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Sequence bias in edited kinetoplastid RNAs.

Uridylate residues (Us) are inserted and deleted at precise positions in mitochondrial transcripts of Trypanosoma brucei. These sequence changes are determined by interactions with small guide RNAs (gRNAs) that are complementary to edited sequence. Adenylate (A) and guanylate (G) residues in gRNAs across from editing sites pair with inserted Us. We evaluate whether sequence bias exists in the bases surrounding insertion sites. Upon analyzing all reported insertion sites in T. brucei, we find that the predicted base pairs flanking insertion sites show a strong bias. Specifically, guiding As and Gs tend to be flanked by cytosine residues and Us. This bias is expected if precise base-pair interactions at the editing site determine the number of inserted Us.

Adenine↗

[A bibliographic study on Tongui-bigan with a special reference to its influence on Japan and China].

In this work my main focus was put on two things; first, to examine the history of publication of Tongui - bogam within the nation with particular interest in the changing aspect observed from the bibliographical terms, and second, to examine the process through which Tongui - bogam was introduced to Japan and China, and the influence the book brought the two nations. Some of the findings concerning the domestic publication of Tongui - bogam are as follows. The first printing of the book was made in 1613, under the auspice of Naeui - won, one of the government organs in the capital in charge of medical affairs. It was printed with wooden movable type carved at Hullyeon - togam, the military training bureau. As for the question of the history of the domestic publication of Tongui - bogam after the first printing in 1613, we don't have enough data yet. Although there are many different editions of Tongui - bogam extant today, with different size and different font each, I could find so far only three copies which carry the data concerning its publication, one printed in 1659 by the Kyongsang provincial government with newly engraved woodblock, one printed in 1754 again by the Kyongsang provincial government with re-engraved woodblock, and one printed in 1814 by the Cholla provincial government with newly re-engraved woodblock. Each of the three was a revised edition at the time of its publication because every time it was based on the copy corrected by Naeui - won. In addition to the above mentioned three different editions of Tongui - bogam, three are quite a few copies originally printed with wooden movable type of different font, at various time and various places. None of them has any record concerning the date and place of its publication, and none of them shows that it was based on the Naeui-won corrected version as a mother copy. Accordingly, all of them carry quite a few erratum misprinting and it seems quite certain that all of them were produced before 1659. I also feel that the 1724 Japanese edition was based on one of the pre - 1659 copies. In Japan, the first publication of Tongui - bogam was made in the year of 1724 (the 9th year of Kyoho in Japanese year title) under the auspice of the Japanese government i.e. the Tokugawa Bakuf. The book carries a preface written by a man named Fubihara, then the vice president of national university, and a postscript written by Minamoto mototoru, a government attached monk physician. It was a woodblock printing and the title of the book was "Kankoku - Teisei Tongui - bogam. The reason the word "Kankoku-Teisei" the Revised Edition Printed with Officially Engraved Woodblocks", was added to the title was that the publication was made by the government and before publication the government ordered Minamoto to read through the original Tongui-bogam throughly and make corrections if any misprintings be found. Minamoto also put the so-called kunto marks, the Japanese way of punctuation system on the original text all the way so that they could read it in the their own way. As the question of what edition of Tongi - bogam the Japanese used as a mother copy and whwn and how the mother copy had been brought to Japan are not clear at all. But judging from the fact that it carries quite a few erratum in spite of their efforts at proofreading before engraving the woodblock, it seems likely that Tongui - bogam they used as a mother copy was the one which was printed in Korea before 1659. In 1659 Tongui-bogam was published in Korea by the Kyongsang provincial government in Taegu with newly engraved woodblock. According to the attached record concerning its publication, it was a revised edition based on the Naeui - won corrected-copy, and this edition carries no misprintings in it at all. On the other hand, among the various editions of the extant Tongui - bogam today we can find some copy which, originally printed from wooden movable type, carries almost the same misprinting as those found in the 1724 Japanese edition. In other words, we are quite certain that the mother copy of the 1724 Japanese edition was brought to Japan before the Naeui - won - corrected - edition began to appear in Korea in 1659. The second publication of Tongui - bogam in Japan was made in 1799 in the city of Osaka. It was reprinted from the original woodblock of 1724 edition, and this second edition was later used in China in 1890 as a mother copy. The first publication of Tongui - bogam in China was made in the year 1766. It was a woodblock edition printed in Kwangtung province, located in the southern end of China. According to the attached preface written by a high ranking official named Nŭngŏ, a native of Kwangtung area, the publication was originally initiated by the governor of that province Mr. Wang, who deeply admired the value of Tongui - bogam. Since the Tongui - bogam at that time was available only in Bigak, the palace library in Peijing, the capital of the Ch'ing dynasty, the governor Mr. Wang had to send a man to Peijing to make a manuscript copy of Tongui - bogam of 25 of the volumes. But unfortunately Mr. Wang left his post before his plan to publish the book was realized and it was thanks to another native man named Chwahanmun who donated big money to cover the expenses of publication. The 1766 edition of Tongui - bogam, one copy of which is now in the possession of Kyungbuk University library, is understandably not a good copy, because it has many erratum in it. But it was reprinted afterwards sometimes with re-engraved woodblock many times at various places in China. The second publication of Tongui - bogam in China appeared in 1890. It carries a preface written by Mincheyusang. It was based on the Japanese edition printed in 1799 in Oosaka. What is interesting with Mr. Min's preface is that it shows their deep admiration of the value of Tongui - bogam on one hand, and at the same time very critical attitude toward the basic philosophy of Hŏjun on the other hand.

