pinecone/core-2020-05-10-deduplication huggingface dataset:
Antimicrobial mechanisms of ortho-phthalaldehyde action

Biocides generally have multiple biochemical targets. Such a feature easily entangles the
analysis of the mechanisms of antimicrobial action. In this study, the action of the dialdehyde biocide ortho-phtalaldehyde (OPA), on bacteria, was investigated using the Gram-negative Pseudomonas fluorescens. The targets of the biocide action were studied using different bacterial
physiological indices. The respiratory activity, membrane permeabilization, physico-chemical
characterization of the bacterial surfaces, outer membrane proteins (OMP) expression,
concomitant influence of pH, contact time and presence of bovine serum albumin (BSA) on
respiratory activity, morphological changes and OPA-DNA interactions were assessed for
different OPA concentrations.
With the process conditions used, the minimum inhibitory concentration was 1500 mg/l, the concentration to promote total loss of bacterial culturability was 65 mg/l and the concentration needed to inactivate respiratory activity was 80 mg/l. These data are evidence that culturability and respiratory activity were markedly affected by the biocide. OPA lead, moreover, to a significant change in cell surface hydrophobicity and induced propidium iodide uptake. Such results suggest cytoplasmic membrane damage, although no release of ATP was detected. At pH 5, the bactericidal action of OPA was stronger, though not influenced by BSA presence.
Nevertheless, at pH 9, BSA noticeably (p < 0.05) impaired biocide action. A time- dependent effect
in OPA action was evident when contemplating respiratory activity variation, mainly for the lower exposure times. Scanning electron microscopy allowed to detect bacterial morphological changes, translated on cellular elongation, for OPA concentrations higher than 100 mg/l.
Interferences at DNA level were, however, restricted to extreme biocide concentrations. The overall bactericidal events occurred without detectable OMP expression changes.
In conclusion, the results indicated a sequence of events responsible for the antimicrobial action of OPA: it binds to membrane receptors due to cross-linkage; impairs the membrane functions allowing the biocide to enter through the permeabilized membrane; it interacts with intracellular reactive molecules, such as RNA, compromising the growth cycle of the cells and, at last, with DNA.Fundação para a Ciência e a Tecnologia (FCT
The role of extracellular polymers on Staphylococcus epidermidis biofilm biomass and metabolic activity

Staphylococcus epidermidis is now well established as a major nosocomial pathogen, associated
with indwelling medical devices. Its major virulence factor is related with the ability to adhere
to indwelling medical devices and form biofilms. In this study, the biofilm matrix of four
S. epidermidis clinical isolates was extracted and the polysaccharides and proteins content was
quantified. The results were correlated with the total biofilm biomass (determined by crystal
violet assay) and cellular metabolic activity (evaluated with XTT reduction assay). According to
the results, the exopolymers studied play an important role not only on structure and biofilm
biomass but also on cellular activity. Thus, the strain forming biofilms with the highest level of
polysaccharides (S. epidermidis 1457) also formed thicker biofilms but with the lowest metabolic
activity. The protein concentration also varied among strains, with the biofilm matrix of
S. epidermidis 9142 presenting a higher concentration of proteins comparing to the remaining
strains. This fact indicates the different levels of importance that matrix proteins can hold on
biofilm composition among strains albeit overall, it is suggested that extracellular protein
production it is not a determinative factor for biofilm total biomass.Fundação para a Ciência e a Tecnologia (FCT) - SFRH/BD/19265/2004, SFRH/BPD/26803/200
Adaptive response of single and binary Pseudomonas aeruginosa and Escherichia coli biofilms to benzalkonium chloride

