• Plant Biotechnology Reports
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• v.2 no.1
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• pp.75-85
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• 2008

Prune dwarf virus (PDV) is an Ilarvirus systemically infecting almond trees and other Prunus species and spreading through pollen, among other means. We have studied strategies based on coat protein (cp) gene to block PDV replication in host plant cells. A Portuguese isolate of PDV was obtained from infected almond leaves and used to produce the cDNA of the cp gene. Various constructs were prepared based on this sequence, aiming for the transgenic expression of the original or modified PDV coat protein (cpPDVSense and cpPDVMutated) or for the expression of cpPDV RNA (cpPDVAntisense and cpPDVwithout start codon). All constructs were tested in a PDV host model, Nicotiana benthamiana, and extensive molecular characterization and controlled infections were performed on transformants and their progenies. Transgenic plants expressing the coat protein RNA were able to block the proliferation of a PDV isolate sharing only 91% homology with the isolate used for cpPDV cloning, as evaluated by DAS-ELISA on newly developed leaves. With cp expression, the blockage of PDV proliferation in newly developed leaves was only achieved with the construct cpPDV Mutated, where the coat protein has a substitution in the 14th aa residue, with arginine replaced by alanine. This result points to a possible role of the mutated amino acid in the virus ability to replicate and proliferate. This work reveals the possibility of achieving protection against PDV through either coat protein RNA or mutated cp sequence.

• Preventive Nutrition and Food Science
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• v.9 no.3
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• pp.276-282
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• 2004

Marginal Zn deficiency is prevalent through the world and yet human zinc status has not been properly assessed due to the lack of a reliable diagnostic indicator. One potential possibility for zinc status assessment using Zn-binding protein, metallothionein (MT)-mRNA, has been proposed. The purpose of the present study was aimed to show whether measurement of mononuclear cell (MNC) MT mRNA, using a competitive-reverse transcriptase-polymerase chain reaction (competitive-RT-PCR) assay, could indicate zinc status in human subjects. In this study, MNC MT-mRNA expression was measured using a competitive-RT-PCR to compare before and after 14 days of zinc supplementation (50 mg Zn/das zinc gluconate). RT-PCR oligonucleotide primers which were designed to amplify both a 278 bp segment of the human MT-2A cDNA and a 198 bp mutant competitor cDNA template from MNCs, were prepared. MT-2A mRNA was normalized by reference to the housekeeping gene, $\beta$-actin, mRNA for which was also measured by competitive-RT-PCR. There was considerable inter-individual variation in MT-mRNA concentration and yet, the mean MT-2A mRNA level increased 4.7-fold after Zn supplementation, as compared to before Zn supplementation. This MT-2A mRNA level was shown as the same pattern and, even more sensitive assay, compared to the conventional plasma and red blood cells (RBCs) Zn assessment in which plasma and RBCs zinc levels increased 2.3- and 1.2-fold, respectively (p<0.05). We suggest that MT competitive-RT-PCR can be a useful assessment tool for evaluating human zinc status.

• Journal of Forest and Environmental Science
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• v.34 no.6
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• pp.435-450
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• 2018

Phenological events of four Rhododendron tree species (viz. R. arboreum, R. arboreum ssp. delavayi var. delavayi, R. barbatum and R. kesangiae) was monitored in temperate mixed broad-leaved forests of Arunachal Pradesh, India. Phenological events like flower bud formation, flowering, fruit setting, fruit maturing, seed dispersal, leaf bud formation, leaf flushing, and leaf shedding were recorded. Indices i.e., phenophase sequence index (PSI), active phenophasic period of the species (APS) and index of reproductive/vegetative activity (RVA) were also calculated. Present study revealed that bark consistency, growth form and leaf pattern of the studied species have showed variations among the species. Rhododendron species exhibited the phenological events overlapping with other phenophases. The peak flower bud formation was observed during the winter; R. arboreum ssp. delavayi var. delavayi start flowering from December, while the flowering in rest three species exhibited during February to April. Fruit setting occurred during summer to autumn while fruit maturation revealed peak during November. Leaf bud formation illustrated two peaks in April and May, leaf flushing exhibited peak in June, while leaf shedding peaked during October to November. Active phenophasic period of the species were found 12 months, which revealed that species engage in various phenophase activities throughout the year. Phenophase sequence index ranged between 0.8 to 0.9 (PSI ${\geq}0.6$), signifies that species have a sequential arrangement of phenophases. Index of reproductive/vegetative activity of the species exemplified >1, indicate that the reproductive phenophases were dominance over vegetative phenophases. The study have provided substantial insight on the life cycle events of Rhododendron species and ecological approaches for further scientific study with recent climate change and effective management and conservation.

