Comparative Analysis of Transcription Start Sites Using Mutual Information

The transcription start site (TSS) region shows greater variability compared with other promoter elements. We are interested to search for its variability by using information content as a measure. We note in this study that the variability is significant in the block of 5 nucleotides (nt) surrounding the TSS region compared with the block of 15 nt. This suggests that the actual region that may be involved is in the range of 5–10 nt in size. For Escherichia coli, we note that the information content from dinucleotide substitution matrices clearly shows a better discrimination, suggesting the presence of some correlations. However, for human this effect is much less, and for mouse it is practically absent. We can conclude that the presence of short-range correlations within the TSS region is species-dependent and is not universal. We further observe that there are other variable regions in the mitochondrial control element apart from TSS. It is also noted that effective comparisons can only be made on blocks, while single nucleotide comparisons do not give us any detectable signals

DeepSegNet: An Innovative Framework for Accurate Blood Cell Image Segmentation

Image segmentation plays a crucial and indispensable role in computer vision, as it allows the partitioning of an image into meaningful regions or objects. Among its numerous applications, image segmentation holds particular significance in the domains of medical diagnosis and healthcare. Its vital role in this field stems from its ability to extract and delineate specific anatomical structures, tumors, lesions, and other critical regions from medical images. In medical diagnosis, accurate and precise segmentation of organs and abnormalities is paramount for effective treatment planning, disease monitoring, and surgical interventions. Blood cell image segmentation is highly valuable for medical diagnosis and research, particularly in the domains of hematology and pathology. Precisely segmenting blood cells from microscopic images is essential, as it offers critical insights into various blood-related disorders and diseases. Although deep learning segmentation models have exhibited promising results in blood cell image segmentation, they suffer from several limitations. These drawbacks encompass scarce data availability, inefficient feature extraction, extended computation time, limited generalization to unseen data, challenges with variations, and artifacts. Consequently, these limitations can adversely impact the overall performance of the models. Blood cell image segmentation encounters persistent challenges due to factors like irregular cell shapes, which pose difficulties in boundary delineation, imperfect cell separation in smears, and low cell contrast, leading to visibility issues during segmentation. This research article introduces the innovative DeepSegNet framework, a powerful solution for precise blood cell image segmentation. The performance of widely-used segmentation models like PSPNet, FPN, and DeepLabv3+ is enhanced through the use of sophisticated preprocessing techniques, improving generalization capability, data diversity, and training stability. Additionally, the incorporation of diverse dilated convolutions and feature fusion further contributes to the improvement of these models. The Improved PSPNet, Improved FPN, Deep Lab V3, and Improved Deep Lab V3+ achieved 98.25%, 99.04%, 98.23%, and 99.31% accuracy, respectively, and the Improved Deep Lab V3+ model outperformed well and produced a Dice Coefficient of 99.32% and Precision of 99.38%. The proposed DeepSegNet framework improves overall performance with an increased accuracy of 8.91%, 3.72%, 17.73%, 22.83%, 7.96%, 9.61%, 17.36%, 6.22%, 13.32%, and 14.32% compared to the existing models. This framework, which can be applied to accurately identify and quantify different cell types from blood cell images, is instrumental in diagnosing a variety of hematological disorders and diseases

Inheritance of male-fertility restoration in A1, A2, A3 and A4(M)cytoplasmic male-sterility systems of sorghum [Sorghum bicolor (L.) Moench]

Almost all the sorghum [Sorghum bicolor (L.) Moench] hybrids commercially exploited to date are based on A1 CMS (cytoplasmic-nuclear male-sterility) system. For genetic diversification and to produce more heterotic hybrids, all the available CMS systems are to be studied for genetics of male-fertility restoration preferably in isonuclear backgrounds. The A1, A2, A3 and A4(M) cytoplasms present in three different nuclear backgrounds were crossed with two common restorers. The segregation of fertile and sterile plants observed in F2 and BC1 populations during rainy and post-rainy seasons of 2007 was tested with c2 for goodness of fit for monogenic, digenic and trigenic ratios. The fertility restoration of A1 CMS system was governed by one basic gene and two duplicate complimentary genes (45F:19S in F2) all acting in dominant fashion while the fertility restoration of A2 and A3 CMS systems was governed by three genes where all of the three complimentary genes in dominant condition restore fertility (27F:37S in F2). The fertility restoration in A4(M) CMS system was governed by three genes where any two of the three dominant duplicate-complimentary genes restored fertility (54F:10S in F2) in post-rainy season while two complementary genes in dominant state restored fertility (9F:7S in F2) in rainy season in the absence of expression of the third gene

Agronomic potential of A4(M) cytoplasmic male-sterility system compared to A1 CMS system of sorghum (Sorghum bicolor)

