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PubMed2005

RNA-conjugated template-switching RT-PCR method for generating an Escherichia coli cDNA library for small RNAs.

The cDNA conversion of RNA molecules is a prerequisite for their analysis. In the case of prokaryotic RNAs, cDNA conversion is difficult due to a lack of the long poly(A) tails that are found in eukaryotic mRNAs. The full cDNAs for eukaryotic mRNAs can be amplified by the reverse transcription polymerase chain reaction (RT-PCR) using the template-switching method together with an oligo(dT) primer. To amplify the full cDNAs for prokaryotic RNAs, we modified the template-switching RT-PCR method by adopting an RNA linker at the 3' end of the target RNAs. Using this method, which we named as RNA-conjugated template-switching RT-PCR (RC/TS RT-PCR), we constructed a cDNA library for small RNAs from cold-shock-treated Escherichia coli cells. To confirm that the cDNAs were amplified by RC/TS RT-PCR without a loss of sequence information, clones carrying the 6S RNA sequence were analyzed from the cDNA library for small RNAs ranging from 130 to 350 nt. We found that the 6S RNA sequences were fully converted into the corresponding cDNAs, confirming that RC/TS RT-PCR is a useful method for constructing a cDNA library for small RNAs in E. coli. This method can be also used to construct a cDNA library for non-poly(A)-containing RNAs from eukaryotic cells.

Blotting, Northern↗
PubMed1989

Calorimetric studies of the effects of cholesterol on the phase transition of C(18):C(10) phosphatidylcholine.

Differential scanning calorimetry (DSC) has been employed to study the effects of cholesterol on the phase transition of C(18):C(10) phosphatidylcholine (C(18):C(10)PC). C(18):C(10)PC is an asymmetric mixed-chain phosphatidylcholine known to form mixed-interdigitated structures below the transition temperature and form partially interdigitated lipid bilayers above the transition. Three types of samples were used. The treated sample is the lipid dispersion that had undergone three freeze-thaw cycles and stored at 4 degrees C for more than 48 h. The untreated sample was made by vortexing the dry lipid in 50 mM KCl, without the above-mentioned pretreatment. The cold-treated sample was prepared by incubating the treated sample at -20 degrees C for 15 d. There is no apparent difference in the DSC curves between the treated and cold-treated samples. The data derived from the treated samples seem to be more reproducible. The DSC curves between the cholesterol/C(18):C(10)PC and cholesterol/symmetric diacylphosphatidylcholine mixtures are different in three aspects: overall appearance, the cholesterol dependence of delta H, and the effect of cholesterol on the maximal transition temperature Tm, the onset temperature To, and the completion temperature Tc. for both the treated and untreated samples, the total enthalpy change delta H of the phase transition of C(18):C(10)PC decreases with increasing cholesterol content, approaching zero at approximately 25 mol%. This level is lower than the total enthalpy changes reported previously for the cholesterol/symmetric diacylphosphatidylcholine mixtures. Both the heating and cooling thermograms show that Tm, To, and Tc decrease with increasing cholesterol content. The decreasing rates of these temperatures with cholesterol are in the neighborhood of -0.24 degree per mol% of cholesterol. This value is greater than those reported previously for cholesterol/symmetric diacylphosphatidylcholine mixtures. The phase transition between interdigitated lipid bilayers appears to be more sensitive to cholesterol than that between noninterdigitated lipid structures. The formation of highly ordered interdigitated lipid bilayers requires stringent structural conditions such as specific chain length differences and high molecular order. Apparently, in the presence of cholesterol, these stringent structural conditions are no longer satisfied. It is likely that cholesterol causes a local disordering effect on the gel phase of C(18):C(10)PC and that as a consequence the physical state of the gel phase changes continuously with the cholesterol content. The implication of the present study is that cholesterol may have a function in preventing lipids from forming highly ordered interdigitated structures in natural membranes.

Calorimetry, Differential Scanning↗
PubMed1989

Effects of warm and cold ischemia on mitochondrial functions in brain, liver and kidney.

