Application of real-time PCR for the identification of the endangered species Galemys pyrenaicus through faecal samples.

BACKGROUND: Currently, many micromammals are important targets for study. The endangered Galemys pyrenaicus is an outstanding example. Globally, their populations have suffered a substantial decline in last 20 years. In the surveyed area, the capture of desman is legally forbidden due to the high conservation concerns. Reason by non-invasive sampling through faeces is proposed for its monitoring. Furthermore, the confusion between faeces from desman and Mediterranean water shrews must be considered. Thus, the aim of this study was focused on developing RT-PCR assays to determine the presence of Galemys pyrenaicus and N. a. anomalus from non-invasive samples. METHODS AND RESULTS: The study was conducted in the mountains of the System Central of Extremadura (Spain). A total of 186 samples were collected from 2018 to 2021 by experts where historically reported and/or our previous studies confirmed their presence. RT-PCR assays using hydrolysis probes were designed to detect genetic material from both desman and Mediterranean water shrews and its specificity was confirmed. The reliability of the method was further assessed by PCR sequencing of mitochondrial Cyb and d-loop, resulting fully compatible with the RT-PCR approach. Intraspecific phylogenetic relationship was reported to improve knowledge about mtDNA variability in the desman from the Central System. CONCLUSIONS: We demonstrated that RT-PCR gives a gold opportunity to further map the species using faeces which minimizes disturbance and reports both population status and individual presence. Cost-effective RT-PCR combined with field-collected faeces allows us to better investigate the full range of occurrence of the species.

Non-Invasive Wildlife Disease Surveillance Using Real Time PCR Assays: The Case of the Endangered Galemys pyrenaicus Populations from the Central System Mountains (Extremadura, Spain).

The Iberian desman (Galemys pyrenaicus) is a small semi-aquatic mammal that inhabits mountainous areas from the centre to the north of the Iberian Peninsula and the Pyrenees and is listed as endangered because it has suffered a serious decline. Since 1960, only three species of digeneans (Omphalometra flexuosa, Maritrema pyrenaica and Mathovius galemydis) and two nematodes (Aonchotheca galemydis and Paracuaria hispanica) have been reported from the desman, but no further information on health status and no data from Extremadura has been available. The aim of our study was to characterise the diversity and distribution of parasites and microbiomes of desmans in different areas of the Central System of Extremadura. Between 2019 and 2021 we collected 238 fecal samples and one tissue (intestine) sample that was obtained from a dead desman. DNA templates were processed by commercial or customised real-time PCR using TaqMan probes. Representative data were obtained for Cryptosporidium spp., Omphalometra spp., Eimeria spp., Salmonella spp., Staphylococcus spp. and Leptospira spp. Omphalometra spp. was studied using a newly developed PCR test. The screening of the dead desman allowed us to obtain, for the first time, a partial sequence of the 18SrDNA. This study is the most complete study of the desman, allowing us to identify parasites and the microbiome in populations of G. pyrenaicus using non-invasive sampling.

Economic and Environmental Performance of an Integrated CO2 Refinery.

The consequences of global warming call for a shift to circular manufacturing practices. In this context, carbon capture and utilization (CCU) has become a promising alternative toward a low-emitting chemical sector. This study addresses for the first time the design of an integrated CO2 refinery and compares it against the business-as-usual (BAU) counterpart. The refinery, which utilizes atmospheric CO2, comprises three synthesis steps and coproduces liquefied petroleum gas, olefins, aromatics, and methanol using technologies that were so far studied decoupled from each other, hence omitting their potential synergies. Our integrated assessment also considers two residual gas utilization (RGU) designs to enhance the refinery's efficiency. Our analysis shows that a centralized cluster with an Allam cycle for RGU can drastically reduce the global warming impact relative to the BAU (by ≈135%) while simultaneously improving impacts on human health, ecosystems, and resources, thereby avoiding burden-shifting toward human health previously observed in some CCU routes. These benefits emerge from (i) recycling CO2 from the cycle, amounting to 11.2% of the total feedstock, thus requiring less capture capacity, and (ii) reducing the electricity use while increasing heating as a trade-off. The performance of the integrated refinery depends on the national grid, while its high cost relative to the BAU is due to the use of expensive electrolytic H2 and atmospheric CO2 feedstock. Overall, our work highlights the importance of integrating CCU technologies within chemical clusters to improve their economic and environmental performance further.

