Frontiers in Biology
Cover Story   2014, Volume 9 Issue 4
The eukaryotic genome is functionally and spatially organized within the cell nucleus. How these spatial organizations regulate genome function remains largely unclear. This review (pages 255-268) provides an overview on cytological observations of subnuclear gene positioning, and summarizes recent findings on the molecular mechanisms of gene posit [Detail] ...
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, Volume 9 Issue 4

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REVIEW
Gene positioning and genome function
Nidhi VISHNOI,Jie YAO
Front. Biol.. 2014, 9 (4): 255-268.  
https://doi.org/10.1007/s11515-014-1313-3

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The eukaryotic genome is packaged as chromatin within the three-dimensional nuclear space. Decades of cytological studies have revealed that chromosomes and genes are non-randomly localized within the nucleus and such organizations have important roles on genome function. However, several fundamental questions remain to be resolved. For example, what is required for the preferential localization of a gene to a nuclear landmark? What is the mechanism underlying gene repositioning in the nucleus? How does subnuclear gene positioning regulate gene transcription? Recent studies have revealed that several factors such as DNA sequence composition, specific regulatory sequences, epigenetic modifications, chromatin remodelers, post-transcriptional regulators and nuclear architectural proteins can influence chromatin dynamics and gene positioning in a gene-specific manner among organisms from yeast to human. In this review, we discuss some recent findings as well as experimental tools to investigate subnuclear gene positioning and to explore its implications in genome functions.

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IRF4 and IRF8: governing the virtues of B lymphocytes
Vipul SHUKLA,Runqing LU
Front. Biol.. 2014, 9 (4): 269-282.  
https://doi.org/10.1007/s11515-014-1318-y

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Interferon regulatory factor 4 (IRF4) and IRF8 are critical regulators of immune system development and function. In B lymphocytes, IRF4 and IRF8 have been shown to control important events during their development and maturation including pre-B cell differentiation, induction of B cell tolerance pathways, marginal zone B cell development, germinal center reaction and plasma cell differentiation. Mechanistically, IRF4 and IRF8 are found to function redundantly to control certain stages of B cell development, but in other stages, they function nonredundantly to play distinct roles in B cell biology. In line with their essential roles in B cell development, deregulated expressions of IRF4 and IRF8 have been associated to the pathogenesis of several B cell malignancies and diseases. Recent studies have elucidated diverse transcriptional networks regulated by IRF4 and IRF8 at distinct B cell developmental stages and related malignancies. In this review we will discuss the recent advances for the roles of IRF4 and IRF8 during B cell development and associated diseases.

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RESEARCH ARTICLE
Age-related peculiarities of change in content of free radical oxidation products in muscle during stress
Vadim V. DAVYDOV,Amjad HAMDALLAH,Evgenya R. GRABOVETSKAYA
Front. Biol.. 2014, 9 (4): 283-286.  
https://doi.org/10.1007/s11515-014-1315-1

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The age-dependent peculiarities of stimulation of free radical processes in subcellular fractions of skeletal muscle of rats subjected to long-term immobilization stress were studied in order to improve knowledge about changes of muscular tissue during ontogenesis. It is found that adult animals do not show accumulation of proteins carbonyls, TBA-reactive substances, and Schiff bases in subcellular fractions of the thigh muscle when immobilized. Long-term immobilization causes apparent manifestation of oxidative stress only in mitochondrial fraction in pubertal rats. Mitochondrial oxidative stress defense systems are sufficiently effective, however, direction of pathways of free radical oxidation carbonyl products catabolism alters in the cytoplasm of myocytes in old rats under long-term immobilization conditions.

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Current trends of antibiotic resistance in clinical isolates of Staphylococcus aureus
Kapil Dev SHARMA, Rajendra Prasad SAINI, Loganathan KARTHIK
Front. Biol.. 2014, 9 (4): 287-290.  
https://doi.org/10.1007/s11515-014-1317-z

