bluuebunny/crossref_metadata_2025_split huggingface dataset:
New Expression System Tightly Controlled by Zinc Availability in
Lactococcus lactis
Authors: Llull D. , Poquet I. 
Published: September 2004

ABSTRACT

Here we developed the new expression system P
Zn
zitR
, based on the regulatory signals (P
Zn
promoter and
zitR
repressor) of the
Lactococcus lactis zit
operon, involved in Zn
2+
high-affinity uptake and regulation. A P
Zn
zitR
-controlled expression vector was constructed, and expression regulation was studied with two reporter genes,
uspnuc
and
lacLM
; these genes encode, respectively, a protein derived from
Staphylococcus aureus
secreted nuclease and
Leuconostoc mesenteroides
cytoplasmic β-galactosidase. Nuclease and β-galactosidase activities of
L. lactis
MG1363 cells expressing either
uspnuc
or
lacLM
under the control of P
Zn
zitR
were evaluated on plates and quantified from liquid cultures as a function of divalent metal ion, particularly Zn
2+
, availability in the environment. Our results demonstrate that P
Zn
zitR
is highly inducible upon divalent cation starvation, obtained either through EDTA addition or during growth in chemically defined medium, and is strongly repressed in the presence of excess Zn
2+
. The efficiency of the P
Zn
zitR
expression system was compared to that of the well-known nisin-controlled expression (NICE) system with the same reporter genes cloned under either P
Zn
zitR
or P

nisA
nisRK

control.
lacLM
induction levels reached with both systems were on the same order of magnitude, even though the NICE system is fivefold more efficient than the P
Zn
zitR
system. An even smaller difference or no difference was observed after 3 h of induction when nuclease was used as a reporter for Western blotting detection. P
Zn
zitR
proved to be a powerful expression system for
L. lactis
, as it is tightly controlled by the zinc concentration in the medium.
Geochemical Rate-RNA Integration Study: Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Gene Transcription and Photosynthetic Capacity of Planktonic Photoautotrophs
Authors: Corredor Jorge E. , Wawrik Boris , Paul John H. , Tran Hiep , Kerkhof Lee , López José M. , Dieppa Angel , Cárdenas Oswaldo 
Published: September 2004

ABSTRACT

A pilot field experiment to assess the relationship between traditional biogeochemical rate measurements and transcriptional activity of microbial populations was carried out at the LEO 15 site off Tuckerton, N.J. Here, we report the relationship between photosynthetic capacity of autotrophic plankton and transcriptional activity of the large subunit gene (
rbcL
) for ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), the enzyme responsible for primary carbon fixation during photosynthesis. Similar diel patterns of carbon fixation and
rbcL
gene expression were observed in three of four time series, with maxima for photosynthetic capacity (
P
max
) and
rbcL
mRNA occurring between 10 a.m. and 1 p.m.. The lowest
P
max
and
rbcL
levels were detected between 6 p.m. and 10:30 p.m.. A significant correlation was found between
P
max
and form ID
rbcL
mRNA (
R
2
= 0.56) and forms IA and IB (
R
2
= 0.41 and 0.47, respectively). The correlation between the abundance of “diatom”
rbcL
and
P
max
mRNA was modest (
R
2
= 0.49;
n
= 12) but improved dramatically (
R
2
= 0.97;
n
= 10) upon removal of two outliers which represented afternoon samples with high
P
max
but lower mRNA levels. Clone libraries from reverse transcription-PCR-amplified
rbcL
mRNA indicated the presence of several chromophytic algae (diatoms, prymnesiophytes, and chrysophytes) and some eukaryotic green flagellates. Analogous results were obtained from amplified small rRNA sequences and secondary pigment analysis. These results suggest that diatoms were a major contributor to carbon fixation at LEO 15 at the time of sampling and that photosynthetic carbon fixation was partially controlled by transcriptional regulation of the RubisCO gene.
Effects of Temperature and Salinity on
Vibrio vulnificus
Population Dynamics as Assessed by Quantitative PCR
Authors: Randa Mark A. , Polz Martin F. , Lim Eelin 
Published: September 2004

