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Genetic testing, including whole genome, whole exome, and other next‐generation sequencing technologies, has evolved vastly in the past decade. With this, the number of identified genes and genetic variants is constantly increasing. Although a variety of databases and online tools exist that summarize, categorize, and classify genes, a clear guideline of which information is needed when reporting a gene and what to do when identifying a new gene is lacking. This includes the correct nomenclature, descriptive information about genetic loci and genetic variation, aliases, and correlated phenotypes. This tutorial is meant to serve as an introduction to reporting genes in a paper and provides an overview of available databases and tools to obtain all necessary information on the genes of interest. [ABSTRACT FROM AUTHOR]

Objectives: This study aimed to elucidate the connection between osteoclastic forkhead transcription factor O1 (FoxO1) and periodontitis and explore the underlying mechanism by which FoxO1 knockdown regulates osteoclast formation. Materials and Methods: A conventional ligature‐induced periodontitis model was constructed to reveal the alterations in the proportion of osteoclastic FoxO1 in periodontitis via immunofluorescence staining. Additionally, RNA sequencing (RNA‐seq) was performed to explore the underlying mechanisms of FoxO1 knockdown‐mediated osteoclastogenesis, followed by western blotting, quantitative polymerase chain reaction, and enzyme‐linked immunosorbent assay. Results: FoxO1+ osteoclasts were enriched in the alveolar bone in experimental periodontitis. Moreover, FoxO1 knockdown led to impaired osteoclastogenesis with low expression of osteoclast differentiation‐related genes, accompanied by an insufficient osteoclast maturation phenotype. Mechanistically, RNA‐seq revealed that the nuclear factor kappa B (NF‐κB) and nucleotide‐binding oligomerization domain‐like receptor family pyrin domain containing 3 (NLRP3) inflammasome signaling pathways were inhibited in FoxO1‐knockdown osteoclasts. Consistent with this, MCC950, an effective inhibitor of the NLRP3 inflammasome, substantially attenuated osteoclast formation. Conclusions: FoxO1 knockdown contributed to the inhibition of osteoclastogenesis by effectively suppressing NF‐κB signaling and NLRP3 inflammasome activation. This prospective study reveals the role of FoxO1 in mediating osteoclastogenesis and provides a viable therapeutic target for periodontitis treatment. [ABSTRACT FROM AUTHOR]

Eucalyptus spp. and their hybrids are frequently cloned and mass planted across farmland tracts and commercial plantations in northern India. It is a viable feeder species to the paper and pulp industries in this region. In 2018 and 2019, during field surveys conducted in northern India, a serious leaf blight disease was frequently observed in E. tereticornis plantations. Isolation from the blighted leaf samples consistently yielded fungal isolates having Calonectria‐like morphology. Morphological features coupled with sequence analysis of partial β‐tubulin (TUB2) and partial translation elongation factor‐alpha (TEF1) gene regions of two fungal isolates confirmed the species as Ca. cerciana. In detached leaf assays and glasshouse inoculation experiments, both isolates produced symptoms similar to those observed on the naturally infected leaves. Koch's postulates were fulfilled by re‐isolating Ca. cerciana from the inoculated leaves. This work is the first to confirm that Ca. cerciana is associated with a serious leaf blight disease of Eucalyptus in northern India and is an important addition to the taxonomy of Calonectria fungi in India. [ABSTRACT FROM AUTHOR]

The article presents the insights of David A. Greenberg and Ryan Subaran on the comments in their article "Blinders, phenotype, and fashionable genetic analysis: a critical examination of the current state of epilepsy genetic studies." The authors say that the statement of Doctor Ingrid E. Scheffer regarding the common genes for the genetic generalized epilepsies (GGEs) was incorrect. They add that the idea of E. W. Johnson on the channel genes may be a good way to look at epilepsy.

Aim: We investigated whether injection of synthetic small interfering siRNAs via renal artery followed by electroporation could be effective in silencing specific genes in glomerulus. Methods: Solution of siRNA targeting enhanced green fluorescent protein (EGFP) was injected via the renal artery of EGFP-transgenic rats followed by delivery of electric pulses. Results: The delivery of siRNA reduced endogenous EGFP expression, mainly in glomerular mesangial cells. Conclusion: Electroporation-mediated gene transfer system via renal artery in rats is very useful for the delivery of a range of different materials including cells, viruses and proteins. Here, we provide a step-by-step description of this perfusion method and a discussion of the key points for the success of the technique. [ABSTRACT FROM AUTHOR]

t(11;18)(q21;q21) is the most frequent chromosomal aberration specifically associated with mucosa-associated lymphoid tissue (MALT) lymphoma. The translocation fuses the API2 gene to the MALT1 gene and generates a functional API2-MALT1 transcript. The breakpoint of the fusion gene is well characterized at the transcript level but poorly understood at the genomic level and the mechanism underlying the translocation is unknown. We identified the genomic breakpoint in 19 t(11;18)-positive MALT lymphoma cases by polymerase chain reaction and sequencing and analysed the junctional sequences. The breakpoints were scattered in intron 7 and exon  8 of the API2 gene, and introns  4, 6, 7 and 8 of the MALT1 gene. Comparative sequence analysis between the API2-MALT1 fusion on der(11) and the MALT1-API2 fusion on der(18) showed extensive alterations including deletions, duplications and non-template-based insertions at the fusion junctions in all cases examined. An extensive sequence search failed to reveal any known sequence motifs that might be associated with chromosomal recombination or any novel consensus sequences at or near the breakpoints on both der(11) and der(18) except in one case, in which Alu repeats spanned the breakpoint of the MALT1-API2 fusion. Our results suggest that t(11;18) may result from illegitimate non-homologous end joining following double strand breaks. [ABSTRACT FROM AUTHOR]

