Chemical Names Research Articles

MODOMICS: a database of RNA modifications and related information. 2023 update.

The MODOMICS database was updated with recent data and now includes new data types related to RNA modifications. Changes to the database include an expanded modification catalog, encompassing both natural and synthetic residues identified in RNA structures. This addition aids in representing RNA sequences from the RCSB PDB database more effectively. To manage the increased number of modifications, adjustments to the nomenclature system were made. Updates in the RNA sequences section include the addition of new sequences and the reintroduction of sequence alignments for tRNAs and rRNAs. The protein section was updated and connected to structures from the RCSB PDB database and predictions by AlphaFold. MODOMICS now includes a data annotation system, with 'Evidence' and 'Estimated Reliability' features, offering clarity on data support and accuracy. This system is open to all MODOMICS entries, enhancing the accuracy of RNA modification data representation. MODOMICS is available at https://iimcb.genesilico.pl/modomics/.

Role of Cytogenetics and Fluorescence In Situ Hybridization in the Laboratory Workup of Acute Myeloid Leukemias

AbstractA new understanding of acute myeloid leukemia as a varied group of unique biologic entity has emerged, as a result of the identification of various chromosomal aberrations and their association with clinical prognosis and diagnosis. Following induction treatment, cytogenetic examination can establish the presence of any residual malignant cells, it's recurrence, clonal evolution if any, or the formation of novel abnormalities. The G-banded karyotype has been the gold standard method for detecting all of these aberrations for years. The capacity to examine the entire genome through karyotype analysis quickly enabled the detection of deletions, duplications, and structural rearrangements across every chromosome, and the more frequent ones were associated with particular aberrant clinical symptoms. Fluorescence in situ hybridization (FISH) is a sensitive technology that aids in differential diagnosis or therapeutic planning and provides rapid results. Furthermore, the combination of cytogenetic and molecular profiling enables a more precise evaluation of disease prognosis, diagnosis, classification, risk stratification, and patient treatment. Interphase FISH analysis, in conjunction with G-banded chromosomal analysis, can be used as a major testing tool for the evaluation of hematological neoplasms. For accurate and consistent descriptions of genomic changes identified by karyotyping and FISH, a specified terminology is necessary. The International System for Human Cytogenomic Nomenclature is the main source and provides instructions for documenting cytogenetic and molecular findings in laboratory reports. This review discusses the two methods, karyotyping and FISH, their advantages and limitations, sample requirements, various FISH probes that are used, nomenclature for results reporting, and the necessary quality control measures.

A Multicenter Study Validates the WHO 2022 Classification for Conjunctival Melanocytic Intraepithelial Lesions With Clinical and Prognostic Relevance

Several nomenclature and grading systems have been proposed for conjunctival melanocytic intraepithelial lesions (C-MIL). The fourth “WHO Classification of Eye Tumors” (WHO-EYE04) proposed a C-MIL classification, capturing the progression of noninvasive neoplastic melanocytes from low- to high-grade lesions, onto melanoma in situ (MIS), and then to invasive melanoma. This proposal was revised to the WHO-EYE05 C-MIL system, which simplified the high-grade C-MIL, whereby MIS was subsumed into high-grade C-MIL. Our aim was to validate the WHO-EYE05 C-MIL system using digitized images of C-MIL, stained with hematoxylin and eosin and immunohistochemistry. However, C-MIL cases were retrieved from 3 supraregional ocular pathology centers. Adequate conjunctival biopsies were stained with hematoxylin and eosin, Melan-A, SOX10, and PReferentially expressed Antigen in Melanoma. Digitized slides were uploaded on the SmartZoom platform and independently scored by 4 ocular pathologists to obtain a consensus score, before circulating to 14 expert eye pathologists for independent scoring. In total, 105 cases from 97 patients were evaluated. The initial consensus diagnoses using the WHO-EYE04 C-MIL system were as follows: 28 benign conjunctival melanoses, 13 low-grade C-MIL, 37 high-grade C-MIL, and 27 conjunctival MIS. Using this system resulted in 93% of the pathologists showing only fair-to-moderate agreement (kappa statistic) with the consensus score. The WHO-EYE05 C-MIL system (with high-grade C-MIL and MIS combined) improved consistency between pathologists, with the greatest level of agreement being seen with benign melanosis (74.5%) and high-grade C-MIL (85.4%). Lowest agreements remained between pathologists for low-grade C-MIL (38.7%). Regarding WHO-EYE05 C-MIL scoring and clinical outcomes, local recurrences of noninvasive lesions developed in 8% and 34% of the low- and high-grade cases. Invasive melanoma only occurred in 47% of the cases that were assessed as high-grade C-MIL. This extensive international collaborative study is the first to undertake a comprehensive review of the WHO-EYE05 C-MIL scoring system, which showed good interobserver agreement and reproducibility.

