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Evolution of machine learning in biosciences: A bibliometric network analysis 生物科学中机器学习的进化:文献计量网络分析
Pub Date : 2022-07-20 DOI: 10.7324/jabb.2022.100505
A. Vanaja, V. Yella
Machine learning, a rapidly evolving field of data analysis, has now become an integral part of life science research. It has been widely utilized for exploring the information encoded by the genome and beyond the genome. In this study, we surveyed the trends of scientific actors and the conceptual structure of machine learning implementation in biomedical research through the published literature retrieved from the PubMed search engine. A longitudinal cohort bibliographic coupling was executed by employing the VOS viewer tool for 4-time periods, 1964–2010, 2011–2015, 2016–2018, and 2019–2020. Scientific actors of machine learning research include 42,629 unique authors, 27,364 organizations with a mean collaboration index of 3.9. Coword analysis revealed that the conceptual framework of machine learning applications in life sciences moved from simple pattern searching to omic science and medical imaging analytic approaches and from Bayes’ theorem to deep learning algorithms. It is observed that presently machine learning is extensively utilized in investigating emerging situations like coronavirus disease. To epitomize, researchers capitalized on advancements in machine learning tools and high-throughput technologies to delve into the intricate and evolving concepts of biology and medicine. © 2022 Vanaja and Yella.
机器学习是一个快速发展的数据分析领域,现在已经成为生命科学研究的一个组成部分。它已被广泛应用于探索基因组编码的信息和基因组之外的信息。在这项研究中,我们通过从PubMed搜索引擎检索的已发表文献,调查了生物医学研究中科学参与者的趋势和机器学习实施的概念结构。采用VOS查看工具对1964-2010年、2011-2015年、2016-2018年和2019-2020年4个时间段进行纵向队列书目耦合。机器学习研究的科学参与者包括42,629位独立作者,27,364个组织,平均合作指数为3.9。Coword分析表明,机器学习在生命科学领域应用的概念框架从简单的模式搜索转向了基因组科学和医学成像分析方法,从贝叶斯定理转向了深度学习算法。据观察,目前机器学习被广泛用于调查新冠肺炎等新情况。研究人员利用机器学习工具和高通量技术的进步,深入研究复杂而不断发展的生物学和医学概念。©2022 Vanaja和Yella。
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引用次数: 0
Abiotic stress signaling in plants and transgenic technology as a triumph: A review 植物中的非生物胁迫信号和转基因技术的成功:综述
Pub Date : 2022-07-20 DOI: 10.7324/jabb.2022.100501
Seetha Babu Manepalli, S. Tomar, Dinkar Gaikwad, S. Maitra
The plants are exposed seasonally and continuously to various environmental and biodiversity stresses that inhibit and affect their life processes from seedling to harvest stage. Several irregularities are seen in light intensity, temperature, mineral and water availability, etc. These changes keep on challenges the plant to grow and reproduce itself and produce several environmental signals. To receive these signals, the plants themselves develop a signaling network with several receptors such as phytohormones, G-protein-coupled receptors, kinases, and hormone receptors. Signal transduction produces a cellular response in plants which initiates the physiological and developmental responses. This article reveals a keen and in-depth analysis of several mechanisms and perceptions of signal transduction during exposure to several kinds of abiotic stresses in plants, along with a generic pathway of signaling in plants. Plant abiotic stress often plays a pivotal role in causing losses through salinity, heat, cold, drought, etc. To understand and overcome these problems through conventional breeding, which was mainly dependent on genetic variations, several studies are going on model plants such as Arabidopsis, rice, and Brachypodium ; the accessibility of sources for these genomes is in the processing stage in wheat. On the other hand, the advancements in genome editing opened the doors for scientists to incorporate the desired trait in a particular plant species. The emerging developments in the second-generation genome editing technologies like CRISPR/cas9 paved the path for plant biologists to develop a trait more efficiently and rapidly, unlike conventional breeding methods. This review plots the importance of signaling during abiotic stress and transgene technology to prevail over abiotic stress in plants by ingesting desired traits in a plant.
