Investigating the molecular mechanisms of learning and memory using Caenorhabditis elegans

Learning is an essential biological process for survival since it facilitates behavioural plasticity in response to environmental changes. This process is mediated by a wide variety of genes, mostly expressed in the nervous system. Many studies have extensively explored the molecular and cellular mechanisms underlying learning and memory. This review will focus on the advances gained through the study of the nematode Caenorhabditis elegans. C. elegans provides an excellent system to study learning because of its genetic tractability, in addition to its invariant, compact nervous system (~300 neurons) that is well-characterised at the structural level. Importantly, despite its compact nature, the nematode nervous system possesses a high level of conservation with mammalian systems. These features allow the study of genes within specific sensory-, inter- and motor neurons, facilitating the interrogation of signalling pathways that mediate learning via defined neural circuits. This review will detail how learning and memory can be studied in C. elegans through behavioural paradigms that target distinct sensory modalities. We will also summarise recent studies describing mechanisms through which key molecular and cellular pathways are proposed to affect associative and non-associative forms of learning.

     

高效表达淀粉酶Bacillus koreensis的培养基响应面优化

为降低烟叶中的淀粉含量,提高烟叶的可用性,从云南马龙C3F-2014烟叶表面筛选出一株高产淀粉酶的细菌,经16sRNA测序鉴定为 Bacillus koreensis 。本研究利用响应面法优化 Bacillus koreensis 的培养基提高了其表达淀粉酶的产量。首先,单因素优化试验表明培养基的最优碳源、氮源和金属离子分别为淀粉、蛋白胨和Ca2+,培养条件单因素试验表明 Bacillus koreensis 最适初始pH、最适温度和最适接种量分别为pH8.0、37 ℃和3%。利用Box-Behnken中心组合设计对可溶性淀粉、蛋白胨、Ca2+设计三因素三水平实验,通过响应面回归分析,得到模型预测的最优培养基条件。在18.74 g/L可溶性淀粉,21.56 g/L蛋白胨,0.52 g/L CaCl2的培养基条件下 Bacillus koreensis 产淀粉酶最高。验证试验得到的淀粉酶活力达到959.39±22.34 U/mL,与模型的预测值相近,比未优化前提高了69.76%。本研究结果为烟草天然源淀粉酶处理烟叶,提高烟叶品质的工业化应用提供了基础。     

Genome Sequence of Weissella cibaria KACC 11862

Weissella cibaria KACC 11862 is a Gram-positive, heterofermentative, Leuconostoc-like lactic acid bacterium that is widely distributed in Korean traditional foods such as kimchi. Here we report the draft genome sequence of the type strain, W. cibaria KACC 11862 (1,599 known genes, 80 RNA genes), which consists of 72 large contigs (>100 bp in size).     

Pseudomonas koreensis promotes tomato growth and shows potential to induce stress tolerance via auxin and polyphenol‐related pathways

Plant and Soil - Pseudomonas koreensis, a subgroup of the P. fluorescens complex, is a potential plant growth-promoting rhizobacterium. This study explored the mechanisms of plant growth promotion...     

Complete genome sequence of Kangiella koreensis type strain (SW-125)

Kangiella koreensis (Yoon et al. 2004) is the type species of the genus and is of phylogenetic interest because of the very isolated location of the genus Kangiella in the gammaproteobacterial order Oceanospirillales. K. koreensis SW-125(T) is a Gram-negative, non-motile, non-spore-forming bacterium isolated from tidal flat sediments at Daepo Beach, Yellow Sea, Korea. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first completed genome sequence from the genus Kangiella and only the fourth genome from the order Oceanospirillales. This 2,852,073 bp long single replicon genome with its 2647 protein-coding and 48 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Fe(III)-enhanced anaerobic transformation of 2,4-dichlorophenoxyacetic acid by an iron-reducing bacterium Comamonas koreensis CY01