The main goal of this work was to examine whether the continuous exposure of single and binary P. aeruginosa and E. coli biofilms to sub-lethal benzalkonium chloride (BC) doses can induce adaptive response of bacteria. Biofilms were formed during 24 h and then put continuously in contact with BC for more 5 days. The six-day-old adapted biofilms were then submitted to BC challenge, characterized and inspected by SEM. Both single and binary adapted biofilms have clearly more biomass, polysaccharides and proteins and less activity even though the number of cells was identical. After BC treatment, adapted biofilms maintained their mass and activity. SEM examination revealed that those adapted biofilms had a slimier and denser matrix that became thicker after BC treatment. Continuous exposure of bacteria to antimicrobials can lead to development of biofilms encompassing more virulent and tolerant bacteria. This adaptive resistance can be the result of a phenotypic adaptation, a genetic acquired resistance or both. Instead of eradicating biofilms and kill microorganisms, the use of a disinfectant can, favour biofilm formation and tolerance. This must be a genuine concern as it can happen in clinical environments, where the use of antimicrobials is unavoidable.The financial support from IBB-CEB and Fundacao para a Ciencia e Tecnologia (FCT) and European Community fund FEDER, through Program COMPETE, in the ambit of the Project PTDC/SAUESA/64609/2006/FCOMP-010124-FEDER-00702 and Idalina Machado PhD Grant (SFRH/BD/31065/2006) and Susana Lopes PhD Grant (SFRH/BD/47613/2008) are gratefully acknowledged
Nutritional requirements and strain heterogeneity in Ashbya gossypii

Colony radial growth rates and specific growth rates of three related Ashbya gossypii strains ATCC10895, IMI31268, MUCL29450 and an unrelated strain, CBS109.26, were measured on various carbon and nitrogen sources at pH 4.5 and pH 6.5 to elucidate physiological growth requirements and strain differences. All strains grew on yeast extract or ammonium as nitrogen sources, but not on nitrate. Substantial growth at pH 4.5 was observed only on complex medium. D-Glucose, glycerol and starch were utilised as carbon sources. Ethanol was produced during growth on glycerol. Conversion of xylose into xylitol demonstrates that the xylose reductase is active. Phenotypic differences between related strains were greater than expected. We demonstrate that A. gossypii utilizes ammonium as sole nitrogen source at pH 6.5, facilitating further physiological studies using chemically defined media in the future.The financial support of Fundacao para a Ciencia e a Tecnologia (FCT), Portugal, is acknowledged, project AshByofactory PTDC/EBB-EBI/101985/2008 and grant SFRH/BD/30229/2006 to O. Ribeiro
Optimization of an automatic counting system for the quantification of Staphylococcus epidermidis cells in biofilms

Biofilm formation is recognized as the main virulence factor in a variety of chronic infections. In vitro evaluation of biofilm formation is often achieved by quantification of viable or total cells. However, these methods depend on biofilm disruption, which is often achieved by vortexing or sonication. In this study, we investigated the effects of sonication on the elimination of Staphylococcus epidermidis cell clusters from biofilms grown over time, and quantification was performed by three distinct analytical techniques. Even when a higher number of sonication cycles was used, some stable cell clusters remained in the samples obtained from 48- and 72-h-old biofilms, interfering with the quantification of sessile bacteria by plate counting. On the other hand, the fluorescence microscopy automatic counting system allowed proper quantification of biofilm samples that had undergone any of the described sonication cycles, suggesting that this is a more accurate method for assessing the cell concentration in S. epidermidis biofilms, especially in mature biofilms.This work was funded by the Fundacao para a Ciencia e a Tecnologia (FCT) and the COMPETE grants PTDC/BIA-MIC/113450/2009 and FCOMP-01-0124-FEDER-014309
Serine protease identification (in vitro) and molecular structure predictions (in silico) from a phytopathogenic fungus, Alternaria solani

