The design of a peptide sequence to inhibit HIV replication: a search algorithm combining Monte Carlo and self-consistent mean field techniques

We developed a search algorithm combining Monte Carlo (MC) and self-consistent mean field techniques to evolve a peptide sequence that has good binding capability to the anticodon stem and loop (ASL) of human lysine tRNA species, tRNA^Lys3, with the ultimate purpose of breaking the replication cycle of human immunodeficiency virus-1. The starting point is the 15-amino-acid sequence, RVTHHAFLGAHRTVG, found experimentally by Agris and co-workers to bind selectively to hypermodified tRNA^Lys3. The peptide backbone conformation is determined via atomistic simulation of the peptide-ASL^Lys3 complex and then held fixed throughout the search. The proportion of amino acids of various types (hydrophobic, polar, charged, etc.) is varied to mimic different peptide hydration properties. Three different sets of hydration properties were examined in the search algorithm to see how this affects evolution to the best-binding peptide sequences. Certain amino acids are commonly found at fixed sites for all three hydration states, some necessary for binding affinity and some necessary for binding specificity. Analysis of the binding structure and the various contributions to the binding energy shows that: 1) two hydrophilic residues (asparagine at site 11 and the cysteine at site 12) “recognize” the ASL^Lys3 due to the VDW energy, and thereby contribute to its binding specificity and 2) the positively charged arginines at sites 4 and 13 preferentially attract the negatively charged sugar rings and the phosphate linkages, and thereby contribute to the binding affinity.     

Reconstituting Corticostriatal Network on-a-Chip Reveals the Contribution of the Presynaptic Compartment to Huntington’s Disease

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Pollen morphology and taxonomic implications of Muscari Miller (Hyacinthaceae) species from Sicily

Pollen morphology of the native Sicilian species of the genus Muscari, one of which is endemic to Sicily, belonging to the subgenera Muscari, Leopoldia and Pseudomuscari, was studied using a light microscope and a scanning electron microscope. Pollen grains are monads, heteropolar and monosulcate; the exine is semitectate reticulate and perforate. The sulcus extends from distal to proximal face and its length is not directly proportional to the size of the granules and varies from one species to another.     

Reproductive costs in terrestrial male vertebrates: insights from bird studies

Reproduction requires resources that cannot be allocated to other functions resulting in direct reproductive costs (i.e. trade-offs between current reproduction and subsequent survival/reproduction). In wild vertebrates, direct reproductive costs have been widely described in females, but their occurrence in males remains to be explored. To fill this gap, we gathered 53 studies on 48 species testing direct reproductive costs in male vertebrates. We found a trade-off between current reproduction and subsequent performances in 29% of the species and in every clade. As 73% of the studied species are birds, we focused on that clade to investigate whether such trade-offs are associated with (i) levels of paternal care, (ii) polygyny or (iii) pace of life. More precisely for this third question, it is expected that fast species (i.e. short lifespan, early maturity, high fecundity) pay a cost in terms of survival, whereas slow species (with opposite characteristics) do so in terms of fecundity. Our findings tend to support this hypothesis. Finally, we pointed out the potential confounding effects that should be accounted for when investigating reproductive costs in males and strongly encourage the investigation of such costs in more clades to understand to what extent our results are relevant for other vertebrates.     

松花江流域沿江重点监控企业水环境潜在污染风险分析

为防控松花江流域水污染风险、优化流域内沿江产业带布局,分析了松花江流域沿江企业潜在污染风险的大小和分布,并揭示导致不同区域间水环境潜在污染风险空间差异的原因。基于《2012年废水国家重点监控企业名单》,本研究将沿松花江(到三级支流)1 km范围内的45家重点废水产生企业识别为松花江流域水环境潜在污染风险源。以沿江企业和重点区域的废水产生量与对应河段的水质状况表征水环境潜在污染风险源强弱与流域水体对潜在污染风险的缓冲能力,并以区域总人口数、第二产业产值及珍稀濒危物种分布情况反映流域社会-经济-自然复合生态系统对潜在污染风险的敏感程度开展评价。结果表明:牡丹江市辖区(牡丹江中游河段)因潜在污染风险源强、水体对潜在污染风险的缓冲能力低且自然生态系统对潜在污染风险的敏感程度高,是松花江流域受沿江企业产生的水环境潜在污染风险最严重的地区;长春市辖区(饮马河、伊通河部分河段)、伊春市辖区(汤旺河全部河段)与敦化市(海浪河全部河段、牡丹江部分河段)由于较低的水体缓冲能力和较高的生态系统敏感程度,应加强水环境潜在污染风险的防治;污染风险源强的吉林市辖区(西流松花江部分河段)与七台河市辖区(倭肯河部分河段),须提高本区域对潜在污染的风险管理能力以降低污染事故发生的可能性。最后,针对不同行业类型、区域潜在污染特点与水污染风险特征,从加快污水处理研究、评估污染治理经济手段、建立产业准入机制及完善污染防治立法等多方面提出流域水环境污染风险管控的相关建议。     

A specific inhibitor of lactate dehydrogenase overcame the resistance toward gemcitabine in hypoxic mesothelioma cells,and modulated the expression of the human equilibrative transporter-1

