Using enzymes to remove biofilms of bacterial isolates sampled in the food-industry

The aim of this study was to analyze the cleaning efficiency of polysaccharidases and proteolytic enzymes against biofilms of bacterial species found in food industry processing lines and to study enzyme effects on the composition of extracellular polymeric substances (EPS) and biofilm removal in a Clean-in-Place (CIP) procedure. The screening of 7 proteases and polysaccharidases for removal of biofilms of 16 bacterial species was first evaluated using a microtiter plate assay. The alkaline pH buffer removed more biofilm biomass as well as affecting a larger range of bacterial species. The two serine proteases and α-amylase were the most efficient enzymes. Proteolytic enzymes promoted biofilm removal of a larger range of bacterial species than polysaccharidases. Using three isolates derived from two bacterial species widely found in food processing lines (Pseudomonas fluorescens and the Bacillus cereus group), biofilms were developed on stainless steel slides and enzymatic solutions were used to remove the biofilms using CIP procedure. Serine proteases were more efficient in removing cells of Bacillus biofilms than polysaccharidases. However, polysaccharidases were more efficient in removing P. fluorescens biofilms than serine proteases. Solubilization of enzymes with a buffer containing surfactants, and dispersing and chelating agents enhanced the efficiency of polysaccharidases and proteases respectively in removing biofilms of Bacillus and P. fluorescens. A combination of enzymes targeting several components of EPS, surfactants, dispersing and chelating agents would be an efficient alternative to chemical cleaning agents.     

Analysis of sequence patterns proximal to the stop codons in Oryza sativa

Abstract

A comprehensive analysis of sequence patterns around the stop codons was performed, by using more than 26,000 rice full-length cDNA sequences. Here it is shown that the bias was most outstanding at the position immediately before the stop codons (?1 codon), where the AAC codon was strongly preferred among ANC codons. Compared with other positions, the codon immediately after the stop codons (+1 codon) also displayed an apparent difference, and had a strong consensus for base A at the first, C at the second, and A at the third letters, respectively. Notably, the base biases at the positions directly downstream of the stop codons, such as the +4, +5 and +6 positions, were much stronger than other positions in the 3′-UTR region, suggesting that those base positions might act as an extended stop signal in the process of protein synthesis. Examination of the relationship between sequence pattern and gene expression level, assessed by CAI values and EST counting, revealed a tendency towards bigger base biases for highly expressed genes. It could be inferred that the translation stop signal is possibly involved in many sequence recognition elements other than the stop codons; highly expressed genes should hold strong sequence consensus around the stop codons for efficient translation termination.     

黄渤海甲壳类的分类多样性

为了解黄渤海甲壳类的分类多样性特征, 我们统计了2010-2015年中国水产科学研究院黄海水产研究所调查捕获的黄渤海甲壳类(软甲纲: 十足目与口足目)物种名录。结合历史文献, 进一步系统整理得到黄渤海甲壳类物种总名录。基于这2个名录, 应用分类阶元包含指数(the inclusion index at taxonomic level, TINCL_i)、平均分类差异指数(average taxonomic distinctness index, Δ⁺)和分类差异变异指数(variation in taxonomic distinctness index, Λ⁺)研究了其分类多样性特征。结果显示: 2010-2015年调查名录中, 甲壳类共93种, 隶属于2目39科66属, 其中10种为新分布种; 对虾科、藻虾科、长臂虾科、梭子蟹科和弓蟹科的物种数最多, 合计占总物种数的38.71%; TINCL_i分别为1.41种/属和2.38种/科; Δ⁺和Λ⁺分别为50.25和35.20。总名录中, 甲壳类共228种, 隶属于2目53科123属, 其中藻虾科、豆蟹科、对虾科、弓蟹科和鼓虾科的物种数最多, 合计占总物种数的30.70%; TINCL_i分别为1.85种/属和4.30种/科, Δ⁺和Λ⁺分别为50.18和30.87。对虾科的相对丰富度指数(the relative richness index, R_r)最高(100), 其次是梭子蟹科(71.43)和长臂虾科(62.50), 豆蟹科最低(6.25)。黄渤海甲壳类的平均分类差异指数(Δ⁺)明显小于鱼类(P < 0.05)。2010-2015年调查的Δ⁺计算值高于理论值, 且在理论值的95%置信区间内, 说明黄渤海甲壳类群落正处在中等程度的干扰中。     