Serine proteases generally share a relatively high degree of sequence identity and play a major role in the diversity of biological processes. Here we focus on three-dimensional molecular architecture of serine proteases from Alernaria solani. The difference in flexibility of active binding pockets and electrostatic surface potential distribution of serine proteases in comparison with other fungal species is reported in this study. In this study we have purified a serine protease from the early blight pathogen, Alernaria solani. MALDI-TOF-MS/MS analysis revealed that protease produced by A. solani belongs to alkaline serine proteases. AsP is made up of 403 amino acid residues with molecular weight of 42.1kDa (Isoelectric point (pI)-6.51) and molecular formula C[subscript 1859]H[subscript 2930]N[subscript 516]O[subscript 595]S[subscript 4]. The follow-up research on the molecular structure prediction is used for assessing the quality of A. solani Protease (AsP). The AsP protein structure model was built based on its comparative homology with serine protease using the program, MODELER. AsP had 16 β-sheets and 10 α-helices, with Ser[superscript 350] (G347-G357), Asp[superscript 158] (D158-H169) and His[superscript 193] (H193-G203) in separate turn/coil structures. Biological metal binding region situated near the 6th-helix and His[superscript 193] residue is responsible for metal binding site. In addition, the calcium ion is coordinated by the carboxyl groups of Lys[superscript 84], Ile[superscript 85], Lys[superscript 86], Asp[superscript 87], Phe[superscript 88], Ala[superscript 89], Ala[superscript 90] (K84-A90) for first calcium (Ca[superscript 2+]) binding site and carbonyl oxygen atom of Lys[superscript 244], Gly[superscript 245], Arg[superscript 246], Thr[superscript 247], Lys[superscript 248], Lys[superscript 249], and Ala[superscript 250] (K244–A250), for second Ca[superscript 2+] binding site. Moreover, Ramachandran plot analysis of protein residues falling into most favored secondary structures were determined (83.3%). The predicted molecular 3D structural model was further verified using PROCHECK, ERRAT and VADAR servers to confirm the geometry and stereo-chemical parameters of the molecular structural design. The functional analysis of AsP 3D molecular structure predictions familiar in the current study may provide a new perspective in the understanding and identification of antifungal protease inhibitor designing
Isolation and partial characterization of bacteriophages infecting Pseudomonas syringae pv. actinidiae, causal agent of kiwifruit bacterial canker

The phytopathogen Pseudomonas syringae pv. actinidiae (Psa) is the causal agent of bacterial canker of kiwifruit. In the last years, it has caused severe economic losses to Actinidia spp. cultivations, mainly in Italy and New Zealand. Conventional strategies adopted did not provide adequate control of infection. Phage therapy may be a realistic and safe answer to the urgent need for novel antibacterial agents aiming to control this bacterial pathogen. In this study, we described the isolation and characterization of two bacteriophages able to specifically infect Psa. φPSA1, a member of the Siphoviridae family, is a temperate phage with a narrow host range, a long latency, and a burst size of 178; φPSA2 is a lytic phage of Podoviridae family with a broader host range, a short latency, a burst size of 92 and a higher bactericidal activity as determined by the TOD value. The genomic sequence of φPSA1 has a length of 51,090 bp and a low sequence homology with the other siphophages, whereas φPSA2 has a length of 40 472 bp with a 98% homology with Pseudomonas putida bacteriophage gh-1. Of the two phages examined, φPSA2 may be considered as a candidate for phage therapy of kiwifruit disease, while φPSA1 seems specific toward the recent outbreak's isolates and could be useful for Psa typin
Antifungal properties of an actinomycin D-producing strain,Streptomycessp. IA1, isolated from a Saharan soil

An actinomycete strain named IA1, which produced an antimicrobial compound, was isolated from a Saharan soil in In Amenas, Algeria. The study of the 16S rDNA sequence of this strain permitted to relate it to Streptomyces mutabilis NBRC 12800T (99.93% of similarity). Strain IA1 exhibited strong activity against a wide range of plant pathogenic fungi. One bioactive compound produced in large amounts (46.7 mg L−1 day−1), named YA, was isolated and purified by TLC and reverse phase HPLC. The structure elucidation of the pure substance, using combined data from UV visible, NMR spectra, and mass spectrometry, permitted to identify it as actinomycin D, and was thus found for the first time in S. mutabilis related species. The biocontrol abilities of the strain IA1 and compound YA were evaluated through two diseases, i.e., chocolate spot of field bean and Fusarium wilt of flax. The occurrence of the two fungal diseases was effectively reduced. The reduction of chocolate spot disease symptoms reached 80 and 91.7% with IA1 and YA seedlings pretreatments, respectively. Soil pretreatment with IA1 or YA also allowed to reduce Fusarium wilt disease impact by almost 60%
Temperate bacteriophages collected by outer membrane vesicles in Komagataeibacter intermedius