Bibliography of Medicine↗

Molecular and transcriptional regulation of plant defense responses to aphid infestation.

Aphids are one of the important agricultural pests causing substantial yield losses in crops grown across the globe. Aphids are known to cause direct feeding damages and indirect losses due to sooty mold development and plant virus transmission. Plants respond to these attacks by mounting a complex defense response at the infested sites and systemic levels. This multilayered defense response involves a highly coordinated network of phytohormones and other signalling components like Ca2+, mitogen activated protein kinases and reactive oxygen species. Key to these complex responses is a well-regulated gene expression involving several transcription factors. A wide range of transcription factors are structurally and functionally characterized across some model plants and in a few agronomically important crops. These transcription factors play diverse roles such as defense gene expression modulation, regulation of hormone signaling, secondary metabolism, oxidative stress response, cell wall modifications, and phloem-based defense. Understanding the integration of signaling pathways, hormone crosstalk, and transcription factor mediated regulation provides a framework for practical applications, including breeding, genome editing, and elicitor-based strategies. This review highlights how plant defense signaling and transcriptional regulation against aphids can be harnessed to develop sustainable and novel pest management solutions.

Aphid↗

A Java-based enterprise system architecture for implementing a continuously supported and entirely Web-based exercise solution.

Since machine-based exercise still uses local facilities, it is affected by time and place. We designed a web-based system architecture based on the Java 2 Enterprise Edition that can accomplish continuously supported machine-based exercise. In this system, exercise programs and machines are loosely coupled and dynamically integrated on the site of exercise via the Internet. We then extended the conventional health promotion model, which contains three types of players (users, exercise trainers, and manufacturers), by adding a new player: exercise program creators. Moreover, we developed a self-describing strategy to accommodate a variety of exercise programs and provide ease of use to users on the web. We illustrate our novel design with examples taken from our feasibility study on a web-based cycle ergometer exercise system. A biosignal-based workload control approach was introduced to ensure that users performed appropriate exercise alone.

Exercise Therapy↗

No melancholia in poststroke depression? A phenomenologic comparison of primary and poststroke depression.

