Correlations of pelvis state to foot placement do not imply within-step active control

Experimental studies of human walking have shown that within an individual step, variations in the center of mass (CoM) state can predict corresponding variations in the next foot placement. This has been interpreted by some to indicate the existence of active control in which the nervous system uses the CoM state at or near mid-stance to regulate subsequent foot placement. However, the passive dynamics of the moving body and/or moving limbs also contribute (perhaps strongly) to foot placement, and thus to its variation. The extent to which correlations of CoM state to foot placement reflect the effects of within-step active control, those of passive dynamics, or some combination of both, remains an important and still open question. Here, we used an open-loop-stable 2D walking model to show that this predictive ability cannot by itself be taken as evidence of within-step active control. In our simulations, we too find high correlations between the CoM state and subsequent foot placement, but these correlations are entirely due to passive dynamics as our system has no active control, either within a step or between steps. This demonstrates that any inferences made from such correlations about within-step active control require additional supporting evidence beyond the correlations themselves. Thus, these within-step predictive correlations leave unresolved the relative importance of within-step active control as compared to passive dynamics, meaning that such methods should be used to characterize control in human walking only with caution.     

Development of a novel MATLAB-based framework for implementing mechanical joint stability constraints within OpenSim musculoskeletal models

The Static Optimization (SO) solver in OpenSim estimates muscle activations and forces that only equilibrate applied moments. In this study, SO was enhanced through an open-access MATLAB interface, where calculated muscle activations can additionally satisfy crucial mechanical stability requirements. This Stability-Constrained SO (SCSO) is applicable to many OpenSim models and can potentially produce more biofidelic results than SO alone, especially when antagonistic muscle co-contraction is required to stabilize body joints. This hypothesis was tested using existing models and experimental data in the literature. Muscle activations were calculated by SO and SCSO for a spine model during two series of static trials (i.e. simulation 1 and 2), and also for a lower limb model (supplementary material 2). In simulation 1, symmetric and asymmetric flexion postures were compared, while in simulation 2, various external load heights were compared, where increases in load height did not change the external lumbar flexion moment, but necessitated higher EMG activations. During the tasks in simulation 1, the predicted muscle activations by SCSO demonstrated less average deviation from the EMG data (6.8% −7.5%) compared to those from SO (10.2%). In simulation 2, SO predicts constant muscle activations and forces, while SCSO predicts increases in the average activations of back and abdominal muscles that better match experimental data. Although the SCSO results are sensitive to some parameters (e.g. musculotendon stiffness), when considering the strategy of the central nervous system in distributing muscle forces and in activating antagonistic muscles, the assigned activations by SCSO are more biofidelic than SO.     

Global secretome analysis of resident cardiac progenitor cells from wild-type and transgenic heart failure mice: Why ambience matters

Resident cardiac progenitor cells (CPCs) have gained attention in cardiac regenerative medicine primarily due to their paracrine activity. In our current study we determined the role of pathological conditions such as heart failure on the autocrine-paracrine action of stem cell antigen-1 (Sca-1) expressing CPC. This comparative secretome profiling of Sca-1⁺ cells derived from transgenic heart failure (αMHC–cyclin-T1/Gαq overexpression [Cyc] cells) versus healthy (wild-type [Wt] cells) mice, achieved via mass-spectrometric quantification, enabled the identification of over 700 proteins. Our results demonstrate that the heart failure milieu caused a 2-fold enrichment of extracellular matrix proteins (ECM) like biglycan, versican, collagen XII, and angiogenic factors like heparan sulfate proteoglycan 2, plasminogen activator inhibitor 1 in the secretome. We further elucidated the direct influence of the secretome on the functional behavior of Sca-1 ⁺ cells via in vitro tube forming assay. Secreted factors present in the diseased milieu induced tube formation in Cyc cells (1.7-fold; p < 0.01) when compared with Wt cells after 24 hr of exposure. The presence of conditioned media moderately increased the proliferation of Cyc cells but had a more pronounced effect on Wt cells. Overall, these findings revealed global modifications in the secretory activity of adult Sca-1 ⁺ cells in the heart failure milieu. The secretion of ECM proteins and angiogenic factors, which are crucial for cardiac remodeling and recovery, was notably enriched in the supernatant of Cyc cells. Thus, during heart failure the microenvironment of Sca-1 ⁺ cells might favor angiogenesis and proliferation suggesting their potential to recover the damaged heart.     