The purpose of this work was to study the effects of warm (37 degrees C) and cold (4 degrees C) ischemia on different mitochondrial functions in rat brain, liver and kidney. After 10 to 60 minutes of ischemia at 37 degrees C the energy coupled respiration as well as the ADP-induced malate-aspartate shuttle activity in brain and liver mitochondria or the rate of mitochondrial ATP synthesis in kidney were significantly decreased. However, the respiratory rates and the shuttle activity in the absence of ADP remained unchanged. These data suggest that ischemia primarily affects electron transport in the respiratory chain rather than the hydrogen shuttle and the energy coupling system. When the temperature during the indicated ischemic periods was decreased to 4 degrees C, in brain and liver no significant alterations of these mitochondrial functions were found in comparison with the non-ischemic controls. When rat kidneys were stored for 36 hours at 4 degrees C according to Collins mimicking transplantation conditions, the mitochondrial respiration and ATP synthesis were only slightly decreased. It therefore appears that hypothermia can prevent effectively mitochondrial dysfunction due to ischemia.

Adenosine Triphosphate↗
PubMed2003

Regulation of coenzyme Q biosynthesis and breakdown.

All animal cells synthesize sufficient amounts of coenzyme Q (CoQ) and the cells also possess the capacity to metabolize the lipid. The main product of the metabolism is an intact ring with a short carboxylated side chain which glucuronidated in the liver and excreted mainly into the bile (Nakamura et al., Biofactors 9 (1999), 111-119). In other cells CoQ is phosphorylated, transferred into the blood and excreted through the urine. The biosynthesis of this lipid is regulated by nuclear receptors. PPARalpha is not required for the biosynthesis, or induction upon cold exposure, but it is necessary for the elevated CoQ synthesis during peroxisomal induction. RXRalpha is involved in the basal synthesis of CoQ and also in the increased synthesis upon cold treatment but is not required for peroxisomal induction. Dietary CoQ in human appear in the blood and it is taken up by mononuclear but not polynuclear cells. The former cells display a specific phospholipid modification, an increase of arachidonic acid content. In monocytes the CoQ administration leads to a significant decrease of the beta2-integrin CD11b and the complement receptor CD35. CD11b is one of the adhesion factors regulating the entry of these cells into the arterial wall which demonstrates that the anti-atherogenic effect of CoQ is mediated by other mechanisms beside its antioxidant protection.

Animals↗
PubMed2006

Unusual presentation of large B cell lymphoma: a case report and review of literature.

Diffuse large B cell lymphoma (DLBCL) is the largest subtype of non-Hodgkin's lymphomas (NHLs) and is characterized by relatively frequent extranodal presentation. In these cases, the most common extranodal localizations are stomach, CNS, bone, testis and liver. Simultaneous detection of multiple extranodal involvement at presentation is quite uncommon, with the majority of these cases characterized by gastric or intestinal disease localization. Retrospective analysis concerning multifocal extranodal NHLs never pointed out disease features such as those described here. We report a patient with an unusual presentation of DLBCL, characterized by adrenal and renal involvement, associated with symptoms and signs of the cold agglutinin disease and a hypercoagulable state. Subsequently, computed tomography (CT) and fluorodeoxyglucose-positron emission tomography (FDG-PET) scanning disclosed a rapidly extensive spread to nodes and bones. Cytofluorimetric analysis of a renal specimen showed medium-to-large lympho-monocytoid elements positive for CD20 with monoclonal expression of immunoglobulin kappa light chain. Histopathological examination confirmed a renal CD20 positive DLBCL localization.

Adrenal Gland Neoplasms↗
PubMed2006

Mercury (micro)biogeochemistry in polar environments.