The present study aimed at the phenomenologic comparison of depressive symptoms in elderly patients with poststroke depression (PSD) or primary depression (depression without a known neuropathology). We investigated 20 patients with PSD and 41 patients with primary depression. A structured clinical interview based on the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, self- and observer-based depression rating scales, a clinical neurologic examination, and neuroradiologic analysis based on standardized computed tomographic scan analysis were applied. The Cornell Depression Scale was used to compare mood-related signs, behavioral disturbances, physical signs, disturbances of cyclic signs, and ideational disturbances in both groups of patients. Those with PSD exhibited no melancholia and fewer cyclic and ideational disturbances but more physical signs of depression. These findings are in line with those of endocrinologic studies. Differences between both groups of patients indicate that careful considerations and further research are needed before treatment strategies developed for and evaluated in patients with primary depression are applied to patients with PSD.

Affect↗

Editing domains of Trypanosoma brucei mitochondrial RNAs identified by secondary structure.

The posttranscriptional insertion and deletion of U residues in trypanosome mitochondrial transcripts called RNA editing initiates at the 3' end of precisely defined editing domains that can be identified independently of the cognate guide RNA. The regions where editing initiates in Trypanosoma brucei cytochrome b and cytochrome oxidase subunit II preedited mRNAs are specifically cleaved by a trypanosome mitochondrial endonuclease that acts like mung bean nuclease and therefore is single strand specific. The regions where editing initiates in virtually all examined preedited mRNAs are predicted to form loop structures, suggesting that editing domains could generally be recognized as prominent single-stranded loops. In contrast to preedited mRNA, edited mRNA can be either resistant or sensitive to cleavage by trypanosome mitochondrial endonuclease, depending on the reaction conditions. This selectivity appears dependent on the availability of extract RNAs, and in model reactions, edited mRNA becomes resistant to cleavage upon base pairing with its guide RNA. Natural partially edited mRNAs are also specifically cleaved with a sensitivity like preedited and unlike edited mRNAs, consistent with their being intermediates in editing. These results suggest that in vivo, the structure of editing domains could initially be recognized by the mitochondrial endonuclease, which could target its associated RNA ligase and terminal U transferase to begin cycles of enzymatic editing modifications.

Animals↗

Importance of terminal base pair hydrogen-bonding in 3'-end proofreading by the Klenow fragment of DNA polymerase I.

We describe studies aimed at evaluating the physical factors governing the rate of 3'-end proofreading by the Klenow fragment of E. coli DNA polymerase I. Two nonpolar deoxynucleoside isosteres containing 2,4-difluorotoluene (F) and 4-methylbenzimidazole (Z), which are non-hydrogen-bonding shape mimics of thymine and adenine, respectively, are used to investigate the effects of base pair geometry and stability on the rate of this exonuclease activity. Steady-state kinetics measurements show that complementary T.A base pairs at the end of a primer-template duplex are edited 14-40-fold more slowly than mismatches. By contrast, a 3'-end T residue in a T. Z pair is edited at a rate equivalent to that of natural base mismatches despite the fact that it resembles a T.A pair in structure. Similarly, the A in an A.F pair is edited as rapidly as a mismatched pair despite its close structural mimicry of an A.T pair. Interestingly, when the base pairs are reversed and F or Z is located at the 3'-end, they are edited more slowly, possibly implicating specific interactions between the exonuclease domain and the base of the nucleotide being edited. Finally, thermal denaturation studies are carried out to investigate the relationship between editing and the ease of unwinding of the duplex. The rapid editing of bases opposite F or Z residues at the duplex terminus seems to correlate well with the stability of these base pairs when placed in a context resembling a primer-template duplex. In general, the rate of 3'-end editing appears to be governed by the rate of fraying of the DNA terminal pair, and base pair geometry appears to have little effect.

3' Untranslated Regions↗

AMA's drug information data base: program capabilities and opportunities for clinical pharmacy.