Mechanistic insight into the attenuation of gouty inflammation by Taiwanese green propolis via inhibition of the NLRP3 inflammasome

Dysregulation of NACHT, LRR, and PYD domains-containing protein 3 (NLRP3) inflammasome is involved in many chronic inflammatory diseases, including gouty arthritis. Activation of the NLRP3 inflammasome requires priming and activation signals: the priming signal controls the expression of NLRP3 and interleukin (IL)-1β precursor (proIL-1β), while the activation signal leads to the assembly of the NLRP3 inflammasome and to caspase-1 activation. Here, we reported the effects of the alcoholic extract of Taiwanese green propolis (TGP) on the NLRP3 inflammasome in vitro and in vivo. TGP inhibited proIL-1β expression by reducing nuclear factor kappa B activation and reactive oxygen species (ROS) production in lipopolysaccharide-activated macrophages. Additionally, TGP also suppressed the activation signal by reducing mitochondrial damage, ROS production, lysosomal rupture, c-Jun N-terminal kinases 1/2 phosphorylation and apoptosis-associated speck-like protein oligomerization. Furthermore, we found that TGP inhibited the NLRP3 inflammasome partially via autophagy induction. In the in vivo mouse model of uric acid crystal-induced peritonitis, TGP attenuated the peritoneal recruitment of neutrophils, and the levels of IL-1β, active caspase-1, IL-6 and monocyte chemoattractant protein-1 in lavage fluids. As a proof of principle, in this study, we purified a known compound, propolin G, from TGP and identified this compound as a potential inhibitor of the NLRP3 inflammasome. Our results indicated that TGP might be useful for ameliorating gouty inflammation via inhibition of the NLRP3 inflammasome.     

天山一号冰川表面冰尘和底部沉积层中可培养酵母菌系统发育类群的分布及生态生理特征

【目的】揭示乌鲁木齐河源天山1号冰川表面冰尘(CS)和底部沉积层(DS)可培养酵母菌系统发育类群及其结构组成差异,分析低温酵母菌代表菌株之间的生态、生理生化特性。【方法】利用4种培养基分离天山1号冰川可培养酵母菌,采用ITS基因序列分析确定菌种的系统进化地位。对分离菌株的最适生长温度、耐盐性和产酶等生态、生理学特性进行分析。【结果】从冰尘和底部沉积层中共分离出152株酵母菌菌株,通过ITSrRNA基因序列的NCBI比对和Rep-PCR指纹分型,结果表明酵母菌类群包括担子菌门(Basidiomycota)和子囊菌(Ascomycota),分属于14个属26种,其中担子菌门柄锈菌亚门(Pucciniomycotina)88株、伞菌亚门(Agariomycotina)24株,子囊菌门40株,冰川广布酵母菌Vishniacozyma victoriae为优势菌株(占比21.84%)。17种酵母的最适生长温度为15°C、2种为10°C、6种为20°C。25株代表酵母菌株产酶分析显示,产脂肪酶、淀粉酶、蛋白酶菌株分别为11株、11株、5株,6株3种酶都不产。【结论】天山1号冰川冰尘及底部沉积层可培养低温酵母系统发育类群结构存在差异,产低温酶活性高、稳定性好,为今后冰川低温酵母菌的研究提供有价值的数据支持。     

中国西藏发现类三角蚌类祖先闯入非海相领域的证据（英文）北大核心CSCD

新发现的双壳类化石命名为Baxoitrigonia baxoiensis gen. et sp. nov.,产地为藏东八宿林卡家东,化石产于景星动物群之下的拉贡塘组下段,同层位有菊石和其他海相双壳类,时代为晚侏罗世Tithonian期;化石的外部特征很接近于三角蛤类Iotrigonia属,但前闭肌痕特征又相似于类三角蚌类,被认为是三角蛤类闯入非海相领域后演变成类三角蚌类的产物。此发现提供了生物和地层两方面的直接证据,证明非海相类三角蚌类(Trigonioidoidea超科)起源于海相三角蛤类(Trigoniida目),而不是起源于珠蚌类(Unionida目)。海相三角蛤类闯入边缘隔绝的洛隆-八宿地区并演变为非海相类三角蚌类,是一次典型的边域成种事件。     

