PANNOTATOR:an automated tool for annotation of pan-genomes

Due to next-generation sequence technologies, sequencing of bacterial genomes is no longer one of the main bottlenecks in bacterial research and the number of new genomes deposited in public databases continues to increase at an accelerating rate. Among these new genomes, several belong to the same species and were generated for pan-genomic studies. A pan-genomic study allows investigation of strain phenotypic differences based on genotypic differences. Along with a need for good assembly quality, it is also fundamental to guarantee good functional genome annotation of the different strains. In order to ensure quality and standards for functional genome annotation among different strains, we developed and made available PANNOTATOR (http://bnet.egr.vcu.edu/iioab/agenote.php), a web-based automated pipeline for the annotation of closely related and well-suited genomes for pan-genome studies, aiming at reducing the manual work to generate reports and corrections of various genome strains. PANNOTATOR achieved 98 and 76% of correctness for gene name and function, respectively, as result of an annotation transfer, with a similarity cut-off of 70%, compared with a gold standard annotation for the same species. These results surpassed the RAST and BASys softwares by 41 and 21% and 66 and 17% for gene name and function annotation, respectively, when there were reliable genome annotations of closely related species. PANNOTATOR provides fast and reliable pan-genome annotation; thereby allowing us to maintain the research focus on the main genotype differences between strains

Microrna let-7: an emerging next-generation cancer therapeutic

In recent years, various rna-based technologies have been under evaluation as potential next-generation cancer therapeutics. Micrornas (mirnas), known to regulate the cell cycle and development, are deregulated in various cancers. Thus, they might serve as good targets or candidates in an exploration of anticancer therapeutics. One attractive candidate for this purpose is let-7 (“lethal-7”)

Improved design for SOI based evanescently coupled multilayer spot-size converter

We report an improved version of a spot-size converter (SSC) consisting of a silicon nanowire evanescently coupled to a phase-matched Poly-Si multilayer structure. With wider transversal dimensions the multilayer structure expands the mode significantly thus increasing the coupling efficiency with the conventional single-mode fiber. Detailed optimization process of a 17-layer based SSC is discussed and its coupling efficiency with a high-NA fiber of radius 2 μm is obtained as 98% providing only 0.087 dB loss. Vertical alignment tolerance between the optimized SSC and a high-NA fiber of radius 2 μm is also shown. This novel design does not consist of a taper and can be fabricated by using CMOS compatible process. It has a short device length and more relaxed alignment tolerances with the fiber. Full-vectorial and computationally efficient finite element method and the least squares boundary residual method have been used for the analysis and optimization of the proposed structure

Syzygium cumini inhibits growth and induces apoptosis in cervical cancer cell lines: a primary study

Cervical cancer is common among women in the Indian subcontinent and the incidences and death rates are gradually increasing over the years. Several dietary phytochemicals have been reported to have growth inhibitory and apoptotic effect on HeLa and other cervical cell lines. In this study, using Hoechst 33342 staining, MTT, Annexin V-FLUOS/PI and TUNEL assays we demonstrated that Syzygium cumini extract inhibits the growth and induces apoptosis in HeLa and SiHa cervical cancer cell lines in a dose- and time-dependent manner. The phytochemical, its mode of action and safety issues are yet to be determined

Phase-matched multi-layer based polarisation-independent spot-size converter for silicon nanowire

The efficient coupling of optical power from a silicon nanowire (NW) to an optical fibre is challenging for both the quasi-TE and quasi-TM polarisations. Here, we propose a polarisation-independent spot-size converter (PI-SSC) based on phase-matched multi-layer waveguides for efficient coupling between a silicon NW and an optical fibre for both the polarisations. The fabrication process of the proposed PI-SSC is compatible with the complementary metal-oxide-semiconductor (CMOS) process. The optimisation for the proposed PI-SSC is studied by using a numerically efficient algorithm, combining a rigorous H-field based full-vectorial finite element method (VFEM) and the least squares boundary residual (LSBR) method. The simulation results show that using an eleven-layer based PI-SSC, the coupling losses between a silicon NW and a lensed fibre of radius 2 μm can be reduced to only 0.34 dB and 0.25 dB for the quasi-TE and quasi-TM polarisations, respectively. Furthermore, the output multi-layer is horizontally tapered, which further reduces the coupling loss for both the polarisations and the end face is easy to be polished

Low Doses of the Carcinogen Furan Alter Cell Cycle and Apoptosis Gene Expression in Rat Liver Independent of DNA Methylation

