Miracle-dz/UniFAR-FTUs huggingface dataset:
Free fatty acid receptor 4 is a nutrient sensor that resolves inflammation to maintain cardiac homeostasis

Background Non-resolving activation of immune responses is central to the pathogenesis of heart failure (HF). Free fatty acid receptor 4 (Ffar4) is a G-protein coupled receptor (GPR) for medium-and long-chain fatty acids (FA) that regulates metabolism and attenuates inflammation in diabetes and obesity. Here, we tested the hypothesis that Ffar4 functions as a cardioprotective nutrient sensor that resolves inflammation to maintain cardiac homeostasis. Methods Mice with systemic deletion of Ffar4 (Ffar4KO) were subjected to pressure overload by transverse aortic constriction (TAC). Transcriptome analysis of cardiac myocytes was performed three days post-TAC. Additionally, Ffar4-mediated effects on inflammatory oxylipin production in cardiac myocytes and oxylipin composition in plasma lipoproteins were evaluated. Results In Ffar4KO mice, TAC induced more severe remodeling, identifying an entirely novel cardioprotective role for Ffar4 in the heart. Transcriptome analysis 3-days post-TAC indicated a failure to induce cell death and inflammatory genes in Ffar4KO cardiac myocytes, as well as a specific failure to induce cytoplasmic phospholipase A2α (cPLA2α) signaling genes. In cardiac myocytes, Ffar4 signaling through cPLA2α-cytochrome p450 ω/ω-1 hydroxylase induced production of the EPA-derived anti-inflammatory oxylipin 18-hydroxyeicosapentaenoic acid (18-HEPE). Systemically, loss of Ffar4 altered oxylipin content in circulating plasma lipoproteins consistent with a loss of anti-inflammatory oxylipins at baseline, and inability to produce both pro-inflammatory and pro-resolving oxylipins following TAC. Finally, we confirmed that Ffar4 is expressed in human heart and down-regulated in HF. Conclusions Our results identify a novel function for Ffar4 in the heart as a FA nutrient sensor that resolves inflammation to maintain cardiac homeostasis.
Microhabitat preferences of the freshwater prawn Macrobrachium jelskii (Decapoda: Palaemonidae)

ABSTRACT We analyzed the microhabitat preferences of Macrobrachium jelskii (Miers, 1877) males and females inhabiting an urban water reservoir in Cruz das Almas, Bahia, Brazil. Prawns were collected monthly, from March 2015 to February 2016, in three microhabitats, using a sieve. Each microhabitat was dominated by one macrophyte species: Eleocharis sp. (M1), Cabomba sp. (M2), and Nymphaea sp. (M3). The prawns were measured (carapace length), and categorized as juvenile males, adult males, juvenile females, non-ovigerous adult females and ovigerous adult females. An analysis of variance (ANOVA) was used to compare the number and size of individuals. The sex ratio and frequency of ovigerous females in the three microhabitats were also calculated. The sex ratio was biased towards females in M1 and did not deviate from 1:1 in M2 and M3. When prawns were separated into five categories we observed that non-ovigerous adult females were more abundant in M1, while adult males were the most abundant demographic category in M2 and M3. Juveniles of both sexes and ovigerous females showed no microhabitat preference, although M1 and M2 appeared to be more suitable for the latter. Adult females were the largest individuals in all microhabitats. Food availability, lower depth and lower predation pressure in M1 are the main factors that make M1 more suitable for M. jelskii, particularly non-ovigerous adult females and larger adult males. Intraspecific competition for shelter in M1 might also occur and adult females win this competition due to their larger body size. Therefore, adult males are found in higher abundance in M2 and M3 and the juvenile of both sexes spread evenly across all microhabitats. Our results help to understand the ecological role and the niche used by M. jelskii. Future studies on the habitat choice and predation under laboratory conditions should help to understand the behavior of this species.
Global ocean resistome revealed: exploring Antibiotic Resistance Genes (ARGs) abundance and distribution on TARA oceans samples through machine learning tools

