Determination of the structure of the DNA binding domain of gamma delta resolvase in solution.

The DNA binding domain (DBD) of gamma delta resolvase (residues 141-183) is responsible for the interaction of this site-specific DNA recombinase with consensus site DNA within the gamma delta transposable element in Escherichia coli. Based on chemical-shift comparisons, the proteolytically isolated DBD displays side-chain interactions within a hydrophobic core that are highly similar to those of this domain when part of the intact enzyme (Liu T, Liu DJ, DeRose EF, Mullen GP, 1993, J Biol Chem 268:16309-16315). The structure of the DBD in solution has been determined using restraints obtained from 2-dimensional proton NMR data and is represented by 17 conformers. Experimental restraints included 458 distances based on analysis of nuclear Overhauser effect connectivities, 17 phi and chi 1 torsion angles based on analysis of couplings, and 17 backbone hydrogen bonds determined from NH exchange data. With respect to the computed average structure, these conformers display an RMS deviation of 0.67 A for the heavy backbone atoms and 1.49 A for all heavy atoms within residues 149-180. The DBD consists of 3 alpha-helices comprising residues D149-Q157, S162-T167, and R172-N183. Helix-2 and helix-3 form a backbone fold, which is similar to the canonical helix-turn-helix motif. The conformation of the NH2-terminal residues, G141-R148, appears flexible in solution. A hydrophobic core is formed by side chains donated by essentially all hydrophobic residues within the helices and turns. Helix-1 and helix-3 cross with a right-handed folding topology. The structure is consistent with a mechanism of DNA binding in which contacts are made by the hydrophilic face of helix-3 in the major groove and the amino-terminal arm in the minor groove. This structure represents an important step toward analysis of the mechanism of DNA interaction by gamma delta resolvase and provides initial structure-function comparisons among the divergent DBDs of related resolvases and invertases.     

Selectively 13C-enriched DNA: 13C and 1H assignments of a triple helix by two-dimensional relayed HMQC experiments

Summary We present NMR studies of an intramolecular triple helix, the three strands of which have been linked by a hexaethylene glycol chain. To overcome the generally encountered difficulties of assignment in the homopyrimidine strands, the carbon C1 of the pyrimidines were selectively ¹³C-enriched. Assignments of the aromatic and sugar protons were obtained from NOESY-HMQC and TOCSY-HMQC spectra. We show that the recognition of a DNA duplex by a third strand via triplex formation is easily carried out in solution by observing the changes of the ¹H1–¹³C1 connectivities as a function of pH. Furthermore, the conformation of the sugars has been found to be C2-endo, on the basis of the coupling constant values directly measured in an HSQC spectrum.     

Effects of Chronic Basic Fibroblast Growth Factor Administration to Rats with Partial Flmbrial Transections on Presynaptic Cholinergic Parameters and Muscarinic Receptors in the Hippocampus: Comparison with Nerve Growth Factor

Abstract: The present study compares the effects of chronic administration of basic fibroblast growth factor (bFGF) and nerve growth factor (NGF) on various hippocampal cholinergic parameters in rats with partial unilateral fimbrial transections. Lesions resulted in marked reductions of several presynaptic cholinergic parameters: choline acetyltransferase (ChAT) activity (by 50%), [³H]-acetylcholine ([³H]ACh) synthesis (by 59%), basal and ve-ratridine (1 μM)-evoked [³H]ACh release (by 44 and 57%, respectively), and [³H]vesamicol binding site densities (by 35%). In addition, [³H]AF-DX 116/muscarinic M₂ binding site densities were also modestly decreased (by 23%). In contrast, [³H]pirenzepine/muscarinic M₁ and [³H]AF-DX 384/muscarinic M₂/M₄ binding site densities were not altered by the lesions, nor were they affected by any of the treatments. Intracerebroventricular administration of bFGF (10 ng, every other day, for 21 days) partially prevented the lesion-induced deficit in hippocampal ChAT activity, an effect that was not markedly different from that measured in the NGF-treated (1 μg intracerebroventricularly, every other day, for 21 days) rats. In rats treated with a combination of bFGF and NGF, ChAT activity was not different from that in rats treated with the individual factors alone. In contrast, the lesion-induced deficits in the other cholinergic parameters were not attenuated by bFGF treatment, although they were at least partially prevented by NGF administration. To determine whether higher concentrations of bFGF are necessary to affect cholinergic parameters other than hippocampal ChAT activity, rats were treated with 1 μg (every other day, 21 days) of the growth factor. In this group of rats, detrimental effects of bFGF, manifested by an increased death rate (46%), and marked reductions in body weight of the survivors, were observed. In addition, this concentration of bFGF appeared to exacerbate the lesion-induced reduction in [³H]ACh synthesis by hippocampal slices; [³H]ACh synthesis in lesioned hippocampi represented 36 and 52% of that in contralateral unlesioned hippocampi for the bFGF-treated and control groups, respectively. In conclusion, although bFGF administration attenuates the deficit in hippocampal ChAT activity induced by partial fimbrial transections, this does not appear to translate into enhanced functional capacity of the cholinergic terminals. This is clearly in contrast to NGF, which enhances not only hippocampal ChAT activity, but also other parameters indicative of increased function in the cholinergic terminals.     