The Ikaros transcription factor has been shown to play an important role in the differentiation of both myeloid and lymphoid lineages. Mice heterozygous for a dominant negative (DN) ikaros isoform develop T-cell leukaemia and lymphoma with 100% penetrance. Overexpression of DN Ikaros isoforms has been reported in some forms of leukaemia, such as childhood acute myelomonocytic and monocytic leukaemias, adult B-cell acute lymphoblastic leukaemias (B ALL) and in childhood and adult pre-B ALL. In this study, the expression of Ikaros isoforms in 49 infant and childhood leukaemia patients was analysed by reverse transcription polymerase chain reaction and Western blot analysis. We found overexpression of the DN Ikaros  6 (Ik6) isoform in a subset of leukaemia patients harbouring t(4;11) translocations. To further study the consequences of Ik6 overexpression in B ALL, we inducibly expressed Ik6 in BaF3 cells and found that Ik6 overexpression delayed cell death after interleukin-3 withdrawal, suggesting that overexpression of Ik6 found in t(4;11) B cells could contribute to leukaemogenesis by preventing the apoptosis of cells in an environment with reduced survival factors. [ABSTRACT FROM AUTHOR]

The frequency and prognostic relevance of translocations t(11;14) and t(4;14), the most common translocations involving the immunoglobulin heavy chain (IgH) gene in multiple myeloma (MM), were investigated in 128 patients treated with intensive chemotherapy and autologous stem cell transplant. Myeloma cells were identified by cytoplasmic light chain immunofluorescence combined with fluorescence in situ hybridization (cIg-FISH) for detection of translocations t(11;14) and t(4;14). Overall, t(11;14) was detected in 16 of 125 (12·8%) and t(4;14) in 15 of 120 (12·5%) patients. Progression-free and overall survivals were similar for patients with or without t(11;14). However, patients with t(4;14) had significantly shorter progression-free (median 9·9 months vs. 25·8 months; P = 0·0003) and overall survivals (median 18·3 months vs. 48·1 months; P < 0·0001) than patients without t(4;14). The t(4;14) was associated with IgA and t(11;14) with light chain MM. There was no association between the t(11;14) or t(4;14) and other biological parameters including age, gender, haemoglobin, β-2 microglobulin, C-reactive protein, calcium, creatinine, albumin, or the percentage of bone marrow plasma cells. Multivariate analysis identified t(4;14) as the only adverse prognostic factor for both progression-free survival and overall survival. Our results indicate that the t(4;14) detected by cIg-FISH is associated with a poor prognosis in MM patients receiving intensive chemotherapy and autotransplant. [ABSTRACT FROM AUTHOR]

Plant secretory phospholipases A2 (sPLA2s) probably play important roles in phospholipid signaling based on the data reported from other organisms, but their functions are poorly understood because of the lack of cloned sPLA2 genes. In this study, we cloned and characterized an Arabidopsis secretory phospholipase A2-γ (AtsPLA2-γ) cDNA, and examined its enzymatic properties. The recombinant protein of AtsPLA2-γ showed maximal enzyme activity at pH 8.0, and required Ca2+ for activity. Moreover, AtsPLA2-γ showed sn-2 position specificity but no prominent acyl preference, though it showed head group specificity to phosphatidylethanolamine rather than to phosphatidylcholine. AtsPLA2-γ was found to predominate in the mature flower rather than in other tissues, and subcellular localization analysis confirmed that AtsPLA2-γ is secreted into the intercellular space. [Copyright &y& Elsevier]

Comments on a study on the effect of the deletion of the p53 gene on the reduced cancer and premature aging phenotypes. Factors that contributed to the deletion of the genes; Background on the phenotypic consequences of the haploinsufficiency of genes; Reasons behind the activation of p53.

The article discusses the role played by epigenetics in the field of reproductive medicine. The natural times when developmental epigenetic reprogramming takes place in gametes almost matches the time of human assisted reproduction when the gametes and embryos are handled in an in vitro environemnt. Information is also given on genomic imprinting and in vitro culture of embryos.

Phylogenetic inference of polyploid species is the first step towards understanding their patterns of diversification. In this paper, we review the challenges and limitations of inferring species relationships of polyploid plants using traditional phylogenetic sequencing approaches, as well as the mischaracterization of the species tree from single or multiple gene trees. We provide a roadmap to infer interspecific relationships among polyploid lineages by comparing and evaluating the application of current phylogenetic, phylogenomic, transcriptomic, and whole‐genome approaches using different sequencing platforms. For polyploid species tree reconstruction, we assess the following criteria: (1) the amount of prior information or tools required to capture the genetic region(s) of interest; (2) the probability of recovering homeologs for polyploid species; and (3) the time efficiency of downstream data analysis. Moreover, we discuss bioinformatic pipelines that can reconstruct networks of polyploid species relationships. In summary, although current phylogenomic approaches have improved our understanding of reticulate species relationships in polyploid‐rich genera, the difficulties of recovering reliable orthologous genes and sorting all homeologous copies for allopolyploids remain a challenge. In the future, assembled long‐read sequencing data will assist the recovery and identification of multiple gene copies, which can be particularly useful for reconstructing the multiple independent origins of polyploids. [ABSTRACT FROM AUTHOR]

The article discusses the concept of evolutionary stable strategy (ESS), as well as the application of game theory in evolutionary problems. It cites the article "The Logic of Animal Conflict," which was written by John Maynard Smith and American polymath George Price in 1973 as the first description of the concept of ESS. It features the history of Price, whose 1978 paper titled "Antlers, Intraspecific Combat, and Altruism" was the basis of the first ESS.

Lists the research papers to be published in the succeeding issues of the "European Journal of Biochemistry." "Stimulation of non-selective cation channels providing Ca2+ influx into platelets by platelet-activating factor and other aggregation inducers," by P.V. Avdonin and colleagues; "Complete nucleotide sequence of the gene for human C1 inhibitor with an unusually high density of Alu elements," by P.E. Carter and colleagues.

Presents several forthcoming papers published on the December 1, 1983 issue of the "European Journal of Biochemistry." "Purification and Properties of a Thiol Protease From Rat-Liver Nuclei"; Changes in Proteoglycan Compositiion of F9 Teratocarcinoma Cells Upon Differentiation"; "Supercoiling and the Mechanism of Restriction Endonucleases"; Identification of the Gene for DNA Helicase II of Escherichia Coli."