ABSTRACT

The abundance of
Vibrio vulnificus
in coastal environments has been linked to water temperature, while its relationship to salinity is less clear. We have developed a culture-independent, most-probable-number quantitative PCR approach to examine
V. vulnificus
population dynamics in Barnegat Bay, N.J. Based on the combined analysis of our results from Barnegat Bay and from the literature, the present data show that (i)
V. vulnificus
population dynamics are strongly correlated to water temperature and (ii) although the general trend is for
V. vulnificus
abundance to be inversely correlated with salinity, this relationship depends on salinity levels. Irrespective of temperature, high abundances of
V. vulnificus
are observed at 5 to 10 ppt, which thus appears to be the optimal salinity regime for their survival. At 20 to 25 ppt,
V. vulnificus
abundances show a positive correlation to salinity. Unsuccessful attempts to resuscitate
V. vulnificus
, combined with our inability to detect cells during the winter despite an assay adapted to detect viable but nonculturable (VBNC) cells, suggest that the decline and eventual disappearance of
V. vulnificus
from the water column during the winter months is due primarily to a significant reduction in population size and is not only the consequence of cells entering the VBNC state. These findings are in line with the hypothesis that the sediment serves as a refuge for a subpopulation of
V. vulnificus
over the winter and weather-driven mixing events during the spring initiate a summer bloom in the water column.
Cloning and Characterization of Gluconolactone Oxidase of
Penicillium cyaneo-fulvum
ATCC 10431 and Evaluation of Its Use for Production of
d
-Erythorbic Acid in Recombinant
Pichia pastoris
Authors: Salusjärvi Tuomas , Kalkkinen Nisse , Miasnikov Andrei N. 
Published: September 2004

ABSTRACT

A
d
-erythorbic acid-forming soluble flavoprotein, gluconolactone oxidase (GLO), was purified from
Penicillium cyaneo-fulvum
strain ATCC 10431 and partially sequenced. Peptide sequences were used to isolate a cDNA clone encoding the enzyme. The cloned gene (accession no.
AY576053
) exhibits high levels of similarity with the genes encoding other known eukaryotic lactone oxidases and also with the genes encoding some putative prokaryotic lactone oxidases. Analysis of the coding sequence of the GLO gene indicated the presence of a typical secretion signal sequence at the N terminus of GLO. No other targeting or anchoring signals were found, suggesting that GLO is the first known lactone oxidase that is secreted rather than targeted to the membranes of the endoplasmic reticulum or mitochondria. Experimental evidence, including the N-terminal sequence of mature GLO and data on glycosylation and localization of the enzyme in native and recombinant hosts, supports this analysis. The GLO gene was expressed in
Pichia pastoris
, and recombinant GLO was produced by using the strong methanol-induced
AOX1
promoter. In order to evaluate the suitability of purified GLO for production of
d
-erythorbic acid, we immobilized it on
N
-hydroxysuccinimide-activated Sepharose and found that the immobilized GLO retained full activity during immobilization but was rather unstable under reaction conditions. Our results show that both soluble and immobilized forms of GLO can, in principle, be used for production of
d
-erythorbic acid from
d
-glucono-δ-lactone or (in combination with glucose oxidase and catalase) from glucose. We also demonstrated the feasibility of glucose-
d
-erythorbic acid fermentation with recombinant strains coexpressing GLO and glucose oxidase genes, and we analyzed problems associated with construction of efficient
d
-erythorbic acid-producing hosts.
Characterization of a Highly Enriched
Dehalococcoides
-Containing Culture That Grows on Vinyl Chloride and Trichloroethene
Authors: Duhamel Melanie , Mo Kaiguo , Edwards Elizabeth A. 
Published: September 2004

ABSTRACT

A highly enriched culture that reductively dechlorinates trichloroethene (TCE),
cis
-1,2-dichloroethene (cDCE), and vinyl chloride (VC) to ethene without methanogenesis is described. The
Dehalococcoides
strain in this enrichment culture had a yield of (5.6 ± 1.4) × 10
8
16S rRNA gene copies/μmol of Cl
−
when grown on VC and hydrogen. Unlike the other VC-degrading cultures described in the literature, strains VS and BAV1, this culture maintained the ability to grow on TCE with a yield of (3.6 ± 1.3) × 10
8
16S rRNA gene copies/μmol of Cl
−
. The yields on an electron-equivalent basis measured for the culture grown on TCE and on VC were not significantly different, indicating that both substrates supported growth equally well. PCR followed by denaturing gradient gel electrophoresis, cloning, and phylogenetic analyses revealed that this culture contained one
Dehalococcoides
16S rRNA gene sequence, designated KB-1/VC, that was identical (over 1,386 bp) to the sequences of previously described organisms FL2 and CBDB1. A second
Dehalococcoides
sequence found in separate KB-1 enrichment cultures maintained on cDCE, TCE, and tetrachloroethene was no longer present in the VC-H
2
enrichment culture. This second
Dehalococcoides
sequence was identical to that of BAV1. As neither FL2 nor CBDB1 can dechlorinate VC to ethene in a growth-related fashion, it is clear that current 16S rRNA gene-based analyses do not provide sufficient information to distinguish between metabolically diverse members of the
Dehalococcoides
group.
Electrophoretic Mobility of
Mycobacterium avium
Complex Organisms
Authors: Lytle Darren , Frietch Christy , Covert Terry 
Published: September 2004

