Studies in Sorghum sudanense, Stapf - the sudan grass

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Time-series clustering of gene expression in irradiated and bystander fibroblasts: an application of FBPA clustering

<p>Abstract</p> <p>Background</p> <p>The radiation bystander effect is an important component of the overall biological response of tissues and organisms to ionizing radiation, but the signaling mechanisms between irradiated and non-irradiated bystander cells are not fully understood. In this study, we measured a time-series of gene expression after α-particle irradiation and applied the Feature Based Partitioning around medoids Algorithm (FBPA), a new clustering method suitable for sparse time series, to identify signaling modules that act in concert in the response to direct irradiation and bystander signaling. We compared our results with those of an alternate clustering method, Short Time series Expression Miner (STEM).</p> <p>Results</p> <p>While computational evaluations of both clustering results were similar, FBPA provided more biological insight. After irradiation, gene clusters were enriched for signal transduction, cell cycle/cell death and inflammation/immunity processes; but only FBPA separated clusters by function. In bystanders, gene clusters were enriched for cell communication/motility, signal transduction and inflammation processes; but biological functions did not separate as clearly with either clustering method as they did in irradiated samples. Network analysis confirmed p53 and NF-κB transcription factor-regulated gene clusters in irradiated and bystander cells and suggested novel regulators, such as KDM5B/JARID1B (lysine (K)-specific demethylase 5B) and HDACs (histone deacetylases), which could epigenetically coordinate gene expression after irradiation.</p> <p>Conclusions</p> <p>In this study, we have shown that a new time series clustering method, FBPA, can provide new leads to the mechanisms regulating the dynamic cellular response to radiation. The findings implicate epigenetic control of gene expression in addition to transcription factor networks.</p

The Ionizing Radiation-Induced Bystander Effect: Evidence, Mechanism, and Significance

It has long been considered that the important biological effects of ionizing radiation are a direct consequence of unrepaired or misrepaired DNA damage occurring in the irradiated cells. It was presumed that no effect would occur in cells in the population that receive no direct radiation exposure. However, in vitro evidence generated over the past two decades has indicated that non-targeted cells in irradiated cell cultures also experience significant biochemical and phenotypic changes that are often similar to those observed in the targeted cells. Further, nontargeted tissues in partial body-irradiated rodents also experienced stressful effects, including oxidative and oncogenic effects. This phenomenon, termed the “bystander response,” has been postulated to impact both the estimation of health risks of exposure to low doses/low fluences of ionizing radiation and the induction of second primary cancers following radiotherapy. Several mechanisms involving secreted soluble factors, oxidative metabolism, gap-junction intercellular communication, and DNA repair, have been proposed to regulate radiation-induced bystander effects. The latter mechanisms are major mediators of the system responses to ionizing radiation exposure, and our knowledge of the biochemical and molecular events involved in these processes is reviewed in this chapter

Studies in para-sorghum snowden - the group with bearded nodes

This paper presents a study of the Para-sorghums consisting of four species, namely S. purpureo- sericeum, S. dimidiatum, S. versicolor and S. nitidum. The group is characterised by the hairiness of the plants, bearded nodes, very long awns (upto 40 mm.) and five pairs of chromosomes.S. purpureosericeum and S. dimidiatum are very closely related to each other, but for the slightly reduced and half coriaceous glume of the latter. The difference is brought about by a single gene.S. versicolor andS. nitidum are more closely related to each other than to the other two. The sorghums of this group do not have much value as fodder in South-India, as they are unable to with-stand cuttings and succumb to the least disturbance to the root system

Studies in sorghum - the non-auriculate and e-ligulate condition

The occurrence of the non-auriculate and e-ligulate condition and its repurcussions on the earhead throw light on the homology between the leaf and the earhead. In non-auriculate and e-ligulate families, the leaves are more erect and the panicle branches likewise. With the suppression of the auricle and ligule there is an absence of the pulvinus and a shortening of the spikelet-free area in the panicle branches and branchlets. This leads to a choking overcrowding of the spikelts on the earhead and consequent risk of sterility. In highly evolved sorghums with auricle and ligule, the presence of the pulvinus and pushing away of the grain-bearing area from the central axis have resulted in producing an economic earhead. These observations are wider in their import in that they throw light on the evolution of the gramineae