM penetration distance was significantly increased in groups treated by RLX compared with NS group (p<0.05), and it was farthest three days after RLX infusion. In the second part, compared with the NS and TACE groups, the tumor growth rates, the positive staining rates of Ki67 and the tumor growth rates were significantly decreased in RLX+TACE group (p<0.05). However, the positive staining rates of TUNEL and the tumor necrosis rates were significantly increased (p<0.05), and HE staining also revealed higher necrosis rates. The intrahepatic metastasis indicates no difference between the three groups (p=0.273). Conclusion An increased penetration distance was obtained by RLX infusion through tumor feeding artery, and better therapeutic effects were achieved by RLX combined with TACE.
The TNF-β Gene Nco I Polymorphism Is Not Associated with Hypertriglyceridemia or Insulin Resistance in Lean and Obese Subjects☆

Interindividual differences in TNF-α monocyte responses can be accounted for by genetic polymorphisms at the TNF-β locus defined by theNco Irestriction enzyme. Higher triglyceride levels in non-insulin-dependent diabetic patients homozygous at the 10.5-kb fragment of the TNF-β gene have been described. The aim of this study was to investigate whether the Ncol polymorphism of the TNF-β gene influences the relationship between insulin resistance and triglyceride levels. Thirty-eight healthy volunteers were divided into two groups according to the absence [homozygous for class 1 allele (1/1), n=16] or presence of the class 2 allele [n=22; 19 heterozygous (1/2), and 3 homozygous (2/2)]. Both groups were comparable in sex, age, BMI, waist/hip ratio, fat mass and percentage of body fat as measured by bioelectric impedance, skinfold measurements, and blood pressure (all p>0.05). There were no differences in serum cholesterol (total, or HDL and VLDL fractions) or in total or VLDL triglycerides between the groups (all p>0.05). The insulin sensitivity index (Minimal Model method) was comparable for the two groups. In summary, the 10.5-kb homozygous genotype of the TNF-β locus does not contribute to differences in triglyceride levels or insulin sensitivity among nondiabetic subjects.
The band and slough technique is effective for management of diminutive type 1 gastric and duodenal neuroendocrine tumors

Abstract Background and study aims Endoscopic resection is recommended as initial treatment for early-stage gastric and duodenal neuroendocrine tumors (G-NETs and D-NETs). However, it can cause serious adverse events. We aimed to evaluate the efficacy and safety of the band and slough (BAS) technique as a novel and less aggressive endoscopic therapy for management of such tumors. Four patients, three diagnosed with < 10-mm D-NET and one with 10-mm type I G-NET, were treated with the BAS technique without endoscopic resection. Initial follow-up endoscopy at 3 months was done to assess for residual tumor. Subsequent endoscopic surveillance was performed. After one session of banding, all patients achieved complete remission at 3-month follow-up. No tumor recurrence was detected on repeat biopsy at 12-month surveillance endoscopy. None of the patients developed any adverse events including bleeding or perforation. The BAS technique may prove to be a safe and effective endoscopic therapy for diminutive, non-metastatic type 1 G-NETs and D-NETs. Studies of larger scale and longer follow-up periods are needed to corroborate these findings.
Host–parasite interactions in clubroot of crucifers

Abstract Clubroot, caused by Plasmodiophora brassicae, is an important root disease of crucifers worldwide. In this review, the molecular aspects of clubroot pathogenesis and resistance are discussed. Topics covered include recent studies on the processes associated with infection by primary and secondary pathogen zoospores, examination of the expression patterns of P. brassicae genes at different stages of infection, and the concurrent identification of candidate genes for functional studies. Although the whole genome sequence of P. brassicae is not yet available, molecular studies of the pathogen are nonetheless moving into the genomics era. Transcriptomics and functional analyses of individual genes involved in the P. brassicae/Brassica interaction have recently been conducted to complement studies on the excellent model host, Arabidopsis thaliana. Two resistance genes have been cloned and their molecular functions illustrated, supporting suggestions that the clubroot pathosystem follows the gene-for-gene model. Although much about the pathogenesis of clubroot remains unknown, significant advances have been made in recent years, which may facilitate the identification of targets for agro-chemical development and resistance breeding.
A Review of Last Decade Developments on Epiretinal Membrane Pathogenesis

Epiretinal membrane (ERM) is a pathologic tissue that develops at the vitreoretinal interface. ERM is responsible for pathological changes of vision with varying degrees of clinical significance. It is either idiopathic or secondary to a wide variety of diseases such as proliferative diabetic retinopathy (PDR) and proliferative vitreoretinopathy (PVR). A great variation in the prevalence of idiopathic ERM among different ethnic groups proposed that genetic and lifestyle factors may play a role in ERM occurrence. Histopathological studies demonstrate that various cell types including retinal pigment epithelium (RPE) cells, fibrocytes, fibrous astrocytes, myofibroblast-like cells, glial cells, endothelial cells (ECs) and macrophages, as well as trophic and transcription factors, including transforming growth factor (TGF), vascular endothelial growth factor (VEGF), platelet-derived growth factor (PDGF) etc., are directly or indirectly involved in the pathogenesis of idiopathic or secondary ERMs. These processes are driven (on the last count) by more than 50 genes, such as Tumor Necrosis Factor (TNF), CCL2 (chemokine (C-C motif) ligand )), Metastasis Associated Lung Adenocarcinoma Transcript 1 )MALAT1(, transforming growth factor (TGF)-β1, TGF-β2, Interleukin-6 (IL-6), IL-10, VEGF and glial fibrillary acidic protein (GFAP), some of which have been studied more intensely than others. The present paper tried to summarize, highlight and cross-correlate the major findings made in the last decade on the function of these genes and their association with different types of cells, genes and gene expression products in the ERM formation.
Indian calcid wasps (Hymenoptera) of the genus Dirhinus Parasitic on synanthropic and other Diptera

