Miracle-dz/UniFAR-FTUs huggingface dataset:
Biochemical and Molecular Characteristics of Vibrio anguillarum Isolated from Alaska Pollock Theragra chalcogramma Seedlings

명태(Theragra chalcogramma)는 대구목(Gadiformes) 대구 과(Gadidae)에 속하는 대표적인 한해성 어류로 우리나라의 동 해안에서부터 오호츠크해, 베링해, 알래스카에 걸친 북태평양 해역에 넓게 분포하고 있다(Oh et al., 2004). 명태의 전 세계 어 획량은 2001년에 약 300 만톤이 어획되었으나 2008년에는 약 260 만톤이 어획되어 총 생산량이 감소하고 있으며, 우리나라 의 경우에도 2001년 약 20 만톤이 어획되었으나 2008년에는 약 2만 5천톤이 어획되어 어획 생산량이 크게 감소하고 있다 (AT, 2010). 명태수급의 대부분을 원양어업에 의존하는 우리나 라는 러시아와 명태 쿼터 협상이 난항을 거듭하고 있어 명태 수 급은 더욱 불안정할 것으로 예상되며 앞으로 수입 의존도가 더 늘어날 것으로 추정되어 명태 자원회복이 매우 시급하다(Kim and Kim, 2014). 일본의 경우 우리나라에 비해 느리기는 하지만 90년대 이 후 명태 자원양이 감소하는 추세가 나타나고 있으며, 주된 원 인으로서 기후변화와의 관련성을 보고하고 있다(Shida et al., 2007). 또한 명태 인공종묘생산 기술을 보유하고 있으나(Ishida et al., 2014), 현재까지 완전양식기술은 개발되어 있지 않다. 우 리나라에서도 최근 명태자원 회복을 위해 명태 인공종묘생산 에 관한 연구가 시작되어 종묘생산에는 성공하였으나(Kwon et al., 2015), 아직 완전양식까지는 불가능한 상황이다. 어류양식의 성공여부를 결정짓는 요인 중 하나로서 종묘생산 과정에서 발생하는 폐사를 들 수 있으며 폐사원인의 규명은 생 산성 향상과도 연결이 되므로 매우 중요하다. 현재까지 명태의 감염성 질병에 관해서는 ichthyophonus 감염증과 바이러스성 출혈성 패혈증(Viral hemorrhagic septicemia, VHS)이 알려져 있다(Meyers et al., 1999; White et al., 2014). 하지만, 이는 자 연산 명태에서 보고된 것으로 양식산 명태에 발생하는 질병에 명태(Theragra chalcogramma) 종묘에서 분리된 Vibrio anguillarum의 생화학적, 분자생물학적 특성 전찬혁·남우화·김정호*
Microbiological study of orofacial infections ofodontogenic origin in Iraqi patients and their sensitivitiesto cefotaxime

Background: This study was carried out to evaluate microbial flora of odontogenic infection in Iraqi patients and to gain further information on the types of micro-organisms in odontogenic infection, and to determine the value of Cefotaxime as an alternative drug in the treatment of odontogenic infection. Materials and methods: The bacteriology of 20 dento-alveolar abscesses was studied using optimal techniques to collect, transport and processing specimen. All specimens yielded bacterial growth when cultured for aerobes and anaerobes. Anaerobes were isolated in all patients. Results and Conclusions: Among the aerobic bacteria, streptococci dominated and among the anaerobes the Gram negative rode, bactericides ruminicola and fusobacterium nucleatum were most frequently isolated followed by Gram positive cocci. All anaerobic isolate were resist to cefotaxime. The results generally showed that Cefotaxime most effective drug against Gram negative rods and less active against Gram positive cocci and this being related to the laboratory results of culture and sensitivity.
Occurrence of Bacteriophages Infecting Bacteroides fragilis and Other Viruses in Polluted Marine Sediments