Phot0, a plausible primeval pigment on Earth and rocky exoplanets.

In view of the existing controversy around the origin of the photosynthesis and, therefore, the first photosynthetic pigments, our work focuses on the theoretical study of a hypothetical first pigment, simpler than those existing today, that collects energy from solar radiation on Earth-like exoplanets. Our theoretical results show that there could exist geochemical conditions that allow the abiotic formation of a primeval pigment that might become sufficiently abundant in the early stages of habitable rocky exoplanets. These conditions would place this pigment before the appearance of life in a very young planet, thanks to chemical routes instead of biochemical transformations. Thus, our results may refute the currently accepted hypothesis that the complex biomolecules that allowed the photosynthesis to be carried out were synthesized through complex and evolved metabolic pathways. In addition, we show that the proposed primeval pigment, which we call Phot0, is also a precursor of the more evolved pigments known today on Earth and demonstrate, for the first time, an abiotic chemical route leading to tetrapyrroles not involving pyrrole derivatives. Our proposal places simple and very abundant raw materials in never-before-proposed geochemical conditions that lead to the formation of biomolecules of biological interest.

Ground-based detection of an extended helium atmosphere in the Saturn-mass exoplanet WASP-69b.

Hot gas giant exoplanets can lose part of their atmosphere due to strong stellar irradiation, and these losses can affect their physical and chemical evolution. Studies of atmospheric escape from exoplanets have mostly relied on space-based observations of the hydrogen Lyman-α line in the far ultraviolet region, which is strongly affected by interstellar absorption. Using ground-based high-resolution spectroscopy, we detected excess absorption in the helium triplet at 1083 nanometers during the transit of the Saturn-mass exoplanet WASP-69b, at a signal-to-noise ratio of 18. We measured line blueshifts of several kilometers per second and posttransit absorption, which we interpret as the escape of part of the atmosphere trailing behind the planet in comet-like form.

The Administration of Escherichia coli Nissle 1917 Ameliorates Development of DSS-Induced Colitis in Mice.

The beneficial effects of probiotics on immune-based pathologies such as inflammatory bowel disease (IBD) have been well reported. However, their exact mechanisms have not been fully elucidated. Few studies have focused on the impact of probiotics on the composition of the colonic microbiota. The aim of the present study was to correlate the intestinal anti-inflammatory activity of the probiotic Escherichia coli Nissle 1917 (EcN) in the dextran sodium sulfate (DSS) model of mouse colitis with the changes induced in colonic microbiota populations. EcN prevented the DSS-induced colonic damage, as evidenced by lower disease activity index (DAI) values and colonic weight/length ratio, when compared with untreated control mice. The beneficial effects were confirmed biochemically, since the probiotic treatment improved the colonic expression of different cytokines and proteins involved in epithelial integrity. In addition, it restored the expression of different micro-RNAs (miR-143, miR-150, miR-155, miR-223, and miR-375) involved in the inflammatory response that occurs in colitic mice. Finally, the characterization of the colonic microbiota by pyrosequencing showed that the probiotic administration was able to counteract the dysbiosis associated with the intestinal inflammatory process. This effect was evidenced by an increase in bacterial diversity in comparison with untreated colitic mice. The intestinal anti-inflammatory effects of the probiotic EcN were associated with an amelioration of the altered gut microbiome in mouse experimental colitis, especially when considering bacterial diversity, which is reduced in these intestinal conditions. Moreover, this probiotic has shown an ability to modulate expression levels of miRNAs and different mediators of the immune response involved in gut inflammation. This modulation could also be of great interest to understand the mechanism of action of this probiotic in the treatment of IBD.