The contamination of polar regions with mercury that is transported as inorganic mercury from lower latitudes has resulted in the accumulation of methylmercury in the food chain of polar environments, risking the health of humans and wildlife. This problem is likely to be particularly severe in coastal marine environments where active cycling occurs. Little is currently known about how mercury is methylated in polar environments. Relating observations on mercury deposition and transport through polar regions to knowledge of the microbiology of cold environments and considering the principles of mercury transformations as have been elucidated in temperate aquatic environments, we propose that in polar regions (1) variable pathways for mercury methylation may exist, (2) mercury bioavailability to microbial transformations may be enhanced, and (3) microbial niches within sea ice are sites where active microorganisms are localized in proximity to high concentrations of mercury. Thus, microbial transformations, and consequently mercury biogeochemistry, in the Arctic and Antarctic are both unique and common to these processes in lower latitudes, and understanding their dynamics is needed for the management of mercury-contaminated polar environments.

Antarctic Regions↗
PubMed2005

Millisecond protein folding studied by NMR spectroscopy.

Proteins are involved in virtually every biological process and in order to function, it is necessary for these polypeptide chains to fold into the unique, native conformation. This folding process can take place rapidly. NMR line shape analyses and transverse relaxation measurements allow protein folding studies on a microsecond-to-millisecond time scale. Together with an overview of current achievements within this field, we present millisecond protein folding studies by NMR of the cold shock protein CspB from Bacillus subtilis.

Bacterial Proteins↗
PubMed2004

Biogeochemical features of lipids in endolithic microbial communities in the Ross Desert (McMurdo Dry Valleys), Antarctica.

Endolithic microbial communities inhabiting porous rocks in the cold, dry mountainous regions of Antarctica have been studied extensively as examples of life's adaptations to extreme environments. Here, we examine hydrocarbons and fatty acids occurring in these communities in order to clarify their biogeochemical features with respect to source organisms, microbial activity, fossilization processes and the influence of Gondwanaland sediments. Unusually, long-chain (>C19) n-alkanes and anteiso-alkanes were often the major hydrocarbons in the samples. A suite of n-alkanoic acids (n-C9-n-C32) and long-chain anteiso-alkanoic acids (a-C20-a-C30) were found, along with short-chain iso- and anteiso-alkanoic acids, and n-alkenoic acids. The relationship between long-chain n-alkanoic acids (n-C20-n-C32) and long-chain anteiso-alkanoic acids suggests that these compounds probably originated from the same group of microorganisms, such as bacteria or endolithic lichens, under moderate pH conditions (pH 3-5). Relatively high trans/cis-C16:1 alkenoic acid ratios suggest the presence of unfavorable environmental conditions in the endolithic microbial habitat. Normal-alkenoic/alkanoic acid ratios may be a useful marker for the fossilization of endolithic microbial communities. Thermally matured triterpanes and steranes from fossilized associations on Mount Fleming strongly suggest the presence of Gondwanaland sediments formed during Devonian and Jurassic (400-180 million years ago).

Alkanes↗
PubMed1989

Reconstitution of the thermostable trimeric phage P22 tailspike protein from denatured chains in vitro.

Intermediates in the intracellular chain folding and association pathway of the P22 tailspike endorhamnosidase have been identified previously by physiological and genetic methods. Conditions have now been found for the in vitro refolding of this large (Mr = 215,000) oligomeric protein. Purified Salmonella phage P22 tailspikes, while very stable to urea in neutral solution, were dissociated by moderate concentrations of urea at acidic pH. The tailspike protein was denatured to unfolded polypeptide chains in 6 M urea, pH 3, as disclosed by analytical ultracentrifugation, fluorescence, and circular dichroism. Upon dilution into neutral buffer at 10 degrees C, the polypeptides fold spontaneously and associate to form trimeric tailspikes with high yield. Like native phage P22 tailspikes, the reconstitution product is resistant to denaturation by dodecyl sulfate in the cold and displays endorhamnosidase activity. Sedimentation coefficients, electrophoretic mobility, and fluorescence emission maxima of native and reconstituted tailspikes are identical within experimental error. By characterization of intermediates, localization of temperature-sensitive steps, and analysis of the effect of previously identified folding mutations, the reconstitution system described should allow comparison of in vivo and in vitro folding pathways of this large protein oligomer.

