Miracle-dz/UniFAR-FTUs huggingface dataset:
Of Bacteria and Bile

The antibacterial activities of bile salts include detergent activity on cell membranes, protein denaturation, and DNA damage. However, many bacterial species are resistant to the antibacterial activity of bile salts. Bile salts may thus be viewed both as antibacterial compounds and as signals used by bacteria to identify bile-containing animal environments. This chapter reviews the mechanisms employed by Escherichia coli, Salmonella enterica, and other intestinal bacteria to respond to bile salts, with emphasis on their relevance for pathogenesis. The reader is also referred to two comprehensive, insightful reviews on bacterial responses to bile. Unconjugated forms of bile salts are amphipatic molecules that can enter the bacterial cell by crossing membrane bilayers. Furthermore, in the outer membrane of gram-negative bacteria, porins provide passage to both unconjugated and conjugated bile salts. Bile salts, especially if unconjugated, may easily reach the bacterial ctyoplasm by diffusion. Bile salts may also bind to specific receptors in the bacterial surface, activating signal transduction pathways that change gene expression patterns. Bile extract or individual bile salts can be added to microbiological media, thus permitting reductionist studies of bacterial bile resistance in the laboratory. It is hypothesized that nonmutational, reversible resistance may involve stochastic activation of one or more efflux systems that transport bile outside the cell.
Azine-carboxamides as anticancer agents

Despite disappointing results with the Raf inhibitor ZM 336372, AstraZeneca claims new B-Raf kinase inhibitors with the same m-phenylenediamine core structure. The new bisamides have two distinct linker groups attached. One is a substituted aromatic carboxylic acid group that constitutes the lipophilic part of the molecule, and the other is usually a pyrimidine carboxylic acid. The new molecules are part of a series of m-phenylenediamine bisamides. The compounds are expected to have anticancer activity due to their B-Raf inhibitory activity. B-Raf is mutated in a number of cancers into a constitutively active enzyme.
Sequential zinc and iron biofortification of bread-wheat grains: from controlled to uncontrolled environments

Abstract. The development of knowledge on bread wheat (Triticum aestivum L.) biofortification in zinc (Zn) and iron (Fe), related to its potential agronomical use and the nutritional and technological implications, is becoming important to strategies for improving human nutrition. In this context, we studied the accumulation of Zn and Fe in grains, considering potential uptake and translocation kinetics, photoassimilate production and deposition, and related yields, in grains of cv. Roxo produced under controlled-environment conditions and used thereafter in field trials. The metabolic plasticity of this wheat genotype grown under controlled-environment conditions allowed a 10- and 4-fold enhancement in accumulation of Zn and Fe in the grains after nutrient supplementation with a 5-fold concentrated Hoagland solution (5S), after two generations. Moreover, when these seeds were sown under field conditions and the resulting plants supplemented with or without Zn and Fe, the accumulation of these nutrients decreased within the next two generations. Such field seeds obtained without further Zn and Fe supplementation (with nitrogen only; F3(S) and F4(S)) maintained enhanced levels of Zn (∼400%) and Fe (40–50%) compared with the initial seeds. If Zn and Fe supplement was given to the plants germinated from F2(5S), the subsequent F3(5S) and F4(5S) seeds maintained the Zn increase (∼400%), whereas a further enhancement was observed for Fe, to 75% and 89%, respectively. Toxic limits were not reached for photosynthetic functioning. Even under the highest Zn and Fe supplement dose given to the F3(5S) plants, there was only a slight effect on photosystem II photochemical performance; in fact, enhanced net photosynthesis values were observed. In conclusion, within this experimental design, Zn and Fe biofortification can be obtained without toxicity effects on photosynthetic performance and with negligible modifications to grain texture and nutritional value (protein quality and contents as well as fatty acids).
WODAN: de invloed van verspreidings- en vestigingsmogelijkheden op het ontstaan van biodiversiteit

