Diving into the vertical dimension of elasmobranch movement ecology

Knowledge of the three-dimensional movement patterns of elasmobranchs is vital to understand their ecological roles and exposure to anthropogenic pressures. To date, comparative studies among species at global scales have mostly focused on horizontal movements. Our study addresses the knowledge gap of vertical movements by compiling the first global synthesis of vertical habitat use by elasmobranchs from data obtained by deployment of 989 biotelemetry tags on 38 elasmobranch species. Elasmobranchs displayed high intra- and interspecific variability in vertical movement patterns. Substantial vertical overlap was observed for many epipelagic elasmobranchs, indicating an increased likelihood to display spatial overlap, biologically interact, and share similar risk to anthropogenic threats that vary on a vertical gradient. We highlight the critical next steps toward incorporating vertical movement into global management and monitoring strategies for elasmobranchs, emphasizing the need to address geographic and taxonomic biases in deployments and to concurrently consider both horizontal and vertical movements

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Prospective dietary polyunsaturated fatty acid intake is associated with trajectories of fatty liver disease: An 8 year follow-up study from adolescence to young adulthood

Background and aim Dietary fat intake has long been associated with fatty liver. Our study aimed to determine the effect of dietary fats on longitudinal fatty liver index (FLI) trajectories from adolescence to young adulthood. Methods Nine hundred eighty-five participants in the Raine Study, Perth, Western Australia, Australia, had cross-sectional assessments at ages 14, 17, 20 and 22 years, during which anthropometric measurements and blood tests were obtained. FLI trajectories were derived from the longitudinal FLI results. Dietary fat intake was measured with a semi-quantitative food frequency questionnaire at 14 years and log multinominal regression analyses were used to estimate relative risks. Results Three FLI trajectories were identified and labelled as stable-low (79.1%, N = 782), low-to-high (13.9%, N = 132), and stable-high (7%, N = 71). The low-to-high group associated with an increased intake of the long-chain polyunsaturated fatty acids EPA, DPA and DHA (RR 1.27, 95% CI 1.10–1.48) relative to the stable-low group. Compared to the stable-low group, omega-6 and the ratio of omega-6 to omega-3 in the stable-high group were associated with an increased relative risk of 1.34 (95% CI 1.02–1.76) and 1.10 (95% CI 1.03–1.16), respectively. Conclusion For those at high risk of fatty liver in early adolescence, high omega-6 fatty acid intake and a high ratio of omega-6 to omega-3 fatty acids are associated with increased risk of fatty liver. There should be caution in assuming these associations are causal due to possible undetected and underestimated confounding factors

Bile acids associate with specific gut microbiota, low-level alcohol consumption and liver fibrosis in patients with non-alcoholic fatty liver disease

© 2020 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd Background: Bile acids (BAs) are synthesized by the liver and modified by gut bacteria, and may play an intermediary role between the gut microbiome and liver in promoting fibrosis in non-alcoholic fatty liver disease (NAFLD). We investigated the associations between serum and faecal BAs, gut microbiome and fibrosis in patients with and without NAFLD and examined the impact of diet and alcohol consumption on these relationships. Methods: Adult patients (n = 122) underwent liver biopsy and BAs characterization by high-performance liquid chromatography/mass spectrometry. Gut microbiome composition was analysed using next-generation 16S rRNA sequencing. Diet and alcohol intake were determined by 3-day food diary. Results: Serum and faecal BA concentrations increased progressively among non-NAFLD controls (n = 55), NAFLD patients with no/mild fibrosis (F0-2, n = 58) and NAFLD with advanced fibrosis (F3/4, n = 9). Progressive increases in serum BAs were driven by primary conjugated BAs including glycocholic acid [GCA] and secondary conjugated BAs. In contrast, faecal BA increase was driven by secondary unconjugated BAs (predominately deoxycholic acid [DCA]). Serum GCA levels and faecal DCA levels correlated with the abundance of Bacteroidaceae and Lachnospiraceae, and stool secondary BAs with an unclassifiable family of the order Bacteroidales (Bacteroidales;other). These bacterial taxa were also associated with advanced fibrosis. Modest alcohol consumption was positively correlated with faecal DCA levels and relative abundance of Lachnospiracaea and Bacteroidales;other. Conclusions: Higher serum and faecal BA levels are associated with advanced fibrosis in NAFLD. Specific gut bacteria link alterations in BA profiles and advanced fibrosis, and may be influenced by low-level alcohol consumption

The borderline cervical smear: colposcopic and biopsy outcome

Aims—To review the outcome of women referred with smears showing borderline nuclear change (BNC), and to determine any differences in outcome if BNC was persistent, preceded by dyskaryosis, or followed treatment for cervical intraepithelial neoplasia (CIN). In addition, to determine criteria that might permit delineation of a BNC subtype, predictive of CIN. Methods—The records of 178 women referred for colposcopy in 1993, with last smear showing BNC, were obtained from our laboratory database. The cytology, colposcopy, and biopsy follow up for a five year period were also obtained. The patients were divided into three categories according to their smear status before the last referral borderline smear: category 1, persistent BNC (n = 39); category 2, BNC preceded by dyskaryotic smears (n = 100); and category 3, BNC after treatment for CIN (n = 39). The referral borderline smears were reviewed on cases with negative outcome and those with a biopsy diagnosis of CIN2 and CIN3. Results—In 50 women (28%) no biopsy was deemed necessary after colposcopic assessment. The biopsy results in the remaining 128 (72%) women were as follows: normal in 18 (10%), koilocytosis in 12 (7%), CIN1 in 45 (25%), CIN2 in 32 (18%), and CIN3 in 21 (12%) women. High grade lesions (CIN2, CIN3) were seen on biopsy in 14 of 39, 33 of 100, and six of 39 cases in category 1, category 2, and category 3, respectively. Blind review of the referral borderline smears from 53 women with a biopsy diagnosis of high grade lesions (32 CIN2, 21 CIN3) confirmed they were borderline in 23, upgraded them to mild dyskaryosis in 15, and found that 14 cases of isolated moderate or severe dyskaryotic cells had been missed originally. The borderline change was in mature squamous cells in five of 23 and in immature metaplastic epithelium in 18 of 23 cases. After smear review in 68 women with negative outcome, 36 smears were reclassified as negative in keeping with inflammation and atrophy, three were considered unsatisfactory, one was upgraded to CIN1, and 28 were confirmed as BNC. Of the latter, 25 of 28 were in mature squamous cells. The five year follow up on women with negative colposcopy (n = 50), negative loop excision of transformation zone (LETZ) (n = 18), and LETZ with koilocytosis (n = 12) showed subsequent high grade CIN on LETZ in 16, 0, and two patients, respectively. Conclusions—On referral of women for colposcopy with last smear showing BNC, the outcome was high grade CIN in over 30% of cases, irrespective of whether the borderline smear was preceded by another borderline smear or by a dyskaryotic smear. In contrast, in those referred because of BNC after treatment of CIN, high grade CIN was seen less frequently (15% of cases). Furthermore, in cases that necessitated loop excisions, high grade CIN was seen in 41%. This study also showed that BNC associated with inflammation or atrophy, or BNC in mature squamous cells, appears to have lower predictive value for CIN than those cases where BNC is associated with immature metaplastic epithelium. The use of terms such as "BNC favour reactive" for the former and "BNC favour dyskaryosis" for the latter is recommended, together with follow up by cytology and colposcopy, respectively. Key Words: borderline nuclear abnormality • cervical cytolog