Automated Cytogenetic Classifier (ACC) to Support Accurate Clinical Decision Making in Acute Myeloid Leukaemia

Introduction Cytogenetic analysis is a recommended test in newly diagnosed AML but requires accurate interpretation of the International System for Human Cytogenomic Nomenclature (ISCN). Keeping up to date across recent published classifications - WHO, the European Leukaemia Net (ELN) and International Consensus Classification (ICC) - is critical for accurate prognostic assessment, but can be challenging for clinicians and laboratory scientists. Furthermore, eligibility to access state-funded treatments in the UK is dictated by certain cytogenetic results. We previously developed a webapp that integrates cytogenetic, molecular and clinical features to aid accurate classification, prognostication and provide treatment recommendations in AML (Coats et al, BJH 2021). To further improve the webapp we have developed a cytogenetic classifier to automatically interpret reports written in ISCN format. In this study we aimed to validate the automated cytogenetic classifier (ACC) in identifying abnormalities that feature in the new WHO, ELN and ICC classifications. Methodology Software for the ACC was written in Python to: 1. count the number and type of karyotypic abnormalities (subdivided into number of monosomies, complete chromosome gains and structural changes) 2. identify presence of clinically relevant, named, abnormalities that feature in international classifications (categorised as an individual abnormalityg. t(9;11)(p21.3;q23.3), or a generic abnormality e.g. any translocation involving 11q23.3). Cytogenetic reports of 50 consecutive AML cases with abnormal karyotypes analysed by Bristol Haematological Oncology Diagnostic Service (BHODS) were selected (training cohort). Each report was uploaded to the ACC and its output independently checked for accuracy. Following review of the software's performance, adjustments to the ACC were made. The updated ACC (Figure 1) analysed 98 additional reports from two other laboratories, UCLH and OUH (validation cohort). Results The ACC analysed 49/50 cytogenetic reports from the BHODS laboratory. One report could not be read by the ACC. The correct quantity of abnormalities was identified in 49/49 cases analysed. Where relevant named abnormalities occurred, these were detected in 79/80 instances. One case of acute promyelocytic leukaemia containing an idic(17p) was not identified as containing an abnormal 17p. Additionally, in one report with a complex karyotype, a monosomy 13 was erroneously detected by the ACC. Adjustments were made to the ACC such that it could analyse all 50 cases with 100% accuracy. The updated ACC then analysed 98 cases from the validation cohort. The correct quantity of abnormalities was detected in 97/ 98 cases. In one case with a highly complex karyotype containing a tetraploid clone, the ACC incorrectly counted 48, as opposed to 45, abnormalities. Clinically relevant, named, abnormalities were correctly identified in 178/179 instances. In one case, containing a 4-way translocation, the ACC did not identify the t(9;11) abnormality. Discussion Here, we show that the updated ACC is accurate in identifying the number and type of karyotypic abnormalities relevant to AML from different laboratories. Reduced accuracy in counting the number of abnormalities in highly complex karyotypes (i.e. >40 abnormalities) is not likely to impact clinical interpretation. Further validation work is needed to analyse 3 and 4-way translocations. User warnings have been added to the ACC for karyotypes containing multiple-translocations and tetraploid/triploid clones to improve clinical safety. The ACC can support clinical decision-making by streamlining cytogenetic interpretation from across multiple clinical classifications. It can be used as a stand-alone programme or integrated into more sophisticated decision support tools. The ACC has the potential to be updated to interpret cytogenetic reports from other classifications or haematological malignancies. The ACC is available as a webapp (Streamlit (ts482-cytogenetics-calculator-extractorstreamlit-w7dq9p.streamlit.app). Figure 1. Flowchart of the methodology of the updated automated cytogenetic classifier (ACC).

