A Method for Cell Culture and Maintenance of Ammonia-Oxidizing Archaea in Agar Stab

Ammonia oxidizing archaea (AOA) are predominantly found and closely linked with geochemical cycling of nitrogen in non-extreme habitats. However, these strains have mainly been investigated using liquid cultures of enriched cells. Here, we provide an agar stab as a simple and reliable means of cultivating and maintaining AOA.     

Protein structure and the spandrels of San Marco: insulin's receptor-binding surface is buttressed by an invariant leucine essential for its stability.

Insulin provides a model of induced fit in macromolecular recognition: the hormone's conserved core is proposed to contribute to a novel receptor-binding surface. The core's evolutionary invariance, unusual among globular proteins, presumably reflects intertwined constraints of structure and function. To probe the architectural basis of such invariance, we have investigated hydrophobic substitutions of a key internal side chain (Leu(A16)). Although the variants exhibit perturbed structure and stability, moderate receptor-binding activities are retained. These observations suggest that the A16 side chain provides an essential structural buttress but unlike neighboring core side chains, does not itself contact the receptor. Among invertebrate insulin-like proteins, Leu(A16) and other putative core residues are not conserved, suggesting that the vertebrate packing scheme is not a general requirement of an insulin-like fold. We propose that conservation of Leu(A16) among vertebrate insulins and insulin-like growth factors is a side consequence of induced fit: alternative packing schemes are disallowed by lack of surrounding covariation within the hormone's hidden receptor-binding surface. An analogy is suggested between Leu(A16) and the spandrels of San Marco, tapering triangular spaces at the intersection of the dome's arches. This celebrated metaphor of Gould and Lewontin emphasizes the role of interlocking constraints in the evolution of biological structures.     

The in vivo distribution of murine lymphokine activated killer cells in splenectomized host

The in vivo distribution of intravenously injected lymphokine activated killer (LAK) cells, generated in vitro with rIL-2 from normal murine splenocytes, was studied in BALB/c mice and compared with that of normal splenocytes. Both normal splenocytes and LAK cells were labeled with 51Cr, and the results were analyzed at 6, 24, and 48 hours after injection by localization index as the parameter. After injection through tail veins of mice, LAK cells were found to migrate to the spleen, lungs, liver, lymph nodes, bones and the kidneys. The apparent increased distribution pattern of LAK cells to the lung at 6 and 24 hours after injection was not detected when normal splenocytes were injected. Since almost one third of the injected LAK cells were found to localize in the spleen, it was postulated that splenectomy would affect the in vivo organ distribution of LAK cells. Accordingly, the in vivo distribution of LAK cells in splenectomized mice was further investigated. Results indicated that splenectomy enhanced the convergence of LAK cells to the lungs, liver, lymph nodes and bones. Therefore, splenectomy may augment the therapeutic effect of the adoptive transfer of LAK cells in pulmonary, hepatic, lymph node and bony metastases.     

Discovery and anti-inflammatory evaluation of benzothiazepinones (BTZs) as novel non-ATP competitive inhibitors of glycogen synthase kinase-3β (GSK-3β)

Glycogen synthase kinase-3β (GSK-3β) has been identified to promote inflammation and its inhibitors have also been proven to treat some inflammatory mediated diseases in animal models. Non-ATP competitive inhibitors inherently have better therapeutical value due to their higher specificity than ATP competitive ones. In this paper, we designed and synthesized a series of new BTZ derivatives as non-ATP competitive GSK-3β inhibitors. Kinetic analysis revealed two typical compounds 6j and 3j showed the different non-ATP competitive mechanism of substrate competition or allosteric modulation to GSK-3β, respectively. As expected, the two compounds showed good specificity in a panel test of 16 protein kinases, even to the closest enzymes, like CDK-1/cyclin B and CK-II. The in vivo results proved that both compounds can greatly attenuate the LPS-induced acute lung injury (ALI) and diminish inflammation response in mice by inhibiting the mRNA expression of IL-1β and IL-6. Western blot analysis demonstrated that they negatively regulated GSK-3β, and the mechanism of the observed beneficial effects of the inhibitors may involve both the increased phosphorylation of the Ser9 residue on GSK-3β and protein expression of Sirtuin 1 (SIRT1). The results support that such novel BTZ compounds have a protective role in LPS-induced ALI, and might be attractive candidates for further development of inflammation pharmacotherapy, which greatly thanks to their inherently high selectivities by the non-ATP competitive mode of action. Finally, we proposed suggesting binding modes by Docking study to well explain the impacts of compounds on the target site.     

