LINE1 Research Articles

Responses of the antioxidative enzymes of few Sub1 rice (Oryza sativa) genotypes to prolonged submergence stress in Odisha

The present experiment was conducted in Department of Plant physiology, OUAT, Bhubaneswar during kharif 2017 and kharif 2019 to screen out the NILs rice genotypes for submergence adaptation traits under coastal regions of Odisha. The potential involvement of activated oxygen species by submergence stress was studied in twenty rice genotypes; thirteen sub1 NILs, two tolerant checks with six susceptible checks. These rice genotypes were subjected to 17 days of complete submergence. Under 17 days of complete submergence and after the submergence, the genotypes IR-85086-Sub 33 -3-2-1 and IR-88760-Sub 93-3-3 showed lower lipid Peroxidation in terms of malondialdehyde (MDA) level and also showed lower levels of ACC Oxidase activity (AAO) and presented higher activities of antioxidative enzymes, superoxide dismutase (SOD), catalase (CAT), Peroxidase (POX) when compared to the susceptible checks. The levels of SOD activity indicated that detoxification of O2 - to H2O2 was maintained at a stable level throughout the submergence stress until up to 17 days in tolerant genotypes. These findings suggested that tolerance to submergence stress in rice might be proven by increased the capacity of antioxidative system. In addition, SOD and CAT activity has much higher affinity for scavenging H2O2 than POX. The present study evaluated thirteen pairs of Sub1 near-isogenic lines (NILs) together with FR13A and other check genotypes in pot culture conditions to assess the survival and growth processes occurring during submergence and recovery that are associated with Sub1.

Biochemical performance of some Sub1 rice (Oryza sativa) genotypes under submergence stress in Odisha

Recurring floods in Asia cause poor crop establishment. Yields decline drastically when plants are completely submerged for a few days. Traditional rice genotypes predominate because they have acquired moderate tolerance to flooding but they carry the penalty of inherently lower grain yields. Genotypes with tolerance to complete submergence were recently developed in the background of popular genotypes by transferring the submergence tolerance gene SUBMERGENCE1 (Sub1) from the highly tolerant Indian landrace FR13A. The present study evaluated thirteen pairs of Sub1 near-isogenic lines (NILs) together with FR13A and other check genotypes in pot culture conditions to assess the survival and growth processes occurring during submergence and recovery that are associated with Sub1. The present experiment was conducted in Department of Plant physiology, OUAT, Bhubaneswar during kharif 2017 and kharif 2019 to screen out the NILs rice genotypes for submergence adaptation traits under coastal regions of Odisha. The present study indicated that among the twenty genotypes, IR-85086-Sub 33-3-2-1(4.87 t ha-1), IR-88760-Sub 93-3-3 (4.7 t ha-1) and Swarna Sub -1 (4.57 t ha-1) contributed highest yield under submergence.

Comparative Transcriptome Analysis of the Response of Two Lines of Rapeseed (Brassica napus L.) to Cold Stress

Comparative Transcriptome Analysis of the Response of Two Lines of Rapeseed (Brassica napus L.) to Cold Stress

Characterizing Repeats in Two Whole-Genome Amplification Methods in the Reniform Nematode Genome.

One of the major problems in the U.S. and global cotton production is the damage caused by the reniform nematode, Rotylenchulus reniformis. Amplification of DNA from single nematodes for further molecular analysis can be challenging sometimes. In this research, two whole-genome amplification (WGA) methods were evaluated for their efficiencies in DNA amplification from a single reniform nematode. The WGA was carried out using both REPLI-g Mini and Midi kits, and the GenomePlex single cell whole-genome amplification kit. Sequence analysis produced 4 Mb and 12 Mb of genomic sequences for the reniform nematode using REPLI-g and SIGMA libraries. These sequences were assembled into 28,784 and 24,508 contigs, respectively, for REPLI-g and SIGMA libraries. The highest repeats in both libraries were of low complexity, and the lowest for the REPLI-g library were for satellites and for the SIGMA library, RTE/BOV-B. The same kind of repeats were observed for both libraries; however, the SIGMA library had four other repeat elements (Penelope (long interspersed nucleotide element (LINE)), RTE/BOV-B (LINE), PiggyBac, and Mirage/P-element/Transib), which were not seen in the REPLI-g library. DNA transposons were also found in both libraries. Both reniform nematode 18S rRNA variants (RN_VAR1 and RN_VAR2) could easily be identified in both libraries. This research has therefore demonstrated the ability of using both WGA methods, in amplification of gDNA isolated from single reniform nematodes.