This work studied the ability of Comamonas koreensis CY01 to reduce Fe(III) (hydr)oxides by coupling the oxidation of electron donors and the enhanced biodegradation of 2,4-dichlorophenoxyacetic acid (2,4-D) by the presence of Fe(III) (hydr)oxides. The experimental results suggested that strain CY01 can utilize ferrihydrite, goethite, lepidocrocite or hematite as the terminal electron acceptor and citrate, glycerol, glucose or sucrose as the electron donor. Strain CY01 could transform 2,4-D to 4-chlorophenol through reductive side-chain removal and dechlorination. Under the anaerobic conditions, Fe(III) reduction and 2,4-D biodegradation by strain CY01 occurred simultaneously. The presence of Fe(III) (hydr)oxides would significantly enhance 2,4-D biodegradation, probably due to the fact that the reactive mineral-bound Fe(II) species generated from Fe(III) reduction can abiotically reduce 2,4-D. This is the first report of a strain of C. koreensis capable of reducing Fe(III) (hydr)oxides and 2,4-D, which extends the diversity of iron-reducing bacteria associated with dechlorination.     

粉拟青霉种内nrDNA ITS分析

通过对20株粉拟青霉(Paecilomyces farinosus)ITS1-5．8S-ITS2(rDNA)区域序列测定,确定了粉拟青霉ITS序列,而韩国学者测定的粉拟青霉ITS序列应为细脚拟青霉(P．tenuipes)的序列。序列比较发现,韩国2株未定名的拟青霉(Paecilomyces spp．)菌株(KACC40219、KACC40221)应为粉拟青霉。基于本研究构建的邻接树推断,粉拟青霉的有性型可能是一种虫草。粉拟青霉的起源应为单源的。不同的粉拟青霉菌株的ITS序列具有多态性,源于同一地区的菌株的ITS变异也较大。ITS序列的证据表明,粉拟青霉菌株间的差异与地理来源及寄主均无相关性。     

Deinococcus swuensis sp. nov., a gamma-radiation-resistant bacterium isolated from soil

Strain DY59^T, a Gram-positive non-motile bacterium, was isolated from soil in South Korea, and was characterized to determine its taxonomic position. Phylogenetic analysis based on the 16S rRNA gene sequence of strain DY59^T revealed that the strain DY59^T belonged to the family Deinococcaceae in the class Deinococci. The highest degree of sequence similarities of strain DY59^T were found with Deinococcus radiopugnans KACC 11999^T (99.0%), Deinococcus marmoris KACC 12218^T (97.9%), Deinococcus saxicola KACC 12240^T (97.0%), Deinococcus aerolatus KACC 12745^T (96.2%), and Deinococcus frigens KACC 12220^T (96.1%). Chemotaxonomic data revealed that the predominant fatty acids were iso-C_15:0 (19.0%), C_16:1 ω7c (17.7%), C_15:1 ω6c (12.6%), iso-C_17:0 (10.3%), and iso-C_17:1 ω9c (10.3%). A complex polar lipid profile consisted of a major unknown phosphoglycolipid. The predominant respiratory quinone is MK-8. The cell wall peptidoglycan contained D-alanine, L-glutamic acid, glycine, and L-ornithine (di-amino acid). The novel strain showed resistance to gamma radiation, with a D₁₀ value (i.e. the dose required to reduce the bacterial population by 10-fold) in excess of 5 kGy. Based on the phylogenetic, chemotaxonomic, and phenotypic data, strain DY59^T (=KCTC 33033^T =JCM 18581^T) should be classified as a type strain of a novel species, for which the name Deinococcus swuensis sp. nov. is proposed.     

Identification of two entomopathogenic bacteria from a nematode pathogenic to the Oriental beetle, Blitopertha orientalis

A pathogenic nematode, Butlerius sp., was isolated from Oriental beetle, Blitopertha orientalis. The infective juveniles exhibited dose- as well as time-dependent entomopathogenicity on the larvae of B. orientalis. Two bacterial species, Providencia vermicola (KACC 91278) and Flavobacterium sp. (KACC 91279), were isolated from the infective juveniles and identified. P. vermicola outnumbered Flavobacterium sp. in the nematode host, in which the colony density of P. vermicola was found to be 21 times higher than that of Flavobacterium sp. However, when the two bacterial species were cocultured in culture media without the nematode host, they showed similar growth rates. Both bacteria induced significant entomopathogenicity against Spodoptera exigua larvae infesting economically important vegetable crops, where P. vermicola was more potent than Flavobacterium sp.     