Electrophoresis, Polyacrylamide Gel↗
PubMedDate not supplied

The role of oxidation in the renal metabolism of glutamine by rat kidney tubules in vitro.

The metabolism of cold and 14C-[U]-glutamine in isolated kidney tubules of normal rats was studied in vitro to establish the relative importance of glucose synthesis and complete oxidation to CO2 for the metabolism of this amino acid in vitro. These metabolic fates were estimated by drawing a complete balance of the nitrogens and of the carbon chains of the extracted glutamine and studying the formation of 14CO2 from 14C-glutamine. It was found that glucose production constitutes the major fate for glutamine metabolism with 1 mM glutamine and that glutamine oxidation constitutes less than 20% of the metabolic fate of the carbon skeleton of this amino acid. With 5 or 10 mM glutamine however, the maximal oxidation to CO2 becomes more important (25%).

Animals↗
PubMed2004

Neonatal management of symptomatic transplacental cryoglobulinaemia.

UNLABELLED: This study reports the first case of symptomatic placental transfer of cryoglobulins and discusses the potential pathogenic processes and the basic guidelines for neonatal management. A 32-y-old woman was affected by essential type I cryoglobulinaemia and displayed the cold-triggered cutaneous symptoms of the disease due to a monoclonal immunoglobulin G (IgG) cryoglobulin. She gave birth to healthy dizygotic twins who were placed in incubators immediately after birth and did not show any cutaneous or visceral lesion in the first 2 d. Cyanotic macules appeared on the hand and foot of one of the newborns when they were removed from the incubators. The same monoclonal IgG-lambda cryoglobulin was identified in the two newborns' cord blood and in the mother's serum. The skin lesions disappeared within 1 wk as both twins were transiently replaced in incubators. No recurrence of skin lesions was observed even at room temperature and, 6 mo later, both twins were healthy and their clinical examination was normal. CONCLUSION: To the authors' knowledge, this is the first report of placental transfer of cryoglobulins and the first description of any neonatal effect. Neonates born to mothers suffering from IgG cryoglobulinaemia should be protected against cold to avoid precipitation of the pathogenic cryoglobulins, until spontaneous resolution.

Adult↗
PubMed2005

[Transformation of Volvariella volvacea with a thermal hysteresis protein gene by particle bombardment].

A cDNA encoding a thermal hysteresis protein was isolated from the Swedish Arctic insect spruce budworm by RT-PCR amplification. Volvariella volvacea strain V34 was transformed with this cDNA through particle bombardment. PCR detection and Southern blotting analysis show that the thermal hysteresis protein gene is integrated into Volvariella volvacea genome. Cold stress assay reveals that transgenic Volvariella volvacea lines exhibit stronger cold tolerance than host strain. The morphological observation of transgenic Volvariella volvacea lines shows that growth rates of most Volvariella volvacea transformants are significantly slower than that of negative control strain. And hypha of most Volvariella volvacea tansformants is thinner than host strain's hypha. Transformant screening result indicates that three-round of selection procedure with first selection on PDSA solid selective medium followed by second and third selection in PDSB liquid selective medium is favorable to get genuine transformants and to eliminate false transformants. Cold tolerance assay of transgenic Volvariella volvacea F1 generation demonstrates that the progeny of transgenic Volvariella volvacea still possesses stronger cold tolerance than non-transformed host strain. This suggests that the cold tolerant characteristic of transgenic Volvariella volvacea is meiotically stable between generations.

Agaricales↗
PubMed1982

Molecular basis for the temperature-dependent insolubility of cryoglobulins--XI. Sequence comparison of the heavy-chain variable regions of the human cryoimmunoglobulins McE and Hil by metric analysis.