Counting Chromosome Abnormalities in Chronic Lymphocytic Leukemia: Comparison of Iscn 2020 and MDS International Working Group Guidelines for Establishing Karyotype Complexity

Karyotype complexity is established by enumerating the number of chromosome abnormalities present in a karyotype. In chronic lymphocytic leukemia (CLL), karyotype complexity, defined as ≥3 chromosome abnormalities, is an important prognostic indicator associated with poor outcomes. Additionally, stratifying patients (pts) by highly complex karyotypes (≥5 chromosome abnormalities) has shown significantly poorer outcomes compared to pts with 3-4 abnormalities (Baliakas, Blood, 2019). In principle, counting chromosome abnormalities is straightforward; however, in practice it can be nuanced, and the number of abnormalities counted for the same karyotype can differ across laboratories. A lack of standardized rules has resulted in variability in establishing complexity across CLL studies. We and others have proposed adapting the international working group on myelodysplastic syndrome (MDS) framework for use in CLL (Chun, Leuk Res, 2010; Jondreville, Am J Hematol, 2020). Additionally, a separate set of guidelines were published in the 2020 International System for Human Cytogenomic Nomenclature (ISCN). To investigate how different guidelines may impact patient categorization in correlative studies, we evaluated karyotype complexity using both guidelines in a previously reported, well-characterized, dataset with long term follow-up of patients with CLL treated with ibrutinib (Kittai, Blood, 2021). 456 patient karyotypes underwent expert review by two cytogeneticists. Discordant scores were discussed to reach consensus. Pts were categorized as not complex (0-2 abnormalities), complex (3-4), or highly complex (≥5) for each set of guidelines. The weighted kappa was used to evaluate agreement between the two guidelines. Progression free survival (PFS) from ibrutinib start and overall survival (OS) were evaluated by the Kaplan-Meier method. Univariable Cox regression model discrimination power for PFS and OS were evaluated by Uno's concordance statistic. MDS guidelines categorized 50.2% as not complex, 19.7% complex and 30.1% as highly complex; similarly, ISCN categorized 50.2% as not complex, 20.2% complex and 29.6% as highly complex. Complexity categories assigned by the two guidelines had a weighted kappa agreement of 0.88 (95% CI 0.84-0.91), with 11% of pts placed in discordant complexity categories. Albeit numbers of pts were small, evaluation of these discordant cases compared to the consensus concordant cases showed outcomes varied. Discordant cases categorized by the MDS guidelines as complex and by ISCN as highly complex showed longer OS compared to the concordant complex and highly complex cases, suggesting ISCN overrated complexity (Fig 1). Conversely, discordant cases categorized by MDS guidelines as highly complex while ISCN categorized as complex showed decreased OS compared to the concordant complex and highly complex cases, suggesting ISCN underrated complexity in these cases (Fig 2). PFS trended similarly for these groups. Both the MDS and the ISCN guidelines showed increased karyotype complexity was significantly associated with shorter PFS (both with p<0.0001) and OS (both with p<0.0001). Comparing the classifiers not complex, complex and highly complex for the entire cohort found no significant difference between the prediction power of the MDS and ISCN guidelines for PFS. For OS, the MDS guidelines had a statistically stronger prediction power compared to ISCN (p=0.0235). Further, when the poorest prognostic group (highly complex) was compared to all others, the MDS guidelines showed significantly stronger prediction power for both PFS (p=0.0359) and OS (p=0.0039) compared to ISCN. Although both sets of guidelines were prognostically significant, in this predominately relapsed/refractory CLL patient population receiving ibrutinib, the MDS guidelines performed more robustly when used as a categorical variable. Clinical trials incorporating karyotype complexity for prognostication, or for treatment stratification, should specify a set of guidelines to apply consistently across the trial. Given the importance of karyotype complexity, particularly with targeted therapies, further studies are needed to evaluate these two sets of guidelines across varying CLL populations to establish recommendations for assigning karyotype complexity uniformly in CLL.