• Genomics & Informatics
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• v.19 no.4
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• pp.44.1-44.9
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• 2021

Autism is a complex neurodevelopmental disorder, the prevalence of which has increased drastically in India in recent years. Neuroligin is a type I transmembrane protein that plays a crucial role in synaptogenesis. Alterations in synaptic genes are most commonly implicated in autism and other cognitive disorders. The present study investigated the neuroligin 3 gene in the Indian autistic population by sequencing and in silico pathogenicity prediction of molecular changes. In total, 108 clinically described individuals with autism were included from the North Karnataka region of India, along with 150 age-, sex-, and ethnicity-matched healthy controls. Genomic DNA was extracted from peripheral blood, and exonic regions were sequenced. The functional and structural effects of variants of the neuroligin 3 protein were predicted. One coding sequence variant (a missense variant) and four non-coding variants (two 5'-untranslated region [UTR] variants and two 3'-UTR variants) were recorded. The novel missense variant was found in 25% of the autistic population. The C/C genotype of c.551T>C was significantly more common in autistic children than in controls (p = 0.001), and a significantly increased risk of autism (24.7-fold) was associated with this genotype (p = 0.001). The missense variant showed pathogenic effects and high evolutionary conservation over the functions of the neuroligin 3 protein. In the present study, we reported a novel missense variant, V184A, which causes abnormal neuroligin 3 and was found with high frequency in the Indian autistic population. Therefore, neuroligin is a candidate gene for future molecular investigations and functional analysis in the Indian autistic population.

• Genomics & Informatics
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• v.19 no.4
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• pp.47.1-47.12
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• 2021

Kaposi's sarcoma-associated herpesvirus (KSHV) is one of the few human oncogenic viruses, which causes a variety of malignancies, including Kaposi's sarcoma, multicentric Castleman disease, and primary effusion lymphoma, particularly in human immunodeficiency virus patients. The currently available treatment options cannot always prevent the invasion and dissemination of this virus. In recent times, siRNA-based therapeutics are gaining prominence over conventional medications as siRNA can be designed to target almost any gene of interest. The ORF57 is a crucial regulatory protein for lytic gene expression of KSHV. Disruption of this gene translation will inevitably inhibit the replication of the virus in the host cell. Therefore, the ORF57 of KSHV could be a potential target for designing siRNA-based therapeutics. Considering both sequence preferences and target site accessibility, several online tools (i-SCORE Designer, Sfold web server) had been utilized to predict the siRNA guide strand against the ORF57. Subsequently, off-target filtration (BLAST), conservancy test (fuzznuc), and thermodynamics analysis (RNAcofold, RNAalifold, and RNA Structure web server) were also performed to select the most suitable siRNA sequences. Finally, two siRNAs were identified that passed all of the filtration phases and fulfilled the thermodynamic criteria. We hope that the siRNAs predicted in this study would be helpful for the development of new effective therapeutics against KSHV.

• KEPCO Journal on Electric Power and Energy
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• v.8 no.1
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• pp.5-7
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• 2022

KEPCO's plan is undergoing a trial operation to replace the open-loop section with ring main units configuration where underground distribution lines are installed, by linking the multi-way circuit breakers auto (MCA) on the power side of each pad-mounted transformer. However, ring main units application mentioned above may cause the ripple effects, when implementing the configuration without a study of protection coordination. Because ring main units with classical pre-set protection devices contribution in fault condition didn't consider yet. For the reliable ring main units operation, it is necessary to resolve several protection issues such as the protection coordination with substation side, prevention of the transformer inrush current. These issues can radically deteriorate the distribution system reliability Hence, it is essential to design proper protection coordination to reduce these types of problems. This paper presents a scheme of ring main units' configuration and MCA's settings of time-current curves to preserve the performance of protection coordination among the switchgears considering constraints, e.g. prevention of the ripple effects (on the branch section when a transformer failure occurs and the mainline when a branch line failure occurs). It was confirmed that the propagation of the failure for each interrupter segment could be minimized by applying the proposed TCC and the interrupter settings for the MCAs (branch, transformer). Further, it was verified that the undetected area of the distribution automation system (DAS) could be supplemented by having the MCA configurated ring main units operate first, instead of the internal protection equipment in the transformer such as the fuse, STP when a transformer failure occurs.

• Journal of Animal Reproduction and Biotechnology
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• v.37 no.4
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• pp.266-275
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• 2022

The impact of heat stress (HS) on reproductive performance and its problems in cows remains to be investigated in Bangladesh. The study was, therefore, aimed to evaluate the effect of HS on fertility and reproductive health problems of dairy cows in a selected area of Bangladesh. A total of 1,095 cows from 500 farms were included in this study. The climate-related data were recorded daily basis for every month in a year and temperature-humidity index (THI) values were calculated to determine the level of HS. Concurrently, data on fertility parameters [number of services per conception (NSC), conception rate (CR) and calving to the first service interval (CFSI)], and reproductive problems were collected through a pre-defined questionnaire. The results show that crossbred [Native x Holstein-Friesian, (HF)] cows were more vulnerable (p < 0.05) to a magnitude of HS effects considering physiological parameters of cows [age, body condition score (BCS), parity and milk yield]. Regarding fertility, HS had no effect on NSC, CR and CFSI in both native and crossbred cows (p > 0.05). The findings on the reproductive problems indicate that HS had significant influence on the prevalence of anestrus (χ² = 21.814, p < 0.05) and retained placenta (χ² = 24.632, p < 0.05) in cows. Of note, the prevalence of repeat breeding syndrome was 2.5 folds higher in stress condition than in no stress condition. Abortion and dystocia were not influenced by HS. In conclusion, HS does not influence the fertility parameters of cows studied; however, anestrus and retained placenta are likely to occur under HS conditions in cows.

