The complete mitochondrial genome of the wild silkworm moth, Actias selene

The complete mitochondrial genome (mitogenome) of Actias selene (Lepidoptera: Saturniidae) was determined to be 15,236 bp, including 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and a control region. The arrangement of 13 PCGs was similar to that of other sequenced lepidopterans. The AT skew of the mitogenome of A. selene was slightly negative, indicating a higher number of T compared to A nucleotides. The nucleotide composition of the mitogenome of A. selene was also biased toward A+T nucleotides (78.91%). All PCGs were initiated by ATN codons, except for the gene encoding cytochrome c oxidase subunit 1 (cox1), which may be initiated by the TTAG, as observed in other lepidopterans. Three genes, including cox1, cox2, and nad5, had incomplete stop codons consisting of just a T. With an exception for trnS1(AGN), all the other tRNA genes displayed a typical clover-leaf structure of mitochondrial tRNA. The A+T-rich region of the mitogenome of A. selene was 339 bp in length, and contains several features common to the Lepidopteras, including non-repetitive sequences, a conserved structure combining the motif ATAGA and an 18-bp poly-T stretch and a poly-A element upstream of trnM gene. Phylogenetic analysis showed that A. selene was close to Saturniidae.     

Recovery of phosphorous from swine wastewater through crystallization

All the phosphate rock Japan needs must be presently imported from abroad because the country has no subterranean phosphorous resources. Therefore, there is a need to accelerate the development of and establish the technologies for phosphorous recovery from waste and wastewater. Swine wastewater has a high potential for phosphorous recovery in Japan. A reactor for removing and recovering phosphorous from swine wastewater was designed with dual functions, crystallization through aeration and separation of formed struvite by settling. However, a dehydration, composting and characterization process was first needed before using sediment sludge, including struvite, on farmland, since the struvite will settle along with huge amounts of other suspended solids (organic matter). For the recovery of pure struvite, an accumulation device was designed and its efficiency examined. The device has a struvite-accumulation face made of stainless steel wire mesh (1 mm in diameter, 1 cm(2) square) to reduce its total weight. During submergence in the aeration column of the demonstration reactor, struvite cross-bridged and accumulated on the face of the device. The struvite could be scraped off easily with only a light brushing, and was found to be approximately 95% pure. Because this device is a very simple structure, it is thought to be acceptable to swine farmers.     

An inducible transgenic Cre mouse line for the study of hippocampal development and adult neurogenesis

The hippocampus is crucial for higher brain functions, such as learning, memory, and emotion. Many diseases like epilepsy and Down's syndrome are associated with abnormalities in early hippocampal development. In addition, adult dentate neurogenesis is thought to be defective in several classes of psychiatric disorders. However, the mechanisms regulating hippocampal development and adult neurogenesis remain unclear. One of the limitations to studying these processes is the scarcity of available specific mouse tools. Here, we report an inducible transgenic Cre mouse line, Frizzled 9‐CreER?, in which tamoxifen administration induces Cre recombinant. Our data show that Cre is expressed in the developing hippocampal primordium, confined to the granule cell layer at P20 and further limited to the subgranular zone in the adult dentate gyrus. Cre recombinase shows very high activity in all of these regions. Thus, this transgenic line will be a powerful tool in understanding the mechanisms of hippocampal development, adult neurogenesis, and associated diseases. genesis 49:919–926, 2011. © 2011 Wiley Periodicals, Inc.     

Metabolomic approach to optimizing and evaluating antibiotic treatment in the axenic culture of cyanobacterium Nostoc flagelliforme

The application of antibiotic treatment with assistance of metabolomic approach in axenic isolation of cyanobacterium Nostoc flagelliforme was investigated. Seven antibiotics were tested at 1–100 mg L^?1, and order of tolerance of N. flagelliforme cells was obtained as kanamycin > ampicillin, tetracycline > chloromycetin, gentamicin > spectinomycin > streptomycin. Four antibiotics were selected based on differences in antibiotic sensitivity of N. flagelliforme and associated bacteria, and their effects on N. flagelliforme cells including the changes of metabolic activity with antibiotics and the metabolic recovery after removal were assessed by a metabolomic approach based on gas chromatography–mass spectrometry combined with multivariate analysis. The results showed that antibiotic treatment had affected cell metabolism as antibiotics treated cells were metabolically distinct from control cells, but the metabolic activity would be recovered via eliminating antibiotics and the sequence of metabolic recovery time needed was spectinomycin, gentamicin > ampicillin > kanamycin. The procedures of antibiotic treatment have been accordingly optimized as a consecutive treatment starting with spectinomycin, then gentamicin, ampicillin and lastly kanamycin, and proved to be highly effective in eliminating the bacteria as examined by agar plating method and light microscope examination. Our work presented a strategy to obtain axenic culture of N. flagelliforme and provided a method for evaluating and optimizing cyanobacteria purification process through diagnosing target species cellular state.     

Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution,new validation tools,and implications for the future

As a discipline, structural biology has been transformed by the three-dimensional electron microscopy (3DEM) “Resolution Revolution” made possible by convergence of robust cryo-preservation of vitrified biological materials, sample handling systems, and measurement stages operating a liquid nitrogen temperature, improvements in electron optics that preserve phase information at the atomic level, direct electron detectors (DEDs), high-speed computing with graphics processing units, and rapid advances in data acquisition and processing software. 3DEM structure information (atomic coordinates and related metadata) are archived in the open-access Protein Data Bank (PDB), which currently holds more than 11,000 3DEM structures of proteins and nucleic acids, and their complexes with one another and small-molecule ligands (~ 6% of the archive). Underlying experimental data (3DEM density maps and related metadata) are stored in the Electron Microscopy Data Bank (EMDB), which currently holds more than 21,000 3DEM density maps. After describing the history of the PDB and the Worldwide Protein Data Bank (wwPDB) partnership, which jointly manages both the PDB and EMDB archives, this review examines the origins of the resolution revolution and analyzes its impact on structural biology viewed through the lens of PDB holdings. Six areas of focus exemplifying the impact of 3DEM across the biosciences are discussed in detail (icosahedral viruses, ribosomes, integral membrane proteins, SARS-CoV-2 spike proteins, cryogenic electron tomography, and integrative structure determination combining 3DEM with complementary biophysical measurement techniques), followed by a review of 3DEM structure validation by the wwPDB that underscores the importance of community engagement.     