ABSTRACT

Malignant pleural mesothelioma (MPM) is a very hypoxic malignancy, and hypoxia has been associated with resistance towards gemcitabine. The muscle-isoform of lactate dehydrogenase (LDH-A) constitutes a major checkpoint for the switch to anaerobic glycolysis. Therefore we investigated the combination of a new LDH-A inhibitor (NHI-1) with gemcitabine in MPM cell lines. Under hypoxia (O₂ tension of 1%) the cell growth inhibitory effects of gemcitabine, were reduced, as demonstrated by a 5- to 10-fold increase in IC₅₀s. However, the simultaneous addition of NHI-1 was synergistic (combination index < 1). Flow cytometry demonstrated that hypoxia caused a G1 arrest, whereas the combination of NHI-1 significantly increased gemcitabine-induced cell death. Finally, the mRNA expression levels of the human equilibrative transporter-1 (hENT1) were significantly down-regulated under hypoxia, but treatment with NHI-1 was associated with a recovery of hENT1 expression. In conclusion, our data show that hypoxia increased MPM resistance to gemcitabine. However, cell death induction and modulation of the key transporter in gemcitabine uptake may contribute to the synergistic interaction of gemcitabine with the LDH-A inhibitor NHI-1 and support further studies for the rational development of this combination.     

A comparative molecular dynamics study on BACE1 and BACE2 flap flexibility

Beta-amyloid precursor protein cleavage enzyme1 (BACE1) and beta-amyloid precursor protein cleavage enzyme2 (BACE2), members of aspartyl protease family, are close homologs and have high similarity in their protein crystal structures. However, their enzymatic properties are different, which leads to different clinical outcomes. In this study, we performed sequence analysis and all-atom molecular dynamic (MD) simulations for both enzymes in their ligand-free states in order to compare their dynamical flap behaviors. This is to enhance our understanding of the relationship between sequence, structure and the dynamics of this protein family. Sequence analysis shows that in BACE1 and BACE2, most of the ligand-binding sites are conserved, indicative of their enzymatic property as aspartyl protease members. The other conserved residues are more or less unsystematically localized throughout the structure. Herein, we proposed and applied different combined parameters to define the asymmetric flap motion; the distance, d₁, between the flap tip and the flexible region; the dihedral angle, φ, to account for the twisting motion and the TriCα angle, θ₂ and θ₁. All four combined parameters were found to appropriately define the observed “twisting” motion during the flaps different conformational states. Additional analysis of the parameters indicated that the flaps can exist in an ensemble of conformations, i.e. closed, semi-open and open conformations for both systems. However, the behavior of the flap tips during simulations is different between BACE1 and BACE2. The BACE1 active site cavity is more spacious as compared to that of BACE2. The analysis of 10S loop and 113S loop showed a similar trend to that of flaps, with the BACE1 loops being more flexible and less stable than those of BACE2. We believe that the results, methods and perspectives highlighted in this report would assist researchers in the discovery of BACE inhibitors as potential Alzheimer’s disease therapies.     

Optimization of compressive loading parameters to mimic in vivo cervical spine kinematics in vitro

The human cervical spine supports substantial compressive load in vivo. However, the traditional in vitro testing methods rarely include compressive loads, especially in investigations of multi-segment cervical spine constructs. Previously, a systematic comparison was performed between the standard pure moment with no compressive loading and published compressive loading techniques (follower load – FL, axial load – AL, and combined load – CL). The systematic comparison was structured a priori using a statistical design of experiments and the desirability function approach, which was chosen based on the goal of determining the optimal compressive loading parameters necessary to mimic the segmental contribution patterns exhibited in vivo. The optimized set of compressive loading parameters resulted in in vitro segmental rotations that were within one standard deviation and 10% of average percent error of the in vivo mean throughout the entire motion path. As hypothesized, the values for the optimized independent variables of FL and AL varied dynamically throughout the motion path. FL was not necessary at the extremes of the flexion–extension (FE) motion path but peaked through the neutral position, whereas, a large negative value of AL was necessary in extension and increased linearly to a large positive value in flexion. Although further validation is required, the long-term goal is to develop a “physiologic” in vitro testing method, which will be valuable for evaluating adjacent segment effect following spinal fusion surgery, disc arthroplasty instrumentation testing and design, as well as mechanobiology experiments where correct kinematics and arthrokinematics are critical.     

施钙对干旱胁迫下花生生理特性、产量和品质的影响

以花生品种606为试材,在旱棚池栽人工控水条件下,研究了钙肥不同用量对花针期和结荚期干旱胁迫下花生的营养生长、生理特性、产量及品质的影响.结果表明:干旱胁迫下施钙,可以促进花生的营养生长,提高叶片的叶绿素含量、净光合速率和根系活力,提高干旱后复水过程中花生的恢复能力,缓解干旱对花生的不利影响;增加了花生荚果和籽仁的产量,尤其是增加了单株结果数和出仁率.施钙提高了籽仁中的脂肪和蛋白质含量,改善了干旱胁迫下花生的籽仁品质.在本试验条件下,施钙量为300 kg·hm-2时效果最佳.