Summary Introduction: The glucose-6-phosphate dehydrogenase (G6PD) fluorescent spot test (FST) is a useful screening test for G6PD deficiency, but is unable to detect heterozygote G6PD-deficient females. We sought to identify whether reporting intermediate fluorescence in addition to absent and bright fluorescence on FST would improve identification of mildly deficient female heterozygotes. Methods: A total of 1266 cord blood samples (705 male, 561 female) were screened for G6PD deficiency using FST (in-house method) and a quantitative enzyme assay. Fluorescence intensity of the FST was graded as either absent, intermediate or normal. Samples identified as showing absent or intermediate fluorescence on FST were analysed for the presence of G6PD mutations using TaqMan@SNP genotyping assays and direct nucleotide sequencing. Results: Of the 1266 samples, 87 samples were found to be intermediate or deficient by FST (49 deficient, 38 intermediate). Of the 49 deficient samples, 48 had G6PD enzyme activity of ≤ 9.5 U/g Hb and one sample had normal enzyme activity. All 38 intermediate samples were from females. Of these, 21 had G6PD activity of between 20% and 60%, and 17 samples showed normal G6PD activity. Twenty-seven of the 38 samples were available for mutation analysis of which 13 had normal G6PD activity. Eleven of the 13 samples with normal G6PD activity had identifiable G6PD mutations. Conclusion: Glucose-6-phosphate dehydrogenase heterozygote females cannot be identified by FST if fluorescence is reported as absent or present. Distinguishing samples with intermediate fluorescence from absent and bright fluorescence improves detection of heterozygote females with mild G6PD deficiency. Mutational studies confirmed that 85% of intermediate samples with normal enzyme activity had identifiable G6PD mutations. [ABSTRACT FROM AUTHOR]

Twin studies of insomnia exhibit heterogeneity in estimates of heritability. This heterogeneity is likely because of sex differences, age of the sample, the reporter and the definition of insomnia. The aim of the present study was to systematically search the literature for twin studies investigating insomnia disorder and insomnia symptoms and to meta‐analyse the estimates of heritability derived from these studies to generate an overall estimate of heritability. We further examined whether heritability was moderated by sex, age, reporter and insomnia symptom. A systematic literature search of five online databases was completed on 24 January 2020. Two authors independently screened 5644 abstracts, and 160 complete papers for the inclusion criteria of twin studies from the general population reporting heritability statistics on insomnia or insomnia symptoms, written in English, reporting data from independent studies. We ultimately included 12 papers in the meta‐analysis. The meta‐analysis focussed on twin intra‐class correlations for monozygotic and dizygotic twins. Based on these intra‐class correlations, the meta‐analytic estimate of heritability was estimated at 40%. Moderator analyses showed stronger heritability in females than males; and for parent‐reported insomnia symptoms compared with self‐reported insomnia symptoms. There were no other significant moderator effects, although this is likely because of the small number of studies that were comparable across levels of the moderators. Our meta‐analysis provides a robust estimate of the heritability of insomnia, which can inform future research aiming to uncover molecular genetic factors involved in insomnia vulnerability. [ABSTRACT FROM AUTHOR]

This article presents a list of some of the forthcoming papers in biochemistry to be published in this journal. Some of the papers listed are "The Organization of the Chloroplast DNA in wheat and maize in the region containing the LS Gene," by B. Koller, H. Delius and T.A. Dyer, "Effect of Carbamination on the Buffering Power of Purified Human Hamoglobins A Solutions At Two Temperatures," by M. Castaing, E. Bursaux and C. Poyart, "The Complete Nucleotide of the Chicken Ovotransferrin mRNA," by J.M. Jeltsch and P. Chambon, "The Primary Structure of Hen Ovotransferrin," by J. Williams, T.C. Elleman, I.B. Kington, A.G. Wilkins and K.A. Kuhn.

The article presents the list of research papers related to biochemistry, that will be published in forthcoming issues of the "European journal of Biochemistry." Some of these papers are--'A novel testis-specific 105-kDa protein related to 90-kDa heatshock protein,' by H. Itoh and Y. Tashima, 'Casein kinase II phosphorylates DNA-polymerase-a-DNA-primase without affecting its basic enzymic properties,' by V. Podust, G. Bialek, H. Stembach and F. Grosse, 'Structural and functional aspects of calcium homeostasis in eukaryotic cells,' by D. Pietrobon, F. di Virgilio and T. Pozzan.

Presents a list of biochemistry papers due for publication after the March 1991 issue of the "European Journal of Biochemistry". "Complete structure of the chicken α2(VI) collagen gene"; "Phosphorylation of keratin intermediate filaments by protein kinase C, by calmodulin-dependent protein kinase and by cAMP-dependent protein kinase".

Front cover: In establishing the left‐right axis of the body in Drosophila, a torsion‐like deformation of the cell occurs (cell chirality). Two myosin Is, Myo1D and Myo1C, are thought to be involved in this process, producing right‐handed and left‐handed cell chirality, respectively. A paper published in the May issue of this journal (Utsunomiya et al. (2024) Genes Cells 29: 380‐396, DOI: 10.1111/gtc.13110) reported that when these myosin Is were expressed in macrophages to observe their interactions with the membrane at the single‐molecule level, Myo1D exhibited mobility consistent with free diffusion, whereas Myo1C showed notably lower mobility. This picture, depicting two vortices in a strait, aptly illustrates their differences. Compared to the fast currents that produce the right‐handed vortex in the back, the currents of the left‐handed vortex in the foreground are docile. Designed by TRAIS Co., Ltd. (Kobe, Japan). [ABSTRACT FROM AUTHOR]