Biodiversiteit is een belangrijk beleidsthema bij het beheer van natuurgebieden in Nederland en daarbuiten. Wat de exacte mechanismen zijn die ten grondslag liggen aan het ontstaan van diversiteit in ecosystemen, is echter nog steeds het onderwerp van hevige discussie. Universiteit Utrecht is een onderzoek gestart onder de naam WODAN (windows of opportunity and dispersal affect number of species) dat zich richt op het beter begrijpen van de vele ecologische processen die samenhangen met de verspreiding en vestiging. De bossen in de IJsselmeerpolders vormen bij uitstek een geschikte locatie om het ontstaan van biodiversiteit te onderzoeken. Daarnaast is de binnenkomst en uitbreiding van nieuwe plantensoorten in de polders goed gedocumenteerd
Influence of age and sex on levels of anti-oxidized LDL antibodies and anti-LDL immune complexes in the general population Published, JLR Papers in Press, December 16, 2004. DOI 10.1194/jlr.M400290-JLR200

Most studies of antibodies to oxidized LDL have been undertaken in patients with different diseases and cardiovascular risk factors. However, very few studies have researched the distribution and determining factors of antibodies to oxidized LDL in the general population. A total of 1,354 persons (817 females and 537 males) aged 5–65 years were included in this study. They were selected randomly from the population census of Málaga, in southern Spain. The females had lower levels of total cholesterol and triglycerides and higher levels of HDL-cholesterol and a very significant increase (P < 0.0001) in levels of anti-oxidized LDL [low density lipoprotein modified by malondialdehyde (MDA-LDL)] antibodies but no difference in levels of immune complexes consisting of LDL and IgG antibodies (anti-LDL immune complex). Younger persons (16–35 years) had higher levels of anti-oxidized LDL (MDA-LDL) antibodies than persons older than 35 years (P = 0.05). Levels of immune complexes were significantly higher (P = 0.05) in persons aged 5–15 years than in persons older than 40 years. A very weak association was found between levels of anti-oxidized LDL (MDA-LDL) antibodies and anti-LDL immune complexes. The higher prevalence of anti-oxidized LDL (MDA-LDL) antibodies in females and young persons is in agreement with studies that found an inverse association between atherosclerosis and the level of these antibodies.
Predictor sets and biodiversity assessment: the evolution and application of an idea

The idea of “indicator species” is a relatively old one with a huge associated literature. The idea that the existence or health of a single species somehow captures the state of an entire ecosystem, though, remains a challenge to those who, like us, study entire assemblages of invertebrates. This challenge is especially marked when the ecosystems of choice are rainforests. Nevertheless there remains a need for a measure of diversity somewhere between the single species and the entire assemblage, which, for invertebrates in rainforests, may add up to many hundreds of species. This need led one of us (RK), in the nineteen nineties, to formulate the idea of a ‘predictor set’: that is, a statistically defined set of species, from within a much larger assemblage, whose spatial or temporal distribution captures the patterns characteristic of the entire assemblage. This essay will trace the origin and development of this idea and present some current applications and future research questions. Of course, the use of single charismatic species as “flagship” or “umbrella” species is undoubtedly of conservation value and remains unchallenged.
Plant enzyme mediated lipolysis of Lolium perenne and Trifolium pratense in an in vitro simulated rumen environment

Lee, M. R. F. , Martinez, E. M. , Scollan, N. D. , Theodorou, M. K. (2003). Plant enzyme mediated lipolysis of Lolium perenne and Trifolium pratense in an in vitro simulated rumen environment. Page 424 in: van der Honing, Y. (Ed.). EAAP Book of abstracts, Volume 9. Wageningen Academic Publishers, ISBN: 978-90-76998-20-6. Book of Abstracts of the Annual Meeting of the European Association for Animal Production (EAPP), Rome, Italy, 30 August-3 September 2003.
In vivo and In vitro Culture of the Red Ring Nematode, Rhadinaphelenchus cocophilus

Inoculations of 100 persistent juveniles (JIII) of the red ring nematode, Rhadinaphelenchus cocophilus, into coconut leaf stalks produced red ring infestations in 50-60% of the stalks after 3-4 weeks. Monoxenic cultures of the fungi, Monilinia fructicola and Botrytis cinerea and undifferentiated sugarcane leaf spindle callus were inoculated with ca. 100 surface-sterilized juveniles (JIII) of R. cocophilus. At 1 week, no nematode survival was observed on either fungus. Molting was observed in one culture of sugarcane callus after 4 weeks. Several oligidic media were tested for R. cocophilus survival and development. Red ring nematodes survived longer than 70 days in autoclaved red ring stem tissue infusion water (RRW) that was unsupplemented or was supplemented with 5.00 g D-glucose/500 ml RRW, 3.85 g lactose/500 ml RRW, or 10.00 g Bacto-lactose broth + 5.00 g D-glucose/500 ml RRW (R + LB + G). A single adult female, four J4's, and nine JIII-J4 intermolts were recovered after 70 days
A Novel Nested Polymerase Chain Reaction (n-PCR) Assay for Identifying Sorghum nitidum