The rise of antibiotic resistance (AR) in clinical settings is one of the biggest modern global public health concerns, therefore, the understanding of its mechanisms, evolution and global distribution is a priority due to its impact on the treatment course and patient survivability. Besides all efforts in the elucidation of AR mechanisms in clinical strains, little is known about its prevalence and evolution in environmental uncultivable microorganisms. In this study, 293 metagenomic and 10 metatranscriptomic samples from the TARA oceans project were used to detect and quantify environmental Antibiotic Resistance Genes (ARGs) using modern machine learning tools. After extensive manual curation, we show their global distribution, abundance, taxonomy and phylogeny, their potential to be horizontally transferred by plasmids or viruses and their correlation with environmental and geographical parameters. After manual curation, we identified a total of 99,205 environmental ORFs as potential ARGs. These ORFs belong to 560 ARG families that confer resistance to 26 antibiotic classes. A total of 149 ORFs were classified as viral sequences. In addition, 24,567 ORFs were found in contigs classified as plasmidial sequences, suggesting the importance of mobile genetic elements in the dynamics of ARGs transmission. From the 13,163 identified ARGs passing all the criteria for quantification analysis, 4,224 were expressed in at least one of the 10 metatranscriptomic samples (FPKM >5). Moreover, 4,804 contigs with more than 2 ARGs were found, including 2 plasmids with 5 different ARGs, highlighting the potential presence of multi-resistant microorganisms in natural environment and/or non-impacted by human presence oceans, together with the possibility of Horizontal Gene Transfer (HGT) between clinical and natural environments. The abundance of ARGs in 293 samples showed different patterns of distribution, with some classes being significatively more abundant in Coastal Biomes. Finally, we identified ARGs conferring resistance to some of the most relevant clinical antibiotics, revealing the presence of 15 ARGs from the recently discovered MCR-1 family with high abundance on Polar Biomes. A total of 5 MCR-1 ORFs are present in the genus Psychrobacter, an opportunistic bacteria that can cause fatal infections in humans. Our results are available on Zenodo in MySQL database dump format and all the code used for the analyses, including jupyter notebooks can be accessed on github (https://github.com/rcuadrat/ocean_resistome).
Genetic variations of cuttlefish Sepia latimanus (Cephalopoda, Sepiidae) in North Sulawesi waters, Indonesia.

This study was aimed at discerning the genetic variations of cuttlefish Sepia latimanus in North Sulawesi, using CO1 gene marker. Sampling was conducted in Kalinaung and Likupang, North Minahasa regency, Manado Bay, Manado municipality and Minahasa regency, Poigar, South Minahasa regency, and Basaan, Southeast Minahasa. All samples were put into 95% alcohol and brought to the molecular biology laboratory of Faculty of Fisheries and Marine Sciences for further analysis. Genome DNA extraction of all samples used innuPREP DNA Micro Kit (Analytic Jena). The CO1 gene was amplified applying universal primer pairs LCO1490: 5’-GGTCAACAAATCATAAAGATATTGG-3’ and HCO2198: 5’TAAACTTCAGGGTGACCAAAAAATCA3’. Polymerase chain reaction (PCR) was carried out in 35 cycles at 95C (30 sec), 50C (30 sec), 72C (50 sec). The PCR product was visualized in 1% (b/v) agarosa gel electrophoresis. Bi-directional sequencing was done by First Base CO (Malaysia) using Big Dye© terminator chemistry (Perkin Elmer). The chromatogram obtained was edited using Geneious v5.6. The sequences were then compared with GenBank data using BLAST (Basic Local Alignment Search Tools) method and BOLDSystems. The phylogenetic tree was built using Neighbor-Joining Method, and genetic similarity was explained by mutation, haplotype and genetic distance. This study found genetic variations in S. latimanus of North Sulawesi waters between and within localities. Haplotype similarity between localities made eleven nucleotide sequences only form 9 haplotypes, while haplotype difference within locality could result from genetic mixture. Wide distribution of the species is supported by its adaptability to the environmental conditions.
Characterization and phylogenetic analysis of the complete mitochondrial genome of Rhinogobius sp. (Perciformes, Gobiidae)

Abstract The genus Rhinogobius was widely distributed in East Asia. In the present study, the complete mitochondrial genome of Rhinogobius sp. , possible a new species of freshwater goby from Anhui province of China, was sequenced for the first time. Sequence analysis showed that it is 16,511 bp in length with A + T content of 52.3%, consisting of 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and a control region (CR). Phylogenetic analyses placed Rhinogobius sp. in a well-supported monophyletic cluster with other Rhinogobius fish and the phylogenetic position of Rhinogobius sp. was closer to Rhinogobius cliffordpopei.
Preliminary phytochemical screening and anticancer potential of Kohautia aspera (Heyne Ex Roth) Bremek

