In-silico identification of putatively functional intergenic small open reading frames in the cucumber genome and their predicted response to biotic and abiotic stresses.

The availability of high-throughput sequencing technologies increased our understanding of different genomes. However, the genomes of all living organisms still have many unidentified coding sequences. The increased number of missing small open reading frames (sORFs) is due to the length threshold used in most gene identification tools, which is true in the genic and, more importantly and surprisingly, in the intergenic regions. Scanning the cucumber genome intergenic regions revealed 420 723 sORF. We excluded 3850 sORF with similarities to annotated cucumber proteins. To propose the functionality of the remaining 416 873 sORF, we calculated their codon adaptation index (CAI). We found 398 937 novel sORF (nsORF) with CAI ≥ 0.7 that were further used for downstream analysis. Searching against the Rfam database revealed 109 nsORFs similar to multiple RNA families. Using SignalP-5.0 and NLS, identified 11 592 signal peptides. Five predicted proteins interacting with Meloidogyne incognita and Powdery mildew proteins were selected using published transcriptome data of host-pathogen interactions. Gene ontology enrichment interpreted the function of those proteins, illustrating that nsORFs' expression could contribute to the cucumber's response to biotic and abiotic stresses. This research highlights the importance of previously overlooked nsORFs in the cucumber genome and provides novel insights into their potential functions.

Robotic-assisted versus laparoscopic-assisted extended mesorectal excision: a comprehensive meta-analysis and systematic review of perioperative and long-term outcomes.

BACKGROUND: Concurrent neoadjuvant chemo-radiation (nCRT) with total mesorectal excision (TME) alone sometimes fails to cure lateral lymph node metastasis (LLNM). Therefore, additional lateral lymph node dissection (LLND) can help in the treatment of these patients. This is what we refer to as extended total mesorectal excision (eTME). Such operations (TME alone or eTME) can be performed using conventional laparoscopic techniques and robotic-assisted techniques as well. Our meta-analysis aims to compare the results of robot-assisted (R-eTME) versus laparoscopic-assisted extended mesorectal excision (L-eTME) in terms of short- and long-term outcomes. METHODOLOGY: Databases searched using title and abstract included Medline (via PubMed), Web of Science, Scopus, and Embase, up to February 20, 2024. All studies that documented robotic versus laparoscopic procedures for extended total mesorectal excision (R-eTME versus L-eTME) and reported more than two relevant outcomes, were included in the study. RESULTS: Our meta-analysis demonstrates four significant outcomes (operative time, urinary complications, overall recurrence, and admission days) between the laparoscopic and robotic groups. The robotic approach shows advantages over the laparoscopic approach in these outcomes except for the operative time (minute), which was longer in the robotic group compared to the laparoscopic group. The laparoscopic group is associated with a higher overall recurrence than the robotic group with an Odds Ratio of 2(95% CI, 1-4, p = 0.05). CONCLUSION: This meta-analysis study showed that the R-eTME group had a lower recurrence rate compared to the L-eTME group. Additionally, hospital admission days increased significantly in the laparoscopic group. Other long-term outcomes did not differ significantly between the two groups. Short-term outcomes were similar, except for more urinary complications in the laparoscopic group. In conclusion, the study suggests that robotic surgery may offer advantages over laparoscopic surgery for eTME. Further research and analysis could provide further insight into the potential benefits of robotic surgery in this procedure, particularly when surgeon experience, center volume, and learning curve are taken into consideration.

Active aspiration versus simple compression to remove residual gas from the abdominal cavity after laparoscopic cholecystectomy: a randomized clinical trial.