Cover Image,Volume 116, Number 2, February 2019

A key point of protein stability engineering is to identify specific target residues whose mutations can stabilize the protein structure without negatively affecting the function or activity of the protein. Here, we propose a method called RiSLnet (Rapid i dentification of Smart mutant Library using residue network) to identify such residues by combining network analysis for protein residue interactions, identification of conserved residues, and evaluation of relative solvent accessibility. To validate its performance, the method was applied to four proteins, that is, T4 lysozyme, ribonuclease H, barnase, and cold shock protein B. Our method predicted beneficial mutations in thermal stability with ~62% average accuracy when the thermal stability of the mutants was compared with the ones in the Protherm database. It was further applied to lysine decarboxylase (CadA) to experimentally confirm its accuracy and effectiveness. RiSLnet identified mutations increasing the thermal stability of CadA with the accuracy of ~60% and significantly reduced the number of candidate residues (~99%) for mutation. Finally, combinatorial mutations designed by RiSLnet and in silico saturation mutagenesis yielded a thermally stable triple mutant with the half-life (T _1/2) of 114.9 min at 58°C, which is approximately twofold higher than that of the wild-type.     

Reconstruction of tricarboxylic acid cycle in Corynebacterium glutamicum with a genome-scale metabolic network model for trans-4-hydroxyproline production

trans-4-Hydroxy- l -proline (Hyp) is an abundant component of mammalian collagen and functions as a chiral synthon for the syntheses of anti-inflammatory drugs in the pharmaceutical industry. Proline 4-hydroxylase (P4H) can catalyze the conversion of l -proline to Hyp; however, it is still challenging for the fermentative production of Hyp from glucose using P4H due to the low yield and productivity. Here, we report the metabolic engineering of Corynebacterium glutamicum for the fermentative production of Hyp by reconstructing tricarboxylic acid (TCA) cycle together with heterologously expressing the p4h gene from Dactylosporangium sp. strain RH1. In silico model-based simulation showed that α-ketoglutarate was redirected from the TCA cycle toward Hyp synthetic pathway driven by P4H when the carbon flux from succinyl-CoA to succinate descended to zero. The interruption of the TCA cycle by the deletion of sucCD-encoding the succinyl-CoA synthetase (SUCOAS) led to a 60% increase in Hyp production and had no obvious impact on the growth rate. Fine-tuning of plasmid-borne ProB* and P4H abundances led to a significant increase in the yield of Hyp on glucose. The final engineered Hyp-7 strain produced up to 21.72 g/L Hyp with a yield of 0.27 mol/mol (Hyp/glucose) and a volumetric productivity of 0.36 g·L ⁻¹·hr ⁻¹ in the shake flask fermentation. To our knowledge, this is the highest yield and productivity achieved by microbial fermentation in a glucose-minimal medium for Hyp production. This strategy provides new insights into engineering C. glutamicum by flux coupling for the fermentative production of Hyp and related products.     

Stabilization and scale-up of photosynthesis-driven ω-hydroxylation of nonanoic acid methyl ester by two-liquid phase whole-cell biocatalysis

Photoautotrophic organisms are promising hosts for biocatalytic oxyfunctionalizations because they supply reduction equivalents as well as O₂ via photosynthetic water oxidation. Thus far, research on photosynthesis-driven bioprocesses mainly focuses on strain development and the proof of principle in small-scale biocatalytic reaction setups. This study investigates the long-term applicability of the previously developed cyanobacterial strain Synechocystis sp. PCC 6803_BGT harboring the alkane monooxygenase system AlkBGT catalyzing terminal alkyl group oxyfunctionalization. For the regiospecific ω-hydroxylation of nonanoic acid methyl ester (NAME), this biocatalyst showed light intensity-independent hydroxylation activity and substantial hydrolysis of NAME to nonanoic acid. Substrate mass transfer limitation, substrate hydrolysis, as well as reactant toxicity were overcome via in situ substrate supply by means of a two-liquid phase system. The application of diisononyl phthalate as organic carrier solvent enabled 1.7-fold increased initial specific activities (5.6 ± 0.1 U/g_CDW) and 7.6-fold increased specific yields on biomass (3.8 ± 0.1 mmol_H-NAME/g_CDW) as compared with single aqueous phase biotransformations. Finally, the whole-cell biotransformation system was successfully scaled from glass tubes to a stirred-tank photobioreactor. This is the first study reporting the application of the two-liquid phase concept for efficient phototrophic whole-cell biocatalysis.