Building a community-based taxonomic resource for digitization of parasites and their hosts

Abstract Classification of the biological diversity on Earth is foundational to all areas of research within the natural sciences. Reliable biological nomenclatural and taxonomic systems facilitate efficient access to information about organisms and their names over time. However, broadly sharing, accessing, delivering, and updating these resources remains a persistent problem. This barrier has been acknowledged by the biodiversity data sharing community, yet concrete efforts to standardize and continually update taxonomic names in a sustainable way remain limited. High diversity groups such as arthropods are especially challenging as available specimen data per number of species is substantially lower than vertebrate or plant groups. The Terrestrial Parasite Tracker Thematic Collections Network project developed a workflow for gathering expert-verified taxonomic names across all available sources, aligning those sources, and publishing a single resource that provides a model for future endeavors to standardize digital specimen identification data. The process involved gathering expert-verified nomenclature lists representing the full taxonomic scope of terrestrial arthropod parasites, documenting issues experienced, and finding potential solutions for reconciliation of taxonomic resources against large data publishers. Although discordance between our expert resources and the Global Biodiversity Information Facility are relatively low, the impact across all taxa affects thousands of names that correspond to hundreds of thousands of specimen records. Here, we demonstrate a mechanism for the delivery and continued maintenance of these taxonomic resources, while highlighting the current state of taxon name curation for biodiversity data sharing.

CerviCell-detector: An object detection approach for identifying the cancerous cells in pap smear images of cervical cancer

Cervical cancer is the second most commonly seen cancer in women. It affects the cervix portion of the vagina. The most preferred diagnostic test required for screening for cervical cancer is the pap smear test. Pap smear is a time-consuming test as it requires detailed analysis by expert cytologists. Cytologists can screen around 100 to 1000 slides depending upon the availability of advanced equipment. It requires substantial time and effort to carefully examine each slide, identify and classify cells, and make accurate diagnoses. Prolonged periods of visual inspection can increase the likelihood of human errors, such as overlooking abnormalities or misclassifying cells. The sheer volume of slides to be screened can exacerbate fatigue and impact diagnostic accuracy. Due to this reason Artificial intelligence (AI) based computer-aided diagnosis system for the classification and detection of pap smear images is needed. There are some AI-based solutions proposed in the literature, still, an effective and accurate system is under research. In this paper, we implement a state-of-the-art object detection model with a newly available CRIC dataset which follows the Bethesda system for nomenclature. Object detection models implemented are YOLOv5 which uses the CSPNet backbone, Faster R–CNN which has Region Proposal Network (RPN) and Detectron2 framework created by Facebook AI Research (FAIR) Group. ResNext model is implemented among the available models from Detectron2. The CRIC dataset is preprocessed and augmented using Roboflow tool. The performance measures of Average Precision and mean Average precision over the Intersection over Union (IoU) are used to evaluate the effectiveness of the models. The models performed better for two classes namely Normal and Abnormal compared to six classes from the Bethesda system. The highest mean Average Precision (mAP) is observed on the augmented dataset for YOLOv5 models for binary classification with 83 % mAP with IoU in the range of 0.50–0.95.

Do You Speak Chemistry?

This article is a broad personal reflection about the language of chemistry, deriving from decades of experience in both research and teaching. The three levels of thought as represented by the Johnstone triangle, a critical attitude towards systematic nomenclature, the concept of pure substance, and the central significance of structural formulas as the most prominent form of representation in chemistry, are the main topics discussed. The chemical transliteration of the Platonic solids is presented as a mean of expression unique to chemistry.

Classification and naming of polymethine dyes used as staining agents for microscopy. A short guide for biomedical investigators

ABSTRACT The scientific literature contains many accounts of application of polymethine dyes, including cyanine dyes, as imaging agents, i.e., “biological stains,” for microscopic investigation of biological materials. Currently, many such dyes are used as probes for living cells, i.e., “fluorescent probes.” Polymethine dyes are defined here by two criteria. First, they possess a conjugated chain of (2n + 1) sp2-hybridized carbon atoms that connect a terminal π-electron-accepting (π-electron withdrawing) group with a terminal π-electron-donating group. Second, they have an odd number (2n + 3) of π-centers and an even number (2n + 4) of π-electrons in this chain, where n equals the number of –CR2=CR3– groups, usually vinylene groups –CH=CH–. Commercialization of diverse chemical types of many polymethine dyes has been attempted. The dyes that have achieved wide application, however, are limited in number and it is these dyes that are emphasized here. Because these polymethine dyes sometimes have been described by confusing, and sometimes confused, names, we clarify here the chemical categories and names of such dyes for the nonchemist, biomedical end user of such imaging agents. Nevertheless, the nomenclature presented here is not intended to replace the traditional “chromophore” categories of dyestuff chemistry, because the latter are held in place both by wide usage and by venerable authorities, such as the Colour Index.

