Comparative Genomics Analysis of a New Exiguobacterium Strain from Salar de Huasco Reveals a Repertoire of Stress-Related Genes and Arsenic Resistance

Indexación: Web of Science; Scopus.The Atacama Desert hosts diverse ecosystems including salt flats and shallow Andean lakes. Several heavy metals are found in the Atacama Desert, and microorganisms growing in this environment show varying levels of resistance/tolerance to copper, tellurium, and arsenic, among others. Herein, we report the genome sequence and comparative genomic analysis of a new Exiguobacterium strain, sp. SH31, isolated from an altiplanic shallow athalassohaline lake. Exiguobacterium sp. SH31 belongs to the phylogenetic Group II and its closest relative is Exiguobacterium sp. S17, isolated from the Argentinian Altiplano (95% average nucleotide identity). Strain SH31 encodes a wide repertoire of proteins required for cadmium, copper, mercury, tellurium, chromium, and arsenic resistance. Of the 34 Exiguobacterium genomes that were inspected, only isolates SH31 and S17 encode the arsenic efflux pump Acr3. Strain SH31 was able to grow in up to 10 mM arsenite and 100 mM arsenate, indicating that it is arsenic resistant. Further, expression of the ars operon and acr3 was strongly induced in response to both toxics, suggesting that the arsenic efflux pump Acr3 mediates arsenic resistance in Exiguobacterium sp. SH31.http://journal.frontiersin.org/article/10.3389/fmicb.2017.00456/ful

Cross-Language Question Re-Ranking

We study how to find relevant questions in community forums when the language of the new questions is different from that of the existing questions in the forum. In particular, we explore the Arabic-English language pair. We compare a kernel-based system with a feed-forward neural network in a scenario where a large parallel corpus is available for training a machine translation system, bilingual dictionaries, and cross-language word embeddings. We observe that both approaches degrade the performance of the system when working on the translated text, especially the kernel-based system, which depends heavily on a syntactic kernel. We address this issue using a cross-language tree kernel, which compares the original Arabic tree to the English trees of the related questions. We show that this kernel almost closes the performance gap with respect to the monolingual system. On the neural network side, we use the parallel corpus to train cross-language embeddings, which we then use to represent the Arabic input and the English related questions in the same space. The results also improve to close to those of the monolingual neural network. Overall, the kernel system shows a better performance compared to the neural network in all cases.Comment: SIGIR-2017; Community Question Answering; Cross-language Approaches; Question Retrieval; Kernel-based Methods; Neural Networks; Distributed Representation

Determinants of copper resistance in Acidithiobacillus ferrivorans ACH isolated from the Chilean altiplano

Indexación; Scopus.The use of microorganisms in mining processes is a technology widely employed around the world. Leaching bacteria are characterized by having resistance mechanisms for several metals found in their acidic environments, some of which have been partially described in the Acidithiobacillus genus (mainly on ferrooxidans species). However, the response to copper has not been studied in the psychrotolerant Acidithiobacillus ferrivorans strains. Therefore, we propose to elucidate the response mechanisms of A. ferrivorans ACH to high copper concentrations (0–800 mM), describing its genetic repertoire and transcriptional regulation. Our results show that A. ferrivorans ACH can grow in up to 400 mM of copper. Moreover, we found the presence of several copper-related makers, belonging to cop and cus systems, as well as rusticyanins and periplasmatic acop protein in the genome. Interestingly, the ACH strain is the only one in which we find three copies of copB and copZ genes. Moreover, transcriptional expression showed an up-regulation response (acop, copZ, cusA, rusA, and rusB) to high copper concentrations. Finally, our results support the important role of these genes in A. ferrivorans copper stress resistance, promoting the use of the ACH strain in industrial leaching under low temperatures, which could decrease the activation times of oxidation processes and the energy costs. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.https://www.mdpi.com/2073-4425/11/8/84

Relationships between caused by drinking of bioactive water Naftussya changes in urine lithogenicity and neuro-humoral-immune factors in humans with theirs abnormalities

Objective. Spa Truskavets' (Ukraine) considered to be indicated for the treatment and metaphylaxis renal stone disease. However, data on the effect of balneotherapy on the parameters of urine Lithogenicity ambiguous. This is due, perhaps, ambiguous influence balneotherapy on the neuroendocrine factors regulating exchange of electrolytes and uric acid. Aim: to find out the influence drinking of bioactive water Naftussya on urine lithogenicity and neuro-humoral-immune factors in humans with theirs abnormalities. Methods. The object of observation were ten women and ten men aged 33-76 years without clinical diagnose but with dysfunction of neuro-endocrine-immune complex and metabolism. In daily urine and blood we determined the content of electrolytes and nitrogenous metabolites, estimated parameters of immunity, recorded conductivity of acupuncture points and heart rate variability (HRV). After examination volunteers within 7 days used bioactive water Naftussya (250 ml three times a day), then repeated the tests listed. Results. Lithogenicity urine Index (Lith) calculated by formula: Lith=(Uric acid•Calcium/Magnesium•Creatinine)0,25. In 3 people initial normal Lith (0,65÷0,81 units) increased by 0,08÷0,16 units. In 4 people with normal or high Lith its changes were not detected (-0,01÷+0,01). In 12 people from a wide range of primary Lith (0,62÷1,07) it lowered by 0,03÷0,12 un. Even in a man maximum level of Lith (1,45 un.) down to the upper limit of normal (0,84 un.). Found a strong correlation between changes in Lith and a number parameters of HRV, metabolism and immunity. Conclusion. The use of bioactive water Naftussya causes ambiguous changes in Lithogenicity of urine, related to ambiguous changes in HRV, metabolism and immunity

