High throughput screening methods for ω-transaminases

Recently, ω-transaminases have been increasingly used to synthesize amine compounds by reductive amination of prochiral ketones which are of high pharmacological significance. However, the conventional methods for evaluating these enzymes are time consuming and have often been regarded as a bottle neck in developing these enzymes as industrial biocatalysts. In the past few years, several high throughput screening methods have been developed for fast evaluation and identification of ω-transaminase. This review summarizes the various methodologies developed for rapidly screening ω-transaminases.     

SNP-PHAGE – High throughput SNP discovery pipeline

Background  

Single nucleotide polymorphisms (SNPs) as defined here are single base sequence changes or short insertion/deletions between or within individuals of a given species. As a result of their abundance and the availability of high throughput analysis technologies SNP markers have begun to replace other traditional markers such as restriction fragment length polymorphisms (RFLPs), amplified fragment length polymorphisms (AFLPs) and simple sequence repeats (SSRs or microsatellite) markers for fine mapping and association studies in several species. For SNP discovery from chromatogram data, several bioinformatics programs have to be combined to generate an analysis pipeline. Results have to be stored in a relational database to facilitate interrogation through queries or to generate data for further analyses such as determination of linkage disequilibrium and identification of common haplotypes. Although these tasks are routinely performed by several groups, an integrated open source SNP discovery pipeline that can be easily adapted by new groups interested in SNP marker development is currently unavailable.     

High‐intensity red light suppresses melatonin

Early studies on rodents indicated that the long‐wavelength portion of the spectrum (orange‐ and red‐appearing light) could influence circadian and neuroendocrine responses. Since then, both polychromatic and analytic action spectra in various rodent species have demonstrated that long‐wavelength light is very weak, if not entirely inactive, for regulating neurobehavioral responses. Since testing of monochromatic light wavelengths above 600 nm is uncommon, many researchers have assumed that there is little to no effect of red light on the neuroendocrine or circadian systems. The aims of the following studies were to test the efficacy of monochromatic light above 600 nm for melatonin suppression in hamsters and humans. Results in hamsters show that 640 nm monochromatic light at 1.1×10¹⁷ photons/cm² can acutely suppress pineal melatonin levels. In normal healthy humans, equal photon density exposures of 1.9×10¹⁸ photons/cm² at 460, 630, and 700 nm monochromatic light elicited a significant melatonin suppression at 460 nm and small reductions of plasma melatonin levels at 630 and 700 nm. These findings are discussed relative to the possible roles of classical visual photoreceptors and the recently discovered intrinsically photosensitive retinal ganglion cells for circadian phototransduction. That physiology, and its potential for responding to red light, has implications for domestic applications involving animal care, the lighting of typical human environments, and advanced applications such as space exploration.     

High Affinity Not in the Vicinity?

Functional interactions between the p75 neurotrophin receptor (p75NTR) and the Trk receptors were demonstrated several years ago, but their mechanistic basis remains uncertain. In this issue of Neuron, Wehrman et al. provide a three-dimensional structure of the full TrkA ectodomain complexed to NGF and examine the possibility of a ternary p75NTR-NGF-TrkA complex.     

High Functional Diversity is Related to High Nitrogen Availability in a Deciduous Forest – Evidence from a Functional Trait Approach

The current study tested the assumption that floristic and functional diversity patterns are negatively related to soil nitrogen content. We analyzed 20 plots with soil N-contents ranging from 0.63% to 1.06% in a deciduous forest near Munich (Germany). To describe species adaptation strategies to different nitrogen availabilities, we used a plant functional type (PFT) approach. Each identified PFT represents one realized adaptation strategy to the current environment. These were correlated, next to plant species richness and evenness, to soil nitrogen contents. We found that N-efficient species were typical for low soil nitrogen contents, while N-requiring species occur at high N-contents. In contrast to our initial hypotheses, floristic and functional diversity measures (number of PFTs) were positively related to nitrogen content in the soil. Every functional group has its own adaptation to the prevailing environmental conditions; in consequence, these functional groups can co-exist but do not out-compete one another. The increased number of functional groups at high N-contents leads to increased species richness. Hence, for explaining diversity patterns we need to consider species groups representing different adaptations to the current environmental conditions. Such co-existing ecological strategies may even overcome the importance of competition in their effect on biodiversity.     

