Baseline Insulin Resistance Is a Determinant of the Small, Dense Low-Density Lipoprotein Response to Diets Differing in Saturated Fat, Protein, and Carbohydrate Contents

Individual responses to diet vary but causes other than genetics are poorly understood. This study sought to determine whether baseline values of homeostasis model assessment (HOMA-IR) was related to changes in small, dense low-density lipoprotein (sdLDL, i.e., LDL4, d = 1.044–1.063 g/mL) amounts quantified by isopycnic density profiling, in mildly hypercholesterolemic subjects (n = 27) consuming one of three low saturated fatty acid (SFA) diets: Dietary Approaches to Stop Hypertension (DASH), Beef in an Optimal Lean Diet (BOLD) and BOLD plus extra protein (BOLD+) when compared to a higher-SFA healthy American diet (HAD). The diets were consumed in random order for 5 wk, with 1 wk between diets. BOLD+ reduced fractional abundance (%) LDL4 (p < 0.05) relative to HAD, DASH and BOLD, and reductions in % LDL4 correlated with reductions in triglycerides (p = 0.044), total cholesterol (p = 0.014), LDL cholesterol (p = 0.004) and apolipoprotein B (p < 0.001). Responses to the four diets were similar (~12% decrease in % LDL4, p = 0.890) in the lower (<2.73 median) HOMA-IR subgroup but differed across diet conditions in the higher HOMA-IR subgroup (p = 0.013), in which % LDL4 was reduced with BOLD+ (−11%), was unchanged in BOLD and increased with the HAD (8%) and DASH (6%) diets (p < 0.05 for BOLD+ vs. HAD). Individual responses to diet interventions are influenced by presence and degree of insulin resistance as measured by HOMA-IR.

Mutational status of plasma exosomal KRAS predicts outcome in patients with metastatic colorectal cancer

Liquid biopsy has become a useful alternative in metastatic colorectal cancer (mCRC) patients when tissue biopsy of metastatic sites is not feasible. In this study we aimed to investigate the clinical utility of circulating exosomes DNA in the management of mCRC patients. Exosomes level and KRAS mutational status in exosomal DNA was assesed in 70 mCRC patients and 29 CRC primary tumor and were analysed at different disease steps evaluating serial blood samples (240 blood samples). There was a significant correlation between the extension of disease and exosomes level and the resection of primary localized tumor was correlated with a decrease of KRAS G12V/ D copies and fractional abundance in metastatic disease. CEA expression and liver metastasis correlated with a higher number of KRAS G12V/D copies/ml and a higher fractional abundance; in the subgroup of mCRC patients eligible for surgery, the size of tumor and the radiological response were related to exosomes level but only the size was related to the number of KRAS WT copies; both KRAS wild-type and mutated levels were identified as a prognostic factor related to OS. Finally, we found that 91% of mutated mCRC patients became wild type after the first line chemotherapy but this status reverted in mutated one at progression in 80% of cases. In a prospective cohort of mCRC patients, we show how longitudinal monitoring using exosome-based liquid biopsy provides clinical information relevant to therapeutic stratification.

IDH1/2 Mutations Are Maintained in a Subset of Patients with Acute Myeloid Leukemia in Complete Remission and Do Not Correlate with Residual Disease

