pinecone/core-2020-05-10-deduplication huggingface dataset:
Leaf breakdown rates : a measure of water quality?

The breakdown rates of Alnus glutinosa leaves and the structure of macroinvertebrate communities were used to evaluate the impact of the village of Montalegre (Portugal) on the water quality of the Cávado river. Chemical and microbial analyses of stream water indicated a high organic load in the vicinity of the village. The abundance of macroinvertebrates associated with leaves increased along the pollution gradient, whereas richness of the community decreased. Biotic indices and multivariate analysis applied to aquatic macroinvertebrate communities discriminated polluted from non-polluted sites. Exponential breakdown rates of alder leaves were high (0.014 to 0.060 day-1) and the differences observed among sites suggested that nutrient enrichment stimulated leaf breakdown significantly. Leaf breakdown rates have not reflected improved biotic conditions as assessed by biotic indices at the most downstream site. These results suggest that both data from the structure and function of a stream are important for assessing water quality
Characterization and partial sequencing of species-specific sarcoplasmic polypeptides from commercial hake species by mass spectrometry following two-dimensional electrophoresis

8 páginas, 1 tabla, 4 figurasThe Merluccidae family comprises marine species, some of them of high commercial value and others less appreciated, whose commercialization in Europe under the generic name of “hake” is highly remarkable. The potential of proteomics was employed in this study with the aim of achieving the differential characterization of five different hake species: Merluccius merluccius (European hake), M. australis (Southern hake), M. hubbsi (Argentinian hake), M. gayi (Chilean hake), and M. capensis (Cape hake), some of them very closely related. Species-specific polypeptides were observed for the five hake species studied in isoelectric focusing (IEF) and/or two-dimensional electrophoresis (2-DE) high-resolution gels. The peptide mass maps of two polypeptide groups, previously selected by 2-DE analysis as potentially species-specific, were obtained by “in-gel” tryptic digestion, followed by matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS). Analysis of group A polypeptides (with pI in the range of 5.0–5.5 and molecular mass of 17 kDa), allowed the differential classification of the hake species into two groups: the East Atlantic coast group and the West Atlantic coast group. Moreover, the peptide mass-maps from the heat-resistant parvalbumin fraction (pI below 4.5; molecular mass <12 kDa) allowed the detection of a peptide characteristic of M. australis not present in the other four hake species tested. A specific 17 kDa protein from M. merluccius was also partially sequenced by nanospray-ion trap-tandem MS, revealing a high homology with rat nucleoside diphosphate kinase A (NDKA). This work opens the way to the application of proteomics to the differential characterization of commercial hake species at the molecular leveThis work was partially supported by the Comision Interministerial\ud
de Ciencia y Tecnologia (CICYT) (Project\ud
ALI95-0053).Peer reviewe
Rapid separation of tetracycline derivatives and their main degradation products by capillary zone electrophoresis

A mixture of five tetracycline (TC) derivatives: minocycline (MC), demeclocycline (DMCTC), doxycycline (DC), and sancycline (SC), as well as each TC derivative from its main degradation product were separated by capillary zone electrophoresis (CZE).\ud
The influence of the pH and the concentration and nature of the background electrolyte (BGE) on the separations was  investigated. Ethylenediaminetetraacetic acid (EDTA; 1mM) was used as additive in a 25 mM phosphate buffer (pH 2.3) because this BGE enabled the rapid separation of the TC derivatives and of each TC derivative from its respective degradation product in less than 6 min. After optimization of the separation conditions, the analytical characteristics of the method were investigated. The parameters involved were linearity, precision (repeatability and reproducibility), and limits of detection (LODs). LODs obtained for the five TC derivatives studied were about 3  g/mL. Finally, the CZE method developed was applied to study the stability of TC derivatives and to analyze the TC derivative content in three different pharmaceutical preparations
Evidence of saxitoxin derivatives as causative agents in the 1997 mass mortality of monk seals in the Cape Blanc peninsula