High Lysine and High Tryptophan Transgenic Maize Resulting from the Reduction of Both 19- and 22-kD α-zeins

The major maize seed storage proteins, zeins, are deficient in lysine and tryptophan content, which contribute to the poor nutritional quality of corn. Whether through the identification of mutations or genetic engineering, kernels with reduced levels of zein proteins have been shown to have increased levels of lysine and tryptophan. It has been hypothesized that these increases are due to the reduction of lysine-poor zeins and a pleiotropic increase in the lysine-rich non-zein proteins. By transforming maize with constructs expressing chimeric double-stranded RNA, kernels derived from stable transgenic plants displayed significant declines in the accumulation of both 19- and 22-kD α-zeins, which resulted in higher lysine and tryptophan content than previously reported for kernels with reduced zein levels. The observation that lysine and tryptophan content is correlated with the protein levels measured in transgenic maize kernels is consistent with the hypothesis that a pleiotropic increase in non-zein proteins is contributing to an improved amino acid balance. In addition, a large increase in accumulation of free amino acids, consisting predominantly of asparagine, asparate and glutamate, was observed in the zein reduction kernels.     

High Level Expression of a Novel Family 3 Neutral β-Xylosidase from Humicola insolens Y1 with High Tolerance to D-Xylose

A novel β-xylosidase gene of glycosyl hydrolase (GH) family 3, xyl3A, was identified from the thermophilic fungus Humicola insolens Y1, which is an innocuous and non-toxic fungus that produces a wide variety of GHs. The cDNA of xyl3A, 2334 bp in length, encodes a 777-residue polypeptide containing a putative signal peptide of 19 residues. The gene fragment without the signal peptide-coding sequence was cloned and overexpressed in Pichia pastoris GS115 at a high level of 100 mg/L in 1-L Erlenmeyer flasks without fermentation optimization. Recombinant Xyl3A showed both β-xylosidase and α-arabinfuranosidase activities, but had no hydrolysis capacity towards polysaccharides. It was optimally active at pH 6.0 and 60°C with a specific activity of 11.6 U/mg. It exhibited good stability over pH 4.0–9.0 (incubated at 37°C for 1 h) and at temperatures of 60°C and below, retaining over 80% maximum activity. The enzyme had stronger tolerance to xylose than most fungal GH3 β-xylosidases with a high K_i value of 29 mM, which makes Xyl3A more efficient to produce xylose in fermentation process. Sequential combination of Xyl3A following endoxylanase Xyn11A of the same microbial source showed significant synergistic effects on the degradation of various xylans and deconstructed xylo-oligosaccharides to xylose with high efficiency. Moreover, using pNPX as both the donor and acceptor, Xyl3A exhibited a transxylosylation activity to synthesize pNPX₂. All these favorable properties suggest that Xyl3A has good potential applications in the bioconversion of hemicelluloses to biofuels.     