Rationale: Isocitrate dehydrogenase 1 and 2 (IDH1/2) mutations may be the nearest signal to in vivo leukemogenesis that we are able to see in overt acute myeloid leukemia (AML). Without immediate transforming activity and slow, metabolism-related effect, IDH1/2 mutations may be considered within the early events that made a myeloid stem cell a malignant one. Methods: With the aim to investigate the behavior of IDH1/2 mutation in AML patients, we prospectively and longitudinally collected clinical data and samples of DNA extracted from bone marrow of consecutive patients. The study was approved by local Ethical Authority (012/2009/U/Tess, 01/2011/U/Tess, 10/2011/U/Tess and 253/2013/O/Tess). Droplet digital polymerase chain reaction (DdPCR) was performed with Bio-Rad's Qx200 DdPCR System© according manufacture instructions. DdPCR for all the samples were performed in duplicate. Serial dilutions were used to identify sensitivity limit of the method for each mutation included in the study. Results : We analyzed 106 samples from 23 patients (median of 5 samples per patient). At database cut-off, 19th September 2020, median follow-up was 23.8 months (IQR 19.5 - 38.8). Fourteen patients were female. Median age at AML diagnosis was 59 years (IQR: 47.5 - 66). Most of the patients had normal karyotype (15/23, 65%) and 1 patient (4%) received diagnosis of AML after a previous myelodysplastic syndrome. Five out of 22 patients tested (23%) harbored FLT3 ITD, 8/21 (38%) had a NPM1 mutation. Almost the entire population (20/23, 87%) received intensive chemotherapy as induction regimen and 55% of these patients obtained complete remission (CR) after induction. Ten out of 23 patients (45%) harbored an IDH1 mutation, 2/23 (9%) R132G and 8/23 (35%) R132H; 13/23 patients (57%) harbored an IDH2 mutation, 7/23 R172K, 1/23 (4%) R172S and 5/23 (22%) R140Q. Most of the samples were collected in complete remission (CR) (54.5%). Other samples were collected at the time of AML diagnosis (15.1%) or relapse/stable disease (37.3%). Median IDH1/2 fractional abundance was 45.3% (IQR 28.6 - 46.8) at diagnosis, 39.5% (IQR 29.5 - 48.0) at relapse/refractory, and .10 % (IQR: .05 - 17.24) in CR. Few cases showed a fractional abundance below 20% at relapse and only one case was IDH1 negative (during an extramedullary relapse). The fractional abundance of IDH1/2 mutation in CR present a bi-modal trend, allowing us to define 2 groups by k-means stratification. Patients in group 1 (42 samples) tend to have a mutation specific fractional abundance that varies with disease burden (figure B, blue box). On the contrary, at the different time points patients in group 2 (group center 45.58%, 12 samples) have fractional abundance values over 30%, comparable to the levels at diagnosis, even in the absence of any other evidence of AML (figure B, orange box). For NPM1, IDH1/2 positive patients, in 18 timepoints, NPM1 qPCR minimal residual disease (MRD) was compared with IDH1/2 fractional abundance selecting the best possible threshold (best possible threshold .083, predicted sensitivity 75%, predicted specificity 60%; R2= .763, 95% C.I.: .521 - .1.00; asymptotic significance = .062). Finally, we selected 15 patients in which we were able to determine IDH1/2 mutation fractional abundance after induction therapy. Our results indicate that IDH1/2 ddPCR positivity does not impact on prognosis in our patient set. Conclusion: Our study shows that IDH1/2 mutations are maintained throughout time in a subset of patients with IDH1/2 positive AML in CR and that they do not univocally correlate with levels of residual disease. In these AML patients, the persistence of IDH1/2 mutations may be part of a more complex process involving clonal hematopoiesis. In such setting, further studies on the biological and clinical significance of IDH1/2 mutations persistence are warranted. Figure 1 Figure 1. Disclosures Martinelli: Abbvie: Consultancy; Astellas: Consultancy, Speakers Bureau; Jazz Pharmaceuticals: Consultancy; Daichii Sankyo: Consultancy; Pfizer: Consultancy, Speakers Bureau; Roche: Consultancy; Celgene /BMS: Consultancy, Speakers Bureau; Incyte: Consultancy; Stemline Therapeutics: Consultancy. Papayannidis: Pfizer, Amgen, Novartis: Honoraria. Cavo: Takeda: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Adaptive Biotechnologies: Consultancy, Honoraria; Novartis: Honoraria; GlaxoSmithKline: Consultancy, Honoraria; Amgen: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Sanofi: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; AbbVie: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Janssen: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: TRAVEL, ACCOMMODATIONS, EXPENSES, Speakers Bureau; Celgene: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel Accommodations, Speakers Bureau; Bristol-Myers Squib: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Curti: Novartis: Membership on an entity's Board of Directors or advisory committees; Pfizer: Membership on an entity's Board of Directors or advisory committees; Jazz Pharma: Membership on an entity's Board of Directors or advisory committees; Abbvie: Membership on an entity's Board of Directors or advisory committees.

Analyses on salt-marsh vegetation composition changes in the Venice lagoon in the last twenty years