Fed-batch cultivation of recombinant escherichia coli JM103 and production of the fusion protein SPA::EcoRI in a 60-L working volume airlift tower loop reactor

SPA::EcoRI fusion protein was produced by Escherichia coli JM103 carrying the multicopy expression plasmid pMTC48, the multicopy repressor plasmid pRK248, and the multicopy protection plasmid pEcoR4 in a 60-L working volume airlift tower loop reactor on M9 minimal medium with glucose. Cell mass concentration, total cell count, number of colony-forming units, specific growth rate, yield coefficient, and metabolite (acetate, pyruvate, succinate, lactate, ethanol) concentrations were monitored during the growth phase and gene expression. Gene expression was induced by temperature shift or chemically by isopropyl-thiogalactosidase in the airlift tower loop reactor (ALTR) at constant cultivation time and in a small stirred tank reactor at different cultivation times. During induction, the cultivation medium was supplemented with concentrated Luria-Bertani (LB) medium. The intracellular enzyme activity was evaluated as a function of the time after the start of the induction. It was found that the reduction of the glucose concentration and increase of the dissolved oxygen concentration reduced the acetate produced and increased the intracellular enzyme activity. (c) 1993 John Wiley & Sons, Inc.     

Analysis of the role of the COL1 domain and its adjacent cysteine-containing sequence in the chain assembly of type IX collagen

The mechanisms of chain selection and assembly of type IX collagen, a heterotrimer 1(IX)2(IX)3(IX), must differ from that of fibrillar collagens since it lacks the characteristic C-propeptide of these latter molecules. We have tested the hypothesis that the information required for this process is contained within the C-terminal triple helical disulfide-bonded region (LMW). The reassociations of the purified LMW fragments of pepsinized bovine type IX collagen were followed by the formation of disulfide-bonded multimers. Our data demonstrate that only three triple helical assemblies form readily, (1)₃, (2)₃, and 123. The information required for chain selection and assembly is thus, at least in part, contained in the studied fragments. Molecular stoichiometries different from the classical heterotrimer may thus also form under certain conditions.     

Sequence and structural homology among membrane-associated domains of CFTR and certain transporter proteins

A sequence comparison of the two membrane-associated (MA) domains of the cystic fibrosis transmembrane conductance regulator (CFTR), multidrug resistance transporter (MDR), and -factor pheromone export system (STE6) proteins, each of which are believed to contain a total of 12 transmembrane (TM) segments, reveals significant amino acid homology and length conservation in the loop regions that connect individual TM sequences. Similar structural homology is observed between these proteins, hemolysin B (HLYB) and the major histocompatibility-linked peptide transporter, HAM1, the latter two which contain a single MA domain composed of six TM segments. In addition, there are specific sequences that are conserved within the TM segments of the five different membrane proteins. This observation suggests that the folding topologies of the MA domains of MDR, STE6, and CFTR in the plasma membrane are likely to be very similar. The sequence analysis also reveals that there are three characteristic motifs (a pair of aromatic residues, LTLXXXXXXP and GXXL) that are conserved in MDR, STE6, HLYB, HAM1, but not in CFTR. We propose that although CFTR may be evolutionarily related to these other membrane proteins, it belongs to a separate subclass.     

Detrending climate data prior to climate–growth analyses in dendroecology: A common best practice?

Tree growth varies closely with high–frequency climate variability. Since the 1930s detrending climate data prior to comparing them with tree growth data has been shown to better capture tree growth sensitivity to climate. However, in a context of increasingly pronounced trends in climate, this practice remains surprisingly rare in dendroecology. In a review of Dendrochronologia over the 2018–2021 period, we found that less than 20 % of dendroecological studies detrended climate data prior to climate-growth analyses. With an illustrative study, we want to remind the dendroecology community that such a procedure is still, if not more than ever, rational and relevant. We investigated the effects of detrending climate data on climate–growth relationships across North America over the 1951–2000 period. We used a network of 2536 tree individual ring-width series from the Canadian and Western US forest inventories. We compared correlations between tree growth and seasonal climate data (Tmin, Tmax, Prec) both raw and detrended. Detrending approaches included a linear regression, 30-yr and 100-yr cubic smoothing splines. Our results indicate that on average the detrending of climate data increased climate–growth correlations. In addition, we observed that strong trends in climate data translated to higher variability in inferred correlations based on raw vs. detrended climate data. We provide further evidence that our results hold true for the entire spectrum of dendroecological studies using either mean site chronologies and correlations coefficients, or individual tree time series within a mixed-effects model framework where regression coefficients are used more commonly. We show that even without a change in correlation, regression coefficients can change a lot and we tend to underestimate the true climate impact on growth in case of climate variables containing trends. This study demonstrates that treating climate and tree-ring time series “like-for-like” is a necessary procedure to reduce false negatives and positives in dendroecological studies. Concluding, we recommend using the same detrending for climate and tree growth data when tree-ring time series are detrended with splines or similar frequency-based filters.     