植物季节性地持续暴露于各种环境和生物多样性胁迫下,这些胁迫抑制和影响了它们从幼苗到收获阶段的生命过程。在光照强度、温度、矿物和水的可用性等方面存在一些不规则性。这些变化不断挑战植物的生长和繁殖,并产生多种环境信号。为了接收这些信号,植物自身发展了一个由多种受体组成的信号网络,如植物激素、g蛋白偶联受体、激酶和激素受体。信号转导在植物中产生细胞反应,启动生理和发育反应。本文深入分析了植物在几种非生物胁迫下信号转导的机制和感知,以及植物信号转导的一般途径。植物的非生物胁迫往往在盐、热、冷、旱等造成的损失中起关键作用。为了通过主要依赖遗传变异的传统育种来了解和克服这些问题,人们正在对拟南芥、水稻和短柄茅等模式植物进行研究;这些基因组源的可及性在小麦中处于加工阶段。另一方面,基因组编辑的进步为科学家们在特定植物物种中加入所需的特性打开了大门。与传统育种方法不同,CRISPR/cas9等第二代基因组编辑技术的新兴发展为植物生物学家更有效、更快速地开发性状铺平了道路。本文综述了在非生物胁迫和转基因技术中信号的重要性,通过摄取植物所需的性状来战胜植物的非生物胁迫。
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引用次数: 2
Purification and physicochemical characterization of exopolysaccharide produced by a novel brown-rot fungus Fomitopsis meliae AGDP-2 一种新型褐腐菌meliae AGDP-2产胞外多糖的纯化及理化性质研究
Pub Date : 2022-07-20 DOI: 10.7324/jabb.2022.100520
Darshankumar Prajapati, A. Bhatt, A. Gupte
The present study represents the purification and characterization of exopolysaccharide produced by Fomitopsis meliae AGDP-2. The water-soluble EPS obtained was purified using Sephadex G-75 column and characterized for its physical and biochemical properties. HPTLC and HPLC analysis indicated that EPS is composed of glucose and mannose residues. Many functional groups such as carboxyl, amide, hydroxyl, and glycosidic linkages were detected by FT-IR spectroscopy. Furthermore, glucose and mannose were detected from NMR spectra with α -(1→6) linkages, thereby signifying the heteropolymeric nature. Using GPC, molecular weight of EPS was estimated to be 2.48 × 10 6 Daltons. The SEM-EDX and AFM analysis revealed that EPS is compact and possesses cube-like structural units and nano-cracks with elemental composition of O, K, Na, Mg, S, Cl, and Ca. While studying its rheological behavior, EPS was found to be pseudoplastic in nature. As the physical properties and biochemical composition influence the bioactivities; the purified EPS from F. meliae AGDP-2 can be further evaluated for various bioactive properties such as antioxidant, anti-cancer, anti-inflammatory, antidiabetic, antibacterial, anti- biofilm, as well as antiviral properties. the present study was conducted to purify and characterize the EPS produced under submerged cultivation of Fomitopsis meliae AGDP-2. The characterization of EPS including monosaccharide composition (high-performance thin-layer chromatography [HPTLC] and HPLC), molecular weight (GPC), rheological behavior, surface morphology (SEM and AFM), as well as IR and nuclear magnetic resonance (NMR) spectra was thoroughly studied.