An investigation was carried out to compare the A4(M) CMS (cytoplasmic-nuclear male-sterility) system to the widely used A1 CMS system in sorghum (Sorghum bicolor (L.) Moench) for agronomic traits and panicle grain mold resistance (PGMR) score at International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh, India in 2006 and 2007 rainy and postrainy seasons. The cytoplasm per se and its first order interaction with A-line seemed to contribute to grain yield, male-fertility restoration % and PGMR during rainy season and male-fertility restoration per cent during postrainy season. The mean days to 50% flowering, plant height and grain yield of A4(M) cytoplasm-based hybrids were comparable with those of A1 cytoplasm-based hybrids during 2006 and 2007 postrainy seasons while during 2006 rainy season, A4(M) cytoplasm based hybrids in few nuclear backgrounds were significantly superior to A1 cytoplasm based hybrids for early flowering and grain yield, while in few nuclear backgrounds A1 cytoplasm-based hybrids were superior. However, the A1 cytoplasm based hybrids were more tolerant for grain mold. Hence the A4(M) cytoplasm can be used to incorporate genetic diversity in grain sorghum hybrids for grain yield in postrainy season, but its use in rainy season is not recommended, where grain mold poses a proble

Genetic variability and plant character association of grain Fe and Zn in selected core collection accessions of sorghum germplasm and breeding lines

Sorghum is the third most important food crop in India after rice and wheat and is the staple food in Central India. It is also the staple for large tribal populations across the country. The poor and vulnerable groups in the society depend upon sorghum for their calorie and micronutrient requirement and in the absence of access and affordability to nutrient-rich foods like vegetables, fruits and animal products, biofortification of sorghum helps in enhancing the nutritional security of this group. Research efforts at ICRISAT and elsewhere showed that there is considerable genetic variability and high heritability for grain Fe and Zn contents and it is possible to genetically enhance the grain micronutrient content (Fe and Zn) in sorghum and other major staples. of variability in the sorghum germplasm accessions and breeding lines and the character association between grain Fe and Zn contents and with other agronomic traits.The main aim of this study was to identify promising donors in the core collection of sorghum germplasm accessions and breeding lines with the objective to use those with high grain Fe and Zn contents in the genetic enhancement program to develop biofortified sorghum cultivars. Significant positive correlation was observed between grain Fe and Zn contents (r=0.75) in the study. The five accessions, IS 5427, IS 5514, IS 55, IS 3760 and IS 3283, identified from the study with high grain Fe (>50 is on a continuing basis. mg kg-1) and Zn (>37 mg kg-1) contents can be utilized to increase the diversity and micronutrient density of sorghum hybrid parents in the futur

Effect of Feeding Differently Processed Sweet Sorghum (Sorghum bicolor L. Moench) Bagasse Based complete Diet on Nutrient Utilization and Microbial N Supply in Growing Ram Lambs

This study was carried out to identify appropriate processing method for efficient utilization of sweet sorghum bagasse (SSB), an agro-industrial by product of ethanol industry after blending with concentrate. SSB based complete diet with roughage to concentrate ratio of 50:50 was processed into mash (SSBM), expander extruded pellet (SSBP), chop form (SSBC) and evaluated in comparison to sorghum stover based complete diet in mash form (SSM). Twenty four Nellore X Deccani ram lambs (9 month age; 21.1 ± 0.57 kg body weight) were randomly divided into four groups of six animals each and the experimental complete diets were allotted at random to each group and evaluated for their intake, nutrient utilization and microbial N supply. Among all the groups, the average dry matter (DM) intake (g/kg w0.75), digested DM, organic matter and crude protein were higher (P < 0.01) in lambs fed SSBP diet. The cellulose digestibility was higher (P < 0.05) in lambs fed SSBP diet than those fed SSM and SSBC diets. Intake of digestible crude protein (DCP, g/d) and metabolizable energy (MJ/d) were higher (P < 0.01) in lambs fed SSBP diet. The SSBP diet had higher (P < 0.01) DCP and N (P < 0.05) balance compared to other three diets. Increased (P < 0.01) purine derivatives and microbial N supply was observed in processed diets. Expander extrusion of SSB based complete diet resulted in improved (P < 0.01) efficiency of microbial protein synthesis. It is concluded that, when SSB was processed into complete diets, in terms of nutrient utilization and microbial N supply, the expander extruded pellet diet was better utilized than chopped or mash form by the growing ram lambs

Evaluation of A1, A2, A3, A4(M), A4(G) and A4(VZM) cytoplasms in iso-nuclear backgrounds for grain mold resistance

Breeding for resistance to grain mold, an economically important disease of sorghum, has been only partially successful. Hybrid technology is well developed in sorghum due to availability of the cytoplasm male sterility (CMS) system and at present almost all commercial hybrids are based on the A1 CMS system. To compare the available alternate CMS systems for grain mold resistance, 72 hybrids were produced by crossing 36 A-lines (six CMS systems; A1, A2, A3, A4(M), A4(G), A4(VZM) each in six nuclear backgrounds) with two common restorers, and were evaluated during the 2006 and 2007 rainy seasons in grain mold nursery at ICRISAT. Data analyses indicated influence of cytoplasm on the responses of hybrids to grain mold infection as measured by panicle grain mold resistance (PGMR) score. The A1 cytoplasm seemed to contribute to grain mold resistance followed by A4(VZM) and A2 cytoplasms. The A4(M) cytoplasm had superior general combining ability (GCA) effects while the A1 and A4(VZM) cytoplasm based hybrids had superior specific combining ability (SCA) effects on the PGMR score. Almost all hybrids had significant mid-parent heterosis. The A1 cytoplasm is the best suited for the development of sorghum hybrids for the rainy season adaptation with grain mold resistance. However, use of alternate cytoplasms (A2 and A4(VZM)) for hybrid development will not increase susceptibility to grain mold in commercial grain production