• Food Science of Animal Resources
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• v.43 no.1
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• pp.124-138
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• 2023

This study was carried out to determine the effects of adding pistachio shell (PIS), pomegranate hull (POM), and olive pulp (OP) to the diet on milk amino acid and fatty acid parameters in Awassi sheep. In the study, 40 head of Awassi sheep, which gave birth at least twice, were used as animal material. Sheep were fed a control diet without added byproducts (CON), rations containing PIS, POM, and OP. Milk amino acid profile was determined by liquid chromatography-tandem mass spectrometry, milk fatty acid gas chromatography-flame ionization detection device. There was a dramatic reduction in alanine, citrulline, glutamine, glutamic acid, glycine, leucine, ornithine and alphaaminoadipic acid in the research groups. In the PIS group, argininosuccinic acid, gammaminobutyric acid, beta-alanine and sarcosine; In the POM group, asparagine, gammaminobutyric acid, beta-alanine, and taurine; In the OP group, a significant positive increase was found in terms of alanine, histidine, gammaminobutyric acid, and taurine amino acids. The applications in the study did not have a statistically significant effect on the ratio of short, medium and long chain fatty acids in milk (p>0.05). In the presented study, it was determined that PIS, POM, and OP, which were added to the sheep rations at a rate of 5%, caused significant changes in the milk amino acid profiles. In this change in milk amino acid profiles, the benefit-harm relationship should be considered.

• Journal of Animal Reproduction and Biotechnology
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• v.38 no.4
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• pp.215-224
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• 2023

Background: Reproductive management practices play crucial roles to maximize the reproductive performance of cows, and thus contribute to farm profitability. We aimed to assess the reproductive management of cows currently practiced in the dairy farms in an urban farming system. Methods: A total of 62 dairy farms were randomly selected considering all size of farms such as small (1-5 cattle), medium (6-20 cattle) and large farms (> 20 cattle) from selected areas of Dhaka city in Bangladesh. The reproductive management-related parameters viz. estrus detection, breeding method, pregnancy diagnosis, dry cow and parturition management, vaccination and treatment of reproductive problems etc. were obtained in a pre-defined questionnaire during the farm visit. Results: The visual observation method was only used (100.0%; 62/62) for estrus detection irrespective of size of the farms; while farmers observed cows for estrus 4-5 times a day, but only for 20-60 seconds each time. Regardless of farm size, 89.0% (55/62) farms used artificial insemination (AI) for breeding the cows. Intriguingly, all farms (100.0%) routinely checked the cows for pregnancy at 35-40 days post-breeding using rectal palpation technique by registered veterinarian. However, only 6.5% (4/62) farms practiced dry cow management. Notably, all farms (100.0%) provided nutritional supplements (Vit D, Ca and P) during late gestation. However, proper hygiene and cleanliness during parturition was not practiced in 77.4% (48/62) farms; even though 96.7% (60/62) farms treated cows by registered veterinarian for parturition-related problems. Conclusions: While farmers used AI service for breeding and timely check their cows for pregnancy; however, they need to increase observation time (30 minutes/ observation, twice in a day: early morning and early night) for estrus detection, consider dry cow management and ensure hygienic parturition for maximizing production.

• International Journal of Computer Science & Network Security
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• v.24 no.8
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• pp.85-104
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• 2024

The DNA (Deoxyribonucleic Acid) database size increases tremendously transmuting from millions to billions in a year. Ergo for storing, probing the DNA database requires efficient lossless compression and encryption algorithm for secure communication. The DNA short pattern repetitions are of paramount characteristics in biological sequences. This algorithm is predicated on probing exact reiterate, substring substitute by corresponding ASCII code and engender a Library file, as a result get cumulating of the data stream. In this technique the data is secured utilizing ASCII value and engendering Library file which acts as a signature. The security of information is the most challenging question with veneration to the communication perspective. The selective encryption method is used for security purpose, this technique is applied on compressed data or in the library file or in both files. The fractional part of a message is encrypted in the selective encryption method keeping the remaining part unchanged, this is very paramount with reference to selective encryption system. The Huffman's algorithm is applied in the output of the first phase reiterate technique, including transmuting the Huffman's tree level position and node position for encryption. The mass demand is the minimum storage requirement and computation cost. Time and space complexity of Repeat algorithm are O(N²) and O(N). Time and space complexity of Huffman algorithm are O(n log n) and O(n log n). The artificial data of equipollent length is additionally tested by this algorithm. This modified Huffman technique reduces the compression rate & ratio. The experimental result shows that only 58% to 100% encryption on actual file is done when above 99% modification is in actual file can be observed and compression rate is 1.97bits/base.