&lt;p&gt;Coastal salt-marshes are important eco-geomorphic features of coastal landscapes providing valuable ecosystem services, but unfortunately, they are among the most vulnerable ecosystems around the world. Their survival is mainly threatened by sea-level rise, wave erosion and human pressure. Halophytic vegetation distribution and dynamics control salt-marsh erosional and depositional patterns, critically determining marsh survival through complex bio-morphodynamic feedbacks. Although a number of studies have proposed species-classification methods and analyzed halophytic vegetation species distribution, our knowledge of the temporal evolution of species composition remains limited. To fill these gaps and better describe vegetation composition changes in time, we developed a novel classification method which is based on the Random Forest soft classification algorithm, and applied the method to two multi-spectral images of the San Felice marsh in the Venice lagoon (Italy) acquired in 2001 and 2019. The Random Forest soft classification achieves high accuracy (0.60 &lt; &lt;em&gt;R&lt;/em&gt;&lt;sup&gt;2&lt;/sup&gt; &lt; 0.96) in the estimation of the fractional abundance of each species in both images. We also determined the local dominant species, i.e. the species with the highest fractional abundance in each pixel. Our observations on the dominant species in 2001 and 2019 show that: 1) the area dominated by &lt;em&gt;Juncus&lt;/em&gt; and &lt;em&gt;Spartina&lt;/em&gt; decreased dramatically in such period; 2) the area dominated by &lt;em&gt;Limonium &lt;/em&gt;almost maintained constant; 3) a noticeable decrease in the bare-soil area occurred due to the encroachment of &lt;em&gt;Salicornia&lt;/em&gt; between 2001 and 2019. We also noticed that the probability distribution of the dominant patch area of each species is consistent with a power-law distribution, with different slopes for different vegetation species at different times. We suggest that vegetation composition changes are related to sea-level rise and to the species-specific inundation tolerance.&lt;/p&gt;

Detection of Somatic Mutations with ddPCR from Liquid Biopsy of Colorectal Cancer Patients

Liquid biopsy and cell-free DNA (cfDNA) show great promise in cancer diagnostics. In this study, we designed a custom droplet digital PCR (ddPCR) assay for the quantification and quality control of cfDNA isolated from serum. The assay was validated on a group of locally advanced colorectal cancer (CRC) patients and two control groups—patients with hemorrhoids and healthy individuals. The assay shows a high correlation with Qubit measurement (r = 0.976) but offers a higher dynamic range. Mean concentrations of cfDNA were 12.36 ng/µL, 5.17 ng/µL, and 0.29 ng/µL for CRC, hemorrhoid patients, and healthy controls, respectively. The quality of cfDNA was assessed with the measurement of B-cell DNA contamination. On a subset of CRC patients, we compared the mutation status on KRAS (G12A, G12D, G12V, G13D) and BRAF (V600E) genes in the primary tumor and cfDNA isolated from the serum. A total of 70.6% of primary tumor samples were mutated, and the mean fractional abundance of mutations was 9.50%. The matching serum samples were mutated in 38% cases with an average fractional abundance of 0.23%. We conclude that any decisions based solely on the amount of cfDNA present in patient serum must be interpreted carefully and in the context of co-morbidities. This study explores the potential of ddPCR somatic mutations detection from liquid biopsy as a supplement to tissue biopsy in targeted personalized CRC patient management.

A LONG-TERM LAND COVER AND LAND USE MAPPING METHODOLOGY FOR THE ANDEAN AMAZON

The data developed by the MapBiomas Amazon initiative ( http://amazonia.mapbiomas.org/ ) led by the Amazon Geo-referenced Socio-environmental Information Network’s (RAISG) is of unprecedented spatial and temporal resolution for the Andes region. It’s comprised by a series of annual maps for the years 2000 to 2017 that allow to monitor the extent of transformation in this region using a single regional methodological approach. Several variables were included to solve Andes-specific methodological challenges and they represent adaptations of RAISG’s Amazonian methodology to the Andean region. Among such, is the use of the novel NDFIb index (Turpo, 2018), an adaptation of the NDFI index that aims at mapping Andean Wetlands. Glaciers identification was aided by the fractional abundance of snow (Turpo, 2018), as well as small water bodies identification with McFeeters (1996) NDWI water index. This experience unfolds promising accessibility to novel land cover and land use regional reconstructions and comparisons possible only by the use of large-scale cloud-computing data processing tools, open source technology, spatially and temporally comprehensive remote sensing data, along with RAISG’s standardized protocols and frameworks.

Adaptation of Gut Microbiotas to Transgenic Pigs Secreting β-Glucanase, Xylanase and Phytase

BackgroundThe gut microbiotas play an important role in digestive function and feed efficiency in pigs. However, the effect of exogenous digestive enzymes on the composition and functional contributions of swine intestinal microbes is unclear. The objective of this study was to investigate the change of gut microbiotas in the transgenic pigs secreting microbial digestive enzymes in their salivary glands.MethodsEGFP marker-free transgenic (MF-TG) pigs were generated by deleted the EGFP coding genes in the transgenic pigs we previously generated. Samples of chyme from the ileum, caecum and colon of five MF-TG and five wild-type (WT) sows were collected for investigating the gut microbiomes via metagenomics analyses.ResultsThe levels of probiotics were abundant in the caecum of MF-TG pigs and higher than those of WT pigs. By contrast, the levels of some harmful microorganisms were higher in the caecum of WT pigs than those of MF-TG pigs. In addition, the microorganisms in the colon of MF-TG pigs had high fractional abundance in DNA (cytosine-5)-methyltransferase 1 and serine-type D-Ala-D-Ala carboxypeptidase, whereas the aspartate carbamoyltransferase regulatory subunit and outer membrane protein pathways were enriched in WT pigs. Moreover, the levels of numerous carbohydrases in the caecum of MF-TG pigs were higher than those of WT pigs. ConclusionsThe results indicated that intestinal microbes can change adaptively to the secretion of transgenic enzymes, thereby forming a benign cooperation with their host.