Minimizing Next-Generation Sequencing Errors for HIV Drug Resistance Testing.

Next-generation sequencing prototypes for the routine diagnosis of resistance to antiretrovirals approved for the treatment of HIV infection are now being used in many clinical diagnostic laboratories. As some of the next-generation sequencing platforms may be a source of errors, it is necessary to improve the currently available protocols and implement bioinformatic tools that may help to correctly identify the presence of resistance mutations with clinical impact. Several studies have addressed these issues in recent years. Some of them are mainly focused on improving protocols for decreasing the magnitude of errors during the polymerase change reaction. Other studies propose specific bioinformatic tools, able to reach both a 93-98% reduction of indels (insertions/deletions) and a sensitivity and specificity close to 100% in single nucleotide polymorphism variant calling. The implementation of new protocols and bioinformatic tools improving the accuracy of next-generation sequencing results must be considered for a correct analysis of HIV resistance mutations for making clinical decisions. This review summarizes the most relevant data available for the optimization of next-generation sequencing applied to HIV resistance testing.

Stem cells protect the bronchial stump in rat, increasing Sox6, Col2a1, and Agc1 expression.

BACKGROUND: Post-pneumonectomy bronchopleural fistulas (BPFs) are associated with high morbidity and mortality. Currently, since the management of BPFs is difficult to assess, the best therapeutic approach is prevention. Our objective was to evaluate the effects of adipose-derived stem cells (ASCs) on the healing of the bronchial stump in an experimental animal model. METHODS: Left pneumonectomy was performed in 37 Sprague-Dawley rats. Animals were randomly assigned to a control group (n = 13), an ASC group (n = 12), and an ASC plus Tissucol(®) group (ASCT) (n = 12). The ASCs and ASCTs were locally administered at the bronchial stump after surgical pneumonectomy. Animals were killed at 10 and 20 days. We analyzed histological changes and changes in the expression of relevant genes involved in wound repair in the bronchial stump. RESULTS: Two control animals, one animal from the ASC group, and one from the ASCT group died from early BPF. All the remaining animals had an adequate postoperative outcome. ASCs and ASCTs significantly decreased the necrosis and ulcerations of the bronchial stump at 10 and 20 days. ASCs significantly decreased mRNA expression of Igf1 at 10 days and Igf1, Tgfb1, Vegfa, and Col2a1 at 20 days, whereas there was increased expression of Agc1 and Col2a1 at 10 days and Sox6 at 20 days. CONCLUSIONS: Our findings indicate that local ASCs protected the bronchial stump after pneumonectomy and induced local changes in gene expression related to their protective action. These results could lead to a potential new therapeutic modality for the prevention of BPF.

Autologous platelet-poor plasma decreases the bronchial stump necrosis in rat.

BACKGROUND: Necrosis of the bronchial stump is a very important trigger for bronchopleural fistula. The administration of local autologous platelet-poor plasma (PPP) could protect the bronchial stump. MATERIALS AND METHODS: Left pneumonectomy was performed in 25 Sprague-Dawley rats. Animals were randomly assigned to a control group (n=13) and PPP group (n=12). PPP was locally administered on the bronchial stump after pneumonectomy. We analyzed histologic changes in the bronchial stump and messenger RNA expression changes of genes involved in wound repair at 10 and 20 d. RESULTS: Local PPP treatment produced a mass of fibrous tissue surrounding the bronchial stump and significantly decreased the presence of necrosis at 20 d. PPP increased the expression of insulin like growth factor 1 at 10 d although it did not reach statistical significance. CONCLUSIONS: Our findings indicate that local PPP treatment of the bronchial stump after pneumonectomy decreased necrosis and could have a protective effect on the bronchial stump.

Increased photovoltaic power output via diffractive spectrum separation.