Phytochemical screening followed by anticancer potential evaluation of Kohautia aspera (Heyne ex Roth) Bremek was the purpose of the study. Successive extraction was performed with four solvents of different polarity as well as hot percolation method for the aqueous extract. The anticancer potential of the plant was investigated by standard MTT assay against (MCF-7) human breast adenocarcinoma cells. The extracts showed many phytoconstituents. In vitro cytotoxic activity of plant increased with increasing concentration of extracts. The presence of important phytoconstituents in plants may provide protection against a number of diseases. The investigation concludes that Kohautia aspera (Heyne ex Roth) Bremek possesses significant anticancer potential.
The complete chloroplast genome of Cymbidium eburneum (Orchidaceae)

Abstract Cymbidium eburneum Lindl. is an endangered species of Orchidaceae and distributed in Guangxi, Yunnan and Hainan of China, and India, Myanmar, Nepal, Vietnam. Here, we report the complete chloroplast (cp) genome sequence and the cp genome features of C. eburneum. The complete chloroplast (cp) genome sequence of C. eburneum is 156,520 bp in length and presented a typical quadripartite structure including one large single-copy region (LSC, 85,518 bp), one small single-copy region (SSC, 20,014 bp), and two inverted repeat regions (IRs, 25,471 bp). The cp genome encoded 135 genes, of which 106 were unique genes (78 protein-coding genes, 24 tRNAs, and 4 rRNAs). The phylogenetic relationships show that C. eburneum is closely related to other species in the genus Cymbidium, and is sister with C. tracyanum.
Diverse, abundant and novel viruses infecting “unculturable” but abundant marine bacteria

Many major marine bacterial lineages such as SAR11, Prochlorococcus, SAR116, and several Roseobacter lineages have members that are abundant, relatively slow-growing, and genome-streamlined. The isolation of phages that infect SAR11 and SAR116 have demonstrated the dominance of these phages in the marine virosphere. However, no phages have been isolated from bacteria in the Roseobacter RCA lineage, another abundant group of bacteria in the ocean. In this study, seven RCA phages that infect three different RCA strains were isolated and characterized. All seven RCA phages belong to the Podoviridae family and have genome sizes ranging from 39.6 to 58.1 kb. Interestingly, three RCA phages (CRP-1, CRP-2 and CRP-3) show a similar genomic content and architecture with SAR116 phage HMO-2011, which represents one of the most abundant known viral groups in the ocean. The high degree of homology between CRP-1, CRP-2, CRP-3 and HMO-2011 resulted in contribution of the RCA phages to the dominance of HMO-2011-type phage in the ocean. CRP-4 and CRP-5 are similar to the Siovirus roseophages in terms of gene content and organization. The remaining two RCA phages, CRP-6 and CRP-7, show limited genomic similarity with known phages and appear to form two new phage genera. Metagenomic fragment recruitment analyses reveal that these RCA phage groups are much more abundant in the ocean compared to most existing marine roseophage groups. The characterization of these RCA phages has greatly expanded our understanding of the genomic diversity and evolution of marine roseophages. Metagenomic fragment recruitment analyses suggest the critical need for isolating phages from the abundant but “unculturable” bacteria in the marine ecosystem.
A system for rapid eDNA detection of aquatic invasive species

This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made. © 2019 The Authors. Environmental DNA published by John Wiley & Sons Ltd 1Molecular Division, Smith-Root Inc., Vancouver, Washington, USA 2Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, USA 3Biology Department, Biomeme Inc, Philadelphia, Pennsylvania, USA 4School of the Environment, Washington State University, Pullman, Washington, USA
Genetic changes of P. vivax tempers host tissue-specific responses in Anopheles stephensi