PURPOSE: After laparoscopic surgical procedures, residual gas in the abdominal cavity can cause post-operative pain, which is commonly located in the shoulder region. Previous studies suggested that post-laparoscopy pain can be prevented by active suctioning of intraabdominal gas at the end of surgery. METHODS: This randomized controlled trial (registered at DRKS 00,023,286) compared active suctioning versus manual compression in their ability to reduce pain after laparoscopic cholecystectomy. Patients scheduled for laparoscopic cholecystectomy were eligible for trial participation. The primary outcome measure was post-operative pain intensity after 12 h. All the patients were examined by MRI scanning to quantify the intraabdominal gas volume after the intervention. RESULTS: As planned, 60 patients were recruited. The two groups (n = 30 each) were very similar at the end of surgery. Active suctioning reduced the amount of residual pneumoperitoneum more than simple compression (median volume 1.5 versus 3.0 ml, p = 0.002). The primary outcome measure, abdominal pain after 12 h, was slightly lower in the intervention group (- 0.5 points, 95% confidence interval + 0.5 to - 1.7), but without reaching statistical significance (p = 0.37). After 12 h, shoulder pain was present in 10 patients in each group (p = 1.0). Independent of group assignment, however, residual gas volume was significantly associated with higher pain intensity. CONCLUSIONS: Active suctioning appears to have only a minor preventive effect on post-laparoscopy pain, probably because evacuation of the pneumoperitoneum remains incomplete in some patients. Other more effective maneuvers for gas removal should be preferred.

Lack of the Major Multifunctional Catalase KatA in Pseudomonas aeruginosa Accelerates Evolution of Antibiotic Resistance in Ciprofloxacin-Treated Biofilms.

During chronic biofilm infections, Pseudomonas aeruginosa bacteria are exposed to increased oxidative stress as a result of the inflammatory response. As reactive oxygen species (ROS) are mutagenic, the evolution of resistance to ciprofloxacin (CIP) in biofilms under oxidative stress conditions was investigated. We experimentally evolved six replicate populations of P. aeruginosa lacking the major catalase KatA in colony biofilms and stationary-phase cultures for seven passages in the presence of subinhibitory levels (0.1 mg/liter) of CIP or without CIP (eight replicate lineages for controls) under aerobic conditions. In CIP-evolved biofilms, a larger CIP-resistant subpopulation was isolated in the ΔkatA strain than in the wild-type (WT) PAO1 population, suggesting oxidative stress as a promoter of the development of antibiotic resistance. A higher number of mutations identified by population sequencing were observed in evolved ΔkatA biofilm populations (CIP and control) than in WT PAO1 populations evolved under the same conditions. Genes involved in iron assimilation were found to be exclusively mutated in CIP-evolved ΔkatA biofilm populations, probably as a defense mechanism against ROS formation resulting from Fenton reactions. Furthermore, a hypermutable lineage due to mutL inactivation developed in one CIP-evolved ΔkatA biofilm lineage. In CIP-evolved biofilms of both the ΔkatA strain and WT PAO1, mutations in nfxB, the negative regulator of the MexCD-OprJ efflux pump, were observed while in CIP-evolved planktonic cultures of both the ΔkatA strain and WT PAO1, mutations in mexR and nalD, regulators of the MexAB-OprM efflux pump, were repeatedly found. In conclusion, these results emphasize the role of oxidative stress as an environmental factor that might increase the development of antibiotic resistance in in vivo biofilms.

Pollen-specific activation of Arabidopsis retrogenes is associated with global transcriptional reprogramming.

Duplications allow for gene functional diversification and accelerate genome evolution. Occasionally, the transposon amplification machinery reverse transcribes the mRNA of a gene, integrates it into the genome, and forms an RNA-duplicated copy: the retrogene. Although retrogenes have been found in plants, their biology and evolution are poorly understood. Here, we identified 251 (216 novel) retrogenes in Arabidopsis thaliana, corresponding to 1% of protein-coding genes. Arabidopsis retrogenes are derived from ubiquitously transcribed parents and reside in gene-rich chromosomal regions. Approximately 25% of retrogenes are cotranscribed with their parents and 3% with head-to-head oriented neighbors. This suggests transcription by novel promoters for 72% of Arabidopsis retrogenes. Many retrogenes reach their transcription maximum in pollen, the tissue analogous to animal spermatocytes, where upregulation of retrogenes has been found previously. This implies an evolutionarily conserved mechanism leading to this transcription pattern of RNA-duplicated genes. During transcriptional repression, retrogenes are depleted of permissive chromatin marks without an obvious enrichment for repressive modifications. However, this pattern is common to many other pollen-transcribed genes independent of their evolutionary origin. Hence, retroposition plays a role in plant genome evolution, and the developmental transcription pattern of retrogenes suggests an analogous regulation of RNA-duplicated genes in plants and animals.

