Miracle-dz/UniFAR-FTUs huggingface dataset:
Degradation of Arginine and Other Amino Acids by Eubacterium nodatum ATCC 33099

The utilisation of a total of 20 amino acids by Eubacterium nodatum , a predominant asaccharolytic anaerobe isolated from human periodontal pockets, was studied. Washed cells of the microorganism produced substantial amounts of acetate, butyrate and ammonia from lysine, and butyrate and ammonia from arginine as main products under anaerobic conditions. They also produced a small amount of formate from histidine. Metabolic products were not detected from any of the other 17 amino acids. These results suggested that lysine and arginine were major substrates which E. nodatum could utilise. In fact, the growth of E. nodatum was markedly enhanced in the presence of lysine or arginine, but not by the other amino acids. Activities of arginine deiminase, ornithine carbamoyltransferase and carbamate kinase were found in the cell-free extract, suggesting that arginine was catabolised through the arginine deiminase pathway and ATP was formed in this pathway. Ornithine was further degraded to butyrate. In addition, the organisms produced arginine-carboxypeptidase, indicating that these bacteria may liberate C-terminal arginine from peptides and utilise it for their growth. Thus, E. nodatum may utilise lysine and arginine as major energy yielding substrates in human periodontal pockets. Keywords: arginine, arginine-carboxypeptidase, arginine deiminase pathway, Eubacterium nodatum , lysine.
GEOGRAPHIC PATTERNS IN PLANT–POLLINATOR MUTUALISTIC NETWORKS

Recent reviews of plant-pollinator mutualistic networks showed that gen- eralization is a common pattern in this type of interaction. Here we examine the ecological correlates of generalization patterns in plant-pollinator networks, especially how interaction patterns covary with latitude, elevation, and insularity. We review the few published anal- yses of whole networks and include unpublished material, analyzing 29 complete plant- pollinator networks that encompass arctic, alpine, temperate, Mediterranean, and subtrop- ical-tropical areas. The number of interactions observed (I) was a linear function of network size (M) the maximum number of interactions: ln I 5 0.575 1 0.61 ln M; R 2 5 0.946. The connectance (C), the fraction of observed interactions relative to the total possible, decreased exponentially with species richness, the sum of animal and plant species in each community (A 1 P): C 5 13.83 exp(20.003(A 1 P)). After controlling for species richness, the residual connectance was significantly lower in highland (.1500 m elevation) than in lowland networks and differed marginally among biogeographic regions, with both alpine and trop- ical networks showing a trend for lower residual connectance. The two Mediterranean networks showed the highest residual connectance. After correcting for variation in network size, plant species were shown to be more generalized at higher latitude and lowland habitats, but showed increased specialization on islands. Oceanic island networks showed an im- poverishment of potential animal pollinators (lower ratio of animal to plant species, A : P, compared to mainland networks) associated with this trend of increased specialization. Plants, but not their flower-visiting animals, supported the often-repeated statements about higher specificity in the tropics than at higher latitudes. The pattern of interaction build- up as diversity increases in pollination networks does not differ appreciably from other
Reduction of RBL–2H3 cells degranulation by nitroaromatic compounds from a Bacillus strain associated to the Amazonian sponge Metania reticulata

Symbionts in sponges must interact with the host immune system, and this can be mediated by immunomodulators. As the bases of the immune system in sponges resemble those of higher metazoans, it is possible that compounds from this microbiota show similar effects in other phyla. It is also known that several antibiotics, in special macrolides, can modulate many components of the immune response and sponges and their associated microorganisms are a rich source of these compounds. Therefore, we tested the immunosuppressive capacity of antibiotic substances produced by bacterial and fungal strains isolated from the Amazon freshwater sponge Metania reticulata. Fourteen bacterial and six fungal strains were obtained from samples of M. reticulata collected in the Negro River (Amazon Central Basin region), during the dry season. These cultures were monitored for natural antimicrobial activity, and two Bacillus strains (MERETb.761 and MERETb.762) and one fungus (MERETf.010) were selected. One Bacillus strain, MERETb.762, showed strong and specific antibiosis on Staphylococcus aureus and two fractions of its extract inhibited the degranulation of RBL–2H3 cells. The predicted formulas of these fractions were C12H6N4O8 and C25H4N2O6, both corresponding to nitroaromatic compounds.
Ultraviolet and violet light: attractive orientation cues for the Indian meal moth, Plodia interpunctella