In our preceding study (Sharma et al., 2019; BioRxiv) we showed that in the gut lumen Plasmodium vivax follows a unique strategy of immuno-suppression by disabling gut flora proliferation. Here, we further demonstrate that post gut invasion, a shrewd molecular relationship with individual tissues such as midgut, hemocyte, salivary glands, and strategic changes in the genetic makeup of P. vivax favors its survival in the mosquito host. A transient suppression of ‘metabolic machinery by early oocysts, and increased immunity’ against late oocysts suggested a unique mechanism of gut homeostasis restoration and Plasmodium population regulation. Though a hyper immune response of hemocyte was a key to remove free circulating sporozoites, but a strong suppression of salivary metabolic activities, may favor successful survival of invaded sporozoites. Finally, genetic alteration of P. vivax ensures evasion of mosquito responses. Conclusively, our system-wide RNAseq analysis provides first genetic evidences of direct mosquito-Plasmodium interaction and establishes a functional correlation. Author Summary Malaria transmission dynamics is heavily influenced by mosquito –parasite interaction. When passing through tissue specific barriers, Plasmodium have to compromise by losing its own population, but genetic relation is unknown. To win the developmental race Plasmodium need to overcome two important immuno-physiological barriers. First one accounts an indirect 24-30hr long pre-invasive gut-microbe-parasite interaction in the gut lumen. And second one follows a direct post gut invasive 14-18 days interaction with midgut, hemocyte and salivary glands. During pre-invasive phase of interaction, we showed Plasmodium vivax follows immuno-suppression strategy by restricting microbial growth in the gut lumen. Here, we demonstrate that switch of parasite from one stage to another stage within mosquito vector is accompanied by genetic changes of parasite. Our data suggests genetic makeup change enables the parasite to manipulate the metabolism of mosquito tissues. This strategy not only clear off multifaceted mosquito’s tissue specific immune responses, but also favors Plasmodium own survival and transmission. Comprehending this tissue specific interaction between host and parasite at molecular level could provide new tool to intervene the plasmodium life cycle within vector.
Pan-Arctic Depth Distribution of Diapausing Calanus Copepods

Diapause at depth is considered an integral part of the life cycle of Calanus copepods, but few studies have focused on the Arctic species Calanus glacialis and Calanus hyperboreus. By analyzing a large set of pan-arctic observational data compiled from multiple sources, we show that Arctic Calanus has a broad depth distribution in winter, indicating that diapause at depth is a facultative strategy. Both species’ vertical distributions tend to deepen in winter and to be deeper and broader with increasing bottom depth, while individuals are aggregated closer to the sea floor in shallow areas. These results indicate that Arctic Calanus species pursue a relatively deep diapause habitat but are topographically blocked on the shelves. Interspecific differences in depth distribution during diapause suggest the importance of predation. The larger C. hyperboreus has a deeper diapause depth than C. glacialis, potentially to alleviate predation pressure or as a result of predation loss near the surface. Moreover, the mean depth of C. hyperboreus in winter is negatively associated with latitude, indicating a shoaling of the diapause population in the central Arctic Ocean where predation pressure is lower. Our results suggest a complex diapause behavior by Arctic Calanus, with implications for our view of the species’ roles in Arctic ecosystems.
Optimizing the role of starch as an energy source for dairy cows.

Although starch is not considered a required nutrient, it is often a topic of discussion, primarily due to its high concentration in corn grain and silage. The objectives of this article are to present and discuss: 1) the effects of dietary starch concentration throughout the lactation, and 2) potential strategies to optimize digestibility of starch in feedstuffs and its utilization by lactating dairy cows. Potential negative effects on either milk yield or feed efficiency when reducing dietary starch exist and underscores that monitoring income over feed costs is recommended rather than price per unit of diet dry matter (DM) when corn prices are high to fully assess economic benefits of reduced-starch diets. Many factors alter starch digestibility of feedstuffs; mean particle is the most important factor in corn silage, corn grain, and high-moisture corn. However, on farm assessment is advised.
Morphological and Molecular Characterization of Potato Black Scurf Disease (Rhizoctonia solani) in Egypt