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Staphyloccus aureus (S. aureus) is a well known human pathogen known to causes a verity of infections in humans. In recent years S. aureus is reported to show drug resistant toward commonly known drugs. Therefore, this study was designed to study the pattern of antibiotic resistance in 50 clinical isolates of S. aureus isolated at Dhanwantri Hospital and Research Centre, Jaipur, Rajasthan, India. S. aureus cultures were isolated from different clinical samples, pus, throat swabs and urine on Blood agar and MacConkey agar and Chrom agar plats and characterized by an array of microscopic and biochemical tests. Antibiotic sensitivity test was performed by standard disc diffusion method (Kirby bayer's method) on Muller Hinton agar plates. During this study, among 50  S. aureus isolates 48 (96%) were found to be resistance toward Aztreonam and Doxicycline followed by Ciprofloxacin (n = 45, 90%), Cefpodoxime and Ceftazidime (n = 44, 88%), Cefuroxime (n = 40, 80%), Pipracillin+ Tazobactum (n = 38, 76%), Cefoparazone (n = 36, 72%), Amoxicillin+ Clavulanic acid and Ceftriaxone (n = 33, 66%), Levofloxacin (n = 32, 64%), Moxifloxacin (n = 31, 62%), Ofloaxacin (n = 25, 50%), Cloxacillin (n = 22, 44%), Azithromycin (n = 21, 42%), Clindamycin (n = 19, 38%), Meropenem (n = 18, 36%), Clarithromycin (n = 16, 32%), Ampicillin+ sulbactam (n = 13, 26%), Amikacin (n = 12, 24%), Impipenem (n = 8, 16%), Linezolid and Methicillin (n = 7, 14%) and Teicoplanin (n = 3, 6%). In conclusion, the isolated S. aureus found to be resistant toward common antibiotics, however all isolates were found to be susceptible to Vancomycin.

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Isolation and partial purification of fungal ligninolytic enzymes from the forest soil fungi isolated from Bhadra Wildlife Sanctuary
SHIVAKUMAR P. BANAKAR,B. THIPPESWAMY
Front. Biol.. 2014, 9 (4): 291-299.  
https://doi.org/10.1007/s11515-014-1319-x

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Screening was done for the isolation of effective lignin degraders from the forest soil samples, by providing lignin as a carbon source through the enrichment method, which leads to the isolation of 8 effective fungal isolates among 14 isolates. Submerged fermentation was done for the production of ligninolytic enzymes with the effective microorganisms by providing Guiaicol as a carbon source. The assay of laccase, lignin peroxidise activity and specific activity was done after the incubation intervals of 2, 4, 6, 7, 8, 10 and 12 days at 27±2°C under shake culture condition. Partially purified protein content was estimated by using Lowry’s method. Pleurotus sp. and Phanerochaetae chrysosporium are more effective at the 2nd and 7th days of incubation for the production of laccase and lignin peroxidases among the effective isolates.

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Bioactive compounds from Caulerpa racemosa as a potent larvicidal and antibacterial agent
Sowmya Rachannanavar NAGARAJ,Jabez William OSBORNE
Front. Biol.. 2014, 9 (4): 300-305.  
https://doi.org/10.1007/s11515-014-1312-4

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Marine algae are rich sources of bioactive compounds capable of harboring secondary metabolites which are structurally and biologically active. In our study, the methanolic extract of marine algae Caulerpa racemosa (green algae) was employed to determine the antibacterial and larvicidal activity. The antibacterial activity showed effective inhibition against five pathogenic bacteria. A significant zone size of 16 mm was observed for Pseudomonas aeruginosa. The methanolic extract of Caulerpa racemosa showed effective larvicidal activity against Culex tritaeniorhynchus and the histopathological studies revealed the rupture in mid gut of larvae. The bioactive compounds in the crude extract were further identified as 2-(-3-bromo-1-adamantyl) acetic acid methyl ester and Chola-5, 22- dien-3-ol by GC-MS. Hence the bioactive compounds obtained from the methanolic extracts could be used for the bactericidal and larvicidal activity which will overcome the harmful impact of synthetic insecticide on environment.

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Isolation and characterization of tyrosinase produced by marine actinobacteria and its application in the removal of phenol from aqueous environment
Suki ROY,Ishita DAS,Minki MUNJAL,Loganathan KARTHIK,Gaurav KUMAR,Sathish KUMAR,Kokati Venkata Bhaskara RAO
Front. Biol.. 2014, 9 (4): 306-316.  
https://doi.org/10.1007/s11515-014-1324-0

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The present study was focused on screening and characterization of tyrosinase enzyme produced by marine actinobacteria and its application in phenolic compounds removal from aqueous solution. A total of 20 strains were isolated from marine sediment sample and screened for tyrosinase production by using skimmed milk agar medium. Among 20 isolates, two isolates LK-4 and LK-20 showed zone of hydrolysis and these were taken for secondary screening by using tyrosine agar medium. Based on the result of secondary screening LK-4 was selected for further analysis, such as tyrosinase assay, protein content and specific activity of the enzyme. The tyrosinase enzyme was produced in a SS medium and was partially purified by ammonium sulfate precipitation, dialysis and SDS PAGE. The isolate (LK-4) was identified as Streptomyces espinosus using 16S rRNA gene sequencing and named as “Streptomyces espinosus strain LK4 (KF806735)”. The tyrosinase enzyme was immobilized in sodium alginate which was applied to remove phenolic compounds from water. The enzyme efficiently removed the phenolic compounds from aqueous solution within few hours which indicated that tyrosinase enzyme produced by Streptomyces espinosus strain LK-4 can be potently used for the removal of phenol and phenolic compounds from wastewater in industries.