The Indian meal moth (IMM), Plodia interpunctella (Hübner) (Lepidoptera: Pyralidae), engages in long‐distance or foraging flights in the twilight hours of the scotophase when blue light dominates the irradiance spectrum of the sky. We tested the hypothesis that IMM uses wavelengths of visible blue/violet light as orientation cues that trigger phototactic responses. In four‐choice laboratory experiments, blue light (400–475 nm) was significantly more effective than green (475–600 nm), orange (575–700 nm), or red (590–800 nm) light in attracting males and mated females. In subsequent experiments that tested light emitting diodes (LEDs) emitting peak wavelengths in the blue/violet‐light range, the 405‐nm ‘violet’ LED was significantly more effective than the 435‐, 450‐, or 470‐nm ‘blue’ LED in attracting males as well as virgin and mated females. In electroretinogram recordings, the 405‐nm wavelength elicited significantly stronger receptor potentials from female and male eyes than the 350‐nm (UV) wavelength, and in a behavioral experiment it significantly enhanced the known attractiveness of UV light. Equal attraction of IMMs to 405‐nm LEDs at 600–700 µW/cm2 with or without UV light, and significantly stronger attraction to a 405‐nm LED than to a 350‐nm LED at maximum light intensities, suggest that the deployment of violet instead of UV light could become one of several management tactics for control of IMMs.
Human GTPBP5 (MTG2) fuels mitoribosome large subunit maturation by facilitating 16S rRNA methylation

Abstract Biogenesis of mammalian mitochondrial ribosomes (mitoribosomes) involves several conserved small GTPases. Here, we report that the Obg family protein GTPBP5 or MTG2 is a mitochondrial protein whose absence in a TALEN-induced HEK293T knockout (KO) cell line leads to severely decreased levels of the 55S monosome and attenuated mitochondrial protein synthesis. We show that a fraction of GTPBP5 co-sediments with the large mitoribosome subunit (mtLSU), and crosslinks specifically with the 16S rRNA, and several mtLSU proteins and assembly factors. Notably, the latter group includes MTERF4, involved in monosome assembly, and MRM2, the methyltransferase that catalyzes the modification of the 16S mt-rRNA A-loop U1369 residue. The GTPBP5 interaction with MRM2 was also detected using the proximity-dependent biotinylation (BioID) assay. In GTPBP5-KO mitochondria, the mtLSU lacks bL36m, accumulates an excess of the assembly factors MTG1, GTPBP10, MALSU1 and MTERF4, and contains hypomethylated 16S rRNA. We propose that GTPBP5 primarily fuels proper mtLSU maturation by securing efficient methylation of two 16S rRNA residues, and ultimately serves to coordinate subunit joining through the release of late-stage mtLSU assembly factors. In this way, GTPBP5 provides an ultimate quality control checkpoint function during mtLSU assembly that minimizes premature subunit joining to ensure the assembly of the mature 55S monosome.
History of the Pipistrellus pipistrellus group in Central Europe in light of its fossil record

ABSTRACT In contrast to proposed paleobiogeographic scenarios based on molecular data, the fossil record suggests that in Central Europe the common pipistrelles, quite rich in the Holocene fossil record, first appeared as late as the present glacial cycle (including the Weichselian interstadials). Bats of this group are completely absent from the rich pre-Weichselian record available from Central Europe but occur in the early Middle Pleistocene record in the Mediterranean (Spain, Malta). Thus, it seems that the European range of common pipistrelles was restricted to the Mediterranean region until their northward spread during the present glacial cycle. The proposed range expansion (supposedly from multiple sources) is explained by climatic specificities of the present glacial cycle, namely with repeated extension of the semiarid, warm open-ground habitats that began in the Mediterranean region by the end of the Eemian.
Synergy of storage management with varietal productivity improvement: the case of maize in Timor-Leste