The AMA drug information base (AMA-DIB) is reviewed and the impact of computerized drug data bases on the practice of clinical pharmacy is discussed. The AMA-DIB is an on-line data base derived from the fifth edition of AMA Drug Evaluations. Thus, it represents consensus information. The data base consists of individual drug records, pharmacologic class records, and therapeutic class records. It is accessed via commands using keyword searches. Computerized on-line drug data bases will have an impact on the practice of clinical pharmacy. Information resource services will either discontinue or proliferate, depending on the quality of the service and the ability of the directors to adapt to future needs. Patient monitoring services will discover that these data bases allow easier access to more information, but the computer will not be able to transfer the data to direct patient care. Thus, their professional roles will remain intact. Clinical pharmacy researchers, in contrast, will notice little or no impact on their practice.

American Medical Association↗

abCRISPR: deep learning-based design of abasic gRNA sequences for specific CRISPR-Cas9 genome editing.

SUMMARY: CRISPR-Cas9 has become a widely used tool for genome editing. However, its off-target cleavage caused by partial sequence matches with guide RNAs (gRNAs) remains a critical limitation. Recently, abasic gRNAs (ØXØ) have been developed to enhance target specificity, but their effects vary depending on the positional sequence context. Here, we present abCRISPR, a deep neural network (DNN) framework for the rational design of ØXØ sequences with minimized off-target activity. abCRISPR leverages informative few-shot training with paired datasets of abasic and unmodified gRNAs, using high-quality random mismatch target libraries, exhaustively sequenced for mismatched off-target substrates (n = 97583) in in vitro CRISPR-Cas9 cleavage experiments. Predicted off-target activities for both abasic and unmodified gRNAs showed strong correlation with experimental data (r ≥ 0.95, 10-fold cross-validation). Notably, these comprehensive training sets provide robust ground-truth negatives, enabling accurate and sensitive prediction of off-targets. For unmodified gRNAs, abCRISPR (AUC = 0.98) was validated to outperform existing deep learning-based methods (AUC = 0.45-0.68). When applied to the human genome, abCRISPR generated ØXØ sequences, covering 58 875 004 potent CRISPR-targetable sites with improved target specificity. Together, this work provides a comprehensive bioinformatics resource for safe and precise CRISPR-Cas9 genome editing. AVAILABILITY AND IMPLEMENTATION: The source code for abCRISPR and training data are available at https://doi.org/10.5281/zenodo.20398246. abCRISPR results for the human genome are available at http://clip.korea.ac.kr/abCRISPR/.

Deep Learning↗

Kinetoplastid RNA editing: in vitro formation of cytochrome b gRNA-mRNA chimeras from synthetic substrate RNAs.

RNA editing in the kinetoplastid Trypanosoma brucei results in the addition and deletion of uridine residues within several mitochondrial mRNAs. The site and number of uridines added appears to be directed by small (approximately 70 nt) guide RNAs (gRNAs), which can base pair to the edited sequences. We examined reactions involving synthetic cytochrome b (CYb) gRNA and pre-edited mRNA in vitro. A major product of the in vitro reaction is a chimeric RNA molecule containing both gRNA and mRNA sequences. Formation of the CYb gRNA-mRNA chimera was specific, since such molecules did not accumulate when either the gRNA or mRNA was substituted with control RNAs. The reaction required a free 3' hydroxyl on the gRNA and was unaffected by capping of the gRNA's 5' end. Direct RNA sequencing indicated that the CYb gRNA is covalently linked via its 3' poly(U) tail to one of the editing sites on the CYb mRNA. These results suggest that the U's added during editing are donated by the poly(U) tail of a gRNA via a chimeric gRNA-mRNA intermediate.

Animals↗

Impact of changes to the American Joint Committee on Cancer T classification on outcome prediction in patients with oropharyngeal cancer.