Since the concept of IoT (Internet of Things) was proposed, it has digitized the real world and has a wide range of applications. However, with tremendous evolution in data acquisition and transfer, a new type of attack represented by advanced persistent threat (APT) has attracted wide attention. APT organization identification for malware is a method to detect APT attacks. However, most of malware is tailored to the goal, it is complex and changeable, or can be updated very quickly. The traditional analysis method is difficult to obtain the source information of APT organization from the malware in the IoT. To this end, we propose a software genes method to solve this problem. Software gene is binary fragment of specific function or information in the software body. In this paper, different from traditional data flow and instruction flow, a new gene model is proposed which combine with knowledge graph of malware behavior. We fill the processed malware information into the gene model to obtain the APT organization gene pool. Of course, the gene pool should be optimized to include the genetic characteristics of APT. In theory, there genetic characteristics can help us identify malware and APT accurately in the IoT. However, biological genetic similarity algorithms cannot be used directly. A genetic similarity algorithm for APT organization identification of malware will be designed instead. Simulations on real‐world dataset corroborate theoretical analysis and reveal the possibility of using genes for malware traceability. [ABSTRACT FROM AUTHOR]

Background and Aims: This study aimed to report nine Charcot–Marie–Tooth disease (CMT) families with six novel IGHMBP2 mutations in our CMT2 cohort and to summarize the genetic and clinical features of all AR‐CMT2S patients reported worldwide. Methods: General information, clinical and neurophysiological data of 275 axonal CMT families were collected. Genetic screening was performed by inherited peripheral neuropathy related genes panel or whole exome sequencing. The published papers reporting AR‐CMT2S from 2014 to 2023 were searched in Pubmed and Wanfang databases. Results: In our CMT2 cohort, we detected 17 AR‐CMT2S families carrying IGHMBP2 mutations and eight were published previously. Among these, c.743 T > A (p.Val248Glu), c.884A > G (p.Asp295Gly), c.1256C > A (p.Ser419*), c.2598_2599delGA (p.Lys868Sfs*16), c.1694_1696delATG (p.Asp565del) and c.2509A > T (p.Arg837*) were firstly reported. These patients prominently presented with early‐onset typical axonal neuropathy and without respiratory dysfunction. So far, 56 AR‐CMT2S patients and 57 different mutations coming from 43 families have been reported in the world. Twenty‐nine of 32 missense mutations were clustered in helicase domain and ATPase region. The age at onset ranged from 0.11to 20 years (Mean ± SD: 3.43 ± 3.88 years) and the majority was infantile‐onset (<2 years). The initial symptoms included weakness of limbs (19, 29.7%), delayed milestones (12, 18.8%), gait disturbance (11, 17.2%), feet deformity (8, 12.5%), feet drop (8, 12.5%), etc. Interpretation: AR‐CMT2S accounted for 6.2% in our CMT2 cohort. We firstly reported six novel IGHMBP2 mutations which expanded the genotypic spectrum of AR‐CMT2S. Furthermore, 17 AR‐CMT2S families could provide more resources for natural history study, drug research and development. [ABSTRACT FROM AUTHOR]

Summary: Greenbeards are selfish genetic elements that make their bearers behave either altruistically towards individuals bearing similar greenbeard copies or harmfully towards individuals bearing different copies. They were first proposed by W. D. Hamilton over 50 yr ago, to illustrate that kin selection may operate at the level of single genes. Examples of greenbeards have now been reported in a wide range of taxa, but they remain undocumented in plants. In this paper, we discuss the theoretical likelihood of greenbeard existence in plants. We then question why the greenbeard concept has never been applied to plants and speculate on how hypothetical greenbeards could affect plant–plant interactions. Finally, we point to different research directions to improve our knowledge of greenbeards in plants. [ABSTRACT FROM AUTHOR]

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The current paper is a commentary on the Metabolic reprogramming‐associated genes predict overall survival for rectal cancer (Jian‐Qing Lin et al 2020). The authors concluded that 'Patients with high‐risk demonstrated significantly poorer survival outcomes than patients with low‐risk in the TCGA database. Also, patients with high‐risk still showed significantly poorer survival outcomes than patients with low‐risk in the GEO database'. But the figure 3 in their published paper, 'Survival analyses for the prognostic metabolic genes in rectal cancer', presented that there was type I error in their study during the hypothesis testing process, obviously. [ABSTRACT FROM AUTHOR]

For cell‐based assays studying monocytes and macrophages, the immortalized monocyte cell line THP‐1 is widely used and stimulated with phorbol 12‐myristate 13‐acetate, lipopolysaccharide (LPS) and/or interferon‐γ (IFN‐γ), after which it differentiates and polarizes into proinflammatory M1‐like macrophages. For the quantification of this and the effect of different factors affecting these processes, the expression levels of various maturation markers are determined using reverse transcription‐quantitative PCR. For this purpose, stably expressed reference genes are crucial. However, no studies evaluating the stability of reference genes in THP‐1 cells stimulated with LPS and IFN‐γ have been performed. Therefore, this paper describes the selection of the most used reference genes [RPL37A (ribosomal protein L37a), GAPDH (glyceraldehyde‐3‐phosphate dehydrogenase), UBC (ubiquitin C), B2M (0β2‐microbulin), ACTB (β‐actin) and PPIA (cyclophilin A)], the in silico primer design, the analysis and the validation of these in accordance with the MIQE (Minimum Information for Publication of Quantitative Real‐Time PCR Experiments) guidelines and more recent recommendations for the validation of the stability of reference genes. Using the RefFinder platform, including the four most popular algorithms for reference gene validation, the Delta CT, BestKeeper, NormFinder and geNorm, we find the reference genes GAPDH and UBC to be the most stable. Furthermore, we demonstrate that the normalization of gene expression data using the least stable reference genes, ACTB and B2M, dramatically affects the interpretation of experimental data. Taken together, it is vital to validate the stability of reference genes under the specific experimental conditions used when utilizing the THP‐1 monocyte model system. [ABSTRACT FROM AUTHOR]