生物多样性相关传统知识调查与评估: 以澜沧与康定两县域为例

本研究依据《县域生物多样性相关传统知识调查与评估技术规定》, 调查评估了云南省澜沧县和四川省康定市两县域生物多样性相关传统知识的分布数量与特征, 分析了传统知识保护与传承状况, 识别了主要受威胁因素和保护空缺, 旨在为我国传统知识保护和民族地区实施传统知识获取与惠益分享制度提供科学依据, 推动《生物多样性公约》与《名古屋议定书》等国际公约的履行。研究结果如下: 分别调查编目澜沧县、康定市的生物多样性相关传统知识145项、98项; 这些传统知识具有明显的地区气候与自然环境特征、生产生活实践特征、传统文化特征和地区社会经济特征; 相关部门在传统知识保护管理方面做出了积极努力, 同时包括习惯法、传统节庆等传统文化和包括祭祀、神山、神林等宗教方式在内的地方社区行动在传统知识保护与传承方面也发挥了重要作用; 生物多样性相关传统知识、创新和做法已被广泛应用于地方社区脱贫攻坚和产业发展; 传统知识保护立法仍不健全、受到威胁、保护意识薄弱及承载传统知识的生物资源减少是制约传统知识保护传承的主要因素。两县域生物多样性相关传统知识丰富, 并且地方社区有效参与了生物多样性相关传统知识的保护与可持续利用。今后应建立传统知识获取与惠益分享国家制度; 加强宣传教育, 提升保护传承意识; 因地制宜开展传统知识保护; 推动传统知识相关生物资源的保护与可持续利用。     

Structural and Dynamic Properties of Allergen and Non-Allergen Forms of Tropomyosin

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Use of inexpensive pressure transducers for measuring water levels in wells

Frequent measurement of below ground water levels at multiple locations is an important component of many wetland ecosystem studies. These measurements, however, are usually time consuming, labor intensive, and expensive. This paper describes a water-level sensor that is inexpensive and easy to construct. The sensor is placed below the expected low water level in a shallow well and, when connected to a datalogger, uses a pressure transducer to detect groundwater or surface water elevations. Details of pressure transducer theory, sensor construction, calibration, and examples of field installations are presented. Although the transducers must be individually calibrated, the sensors have a linear response to changing water levels (r ² .999). Measurement errors resulting from temperature fluctuations are shown to be about 4 cm over a 35°C temperature range, but are minimal when the sensors are installed in groundwater wells where temperatures are less variable. Greater accuracy may be obtained by incorporating water temperature data into the initial calibration (0.14 cm error over a 35C temperature range). Examples of the utility of these sensors in studies of groundwater/surface water interactions and the effects of water level fluctuations on tree growth are provided.     

The periodic change in adenosine 3′,5′-monophosphate concentration in sea-urchin eggs

The level of adenosine 3′,5′-monophosphate (cyclic AMP) in the eggs of the sea urchin, Anthocidaris crassispina, was found to change periodically after fertilization. The minimum and maximum levels of cyclic AMP were 1.0·10^?7 M and 1.5·10^?6 M, respectively. The activity of adenylate cyclase in a 105 000 × g precipitate reached a plateau at 20 min after fertilization and stayed constant for at least 2 h. It was also found that 1.0 mM CaCl₂ increased the activity of adenylate cyclase in the same precipitate from unfertilized eggs. In contrast, phosphodiesterase activity changed periodically and correlated with cyclic AMP levels in the eggs. Up to a concentration of 1.5·10^?6 M cyclic AMP, phosphodiesterase activity was low, but it became activated when the level of cyclic AMP rose beyond this level. These results indicate that the change in the intracellular level of cyclic AMP is regulated mainly by the change in phosphodiesterase activity.     

Diet and temperature modify the relationship between energy use and ATP production to influence behavior in zebrafish (Danio rerio)

Food availability and temperature influence energetics of animals and can alter behavioral responses such as foraging and spontaneous activity. Food availability, however, is not necessarily a good indicator of energy (ATP) available for cellular processes. The efficiency of energy transduction from food‐derived substrate to ATP in mitochondria can change with environmental context. Our aim was to determine whether the interaction between food availability and temperature affects mitochondrial efficiency and behavior in zebrafish (Danio rerio). We conducted a fully factorial experiment to test the effects of feeding frequency, acclimation temperature (three weeks to 18 or 28°C), and acute test temperature (18 and 28°C) on whole‐animal oxygen consumption, mitochondrial bioenergetics and efficiency (ADP consumed per oxygen atom; P:O ratio), and behavior (boldness and exploration). We show that infrequently fed (once per day on four days per week) zebrafish have greater mitochondrial efficiency than frequently fed (three times per day on five days per week) animals, particularly when warm‐acclimated. The interaction between temperature and feeding frequency influenced exploration of a novel environment, but not boldness. Both resting rate of producing ATP and scope for increasing it were positively correlated with time spent exploring and distance moved in standardized trials. In contrast, behavior was not associated with whole‐animal aerobic (oxygen consumption) scope, but exploration was positively correlated with resting oxygen consumption rates. We highlight the importance of variation in both metabolic (oxygen consumption) rate and efficiency of producing ATP in determining animal performance and behavior. Oxygen consumption represents energy use, and P:O ratio is a variable that determines how much of that energy is allocated to ATP production. Our results emphasize the need to integrate whole‐animal responses with subcellular traits to evaluate the impact of environmental conditions on behavior and movement.