The acetic acid bacteria have mainly relevance for bacterial cellulose production and
fermented bio-products manufacture. The purpose of this study was to identify temperate
bacteriophages in a cellulose-producing bacterial strain Komagataeibacter intermedius
IMBG180. Prophages from K. intermedius IMBG180 were induced with mitomycin C and
nalidixic acid. Transmission electron microscopy analysis exhibited tailed bacteriophages
belonging to Myoviridae. A PCR assay targeting the capsid gene of the myoviruses proved
phylogenetic position of induced phages. Nalidixic acid was poor inducer of prophages,
however, it induced the OMV-like particles release. Size of OMVs depended on an antibiotic
applied for phage induction and varied in the range of 30–80 and 120–200 nm. Inside some of
them, tails of phages have been visible. Under conditions, inducing prophages, OMVs acted
as the collectors of formed phage particles, using outer membrane receptors for phage
detection (in this case, outer membrane siderophore receptor), and fulfilled therefore ―a
cleaning,‖ as well as defensive functions, preventing bacteriophage spread outside
population. This is the first description of myoviruses affiliated to K. intermedius, as well as
outer membrane vesicles interaction with phages within this host.This research was supported by grant 47/2014 from
National Academy of Sciences, Ukraine.http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1521-4028hb2016Biochemistr
Elemental biochemical analysis of the polysaccharides in the extracellular matrix of the yeast Saccharomyces cerevisiae

In yeast multicellular aggregates, such as biofilms and colonies, cells are supported by a yeast extracellular matrix (yECM) of glycosidic nature, the composition of which is mostly unknown. Saccharomyces cerevisiae ECM was produced, extracted and partitioned. An analytical-grade pure glycoside fraction was obtained, fractionated by anionic exchange liquid chromatography and analyzed by gas chromatography–mass spectrometry and polyacrylamide gel electrophoresis. Two different molecular weight polysaccharides were found, composed of glucose, mannose and small relative amounts of galactose. One of the polysaccharides had a low molecular weight, compatible with the association with glycoproteins abundantly occurring in yECM. In addition, these polysaccharide species were separated by diaminopropane agarose gel electrophoresis and induced metachromatic shift, suggesting chemical substitution, which was corroborated by anticoagulation activity. This was shown to be associated with the double deletion of the yeast homologues of the mammalian Hedgehog modulators Hhatl and Hhat, respectively yeast Gup1 and Gup2. These results pioneer the study of the molecular biology of the ECM supporting S. cerevisiae multicellular aggregates such as biofilms.The polysaccharide analysis was performed at the
Laboratory of Glycoconjugates Biochemistry and Cellular
Biology, UFRJ, Brazil. Fábio Faria-Oliveira was
supported by a PhD scholarship (SFRH/BD/45368/2008) from FCT (Fundação para a Ciência e a Tecnologia). This
work was funded by Marie Curie Initial Training
Network GLYCOPHARM (PITN-GA-2012-317297), and
FCT/MEC through Portuguese funds (PIDDAC)–PEst-OE/
BIA/UI4050/2014.info:eu-repo/semantics/publishedVersio
Evidence of novel plant-species specific ammonia oxidizing bacteria clades in acidic South African fynbos soils

Ammonia-oxidizing bacteria (AOB) are essential in the biogeochemical cycling of nitrogen as they catalyze the rate-limiting oxidation of ammonia into nitrite. Since their first isolation in the late 19th century, chemolithoautotrophic AOBs have been identified in a wide range of natural (e.g., soils, sediments, estuarine, and freshwaters) and man created or impacted habitats (e.g., wastewater treatment plants and agricultural soils). However, little is known on the plant-species association of AOBs, particularly in the nutrient-starved fynbos terrestrial biome. In this study, we evaluated the diversity of AOBs in the plant canopy of three South African fynbos-specific plant species, namely Leucadendron xanthoconus, Leucospermum truncatulum and Leucadendron microcephalum, through the construction of amoA-gene clone libraries. Our results clearly demonstrate that plant-species specific and monophyletic AOB clades are present in fynbos canopy soils.Claude Leon Foundation, the South African National Research Foundation
(NRF) and University of Pretoria.http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1521-40282016-08-28hb201
Influence of the metabolic state on the tolerance of Pichia kudriavzevii to heavy metals