Genomic Variation and Arsenic Tolerance Emerged as Niche Specific Adaptations by Different Exiguobacterium Strains Isolated From the Extreme Salar de Huasco Environment in Chilean – Altiplano

Indexación: Scopus.Polyextremophilic bacteria can thrive in environments with multiple stressors such as the Salar de Huasco (SH). Microbial communities in SH are exposed to low atmospheric pressure, high UV radiation, wide temperature ranges, salinity gradient and the presence of toxic compounds such as arsenic (As). In this work we focus on arsenic stress as one of the main adverse factors in SH and bacteria that belong to the Exiguobacterium genus due to their plasticity and ubiquity. Therefore, our aim was to shed light on the effect of niche conditions pressure (particularly arsenic), on the adaptation and divergence (at genotypic and phenotypic levels) of Exiguobacterium strains from five different SH sites. Also, to capture greater diversity in this genus, we use as outgroup five As(III) sensitive strains isolated from Easter Island (Chile) and The Great Salt Lake (United States). For this, samples were obtained from five different SH sites under an arsenic gradient (9 to 321 mg/kg: sediment) and isolated and sequenced the genomes of 14 Exiguobacterium strains, which had different arsenic tolerance levels. Then, we used comparative genomic analysis to assess the genomic divergence of these strains and their association with phenotypic differences such as arsenic tolerance levels and the ability to resist poly-stress. Phylogenetic analysis showed that SH strains share a common ancestor. Consequently, populations were separated and structured in different SH microenvironments, giving rise to multiple coexisting lineages. Hence, this genotypic variability is also evidenced by the COG (Clusters of Orthologous Groups) composition and the size of their accessory genomes. Interestingly, these observations correlate with physiological traits such as growth patterns, gene expression, and enzyme activity related to arsenic response and/or tolerance. Therefore, Exiguobacterium strains from SH are adapted to physiologically overcome the contrasting environmental conditions, like the arsenic present in their habitat. © Copyright © 2020 Castro-Severyn, Pardo-Esté, Mendez, Morales, Marquez, Molina, Remonsellez, Castro-Nallar and Saavedra.https://www.frontiersin.org/articles/10.3389/fmicb.2020.01632/ful

Identification of the Neogenin-Binding Site on the Repulsive Guidance Molecule A

Repulsive guidance molecule (RGM) is a membrane-bound protein that was originally identified as an axon guidance molecule in the chick retinotectal system. RGMa, one of the 3 isoforms found in mammals, is involved in laminar patterning, cephalic neural tube closure, axon guidance, and inhibition of axonal regeneration. In addition to its roles in the nervous system, RGMa plays a role in enhancing helper T-cell activation. Binding of RGM to its receptor, neogenin, is considered necessary to transduce these signals; however, information on the binding of RGM to neogenin is limited. Using co-immunoprecipitation studies, we have identified that the RGMa region required for binding to neogenin contains amino acids (aa) 259–295. Synthesized peptide consisting of aa 284–293 directly binds to the extracellular domain (ECD) of recombinant neogenin, and addition of this peptide inhibits RGMa-induced growth cone collapse in mouse cortical neurons. Thus, we propose that this peptide is a promising lead in finding reagents capable of inhibiting RGMa signaling

Lawson criterion for ignition exceeded in an inertial fusion experiment

For more than half a century, researchers around the world have been engaged in attempts to achieve fusion ignition as a proof of principle of various fusion concepts. Following the Lawson criterion, an ignited plasma is one where the fusion heating power is high enough to overcome all the physical processes that cool the fusion plasma, creating a positive thermodynamic feedback loop with rapidly increasing temperature. In inertially confined fusion, ignition is a state where the fusion plasma can begin "burn propagation" into surrounding cold fuel, enabling the possibility of high energy gain. While "scientific breakeven" (i.e., unity target gain) has not yet been achieved (here target gain is 0.72, 1.37 MJ of fusion for 1.92 MJ of laser energy), this Letter reports the first controlled fusion experiment, using laser indirect drive, on the National Ignition Facility to produce capsule gain (here 5.8) and reach ignition by nine different formulations of the Lawson criterion