Presentation and implementation multi-objective mathematical models to balance the assembly line

The use of assembly lines is one of the important approaches in mass production of industrial products. Imbalance of assembly lines increases cycle time and idle times, resulting in reduced production rates, line efficiency, and increased system costs, which ultimately lead to low productivity. A hybrid model assembly line is a type of production line on which various models of products are assembled. These assembly lines are increasingly accepted in the industry in order to overcome the diversity of customer demand. The hybrid model assembly line is able to respond quickly to sudden changes in demand for different models of a product without maintaining a large inventory.The purpose of this paper is to present a multi-objective integer linear mathematical programming model for balancing assembly lines, which is solved using the general criteria method. The three objective functions considered in this model are: (1) Minimizing cycle time (2) Minimize the idle time of each station and (3) increase the efficiency of the assembly line. In order to investigate the model, Iran-Shargh Neishabour Company has been considered as a case study. After implementing the proposed model of the paper, the results show the optimal performance of the proposed model and the studied parameters in line balancing have been significantly improved.

Op Ed- Blurring Lines — The End of the Open Ed Conference: Who Wins? Who Loses?

Op Ed- Blurring Lines — The End of the Open Ed Conference: Who Wins? Who Loses?

Mixed and separate gender feeding influenced the growth performance for two lines of Korean native chickens when compared to a white semi-broiler and a commercial broiler from day 1 to 35 post-hatch

Mixed and separate gender feeding influenced the growth performance for two lines of Korean native chickens when compared to a white semi-broiler and a commercial broiler from day 1 to 35 post-hatch

COVID-19, spatio-epidemiology and urban planning

Urban life has always been characterized by the trappings of anonymity, opportunity and even risk COVID-19 has fundamentally intensified the risks of urban life;the pandemic has been a particularly urban -- possibly peri-urban -- phenomenon It has introduced a form of epidemiological relation in urban spaces, blurring the lines between health and infirmity The hospital has always occupied a fringe aspect of the urban imagination, providing a space for treatment, observation, inoculation and recovery from ailments With the emergence of COVID-19 however, the spaces of epidemiological observation and treatment have extended beyond hospitals into urban spaces in general COVID-19 is characterized by different strains and susceptibilities to infection;for instance, younger people have comparatively milder symptoms In effect, urban social relations have become epidemiological relations;mere proximity and movement prompt questions of one's state of health Everyday spaces are deemed potential hotspots, every urbanite potentially infectious Proximity, movement and location have become matters of urban-health and public policy Various urban planning strategies have therefore been introduced to regulate urban spaces, movement, proximity and risks of infection One such strategy is the tracking of potential COVID-19 urban hotspots and populations

MAGIC-f gel dosimeter reading: a comparison between an in-house optical CT and MRI imaging

Introduction: According to new developments in radiation therapy techniques, accurate ‎dose verification in three-dimensions has become more critical. Polymer gel dosimeters ‎‎(PGDs) are valuable tools to be used for this purpose. Nowadays, various imaging ‎modalities are employed to read out the gels. This study was aimed to investigate the ‎measured dose distribution recorded in MAGIC-f PGD with optical computed tomography ‎‎(OCT) by comparison with MRI. ‎Material and methods: We developed an in-house CCD based cone-beam OCT scanner. A ‎phantom of MAGIC-f PGD was used to measure a four-field box dose distribution. MRI and ‎OCT scanners were performed for gel readouts. Both measurement results were compared ‎by gamma index analysis with various acceptance criteria. The temporal stability of the gel ‎was also evaluated with the OCT readout system.‎Results: The percentage of isodose lines from two measured datasets agreed well together. ‎The pass rates were 99.02%, 96.8%, and 89.8% with 5%/5mm, 4%/4mm, and 3%/3mm ‎criteria, respectively, at the phantom's central axial slice. ‎Conclusion: The results indicate that the performance of this OCT system is almost the ‎same with acceptable discrepancies to the MRI as accepted standard readout modality, and ‎it can be used for three-dimensional dose verifications.‎