本研究对meliae Fomitopsis AGDP-2产生的胞外多糖进行了纯化和鉴定。所得水溶性EPS采用Sephadex G-75柱进行纯化,并对其物理生化性质进行表征。HPLC和HPTLC分析表明,EPS由葡萄糖和甘露糖残基组成。许多官能团,如羧基,酰胺,羟基和糖苷键被检测到FT-IR光谱。此外,葡萄糖和甘露糖在核磁共振光谱中被检测到具有α -(1→6)键,从而表明其异聚性。用GPC法测定EPS的分子量为2.48 × 106道尔顿。SEM-EDX和AFM分析表明,EPS结构紧凑,具有立方体结构单元和纳米裂纹,元素组成为O, K, Na, Mg, S, Cl和Ca。在研究其流变行为时,发现EPS本质上是假塑性的。由于物理性质和生化成分影响生物活性;从meliae AGDP-2中纯化的EPS可以进一步评价其抗氧化、抗癌、抗炎、抗糖尿病、抗菌、抗生物膜和抗病毒等生物活性。本研究对深层培养的meliae Fomitopsis AGDP-2产生的EPS进行了纯化和表征。对EPS的单糖组成(高性能薄层色谱[HPTLC]和高效液相色谱])、分子量(GPC)、流变行为、表面形貌(SEM和AFM)以及IR和核磁共振(NMR)谱进行了深入的表征。
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引用次数: 2
An epidemiological outbreak of scrub typhus caused by Orientia tsutsugamushi – A comprehensive review 一起恙虫病东方体引起的恙虫病流行病学暴发——综合回顾
Pub Date : 2022-07-20 DOI: 10.7324/jabb.2022.100509
Subhasmita Panda, S. Swain, Rachita Sarangi
Scrub typhus is a vector-borne infectious disease caused by Orientia tsutsugamushi a gram-negative bacterium belonging to order Rickettsiales, endemic in Asia–Pacific region known as “Tsutsugamushi triangle.” This review aims to describe the seasonal outbreak of scrub typhus endemic in many places of India and in a global map which will be systematically analyze the current situation. The review focused on the diagnosis methods used to detect the disease also on the severity and complications during the clinical presentation. The data of scrub typhus outbreaks in different countries from 2000 to 2020 were retrieved from various sources. Gradually, increased case load and incidence rates have been recorded. The majority of the reported cases were from the North-East region of India during the cooler months. In Odisha, very few case reports were found, mostly from the capital, Bhubaneswar, but other areas have no records as it is still considered as an underreported disease. We concluded that India has experienced a large increase in scrub typhus incidence and documented an expansion in geographic distribution throughout the country. Therefore, people in rural areas need to be more conscious and aware to prevent the spread. Although no vaccine is available, several other preventive measures can be taken.
恙虫病是一种由恙虫病东方体引起的媒介传播传染病,恙虫病东方体是一种革兰氏阴性细菌,属于立克次体目,在亚太地区流行,被称为“恙虫病三角”。这篇综述的目的是描述印度许多地方地方性丛林斑疹伤寒的季节性暴发,并绘制全球地图,系统地分析目前的情况。本文综述了用于检测疾病的诊断方法,以及临床表现时的严重程度和并发症。从各种来源检索了2000年至2020年不同国家恙虫病暴发的数据。逐渐记录到病例量和发病率的增加。大多数报告的病例发生在印度东北部较冷的月份。在奥里萨邦,发现的病例报告很少,主要来自首都布巴内斯瓦尔,但其他地区没有记录,因为它仍然被认为是一种漏报的疾病。我们的结论是,印度经历了丛林斑疹伤寒发病率的大幅增加,并在全国范围内记录了地理分布的扩大。因此,农村地区的人们需要更多的意识和意识来防止传播。虽然没有可用的疫苗,但可以采取其他几种预防措施。
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引用次数: 2
Isolation and characterization of starch degrading bacteria from disparate soil samples 不同土壤样品中淀粉降解菌的分离与特性研究
Pub Date : 2022-07-20 DOI: 10.7324/jabb.2022.100524
V. Srivathsan, Mahima Bhandari, P. Swaminathan
Amylases are starch degrading enzymes. These enzymes play a pivotal role in the biotechnology industries in food, fermentation, textiles, and paper production. Many industries lack local amylase supply, so the demand for amylase is often high. The study focuses on the screening and isolation of amylase producing bacteria from disparate samples of soil. The promising hydrolytic strains of bacteria from the collected samples were characterized using enzyme kinetics and further investigation is carried out to characterize the amylase enzyme produced by optimization of pH and temperature. The shortlisted isolate was identified using 16s rRNA sequencing. This study is an initial result of an exploration where soil is a source of industrially important amylase producing bacterial strains.
