Biogeochemical Typing of Paddy Field by a Data-Driven Approach Revealing Sub-Systems within a Complex Environment - A Pipeline to Filtrate,Organize and Frame Massive Dataset from Multi-Omics Analyses

We propose the technique of biogeochemical typing (BGC typing) as a novel methodology to set forth the sub-systems of organismal communities associated to the correlated chemical profiles working within a larger complex environment. Given the intricate characteristic of both organismal and chemical consortia inherent to the nature, many environmental studies employ the holistic approach of multi-omics analyses undermining as much information as possible. Due to the massive amount of data produced applying multi-omics analyses, the results are hard to visualize and to process. The BGC typing analysis is a pipeline built using integrative statistical analysis that can treat such huge datasets filtering, organizing and framing the information based on the strength of the various mutual trends of the organismal and chemical fluctuations occurring simultaneously in the environment. To test our technique of BGC typing, we choose a rich environment abounding in chemical nutrients and organismal diversity: the surficial freshwater from Japanese paddy fields and surrounding waters. To identify the community consortia profile we employed metagenomics as high throughput sequencing (HTS) for the fragments amplified from Archaea rRNA, universal 16S rRNA and 18S rRNA; to assess the elemental content we employed ionomics by inductively coupled plasma optical emission spectroscopy (ICP-OES); and for the organic chemical profile, metabolomics employing both Fourier transformed infrared (FT-IR) spectroscopy and proton nuclear magnetic resonance (¹H-NMR) all these analyses comprised our multi-omics dataset. The similar trends between the community consortia against the chemical profiles were connected through correlation. The result was then filtered, organized and framed according to correlation strengths and peculiarities. The output gave us four BGC types displaying uniqueness in community and chemical distribution, diversity and richness. We conclude therefore that the BGC typing is a successful technique for elucidating the sub-systems of organismal communities with associated chemical profiles in complex ecosystems.     

Glutaric acid stimulates glutamate binding and astrocytic uptake and inhibits vesicular glutamate uptake in forebrain from young rats

Glutaric acidemia type I (GA I) is an inherited neurometabolic disorder caused by glutaryl-CoA dehydrogenase deficiency, which leads to accumulation in body fluids and in brain of predominantly glutaric acid (GA), and to a lesser extent of 3-hydroxyglutaric and glutaconic acids. Neurological presentation is common in patients with GA I. Although the mechanisms underlying brain damage in this disorder are not yet well established, there is growing evidence that excitotoxicity may play a central role in the neuropathogenesis of this disease. In the present study, preparations of synaptosomes, synaptic plasma membranes and synaptic vesicles, as well as cultured astrocytes from rat forebrain were exposed to various concentrations of GA for the determination of the basal and potassium-induced release of [(3)H]glutamate by synaptosomes, Na(+)-independent glutamate binding to synaptic membranes and vesicular glutamate uptake and Na(+)-dependent glutamate uptake into astrocytes, respectively. GA (1-100 nM) significantly stimulated [(3)H]glutamate binding to brain plasma membranes (40-70%) in the absence of extracellular Na(+) concentrations, reflecting glutamate binding to receptors. Furthermore, this stimulatory effect was totally abolished by the metabotropic glutamate ligands DHPG, DCG-IV and l-AP4, attenuated by the ionotropic non-NMDA glutamate receptor agonist AMPA and had no interference of the NMDA receptor antagonist MK-801. Moreover, [(3)H]glutamate uptake into synaptic vesicles was inhibited by approximately 50% by 10 and 100 nM GA and Na(+)-dependent [(3)H]glutamate uptake by astrocytes was significantly increased (up to 50%) in a dose-dependent manner (maximal stimulation at 100 microM GA). In contrast, synaptosomal glutamate release was not affected by the acid at concentrations as high as 1 mM. These results indicate that the inhibition of glutamate uptake into synaptic vesicles by low concentrations GA may result in elevated concentrations of the excitatory neurotransmitter in the cytosol and the stimulatory effect of this organic acid on glutamate binding may potentially cause excitotoxicity to neural cells. Finally, taken together these results and previous findings showing that GA markedly decreases synaptosomal glutamate uptake, it is possible that the stimulatory effect of GA on astrocyte glutamate uptake might indicate that astrocytes may protect neurons from excitotoxic damage caused by GA by increasing glutamate uptake and therefore reducing the concentration of this excitatory neurotransmitter in the synaptic cleft.     