The amino acid sequences of the VH-domains from two human cryoimmunoglobulins have been compared with one another and with the VH-domains of noncryoglobulins by the mathematical method of metric analysis. The VHII sequence of McE [Gerber-Jenson et al. (1981), J. Immun. 126, 1212-1216] and the VHIII sequence of Hil [Chiu et al (1979), Biochemistry, 18, 553-560] resemble much more closely the VH-sequences of noncryoglobulins from their own subgroups than they resemble one another. Neither cryoglobulin sequence contains an unusual insertion or deletion of residues. Based on the crystallographic structure of the VHII domain in the Fab fragment of the human noncryoglobulin Newm [Saul et al. (1978), J biol. Chem., 253, 585-597], McE and Hil each contain two unprecedented residues in the outer beta-sheet structure of the VH-domain. The inwardly directed sidechains of Gly-71 and Ile-84 in McE may perturb the internal hydrophobic interactions and normal folding of adjacent segments of the outer beta-sheet from the third framework region. In contrast, the outwardly directed sidechains of Ile-23 and Arg-77 in Hil may perturb the external hydrophilic properties and folding of adjacent segments of the outer beta-sheet from the first and third framework regions. Thus, the monoclonal immunoglobulins McE and Hil may display cold-induced insolubility by different perturbations of the outer surface of the VH-domain. In each case, the unprecedented framework residues that mnay be responsible could have arisen by two point mutations involving single base changes.

Amino Acid Sequence↗
PubMed1986

Usefulness of fingertip skin temperature for examining peripheral circulatory disturbances of vibrating tool operators.

The data on skin temperature obtained in a cold provocation test (immersing one hand in water at 10 degrees C for 10 min) were analyzed to confirm their usefulness for examining the peripheral circulatory functions of vibrating tool operators. Under room temperatures from 20 to 23 degrees C in winter, the skin temperatures after the end of provocation of the VWF (vibration-induced white finger) group were generally significantly lower than those of the age-matched non-VWF and reference groups, and the non-VWF operators with over 5,000 h of chain-saw experience showed significantly lower skin temperatures 5 and 10 min after provocation than the age-matched referents. In this study skin temperature was used as a screening test for VWF. The highest sensitivity (91.1%) was obtained at 19.0 degrees C at the fifth minute after the end of the provocation, and the highest specificity (93.3%) at 15.5 degrees C at the third minute after provocation, both the sensitivity and specificity being over 70% and the correct diagnosis rate being over 80% among the screening levels.

Cold Temperature↗
PubMed2003

A tomato alternative oxidase protein with altered regulatory properties.

We have investigated the expression and regulatory properties of the two alternative oxidase (Aox) proteins that are expressed in tomato (Lycopersicon esculentum L. Mill cv. Sweetie) after storage of green fruit at 4 degrees C. Four Aox genes were identified in the tomato genome, of which two (LeAox1a and LeAox1b) were demonstrated to be expressed in cold-treated fruit. The activity and regulatory properties of LeAox1a and LeAox1b were assayed after expression of each protein in yeast cells (Saccharomyces cerevisiae), proving that each is an active Aox protein. The LeAox1b protein was shown to have altered regulatory properties due to the substitution of a Ser for the highly conserved Cys(I) residue. LeAox1b could not form inactive disulfide-linked dimers and was activated by succinate instead of pyruvate. This is the first example of a dicot species expressing a natural Cys(I)/Ser isoform. The implications of the existence and expression of such Aox isoforms is discussed in the light of the hypothesised role for Aox in plant metabolism.

Amino Acid Sequence↗
PubMed1991

Thermal unfolding pathway for the thermostable P22 tailspike endorhamnosidase.