SUMMARY Maize (Zea mays L.) is the major staple crop in Timor-Leste, but yields are low, averaging 1·0–1·7 t/ha, and losses during storage are high from maize weevil (Sitophilus zeamais Motschulsky) damage. The current research, assessing both weevil damage and management options, studied household storage of traditional and introduced maize varieties in 18 farmer groups for 33 weeks, and then evaluated the weevil damage in cobs stored for 9 months of 19 populations from different multi-location yield trials in 2007 and 2010. Storage of shelled grain in airtight containers for 33 weeks had no weevil damage on-farm. In contrast, storing shelled maize in a woven sack was the worst storage method with an average of 0·96 of grain attacked by weevils by Week 33, with local and introduced varieties damaged similarly. Shelled grain stored in a woven sack were infested significantly more than in traditional storage methods husked on the cob – above a fireplace, in a tree or an elevated house. Importantly, modern varieties were damaged more extensively by weevils than local maize types when the husked maize was stored using traditional methods. In the yield trials, grain weevil damage averaged 0·39 in both years after storage in the husk for 9 months. Varietal and location effects were significant for proportion of weevil damage, but the interaction effect was not significant in either year. The broadsense heritabilities were intermediate/high for proportion of weevil-damaged grain (H 2=0·81 in 2007 and 0·59 in 2010), and there is potential that populations can be found combining a substantial yield increase with no increase in weevil susceptibility for households using traditional storage methods. For those households with access to airtight storage systems, the results emphasize the need to exploit the interaction of variety with storage method to benefit from the yield advantage of introduced varieties through the concurrent dissemination of improved seed with subsidized, airtight storage drums.
Overexpression of Wild-Type Retinoic Acid Receptor (RAR) Recapitulates Retinoic Acid-Sensitive Transformation of Primary Myeloid Progenitors by Acute Promyelocytic Leukemia RAR-Fusion Genes

Retinoic acid receptor  (RAR) is the target of several chromosomal translocations associated with acute promyelocytic leukemias (APLs). These rearrangements fuse RAR to different partner genes creating the chimeric proteins: PML-RAR, PLZF-RAR, and NPM-RAR. Although the vast majority of APLs respond to retinoic acid therapy, those associated with PLZF-RAR are resistant. We have used retroviruses to express PML-RAR, PLZF-RAR, NPM-RAR, RAR403 (a dominant negative mutant of RAR), and wild-type RAR in murine bone marrow progenitors and found that all of these constructs blocked differentiation and led to the immortalization of myeloid progenitors. This cellular transformation is specific to an alteration of the RAR pathway because overexpression of RARβ, RARγ, or RXR did not result in similar growth perturbations. Pharmacological doses of RA induced differentiation and inhibited proliferation of cells transformed with either of the APL fusion genes, including PLZF-RAR, whereas physiological retinoic acid concentrations were sufficient to reverse the phenotype of cells transformed with wild-type RAR. The cellular responses to retinoic acid were accompanied by a sharp decrease in the amount of the RAR-fusion proteins expressed in the cells. Our findings suggest that the oncogenicity of RAR-fusion proteins results from their nature to behave as unliganded RAR in the presence of physiological concentrations of retinoic acid.
Cro’s role in the CI–Cro bistable switch is critical for λ’s transition from lysogeny to lytic development

CI represses cro; Cro represses cI. This double negative feedback loop is the core of the classical CI–Cro epigenetic switch of bacteriophage . Despite the classical status of this switch, the role in development of Cro repression of the PRM promoter for CI has remained unclear. To address this, we created binding site mutations that strongly impaired Cro repression of PRM with only minimal effects on CI regulation of PRM. These mutations had little impact on development after infection but strongly inhibited the transition from lysogeny to the lytic pathway. We demonstrate that following inactivation of CI by ultraviolet treatment of lysogens, repression of PRM by Cro is needed to prevent synthesis of new CI that would otherwise significantly impede lytic development. Thus a bistable CI–Cro circuit reinforces the commitment to a developmental transition.
Comparison of crop yields and soil conditions during 30 years under annual tillage or grazed pasture