Non-Trivial, Left-Covariant, Continuously Closed Paths over Lines

LetTbe a countably abelian, totally sub-projective random vari-able. It is well known thatC′′is naturally generic, contra-n-dimensional,meromorphic and contra-Hamilton. We show that there exists a com-pact and differentiablep-adic subring. Unfortunately, we cannot as-sume that every globally connected path is local. It is well known that ̄Pis homeomorphic to Ω.

Introduction. Ian Hacking and the Historical Reason of the Sciences

Ian Hacking is among the few that have successfully undermined the Analytic/Continental divide, by working on the “trading zones” between these two strands, and forged their conceptual instruments by drawing these latter from different sources and applying them to widely diverse philosophical debates, across natural, social and medical sciences: debates ranging from the problem of induction and proofs and deduction in mathematics to the theories of meaning and truth as well as to the controversy between realism and constructivism in natural and social sciences. Albeit well-known and widely inspiring, Hacking is still rarely studied, and his wide-ranging production has not yet received an accurate and comprehensive analysis. This Focus aims to precisely fill this gap, by providing one of the first extensive studies dedicated to Hacking’s philosophy. It does not wish, however, to cover all the philosophical areas to which he has possibly contributed, neither does it aim, more generally, to provide a commentary nor an exegesis of his works. By collecting papers by both established and young scholars, this Focus rather intends to explore why Hacking has so largely in- fluenced the field of history and philosophy of science. Analyzing Hacking’s contribution to the 20th-century attempts to bring together history and philosophy of science as well as discussing his arguments on scientific stability, the Focus tackles, from different perspectives, the question of the historicity of reason. Without aspiring to definitive answers, this Focus wishes to open up lines of further research on Hacking’s works as well as along their path.

HRV16 Infection Induces Changes in the Expression of Multiple piRNAs.

Human rhinovirus (HRV) is one of the most important cold-causing pathogens in humans. Piwi-interacting RNAs (piRNAs) are a recently discovered class of small non-coding RNAs whose best-understood function is to repress mobile element (ME) activity in animal germline. However, the profile of human/host piRNA during HRV infection is largely unknown. Here we performed high-throughput sequencing of piRNAs from H1-HeLa cells infected with HRV16 at 12h, 24h, and 36h. The results showed that22,151,664, 24,362,486 and 22,726,546 piRNAs displayed differential expression after HRV16 infection for three time points. A significant differential expression of 21 piRNAs was found in all time points and further verified by RT-qPCR, including 7 knownpiRNAs and 14 newly found piRNAs. In addition, piRNA prediction was performed on Piano using the SVM algorithm and transposon information. It found that novel_pir78110, novel_pir78107, novel_pir78097, novel_pir78094 and novel_pir76584 are associated with the DNA/hobo of Drosophila, Ac of maize and Tam3 of snapdragon (hAT)-Charlie transposon. The novel_pir97924, novel_pir105705 and novel_pir105700 recognize long interspersed nuclear elements 1 (LINE-1). The novel_pir33182 and novel_pir46604 are related to the long terminal repeat (LTR)/(Endogenous Retrovirus1) ERV1 repetitive element. The novel_pir73855 is related to the LTR/ERVK repetitive element. Both novel_pir70108 and novel_pir70106 are associated with the LTR/ERVL-MaLR repetitive element. The novel_pir15900 is associated with the DNA/hAT-Tip100 repetitive element. Overall, our results indicated that rhinovirus infection could reduce theexpression of some piRNAs to facilitate upregulation of LINE-1 transcription or retrotransposons' expression, which is helpful to further explore the mechanism of rhinovirus infection.