5 páginas, 1 tabla, 2 figurasMonk seals in Cape Blanc (Western Sahara coast) suffered a mass mortality during May–July 1997 which was attributed to a morbillivirus. High performance liquid chromatography (HPLC) analysis on tissues of seals killed during the outbreak and on related fauna showed peaks with retention times coincident with those of some saxitoxin derivatives but their identity was not proved. Here we present results of further HPLC analyses that unambiguously prove the identity of these toxins by mass spectrometry (MS), supporting the hypothesis that this mortality of monk seals was caused by biotoxins rather than by a morbillivirus.Peer reviewe
The role of the EMA software in integrated crop management and its commercial uptake

This document is the Accepted Manuscript version of the following article: Kathleen Lewis and John Tzilivakis, ???The role of the EMA software in integrated crop management and its commercial uptake???, Pest Management Science, Vol. 56 (11): 969-973, first published online 13 October 2000. The version of record is available online at doi: DOI: 10.1002/1526-4998(200011). Copyright ?? 2000 Society of Chemical Industry. Based on a paper presented at the symposium ???The Economic and Commercial Impact of Integrated Crop Management???, organised by the SCI Crop Protection Group in collaboration with the Volcani Center, Israel and the Fresh Produce Consortium and held on 3???4 April 2000 at 14/15 Belgrave Square, London SW1X 8PS, UK.Integrated crop management (ICM) balances the issues of profitability and sustainability with the need for concern for the environmental as a whole. As such, it requires sound decision-making based on detailed knowledge of the integrated nature of farming and how any single activity can impact on the business viability (short- and long-term) and on the environment. This paper reports the development and use of a practical software package, Environmental Management for Agriculture (EMA), designed to support farmers, advisers and others in developing ICM practices. An exercise in technology transfer, the package uses a simple, but effective, technique relying on input data and information readily available on farm or stored in the system's databases. The paper explains how EMA can support ICM, provides an analysis of the identified user-groups and an insight into how the package is being used by these different groups. It also discusses advantages and disadvantages of using software tools in ICM decision making
Supporting the model of ductile iron dendritic solidification

The literature about graphite formation in ductile iron proposes the experimentally supported theory lhat this phase forms in the melt.
This is naturally accepted as a consequence af the euteclic reaction of the iron-carbon equib"briumdiagram. This reaction requires that during cooling, at 1150-1100°C, the liquid with a eutectic composition decomposes into two solid phases, pure graphite aOOaustenite with a earbon content dose to 2% in weight. li the ductile irons have a generaIly eutectic composition, the presence of neither pro-eutectic graphite nor austenite
seems necessary for eutectic graphite formation.
According to the proposed solidification path, the graphite nodules become encapsulated by an austenite case, resulting in a 10ss of conmct between liquid and graphite. Carbon will then have to diffuse from the liquid through the austenite to the graphite to allow further growth 01both solid phases
Multipotent mesenchymal stem cells from adult human synovial membrane

OBJECTIVE: To characterize mesenchymal stem cells (MSCs) from human synovial membrane (SM). METHODS: Cell populations were enzymatically released from the SM obtained from knee joints of adult human donors and were expanded in monolayer with serial passages at confluence. Cell clones were obtained by limiting dilution. At different passages, SM-derived cells were subjected to in vitro assays to investigate their multilineage potential. Upon treatments, phenotypes of cell cultures were analyzed by histo- and immunohistochemistry and by semiquantitative reverse transcription-polymerase chain reaction for the expression of lineage-retated marker genes. RESULTS: SM-derived cells could be expanded extensively in monolayer, with limited senescence. Under appropriate culture conditions, SM-derived cells were induced to differentiate to the chondrocyte, osteocyte, and adipocyte lineages. Sporadic myogenesis was also observed. Five independent cell clones displayed multilineage potential. Interestingly, only 1 clone was myogenic. Donor age, cell passaging, and cryopreservation did not affect the multilineage potential of SM-derived cells. In contrast, normal dermal fibroblasts under the same culture conditions did not display this potential. CONCLUSION: Our study demonstrates that human multipotent MSCs can be isolated from the SM of knee joints. These cells have the ability to proliferate extensively in culture, and they maintain their multilineage differentiation potential in vitro, establishing their progenitor cell nature. SM-derived MSCs may play a role in the regenerative response during arthritic diseases and are promising candidates for developing novel cell-based therapeutic approaches for postnatal skeletal tissue repair.status: publishe
Integrating plant- and animal-based perspectives for more effective restoration of biodiversity