Numbers of B.fragilis bacteriophages in comparison to coliphages, enteroviruses and rotaviruses were evaluated by different methods in sediments of a coastal area near Barcelona which receives substantial amounts of pollution of domestic origin. Phages infecting B.fragilis should be eluted from sediments prior to their enumeration, in the same way as solid-associated animal viruses have to.Phages infecting B.fragilis were better eluted by glycine buffer at alkaline pH than by a caotropic agent (beef extract-sodium nitrate). Such differences between glycine buffer and sodium nitrate were not evident when enteroviruses and rotaviruses were eluted from sediments. This suggests that elution with glycine buffer is preferable for bacteriophages, while the use of caotropic agents is advisable for animal viruses, because of the simplicity of the methodology. In the studied area, coliphages were the more abundant viruses. Also, B.fragilis phages outnumbered rotaviruses and enteroviruses by a factor of more than ten. The ratios between phages active against B.fragilis and either enteroviruses or rotaviruses in marine sediments were similar to the ratios found in sewage, thus indicating that they have a similar fate.
Developmental Changes in Gene Expression Drive Accumulation of Lycopene and β-Carotene in Watermelon

A BSTRACT . Citrullus lanatus (watermelon) is an excellent daily source of dietary lycopene and b -carotene. To investigate the transcriptional regulation of carotenoid biosynthesis genes relative to lycopene and b -carotene accumulation in watermelon fruit, six watermelon accessions with different ﬂesh colors were examined in this study: white-ﬂeshed PI 459074, pale-yellow-ﬂeshed ‘Cream of Saskatchewan’, light-pink-ﬂeshed PI 482255, orange-yellow-ﬂeshed ‘WM-Clr-1’, and red-ﬂeshed ‘LSW177’ and ‘MSW28’. The expression patterns of eight genes ( PSY1 , PSY2 , PDS , ZDS , CRTISO , LCYB , NCED1 , and NCED7 ) involved in lycopene and b -carotene biosynthesis and bio-degradation were analyzed. The results conﬁrmed the accumulation of large quantities of lycopene in red-ﬂeshed ‘LSW177’ and ‘MSW28’, reﬂecting the elevated expression of PSY1 and the low transcriptional expression of NCED1 . The relative expression levels of NCED1 likely play an important role in the color development of the light-pink-ﬂeshed PI 482255, whereas the reduced transcriptional expression of PSY1 and the increased expression of NCED1 appear to be the main factors contributing to the formation of white ﬂesh in the fruit of PI 459074. Low transcriptional expression of PSY1 results in the pale-yellow ﬂesh of the ‘Cream of Saskatchewan’ fruit.
Mitochondria and lysosomes play a key role in HepG2 cell apoptosis induced by microcystin-LR

Abstract The aim of the present study was to investigate the toxicological mechanism of microcystin-LR (MC-LR) on HepG2 cells to understand MC-related human hepatitis and primary liver cancer. The results showed that MC-LR induced the time- and concentration-dependent apoptosis of HepG2 cells, and MC-LR exposure promoted the expression of Smac/Diablo in HepG2 cells. In addition, Bad and cleaved-Bid protein levels were also altered. Moreover, MC-LR exposure promoted the expression of Fas and FasL and increased caspase-8 transcription and enzymatic activity, suggesting that the MC-LR-induced apoptosis of HepG2 cells may be mediated via mitochondrial and Fas/FasL pathways in which lysosomal destabilization might play an important role.
Regulation and Function of the dlx Genes in the Zebrafish Forebrain

The Dlx genes encode a family of transcription factors important to the development of the vertebrate forebrain. The expression of the Dlx genes is controlled by a number of highly conserved regulatory elements, which have been extensively studied in the mouse. The Dlx genes have been shown to have highly overlapping expression during the development of the telencephalon/diencephalon and play a role in GABAergic interneuron differentiation and in the regulation of the Gad genes, responsible for GABA synthesis. Using fluorescent in situ hybridizations, we show the dlx genes are expressed in highly overlapping domains within the zebrafish forebrain and appear to follow a conserved pathway involved in the differentiation of GABAergic interneurons. We have identified one of the dlx regulatory elements, URE2, in the three major branches of jawed vertebrates and tested the orthologous sequences for regulatory function. These regulatory sequences have similar activity in the forebrain of mice and zebrafish. Transgenic and dlx expression data indicate there may be similar genetic cascades controlling Dlx expression in the mammalian and teleost forebrain. To elucidate the genetic cascade regulating the expression of the dlx and gadl genes in zebrafish, we knocked down the function of asclla, a Mas hi ortholog known to regulate Dlx expression in the mouse. Knockdown of asclla function resulted in a loss of dlx and gadl expression in the prethalamus. We also impaired the function of the dlx genes in the zebrafish forebrain. Double knockdown of the dlxla/2a genes resulted in a loss of gadl expression in the prethalamus, but not in the telencephalon, in contrast to observations made in the mouse. We propose the asclla and dlx genes are involved in an
Post-Transcriptional Shaping of Neurons: The Role of miRNAs and FMRP-Interacting P-Body Components in Regulating Neuronal Structure