淀粉酶是淀粉降解酶。这些酶在食品、发酵、纺织和造纸等生物技术产业中发挥着关键作用。许多行业缺乏当地的淀粉酶供应,因此对淀粉酶的需求往往很高。本研究的重点是从不同土壤样品中筛选和分离产生淀粉酶的细菌。利用酶动力学对所收集的样品中有潜力的水解菌株进行了表征,并对pH和温度优化产生的淀粉酶进行了进一步的表征。通过16s rRNA测序对候选分离物进行鉴定。这项研究是一项探索的初步结果,其中土壤是工业上重要的淀粉酶生产菌株的来源。
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引用次数: 1
Evaluation of plant growth-promoting activities of endophytic bacteria of Musa acuminata and their characterization 荆芥内生细菌促植物生长活性评价及其特性研究
Pub Date : 2022-07-20 DOI: 10.7324/jabb.2022.100511
Shilpi Singh, Kamlesh Choure, P. Rai, S. Gour, V. Agnihotri
The study was conducted with an aim of isolating and identifying bacterial endophytes associated with Musa acuminata and assessing their plant growth-promoting properties. Endophytic bacteria show mutualistic relationship with plants and help them in alleviating several biotic and abiotic stress without showing any apparent negative effect to the host plant. In the present study, explants samples from different parts of M. acuminata plant such as root, stem, and leaves were collected and cultured. A total of 33 bacterial isolates were obtained and screened for their biotechnological potential for promoting plant growth. From which, 19 isolates were selected for further analysis based on their in vitro plant growth-promoting activities that include indole-3-acetic acid production, phosphate solubilization, nitrogen fixation, ammonia production, hydrogen cyanide (HCN) production, and siderophore production. In addition, these isolates also evaluated for the antagonist activity against Fusarium oxysporum and Macrophomina phaseolina. Among them, five isolates were sequenced, on the basis of 16S rRNA gene sequencing homology of the representative strains was identified EMS1 and EMS4 as Bacillus cereus , EMS13, 14, and 18 as Enterobacter cloacae, and EMS16 as Enterobacter hormaechei. Phylogenetic tree indicated evolutionary relationship of these bacteria to their closely related species. The result of this study demonstrated that based on growth-promoting competencies, all isolated strains have ability that influence the growth of host plants and have potential to be used as effective growth promoting bioinoculant for M. acuminata .
本研究的目的是分离和鉴定与尖锐木有关的细菌内生菌,并评估其促进植物生长的特性。内生细菌与植物表现出共生关系,帮助植物缓解多种生物和非生物胁迫,而对寄主植物没有明显的负面影响。本研究从荆芥的根、茎、叶等不同部位采集外植体进行培养。共分离得到33株细菌,并对其促进植物生长的生物技术潜力进行了筛选。从中选择了19株菌株,根据其体外植物生长促进活性进行进一步分析,这些活性包括吲哚-3-乙酸的产生、磷酸盐的溶解、固氮、氨的产生、氰化氢(HCN)的产生和铁载体的产生。此外,还对分离菌株对尖孢镰刀菌和菜绿大霉的拮抗活性进行了评价。其中,对5株菌株进行测序,根据代表性菌株的16S rRNA基因测序同源性,确定EMS1和EMS4为蜡样芽孢杆菌,EMS13、14和18为阴沟肠杆菌,EMS16为贺氏肠杆菌。系统发育树显示了这些细菌与近缘种的进化关系。本研究结果表明,基于促生长能力,所有分离菌株都具有影响寄主植物生长的能力,有潜力作为有效的促生长生物接种剂。
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引用次数: 2
Bioremediation— sustainable tool for diverse contaminants management: Current scenario and future aspects 生物修复-各种污染物管理的可持续工具:目前的情况和未来的方面
Pub Date : 2022-06-20 DOI: 10.7324/jabb.2022.10s205
Manali Singh, K. Jayant, Anshi Mehra, Shivani Bhutani, T. Kaur, Divjot Kour, D. Suyal, Sangram Singh, A. Rai, Ajar Nath Yadav
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引用次数: 1
Extraction and quantification of acrylic acid from acrylamidase-catalyzed reaction produced by Bacillus tequilensis 龙舌兰芽孢杆菌丙烯酰胺酶催化反应中丙烯酸的提取与定量
Pub Date : 2022-06-20 DOI: 10.7324/jabb.2022.10s208
R. Prabha, V. Nigam