Assessing the Fractional Abundance of Highly Mixed Salt-Marsh Vegetation Using Random Forest Soft Classification

Coastal salt marshes are valuable and critical components of tidal landscapes, currently threatened by increasing rates of sea level rise, wave-induced lateral erosion, decreasing sediment supply, and human pressure. Halophytic vegetation plays an important role in salt-marsh erosional and depositional patterns and marsh survival. Mapping salt-marsh halophytic vegetation species and their fractional abundance within plant associations can provide important information on marsh vulnerability and coastal management. Remote sensing has often provided valuable methods for salt-marsh vegetation mapping; however, it has seldom been used to assess the fractional abundance of halophytes. In this study, we developed and tested a novel approach to estimate fractional abundance of halophytic species and bare soil that is based on Random Forest (RF) soft classification. This approach can fully use the information contained in the frequency of decision tree “votes” to estimate fractional abundance of each species. Such a method was applied to WorldView-2 (WV-2) data acquired for the Venice lagoon (Italy), where marshes are characterized by a high diversity of vegetation species. The proposed method was successfully tested against field observations derived from ancillary field surveys. Our results show that the new approach allows one to obtain high accuracy (6.7% < root-mean-square error (RMSE) < 18.7% and 0.65 < R2 < 0.96) in estimating the sub-pixel fractional abundance of marsh-vegetation species. Comparing results obtained with the new RF soft-classification approach with those obtained using the traditional RF regression method for fractional abundance estimation, we find a superior performance of the novel RF soft-classification approach with respect to the existing RF regression methods. The distribution of the dominant species obtained from the RF soft classification was compared to the one obtained from an RF hard classification, showing that numerous mixed areas are wrongly labeled as populated by specific species by the hard classifier. As for the effectiveness of using WV-2 for salt-marsh vegetation mapping, feature importance analyses suggest that Yellow (584–632 nm), NIR 1 (near-infrared 1, 765–901 nm) and NIR 2 (near-infrared 2, 856–1043 nm) bands are critical in RF soft classification. Our results bear important consequences for mapping and monitoring vegetation-species fractional abundance within plant associations and their dynamics, which are key aspects in biogeomorphic analyses of salt-marsh landscapes.

The abundance of S- and Si-bearing molecules in O-rich circumstellar envelopes of AGB stars

Aims. We aim to determine the abundances of SiO, CS, SiS, SO, and SO2 in a large sample of oxygen-rich asymptotic giant branch (AGB) envelopes covering a wide range of mass loss rates to investigate the potential role that these molecules could play in the formation of dust in these environments. Methods. We surveyed a sample of 30 oxygen-rich AGB stars in the λ 2 mm band using the IRAM 30m telescope. We performed excitation and radiative transfer calculations based on the large velocity gradient method to model the observed lines of the molecules and to derive their fractional abundances in the observed envelopes. Results. We detected SiO in all 30 targeted envelopes, as well as CS, SiS, SO, and SO2 in 18, 13, 26, and 19 sources, respectively. Remarkably, SiS is not detected in any envelope with a mass loss rate below 10−6 M⊙ yr−1, whereas it is detected in all envelopes with mass loss rates above that threshold. From a comparison with a previous, similar study on C-rich sources, it becomes evident that the fractional abundances of CS and SiS show a marked differentiation between C-rich and O-rich sources, being two orders of magnitude and one order of magnitude more abundant in C-rich sources, respectively, while the fractional abundance of SiO turns out to be insensitive to the C/O ratio. The abundance of SiO in O-rich envelopes behaves similarly to C-rich sources, that is, the denser the envelope the lower its abundance. A similar trend, albeit less clear than for SiO, is observed for SO in O-rich sources. Conclusions. The marked dependence of CS and SiS abundances on the C/O ratio indicates that these two molecules form more efficiently in C- than O-rich envelopes. The decline in the abundance of SiO with increasing envelope density and the tentative one for SO indicate that SiO and possibly SO act as gas-phase precursors of dust in circumstellar envelopes around O-rich AGB stars.