SUMMARY Crop yields and soil properties of grazed grass–clover pasture and arable plots at the Grasslands Research Institute, Hurley, UK. were measured over 30 years (1955–84). Yields of herbage declined from 9·6 t DM/ha in the first harvest year to 4–6 t in years 5 to 8 but subseque8tly increased (after liming) to give a mean yield of 8·2 t for 1963–84. Yields of barley in plots receiving a seed-bed application of 45 kg N/ha averaged (1962–80) 3·1 t/ha and, in plots top dressed with an additional 100 kg N/ha, 4·1 t/ha but after 1969, response to additional N and yield under both N treatments showed a marked decline. Soil carbon increased during the first 10 years under pasture from 1·2 to 1·8% and soil N from 0·13 to 0·17%. These increases, equivalent to 1 t C and 75 kg N/ha per year, occurred at the same time as the initial decline in herbage yield noted above. During the subsequent 20 years, C and N remained relatively constant and herbage yields increased. Soil C and N decreased under 30 years' arable management to 0·8% C and 0·1% N, equivalent to a loss of 290 kg C and 25 kg N/ha per year. Major factors that appear to have influenced herbage yields were (i) soil moisture, (ii) accumulation of N in the soil organic matter during the first 8 years and the subsequent increase in the rate of mineralization, and (iii) the action of the earthworm population in creating a stone-free, fertile layer of top soil. As for barley, it was concluded that yields could not be maintained indefinitely on this soil series, as a result of the loss of soil structure and the development of a compact layer of soil at plough depth.
Methods for Selection of Mutants and In Vitro Culture of Cochliobolus heterostrophus

SUMMARY: Auxotrophic, morphological and drug-resistant mutants of Cochliobolus heterostrophus (= Bipolaris maydis = Helminthosporium maydis = Drechslera maydis) were isolated after mutagenesis with ethyl methanesulphonate. Exposure of the fungus to other mutagens (N-methyl-N'-nitro-N-nitrosoguanidine, nitrous acid, and UV light) resulted in recovery of morphological but not auxotrophic mutants. Antibiotic enrichment or filtration enrichment in medium containing high levels of sorbose increased the proportion of auxotrophs in the surviving population. All sexually fertile mutants were found to have single gene lesions; those with the same phenotype were allelic in some cases but not in others. Defined minimal and complete media, designed to facilitate genetic and molecular biological manipulations, supported maximal growth rate at 30 °C and maximal conidiation of the fungus at 23 °C with a 16 h long-wave UV light photoperiod. Under all in vitro growth conditions tested, near-isogenic lines of two known races of the fungus were essentially identical. Sexual fertility was improved by a programme of breeding and selection, but not by physical or chemical changes in the medium used for crossing. The fungus can be stored conveniently on silica gel.
Amended Descriptions of the Genus Leptospira Noguchi 1917 and the Species L. interrogans (Stimson 1907) Wenyon 1926 and L. biflexa (Wolbach and Binger 1914) Noguchi 1918

The current descriptions of the genus Leptospira Noguchi and the species L. interrogans and L. biflexa (Int. J. Syst. Bacteriol. 30:225–420) are inadequate and out of date. On behalf of the members of the Subcommittee on the Taxonomy of Leptospira of the International Committee on Systematic Bacteriology, amended descriptions of these taxa are presented.
Gene mapping in complex traits gene expression profiling and copy number variability in gene mapping of age-related cognitive decline