Changes in synaptic structure in response to neuronal stimulation are believed to underlie the processes of learning and long-term memory. However, the mechanisms for these structural modifications are poorly understood. It is well-known that activitydependent synaptic modifications rely upon new protein synthesis, and rapid new protein synthesis, at that. Therefore, it is widely believed that pools of messenger RNAs held in a state of translational repression are transcribed in a neuronal cell body prior to stimulation, and transported to the synapse, where they reside until stimulation occurs. This study investigates the roles and interactions of translational repression mechanisms to better understand how new synaptic growth is repressed or enhanced for the purposes of long-term memory and learning. We found that miRNAs -315, -275, -11 and the miR-9 family are of particular interest for neuronal growth in Drosophila larvae because they are extremely enriched in the larval CNS compared to the adult brain, and are predicted to regulate mRNA targets that significantly contribute to neuronal development. Furthermore, miR-315 and the miR-9 family bind and regulate a Futsch (Drosophila homolog of mammalian MAP1B known to affect synaptic growth) reporter in vitro, and the miR-9 family exhibits an increase in bouton numbers at muscles 6/7 of the NMJ characteristic of an increase in Futsch levels when under-expressed. Curiously, this same effect with seen with miR-9 family overexpression.
Identification and Characterization of Bacterial Chemoreceptors Using Quantitative Capillary and Gradient Plate Chemotaxis Assays

[Abstract] Bacterial chemotaxis is a motility-based response that biases cell movement toward beneficial molecules, called attractants, and away from harmful molecules, also known as repellents. Since the species of the genus Pseudomonas are characterized by a metabolic versatility, these bacteria have developed chemotactic behaviors towards a wide range of different compounds. The specificity of a chemotactic response is determined by the chemoreceptor, which is at the beginning of the signaling cascade and which receives the signal input. The basic elements of a typical chemoreceptor are the periplasmic ligand binding domain (LBD), responsible for sensing environmental stimuli, and the cytosolic methyl-accepting (MA) domain, that interacts with other components of the cellular signaling cascade. Escherichia coli (E. coli), the traditional model in chemotaxis research, has 5 well-characterized chemoreceptors. However, genome sequence analyses have revealed that many other bacteria possess many more chemoreceptors, some of which with partially overlapping signal profiles. This high number of chemoreceptors complicates their study by the analysis of single chemoreceptor mutants. We have pursued an alternative strategy for chemoreceptor characterization which corresponds to the generation of chimeric receptors composed of the LBD of the chemoreceptor under investigation and the MA domain of an E. coli receptor (Tar). The chimer is then introduced into a chemoreceptor free mutant of E. coli and the chemotaxis of the resulting strain is entirely due to the action of this chimeric receptor. In this publication we describe the use of quantitative capillary and gradient plate assays to study Pseudomonas chemotaxis as well as E. coli strains harboring chimeric receptors.
Thermotolerant yeasts capable of producing bioethanol: isolation from natural fermented sources, identification and characterization

ABSTRACT Recently, the demands of biofuels have increased, because of their significant role in reducing various pollutants created by fossil fuels. Here, we have collected 25 samples containing various thermotolerant microorganisms from the nine natural fermented sources of Bangladesh, such as Boiled potato (Bp), Decomposed foods (Df), Municipal liquid waste (Mlw), Municipal solid waste (Msw), Sugarcane juice (Sc), Pantavat (Pv), Sugar molasses (Sm), Tari (Tari) and Watermelon juice (Wm) for bioethanol production. Among them, 18 isolates are capable of producing bioethanol. Cultural, morphological, physiological, biochemical and genetic analyses were carried out under various physiological conditions. Ethanol fermentation was checked by different carbon sources, temperatures and pH. All of the isolates could grow well in the medium containing Dextrose and Arabinose and only two strains Pv-1 and Bp-2 could ferment Xylose as a sole carbon source. At 42 °C, the highest ethanol concentration 6.58% (v/v) was obtained by a strain Wm-1 isolated from Watermelon juice. At 37 °C, maximal ethanol concentrations of 6.74% (v/v), 6.50% (v/v) and 6.22% (v/v) were obtained by the strains Bp-2, Wm-l and Pv-1, respectively. Among the various pH tested, the highest ethanol concentration 6.6% (v/v) was obtained at pH 4.5 by a strain named Tari-2. Finally, yeast 26S rDNA sequencing information identified the strains Sc-2 as Saccharomyces cerevisiae Pv-2, Tari-2 and Df-1 as Pichia kudriavzevii, Mlw-l and Bp-2 as Candida tropicalis, Pv-1 as Pichia guilliermondii and Df-2 as Candida rugosa.
UCHIME2: improved chimera prediction for amplicon sequencing