Extracted DC component‐based pilot relaying for series‐compensated lines

Extracted <scp>DC</scp> component‐based pilot relaying for <scp>series‐compensated</scp> lines

LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions

BackgroundTo investigate the mechanisms driving regulatory evolution across tissues, we experimentally mapped promoters, enhancers, and gene expression in the liver, brain, muscle, and testis from ten diverse mammals.ResultsThe regulatory landscape around genes included both tissue-shared and tissue-specific regulatory regions, where tissue-specific promoters and enhancers evolved most rapidly. Genomic regions switching between promoters and enhancers were more common across species, and less common across tissues within a single species. Long Interspersed Nuclear Elements (LINEs) played recurrent evolutionary roles: LINE L1s were associated with tissue-specific regulatory regions, whereas more ancient LINE L2s were associated with tissue-shared regulatory regions and with those switching between promoter and enhancer signatures across species.ConclusionsOur analyses of the tissue-specificity and evolutionary stability among promoters and enhancers reveal how specific LINE families have helped shape the dynamic mammalian regulome.

A first look at the ‘repeatome’ of Benedenia humboldti, a major pathogen in yellowtail aquaculture: Repetitive element characterization, nuclear rRNA operon assembly, and microsatellite discovery

The monogenean Benedenia humboldti is a pathogen of the yellowtail Seriola lalandi in the South-Eastern Pacific ocean. Using low-coverage short Illumina 150bp pair-end reads sequencing, this study examines, for the first time, the 'repeatome' (= repetitive genomic elements), including the 45S ribosomal RNA DNA operon and microsatellites, in B. humboldti. Repetitive elements comprised a large fraction of the nuclear genome and a considerable proportion of them could not be assigned to known repeat element families. Taking into account only annotated repetitive elements, the most frequent belonged to the 45S ribosomal RNA operon or were classified as satellite DNA and Class I - Long Interspersed Nuclear Elements (LINEs) which were considerably more abundant than Class I - LTR elements. The ribosomal RNA gene operon in B. humboldti is comprised of, in the following order, a 5' ETS (length=233bp), ssrDNA (2082bp), ITS1 (346bp), 5.8S rDNA (150bp), ITS2 (572bp), lsrDNA (3887bp), and a 3' ETS (1097bp). A total of 15 SSRs were identified. These newly developed genomic resources will contribute to the better understanding of meta-population connectivity in this species, cryptic species in the genus, and will advance pest management strategies.

Desempenho agronômico de rúcula (Eruca sativa L.) em diferentes manejos da cobertura de solo

O presente trabalho teve como objetivo avaliar o desempenho agronômico da rúcula sob diferentes manejos da cobertura de solo. O experimento foi realizado em Florianópolis – SC com delineamento em blocos casualizados, com quatro tratamentos e quatro repetições. Foi utilizada a cultivar Rococó, semeada diretamente em campo em um espaçamento de 5 x 15 cm entre plantas e entre linhas, respectivamente. Os tratamentos consistiram na testemunha (sem capina), cobertura morta, lona plástica e capina manual. Avaliou-se o número de folhas, área foliar e massa fresca. O experimento foi finalizado aos 33 dias após a semeadura. Os dados foram submetidos à análise de variância e ao teste de Tukey para diferenciar as médias a 5% de probabilidade. A capina manual das plantas espontâneas foi significativamente superior à ausência de capina para a área foliar, massa fresca e produtividade. Não houve diferenças entre os tratamentos para o número de folhas. Os resultados demonstraram melhor desempenho da rúcula quando manejada com capina manual, mas os manejos com cobertura morta ou lona plástica apresentaram desempenho similar, também sendo alternativas viáveis.

