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An open reading frame encoding an 88 amino acid protein was present downstream of the previously characterized endolysin of Streptomyces aureofaciens phage µ1/6. Structural analysis of its sequence revealed features characteristic for holin. This open reading frame encoding the putative holin was amplified by polymerase chain reaction and cloned into the expression vector pET-21d(+). Synthesis of the holin-like protein resulted in bacterial cell death but not lysis. The holµ1/6 gene was able to complement the defective λ S allele in the nonsuppressing Escherichia coli HB101 strain to produce phage progeny. This fact suggests that the proteins encoded by both phage genes have analogous function, i.e. the streptomycete holin induces nonspecific lesions in the cytoplasmic membrane, through which the λ endolysin gains an access to its substrate, the cell wall. The concomitant expression of both S. aureofaciens holµ1/6 and λ endolysin in E. coli resulted in abrupt cell lysis. This result provided further evidence that the product of holµ1/6 gene is a holin. [ABSTRACT FROM AUTHOR]

Abstract Background Polyploidization is considered one of the main mechanisms of plant genome evolution. The presence of multiple copies of the same gene reduces selection pressure and permits sub-functionalization and neo-functionalization leading to plant diversification, adaptation and speciation. In bread wheat, polyploidization and the prevalence of transposable elements resulted in massive gene duplication and movement. As a result, the number of genes which are non-collinear to genomes of related species seems markedly increased in wheat. Results We used new-generation sequencing (NGS) to generate sequence of a Mb-sized region from wheat chromosome arm 3DS. Sequence assembly of 24 BAC clones resulted in two scaffolds of 1,264,820 and 333,768 bases. The sequence was annotated and compared to the homoeologous region on wheat chromosome 3B and orthologous loci of Brachypodium distachyon and rice. Among 39 coding sequences in the 3DS scaffolds, 32 have a homoeolog on chromosome 3B. In contrast, only fifteen and fourteen orthologs were identified in the corresponding regions in rice and Brachypodium, respectively. Interestingly, five pseudogenes were identified among the non-collinear coding sequences at the 3B locus, while none was found at the 3DS locus. Conclusion Direct comparison of two Mb-sized regions of the B and D genomes of bread wheat revealed similar rates of non-collinear gene insertion in both genomes with a majority of gene duplications occurring before their divergence. Relatively low proportion of pseudogenes was identified among non-collinear coding sequences. Our data suggest that the pseudogenes did not originate from insertion of non-functional copies, but were formed later during the evolution of hexaploid wheat. Some evidence was found for gene erosion along the B genome locus.

Abstract Background We generated the gene expression profile of the total testis from the adult C57BL/6J male mice using serial analysis of gene expression (SAGE). Two high-quality SAGE libraries containing a total of 76 854 tags were constructed. An extensive bioinformatic analysis and comparison of SAGE transcriptomes of the total testis, testicular somatic cells and other mouse tissues was performed and the theory of male-biased gene accumulation on the X chromosome was tested. Results We sorted out 829 genes predominantly expressed from the germinal part and 944 genes from the somatic part of the testis. The genes preferentially and specifically expressed in total testis and testicular somatic cells were identified by comparing the testis SAGE transcriptomes to the available transcriptomes of seven non-testis tissues. We uncovered chromosomal clusters of adjacent genes with preferential expression in total testis and testicular somatic cells by a genome-wide search and found that the clusters encompassed a significantly higher number of genes than expected by chance. We observed a significant 3.2-fold enrichment of the proportion of X-linked genes specific for testicular somatic cells, while the proportions of X-linked genes specific for total testis and for other tissues were comparable. In contrast to the tissue-specific genes, an under-representation of X-linked genes in the total testis transcriptome but not in the transcriptomes of testicular somatic cells and other tissues was detected. Conclusion Our results provide new evidence in favor of the theory of male-biased genes accumulation on the X chromosome in testicular somatic cells and indicate the opposite action of the meiotic X-inactivation in testicular germ cells.