Genome sequence of an ammonia-oxidizing soil archaeon, "Candidatus Nitrosoarchaeum koreensis" MY1

Ammonia-oxidizing archaea are ubiquitous microorganisms which play important roles in global nitrogen and carbon cycle on earth. Here we present the high-quality draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus koreensis" MY1, that dominated an enrichment culture of a soil sample from the rhizosphere. Its genome contains genes for survival in the rhizosphere environment as well as those for carbon fixation and ammonium oxidation to nitrite.     

Mannitol production by Leuconostoc citreum KACC 91348P isolated from Kimchi

Leuconostoc genus, which comprise heterofermentative lactic acid bacteria, reduces fructose to mannitol by recycling intracellular NADH. To evaluate the mannitol productivities of different Leuconostoc species, 5 stock cultures and 4 newly isolated strains were cultivated in MRS and simplified media containing glucose and fructose (1:2 ratio). Among them, L. citreum KACC 91348P, which was isolated from kimchi, showed superior result in cell growth rate, mannitol production rate, and yield in both media. The optimal condition for mannitol production of this strain was pH 6.5 and 30°C. When L. citreum KACC was cultured in simplified medium in a 2 l batch fermenter under optimal conditions, the maximum volumetric productivity was 14.83 g·l(-1)h(-1) and overall yield was 86.6%. This strain is a novel and efficient mannitol producer originated from foods to be used for fermentation of fructose-containing foods.     

Probiotic‐mediated competition,exclusion and displacement in biofilm formation by food‐borne pathogens

The objective of this study was to examine the inhibitory effect of probiotic strains on pathogenic biofilm formation in terms of competition, exclusion and displacement. Probiotic strains (Lactobacillus acidophilus KACC 12419, Lact. casei KACC 12413, Lact. paracasei KACC 12427 and Lact. rhamnosus KACC 11953) and pathogens (Salmonella Typhimurium KCCM 40253 and Listeria monocytogenes KACC 12671) were used to evaluate the auto‐aggregation, hydrophobicity and biofilm formation inhibition. The highest auto‐aggregation abilities were observed in Lact. rhamnosus (17·5%), Lact. casei (17·2%) and Lact. acidophilus (15·1%). Salm. Typhimurium had the highest affinity to xylene, showing the hydrophobicity of 53·7%. The numbers of L. monocytogenes biofilm cells during the competition, exclusion and displacement assays were effectively reduced by more than 3 log when co‐cultured with Lact. paracasei and Lact. rhamnosus. The results suggest that probiotic strains can be used as alternative way to effectively reduce the biofilm formation in pathogenic bacteria through competition, exclusion and displacement.

Significance and Impact of the Study

This study provides new insight into biofilm control strategy based on probiotic approach. Probiotic strains effectively inhibited the biofilm formation of Listeria monocytogenes through the mechanisms of competition, exclusion and displacement. These findings contribute to better understand the probiotic‐mediated competition, exclusion and displacement in biofilm formation by pathogens.     

Draft Genome Sequence of Escherichia coli W26, an Enteric Strain Isolated from Cow Feces

An enteric bacterium, Escherichia coli W26 (KACC 16630), was isolated from feces from a healthy cow in South Korea. Here, we report the draft genome sequence of the isolate, which is closely affiliated with commensal strains belonging to E. coli phylogroup B1.     

Pedobacter jeongneungensis sp. nov., isolated from forest soil

Strain BH45(T) was isolated from forest soil of Mt. Bukhan in Jeongneung, Seoul, Korea. The Gram-staining-negative strain BH45(T) grows at 4-30°C (optimum of 25-30°C) and between pH 5-8 (optimum of pH 6-8). Its major cellular fatty acids are C(18:3) ω6c (6,9,12) and C(10:0). The G+C content of genomic DNA was 40.2 mol%. The major respiratory quinone system in strain BH45(T) is menaquinone-7. Phylogenetic analysis based on 16S rRNA gene sequences indicates that strain BH45(T) is closely related to the genus Pedobacter. Sequence similarities with P. terrae KCTC 12762(T), P. suwonensis KACC 11317(T), P. soli KACC 14939(T), P. alluvionis DSM 19624(T), P. roseus KCCM 42272(T), P. yonginense KCTC 22721(T) were 97.5, 97.1, 97.0, 97.0, 97.0, and 96.0%, respectively. DNA-DNA hybridization results distinguish strain BH45(T) from two Pedobacter species with high 16S rRNA gene sequence similarities. According to the phenotypic and molecular data, the strain BH45(T) clearly represents a novel species within the genus Pedobacter; thus, the name Pedobacter jeongneungensis sp. nov. is proposed for this strain. The type strain is BH45(T) (=KACC 15514(T) =JCM 17626(T)).     