Purification and structure elucidation of Penicillium chrysogenum derived antifungal compound with potential anti-Candida property: in silico and in vitro evidence

Following preliminary bioactivity testing, the fungal strain identified as Penicillium crysogenum was cultured in a modified Czapec Yeast Broth medium (CYB) for the production of antifungal compounds. Several chromatographic techniques including HPLC were used to purify the fungal metabolites from the crude extract. The mass determination of the purified compound was performed using Water’s LCMS system while the structure of the compound was elucidated using 400 and 500 Varian NMR machines. The chemical name of the purified compound is (2 R, 4S) −2, 4-dimethyl-4-((E)-2-((3S, 4S)-2, 4, 5-trihydroxy-3-methoxy-4-phenyl–1, 2, 3, 4-tetrahydroquinolin-6-yl) vinyl) cyclohexanone with the chemical formula C26H31NO5 and exact mass of 437.2. Molecular docking predicted compound docking score with dihydrofolate reductase enzyme and lanosterol 14α-demethylase enzyme as −8.1 kcal/mol and −9.8 kcal/mol respectively. Further, the compounds showed stable binding mode with the enzymes and reported robust binding energies. After insilico analysis, the compound with mass 437 was tested for its antifungal potential in vitro against two pathogenic yeast species (i.e. Candida albicans and Candida glaberata) using the agar tube diffusion method. Using sterile di-methyl sulfoxide (DMSO) the compound was prepared in four dose concentrations (100, 250, 500, 1000 µg mL−1) and mixed with autoclaved semisolid Potato Dextrose Agar (PDA) medium in screw-capped test tubes labelled with the corresponding dose concentration. The fungal strains were inoculated on this medium and linear growth inhibition of the fungal strains was calculated using fluconazole as the control drug. The results from in vitro experiments were encouraging as at concentrations of 500 and 1000 μg mL−1 the compound inhibited the growth of C. albicans by 17% and 38% while 19% and 41% inhibition were recorded against C. glaberata. The compound showed antifungal activity in silico and in vitro against both the Candida species and can act as a potent antifungal candidate in the future upon further investigation. Communicated by Ramaswamy H. Sarma

Assessment of COVID-19-related medical device regulator policies on entry to market for prioritised devices: a case study

Background/Aims In response to the COVID-19 pandemic, medical devices were given exceptional use authorisations. Medical device regulators around the world modified their administrative approach to medical device approval to ensure that relevant devices and personal protection equipment would be available to healthcare professionals and patients. Using data from medical device regulators in the US and Australia, this study assessed the impact of COVID-19-related regulatory modifications implemented to allow quick market entry of relevant equipment, and how data science techniques can help to inform future policy. Methods Data from the US Food and Drug Administration's Global Unique Device Identification Database and the Australian Therapeutic Goods Administration's Australian Register of Therapeutic Goods were used as case studies to explore the effects of policy changes. All COVID-19-related devices and personal protective equipment were identified in the data using the Global Medical Device Nomenclature system and device descriptions. A 10-day and 20-day moving average was applied to assess how many of these devices reached the market between 30 July 2019 and 24 June 2020. Results In both the US and Australian datasets, the number of market entries increased after the pandemic began. However, the impact of the Australian policy appeared to be greater than that of the US, as there was a considerable increase in the number of personal protective equipment and COVID-19-related device registrations following the declaration of the pandemic in Australia, while the impact on the US data was relatively minimal. Conclusions In general, market entry of relevant equipment increased during the COVID-19 pandemic, indicating the possible impact of policy changes. The kind of data captured in national databases greatly influences the ability to accurately track performance of regulatory policy changes. This work shows the potential of using data science in a regulatory context to assess if a policy change creates the desired effect.