西双版纳热带季节雨林风时空变化特征初步分析

利用西双版纳热带季节雨林观测铁塔不同高度的风速及风向观测资料,分析了风的年、季节和日变化特征.结果表明,林冠上风速较强,林冠下风速较弱;林内风速的日变化和垂直变化均不明显.30～50 m范围内,风速垂直变化最显著,但年变化不大;50 m以上风速年变化显著,但垂直变化稍小.干热季(3～4月)风速最大,雨季(5～10月)次之,雾凉季(11～翌年2月)最小.昼间风速大于夜间.在昼间,上午风速最小,下午次之,中午最大.受地理位置和地形影响,风向具有明显的日变化特征,主导风向昼间为偏东南风,夜间为偏西风.昼间零平面位移(d) 值上午最大,中午次之下午最小,其年变化幅度呈现下午幅度大,上午和中午幅度小的趋势.粗糙度(Z₀)昼间值呈现下午>中午>上午的趋势,且下午Z₀值显著大于其他两个时段.     

Lipids,lipid metabolism and Kaposi’s sarcoma-associated herpesvirus pathogenesis

Lipids are essential for mammalian cells to maintain many physiological functions. Emerging evidence has shown that cancer cells can develop specific alterations in lipid biosynthesis and metabolism to facilitate their survival and various malignant behaviors. To date, the precise role of cellular lipids and lipid metabolism in viral oncogenesis is still largely unclear with only a handful of literature covering this topic to implicate lipid metabolism in oncogenic virus associated pathogenesis. In this review, we focus on the role of lipid biosynthesis and metabolism in the pathogenesis of the Kaposi’s sarcoma-associated herpesvirus, a common causative factor for cancers arising in the immunocompromised settings.

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Sugar induced cell death in yeast is dependent on the rate of sugar phosphorylation as determined by Arabidopsis thaliana hexokinase

Sugars like glucose and fructose induce death of yeast cells within a few hours, in the absence of additional nutrients to support growth, while cells incubated in water remain viable for weeks. This sugar-induced cell death (SICD) by glucose and fructose required glucose or fructose phosphorylation since yeast cells deficient in hexose phosphorylation did not die. However, when hexose phosphorylation is restored by complementation with Arabidopsis thaliana hexokinase, the cells died. The affinity of A. thaliana hexokinase is about 400 times higher for glucose than for fructose, therefore, A. thaliana hexokinase was further utilized to study the role of hexose phosphorylation in SICD. The rate of SICD of hexokinase-deficient yeast cells expressing A. thaliana hexokinase was significantly slower in fructose than in glucose, indicating that SICD is determined by the rate of hexose phosphorylation. The significance of hexose phosphorylation and its role in SICD is discussed.     

荧光假单胞菌抗噬菌体菌株的选育

本实验从荧光假单胞菌（Ｐｓｅｕｄｏｍｏｎａｓｆｌｕｏｒｅｓｃｅｎｓ）ＡＳ—３菌株的不正常发酵液中分离到一种噬菌体,将其命名为ＰＦＡＳ。ＡＳ—３菌株能利用葡萄糖发酵产生Ｄ－异维生素Ｃ的前体物质２－酮基－Ｄ－葡萄糖酸。电镜观察表明ＰＦＡＳ噬菌体呈蝌蚪形,具有直径为６６ｎｍ的六角形头部及长１１７ｎｍ的尾部。通过紫外线诱变及自然选育两种途径,配合简便有效的初筛方法,经多次分离、纯化、复筛最终在摇并发酵试验中获得６株产量稳定地高于对照敏感菌的抗噬菌体菌株,可望用于生产。     

Protein Kinase LTRPK1 Influences Cold Adaptation and Microtubule Stability in Rice

Rice LTRPK1, which encodes a member of the casein kinase I family, has been reported to be involved in root development, hormone response, and metabolic processes. Here we further show that LTRPK1 participates in stress resistance by regulating cytoskeleton rearrangement and formation of cold tolerance and adaptation. Semiquantitative RT-PCR analysis revealed enhanced expression of LTRPK1 in plants subject to low-temperature stress at 4 °C, suggesting a role in low-temperature-related cell responses and signal transduction pathways. Further analysis of LTRPK1-deficient transgenic plants showed that under low-temperature treatment, the growth rate of transgenic plant primary roots, which is commonly used as an indicator for cold stress response abilities, was less inhibited than that of control plants. Moreover, damage to the plasma membrane of root cells in LTRPK1-deficient plants was greater than that of controls as measured by relative electrical conductivity (REC). The malondialdehyde (MDA) content of LTRPK1-deficient plants also increased over that of the control, indicating increased plasma membrane permeability. Further immunofluorescence localization observations indicated that microtubules of transgenic plants subject to low temperature disassembled more rapidly, whereas the control plant microtubules in most cells of the root elongation zone kept their normal habitus, which suggested that LTRPK1-deficient plants had reduced capacity to resist low-temperature stress through regulation of microtubule assembly. These results demonstrate involvement of LTRPK1 in low-temperature stress and provide new insight for rice breeding and germplasm innovation to improve crop cold tolerance.