Rhizoctonia solani is the biological causal agent of the potato black scurf disease. The symptoms were examined on vegetative and tuber potato plants in eight Egyptian governorates (Aswan, Behera, Dakahlyia, Gharbia, Giza, Ismailia, Menofyia, and New Valley) during 2012-13 and 2013-14. Representative infected samples of Diamant, Hermes, Lady Rosetta and Spunta cultivars were collected randomly from different conventional and organic farms. Field survey produced a total of 182 isolates. The highest disease severity occurred in Ismailia and Behera, while the lowest severity was in Menofyia. The cultivar Herms was resistant in greenhouse and field trials, while Lady Rosetta was the susceptible. Disease incidence and severity were higher in organic than conventional cultivation farms. The ١٨٢ isolates were subdivided into 14 group based on the morphological examination. The anastomosis test on ٥٠ selected isolates produced four different interactive groups (C0-C3). Sequence analysis was performed on the internal transcribed spacer (ITS) 18s rDNA of 35 selected isolates and confirmed the identified groups. High molecular similarity and single nucleotide polymorphisms (SNP) were produced between the representing ITS sequences of the (AG3, AG4, AGA, and AGF) groups using the comparative analysis. The AG3 and AG4 groups included 25 and six isolates; respectively, and severely infected potato. The AGA and AGF groups included three and one isolates; respectively, and unregistered for potato invasion. These results of great applications at the level of potato black scurf disease characterization in Egypt.
Inter- and intraspecific differences in Drosophila cold tolerance are linked to hindgut reabsorption capacity

Maintaining extracellular osmotic and ionic homeostasis is crucial to maintain organismal function. In insects, hemolymph volume and ion content is regulated by the combined actions of the secretory Malpighian tubules and reabsorptive hindgut. When exposed to stressful cold, homeostasis is gradually disrupted, characterized by a debilitating increase in extracellular K+ concentration (hyperkalemia). In accordance with this paradigm, studies have found a strong link between the cold tolerance of insect species and their ability to maintain ion and water homeostasis at low temperature. This is also the case for drosophilids where studies have already established how inter- and intra-specific differences in cold tolerance are linked to the secretory capacity of Malpighian tubules. However, presently there is little information on the effects of temperature on the reabsorptive capacity of the hindgut in Drosophila. To address this question we developed a novel method that allows for continued measurements of hindgut ion and fluid reabsorption in Drosophila. Firstly we demonstrate that this assay is temporally stable (> 3 hours) and that the preparation is responsive to humoral stimulation and pharmacological intervention of active and passive transport in accordance with the current insect hindgut reabsorption model. Using this method at benign (24°C) and low temperature (3°C) we investigated how cold acclimation or cold adaptation affected the thermal sensitivity of osmoregulatory function. We found that cold tolerant Drosophila species and cold-acclimated D. melanogaster are innately better at maintaining rates of fluid and Na+ reabsorption at low temperature. Furthermore, cold adaptation and acclimation causes a relative reduction in K+ reabsorption at low temperature. These characteristic responses of cold adapted/acclimated Drosophila will act to promote maintenance of ion and water homeostasis at low temperature and therefore provide further links between adaptations in osmoregulatory capacity of insects and their ability to tolerate cold exposure.
Cardioprotective Role of the Mitochondrial ATP-Binding Cassette Protein 1

The mechanism by which mitochondria exert protection against oxidant stress is not clear. We recently showed that a purified mitochondrial fraction containing 5 coimmunoprecipitating proteins (succinate dehydrogenase, adenine nucleotide translocator, ATP synthase, inorganic phosphate carrier, and mitochondrial ATP-binding cassette protein 1 or mABC1) displayed mitochondrial ATP-sensitive K+-channel activity. mABC1, a member of the ABC family of proteins, is the only protein in this complex whose function is not known. A yeast homologue of mABC1 protein, Mdl1p, was recently identified to have a novel role for induction of cellular resistance to oxidant stress. Based on these observations, we hypothesized that mABC1 plays a key role in protection of myocardial cells against oxidant stress. We studied the function of mABC1 by modulating the levels of this protein in neonatal rat cardiomyocytes using various molecular techniques, followed by assessment of cell viability and measurement of mitochondrial membra.
Proceedings of the Workshop on Language Analysis in Social Media

We explore improving parsing social media and other web data by altering the input data, namely by normalizing web text, and by revising output parses. We find that text normalization improves performance, though spell checking has more of a mixed impact. We also find that a very simple tree reviser based on grammar comparisons performs slightly but significantly better than the baseline and well outperforms a machine learning model. The results also demonstrate that, more than the size of the training data, the goodness of fit of the data has a great impact on the parser.