Ecological restoration of modified and degraded landscapes is an important challenge for the 21st century, with potential for major gains in the recovery of biodiversity. However, there is a general lack of agreement between plant- and animal-based approaches to restoration, both in theory and practice. Here, we review these approaches, identify limitations from failing to effectively integrate their different perspectives, and suggest ways to improve outcomes for biodiversity recovery in agricultural landscapes. We highlight the need to strengthen collaboration between plant and animal ecologists, to overcome disciplinary and cultural differences, and to achieve a more unified approach to restoration ecology. Explicit consideration of key ecosystem functions, the need to plan at multiple spatial and temporal scales, and the importance of plant–animal interactions can provide a bridge between plant- and animal-based methods. A systematic approach to restoration planning is critical to achieving effective biodiversity outcomes while meeting long-term social and economic needs.Full Tex
Monitoring the stereoselectivity of biodegradation of chiral polychlorinated biphenyls using electrokinetic chromatography

A study of the biodegradation of several chiral polychlorinated biphenyls (PCBs,\ud
IUPAC numbers 45, 88, 91, 95, 136, 144, 149, and 176) by a naturally occurring soil\ud
bacterium as well as the stereoselectivity of such process has been performed using\ud
Electrokinetic Chromatography with cyclodextrins (CD-EKC). In order to achieve the\ud
analysis of chiral PCBs, a CD-EKC system based on 50 mM 2-morpholinoethanesulfonic\ud
acid (MES) buffer (pH 6.5) containing 2 M urea, 20 mM carboxymethylated ccyclodextrin\ud
(CM-c-CD), and 10 mM b-cyclodextrin (b-CD) was used. First, the percentage\ud
degradation of PCBs by the microorganism used in this work was measured\ud
for different incubation times (22, 46, 71, 93, 165, 213, and 262 hours). The results\ud
showed a high degree of biodegradation (from 61% to 94%) for the eight PCBs studied\ud
after 262 hours of incubation with the microorganism, degradation being favoured\ud
for the least chlorinated congeners. Secondly, measurement of the atropisomeric\ud
ratio of the PCB atropisomers during the biodegradation process revealed no significant\ud
variation of the atropisomeric ratios with the degradation time, indicating a nonstereoselective\ud
degradation of PCBs by the microorganismThe authors thank the Comunidad Autónoma de Madrid (Spain)  for projects 07 M/0640/1997 and 07 M/0049/1998
Highly reproducible Capillary Gel Electrophoresis (CGE) of DNA fragments using uncoated columns. Detection of genetically modified maize by PCR-CGE

In this work a capillary gel electrophoresis (CGE) method is presented that yields reproducible separations of DNA fragments using commercially available polymers together with bare fused silica capillaries. The method combines a washing routine of the column with 0.1 M hydrochloride acid followed by a rinsing step with a solution containing 1% polyvinyl alcohol. The use of this procedure together with a running Tris-phosphate-EDTA buffer containing 2-hydroxyethyl cellulose (HEC) at pH 7.3 gives highly resolved separations of DNA fragments ranging from 80 to 500 bp. The separation of these DNA fragments is achieved in ca. 20 min with efficiencies up to 1.8×106 plates/m. Reproducibility values of migration times (given as %RSD) of the DNA fragments separated by this CGE method are better than 0.86% (n = 10) for the same day, 1.61% (n = 40) for four different days, and 1.4% (n = 15) for three different capillaries. The length up to 500 bp corresponds to the DNA sizes more frequently amplified by PCR for detecting genetically modified organisms (GMOs) in foods. The usefulness of this separation method is demonstrated by detecting genetically modified insect-resistant Bt maize after amplification of a DNA fragment by PCR. Detection of 1% of Bt maize in flour is carried out using this CGE procedure with UV absorbance and laser induced fluorescence (LIF).Peer reviewe
Structural plasticity of the Salmonella FliS flagellar export chaperone

The Salmonella FliS flagellar export chaperone is a highly α-helical protein. Proteolytic experiments suggest that FliS has a compact core. However, the calorimetric melting profile of FliS does not show any melting transition in the 25-110 °C temperature range. CD measurements reveal that FliS is losing its helical structure over a broad temperature range upon heating. These observations indicate that FliS unfolds in a non-cooperative way and its native state shows features reminiscent of the molten globule state of proteins possessing substantial structural plasticity. As FliS has several binding partners within the cell, conformational adaptability seems to be an essential requirement to fulfill its multiple roles. This article is protected by copyright. All rights reserved
Hematopoietic (stem) cell development — how divergent are the roads taken?