ABSTRACT

The electrophoretic mobilities (EPMs) of 30
Mycobacterium avium
complex organisms were measured. The EPMs of 15 clinical isolates ranged from −1.9 to −5.0 μm cm V
−1
s
−1
, and the EPMs of 15 environmental isolates ranged from −1.9 to −4.6 μm cm V
−1
s
−1
at pH 7.
Inhibition of
Listeria monocytogenes
in Fish and Meat Systems by Use of Oregano and Cranberry Phytochemical Synergies
Authors: Lin Y. T. , Labbe R. G. , Shetty Kalidas 
Published: September 2004

ABSTRACT

Optimized phenolics from oregano and cranberry extracts were evaluated for antimicrobial activity against
Listeria monocytogenes
in laboratory media and in beef and fish. The antimicrobial activity increased when oregano and cranberry extracts were mixed at a ratio of 75% oregano and 25% cranberry (wt/wt) with 0.1 mg of phenolic per disk or ml, and the efficacy was further enhanced by lactic acid. The inhibition by phytochemical and lactic acid synergies was most effective when beef and fish slices were stored at 4°C.
Rapid Estimation of Numbers of Fecal
Bacteroidetes
by Use of a Quantitative PCR Assay for 16S rRNA Genes
Authors: Dick Linda K. , Field Katharine G. 
Published: September 2004

ABSTRACT

Assessment of health risk associated with fecal pollution requires a reliable fecal indicator and a rapid quantification method. We report the development of a
Taq
nuclease assay for enumeration of 16S rRNA genes of
Bacteroidetes
. Sensitivity and correlation with standard fecal indicators provide experimental evidence for application of the assay in monitoring fecal pollution.
PCR-Based Identification of Hyperthermophilic Archaea of the Family
Thermococcaceae
Authors: Slobodkina Galina B. , Chernyh Nikolai A. , Slobodkin Alexander I. , Subbotina Irina V. , Bonch-Osmolovskaya Elizaveta A. , Lebedinsky Alexander V. 
Published: September 2004

ABSTRACT

A method for rapid detection and identification of hyperthermophilic archaea of the family
Thermococcaceae
based on PCR amplification of 16S rRNA gene fragments with primers TcPc 173F (5′-TCCCCCATAGGYCTGRGGTACTGGAAGGTC-3′) and TcPc 589R (5′-GCCGTGRGATTTCGCCAGGGACTTACGGGC-3′) was developed and used for identification of new isolates.
Sodium nitroprusside and peroxynitrite effect on hepatic DNases: an in vitro and in vivostudy
Authors: Kocic Gordana , Pavlovic Dusica , Pavlovic Radmila , Nikolic Goran , Cvetkovic Tatjana , Stojanovic Ivana , Jevtovic Tatjana , Kocic Radivoj , Sokolovic Dusan 
Published: September 2004

Abstract
Background
It has been documented that nitric oxide (NO) donor sodium nitroprusside (SNP) and authentic peroxynitrite are capable of promoting apoptosis in a number of different cell types. Various endonucleases have been proposed as candidates responsible for the internucleosomal cleavage of the genomic DNA observed during apoptosis, but the main effect is attributed to the alkaline-DNases (Mg2+- and caspase-dependent) and acid-DNase. The aim of this study was to examine an in vivo and in vitro possibility for alkaline- and acid-DNases to be activated by SNP and peroxynitrite.

Results
The effect on liver tissue alkaline and acid DNase activity together with the markers of tissue and plasma oxidative and nitrosative stress (lipid peroxidation, SH group content, carbonyl groups and nitrotyrosine formation) was investigated in plasma and liver tissue. The activity of liver alkaline DNase increased and that of acid DNase decreased after in vivo treatment with either SNP or peroxynitrite. A difference observed between the in vivo and in vitro effect of oxide donor (i.e., SNP) or peroxynitrite upon alkaline DNase activity existed, and it may be due to the existence of the "inducible" endonuclease. After a spectrophotometric scan analysis of purified DNA, it was documented that both SNP and peroxynitrite induce various DNA modifications (nitroguanine formation being the most important one) whereas DNA fragmentation was not significantly increased.