ShinyTPs: Curating Transformation Products from Text Mining Results.

Transformation product (TP) information is essential to accurately evaluate the hazards compounds pose to human health and the environment. However, information about TPs is often limited, and existing data is often not fully Findable, Accessible, Interoperable, and Reusable (FAIR). FAIRifying existing TP knowledge is a relatively easy path toward improving access to data for identification workflows and for machine-learning-based algorithms. ShinyTPs was developed to curate existing transformation information derived from text-mined data within the PubChem database. The application (available as an R package) visualizes the text-mined chemical names to facilitate the user validation of the automatically extracted reactions. ShinyTPs was applied to a case study using 436 tentatively identified compounds to prioritize TP retrieval. This resulted in the extraction of 645 reactions (associated with 496 compounds), of which 319 were not previously available in PubChem. The curated reactions were added to the PubChem Transformations library, which was used as a TP suspect list for identification of TPs using the open-source workflow patRoon. In total, 72 compounds from the library were tentatively identified, 18% of which were curated using ShinyTPs, showing that the app can help support TP identification in non-target analysis workflows.

BFGF-like Activity Supported Tissue Regeneration, Modulated Neuroinflammation, and Rebalanced Ca2+ Homeostasis following Spinal Cord Injury.

A spinal cord injury (SCI) is a well-defined debilitating traumatic event to the spinal cord that usually triggers permanent changes in motor, sensory, and autonomic functions. Injured tissue becomes susceptible to secondary mechanisms caused by SCIs, which include pro-inflammatory cytokine release, the activation of astrocytes and microglia, and increased neuronal sensibility. As a consequence, the production of factors such as GFAP, IBA-1, TNF-α, IL-1β, IFN-γ, and S100-β slow down or inhibit central nervous system (CNS) regeneration. In this regard, a thorough understanding of the mechanisms regulating the CNS, and specifically SCI, is essential for the development of new therapeutic strategies. It has been demonstrated that basic fibroblast growth factor (bFGF) was successful in the modulation of neurotrophic activity, also promoting neurite survival and tissue repair, thus resulting in the valuable care of CNS disorders. However, bFGF therapeutic use is limited due to the undesirable effects developed following its administration. Therefore, the synthetic compound mimetic of bFGF, SUN11602 (with chemical name 4-[[4-[[2-[(4-Amino-2,3,5,6-tetramethylphenyl)amino]acetyl]methylamino]-1-piperidinyl]methyl]benzamide), has been reported to show neuroprotective activities similar to those of bFGF, also demonstrating a good pharmacokinetic profile. Here, we aimed to investigate the neuroprotective activity of this bFGF-like compound in modulating tissue regeneration, neuroinflammation, and Ca2+ overload by using a subacute mouse model of SCI. SUN11602 (1, 2.5, and 5 mg/kg) was administered orally to mice for 72 h daily following the in vivo model of SCI, which was generated by the extradural compression of the spinal cord. The data obtained demonstrated that SUN11602 treatment considerably decreased motor alteration and diminished the neuroinflammatory state through the regulation of glial activation, the NF-κB pathway, and kinases. Additionally, by controlling Ca2+-binding proteins and restoring neurotrophin expression, we showed that SUN11602 therapy restored the equilibrium of the neuronal circuit. Because of these findings, bFGF-like compounds may be an effective tool for reducing inflammation in SCI patients while enhancing their quality of life.

Spatial atlas of the mouse central nervous system at molecular resolution

Spatially charting molecular cell types at single-cell resolution across the 3D volume is critical for illustrating the molecular basis of brain anatomy and functions. Single-cell RNA sequencing has profiled molecular cell types in the mouse brain1,2, but cannot capture their spatial organization. Here we used an in situ sequencing method, STARmap PLUS3,4, to profile 1,022 genes in 3D at a voxel size of 194 × 194 × 345 nm3, mapping 1.09 million high-quality cells across the adult mouse brain and spinal cord. We developed computational pipelines to segment, cluster and annotate 230 molecular cell types by single-cell gene expression and 106 molecular tissue regions by spatial niche gene expression. Joint analysis of molecular cell types and molecular tissue regions enabled a systematic molecular spatial cell-type nomenclature and identification of tissue architectures that were undefined in established brain anatomy. To create a transcriptome-wide spatial atlas, we integrated STARmap PLUS measurements with a published single-cell RNA-sequencing atlas1, imputing single-cell expression profiles of 11,844 genes. Finally, we delineated viral tropisms of a brain-wide transgene delivery tool, AAV-PHP.eB5,6. Together, this annotated dataset provides a single-cell resource that integrates the molecular spatial atlas, brain anatomy and the accessibility to genetic manipulation of the mammalian central nervous system.