Background: In Tanzania, inadequate infrastructures and shortages of trauma-response training exacerbate trauma-related fatalities. McGill University's Centre for Global Surgery introduced the Trauma and Disaster Team Response course (TDTR) to address these challenges. This study assesses the impact of simulation-based TDTR training on care providers' knowledge/skills and healthcare processes to enhance patient outcomes., Methods: The study used a pre-post-interventional design. TDTR, led by Tanzanian instructors at Muhimbili Orthopedic Institute from August 16-18, 2023, involved 22 participants in blended online and in-person approaches with simulated skills sessions. Validated tools assessed participants' knowledge/skills and teamwork pre/post-interventions, alongside feedback surveys. Outcome measures included evaluating 24-h emergency department patient arrival-to-care time pre-/post-TDTR interventions, analyzed using parametric and non-parametric tests based on data distributions., Results: Participants' self-assessment skills significantly improved (median increase from 34 to 58, p < 0.001), along with teamwork (median increase from 44.5 to 87.5, p < 0.003). While 99% of participants expressed satisfaction with TDTR meeting their expectations, 97% were interested in teaching future sessions. The six-month post-intervention arrival-to-care time significantly decreased from 29 to 13 min, indicating a 55.17% improvement (p < 0.004). The intervention led to fewer ward admissions (35.26% from 51.67%) and more directed to operating theaters (29.83% from 16.85%), suggesting improved patient management (p < 0.018)., Conclusion: The study confirmed surgical skills training effectiveness in Tanzanian settings, highlighting TDTR's role in improving teamwork and healthcare processes that enhanced patient outcomes. To sustain progress and empower independent trauma educators, ongoing refresher sessions and expanding TDTR across low- and middle-income countries are recommended to align with global surgery goals., (© 2024 The Authors. World Journal of Surgery published by John Wiley & Sons Ltd on behalf of International Society of Surgery/Société Internationale de Chirurgie (ISS/SIC).)

All eukaryotic organisms contain mitochondria or organelles that evolved from the same endosymbiotic event like classical mitochondria. Organisms inhabiting low oxygen environments often contain mitochondrial derivates known as hydrogenosomes, mitosomes or neutrally as mitochondrion-like organelles. The detailed investigation has shown unexpected evolutionary plasticity in the biochemistry and protein composition of these organelles in various protists. We investigated the mitochondrion-like organelle in Trimastix pyriformis, a free-living member of one of the three lineages of anaerobic group Metamonada. Using 454 sequencing we have obtained 7 037 contigs from its transcriptome and on the basis of sequence homology and presence of N-terminal extensions we have selected contigs coding for proteins that putatively function in the organelle. Together with the results of a previous transcriptome survey, the list now consists of 23 proteins - mostly enzymes involved in amino acid metabolism, transporters and maturases of proteins and transporters of metabolites. We have no evidence of the production of ATP in the mitochondrion-like organelle of Trimastix but we have obtained experimental evidence for the presence of enzymes of the glycine cleavage system (GCS), which is part of amino acid metabolism. Using homologous antibody we have shown that H-protein of GCS localizes into vesicles in the cell of Trimastix. When overexpressed in yeast, H- and P-protein of GCS and cpn60 were transported into mitochondrion. In case of H-protein we have demonstrated that the first 16 amino acids are necessary for this transport. Glycine cleavage system is at the moment the only experimentally localized pathway in the mitochondrial derivate of Trimastix pyriformis.

Tumor stroma is an active part influencing the biological properties of malignancies via molecular cross-talk. Cancer-associated fibroblasts play a significant role in this interaction. These cells frequently express smooth muscle actin and can be classified as myofibroblasts. The adhesion/growth-regulatory lectin galectin-1 is an effector for their generation. In our study, we set the presence of smooth muscle actin-positive cancer-associated fibroblasts in relation to this endogenous lectin and an in vivo competitor (galectin-3). In squamous cell carcinomas of head and neck, upregulation of galectin-1 presence was highly significantly correlated to presence of smooth muscle actin-positive cancer-associated fibroblasts in the tumor (p = 4 × 10(-8)). To pinpoint further correlations on the molecular level, we applied microarray analyses to the transcription profiles of the corresponding tumors. Significant correlations of several transcripts were detected with the protein level of galectin-1 in the cancer-associated fibroblasts. These activated genes (MAP3K2, TRIM23, PTPLAD1, FUSIP1, SLC25A40 and SPIN1) are related to known squamous-cell-carcinoma poor-prognosis factors, NF-κB upregulation and splicing downregulation. These results provide new insights into the significance of presence of myofibroblasts in squamous cell carcinoma., (Copyright © 2012 UICC.)