Conclusion
Alkaline DNase activation seems to be associated with the programmed destruction of the genome, leading to the fragmentation of damaged DNA sites. Thus, the elimination of damaged cells appears to be a likely factor in prevention against mutation and carcinogenesis.
Recurrence of primary extramedullary plasmacytoma in breast both simulating primary breast carcinoma
Authors: Kaviani Ahmad , Djamali-zavareie Mansoor , Noparast Maryam , Keyhani-Rofagha Sedigheh 
Published: September 2004

Abstract
Background
Extramedullary myelomas (plasmacytoma) are malignant proliferations of plasma cells in the absence of bone involvement. When they occur in the soft tissue they usually involve the upper respiratory tract and oral cavity. Extramedullary plasmacytomas of breast are uncommon.

Case presentation
A 70 year-old woman with bilateral breast masses underwent excisional biopsy for suspected primary carcinoma that subsequently proved to be a recurrence from extramedullary plasmacytoma of the mediastinum. This was diagnosed and treated 5-years prior to appearance of breast lumps.

Conclusion
Though uncommon, considering the possibility of metastatic carcinoma and primary, secondary or recurrent lymphoproliferative disease presenting as a breast mass may avoid unnecessary surgeries.
Risk of Stroke and Myocardial Infarction Among Initiators of Triptans
Authors: Petersen Christian Lund , Hougaard Anders , Gaist David , Hallas Jesper 
Published: February 2024

ImportanceTriptans are contraindicated in patients with ischemic heart disease or previous myocardial infarction, and caution is advised when prescribing these drugs to patients with vascular risk factors. However, controlled observational studies have either shown no association or an apparent lower risk, possibly owing to a channeling of triptans to individuals at low risk of cardiovascular outcomes, and it remains unclear whether avoiding triptan treatment for these patients is meaningful.ObjectiveTo establish whether an association between triptans and ischemic events could be demonstrated using a self-controlled design because this type of design is robust to the previously mentioned type of confounding.Design, Setting, and ParticipantsAll people in nationwide Danish registries who were initiating triptans and all the ischemic events that they experienced were identified. A case-crossover design was used to estimate odds ratios (OR) for associations between first-ever triptan use and ischemic outcomes, comparing triptan exposure in the 2-week period up to the event with four 2-week reference periods. Data were obtained for the period January 1995 to August 2022. Included from the population of Denmark were individuals redeeming a prescription for any triptan and experiencing at least 1 of 3 predefined ischemic outcomes. No one was excluded.ExposureInitiation of any triptan.Main Outcomes and MeasuresAcute myocardial infarction, ischemic stroke, or nonspecified stroke.ResultsIdentified were a total of 429 612 individuals (median [IQR] age, 38 [28-48] years; 325 687 female [75.8%]) who redeemed a first prescription for a triptan in the study period. Of these patients, 11 (0.003%) had a myocardial infarction with the first triptan prescription in either a focal or referent window (odds ratio [OR], 3.3; 95% CI, 1.0-10.9), 18 (0.004%) had ischemic stroke (OR, 3.2; 95% CI, 1.3-8.1), and 35 (0.008%) had ischemic/nonspecified stroke (OR, 3.0; 95% CI, 1.5-5.9). Case patients had a median age of approximately 60 years and had a high-risk cardiovascular profile.Conclusions and RelevanceResults of this case-crossover study suggest that triptan initiation was associated with higher risk of ischemic stroke and myocardial infarction. For the individual patient with low background cardiovascular risk, the risk of an ischemic event after triptan initiation was very low.
Spontaneous Topological (Anti)meron Chains in the Domain Walls of Centrosymmetric Rare‐Earth Magnet
Authors: Xu Jiawang , Wang Liming , Xi Lei , Gao Yang , Gao Yawei , Wang Dingsong , Huang He , Zheng Xinqi , Zhang Jingyan , Yang Mengmeng , Ma Tianping , Yang Hongxin , Zhang Ying , Shen Baogen , Wang Shouguo 
Published: February 2024

AbstractExploration and manipulation of topological protected magnetic swirls, such as skyrmion, antiskyrmion, meron, and vortex, holds significance for fundamental research and practical applications in high‐density magnetic information storage and spintronics because of their high storage density and low driven current. This study unveils the existence of field‐free spontaneous (anti)meron chains with a topological charge of ±1/2 in the centrosymmetric rare‐earth magnet Tb6Co2.17Si2.5 via in situ real‐space observation. The spin reorientation transition from in‐plane to uniaxial anisotropy contributes to the spontaneous transformation from straight domain walls to topological (anti)meron chains and to stripe domains along the [110] zone axis during in situ cooling. The study further confirms the critical role of the noncollinear magnetic structure of Tb atoms in the formation of topological (anti)meron chains via real‐space observations, first‐principles calculations, and micromagnetic simulations. The spontaneous topological magnetic texture is strongly correlated with the 4f electrons of rare‐earth atoms, enriching and stimulating alternative generation mechanisms of topological spin textures from emerging rare‐earth magnets, and further applications in spintronics.
Hetero MOF‐On‐MOF of Ni‐BDC/NH2‐MIL‐88B(Fe) Enables Efficient Electrochemical Seawater Oxidation
Authors: Bao Yanji , Ru Haifeng , Wang Yifeng , Zhang Kexi , Yu Rentong , Wu Qiang , Yu Aimin , Li Dong‐Sheng , Sun Chenghua , Li Weiwei , Tu Jinchun 
Published: February 2024