The reduction of non-renewable material has raised significant concerns for several years over the sustainable production of organic acids through bio-based methods in the world. One such way to overcome this problem is to use reactive extractants, in which appropriate extractants are employed to recover various organic and inorganic acids. The extraction of acrylic acid by solvent extraction is an illustration of this technique. The current study focuses on the synthesis of acrylic acid from acrylamidase produced by Bacillus tequilensis , succeeded by acid extraction from the amidase-catalyzed reaction by a solvent technique. Among the various solvents, ethyl acetate (2:1, v/v) was established as the most appropriate solvent for the extraction. Exactly 65 mg of raw acrylic acid was recovered from 20 ml of the amidase-catalyzed reaction. Various analytical methods such as thin layer chromatography, fourier transform infrared spectroscopy, high-performance liquid chromatography (HPLC), and mass spectrophotometry were accomplished for the identification, validation, and quantification of the extracted acrylic acid. The m / z value of acrylic acid obtained in the extracted product was 73.18, which was similar to the standard acrylic acid. From HPLC, almost 34% of bioconversion was quantified (3.4 mM) from 10 mM of acrylamide consumed. The extracted acrylic acid can be further exploited as chemical intermediates and pharmaceuticals in the future.
近年来,不可再生材料的减少引起了世界各国对通过生物基方法可持续生产有机酸的重大关注。克服这一问题的一种方法是使用活性萃取剂,其中使用适当的萃取剂来回收各种有机酸和无机酸。溶剂萃取法提取丙烯酸是该技术的一个实例。本研究以龙舌兰芽孢杆菌产生的丙烯酰胺酶为原料,采用溶剂法对酰胺酶催化反应进行酸萃取,合成丙烯酸。在各种溶剂中,确定乙酸乙酯(2:1,v/v)为最合适的萃取溶剂。从20毫升的酰胺酶催化反应中回收了65毫克的原料丙烯酸。采用薄层色谱法、傅里叶变换红外光谱法、高效液相色谱法、质谱法等多种分析方法对提取的丙烯酸进行鉴定、验证和定量。提取产物中丙烯酸的m / z值为73.18,与标准丙烯酸的m / z值相近。通过高效液相色谱法,从消耗的10毫米丙烯酰胺中,几乎量化了34%的生物转化(3.4毫米)。提取的丙烯酸在未来可进一步开发为化工中间体和医药。
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引用次数: 0
Bioremediation and Waste Management for Environmental Sustainability 促进环境可持续发展的生物修复和废物管理
Pub Date : 2022-06-20 DOI: 10.7324/jabb.2022.10s201
Ajar Nath Yadav, D. Suyal, Divjot Kour, V. Rajput, A. Rastegari, Joginder Singh
gricultural practices, industrial manufacturing, and lifestyle of human beings have raised the accumulation of hazardous compounds into the surrounding. It has drastically increased health issues and environmental concerns. Therefore, there is an urgent need for eco-friendly approaches to solving these multiple issues at a time. Contrary to the harmful chemical methods, bioremediation has emerged as an eco-friendly substitute for sustainable development. Bioremediation utilizes living microbiomes for cleaning environment and their sustainability. As advancement in science and technology, researchers have developed various bioremediation techniques but because of nature and type of pollutant, there is no single ‘silver bullet’ which can be applied to restore the polluted environment. The ever-increasing population and our reckless acts are turning the Earth into a huge garbage dump. The indiscriminate exploitation of resources making this condition worsen. Moreover, it is a major cause of climatic irregularities, environmental destructions, biodiversity shrinking, disease outbreaks, and agricultural issues. The present waste management efforts are proving insufficient to handle this situation.