Amplicon sequencing generates chimeric reads which can cause spurious inferences of biological variation. I describe UCHIME2, an update of the popular UCHIME chimera detection algorithm with new modes optimized for high-resolution biological sequence reconstruction (“denoising”) and other applications. I show that chimera frequency correlates inversely with divergence, that error-free chimera prediction from sequence is impossible in principle, and that UCHIME2 achieves higher detection accuracy than previous methods.
A new species of Pseudopaludicola (Anura, Leptodactylidae) from northern Brazil

We describe a new species, Pseudopaludicola canga, from the Serra dos Carajas highlands in Brazilian Amazonian forest. The new species is a member of the Pseudopaludicola pusilla group and is characterized mainly by its large size. The described species may represent another endemic species of the Serra dos Carajas.
Use of a Modified Gompertz Equation to Model Nonlinear Survival Curves for Listeria monocytogenes Scott A.

The heat resistance of Listeria monocytogenes was determined in 0.1 M KH2PO4 buffer at three temperatures (50, 55, and 60°C), three pH levels (5, 6, and 7), and three NaCl concentrations (0, 2, and 4%). Survival curves were fit using nonlinear regression with a modified Gompertz equation. The Gompertz equation is capable of fitting survival curves which are linear, those which display an initial lag region followed by a linear region, and those which are sigmoidal. Parameter estimates were used to describe the lag region, death rate, and the tailing region of a survival curve. These estimates were also used to predict single and interactive effects of temperature, pH, and percentage of NaCl on the log surviving fraction (LSF) of bacteria. Interactions among these variables significantly (P < .05) affected the LSF. Generally, increased pH or NaCl concentration lead to an increased (P < .05) LSF, where as increased time or temperature lead to a decreased (P < .05) LSF. All multiple factor interactions significantly (P < .05) affected the LSF. These interactions differed depending on the heating medium and the region of the survival curve. The correlation of observed LSF and predicted LSF (R2 = .89) indicated that the Gompertz equation was in close agreement with the observations. This study demonstrated that the Gompertz equation and nonlinear regression can be used as an effective means to predict survival curve shape and response to heat of L. monocytogenes in many different environmental conditions.
Microbial Community Characteristics in Industrial Matured Chinese paocai, a Fermented Vegetable Food, from Different Factories

Paocai was a traditional fermented food in China and produced by spontaneous fermentation of various vegetables. The microbial community occurring in industrial matured Chinese paocai (IMCP) from different factories was investigated by PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR). The dominant bacteria were different in IMCP from different factories. Three genera including Debaryomyces, Pichia and Candida were identified and Debaryomyces was mutual and dominant yeast in all IMCP. Fifteen bands from DGGE profiles of lactic acid bacteria (LAB) were identified and four genera were detected. Alkalibacterium and Lactobacillus were dominant in all IMCP. In conclusion, the IMCP from different factories possessed different dominant bacteria. The community of LAB in IMCP from different factories was different, and Lactobacillus and Alkalibacterium were main LABs in all IMCP. The quantity of LAB was quantitated and shown to exist at 10 _ 10 copies in the IMCP from different factories.
Antioxidant properties of ethanol and fractions of ocimum gratissimum leave in paracetamol-induced oxidative stress in Wistar albino rats. -