Sixty years ago, the geneticist James Neel proposed that the epidemics of obesity and diabetes today may have evolutionary roots. Specifically, he suggested that our ancestors may have accumulated mutations during periods of famine that provided a survival advantage at that time. However, the presence of this "thrifty genotype" in today's world, where food is plentiful, would predispose us to obesity and diabetes. The "thrifty gene" hypothesis, attractive to some, has been challenged over the years. The authors have previously postulated that the loss of the uricase gene, resulting in a rise in serum and intracellular uric acid levels, satisfies the criteria of a thrifty genotype mutation. This paper reviews and brings up-to-date the evidence supporting the hypothesis and discusses the current arguments that challenge this hypothesis. Although further studies are needed to test the hypothesis, the evidence supporting a loss of uricase as a thrifty gene is substantial and supports a role for evolutionary biology in the pathogenesis of the current obesity and diabetes epidemics. [ABSTRACT FROM AUTHOR]

Genetic and early environmental differences including early health habits associate with future health. To provide insight on the causal nature of these associations, monozygotic (MZ) twin pairs discordant for health habits provide an interesting natural experiment. Twin pairs discordant for leisure‐time physical activity (LTPA) in early adult life is thus a powerful study design to investigate the associations between long‐term LTPA and indicators of health and wellbeing. We have identified 17 LTPA discordant twin pairs from two Finnish twin cohorts and summarize key findings of these studies in this paper. The carefully characterized rare long‐term LTPA discordant MZ twin pairs have participated in multi‐dimensional clinical examinations. Key findings highlight that compared with less active twins in such MZ twin pairs, the twins with higher long‐term LTPA have higher physical fitness, reduced body fat, reduced visceral fat, reduced liver fat, increased lumen diameters of conduit arteries to the lower limbs, increased bone mineral density in loaded bone areas, and an increased number of large high‐density lipoprotein particles. The findings increase our understanding on the possible site‐specific and system‐level effects of long‐term LTPA. [ABSTRACT FROM AUTHOR]

Psychiatric and neurocognitive symptoms due to hypercortisolism were already described by Harvey Cushing in his original paper on patients with Cushing's syndrome (CS). Nowadays, it is well known that psychiatric and cognitive complaints are two of the most common, and most distressing, symptoms in patients with CS. Psychiatric symptoms are indeed a major clinical manifestation of CS. The most commonly observed psychiatric conditions are depression and anxiety, whilst mania and psychosis are less common. Several domains of cognitive function are impaired at diagnosis, including episodic and working memory, executive function and attention. Following treatment, one-fourth of the patients still experience depressed mood, and the cognitive impairments are only partially restored. Consequently, quality of life in patients with CS is severely and persistently affected. Neuroimaging studies have also illustrated the deleterious effects of hypercortisolism on the brain by demonstrating reduced grey matter volumes and cortical thickness, altered resting-state functional responses and during cognitive tasks, as well as widespread reduced white matter integrity, especially in structures important for cognitive function and emotional processing, both before and after successful abrogation of hypercortisolism. In this paper, we summarize the current knowledge on the psychiatric and neurocognitive consequences of hypercortisolism in patients with CS, both before, and after successful treatment. In addition, we review the structural and functional brain abnormalities associated with hypercortisolism and discuss the influence of these factors on quality of life. [ABSTRACT FROM AUTHOR]

Summary: The review aimed at searching for DNA structure markers of epigenetic modifications leading to intrauterine growth restriction (IUGR) in three livestock species, mouse and human. IUGR affects mammals by harming their wellbeing and the profitability of breeding enterprises. Of the livestock species, we chose cow, pig and sheep owing to there being many reports on the epigenetics of IUGR. IUGR investigations in human and mouse are particularly numerous, as we are interested in our own wellbeing and the mouse is a model species. We decided to focus on five genes (Igf2r, Igf2, H19, Peg3 and Mest) of known IUGR association, reported in all of those species. Despite the abundance of papers on IUGR, naturally occurring mutations responsible for epigenetic modifications have been described only in human and cow. The effect of induced DNA structural modifications upon epigenetics has been described in mouse and pig. One paper regarding mouse was chosen from among those describing DNA modifications performed to obtain parthenogenetic progeny. Papers regarding pig parthenogenetic progeny described the epigenetics of genes involved in foetal development, with no interference with the genome structure. No reports on DNA modifications altering IUGR epigenetics in sheep were found. Only environmental effects were studied and we could not conclude from the experiment designs whether the gene setup could affect the expression of involved genes, as different populations were not included or not specified within particular experiments. Apparently, DNA markers of IUGR epigenetics exist. It has been reported that the small number of them, occurring naturally, may result from neglecting existing evidence of such selection or health status forecasting markers. [ABSTRACT FROM AUTHOR]

Metagenomics provides a tool to assess the functional potential of environmental and host‐associated microbiomes based on the analysis of environmental DNA: assembly, gene prediction and annotation. While gene prediction is straightforward for most bacterial and archaeal taxa, it has limited applicability in the majority of eukaryotic organisms, including fungi that contain introns in gene coding sequences. As a consequence, eukaryotic genes are underrepresented in metagenomics datasets and our understanding of the contribution of fungi and other eukaryotes to microbiome functioning is limited. Here, we developed a machine intelligence‐based algorithm that predicts fungal introns in environmental DNA with reasonable precision and used it to improve the annotation of environmental metagenomes. Intron removal increased the number of predicted genes by up to 9.1% and improved the annotation of several others. The proportion of newly predicted genes increased with the share of eukaryotic genes in the metagenome and—within fungal taxa—increased with the number of introns per gene. Our approach provides a tool named SVMmycointron for improved metagenome annotation, especially of microbiomes with a high proportion of eukaryotes. The scripts described in the paper are made publicly available and can be readily utilized by microbiome researchers analysing metagenomics data. [ABSTRACT FROM AUTHOR]

Malignancies and diseases of various genetic origins can be diagnosed and classified with microarray data. There are many obstacles to overcome due to the large size of the gene and the small number of samples in the microarray. A combination strategy for gene expression in a variety of diseases is described in this paper, consisting of two steps: identifying the most effective genes via soft ensembling and classifying them with a novel deep neural network. The feature selection approach combines three strategies to select wrapper genes and rank them according to the k‐nearest neighbour algorithm, resulting in a very generalisable model with low error levels. Using soft ensembling, the most effective subsets of genes were identified from three microarray datasets of diffuse large cell lymphoma, leukaemia, and prostate cancer. A stacked deep neural network was used to classify all three datasets, achieving an average accuracy of 97.51%, 99.6%, and 96.34%, respectively. In addition, two previously unreported datasets from small, round blue cell tumors (SRBCTs)and multiple sclerosis‐related brain tissue lesions were examined to show the generalisability of the model method. [ABSTRACT FROM AUTHOR]