Chromosome Rearrangement in Elymus dahuricus Revealed by ND-FISH and Oligo-FISH Painting.

As a perennial herb in Triticeae, Elymus dahuricus is widely distributed in Qinghai-Tibetan Plateau and Central Asia. It has been used as high-quality fodders for improving degraded grassland. The genomic constitution of E. dahuricus (2n = 6x = 42) has been revealed as StStHHYY by cytological approaches. However, the universal karyotyping nomenclature system of E. dahuricus is not fully established by traditional fluorescent in situ hybridization (FISH) and genomic in situ hybridization (GISH). In this study, the non-denaturing fluorescent in situ hybridization (ND-FISH) using 14 tandem-repeat oligos could effectively distinguish the entire E. dahuricus chromosomes pairs, while Oligo-FISH painting by bulked oligo pools based on wheat-barley collinear regions combined with GISH analysis, is able to precisely determine the linkage group and sub-genomes of the individual E. dahuricus chromosomes. We subsequently established the 42-chromosome karyotype of E. dahuricus with distinctive chromosomal FISH signals, and characterized a new type of intergenomic rearrangement between 2H and 5Y. Furthermore, the comparative chromosomal localization of the centromeric tandem repeats and immunostaining by anti-CENH3 between cultivated barley (Hordeum vulgare L.) and E. dahuricus suggests that centromere-associated sequences in H subgenomes were continuously changing during the process of polyploidization. The precise karyotyping system based on ND-FISH and Oligo-FISH painting methods will be efficient for describing chromosomal rearrangements and evolutionary networks for polyploid Elymus and their related species.

Updated knowledge and a proposed nomenclature for nuclear receptors with two DNA binding domains (2DBD-NRs).

Nuclear receptors (NRs) are important transcriptional modulators in metazoans. Typical NRs possess a conserved DNA binding domain (DBD) and a ligand binding domain (LBD). Since we discovered a type of novel NRs each of them has two DBDs and single LBD (2DBD-NRs) more than decade ago, there has been very few studies about 2DBD-NRs. Recently, 2DBD-NRs have been only reported in Platyhelminths and Mollusca and are thought to be specific NRs to lophotrochozoan. In this study, we searched different databases and identified 2DBD-NRs in different animals from both protostomes and deuterostomes. Phylogenetic analysis shows that at least two ancient 2DBD-NR genes were present in the urbilaterian, a common ancestor of protostomes and deuterostomes. 2DBD-NRs underwent gene duplication and loss after the split of different animal phyla, most of them in a certain animal phylum are paralogues, rather than orthologues, like in other animal phyla. Amino acid sequence analysis shows that the conserved motifs in typical NRs are also present in 2DBD-NRs and they are gene specific. From our phylogenetic analysis of 2DBD-NRs and following the rule of Nomenclature System for the Nuclear Receptors, a nomenclature for 2DBD-NRs is proposed.

Polymorphic Solid Solutions in Molecular Crystals: Tips, Tricks, and Switches.

Crystal polymorphism has been a topic of much interest for the past 20 years or so, especially since its scientific (and legal) importance to the pharmaceutical industry was realized. By contrast, the formation of solid solutions in molecular crystals has been overlooked despite its long-standing prevalence in the analogous field of inorganic crystals. Wilfully forgotten, crystalline molecular solid solutions may be very common in our world since molecular compounds are rarely produced with 100% purity, and impurities able to form solid solutions are difficult to reject via recrystallization. Given the importance of both polymorphism and solid solutions in molecular crystals, we share here some tips, tricks, and observations to aid in their understanding. First, we propose a nomenclature system fit for the description of molecular crystalline solid solutions capable of polymorphism (tips). Second, we highlight the challenges associated with their experimental and computational characterization (tricks). Third, we show that our recently reported observation that polymorph stabilities can change by virtue of solid solution formation is a general phenomenon, reporting it on a second system (switches). Our work focuses on the historically important compound benzamide forming solid solutions with nicotinamide and 3-fluorobenzamide.