Abstract The species of Dirhinini from the Indian Subcontinent are revised and a key given to the ten recognized species. These are classified in one genus, Dirhinus Dalman, with two subgenera. Four new species, claviger, deplanatus, pilifer and altispina, are described and seventeen new synonyms (sixteen specific, one generic) proposed. All pertinent biological data are critically reviewed, all host records being from Diptera, especially synanthropic muscoid flies, noxious fruitflies and tachinids. Observations are made on geographic distributions, two species being found to extend from Africa to the Hawaiian Islands.
PHOTOSYNTHESIS AND RESPIRATION IN THE SUB‐ANTARCTIC TUSSOCK GRASS POA COOKII

SUMMARY Poa cookii dominates the tussock grasslands at islands of the Kerguelen Province of the sub-Antarctic. In common with other sub-Antarctic Poa species it is highly productive. Infra-red gas analysis studies at Marion Island (46° S, 37° E) showed that P. cookii is a C3 photosynthetic type plant, possessing a high CO2 compensation concentration (c. 100 p.p.m.) and apparently high rates of photorespiration. However, photosynthetic light saturation was not attained at a photosynthetic photon flux density (PPFD) of 2000μmol m−2s−1, possibly due to leaf anatomical features causing shading of the chlorophyllous mesophyll. Compensating irradiance values were 5 to 11 μmol m−2s−1. Net photosynthesis occurred below 0 °C and increased with temperature up to 10 to 12 °C, remaining constant up to 19 to 23 °C, depending in PPFD. Dark respiration increased exponentially with temperature and at 32 °C the temperature optimum had not been reached. Photorespiration also increased with temperature but rates were lower than those of dark respiration. Increasing the wind velocity over a leaf immediately decreased the net assimilation rate, which then slowly recovered to almost the original level. It appears that the grass is well-adapted to sub-Antarctic conditions of low light, low (seldom freezing) temperatures and high wind.
Photodynamic therapy for the eradication of biofilms formed by catheter associated Pseudomonas aeruginosa strains

Pseudomonas aeruginosa has emerged as a major opportunistic pathogen causing catheter-associated urinary tract infections (CA-UTIs) associated with high mortality and morbidity. In this study 18 P. aeruginosa isolates from urine of catheterized patients were evaluated for in vitro biofilm formation.All the tested strains showed the ability to form biofilm more thicker than those formed by a cohort of 29 blood culture strains belonging to the same species. Photodynamic antimicrobial chemotherapy (PACT) is a novel antimicrobial treatment that exploits a photosensitizer (PS) and visible light to induce lethal oxidative damages in bacterial cells and could be used as local antimicrobial approach in CA-UTIs. Here we tested the susceptibility of planktonic and sessile cultures of P. aeruginosa strains, the model strain PAO1 and CA-UTI isolates, to photodynamic inactivation with a di cationic porphyrinic photosensitizer, the 5, 15-di (N-benzyl-4-pyridynium)-porphyrin di chloride.Although Pseudomonas aeruginosa is regarded as a difficult target for antimicrobial chemotherapy, satisfactory bactericidal activities on both planktonic and biofilm cultures were observed.
A four‐factor immune risk score signature predicts the clinical outcome of patients with spinal chordoma

Abstract Background Currently, the measurement of immune cells in previous studies is usually subjective, and no immune‐based prognostic model has been established for chordoma. In this study, we sought to simultaneously measure tumor‐infiltrating lymphocyte (TIL) subtypes in chordoma samples using an objective method and develop an immune risk score (IRS) model for survival prediction. Methods Multiplexed quantitative immunofluorescence staining was used to determine the TIL levels in the tumoral and stromal subareas of 114 spinal chordoma specimens (54 in the training and 60 in the validation cohort) for programmed death‐1 (PD‐1), CD3, CD8, CD20 (where CD is cluster of differentiation), and FOXP3. Flow cytometry was performed to validate the immunofluorescence assay for lymphocyte measurement on an additional five fresh chordoma specimens. Subsequently, the IRS model was built using the least absolute shrinkage and selection operator (LASSO) Cox regression method. Results Flow cytometry and quantitative immunofluorescence showed similar lymphocytic percentages and TIL subpopulation proportions in the fresh tumor specimens. With the training data, the LASSO model identified four immune features for IRS construction: tumoralFOXP3, tumoralPD‐1, stromalFOXP3, and stromalCD8. In both cohorts, a high IRS was significantly associated with tumoral programmed cell death‐1 ligand 1 expression, Enneking inappropriate tumor resection, and surrounding muscle invasion by tumor. Multivariate Cox regression and stratified analysis in the two cohorts revealed that the IRS was an independent predictor and could effectively separate patients with similar Enneking staging into different risk subgroups, with significantly different survival rates. Further receiver operating characteristic analysis found that the IRS classifier had a better prognostic value than the traditional clinicopathological factors and compensated for the deficiency of Enneking staging for outcome prediction. More importantly, a nomogram based on the IRS and clinical predictors showed adequate performance in estimating disease recurrence and survival of patients. Conclusions These data support the use of the IRS signature as a reliable prognostic tool in spinal chordoma and may facilitate individualized therapy decision making for patients.