Listeriosis is one of the most common nervous diseases in ruminants, and is caused almost exclusively by the Gram‐positive bacterium, Listeria monocytogenes. However, there are few reports of listeriosis associated with L. innocua, which is genetically closely related to L. monocytogenes, but considered non‐pathogenic. In this work, we report two cases of suppurative meningoencephalitis in apparently previously healthy ruminants from different farms, in which two strains of L. innocua were recovered. The whole genomes from both isolates were sequenced, allowing phylogenetic analyses to be performed, which indicated that the two strains were very closely related. Virulence determinants were searched, especially genes coding for the main L. monocytogenes virulence factors which have been previously described in L. innocua. Surprisingly, the two isolates do not possess such virulence determinants. Instead, both strains carried a set of genes that encode for other virulence factors of the genus Listeria detected using the Virulence Factor Database (VFDB): iap (division and invasion of host cells), lpeA (entry into non‐professional phagocytes cells), fbpA (multifunctional virulence factor, including adherence to host cells), lspA (surface protein anchoring), lap (adhesion to enterocytes and trans epithelial translocation), pdgA (resistance to lysozyme), oatA (resistance to different antimicrobial compounds and also required for growth inside macrophages), lplA1 (use of host‐metabolites for in vivo growth), gtcA (catalyses teichoic acid of bacterial wall), prsA2 (cell invasion, vacuole lysis and intracellular growth), clpC, clpE and clpP (survival under several stress conditions). These genes among others detected, could be involved in the ability of L. innocua to produce damage in animal and human hosts. These results highlight the multifactorial profile of Listeria pathogenesis and the need for comprehensive scientific research that address microbiological, environmental and veterinary aspects of listeriosis. This paper report two cases of nervous listeriosis in ruminants due to L. innocua in which their genomes were sequenced, and the presence of virulence factors were studied. [ABSTRACT FROM AUTHOR]

Conradi‐Hünermann‐Happle syndrome is a rare X‐linked dominant syndrome affecting the skin, skeletal system, and eyes. Here, we report on a female patient with a de novo heterozygous missense mutation c.301C>T (p.Trp101Arg) of the EMP (emopamil binding protein) gene. [ABSTRACT FROM AUTHOR]

SUMMARY: Whole genome duplication (WGD) in plants is typically followed by genomic downsizing, where large portions of the new genome are lost. Whether this downsizing is accompanied by increased or decreased evolutionary rates of the remaining genes is poorly known, not least because homeolog pairings are often obscured by chromosomal rearrangement. Here, we use the newly published genome from a sedge, namely Kobresia littledalei, and CRISPR/Cas‐9 editing to investigate how the Rho WGD event 70 million years ago (MYA) affected transcription factor evolutionary rates, fates, and function in rice (Oryza sativa) and sorghum (Sorghum bicolor). We focus on the 30‐member DNA‐binding with one zinc finger (Dof) transcription factor family in both crops due to their agronomic importance. Using the known speciation dates of rice from Kobresia (97 MYA) and sorghum (50 MYA), we find that rates of amino acid substitution in the critical Dof domain region were over twofold higher during the 20‐million‐year period following the WGD than before or afterward. Through comparison of synteny blocks, we report that at least 11% of Dof genes were purged from 70 to 50 MYA, while only 6% have been lost in the most recent 50‐million‐year interval. CRISPR/Cas9 editing revealed widespread fitness‐related defects in flowering and lack of redundancy of paired members, as well as significant differences in expression between gene pairs. Together these findings demonstrate the strength of Dof genes as a model for deep evolutionary study and offer one of the most detailed portraits yet of the Rho WGD impact on a gene lineage. Significance Statement: This study leverages the newly published Kobresia genome to assess evolutionary rates in Dof transcription factors before and after the Rho whole genome duplication (WGD) 70 million years ago (MYA) in monocots and reports dramatic loss of gene members and increased amino acid substitution rates from 70 to 50 MYA, but lower rates in the 27 million years before and 50 million years after the WGD event. CRISPR/Cas9 editing reveals non‐redundancy in remaining duplicate retained pairs of OsDof genes. [ABSTRACT FROM AUTHOR]

Laboratory practical sessions are critical to scientific training in biology but usually fail to promote logical and hypothesis‐driven reasoning and rely heavily on the teacher's instructions. This paper describes a 2‐day laboratory practicum in which students prepare and analyze larval cuticle preparations of Drosophila segmentation gene mutant strains. Embryonic segmentation involves three major classes of genes according to their loss‐of‐function phenotypes: the establishment of broad regions by gap genes, the specification of the segments by the pair‐rule genes, and the compartments within segments by the segment polarity genes. Students are asked to sort undefined segmentation mutants into gap, pair‐rule, or segment polarity categories based on their knowledge of the Drosophila segmentation process and the microscopic anatomical traits they are capable of finding in the sample preparations. This technically simple practicum prompts students to pay attention to detailed observation to detect anatomic markers of intrasegmental compartments and thorax versus abdomen cuticle, and promote their logical reasoning in hypothesizing to which segmentation type a given mutant fits best. [ABSTRACT FROM AUTHOR]