Parasitic diseases of rabbits (distribution, diagnosis and treatment)

This review presents data on the most common causative agents of protozooses, helminthiases, and ectoparasitic diseases of rabbits (Oryctolagus cuniculus, Linnaeus, 1758), which are of interest to veterinarians. Modern methods of diagnosing parasitic diseases in rabbits have been determined. Chemotherapeutic drugs available on the world pharmaceutical market for therapeutic and preventive treatments in rabbits are listed. The main causative agents of protozoan, helminthic, and ectoparasitic diseases of rabbits are considered, considering the modern systematic position of parasites. The features of the distribution of parasitic diseases in Ukraine and the world, according to the data of well-known scientists in the field of veterinary parasitology, are briefly given. Information on the specifics of the use of antiparasitic drugs in the case of animals affected by protozooses, helminths, and ticks is summarized. The work briefly provides information on the most common medicines and chemical combinations that are the active ingredients of these drugs (their chemical names existing in different countries, synonyms, and main pharmacological properties). Information on the dosage and features of the use of antiparasitic agents in the case of rabbit diseases is given following the data of modern scientific literature and the relevant recommendations for their industrial use. During the inspection, it was established that rabbits are most often affected by eimeriosis (coccidiosis). Currently, 15 species of Eimeria spp. have been identified. Young animals (2–6 months) are most susceptible to eimeriosis. The peak of infestation in the territory of Ukraine falls in the spring-summer period. It was found that P. ambiguus is most often detected among helminthiases in rabbits in our country. Rabbits aged 1 to 2 years are most susceptible to these helminths, and the peak of infestation occurs in January. In rabbits, psoroptosis is one of the most common acaroses, the causative agent of which is ticks of the P. cuniculi species. The purpose of this work was to show the current state of rabbits' most common parasitic diseases on the territory of Ukraine and in the world in general, highlight the existing antiparasitic drugs, and summarize information on their use. It has been established that animals with encephalitozoonosis are the most difficult to diagnose and treat. At the same time, there is a wide range of coccidiostats and coccidiolytics for treating rabbits affected by eimeries. For the infestation of animals with helminths, it is appropriate to use benzimidazoles and ivermectins. In the case of acaroses, ivermectin and fungicidal-acaricidal ointments remain effective drugs. The analysis of literary sources will allow for the expansion of the already available data on the spread, prevention, and treatment of parasitic diseases in rabbits. The given information will help ensure the rabbits' veterinary well-being on Ukraine's territory.

Awareness and Advertisement of Red Meat Carcinogens in Low Income Grocery Stores

Previous studies regarding the association between increased cancer rates and socioeconomically challenged locations have not pinpointed specific products that contribute the most toward the risk of cancer. This study aimed to find a few of the most highly advertised carcinogenic products in one area, and how they may be generalized to a larger scale. In this project, multiple methods of data collection were performed; a census map of the counties in central Texas was used and a rural, socioeconomically impoverished was chosen as the site for this study. Personal perceptions of products and product placement in a few randomly selected stores as well as interviews with store employees were some of the research methods used to collect data. Overall, the three most advertised products were beef jerky ( coming in assorted flavors and sizes), instant noodles, and sausages/meat sticks. Other products were also found to be advertised, however, not to the extent of these products, and not to the rate of successful purchase as well. With elevated cancer levels around the world, it is important to increase awareness of the risks that certain common foods may pose, but go unnoticed due to the details involving long, unknown chemical names and terms. The results of this study might shine light upon some of the most commonly advertised products containing carcinogens so that customers can be more aware of what they are purchasing before consuming them.

Name and shame: can taxonomists agree on systematic reforms?

The Linnean nomenclatural system dominates in taxonomy, despite various ethical issues being raised regarding the rules applied to this approach. Some recent proposals to adapt the system have been dismissed as destabilizing by many taxonomists. However, simple rule changes and amendments to address these issues could be implemented without excessive disruption.