Early maternal care restores LINE-1 methylation and enhances neurodevelopment in preterm infants

BackgroundPreterm birth affects almost 9–11% of newborns and is one of the leading causes of childhood neurodevelopmental disabilities; the underlying molecular networks are poorly defined. In neurons, retrotransposons LINE-1 (L1) are an active source of genomic mosaicism that is deregulated in several neurological disorders; early life experience has been shown to regulate L1 activity in mice.MethodsVery preterm infants were randomized to receive standard care or early intervention. L1 methylation was measured at birth and at hospital discharge. At 12 and 36 months, infants’ neurodevelopment was evaluated with the Griffiths Scales. L1 methylation and CNVs were measured in mouse brain areas at embryonic and postnatal stages.ResultsHere we report that L1 promoter is hypomethylated in preterm infants at birth and that an early intervention program, based on enhanced maternal care and positive multisensory stimulation, restores L1 methylation levels comparable to healthy newborns and ameliorates neurodevelopment in childhood. We further show that L1 activity is fine-tuned in the perinatal mouse brain, suggesting a sensitive and vulnerable window for the L1 epigenetic setting.ConclusionsOur results open the field on the inspection of L1 activity as a novel molecular and predictive approach to infants’ prematurity-related neurodevelopmental outcomes.Trial registrationClinicalTrial.gov (NCT02983513). Registered on 6 December 2016, retrospectively registered.

The enhancer activity of long interspersed nuclear element derived microRNA 625 induced by NF-\u03baB

Transposable elements (TEs) are DNA sequences that cut or introduced into the genome, and they represent a massive portion of the human genome. TEs generate a considerable number of microRNAs (miRNAs) are derived from TEs (MDTEs). Numerous miRNAs are related to cancer, and hsa-miRNA-625 is a well-known oncomiR derived from long interspersed nuclear elements (LINEs). The relative expression of hsa-miRNA-625-5p differs in humans, chimpanzees, crab-eating monkeys, and mice, and four primers were designed against the 3′UTR of GATAD2B to analyze the different quantities of canonical binding sites and the location of miRNA binding sites. Luciferase assay was performed to score for the interaction between hsa-miRNA-625 and the 3′UTR of GATAD2B, while blocking NF-κB. In summary, the different numbers of canonical binding sites and the locations of miRNA binding sites affect gene expression, and NF-κB induces the enhancer activity of hsa-miRNA-625-5p by sharing the binding sites.

Genetic and Agronomic Analysis of a Recombinant Inbred Line Population to Map Quantitative Trait Loci for Blast Resistance and Select Promising Lines in Rice

Genetic and Agronomic Analysis of a Recombinant Inbred Line Population to Map Quantitative Trait Loci for Blast Resistance and Select Promising Lines in Rice

Sex dimorphism of Yunnanilus analis and its habitat adaptation in Xingyun Lake, Yunnan, China.

Yunnanilus is a group of endemic fish inhabit in Yun-Gui Plateau and its adjacent areas. They show the characteristic of sex dimorphism, which could be an important reason for their adaptation to karst habitats. Here, we used Yunnanilus analis as the model to understand the sex dimorphism characteristics and its adaptation to the karst habitats. The sex dimorphism, female fecundity, and food specialization of Y. analis were investigated in Xingyun Lake, Jiangchuan, Yunnan. Our results showed that Y. analis exhibit sex size dimorphism (sex dimorphism index=0.23; female with larger body size). There were stains on the transverse sections at females body, but not in males. Males had dark longitudinal lines at their body sides. Morphological differences between males and females were confirmed by the results of one-way analyses of variance (ANOVA), multivariate statistical analyses, principal component analyses, discriminant analyses, and one-way analyses of similarity (ANOSIM) on total length, standard body length, fork length, head width vs. heal length, and the distance between the starting point of ventral fin to the starting point of pectoral fin vs. standard body length. Fecundity of female fish was 1364.5±489.3 (470-2430) eggs, which were positively correlated with their body size. Both female and male Y. analis mainly feed on Chironomid larvae and mayfly naiads. Their food composition was somehow similar, with significantly statistical difference. In conclusion, fecundity selection pressure and food specialization should be the main factors contributing to the evolution of Y. analis' sex dimorphism. More importantly, sex dimorphism of Y. analis is a significant adaptation to the karstic habitats.