Cancer database is a systematic collection and analysis of information on various human cancers at genomic and molecular level that can be utilized to understand various steps in carcinogenesis and for therapeutic advancement in cancer field. Oral cancer is one of the leading causes of morbidity and mortality all over the world. The current research efforts in this field are aimed at cancer etiology and therapy. Advanced genomic technologies including microarrays, proteomics, transcrpitomics, and gene sequencing development have culminated in generation of extensive data and subjection of several genes and microRNAs that are distinctively expressed and this information is stored in the form of various databases. Extensive data from various resources have brought the need for collaboration and data sharing to make effective use of this new knowledge. The current review provides comprehensive information of various publicly accessible databases that contain information pertinent to oral squamous cell carcinoma (OSCC) and databases designed exclusively for OSCC. The databases discussed in this paper are Protein-Coding Gene Databases and microRNA Databases. This paper also describes gene overlap in various databases, which will help researchers to reduce redundancy and focus on only those genes, which are common to more than one databases. We hope such introduction will promote awareness and facilitate the usage of these resources in the cancer research community, and researchers can explore the molecular mechanisms involved in the development of cancer, which can help in subsequent crafting of therapeutic strategies. [ABSTRACT FROM AUTHOR]

Genetic variation is responsible for a large amount of the inter-individual performance disparities seen in sport. As such, in the last ten years genetic association studies have become more common; with one of the most frequently researched sports being football. However, the progress and methodological rigour of genetic association research in football is yet to be evaluated. Therefore, the aim of this paper was to identify and evaluate all genetic association studies involving football players and outline where and how future research should be directed. Firstly, a systematic search was conducted in the Pubmed and SPORTDiscus databases, which identified 80 eligible studies. Progression analysis revealed that 103 distinct genes have been investigated across multiple disciplines; however, research has predominately focused on the association of the ACTN3 or ACE gene. Furthermore, 55% of the total studies have been published within the last four years; showcasing that genetic association research in football is increasing at a substantial rate. However, there are several methodological inconsistencies which hinder research implications, such as; inadequate description or omission of ethnicity and on-field positions. Furthermore, there is a limited amount of research on several key areas crucial to footballing performance, in particular; psychological related traits. Moving forward, improved research designs, larger sample sizes, and the utilisation of genome-wide and polygenic profiling approaches are recommended. Finally, we introduce the Football Gene Project, which aims to address several of these limitations and ultimately facilitate greater individualised athlete development within football. [ABSTRACT FROM AUTHOR]

Striga hermonthica, causes up to 100% yield loss in maize production in Sub‐Saharan Africa. Developing Striga‐resistant maize cultivars could be a major component of integrated Striga management strategies. This paper presents a comprehensive overview of maize breeding activities related to Striga resistance and its management. Scientific surveys have revealed that conventional breeding strategies have been used more than molecular breeding strategies in maize improvement for Striga resistance. Striga resistance genes are still under study in the International Institute for Tropical Agriculture (IITA) maize breeding programme. There is also a need to discover QTL and molecular markers associated with such genes to improve Striga resistance in maize. Marker Assistance Breeding is expected to increase maize breeding efficiency with complex traits such as resistance towards Striga because of the complex nature of the host‐parasite relationship and its intersection with other environmental factors. Conventional alongside molecular tools and technical controls are promising methods to effectively assess Striga in Sub‐Saharan Africa. [ABSTRACT FROM AUTHOR]

To understand how organisms adapt to their environment, a gene‐environmental association (GEA) analysis is commonly conducted. GEA methods based on mixed models, such as linear latent factor mixed models (LFMM) and LFMM2, have grown in popularity for their robust performance in terms of power and computational speed. However, it is unclear how the assumption of a Gaussian distribution for the response variables influences model performance. In this paper, we develop a generalized linear model (GLM) that allows for non‐Gaussian distribution in the genotypic response variables, and treatment of multiallelic nucleotide polymorphisms. Moreover, this multinomial logistic regression model (MLR) is combined with an admixture‐based model or principal components analysis to correct for population structure (MLR‐ADM and MLR‐PC). Using simulations, we evaluate the type 1 error, false discovery rates (FDR), and power to detect selected SNPs, to guide model choice and best practices. With genomic control, MLR‐PC and LFMM2 have similar type 1 error, FDRs, and power when analysing biallelic SNPs, while dramatically outperforming models not accounting for population structure. Differences in performance occur under continuous population structure where MLR‐PC outperforms LFMM/LFMM2, especially when a larger number of clusters or triallelic SNPs are analysed. The Human Genome Diversity Project (HGDP) data set shows that both MLR‐PC and LFMM2 control the inflation of P‐values. Analysis of the 1,000 Genome Project Phase 3 data set illustrates that MLR‐PC and LFMM2 produce consistent results for most significant SNPs, while MLR‐PC discovered additional SNPs corresponding to certain genes, suggesting MLR‐PC may be a useful alternative to GEA inference. [ABSTRACT FROM AUTHOR]

The purpose of this paper is to investigate the immune function of the tumor microenvironment and its clinical correlation with colonic carcinoma. Immune genes were downloaded from the The Cancer Genome Atlas database. Five subtypes are obtained by cluster screening based on immune gene expression data. The C3 and C4 subtypes show stronger immune activity. In addition, the C4 subtype has the largest number of gene mutations and the worst prognosis. Most of the immune signatures are upregulated in the C4 subtype, while most of the immune infiltration‐related cells are upregulated in the C3 and C4 subtypes. The different immune microenvironments between these subtypes may provide new ideas for immunotherapy strategies in colon carcinoma. [ABSTRACT FROM AUTHOR]

A hybridization probe was used to study the regulation of expression of the gene coding for the small subunit of ribulose 1,5-bisphosphate carboxylase, during functional differentiation of protoplasts. A library of cDNA from poly(A)-containing RNA extracted from specially treated tobacco leaves was constructed in the plasmid pBR322, by blunt-end ligation. This library was screened by colony hybridization with 32P-labelled cDNA prepared from rnRNA coding for the precursor of the small subunit. A positive colony was identified containing recombinant plasmids with a nucleotide sequence homologous to this mRNA. These plasmids, bound to diazobenzyloxymethylated cellulose paper. were then used as a hybridization probe. The results showed unambiguously that the small subunit was not transcribed in protoplasts but was transcribed in undifferentiated white and chiorophylle containing green callus cultures derived from protoplasts. The discrepancy between these results and those obtained with classical techniques is discussed. [ABSTRACT FROM AUTHOR]