AbstractSeawater electrolysis is a sustainable technology for producing hydrogen that would neither cause global freshwater shortages nor create carbon emissions. However, this technology is severely hampered by the insufficient stability and the competition from the chlorine evolution reaction (ClER) in actual application. Herein, a metal–organic framework (MOF)‐on‐MOF heterojunction (Ni‐BDC/NH2‐MIL‐88B(Fe)) denoted as (Ni‐BDC/NM88B(Fe)) is synthesized as an effective oxygen evolution reaction (OER) electrocatalyst for high‐performance seawater electrolysis, which exhibits a long stability of 200 h and low overpotentials of 232 and 299 mV at 100 mA cm−2 in alkaline freshwater and seawater solution, respectively. The exceptional performance is attributed to the rapid self‐reconstruction of Ni‐BDC/NM88B(Fe) to produce NiFeOOH protective layer, thereby avoiding ClER‐induced dissolution. Moreover, the interface interaction between Ni‐BDC and NM88B(Fe) could form the Ni─O─Fe bonds in Ni‐BDC/NM88B(Fe) to promote the electron transfer and lower the energy barrier of the rate‐determining step, thereby accelerating the OER. These electrochemical properties make it intriguing candidate as an efficient electrocatalyst for practical alkaline seawater electrolysis.
A 3D Phosphorescent Supramolecular Organic Framework in Aqueous Solution
Authors: Yin Chenjia , Yan Zi‐Ang , Yan Ruijian , Xu Chen , Ding Bingbing , Ji Yuanhui , Ma Xiang 
Published: February 2024

AbstractSupramolecular organic framework (SOF) has recently garnered significant research interest in the field of luminescent materials. However, SOF with room‐temperature phosphorescence emission in solution is very rare due to the quenching of dissolved oxygen and free molecular motions, which would lead to nonradiative deactivation of triplet exciton in liquid state. In this work, a 3D cationic phosphorescent SOF is synthesized through host‐guest interaction between CB[8] and a tetrahedral monomer TBBP, which can rapidly adsorb anionic guests in solution. When anionic dyes are introduced, triplet to singlet Förster resonance energy transfer (TS‐FRET) in solution can be achieved, and delayed fluorescence with large Stokes shift can be realized. Additionally, when anionic drugs are introduced, the phosphorescence of TBBP‐CB[8] can be quenched due to charge transfer, enabling the detection of drugs through phosphorescence signals. Taking advantage of the fast adsorption property of 3D SOF, an INHIBIT logic gate with three inputs and two outputs is constructed. These findings provide a novel method to prepare phosphorescent functional materials and a new pathway to construct TS‐FRET system in solution.
Halide Ion Mobility in Paired 2D Halide Perovskites: Ruddlesden–Popper Versus Dion–Jacobson Phases
Authors: Min Seonhong , Cho Junsang 
Published: February 2024

Abstract2D lead halide perovskites with tunable optoelectronic properties through modulating inorganic components and organic spacer ligands represent a promising candidate in perovskite optoelectronics. However, an intrinsic soft lattice of perovskites gives rise to a vacancy‐mediated halide ion migration, which further affects the long‐term stability of materials as well as devices. Here, halide ion mobility is evaluated using two different 2D perovskites yielded with butylammonium (BA) for the Ruddlesden–Popper (RP) phase and butane‐1,4‐diamine (BDA) for the Dion–Jacobson (DJ) phase, respectively. By probing the halide ion migration kinetics in the physically paired 2D bromide and iodide perovskite films, the softer lattice (RP) shows a lower activation energy of 50.9 kJ mol−1 as compared to that of more rigid lattice (DJ) of 60.8 kJ mol−1. Given similar halide diffusion pathlength and halide mixing chemical potential, the binding mode (RP and DJ) can indeed dictate the overall halide ion stability. Understanding such halide ion mobility is important in designing perovskites with increased stability and performances at material and device levels.