Alternative strategies for mapping genes involved in common traits are needed due to the complexity of the underlying genetic and environmental causes. Improvements in technology have provided the ability to genotype increasing numbers of single nucleotide polymorphisms (SNPs) in multiple individuals in a cost effective manner. The advent of whole genome expression profiling technology has enabled investigators to combine functional genomics with genetic variation such as SNPs and copy number polymorphisms to inform the choice of possible candidate genes for further study In this study, genes involved in age-related cognitive decline as defined by Alzheimer’s disease (AD) were identified through the use of current high-throughput technologies. Gene profiling was used to identify functional candidates and associated pathways implicated in neuropathological phenotypes related to cognitive decline. Whole genome association (WGA) techniques were investigated to assess both the low level characteristics of the genotyping algorithms and the impact of DNA structural variation on the previous gene expression results.
Analysis of the country of origin effect for the Romanian consumer of food products.

In the case of food products, the concept of country of origin is frequently present because of the shorter time spend by the consumer during the evaluation of alternatives phase. The aim of this study is to determine the influence of country of origin attribute over the consumer in the case of food products by comparing to attributes like brand, price, package and ingredients. A study was conducted among the people from Cluj-Napoca in 2013, on a sample of 277 people. The instrument used was the questionnaire which had four parts. A major objective of this study was to investigate if the results obtained by Dosen (2006) in his study will be the same among the Romanian consumers. The first hypothesis considers that the brand is more important in the buying decision-making process that the country of origin. The second one refers to price as being more important than the country of origin. Results indicate that price is more important than all the attributes mentioned: country of origin, ingredients, brand, and package. Country of origin is more important than brand and package. Brand is more important than package. In the present study brand is not more important than the country of origin and price is more important than the country of origin. It can be concluded that the country of origin is an important attribute when referring to food products, but price is the most important one. Package is the least important attribute, so not so many efforts must be spent for it.
Repetitive-Motion Display: A New Behaviour in a Burrowing Alpheid Shrimp

ABSTRACT Alpheidae are a highly diverse group of carideans with various life histories. They are known to possess specialized body forms and appendages, form facultative and obligate symbiotic relationships, and even exhibit complex behaviors like eusociality. This study represents the first documented association between the alpehid shrimp Alpheus rapax Fabricius, 1798 and the gobiid fish Myersina macrostoma. An undocumented behavioral display was observed in eight A. rapax individuals. The display was only performed in newly molted individuals while within their respective burrows in the presence of light. The display consisted on the following repetition: shrimp shifted its entire body forwards, with the cephalothorax angled downwards with respect to the pleon and both chelipeds extended forwards and towards each other; body jerked rapidly backwards with pleon curled and walking pereiopods extended; cephalothorax angled upwards, while the chelipeds were spread apart and moved backwards; and continuous undulations of pleopods. The display was hypothesized to either contribute to physiological requirements post molting or as a dishonest signal.
A study on wheat middling's usage on turkey's performances.

Two trials were conducted to determination of chemical composition and nutritive value of grade 1 wheat middlings wastes and its suitable levels in turkey diets were investigated.Experiment 1 evaluated the chemical composition, and energy and protein content. The experiment 2 was conducted by 160 day old unsexed white wide breast turkeys. Four rations were used as a four treatments includes (0, 10, 20,30%) of wheat middlings in turkeys diets. Four replicates with 10 birds were arranged in each.All of diets were Isoenergetic and isonetrogenous. The experiment was started from 30 days of age to the 120 days of old. Experiment statistical was in complete random design (CRD), data analysed by SAS program and means were examined by Duncan multiple test. The metabolizable energy and protein content were 3220 kcal/ kg and 14.2% respectively. No significant differences were found in body weight (BW), feed conversion ratio (FCR) and body weight gain and cost of 1kg meat production in the turkey feeding trial and in by different levels of wheat middlings(p>0.05). There were no significant variables in breast and thigh and abdominal fat and viscera percent of slaughtered turkeys too (p>0.05). However, in this study, these variations did not significantly affect the performance of turkeys. It would suggested that 30% of wheat middlings in turkey's ration could leads to decrease the ration price and approach more benefits for turkey industry