This work aims to examine the influence of the metabolic state of the yeast Pichia kudriavzevii on the susceptibility to a metals mixture (5mgL1 Cd, 10mgL1 Pb, and 5mgL1 Zn). Cells exposed to the metals mixture in the presence of 25mmolL1 glucose displayed a higher loss of membrane integrity and proliferation capacity, compared to cells incubated in the absence of glucose. The analysis of the effect of individual metals revealed that glucose increased the toxic effect of Cd marginally, and of Pb significantly. The increased susceptibility to heavy metals due to glucose was attenuated in the simultaneous presence of a mitochondrial respiration inhibitor such as sodium azide (NaN3). ATP-depleted yeast cells, resulting from treatment with the non-metabolizable glucose analogue 2-deoxy-d-glucose, showed an increased susceptibility to heavy metals mixture. Pre-incubation of yeast cells with 1 or 1.5mmolL1 Ca2+ reduced significantly (P<0.05) the loss of membrane integrity induced by the metals mixture. These findings contribute to the understanding of metals mechanisms of toxicity in the non-conventional yeast P. kudriavzevii.This study was supported by the Portuguese Foundation
for Science and Technology (FCT) under the scope of the
strategic funding of UID/BIO/04469/2013 unit and
COMPETE 2020 (POCI-01-0145-FEDER-006684) and the
Project RECI/BBB-EBI/0179/2012 (FCOMP-01-0124-FEDER-
027462). Vanessa A. Mesquita and Manuela D. Machado
gratefully acknowledge the grant from Coordenaç~ao de
Aperfeiçoamento de Pessoal de N ıvel Superior (CAPES) and the post-doctoral grant from FCT (SRH/BPD/72816/
2010), respectively
Biofilm forming bacteria and archaea in thermal karst springs of Gellért Hill discharge area (Hungary)

The Buda Thermal Karst System (BTKS) is an extensive active hypogenic cave system located beneath the residential area of the Hungarian capital. At the river Danube, several thermal springs discharge forming spring caves. To reveal and compare the morphological structure and prokaryotic diversity of reddish-brown biofilms developed on the carbonate rock surfaces of the springs, scanning electron microscopy (SEM), and molecular cloning were applied. Microbial networks formed by filamentous bacteria and other cells with mineral crystals embedded in extracellular polymeric substances were observed in the SEM images. Biofilms were dominated by prokaryotes belonging to phyla Proteobacteria, Chloroflexi and Nitrospirae (Bacteria) and Thaumarchaeota (Archaea) but their abundance showed differences according to the type of the host rock, geographic distance, and different water exchange. In addition, representatives of phyla Acidobacteria, Actinobacteria, Caldithrix, Cyanobacteria, Firmicutes Gemmatimonadetes, and several candidate divisions of Bacteria as well as Crenarchaeota and Euryarchaeota were detected in sample-dependent higher abundance. The results indicate that thermophilic, anaerobic sulfur-, sulfate-, nitrate-, and iron(III)-reducing chemoorganotrophic as well as sulfur-, ammonia-, and nitrite-oxidizing chemolithotrophic prokaryotes can interact in the studied biofilms adapted to the unique and extreme circumstances (e.g., aphotic and nearly anoxic conditions, oligotrophy, and radionuclide accumulation) in the thermal karst springs
Climate signature of solar irradiance variations: Analysis of long-term instrumental, historical, and proxy data

The signature of solar irradiance variations on decadal-to-centennial climate variability is analyzed by means of statistical analysis of long-term instrumental, historical and proxy data sets. Solar variations associated with the Schwabe, Hale, and Gleissberg cycles are detected by their spatial patterns in sea surface temperature and seal level pressure. Different statistical methods of instrumental and proxy data show that the mode related to solar irradiance fluctuations on multidecadal timescales (Gleissberg cycle) is distinct from the Atlantic multidecadal mode associated to ocean circulation changes. From this, one can infer the degree to which solar variability has contributed to long-term temperature variations during the instrumental and pre-instrumental era
Northeast monsoon rainfall variability over south peninsular India vis-à-vis the Indian Ocean dipole mode

Whereas the June through to September southwest summer monsoon season over the Indian subcontinent has been the main focus of research, the October through to December northeast monsoon season over south peninsular India has received less attention. Hence, this study focuses on the northeast monsoon rainfall (NEMR) variability using historical data for a 131 year period (1871–2001) and its relationship with the neighbouring Indian Ocean sea-surface temperature (SST). Based on the observed available rainfall data, a time series of NEMR over the coherent south peninsular India has been developed. Similarly, an index to quantify the Indian Ocean dipole mode (IODM), exhibiting warm (cool) waters over the equatorial western (southeastern) Indian Ocean, has been developed using GISST data for the same period. The dynamics of the NEMR–IODM relationship are examined with the National Centers for Environmental Prediction–National Center for Atmospheric Research reanalysis data