The “High Irradiance Responses” of plant photomorphogenesis

Plants growing in the natural environment are exposed daily to prolonged periods of high intensity irradiation. Many plant photomorphogenic responses are fully expressed only under prolonged exposures to high irradiances of light. The intensive study of these responses, the “High Irradiance Responses” (HIR) of plant photomorphogenesis, which started about 20 years ago, has been essentially directed—so far—toward the identification of the HIR photoreceptor, or photoreceptors, a problem that has not been satisfactorily and definitively solved, as yet. There is a great deal of evidence in support of the hypothesis that phytochrome, the pigment mediating the redfar red reversible plant photo-responses to low fluences of light, is involved in the photocontrol of the HIR. It seems likely that phytochrome may be the only photomorphogenic receptor responsible for the photocontrol of HIR responses brought about by irradiation at wavelengths longer than 600 nm. Phytochrome is probably also involved in the photocontrol of the HIR effects brought about by irradiation in the 350 to 500 nm region of the spectrum, but it cannot be excluded that other photochemical systems may also be involved. From a theoretical point of view, it does not seem unreasonable that the final expression of an HIR response may involve an interaction between phytochrome and other photochemical systems, with phytochrome probably playing the primary role and being responsible for the control of the activity of the other systems. Numerous “phytochrome only” interpretations (models) of the HIR have been proposed. Some of them have been developed to a fairly high degree of elaboration and have allowed the prediction of at least some of the features of the HIR. These “models,” although not rigorously and completely tested yet, seem to provide a reasonable interpretation for the HIR effects displayed under prolonged far red irradiation and for those HIR responses for which far red is the most effective spectral region. However, they do not provide a satisfactory explanation for the HIR responses for which blue is the most or the only effective spectral region, nor for the high effectiveness of white light. But, in spite of these problems, the “phytochrome only” interpretations of the HIR can be considered more satisfactory than those based on an interaction between phytochrome and other photochemical systems, especially in relation to the fact that the identity of these other photochemical systems has not been defined yet.     

High Concentration—Ethanol Fermentation of Raw Ground Corn

1-Pyrroline-5-carboxylate dehydrogenase was purified and crystallized from Bacillus sphaericus. The crystalline preparation gave a single band on polyacrylamide slab gel electrophoresis. The molecular weight of the enzyme was determined to be about 100,000 by gel filtration. The enzyme consists of two subunits which are identical in molecular weight (50,000), as judged on SDS slab gel electrophoresis. The enzyme shows an optimum pH of 6.5 to 7.0. Its activity was 8.1 times higher with NADP⁺ than with NAD ⁺, and the enzyme was stabilized by NADP⁺. The apparent Km values for l-l-pyrroline-5-carboxylate, NADP⁺ and NAD⁺ are 4.2 × 10^–5m (with NADP⁺), 9.5 × 10~⁶m and 2.5 × IO^-3 m, respectively. The enzyme reaction is irreversible. A simple method for the determination of l-ornithine involving ornithine ¿-aminotransferase and 1- pyrroline-5-carboxylate dehydrogenase from B. sphaericus was developed. A linear relationship was found between the absorbance at 340 nm and the amount of l-ornithine (50 ~ 400 nmol), and between the fluorescence and the amount of l-ornithine (0.2 ~ 10 nmol).     

Puerperal Thromboembolic Disease in “High Risk” Cases

One hundred obstetric patients were studied for evidence of puerperal thromboembolic disease. Only one case of deep vein thrombosis was detected in patients thought to be in a “high risk” category because of age or operative intervention. Clinical findings were unreliable compared with measurements of ¹²⁵I-labelled fibrinogen uptake. Doppler ultrasound flow detection proved a simple screening technique but produced no abnormal findings in this series.     

High throughput platform to explore RNA–protein interactomes

RNA binding proteins (RBPs) and RNA interaction is an emerging topic in molecular biology. Many reports showed that such interactions contribute to many cellular processes as well as disease development. Several standard in vitro and in vivo methods were developed to fulfill the needs of this RBP–RNA interaction study to explore their biological functions. However, these methods have their limitations in terms of throughput. In this review, we emphasize two important high throughput methods to studying RBP–RNA interactions, affinity purification and protein microarray. These methods have recently become robust techniques regarding their efficiency in systematically analyzing RBP–RNA interactions. Here, we provide technique overviews, strategies and applications of these methods during biological research. Although these technologies are just beginning to be explored, they will be most important methods in this study.     