This work developed a novel nested polymerase chain reaction (n-PCR) assay to identify Sorghum nitidum (S. nitidum). It has been designed a set of specific n-PCR inner primers Snit5/Snit2 and outer primers Nout1/Nout2 based on a conserved nucleotide sequence of adh1-like gene of S. nitidum. Fourteen samples of sorghum were used to investigate the specificity of the primers and the n-PCR assay. The result showed that 9 samples of S. nitidum displayed a positive strong, specific amplified band at ~873 bp in gel spectra, while other relatives, including Sorghum halepense, Sorghum almum, Sorghum bicolor, Sorghum propinum and Sorghum sudanse exhibited negative amplifications. This assay was able to specifically identify S. nitidum fast and effectively, which could be applied widely in field inspection, agriculture production and plant protection.
Strong sexual dimorphism unraveled by DNA analysis – towards a better understanding of Pseudothyretes classification (Lepidoptera: Erebidae: Arctiinae)

Pseudothyretes Dufrane, 1945 is one of the least known genera of the subtribe Thyretina. The association of the sexes is not known for any of the seven species in the genus because of the very strong sexual dimorphism and the lack of appropriate data. With the help of molecular data we elucidate the previously unknown females of two species [Pseudothyretes kamitugensis (Dufrane, 1945) and Pseudothyretes perpusilla (Walker, 1856)]. The same procedure revealed the synonymy of Pseudothyretes carnea (Hampson, 1898) and Pseudothyretes rubicundula (Strand, 1912) syn. nov., treated previously as two separate taxa described from the opposite sexes. The morphological analysis of almost 750 specimens yielded the discovery of two new species (Pseudothyretes mirus Przybylowicz sp. nov. and Pseudothyretes obscurus Przybylowicz sp. nov.), for which we give detailed descriptions, including morphological characters of both sexes. We provide for the first time a dichotomous key for the identification of males based on habitus and genitalia. A molecular analysis of 61 samples representing seven species allows a preliminary recognition of molecular variation. The paper also includes a historical background of the genus, distributional analysis of the species, and an extensive discussion of the identity of the female holotype of Pseudothyretes carnea (Hampson, 1898). Female genitalia and labial palpus morphology are illustrated for the first time in this genus. © 2015 The Linnean Society of London
Penampilan Produksi Ayam Broiler yang Diberi Bacillus circulans dan Bacillus sp. Selama Periode Pemulihan Setelah Pembatasan Ransum

The present study was designed to investigate the efficacy of Bacillus circulans and Bacillus sp. as probiotic during realimentation period on performance of broiler chickens. Three hundred of 7 days-old unsexed broiler chicken of Cobb commercial strain were used in the experiment. The treatments were: control ration was fed ad libitum (P-0), ration with energy restriction at 1.5xBW 0.67 EM kcal/day without (P-1) and with (P-2) probiotic supplementation during realimentation period, and ration with energy restriction at 2.25xBW 0.67 EM kcal/day without (P-3) and with (P-4) probiotic supplementation during realimentation period. Feed restriction was applied from 7 to 14 days of age. The experiment was arranged as a completely randomized design with 5 treatments and 6 replications. The results showed that feed intake and body weight gain of chickens submitted to early feed restriction on P-1, P-2, P-3 and P-4 were significantly lower (P 0.67 EM kcal/day for 7 days (7 to 14 days of age) with supplementation of probiotic B. circulans and Bacillus sp. (P-4) during realimentation period showed similar compensatory growth and body weight, but production index and feed cost better than control. Key words: feed restriction, probiotic, realimentation
Antimicrobial Efficacy of Methanobactin against Bacillus Subtilis