BACKGROUND: The efficacy of the current 6th edition of the American Joint Committee on Cancer (AJCC) tumor staging criteria in improving outcome prediction for patients with oropharyngeal cancer was analyzed. METHODS: From the database of the Department of Radiation Oncology at the University of Texas M. D. Anderson Cancer Center the authors identified 875 patients irradiated at the study institution for oropharyngeal cancer between January 1975 and December 1998. The tumors were restaged based on the 6th edition of AJCC tumor staging criteria to reassess the original outcome predictions, specifically overall survival (OS) and local control (LC). RESULTS: Applying the new 6th edition staging system resulted in the following T classification distributions: T2, 301 tumors (34%); T3, 248 tumors (28%); T4a, 224 tumors (26%), and T4b, 102 tumors (12%). The 5-year and 10-year OS rates based on the new system were: T2, 65% and 45%; T3, 44% and 28%; T4a, 30% and 23%; and T4b, 26% and 12%, respectively. The 5-year and 10-year actuarial local LC rates based on the new system were: T2, 85% and 83%; T3, 73% and 71%; T4a, 61% and 58%; and T4b, 42% and 42%, respectively. Differences in OS and LC rates stratified by stage were found to be statistically significant both for the overall distribution of survival and pairwise comparisons of the 4 tumor stage groups. CONCLUSIONS: The modifications established in the 6th edition of the AJCC tumor staging system for oropharyngeal tumors appear to be useful to distinguish prognostic groups for both LC and OS based on tumor stage.

Adult↗

Evaluation of the newly updated TNM classification of head and neck carcinoma with data from 3247 patients.

BACKGROUND: The fifth edition of the TNM classification contains a number of changes concerning head and neck tumors. The division of Stage IV tumors into three subcategories marks a significant expansion of the stage grouping procedure. METHODS: In a retrospective study, the clinical courses of 3247 patients with carcinoma of the oral cavity, the oro- and hypopharynx, the larynx, the salivary glands, and the maxillary sinus were comparatively evaluated according to the fourth and fifth editions of the TNM classification agreed upon by the International Union Against Cancer and the American Joint Committee on Cancer. The particular aim of this study was to test the prognostic relevance of the subdivision of Stage IV, especially for mucosal carcinoma. RESULTS: In classifying the primary tumor, the most extensive changes were noted for supraglottic and salivary gland tumors. On the basis of the fourth edition of the TNM classification, the following recurrence free 5-year survival rates for 3033 cases of mucosal cancer were calculated: Stage I, 91.0%; Stage II, 78.6%; Stage III, 61.4%; Stage IV, 31.0%. The calculations based on the fifth edition yielded the following: Stage I, 91.0%; Stage II, 77.2%; Stage III, 61.2%; Stage IVA, 32.4%; Stage IVB, 25.3%; Stage IVC, 3.6%. CONCLUSIONS: The adequacy of the revised stage classification in establishing a prognostic hierarchy was confirmed. However, a significant prognostic distinction between N2 metastasis (Stage IVA) and N3 metastasis (Stage IVB) could not be found.

Carcinoma↗

[Reference population values for the Spanish Child Health and Illness Profile-Adolescent Edition (CHIP-AE) using a representative school-based sample].

AIM: The Child Health and Illness Profile (CHIP-AE) is a generic health status instrument for adolescents aged 12-19 years adapted for use in Spain. The aim of this study was to obtain reference population values of the Spanish version of the CHIP-AE. METHODS: The CHIP-AE was administered to a representative sample of adolescents from schools in Barcelona. The sample was selected by using cluster-sampling, stratified by type of school (public or private) and an ecological socioeconomic index (Indice de Capacidad Familiar: low, middle, and high). The CHIP-AE scores were standardized to a mean of 20 and a standard deviation (SD) of 5. Means and percentiles were computed. Means were compared by age, gender, and socioeconomic status using analysis of variance. RESULTS: The response rate was 81% (n = 902). The distribution of the CHIP-AE scores presented a wide range with scores generally skewed toward positive health status. Nevertheless, the results suggest that the sample selected from a general population was not free of health problems. Twenty-five percent of adolescents presented scores below 17.2 in the domain of discomfort, indicating an effect size of 0.56 standardized SD units. The distribution of scores in the reference samples from Barcelona was similar to the original results in Baltimore (USA), with some marginal differences in individual risks. CONCLUSIONS: The CHIP-AE systematically gathers information on health domains in adolescents. The results from this reference sample will allow comparisons with adolescents from other regions, and/or with different health problems, as well as description of inequalities in health during adolescence.