The development of the hematopoietic system during early embryonic stages occurs in spatially and temporally distinct waves. Hematopoietic stem cells (HSC), the most potent and self-renewing cells of this system, are produced in the final ‘definitive’ wave of hematopoietic cell generation. In contrast to HSCs in the adult, which differentiate via intermediate progenitor populations to produce functional blood cells, the generation of hematopoietic cells in the embryo prior to HSC generation occurs in the early waves by producing blood cells without intermediate progenitors (such as the ‘primitive’ hematopoietic cells). The lineage relationship between the early hematopoietic cells and the cells giving rise to HSCs, the genetic networks controlling their emergence, and the precise temporal determination of HSC fate remain topics of intense research and debate. This Review article discusses the current knowledge on the step-wise embryonic establishment of the adult hematopoietic system, examines the roles of pivotal intrinsic regulators in this process, and raises questions concerning the temporal onset of HSC fate determination
The E3 ubiquitin ligase MARCH3 controls the endothelial barrier

International audienceCell-cell contacts coordinate the endothelial barrier function in response to external cues. To identify new mediators involved in cytokine-promoted endothelial permeability, we screened a siRNA library targeting E3 ubiquitin ligases. Here, we report that silencing of the late endosome/lysosomal membrane-associated RING-CH-3 (MARCH3) enzyme protects the endothelial barrier. Furthermore, transcriptome analysis unmasked the upregulation of the tight junction-encoding gene occludin (OCLN) in MARCH3-depleted cells. Indeed, MARCH3 silencing results in the strengthening of cell-cell contacts, as evidenced by the accumulation of junctional proteins. From a molecular standpoint, the FoxO1 forkhead transcription repressor was inactivated in the absence of MARCH3. This provides a possible molecular link between MARCH3 and the signaling pathway involved in regulating the expression of junctional proteins and barrier integrity
Apolipoprotein A-I: the dual face of a protein

Conformational plasticity and flexibility are key structural features of ApoAI\ud
in lipid metabolism. Amyloidogenic single point mutations, associated with\ud
incurable familial amyloidosis with fibril deposition in peripheral organs, may\ud
have a dramatic impact on the structural and functional features of ApoAI.\ud
Here, the consistent body of data on ApoAI variants has been reviewed, with\ud
the aim of highlighting the hallmarks of the pathology. In accordance with our\ud
observations, as well as that of others, we propose a model that accounts for the\ud
alteration of the delicate balance between lipid-free/lipid-bound dynamic states\ud
which is based on monomer-to-dimer interconversion via domain swapping
Identification of amino acid residues important for the arsenic resistance function of Arabidopsis ABCC1

The Arabidopsis ATP-Binding Cassette (ABC) transporter ABCC1 sequesters arsenic (As)-phytochelatin conjugates into the vacuole, thereby conferring As resistance. Here, we report the results of a screen for phosphorylation-dependent regulation sites of AtABCC1. Variants of AtABCC1 harboring mutations that replaced amino acid residues Tyr682 , Tyr709 , Tyr822 , Ser846 , Ser1278 , or Thr1408 with alanine confer reduced resistance and decrease the intracellular As content relative to wild-type AtABCC1 when heterologously expressed in the SM7 yeast strain. This suggests that these mutations compromise the vacuolar sequestration of As by AtABCC1. Furthermore, through a phosphomimic mutant study, we found that phosphorylation of Ser846 is required for the As resistance function of AtABCC1. Our analysis provides a first clue as to the phosphorylation-mediated regulation of AtABCC1 activity
Effect of the Endosomal Acidification on Small Ion Transport through the Anthrax Toxin PA63 Channel