Resource use efficiency in urban and peri-urban sheep, goat and cattle enterprises

Urban livestock husbandry receives growing attention given the increasing urban demand for livestock products. At the same time, little is known about the resource use efficiency in urban livestock enterprises and eventual negative externalities. In livestock production, feeds are an important resource whose nutrients are transformed into products (meat and milk) to generate financial return to the producer. The lack of knowledge on nutrient supply through feed might lead to oversupply with severe environmental impacts. In Niamey, a typical West African city and capital of the Republic of Niger, urban livestock production is constrained by feed scarcity, especially during the dry season. Here, the issue of resource use efficiency was studied in 13 representative and differently managed sheep/goat and cattle enterprises characterized by high and low feed inputs, respectively, during a period of 28 months. Nitrogen (N), phosphorus (P) and potassium (K) inflows into each farm through livestock feeds and outflows through manure were determined using a semi-structured questionnaire; interviews were accompanied by regular weighing of feed supplied and dung produced. Live weight gain (LWG) and efficiency of conversion of total feed dry matter offered (kg TDMO/kg LWG) were computed along with nutrient balances (NBs) per metabolic body mass (kg0.75). NBs (per kg0.75/day) in the high-input (HI) sheep/goat enterprises were +1762.4 mg N, +127.2 mg P and +1363.5 mg K and were significantly greater (P < 0.05) than those in low-input (LI) units (+69.1 mg N, -98.3 mg P and +16.5 mg K). In HI cattle enterprises, daily balances averaged +454.1 mg N, +40.1 mg P and +341.8 mg K compared to +34.4 mg N, -9.0 mg P and +68.3 mg K (P > 0.05) in LI cattle systems. All systems were characterized by poor conversion efficiencies of offered feed, which ranged from 13.5 to 46.1 kg TDMO/kg LWG in cattle and from 15.7 to 43.4 kg TDMO/kg LWG in sheep/goats. LWG in HI sheep/goats was 53 g/day in the rainy season, 86 g/day in the hot dry season and 104 g/day in the cool dry season, while HI cattle lost 79 g/day in the hot dry season and gained 121 g/day and 92 g/day in the cool dry and rainy seasons, respectively. The data indicate that there is nutrient wasting and scope for improvement of feeding strategies in Niamey's livestock enterprises, which might also decrease nutrient losses to the urban environment.     

MAFCO: A Compression Tool for MAF Files

In the last decade, the cost of genomic sequencing has been decreasing so much that researchers all over the world accumulate huge amounts of data for present and future use. These genomic data need to be efficiently stored, because storage cost is not decreasing as fast as the cost of sequencing. In order to overcome this problem, the most popular general-purpose compression tool, gzip, is usually used. However, these tools were not specifically designed to compress this kind of data, and often fall short when the intention is to reduce the data size as much as possible. There are several compression algorithms available, even for genomic data, but very few have been designed to deal with Whole Genome Alignments, containing alignments between entire genomes of several species. In this paper, we present a lossless compression tool, MAFCO, specifically designed to compress MAF (Multiple Alignment Format) files. Compared to gzip, the proposed tool attains a compression gain from 34% to 57%, depending on the data set. When compared to a recent dedicated method, which is not compatible with some data sets, the compression gain of MAFCO is about 9%. Both source-code and binaries for several operating systems are freely available for non-commercial use at: http://bioinformatics.ua.pt/software/mafco.     

