Detecting Site-Specific Physicochemical Selective Pressures: Applications to the Class I HLA of the Human Major Histocompatibility Complex and the SRK of the Plant Sporophytic Self-Incompatibility System

Models of codon substitution are developed that incorporate physicochemical properties of amino acids. When amino acid sites are inferred to be under positive selection, these models suggest the nature and extent of the physicochemical properties under selection. This is accomplished by first partitioning the codons on the basis of some property of the encoded amino acids. This partition is used to parametrize the rates of property-conserving and property-altering base substitutions at the codon level by means of finite mixtures of Markov models that also account for codon and transition:transversion biases. Here, we apply this method to two positively selected receptors involved in ligand-recognition: the class I alleles of the human major histocompatibility complex (MHC) of known structure and the S-locus receptor kinase (SRK) of the sporophytic self-incompatibility system (SSI) in cruciferous plants (Brassicaceae), whose structure is unknown. Through likelihood ratio tests we demonstrate that at some sites, the positively selected MHC and SRK proteins are under physicochemical selective pressures to alter polarity, volume, polarity and/or volume, and charge to various extents. An empirical Bayes approach is used to identify sites that may be important for ligand recognition in these proteins.Reviewing Editor : Dr. Willie Swanson     

Role of pollination in yield and physicochemical properties of tomatoes (Lycopersicon esculentum)

Very little is known about pollination and its effects on the yield and physicochemical properties of flowering plants in tropical countries. Wind and insect pollinators are among our natural resources because pollination is the most important ecosystem service performed by wind and insects, and is vital to the socio-economic status of human beings. In this experiment, different pollination methods for tomato plants were examined. Self-pollination was encouraged by covering the plants with a plastic sheet. Wind and insects were excluded from these plants, and thus only self-pollination was possible. The experiment occurred during the flowering stage. Wind-pollinated plants were covered with a muslin cloth, which excluded insects, and only wind could pass through the cloth. For insect pollination, plants remained uncovered, allowing free access to insects to pollinate the flowers. At fruit maturity, when fruits were completely red, fruits from each treatment were harvested on the same date and under the same conditions. Results illustrated the substantial importance of insects as pollinators of tomato crops. Open field had greater tomato yield and positive effects on physicochemical properties on fruit than under self and wind pollination.     

Synthesis,biological evaluation,and physicochemical property assessment of 4-substituted 2-phenylaminoquinazolines as Mer tyrosine kinase inhibitors

Current results identified 4-substituted 2-phenylaminoquinazoline compounds as novel Mer tyrosine kinase (Mer TK) inhibitors with a new scaffold. Twenty-one 2,4-disubstituted quinazolines (series 4–7) were designed, synthesized, and evaluated against Mer TK and a panel of human tumor cell lines aimed at exploring new Mer TK inhibitors as novel potential antitumor agents. A new lead, 4b, was discovered with a good balance between high potency (IC₅₀ 0.68 μM) in the Mer TK assay and antiproliferative activity against MV4-11 (GI₅₀ 8.54 μM), as well as other human tumor cell lines (GI₅₀ < 20 μM), and a desirable druglike property profile with low log P value (2.54) and high aqueous solubility (95.6 μg/mL). Molecular modeling elucidated an expected binding mode of 4b with Mer TK and necessary interactions between them, thus supporting the hypothesis that Mer TK might be a biologic target of this kind of new active compound.     

新分离呼吸道肠道病毒生物学特性和S4片段的序列测定

新分离呼吸道肠道病毒(简称呼肠病毒)经过空斑分纯后进行生物学和部分基因序列的鉴定.首先通过BYD株(由端青从北京于某患者标本中分离到的第一株呼肠病毒)对4种传代细胞的敏感性试验,选出L929和LLC-MK2敏感细胞,然后用LLC-MK2细胞进行理化性质试验,血凝试验和形态学鉴定.结果显示该病毒为耐乙醚、不耐酸、不耐热的RNA病毒;对人O型红细胞能产生凝集,滴度达132;电镜下可查见细胞胞浆内有球形、直径为70nm～80nm、双层衣壳的病毒颗粒.提取BYD株RNA并进行S4片段序列分析,结果显示该片段的氨基酸序列与已知呼肠病毒1～3型标准株的同源性分别为95%、90%和95%.以上这些生物学以及S4片断的序列分析结果表明新分离BYD株病毒符合呼肠病毒科的特性.     

伪狂犬病病毒基因缺失疫苗制苗用毒种特性研究

本试验通过对PRV基因缺失株SA215(gE -/gI -/TK -)细胞培养特性、理化特性及形态发生过程进行研究,来确定gE、gI和TK基因缺失对病毒特性的影响.结果表明,基因缺失对该毒株在培养细胞的吸附和穿入过程没有影响,但与亲本株相比,表现为生长掩蔽期延长,增殖速度减缓,但能达到相似的增殖滴度,并且基因缺失对病毒的理化特性影响很小.形态发生过程观察结果表明,PRV SA215株在细胞培养上形态发生正常,能形成感染性病毒粒子,但在由核膜出芽和囊膜形成上受到一定程度的阻碍.本研究为疫苗研制和生产提供指导和依据.     