Objective: The present study is aimed at evaluating the antioxidant activity of different solvent fractions (ethylacetate, ethanol, hexane, aqueous) of Ocimum gratissimum (OG) on oxidative stress indices in Paracetamol-induced oxidative stress in Wistar albino rats. Methods: Thirty five Wistar albino rats of both sexes were divided into seven groups (n=5). Paracetamol (PCM) (500mg/ kg BW) dissolved in olive oil was administered daily for 28 days to induce hepatic damage in experimental rats. Control group received 1 ml olive oil only. 400 mg/kg BW doses of ethyl acetate, ethanol, hexane, aqueous fractions of OG and silymarin (SIL) (100mg/kg) in addition to 500mg/kg body weight of PCM dissolved in 1ml of olive oil respectively were used as treatment groups daily for 28 days. Blood samples were collected by cardiac puncture and activities of Superoxide dismutase (SOD), catalase (CAT), glutathione (GSH) using standard biochemical methods. Lipid peroxidation was estimated by measuring Malondialdehyde (MDA) concentration. Results: SOD activity increased significantly (p≤ 0.05) in groups administered different fractions of OG and SIL when compared with control. CAT activity showed significant (p≤ 0.05) increase in ethanol and ethyl acetate fractions of OG while group treated with SIL and groups administered hexane and aqueous fractions showed a marked increase when compared with rats treated with PCM only. Reduced GSH level increased significantly (p≤ 0.05) in aqueous fraction while SIL-treated group and groups administered fractions of OG (ethyl acetate, ethanol and hexane) showed a marked increase when compared with PCM only treated group. MDA concentration decreased significantly (p≤ 0.05) in groups administered different fractions of OG when compared with PCM only treated group. Conclusion: These findings are suggestive of the antioxidant properties of different solvent fractions of Ocimum gratissimum extract in paracetamol-induced oxidative stress with ethyl acetate fraction showing the highest activity.
A three-dimensional co-culture system to investigate macrophage-dependent tumor cell invasion

Macrophages infiltrate cancers and promote progression to invasion and metastasis. To directly examine tumor-associated macrophages (TAMs) and tumor cells interacting and co-migrating in a three-dimensional (3D) environment, we have developed a co-culture model that uses a PyVmT mouse mammary tumor-derived cell line and mouse bone marrow-derived macrophages (BMM). The Py8119 cell line was cloned from a spontaneous mammary tumor in a Tg(MMTV:LTR-PyVmT) C57Bl/6 mouse and these cells form 3-dimensional (3D) spheroids under conditions of low adhesion. Co-cultured BMM infiltrate the Py8119 mammospheres and embedding of the infiltrated mammospheres in Matrigel leads to subsequent invasion of both cell types into the surrounding matrix. This physiologically relevant co-culture model enables examination of two critical steps in the promotion of invasion and metastasis by BMM: 1) macrophage infiltration into the mammosphere and, 2) subsequent invasion of macrophages and tumor cells into the matrix. Our methodology allows for quantification of BMM infiltration rates into Py8119 mammospheres and demonstrates that subsequent tumor cell invasion is dependent upon the presence of infiltrated macrophages. This method is also effective for screening macrophage motility inhibitors. Thus, we have developed a robust 3D in vitro co-culture assay that demonstrates a central role for macrophage motility in the promotion of tumor cell invasion.
A series of amino-2-cyclohexyl esters, their electrophysiological and antiarrhythmic effects as related to actions on ischemia-induced arrhythmias

Indiscriminate blockade of cardiac ion channels, in addition to affects on extracardiac tissues, is primarily responsible for cardiac side-effects associated with conventional antiarrhythmic drug use. The inactive R,R-enantiomers of cyclohexylbenzenacetamide analgesics (e.g., U 50,488H and RSD920, Parke Davis compounds) exhibited antiarrhythmic activity independent of central or peripheral opioid activity. This pharmacophore offered a novel approach for rational drug design for the purpose of limiting drug toxicity. The cyclohexylbenzenacetamide structure was soon replaced with less cardiac-depressant ester derivatives. The present thesis examined a series of 16 structurally-related amino-2cyclohexyl ester compounds to identify the chemical components within this series for cardiac ion channel blockade and, ultimately, antiarrhythmic actions against ischemiainduced arrhythmias. The compounds were tested against arrhythmias produced by myocardial ischemia and by electrical stimulation. Additional studies were performed in isolated rat ventricular cells to characterize their actions on the major depolarizing and repolarizing currents (Kja and ITo, respectively). Cloned sodium channels expressed in Xenopus oocytes served as a separate cell line in which to directly evaluate effects on lN aThe major conclusions from this study were as follows: 1. In this series, antiarrhythmic activity against ischemia-induced arrhythmias was dependent on chemical structure, in particular, with the nature of the aromatic group (Ri) and amine heterocyclic group (R 2) held in a trans position by the cyclohexyl backbone.