BACKGROUND: Evidence of potent rodent carcinogenicity via an unclear mechanism suggests that furan in various foods [leading to an intake of up to 3.5 mu g/kg body weight (bw)/day] may present a potential risk to human health

A Complex Relationship Among the Circadian Rhythm, Reward Circuit and Substance Use Disorder (SUD)

Saptadip Samanta,1 Debasis Bagchi,2,3 Mark S Gold,4 Rajendra D Badgaiyan,5 Debmalya Barh,6 Kenneth Blum7– 12 1Department of Physiology, Midnapore College, Midnapore, West Bengal, 721101, India; 2Department of Biology, College of Arts and Sciences, Adelphi University, Garden City, NY, USA and Department of Psychology, Gordon F. Derner School of Psychology, Adelphi University, Garden City, NY, USA; 3Department of Pharmaceutical Sciences, College of Pharmacy, Southern University, Houston, TX, 77004, USA; 4Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA; 5Department of Psychiatry, Case Western Reserve University School of Medicine, Cleveland, OH, USA; 6Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Nonakuri, Purba Medinipur 721172, West Bengal, India; 7Division of Addiction Research & Education, Center for Sports, Exercise, and Mental Health, Western University Health Sciences, Pomona, CA, 91766, USA; 8Institute of Psychology, Eotvos Loránd University, Budapest, 1053, Hungary; 9Department of Psychiatry, Wright State University Boonshoft School of Medicine and Dayton VA Medical Center, Dayton, OH, 45435, USA; 10Department of Psychiatry, University of Vermont, Burlington, VT, 05405, USA; 11Division of Nutrigenomics, The Kenneth Blum Behavioral & Neurogenetic Institute, Austin, TX, 78701, USA; 12Department of Molecular Biology, Adelson School of Medicine, Ariel University, Ariel, IsraelCorrespondence: Saptadip Samanta; Debasis Bagchi, Email [email protected]; [email protected]; [email protected]: The human brain not only controls the various physiological functions but is also the prime regulator of circadian rhythms, rewards, and behaviors. Environmental factors, professional stress, and social disintegration are regarded as the initial causative factors of addiction behavior. Shift work, artificial light exposure at night, and chronic and acute jet lag influence circadian rhythm dysfunction. The result is impaired neurotransmitter release, dysfunction of neural circuits, endocrine disturbance, and metabolic disorder, leading to advancement in substance use disorder. There is a bidirectional relationship between chronodisruption and addiction behavior. Circadian rhythm dysfunction, neuroadaptation in the reward circuits, and alteration in clock gene expression in the mesolimbic areas influence substance use disorder (SUD), and chronotherapy has potential benefits in the treatment strategies. This review explores the relationship among the circadian rhythm dysfunction, reward circuit, and SUD. The impact of chronotherapy on SUD has also been discussed.Keywords: SCN, circadian rhythm dysfunction, melatonin, cortisol, drug addictio

To other planets with upgraded millennial kombucha in rhythms of sustainability and health support

Humankind has entered a new era of space exploration: settlements on other planetary bodies are foreseen in the near future. Advanced technologies are being developed to support the adaptation to extraterrestrial environments and, with a view on the longer term, to support the viability of an independent economy. Biological processes will likely play a key role and lead to the production of life-support consumables, and other commodities, in a way that is cheaper and more sustainable than exclusively abiotic processes. Microbial communities could be used to sustain the crews’ health as well as for the production of consumables, for waste recycling, and for biomining. They can self-renew with little resources from Earth, be highly productive on a per-volume basis, and be highly versatile—all of which will be critical in planetary outposts. Well-de!ned, semi-open, and stress-resistant microecosystems are particularly promising. An instance of it is kombucha, known worldwide as a microbial association that produces an eponymous, widespread soft drink that could be valuable for sustaining crews’ health or as a synbiotic (i.e., probiotic and prebiotic) after a rational assemblage of de!ned probiotic bacteria and yeasts with endemic or engineered cellulose producers. Bacterial cellulose products offer a wide spectrum of possible functions, from leather-like to innovative smart materials during long-term missions and future activities in extraterrestrial settlements. Cellulose production by kombucha is zero-waste and could be linked to bioregenerative life support system (BLSS) loops. Another advantage of kombucha lies in its ability to mobilize inorganic ions from rocks, which may help feed BLSS from local resources. Besides outlining those applications and others, we discuss needs for knowledge and other obstacles, among which is the biosafety of microbial producers