High Five昆虫细胞系的致瘤性研究

目的检测High Five昆虫细胞系对BALB/c裸鼠致瘤性情况,以确保其作为疫苗生产细胞株的安全性。方法将裸鼠随机分为5组,分别为High Five基础细胞库细胞试验组、High Five最高限制代次细胞试验组、HEp-2细胞阳性对照组、CEF细胞阴性对照组和不作任何处理的空白对照组,用细胞悬液背部皮下接种裸鼠。3周和12周后对裸鼠解剖及病理组织学检查,其是否有肿瘤形成。结果阳性对照HEp-2细胞组裸鼠接种后3周注射部位形成结节,病理组织学检查为鳞状细胞癌;阴性对照CEF细胞组和High Five细胞组均无结节形成,接种后12周经解剖用病理组织学检查,均无肿瘤形成。结论基础代次和最高限制代次High Five细胞均不具有致瘤性,可安全地应用于疫苗生产。     

High plant endemism in an Indian hotspot – eastern Himalaya

A preliminary investigation in the Subansiri area of the eastern Himalaya recorded high plant endemism. As a regular exercise of field sampling of various forest types to map the biorich areas, the number of species observed was evaluated to analyze their endemic status in one of the important hotspot regions of the world. The total number of individuals, species, genera and families observed were recorded in various natural and semi-natural forest types. A total of 122 plots sampled randomly in various forest types recorded 764 plant species, of which 59 were found to be endemic. The overall species endemism is observed to be 13 per ha. These 59 species belong to 27 families and 46 genera. Fifty percent of species were from just five families, Rubiaceae, Lauraceae, Acanthaceae, Magnoliaceae and Rosaceae. Stem size class distribution of the most abundantly found endemic tree species in three primary forest types indicated a quantitative status. This study envisages the status of plant endemism carried out following a proportional stratified random sampling method for various classified vegetation cover types using satellite remote sensing data. Many primitive genera and families were recorded which are indicative of long evolutionary age and affinities of the area with respect to species endemism.     

High Intensity Exercise: A Cause of Lymphocyte Apoptosis?

Post exercise lymphocytopenia is well documented and attributed to egress of lymphocytes from the vascular compartment. Recent studies have reported exercise induced DNA damage in leukocytes and have questioned a possible link to apoptosis. Eleven subjects underwent a ramped treadmill test to exhaustion. Venous blood samples were taken before, immediately post exercise, and 24 and 48 hours after exercise. Single cell gel electrophoresis revealed evidence of single strand DNA damage in 10% of lymphocytes immediately after exercise, but not at other times. Fluorescent microscopy showed three patterns of DNA distribution, similar to those seen in apoptosis, at all times after exercise. Three subjects underwent the same exercise protocol, and lymphocytes were prepared for flow cytometry to determine apoptosis using the TUNEL method. Flow cytometry revealed lymphocyte apoptosis in 63% of lymphocytes immediately after exercise and 86.2%, 24 hours after exercise. Lymphocyte apoptosis is documented for the first time after exercise and may in part account for exercise induced lymphocytopenia and reduced immunity.     

High human disturbance decreases individual variability in skink escape behavior

Animals living around people may modify their antipredator behavior as a function of proximity to humans,and this response has profound implications for whether or not a population can coexist with humans.We asked whether inland blue-tailed skinks Emoia impar modified their individual antipredator behavior as a function of differential exposure to humans.We conducted multiple consecutive flushes and recorded 2 measures of antipredator response:flight initiation distance(FID),the distance from a threatening stimulus at which an individual flees,and distance fled,the distance an individual fled after a flush.We used a multiple model comparison approach to quantify variation in individual escape behavior across multiple approaches and to test for differences in between-individual variation among populations.We found that individuals tolerated closer approach and fled shorter distances at locations with relatively less human disturbance than at locations with medium and high human disturbance,respectively.In addition,skinks living at high human disturbance sites had less variable FIDs than at low human disturbance sites.Two theories may explain these results.Selection against less favorable phenotypes has reduced behavioral variation in urban habitats and behavioral plasticity allows individuals to flexibly adjust their behavioral patterns in response to human disturbance.These results highlight the importance of studying variation within populations,at the individual level,which may better elucidate the impact that human disturbance has on the behavioral composition of populations.