The conditions in which protein stability is biologically or industrially relevant frequently differ from those in which reversible denaturation is studied. The trimeric tailspike endorhamnosidase of phage P22 is a viral structural protein which exhibits high stability to heat, proteases, and detergents under a range of environmental conditions. Its intracellular folding pathway includes monomeric and trimeric folding intermediates and has been the subject of detailed genetic analysis. To understand the basis of tailspike thermostability, we have examined the kinetics of thermal and detergent unfolding. During thermal unfolding of the tailspike, a metastable unfolding intermediate accumulates which can be trapped in the cold or in the presence of SDS. This species is still trimeric, but has lost the ability to bind to virus capsids and, unlike the native trimer, is partially susceptible to protease digestion. Its N-terminal regions, containing about 110 residues, are unfolded whereas the central regions and the C-termini of the polypeptide chains are still in the folded state. Thus, the initiation step in thermal denaturation is the unfolding of the N-termini, but melting of the intermediate represents a second kinetic barrier in the denaturation process. This two-step unfolding is unusually slow at elevated temperature; for instance, in 2% SDS at 65 degrees C, the unfolding rate constant is 1.1 x 10(-3) s-1 for the transition from the native to the unfolding intermediate and 4.0 x 10(-5) s-1 for the transition from the intermediate to the unfolded chains. The sequential unfolding pathway explains the insensitivity of the apparent Tm to the presence of temperature-sensitive folding mutations [Sturtevant, J. M., Yu, M.-H., Haase-Pettingell, C., & King, J. (1989) J. Biol. Chem. 264, 10693-10698] which are located in the central region of the chain. The metastable unfolding intermediate has not been detected in the forward folding pathway occurring at lower temperatures. The early stage of the high-temperature thermal unfolding pathway is not the reverse of the late stage of the low-temperature folding pathway.

Binding Sites↗
PubMed2005

Identification of a rice zinc finger protein whose expression is transiently induced by drought, cold but not by salinity and abscisic acid.

A C2H2-type zinc finger protein gene ZFP245 was cloned by RT-PCR approach from cold treated rice seedlings. ZFP245 is 712 bp in length and encodes a 24.5 KDa protein, which has 35% identity in amino acid with SCOF-1, a cold-inducible zinc finger protein from soybean. By database search, ZFP245 was mapped on chromosome 7 and clustered together with another C2H2 zinc finger gene. Tissue expression analysis showed that ZFP245 was constitutively expressed in various rice tissues including roots, stems, leaves and spikes. The semi-quantitative-RT-PCR assay revealed ZFP245 was strongly induced after 6 h exposure to cold and drought stresses, and then reduced to the baseline. However, ZFP245 was not regulated by high salt or abscisic acid treatment. The promoter sequence of 1017 nucleotides, upstream of ZFP245, was cloned directly by PCR approach. Sequence analysis revealed a CRT/DRE element was found within the ZFP245 promoter region. Taken together, ZFP245, as the first identified C2H2-type zinc finger protein involved in stress response in monocots probably plays a role as a transcription regulator in plant cold and drought responses through an ABA-independent pathway.

Abscisic Acid↗
PubMed2004

Photoperiod and temperature differentially regulate the expression of two dehydrin genes during overwintering of birch (Betula pubescens Ehrh.).

The overwintering of trees in northern areas depends on processes regulated by photoperiod and temperature. To identify the physiological and genetic factors involved in this environmental control, three latitudinal ecotypes of pubescent birch (Betula pubescens Ehrh.) growing in a common garden experiment were used. Each ecotype responded to the shortening of the photoperiod according to its specific critical daylength, resulting in the induction of freezing tolerance and dehydration of buds first in the northern ecotype, followed by the central and southern ecotypes, respectively. By contrast, there was no clear difference in the timing of dormancy release, bud rehydration, and deacclimation in the spring, suggesting that these traits were controlled mainly by temperature. To elucidate the role of dehydrins (DHN) in the overwintering process, two DHN genomic clones were isolated from pubescent birch and expression of the corresponding genes, both in field and under controlled conditions, was characterized. BpuDhn1 was found to encode an Y(n)K(n)-type of basic DHN, while BpuDhn2 encoded an acidic, SK(n)-type of DHN. In field-grown trees the level of BpuDhn1 increased in buds during the autumn, while the level of BpuDhn2 was highest during the coldest winter months. Under controlled conditions BpuDhn1 increased in response to the combined effect of short daylength and low, non-freezing temperatures whereas the expression of BpuDhn2 was mainly controlled by low temperature while photoperiod had less effect on its expression. These results suggest that DHNs participate in the sensitive environmental regulation of the overwintering process in birch.

Amino Acid Sequence↗