The anticancer drug perillyl alcohol is a Na/K-ATPase inhibitor

Indoleamine 2,3-dioxygenase (IDO) is an enzyme that suppresses adaptive T-cell immunity by catabolizing tryptophan from the cellular microenvironment. Inhibition of IDO pathway might enhance the efficacy of immunotherapeutic strategies for cancer. We synthesized 1-alkyl-tryptophan targeted IDO inhibitors and compared their effects on IDO expression and activity in dendritic cells (DCs) with the common IDO inhibitor 1-methyl-dl-tryptophan (1-MT). The IDO gene expression was examined by RT-PCR and realtime PCR. The toxicity of these analogs on the proliferation of DCs was detected by MTT assay. All of these analogs inhibited IDO expression and activity induced by IFN-γ and showed no cytotoxicity to DCs at 100 μM. 1-MT intensively suppressed IDO1 expression and activity in DCs, and 1-propyl-tryptophan (1-PT) and 1-isopropyl-tryptophan (1-isoPT) moderately inhibited them. 1-Butyl-tryptophan (1-BT) and 1-ethyl-tryptophan (1-ET) mainly inhibited IDO2 expression. Our results suggest that those analogs differed in their inhibitory activity on IDO expression may give us a clue for developing active IDO inhibitors.     

Olfactory responses of Anaphes nitens (Hymenoptera,Mymaridae) to host and habitat cues

The eucalyptus weevil, Gonipterus spp. Schoenherr, 1833 (Coleoptera, Curculionidae) is considered a major pest of eucalyptus plantations. In regions where control is achieved, success is usually brought by the action of the solitary egg parasitoid Anaphes nitens (Girault, 1928) (Hymenoptera, Mymaridae). Research was conducted to ascertain which cues might mediate female wasp host location and selection. In Petri dish arenas, females were attracted to Gonipterus platensis Marelli, 1927 egg capsules, to G. platensis mated female faeces and to leaves of Eucalyptus globulus Labillardière, 1799. Gas chromatography–mass spectrometry electroantennographic detection analysis was conducted using extracts obtained from leaves of E. globulus, from G. platensis egg capsules, as well as from adults of both sexes and their faeces, in order to detect and identify compounds perceived by the wasp's olfactory system. The parasitoids were shown to detect a wide range of compounds emitted by each one of these sources, and for 31 compounds, antennal response was confirmed by dose-response tests. Further behavioural trials were conducted in Petri dishes in order to decode the effect, on parasitoid behaviour, of selected compounds emitted by E. globulus and of the pheromones, emitted by the weevils on parasitoid behaviour. Attraction was observed to two compounds emitted by E. globulus, namely 1,8-cineole and γ-terpinene, and to the main component of the male sex/aggregation pheromone, cis-verbenol. To our knowledge, this is the first report of attraction of a parasitoid from the family Mymaridae to a component of its host's sexual/aggregation pheromone. Similarly, to other egg parasitoid species, A. nitens females are likely to use the host plant volatiles as long-range host location cues and to adopt the ‘infochemical detour’ strategy in order to get in the vicinity of their hosts.     

Oral manifestations in chikungunya patients: A systematic review

BackgroundChikungunya fever is considered an abrupt onset arbovirus transmitted by mosquitoes, mainly Aedes aegypti and Aedes albopictus. The disease has a significant impact on the quality of life of affected persons, and many of its numerous symptoms have not yet been properly clarified, such as the manifestations that can occur in the oral cavity. The aim of this study was to identify the main oral manifestations related to chikungunya fever, as well as describe the demographic characteristics of patients, by conducting a systematic review of the literature.Methods and findingsSearches were performed in MEDLINE (PubMed), Embase (Elsevier), LILACS (VHL), Cochrane Library, Scopus, and CAPES electronic databases for theses and dissertations published up to January 16, 2021 without language and date restrictions. Additional manual searches of gray literature, reference list, and Google Scholar were carried out. We included 27 studies highlighting mainly oral manifestations that cause masticatory discomfort such as ulcers and oral thrush, gingival bleeding, pain and burning of the oral mucous membranes, temporomandibular joint (TMJ) arthralgia, opportunistic infections, and changes in taste.ConclusionsThere seems to be a predominance of oral manifestations that cause discomfort when chewing, such as ulcerations in the acute phase of the disease, with complete remission within 3 to 10 days after the onset, apparently mostly affecting women and older persons. These oral manifestations can be compatible with basic viral infections related to inflammatory response and transitory immunosuppression.