Molecular cloning and in-depth bioinformatics analysis of type II ribosome-inactivating protein isolated from Sambucus ebulus

Plant ribosome–inactivating proteins (RIPs) are N–glycosidases which inhibit protein synthesis through depurination of the ribosomal RNA sequence. Type II RIPs are heterodimer proteins which can bind to cell surfaces. The cytotoxicity of these RIPs is different. Sambucus spp. are a rich source of RIP proteins with different properties. In the present study, a type II RIP was isolated from S. ebulus plant that grows widely in the north of Iran, and different bioinformatics tools were used for the evaluation of physicochemical, functional and 3D protein characteristics. The results showed significant differences among isolated RIP and other Sambucus RIP proteins. The study of these differences can not only expand our insight into the functioning mechanisms of plant RIPs but also provide information about a novel RIP protein with potential biological applications.     

Cytotoxicity in the age of nano: The role of fourth period transition metal oxide nanoparticle physicochemical properties

A clear understanding of physicochemical factors governing nanoparticle toxicity is still in its infancy. We used a systematic approach to delineate physicochemical properties of nanoparticles that govern cytotoxicity. The cytotoxicity of fourth period metal oxide nanoparticles (NPs): TiO₂, Cr₂O₃, Mn₂O₃, Fe₂O₃, NiO, CuO, and ZnO increases with the atomic number of the transition metal oxide. This trend was not cell-type specific, as observed in non-transformed human lung cells (BEAS-2B) and human bronchoalveolar carcinoma-derived cells (A549). Addition of NPs to the cell culture medium did not significantly alter pH. Physiochemical properties were assessed to discover the determinants of cytotoxicity: (1) point-of-zero charge (PZC) (i.e., isoelectric point) described the surface charge of NPs in cytosolic and lysosomal compartments; (2) relative number of available binding sites on the NP surface quantified by X-ray photoelectron spectroscopy was used to estimate the probability of biomolecular interactions on the particle surface; (3) band-gap energy measurements to predict electron abstraction from NPs which might lead to oxidative stress and subsequent cell death; and (4) ion dissolution. Our results indicate that cytotoxicity is a function of particle surface charge, the relative number of available surface binding sites, and metal ion dissolution from NPs. These findings provide a physicochemical basis for both risk assessment and the design of safer nanomaterials.     

The design and synthesis of a potent glucagon receptor antagonist with favorable physicochemical and pharmacokinetic properties as a candidate for the treatment of type 2 diabetes mellitus

A novel and potent small molecule glucagon receptor antagonist for the treatment of diabetes mellitus is reported. This candidate, (S)-3-[4-(1-{3,5-dimethyl-4-[4-(trifluoromethyl)-1H-pyrazol-1-yl]phenoxy}butyl)benzamido]propanoic acid, has lower molecular weight and lipophilicity than historical glucagon receptor antagonists, resulting in excellent selectivity in broad-panel screening, lower cytotoxicity, and excellent overall in vivo safety in early pre-clinical testing. Additionally, it displays low in vivo clearance and excellent oral bioavailability in both rats and dogs. In a rat glucagon challenge model, it was shown to reduce the glucagon-elicited glucose excursion in a dose-dependent manner and at a concentration consistent with its rat in vitro potency. Its properties make it an excellent candidate for further investigation.     

Structural and physicochemical properties of starch gels prepared from partially modified starches using Thermus aquaticus 4-α-glucanotransferase

The modified starch gels prepared from partial enzyme treatments (1, 3, and 6 U/g starch; 2-h incubation) of the corn and rice starch pastes using Thermus aquaticus 4-α-glucanotransferase (TAαGT) were investigated for their molecular characteristics, microstructures, and physicochemical properties. Unlike the native and partially modified normal starches, the native and partially modified waxy starches could not form gels strong enough for textural analysis after 24 h for gel setting. Features of the partially modified normal starches were the specific apparent amylose contents and maximum iodine absorption wavelength (λ_max, ∼567 nm), as well as the tri-modal molecular weight profiles and flatter side-chain distributions. Also, the partially modified normal starch gels possessed fractured surfaces with discontinuous crystalline fibrous assembly that differed from the native starch gels’ porous continuous network, which resulted in more brittle, rigid, and resilient gels compared with the native gels.     

Improvement in aqueous solubility achieved via small molecular changes

Overcoming poor solubility is a significant issue in drug discovery. The most common solution is to replace carbon atoms with polar heteroatoms such as N and O or by attaching a solubilizing appendage. This approach can lead to other issues such as poor activity and PK or the increased risk for toxicity. However, there are more subtle structural changes which can be employed that lead to an increase in solubility. These include, excising hydrophobic groups which do not efficiently contribute to binding, modifying stereo- and regiochemistry, increasing or decreasing the degree of unsaturation or adding small hydrophobic groups such as fluorine or methyl.