Summary: Intra‐specific variability is a cornerstone of evolutionary success of species. Acquiring genetic material from distant sources is an important adaptive mechanism in bacteria, but it can also play a role in eukaryotes. In this paper, we investigate the nature and evolution of a chromosomal segment of panicoid (Poaceae, Panicoideae) origin occurring in the nuclear genomes of species of the barley genus Hordeum (Pooideae). The segment, spanning over 440 kb in the Asian Hordeumbogdanii and 219 kb in the South American Hordeumpubiflorum, resides on a pair of nucleolar organizer region (NOR)‐bearing chromosomes. Conserved synteny and micro‐collinearity of the segment in both species indicate a common origin of the segment, which was acquired before the split of the respective barley lineages 5–1.7 million years ago. A major part of the foreign DNA consists of several approximately 68 kb long repeated blocks containing five stress‐related protein‐coding genes and transposable elements (TEs). Whereas outside these repeats, the locus was invaded by multiple TEs from the host genome, the repeated blocks are rather intact and appear to be preserved. The protein‐coding genes remained partly functional, as indicated by conserved reading frames, a low amount of non‐synonymous mutations, and expression of mRNA. A screen across Hordeum species targeting the panicoid protein‐coding genes revealed the presence of the genes in all species of the section Stenostachys. In summary, our study shows that grass genomes can contain large genomic segments obtained from distantly related species. These segments usually remain undetected, but they may play an important role in the evolution and adaptation of species. [ABSTRACT FROM AUTHOR]

Background: Gaining insight into microRNAs (miRNAs) and genes that regulate the therapeutic response of cancer diseases in general and prostate cancer (PCa) in particular is an important issue in current molecular biomedicine and allows the discovery of predictive miRNA targets. Objectives: The aim of this study was to analyze the available data on the influence of radiotherapy (RT) on miRNA expression and on miRNA involved in radiotherapy response in PCa. Materials and methods: The data used in this review were extracted from research papers and the DIANA, STRING, and other databases with a special focus on the mechanisms of radiotherapy PCa response and the miRNA involved and associated genes. Results and Discussion: A search for miRNA prognostic and therapeutic effectiveness markers should rely on both the data of recent experimental studies on the influence of RT on miRNA expression and miRNAs involved in regulation of radiosensitivity in PCa and on bioinformatics resources. miRNA panels and genes targeted by them and involved in radioresponse regulation highlighted by meta‐analysis and cross‐analysis of the data in the present review have. Conclusion: Selected miRNA and gene panel has good potential as prognostic and radiotherapy effectiveness markers for PCa and, moreover, as radiotherapy effectiveness markers in other types of cancer, as the proposed model is not specific to PCa, which opens up opportunities for the development of a universal diagnostic system (or several intersecting systems) for oncology radiotherapy in general. [ABSTRACT FROM AUTHOR]

It has long been observed that human protein‐coding genes have a particular distribution of GC‐content: the 5′ end of these genes has high GC‐content while the 3′ end has low GC‐content. In 2012, it was proposed that this pattern of GC‐content could act as an mRNA identity feature that would lead to it being better recognized by the cellular machinery to promote its nuclear export. In contrast, junk RNA, which largely lacks this feature, would be retained in the nucleus and targeted for decay. Now two recent papers have provided evidence that GC‐content does promote the nuclear export of many mRNAs in human cells. [ABSTRACT FROM AUTHOR]

Rht14, was considered as a GA‐responsive dwarf gene in durum wheat (Triticum durum L.). The object of this paper is to understand the responsiveness of Rht14 after applying exogenous GA3 on important morphological and agronomic traits, and its potential application in wheat breeding. In this study, the F2:3 lines, F3:4 lines and F4:5 lines derived from the reciprocal crosses between the Castelporziano (CP), the donor of Rht14, and tall cultivar Langdon (L) were used to evaluate the effects of Rht14 with exogenous GA3 application on crucial traits. After application of GA3, the plant height of the dwarf lines was more significantly increased by an average of 51.21% and 52.27% than that of the tall lines by 14.70% and 15.16% of the two populations, respectively, while their diameter and thickness of internodes were remarkably reduced, and their flag leaf area, SPAD value and net photosynthetic rate were markedly decreased, compared with the controls. After application of GA3, the spikelet number spike−1, grain number spike−1, and 1000‐kernel weight of the dwarf lines notably increased, while no significant differences were observed on the seed length, width and thickness. Exogenous GA3 significantly increased the coleoptile length, whereas notably reduced the max root length and total root length of the dwarf lines. Significant increases of crude protein, wet gluten, sedimentation value, stability time and development time were observed in the dwarf lines treated with GA3. This study indicated the dwarf gene Rht14 was a GA‐deficient gene and application GA3 could rescue some negative effects by Rht14. [ABSTRACT FROM AUTHOR]

Summary: With the availability of a new highly contiguous Bos taurus reference genome assembly (ARS‐UCD1.2), it is the opportune time to upgrade the bovine gene set by seeking input from researchers. Furthermore, advances in graphical genome annotation tools now make it possible for researchers to leverage sequence data generated with the latest technologies to collaboratively curate genes. For many years the Bovine Genome Database (BGD) has provided tools such as the Apollo genome annotation editor to support manual bovine gene curation. The goal of this paper is to explain the reasoning behind the decisions made in the manual gene curation process while providing examples using the existing BGD tools. We will describe the sources of gene annotation evidence provided at the BGD, including RNA‐seq and Iso‐Seq data. We will also explain how to interpret various data visualizations when curating gene models, and will demonstrate the value of manual gene annotation. The process described here can be applied to manual gene curation for other species with similar tools. With a better understanding of manual gene annotation, researchers will be encouraged to edit gene models and contribute to the enhancement of livestock gene sets. [ABSTRACT FROM AUTHOR]

Heatmap of differentially expressed genes between cetuximab‐resistant and cetuximab‐sensitive patients; image adapted from the Regular Paper by Kwang‐Hyun Cho and co‐authors (pp. 1305–1318). [ABSTRACT FROM AUTHOR]