农业生产、工业生产和人类的生活方式增加了有害化合物在周围环境中的积累。它大大增加了健康问题和环境问题。因此,迫切需要采用生态友好的方法来同时解决这些多重问题。与有害的化学方法相反,生物修复已成为可持续发展的环保替代品。生物修复利用活的微生物群来清洁环境及其可持续性。随着科学技术的进步,研究人员开发了各种生物修复技术,但由于污染物的性质和类型,没有单一的“银弹”可以用于恢复被污染的环境。不断增长的人口和我们鲁莽的行为正在把地球变成一个巨大的垃圾场。不分青红皂白地开发资源使这种情况更加恶化。此外,它也是造成气候异常、环境破坏、生物多样性减少、疾病爆发和农业问题的主要原因。目前的废物管理工作不足以处理这种情况。
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引用次数: 5
Ex-situ biofilm mediated approach for bioremediation of selected heavy metals in wastewater of textile industry 脱位生物膜介导法处理纺织废水中重金属
Pub Date : 2022-06-20 DOI: 10.7324/jabb.2022.10s209
Anu Kumar, S. Shivani, B. Krishan, M. Samtiya, T. Dhewa
Industrialization plays a major role in strengthening the economy of any country. However, these industries directly or indirectly affect the environment. Industrial wastewater discharge has been reported with certain heavy metals such as chromium, lead, cobalt, and others which are a potential hazard to the water bodies and humans as well. Biofilm is an applied method in the fields of bioremediation for reliving this emerging problem and in the efficient removal of heavy metals from wastewater. Biofilms of Escherichia coli and petroleum soil isolated microorganisms ( PSIM ) were developed at the V bottom of 96 well microtiter plate. The contaminated water sample was collected from the textile industry, Solan, Himachal Pradesh, India. The biofilms were incubated with the industrial water tested for heavy metals assuming the microbes have the potential to assimilate the heavy metals up to 5 mg/mL of concentration. After the incubation for 1–2 weeks, the microorganisms were able to reduce the level of heavy metals present in the samples which was conveyed by biomass comparison of microorganisms in the successive intervals of time. 0.74 × 10 10 cells/mL and 0.77 × 10 10 cell/mL of E. coli and PSIM biofilms were able to tolerate the metal toxicity on incubation for 2 weeks at the highest concentration due to the functional group present extracellular polymeric substance which forms complexes with heavy metals. This leads to the fact that these biofilms have assimilated the heavy metals and are potent for the removal of heavy metals from industrial wastewater.
工业化在加强任何国家的经济方面都起着重要作用。然而,这些行业直接或间接地影响着环境。据报道,工业废水排放中含有某些重金属,如铬、铅、钴等,对水体和人类都有潜在的危害。生物膜是解决这一新兴问题和有效去除废水中重金属的一种生物修复方法。在96孔微滴板的V底培养大肠杆菌和石油土壤分离微生物(PSIM)的生物膜。受污染的水样取自印度喜马偕尔邦索兰的纺织业。生物膜与重金属测试的工业用水孵育,假设微生物有可能吸收浓度高达5毫克/毫升的重金属。经过1-2周的培养,微生物能够降低样品中存在的重金属水平,这是通过微生物在连续时间间隔内的生物量比较来传递的。0.74 × 10 10细胞/mL和0.77 × 10 10细胞/mL的大肠杆菌和PSIM生物膜在培养2周后,由于功能基团存在与重金属形成络合物的胞外聚合物物质,在最高浓度下能够耐受金属毒性。这导致了这些生物膜已经吸收了重金属,并且对于去除工业废水中的重金属是有效的。
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引用次数: 0
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Journal of Applied Biology & Biotechnology
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