Background Information: Considering an analogy between wound healing and tumour progression, we studied chemokine and cytokine transcription and expression in normal fibroblasts by co-culture and in situ., Results: Whole-genome transcriptome profiling revealed strong upregulation for the interleukin (IL)-6, IL-8 and the chemokine CXCL-1 in in vitro co-cultures of normal fibroblasts with either normal or malignant epithelial cells compared to fibroblast cultures. The same ILs/chemokines were distinctly upregulated in clinical samples of squamous cell carcinoma when compared with paired normal mucosae. Analysis of culture supernatants showed that during the course of co-culture of the fibroblasts with the epithelial cells, IL-6, IL-8 and CXCL-1 were secreted to the culture medium. Experiments with addition of any of the proteins to the culture medium supported the notion that these ILs/chemokines strongly contributed to maintenance of a low-differentiation phenotype of epithelial cells, evaluated by the detection of keratin-8. Simultaneous addition of all factors increased the extent of the effect. These studies were extended by experiments with epithelial cells, either cultured in medium conditioned by preceding use for malignant keratinocytes without and in the presence of normal or cancer-associated fibroblasts or medium containing antibodies against IL-6, IL-8 and CXCL-1., Conclusions: Our results indicate an analogy between wound healing and tumour growth, support the importance of epithelial-mesenchymal interaction in this model system and establish a potential bio-inspired anticancer therapy., (Copyright © 2012 Wiley-Liss, Inc.)

Soils of coniferous forest ecosystems are important for the global carbon cycle, and the identification of active microbial decomposers is essential for understanding organic matter transformation in these ecosystems. By the independent analysis of DNA and RNA, whole communities of bacteria and fungi and its active members were compared in topsoil of a Picea abies forest during a period of organic matter decomposition. Fungi quantitatively dominate the microbial community in the litter horizon, while the organic horizon shows comparable amount of fungal and bacterial biomasses. Active microbial populations obtained by RNA analysis exhibit similar diversity as DNA-derived populations, but significantly differ in the composition of microbial taxa. Several highly active taxa, especially fungal ones, show low abundance or even absence in the DNA pool. Bacteria and especially fungi are often distinctly associated with a particular soil horizon. Fungal communities are less even than bacterial ones and show higher relative abundances of dominant species. While dominant bacterial species are distributed across the studied ecosystem, distribution of dominant fungi is often spatially restricted as they are only recovered at some locations. The sequences of cbhI gene encoding for cellobiohydrolase (exocellulase), an essential enzyme for cellulose decomposition, were compared in soil metagenome and metatranscriptome and assigned to their producers. Litter horizon exhibits higher diversity and higher proportion of expressed sequences than organic horizon. Cellulose decomposition is mediated by highly diverse fungal populations largely distinct between soil horizons. The results indicate that low-abundance species make an important contribution to decomposition processes in soils.

The genus Luzula consists of 115 species distributed throughout the world. Luzula is monophyletic, but species relationships within the genus are difficult to determine primarily due to the similar morphology even within geographically remote taxa (especially within the section Luzula). The plastome trnL intron, trnL-F intergenic spacer and the nuclear ribosomal ITS1-5.8S-ITS2 regions were analysed using maximum parsimony and maximum likelihood reconstruction in 93 species of Luzula. The incongruent phylogenetic signals obtained from the chloroplast and the nuclear genomes point to incomplete lineage sorting as well as recent hybridisation in this group. Although tree-building analyses revealed several well-supported lineages, the outcomes for many groups were ambiguous. In the total evidence tree, Luzula species were grouped within six main clades (1. subgenus Marlenia, 2. subgenus Pterodes except for L. pilosa, 3. sections Anthelaea and Nodulosae, 4. sections Diprophyllatae and Thyrsanochlamydeae, 5. section Alpinae except for a few species and 6. section Luzula). The subgenus Marlenia occupies the early derived lineage within the genus Luzula. The traditionally accepted subgenera Pterodes and Luzula (and its sections) appear to be non-monophyletic. A statistical parsimony network approach showed that ancient haplotypes and ribotypes co-occur with their descendants in Luzula. Furthermore, many haplotypes are shared among different species. Within the Luzula section Luzula, both recent hybridisation and incomplete lineage sorting of ancestral polymorphisms may represent potential sources of the incongruence between chloroplast and nuclear data., (Copyright © 2010 Elsevier Inc. All rights reserved.)