Adolescent↗

[Evaluation of the "new" TNM classification of head and neck tumors in 3247 patients].

UNLABELLED: The 5th edition of the TNM classification entails a number of changes concerning head and neck tumors. The division of stage IV tumors into three subcategories marks a significant expansion of the stage grouping procedure. METHODS: In a retrospective study the clinical course of 3247 patients with head and neck carcinomas were comparatively evaluated according to the 4th and 5th editions of the new TNM classification. In particular it was the aim of the study to test the prognostic relevance of the subdivision of stage IV especially in mucosal cancer. RESULTS: In classifying the primary tumor the most extensive changes were noted for supraglottic and salivary gland tumors. On the basis of the 4th edition of the TNM classification the following recurrence-free 5-year survival rates for 3033 cases of mucosal cancer were calculated: stage I 91,0%, stage II 78.6%, stage III 61.4%, stage IV 31.0%. The calculations based on the 5th edition yielded: stage I 91.0%, stage II 77.2%, stage III 61.2%, stage IVA 32.4%, stage IVB 25.3%, stage IVC 3.6%. CONCLUSIONS: The adequacy of the revised stage classification in establishing a prognostic hierarchy was confirmed. However, a significant prognostic distinction between N2- (stage IVA) and N3-metastasis (stage IVB) could not be found.

Adult↗

RNA editing: transfer of genetic information from gRNA to precursor mRNA in vitro.

RNA editing in the mitochondrion of Trypanosoma brucei extensively alters the adenosine triphosphate synthase (ATPase) subunit 6 precursor messenger RNA (pre-mRNA) by addition of 447 uridines and removal of 28 uridines. In vivo, the guide RNA gA6[14] is thought to specify the deletion of two uridines from the editing site closest to the 3' end. In this study, an in vitro system was developed that accurately removed uridines from this editing site in synthetic ATPase 6 pre-mRNA when gA6[14] and ATP were added. Mutations in both the guide RNA and the pre-mRNA editing site suggest that base-pairing interactions control the number of uridines deleted in vitro. Thus, guide RNAs are required for RNA editing and for the transfer of genetic information to pre-mRNAs.

Adenosine Triphosphatases↗

Rewriting the information in DNA: RNA editing in kinetoplastids and myxomycetes.

RNA editing has a major impact on the genes and genomes that it modifies. Editing by insertion, deletion and base conversion exists in nuclear, mitochondrial and viral genomes throughout the eukaryotic lineage. Editing was first discovered in kinetoplastids, and recent work has resulted in the characterization of some components of the editing machinery. Two proteins with ligase activity have been identified in Trypanosoma brucei, and other proteins in the editosome complex are yielding to the probe of research. A second group of protists, myxomycetes, are unique in their use of four different types of editing within a single transcript. Phylogenetic analysis of editing in representative myxomycetes revealed a different history of the four types of editing in this lineage. Development of a soluble in vitro editing system has provided further support for the co-transcriptional nature of editing in Physarum polycephalum, and will certainly provide future opportunities for understanding this mysterious process.

Cytidine↗

From scissors to editors: how the evolution of precision is redefining therapeutic genome editing.

Since its introduction as a genome-editing tool, CRISPR-based technology has undergone rapid refinement, with precision emerging as a central focus of development. Early CRISPR-Cas9 systems demonstrated unprecedented ease and efficiency in targeting specific DNA sequences, but concerns over off-target effects and variable editing outcomes limited their broader application. This review outlines the progression of CRISPR from its discovery in prokaryotes to its application as a versatile tool in precision medicine, where it supports targeted therapies for genetic disorders in various ways. Although technical challenges, including off-target editing and delivery inefficiencies, persist alongside ethical considerations of accessibility and long-term consequences, CRISPR's ongoing refinements and innovations reflect a clear trajectory toward greater specificity, safety, and predictability, positioning CRISPR as an increasingly precise platform for both fundamental research and therapeutic use.

Gene Editing↗