Ecological and methodological drivers of non-stationarity in tree growth response to climate

Radial tree growth is sensitive to environmental conditions, making observed growth increments an important indicator of climate change effects on forest growth. However, unprecedented climate variability could lead to non-stationarity, that is, a decoupling of tree growth responses from climate over time, potentially inducing biases in climate reconstructions and forest growth projections. Little is known about whether and to what extent environmental conditions, species, and model type and resolution affect the occurrence and magnitude of non-stationarity. To systematically assess potential drivers of non-stationarity, we compiled tree-ring width chronologies of two conifer species, Picea abies and Pinus sylvestris, distributed across cold, dry, and mixed climates. We analyzed 147 sites across the Europe including the distribution margins of these species as well as moderate sites. We calibrated four numerical models (linear vs. non-linear, daily vs. monthly resolution) to simulate growth chronologies based on temperature and soil moisture data. Climate–growth models were tested in independent verification periods to quantify their non-stationarity, which was assessed based on bootstrapped transfer function stability tests. The degree of non-stationarity varied between species, site climatic conditions, and models. Chronologies of P. sylvestris showed stronger non-stationarity compared with Picea abies stands with a high degree of stationarity. Sites with mixed climatic signals were most affected by non-stationarity compared with sites sampled at cold and dry species distribution margins. Moreover, linear models with daily resolution exhibited greater non-stationarity compared with monthly-resolved non-linear models. We conclude that non-stationarity in climate–growth responses is a multifactorial phenomenon driven by the interaction of site climatic conditions, tree species, and methodological features of the modeling approach. Given the existence of multiple drivers and the frequent occurrence of non-stationarity, we recommend that temporal non-stationarity rather than stationarity should be considered as the baseline model of climate–growth response for temperate forests.     

Microbial nitrogen and phosphorus co-limitation across permafrost region

The status of plant and microbial nutrient limitation have profound impacts on ecosystem carbon cycle in permafrost areas, which store large amounts of carbon and experience pronounced climatic warming. Despite the long-term standing paradigm assumes that cold ecosystems primarily have nitrogen deficiency, large-scale empirical tests of microbial nutrient limitation are lacking. Here we assessed the potential microbial nutrient limitation across the Tibetan alpine permafrost region, using the combination of enzymatic and elemental stoichiometry, genes abundance and fertilization method. In contrast with the traditional view, the four independent approaches congruently detected widespread microbial nitrogen and phosphorus co-limitation in both the surface soil and deep permafrost deposits, with stronger limitation in the topsoil. Further analysis revealed that soil resources stoichiometry and microbial community composition were the two best predictors of the magnitude of microbial nutrient limitation. High ratio of available soil carbon to nutrient and low fungal/bacterial ratio corresponded to strong microbial nutrient limitation. These findings suggest that warming-induced enhancement in soil nutrient availability could stimulate microbial activity, and probably amplify soil carbon losses from permafrost areas.     

Long-term changes in Noctiluca scintillans blooms along the Chinese coast from 1933 to 2020

Noctiluca scintillans is one of the most common harmful algal species and widely known due to its bioluminescence. In this study, the spatial distribution, seasonal variations, and long-term trends of N. scintillans blooms in China and the related drivers were analyzed and discussed. From 1933 to 2020, a total of 265 events of N. scintillans blooms were recorded in Chinese coastal waters, with a total duration of 1052 days. The first N. scintillans bloom occurred in Zhejiang in 1933, and only three events were recorded before 1980. From 1981 to 2020, N. scintillans caused harmful algal blooms (HABs) almost every year, both the average duration and the proportion of multiphase HABs showed an increasing trend. 1986–1992, 2002–2004, and 2009–2016 were the three peak periods with a frequency of no less than five events of N. scintillans blooms per year. In terms of spatial distribution, N. scintillans blooms spread from the Southeast China Sea to the Bohai Sea after 2000, Guangdong, Fujian, and Hebei were the three provinces with the highest numbers of recorded events of N. scintillans blooms. Moreover, 86.8% of the events of N. scintillans blooms occurred in spring (March, April, and May) and summer (June, July, and August). Among environmental factors, the dissolved inorganic phosphate, dissolved silicate and chemical oxygen demand were significantly correlated with the cell density of N. scintillans during N. scintillans blooms, and most of N. scintillans blooms were recorded in the temperature range of 18.0–25.0°C. Precipitation, hydrodynamics, water temperature, and food availability might be the main factors affecting the spatial–temporal distribution of N. scintillans blooms along the Chinese coast.