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Lucrative pectinase production by novel strain Pseudozyma sp. SPJ with statistical optimization techniques using agro-industrial residues
Sampriya SHARMA,Jitender SHARMA,Rishi Pal MANDHAN
Front. Biol.. 2014, 9 (4): 317-323.  
https://doi.org/10.1007/s11515-014-1316-0

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Production of high titers of an alkaline, extracellular and thermo-tolerant pectinase by a newly isolated yeast Pseudozyma sp. SPJ was carried out under solid state fermentation. Citrus peel, the inexpensive agro-industrial residue used as substrate, was experienced to be unsurpassed. Response surface methodology was conducted to optimize the culture conditions for Pseudozyma sp. SPJ for hyper production of pectinase. Plackett Burman design was applied to identify the most effective culture variables. Out of nine variables studied, incubation time, moisture content and ammonium sulfate were detected as most important. A full factorial Central Composite Design was used to optimize the levels of these variables, which resulted in 17-fold increase (71.19 IU/g to 1215.66 IU/g dry substrate) in the enzyme yield. The results of analysis of variance and multiple regression analysis implies that the effect of incubation time (p<0.000) and moisture content (p<0.018) is more than ammonium sulfate. And also the interaction of moisture content with ammonium sulfate (p<0.002) is more significant.

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Apathy in Parkinson disease
Marina NODEL,Nikolay YAKHNO,Anastasia MEDVEDEVA,Michail KULIKOV
Front. Biol.. 2014, 9 (4): 324-331.  
https://doi.org/10.1007/s11515-014-1322-2

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Apathy is one of the least investigated symptom of Parkinson disease (PD). In the article there are data of frequency, diagnostic features, pathophysiology and treatment of apathy in PD. The aim of the investigation was to evaluate the frequency of apathy in PD without dementia, evaluate the relationship with other neuropsychiatric and motor disorders, influence on the life quality. 115 patients (age-63.84±0.6 years, stage-2.6±0.3) with PD without dementia were included in the investigation. There were used the following scales: scale of evaluation stages of PD by Hoehn-Yahr, UPDRS (part ?activity of daily living?, ?motor functions ?); Beck Depression Inventory, Spielberger State Trait Anxiety Inventory, Parkinson Disease Sleep Scale- PDSS, Epworth Sleepiness Scale, Parkinson Fatigue Scale-PFS-16, SCOPA-Cog, Lilli Apathy Rating Scale LARS and Apathy Scale AS.

Apathy was found in 25% of patients. The frequency and severity of apathy does not depend on stage and duration of PD. It was found positive correlation of apathy and hypokinesia. In different stages of PD there was variability of relationships of apathy with depression, executive functions and sleep disorders. We suppose the heterogeneity of apathy in PD because of the variability of the association with other neuropsychiatric (affective, cognitive, sleep) disorders. It was found the negative influence of apathy on daily activity, emotional and social aspects of life quality.

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Cognitive disorder in brain concussion
Vladimir ZAKHAROV,Ekaterina DROZDOVA,Nikolay YAKHNO
Front. Biol.. 2014, 9 (4): 332-337.  
https://doi.org/10.1007/s11515-014-1323-1

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This paper presented original study results concerning the prevalence and clinical characteristics of cognitive impairment associated with brain concussion. The cognitive functions of 80 consecutive patients (mean age= 37.40±11.74 years; 50 men and 30 women) admitted to the hospital with brain concussions were evaluated. Their cognitive scores were compared with 40 age- and education-matched healthy volunteers without history of cranial trauma. Cognitive impairment without dementia was found in 93% of the patients. Cognitive impairment in brain concussion was also characterized by prominent cognitive slowness (bradyphrenia), concentration decrease, free recall insufficiency, and visual-spatial dysfunction. Age and severity of anxiety significantly influence the cognitive performance of patients.

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10 articles