Methanobactin is a novel extracellular fluorescent chromopeptide produced by methanotrophys. Its recent characterization has placed it in a new class of compounds, which is now known as chalkophores. They are analogous to iron-binding siderophores. The present study investigated the antimicrobial efficacy of copper-bound methanobactin (Mb-Cu) against Bacillus Subtilis in LB medium. Minimum inhibitory concentrations (MICs) determined that at 24 h for stationary-phase Bacillus Subtilis cultures in liquid LB medium (36° C) via use of a two-fold dilutions method, was 5 mg/mL. Minimum bactericidal concentrations (MBC) for Mb-Cu observed in the plate after 72 h at 36° C was 10 mg/mL. Effect of different pH value (2 to 9) on antibacterial activity of Mb-Cu was measured by bacteriostatic circle method; the results showed that there was a non-liner re lationship between the antimicrobial activity of Mb-Cu against Bacillus Subtilis and pH. M ethanobactin was active in the range of pH 2~9 and has the best antimicrobial activity at near pH 6.0. Growth curve of Bacillus subtilis results showed that the maximum growth rate of Bacillus Subtilis was reduce and the lag phase was extended for 3 h.
THE REGULATION OF WATER AND SALT BY THE FIDDLER CRABS, UCA PUGNAX AND UCA PUGILATOR

1. Analyses were made of the serum, urine, gill and stomach fluids for total osmotic concentration and the electrolytes Na, Mg, K, Ca. NH4, Cl and SO4 in Uca pugnax and U. pugilator when these two species were kept in 100% and 175% sea water.2. For crabs in 100% sea water the serum electrolyte values for Na, Mg and Cl are lower and those for K, Ca, NH4 and SO4 higher than in the medium; for crabs in 175% sea water the serum electrolyte values of Na, Mg, K, Ca, NH4 and Cl are lower and only SO4 higher than the values in the medium. The sera of crabs from both media are hypotonic to their saline environment.3. The electrolyte values of sera from crabs in normal sea water differ significantly from the gill fluid electrolytes for Mg, Ca and Cl only; while similar sera values from crabs in concentrated sea water differ significantly for Na, Mg, Ca, Cl and SO4. In all cases except for Ca from crabs in normal sea water the significant gill fluid electrolyte concentrations are greater than the corresponding sera .
Regulatory T Cells CD4+ CD25+ Expression in Biliary Atresia Mice Model after Exposure with Rhesus Rotavirus (RRV)

Billiary atresia (BA) is still a major challenge for clinicians, as without surgical intervention, more than 80% of patients will develop liver cirrhosis, or die within 2 years of life. The pathogenesis is still unknown, but a theory of primary perinatal hepatobiliary viral infection followed by auto- immune-mediated bile duct injury had been hypothesized. The objective of this study is to determine the change of regulatory T cells and inflammatory reaction in liver after rhesus rotavirus (RRV) infection in BA mice model. Two groups of newborn mice, those were RRV group consisting of 24 newborn mice injected by RRV 1.5 x 106 PFU intraperitoneally less than 24 hours after birth, and control group comprising of 24 newborn mice injected with buffered saline were used as BA model. The expression of Tregs and infiltration of inflammatory cells in the liver of the two groups of newborn mice were studied on day 3, 7, 14, and 21 after birth. The results shows that tregs expressions of RRV group on day 3, 7, 14 and 21 were significantly higher than control group (p<0.05). There were also significant increases of Tregs expressions on day by day, both in RRV group (p<0.001), as well as in control groups (p=0.002). The excessive infiltration of inflammatory cells and narrowing of bile duct lumens were detected on day 14. As a conclusion we can say that the Induction of Rotavirus (RRV) in newborn mice model BA increases the expressions of Tregs, and may cause damage of bile ducts within two weeks of life.
The Aqueous Extract of a Popular Herbal Nutrient Supplement, Angelica sinensis, Protects Mice against Lethal Endotoxemia and Sepsis

Despite recent advances in antibiotic therapy and intensive care, sepsis remains a widespread problem in critically ill patients. The high mortality from sepsis is in part mediated by bacterial endotoxin, which stimulates macrophages/monocytes to sequentially release early (e.g., tumor necrosis factor, interleukin-1, and interferon-γ) and late [e.g., high mobility group box 1 protein (HMGB1)] proinflammatory cytokines. Our discovery of HMGB1 as a late mediator of lethal systemic inflammation has initiated a new field of investigation for the development of experimental therapeutics. A popular Chinese herb, Angelica sinensis (also known as Dang Gui or Dong Quai) has been used traditionally for treating women with gynecological disorders (such as dysmenorrheal and hot flashes). Here we examined the effect of Angelica sinensis extract on endotoxin-induced HMGB1 release in vitro, and explored its therapeutic potential in animal models of lethal endotoxemia and sepsis [induced by cecal ligation and puncture (CLP)] in vivo. We demonstrated that a low-molecular-weight (<10 kDa) fraction of A. sinensis extract significantly attenuated endotoxin-induced HMGB1 release in part through interfering with its cytoplasmic translocation in macrophage cultures. Prophylactic administration of an aqueous extract of A. sinensis significantly attenuated systemic HMGB1 accumulation in vivo, and conferred a dose-dependent protection against lethal endotoxemia. Furthermore, delayed administration of A. sinensis extract beginning 24 h after CLP attenuated systemic HMGB1 accumulation, and significantly rescued mice from lethal sepsis. Taken together, these data suggest that A. sinensis contains water-soluble components that exert protective effects against lethal endotoxemia and experimental sepsis in part by attenuating systemic accumulation of a late proinflammatory cytokine, HMGB1.
Rates of local colonization and extinction reveal different plant community assembly mechanisms on road verges in central Spain