Tight regulation of pH is critical for the structure and function of cells and organelles. The pH environment changes dramatically along the endocytic pathway, an internalization transport process that is ‘hijacked’ by many intracellularly active bacterial exotoxins, including the anthrax toxin. Here we investigate the role of pH on single-channel properties of the anthrax toxin channel, PA63. Using conductance and current noise analysis, blocker binding, ion selectivity, and PEG partitioning measurements, we show that the channel exists in two different open states (‘maximum’ and ‘main’) at pH  5.5, while only a maximum conductance state is detected at pH  5.5. We describe two substantially distinct patterns of PA63 conductance dependence on KCl concentration uncovered at pH 6.5 and 4.5
Mitochondrial intermediate peptidase is a novel regulator of sirtuin-3 activation by caloric restriction

Sirtuin-3 (SIRT3) regulates mitochondrial quality and is involved in the anti-ageing and pro-longevity actions of caloric restriction (CR). Here, we show that CR upregulates the mature form of SIRT3 and mitochondrial intermediate peptidase (MIPEP), a mitochondrial signal peptidase (MtSPase), in white adipose tissue. We also demonstrate that upregulation of mature SIRT3 is dependent on MIPEP in 3T3-L1 cells, suggesting that MIPEP may contribute to the maintenance of mitochondrial quality during CRvia activation of SIRT3. This novel mechanism of SIRT3 activation through MIPEP facilitates the elucidation of additional molecular pathways of CR
Nuclear cytochrome c - a mitochondrial visitor regulating damaged chromatin dynamics

Over the past decade, evidence has emerged suggesting a broader role for cytochrome c (Cyt c) in programmed cell death. Recently, we demonstrated the ability of Cyt c to inhibit the nucleosome assembly activity of histone chaperones SET/template-activating factor Iß and NAP1-related protein during DNA damage in humans and plants respectively. Here, we hypothesise a dual concentration-dependent function for nuclear Cyt c in response to DNA damage. We propose that low levels of highly cytotoxic DNA lesions - such as double-strand breaks - induce nuclear translocation of Cyt c, leading to the attenuation of nucleosome assembly and, thereby, increasing the time available for DNA repair. If DNA damage persists or is exacerbated, the nuclear Cyt c concentration would exceed a given threshold, causing the haem protein to block DNA remodelling altogether.Peer Reviewe
Identification of a novel botulinum neurotoxin gene cluster in Enterococcus

The deadly neurotoxins of Clostridium botulinum (BoNTs) comprise eight serotypes (A–G; X). The neurotoxin gene cluster encoding BoNT and its accessory proteins includes an operon containing an ntnh gene upstream of the boNT gene. Another operon contains either ha (haemagglutinin) or orfX genes (of unknown function). Here we describe a novel boNT gene cluster from Enterococcus sp. 3G1_DIV0629, with a typical ntnh gene and an uncommon orfX arrangement. The neurotoxin (designated putative eBoNT/J) contains a metallopeptidase zinc-binding site, a translocation domain and a target cell attachment domain. Structural properties of the latter suggest a novel targeting mechanism with consequent implications for application by the pharmaceutical industry. This is the first complete boNT gene cluster identified in a non-clostridial genome
The tale of two talins – two isoforms to fine-tune integrin signalling

Talins are cytoplasmic adapter proteins essential for integrin-mediated cell adhesion to the \ud
extracellular matrix. Talins control the activation state of integrins, link integrins to cytoskeletal \ud
actin, recruit numerous signalling molecules that mediate integrin signalling, and coordinate \ud
recruitment of microtubules to adhesion sites via interaction with KANK (kidney ankyrin repeat-\ud
containing) proteins. Vertebrates have two talin genes, TLN1 and TLN2. Although talin1 and \ud
talin2 share 76% protein sequence identity (88% similarity), they are not functionally redundant, \ud
and the differences between the two isoforms are not fully understood. In this Review, we focus \ud
on the similarities and differences between the two talins in terms of structure, biochemistry \ud
and function, which hint at subtle differences in fine-tuning adhesion signalling