Complete genome sequence of Bifidobacterium longum subsp. longum KACC 91563

Bifidobacterium longum strains predominate in the colonic microbiota of breast-fed infants. Here we report the complete genome sequence of B. longum subsp. longum KACC 91563, isolated from feces of neonates. A single circular chromosome of 2,385,301 bp contains 1,980 protein-coding genes, 56 tRNA genes, and 3 rRNA operons.     

Vespidae of Viet Nam (Insecta: Hymenoptera) 2. Taxonomic notes on Vespinae

The taxonomy of the Vietnamese species of the social wasp subfamily Vespinae is revised. Vespa auraria Smith, 1852, is synonymized under V. velutina Lepeletier, 1836. Vespula koreensis (Radoszkowski, 1887) is recorded as new for Viet Nam, and its color characters are described. A key to vespine species of Viet Nam based on morphological characters is provided.     

Draft Genome Sequence of Staphylococcus saprophyticus subsp. saprophyticus M1-1, Isolated from the Gills of a Korean Rockfish, Sebastes schlegeli Hilgendorf, after High Hydrostatic Pressure Processing

A bacterium designated M1-1 was isolated from the gills of a Korean rockfish, Sebastes schlegeli Hilgendorf, after high hydrostatic pressure processing. Studies of 16S rRNA phylogeny and comparative genomics demonstrated that the isolate belongs to Staphylococcus saprophyticus subsp. saprophyticus. Here, we report the draft genome sequence of S. saprophyticus subsp. saprophyticus M1-1 (KACC 16562).     

Genome sequence of Escherichia coli J53, a reference strain for genetic studies

Escherichia coli J53 (F(-) met pro Azi(r)) is a derivative of E. coli K-12 which is resistant to sodium azide. This strain has been widely used as a general recipient strain for various conjugation experiments. Here, we report the genome sequence of E. coli J53 (=KACC 16628).     

Functional analysis of <Emphasis Type="Italic">pilQ</Emphasis> gene in <Emphasis Type="Italic">Xanthomanas oryzae</Emphasis> pv. <Emphasis Type="Italic">oryzae</Emphasis>, bacterial blight pathogen of rice

Bacterial blight (BB) of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), is the most devastating bacterial disease in rice. A virulence-attenuated mutant strain HNU89K9 of X. oryzae pv. oryzae (KACC10331), with a transposon insertion in the pilQ gene was used for this study. The pilQ was involved in the gene cluster pilMNOPQ of the Xoo genome. Growth rate of the pilQ mutant was similar to that of wild-type. At level of amino acids, PilQ of Xoo showed that a high sequence identities more than 94% and 70% to Xanthomonas species and to Xyllela fastidiosa, respectively but a low sequence homology less than 30% to other bacterial species. The twitching motility forming a marginal fringe on PSA media was observed on colony of the wild-type strain KACC10331, but not in mutant HNU89K9. Wild-type Xoo cells formed a biofilm on the surface of the PVC plastic test tube, while the mutant strain HNU89K9 did not form a biofilm. The results suggest that the pilQ gene of X. oryzae pv. oryzae plays a critical role in pathogenicity, twitching motility, and biofilm formation.     

Genome sequence of Escherichia coli AA86, isolated from cow feces

Escherichia coli AA86 (=KACC 15541) is an enteric bacterium that was isolated from a sample of healthy cow feces. Its genome sequence revealed that it is most closely related to the human fecal strain E. coli SE15 and could be classified under E. coli phylogenetic group B2. Here, we report the genome sequence of E. coli AA86, consisting of 3 contigs and 2 plasmids.