Question: Does community assembly on roadsides differ between two contrasting habitats along a stress–productivity gradient? Is establishment success determined by the regional pool, environmental filters or historical events? Location: Highway roadcuts and embankments in central Spain (40°29′N, 03°34′W). Methods: Species composition was recorded annually in 45 plots distributed on steep slopes with newly exposed surfaces (roadcuts) or newly built topsoiled substrates (embankments), for 4 years following hydroseeding with standard or native seed mixture. Frequency of appearance and local colonization and extinction rates of individual species were clustered in establishment success groups. We examined the correspondence between descriptive plant traits and species performance on both roadslope types. Results: Roadslope species richness showed a sustained increase over time, although at consistently lower levels and rates on the more productive embankments. Sixty per cent of the colonization events involved species from the surrounding vegetation. Hydroseeded species persisted through time, but did not modify community composition or dynamics. A higher establishment success rate was found in wind-pollinated species with large seeds and in exotic species. Those species growing on embankments showed an equal or higher establishment success rate on roadcuts and, conversely, species from roadcuts exhibited an equal or lower success rate on embankments. Conclusions: At the initial stages of community assemblage on unproductive newly created areas, species richness was shaped by the regional species pool. Communities on less harsh topsoiled embankments were subjected, however, to the filtering effect of competitive exclusion. In a reclamation context, efforts to increase site productivity may have detrimental consequences for in situ conservation of local diversity.
Interpretation of genotype × environment interaction for winter wheat yield in Ontario

An understanding of the causes of genotype × environment (GE) interaction can help identify traits that contribute to better cultivar performance and environments that facilitate cultivar evaluation. Through subjecting environment-centered yield of a multi-environment trial data to singular value decomposition, the portion of yield variation that is relevant to cultivar evaluation is partitioned into noncrossover and crossover GE interaction, quantified by the first two principal components (PC), respectively. Each PC is a set of genotypic scores multiplied by a set of environmental scores. By relating the PC scores to genotypic and environmental covariates, GE interaction represented by each PC can be interpreted in terms of trait × factor interactions. This strategy was employed in analysis of the 1992 to 1998 Ontario winter wheat (Triticum aestivum L.) performance trial data. Results indicated that plant height and maturity were the major genotypic causes of GE interaction, whereas cold temperature in the winter and hot temperature in the summer were the major environmental causes of GE interaction. Positive interactions were found between earlier maturity vs. warmer winters or hotter summers, and between shorter plant height vs. warmer winters or cooler summers. In addition, better resistance to septoria leaf blotch (caused by Septoria secalis Prill. & Delacr.) was frequently associated with overall performance. The results of this study should help in determining breeding objectives and for selecting test sites or environments for winter wheat breeding in Ontario.
Global patterns of functional diversity and assemblage structure of island parasitoid faunas

A.M.C.S. was supported by a Brazilian CNPq junior postdoctoral fellowship (159763/2010-0), a Portuguese Fundacao para a Ciencia e a Tecnologia grant (SFRH/BPD/70709/2010) co-funded by the European Social Fund POPH-QREN programme, a Marie Curie Intra-European Fellowship (IEF 331623 ‘COMMSTRUCT’) and by the projects ‘Developing tools to unify range dynamics and community-level processes into a single analytical framework’ (cooperation project CSIC-CNPq P2011BR0071) and ‘Disentangling the geographic and evolutionary determinants of the diversity of Western Palaeartic dung beetles’ [Spanish DGCyT project CGL2011-29317/BOS].