In this Letter, we report the preliminary demonstration of a new paradigm for photovoltaic power generation that utilizes a broadband diffractive-optical element (BDOE) to efficiently separate sunlight into laterally spaced spectral bands. These bands are then absorbed by single-junction photovoltaic cells, whose band gaps correspond to the incident spectral bands. We designed such BDOEs by utilizing a modified version of the direct-binary-search algorithm. Gray scale lithography was used to fabricate these multilevel optics. They were experimentally characterized with an overall optical efficiency of 70% over a wavelength range of 350-1100 nm, which was in excellent agreement with simulation predictions. Finally, two prototype devices were assembled: one with a pair of copper indium gallium selenide based photovoltaic devices, and another with GaAs and c-Si photovoltaic devices. These devices demonstrated an increase in output peak electrical power of ∼ 42% and ∼ 22%, respectively, under white-light illumination. Because of the optical versatility and manufacturability of the proposed BDOEs, the reported spectrum-splitting approach provides a new approach toward low-cost solar power.

Design and analysis of multi-wavelength diffractive optics.

We present an extension of the direct-binary-search algorithm for designing high-efficiency multi-wavelength diffractive optics that reconstruct in the Fresnel domain. A fast computation method for solving the optimization problem is proposed. Examples of three-wavelength diffractive optics with over 90% diffraction efficiency are presented. These diffractive optical elements reconstruct three distinct image patterns when probed using the design wavelengths. Detailed parametric and sensitivity studies are conducted, which provide insight into the diffractive optic's performance when subject to different design conditions as well as common systematic and fabrication errors.

Searching for novel molecular targets of chronic rejection in an orthotopic experimental lung transplantation model.

BACKGROUND: Chronic rejection (CR) is the main reason for the limited survival rates among lung transplant (LT) recipients. There remains no effective treatment for CR. The aim of this study was to identify new molecular mechanisms involved in CR by using DNA microarray analysis. METHODS: We performed 10 left LTs using the microsurgical cuff technique in inbred Sprague-Dawley rats. Lung isograft samples were obtained 3 months after surgery. We analyzed histologic, apoptotic and gene expression changes by DNA microarray and quantitative PCR analysis. RESULTS: Histologic analyses confirmed signs of CR in all lungs and positive labeling for apoptotic and anti-apoptotic markers. A total of 702 genes were regulated in the CR lungs: 317 genes were upregulated and 385 were downregulated. Significant changes for about 30 biologic processes, including regulation of the cytoskeleton, and 15 signaling pathways, such as adherens junctions, were observed. We found significantly increased mRNA expression of the Cldn5, Epas1, Tgfb1, Vegf, Selp1, Hsp27 and Igf1 genes. CONCLUSIONS: This is the first experimental study performed in an orthotopic model of LT using DNA microarray analysis. The individual genes, biologic process and pathways identified may represent novel targets that could be manipulated and contribute to the development of treatments capable of providing protection from CR.

Nanostructured gradient-index antireflection diffractive optics.

We describe the fabrication and characterization of a nanostructured diffractive element with near-zero reflection losses. In this element, subwavelength nanostructures emulating adiabatic index matching are integrated on the surface of a diffractive microstructure to suppress reflected diffraction orders. The fabricated silicon grating exhibits reflected efficiencies that are suppressed by 2 orders of magnitude over broad wavelength bands and wide incident angles. Theoretical models of the fabricated structure based on rigorous coupled-wave analysis and effective medium theory are in agreement with the experimental data. The proposed principles can be applied to improve the performance of any diffractive structures, potentially leading to more efficient Fresnel lenses, holographic elements, and integrated optical systems.

Quantitative measurement of size and three-dimensional position of fast-moving bubbles in air-water mixture flows using digital holography.

We present a digital in-line holographic imaging system for measuring the size and three-dimensional position of fast-moving bubbles in air-water mixture flows. The captured holograms are numerically processed by performing a two-dimensional projection followed by local depth estimation to quickly and efficiently obtain the size and position information of multiple bubbles simultaneously. Statistical analysis on measured bubble size distributions shows that they follow lognormal or gamma distributions.