氮磷肥配施对苦荞根系生理生态及产量的影响

以苦荞品种‘迪庆’为材料,在盆栽试验条件下,研究了氮(纯氮用量分别为0g/kg、0.1g/kg、0.2g/kg)、磷(P2O5用量分别为0.1g/kg和0.2g/kg)配施对苦荞根系生长、生理指标及其产量的影响,旨在为黄土高原苦荞高产优质栽培提供理论依据。结果表明:(1)在相同施磷量条件下,苦荞幼苗的株高、茎粗、茎叶干重、主根长、根表面积、根系体积、根系直径、根系干重以及壮苗指数等均随施氮量的增加而呈先升后降的趋势,但根冠比随施氮量的增加而呈先降后升的趋势;叶片叶绿素含量以及根系活力、酸性磷酸酶(Apase)活性、可溶性蛋白含量和植株氮积累量随施氮量的增加呈抛物线变化趋势,根系硝酸还原酶(NR)活性和植株氮含量随施氮量的增加而增加;而根系可溶性糖含量、超氧化物歧化酶(SOD)活性、过氧化物酶(POD)活性、丙二醛(MDA)含量和游离脯氨酸含量等指标均随施氮量的增加而呈先降后升的趋势,0.1g/kg施氮处理各指标均显著低于其他处理;成熟期单株粒重、百粒重随施氮量的增加呈先升后降的趋势,0.1g/kg施氮处理各指标均显著高于其他处理。(2)在相同施氮量条件下,随着施磷量的增加,苦荞根系酸性磷酸酶(Apase)活性、SOD活性、POD活性、MDA含量、可溶性糖含量、可溶性蛋白以及游离脯氨酸含量等指标均降低,其余各指标则呈增加趋势。(3)无论施磷量条件如何,0.1g/kg的施氮处理下苦荞产量最高,与其他施氮处理相比,在低磷和高磷处理下的增产幅度分别为7.04%~37.40%和14.73%~68.26%;在施氮量一定的情况下,高磷处理比低磷处理增产15.96%~42.00%。(4)在该试验条件下,适当的氮磷肥配施表现出了明显的正加和效应,但过量施肥也有可能导致增产幅度下降,中氮高磷(施纯N量0.1g/kg,施P2O5量0.2g/kg)配施效果最优。     

Fast seedling root growth leads to competitive superiority of invasive plants

The competitive superiority of invasive plants plays a key role in the process of plant invasions, enabling invasive plants to overcome the resistance of local plant communities. Fast aboveground growth and high densities lead to the competitive superiority of invasive species in the competition for light. However, little is understood of the role belowground root competition may play in invasion. We conducted an experiment to test the effect of root growth on the performance of an invasive shrub Cassia alata, a naturalized, non-invasive shrub Corchorus capsularis, and a native shrub Desmodium reticulatum. We compared seedling growth of the three species and their competitive ability in situ. The roots of the C. alata seedlings grew much faster than those of C. capsularis and D. reticulatum during the entire growth period although C. alata had shorter shoots than D. reticulatum. Furthermore, C. alata showed an apparent competition advantage compared to the other two species as evidenced by less biomass reduction in intraspecific competition and higher competitive effects in interspecific competition. Our study reveals that fast seedling root growth may be important in explaining the competitive advantages of invasive plants. Future studies should pay more attention to the belowground traits of invasive plants, the trade-off between shoot and root growth, and the role of root competition in affecting the population dynamics of invasive plants and the structures of invaded communities.     

Modeling and correct the GC bias of tumor and normal WGS data for SCNA based tumor subclonal population inferring

Background

Somatic copy number alternations (SCNAs) can be utilized to infer tumor subclonal populations in whole genome seuqncing studies, where usually their read count ratios between tumor-normal paired samples serve as the inferring proxy. Existing SCNA based subclonal population inferring tools consider the GC bias of tumor and normal sample is of the same fature, and could be fully offset by read count ratio. However, we found that, the read count ratio on SCNA segments presents a Log linear biased pattern, which influence existing read count ratios based subclonal inferring tools performance. Currently no correction tools take into account the read ratio bias.

Results

We present Pre-SCNAClonal, a tool that improving tumor subclonal population inferring by correcting GC-bias at SCNAs level. Pre-SCNAClonal first corrects GC bias using Markov chain Monte Carlo probability model, then accurately locates baseline DNA segments (not containing any SCNAs) with a hierarchy clustering model. We show Pre-SCNAClonal’s superiority to exsiting GC-bias correction methods at any level of subclonal population.

Conclusions

Pre-SCNAClonal could be run independently as well as serving as pre-processing/gc-correction step in conjuntion with exsiting SCNA-based subclonal inferring tools.

     

Engineered Tissue Folding by Mechanical Compaction of the Mesenchyme

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The Strength of Mechanical Forces Determines the Differentiation of Alveolar Epithelial Cells

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Using matrix assisted laser desorption ionisation mass spectrometry (MALDI-MS) profiling in order to predict clinical outcomes of patients with heart failure

Background

Current risk prediction models in heart failure (HF) including clinical characteristics and biomarkers only have moderate predictive value. The aim of this study was to use matrix assisted laser desorption ionisation mass spectrometry (MALDI-MS) profiling to determine if a combination of peptides identified with MALDI-MS will better predict clinical outcomes of patients with HF.

Methods

A cohort of 100 patients with HF were recruited in the biomarker discovery phase (50 patients who died or had a HF hospital admission vs. 50 patients who did not have an event). The peptide extraction from plasma samples was performed using reversed phase C18. Then samples were analysed using MALDI-MS. A multiple peptide biomarker model was discovered that was able to predict clinical outcomes for patients with HF. Finally, this model was validated in an independent cohort with 100 patients with HF.

Results

After normalisation and alignment of all the processed spectra, a total of 11,389 peptides (m/z) were detected using MALDI-MS. A multiple biomarker model was developed from 14 plasma peptides that was able to predict clinical outcomes in HF patients with an area under the receiver operating characteristic curve (AUC) of 1.000 (p?=?0.0005). This model was validated in an independent cohort with 100 HF patients that yielded an AUC of 0.817 (p?=?0.0005) in the biomarker validation phase. Addition of this model to the BIOSTAT risk prediction model increased the predictive probability for clinical outcomes of HF from an AUC value of 0.643 to an AUC of 0.823 (p?=?0.0021). Moreover, using the prediction model of fourteen peptides and the composite model of the multiple biomarker of fourteen peptides with the BIOSTAT risk prediction model achieved a better predictive probability of time-to-event in prediction of clinical events in patients with HF (p?=?0.0005).

Conclusions

The results obtained in this study suggest that a cluster of plasma peptides using MALDI-MS can reliably predict clinical outcomes in HF that may help enable precision medicine in HF.