Laparoscopic retroperitoneal lymphadenectomy for ovarian mixed germ cell tumor in a patient with situs inversus totalis; reporting the first case worldwide with literature review and in silico analysis.

BACKGROUND: Situs inversus totalis (SIT) is a rare autosomal recessive inheritance at which the abdomino-thoracic organs are mirror-image transposed. Germ cell tumors originate from the primitive germ cell of the ovary and testis. CASE REPORT PRESENTATION: A rare association between malignant ovarian mixed germ cell tumor and SIT was presented in a 32-years-old Egyptian female, successfully treated with laparoscopic total abdominal hysterectomy, right salpingo-oophorectomy, and retroperitoneal lymphadenectomy (laparoscopic retroperitoneal lymphadenectomy) of both sides. This case is considered the first of its kind worldwide. CONCLUSION: SIT may be associated with malignant ovarian germ cell tumors. Surgical intervention could be done laparoscopically.

The evolutionary trajectories of P. aeruginosa in biofilm and planktonic growth modes exposed to ciprofloxacin: beyond selection of antibiotic resistance.

Ciprofloxacin (CIP) is used to treat Pseudomonas aeruginosa biofilm infections. We showed that the pathways of CIP-resistance development during exposure of biofilms and planktonic P. aeruginosa populations to subinhibitory levels of CIP depend on the mode of growth. In the present study, we analyzed CIP-resistant isolates obtained from previous evolution experiments, and we report a variety of evolved phenotypic and genotypic changes that occurred in parallel with the evolution of CIP-resistance. Cross-resistance to beta-lactam antibiotics was associated with mutations in genes involved in cell-wall recycling (ftsZ, murG); and could also be explained by mutations in the TCA cycle (sdhA) genes and in genes involved in arginine catabolism. We found that CIP-exposed isolates that lacked mutations in quorum-sensing genes and acquired mutations in type IV pili genes maintained swarming motility and lost twitching motility, respectively. Evolved CIP-resistant isolates showed high fitness cost in planktonic competition experiments, yet persisted in the biofilm under control conditions, compared with ancestor isolates and had an advantage when exposed to CIP. Their persistence in biofilm competition experiments in spite of their fitness cost in planktonic growth could be explained by their prolonged lag-phase. Interestingly, the set of mutated genes that we identified in these in vitro-evolved CIP-resistant colonies, overlap with a large number of patho-adaptive genes previously reported in P. aeruginosa isolates from cystic fibrosis (CF) patients. This suggests that the antibiotic stress is contributing to the bacterial evolution in vivo, and that adaptive laboratory evolution can be used to predict the in vivo evolutionary trajectories.

Tailored CNTs Buckypaper Membranes for the Removal of Humic Acid and Separation of Oil-in-Water Emulsions.

Carbon nanotubes (CNTs) are a robust material and proven as a promising candidate for a wide range of electronic, optoelectronic and environmental applications. In this work, two different methods were utilized for the preparation of CNTs exhibiting different aspect ratios via chemical vapor deposition (CVD). The as-prepared CNTs were analyzed using scanning electron microscopy (SEM), transmission electron microscopy (TEM), N2adsorption isotherms, thermogravimetric analysis and Raman spectroscopy in order to investigate their morphological and structural properties. Free-standing CNTs "buckypaper" membranes were fabricated, characterized and tailored to meet the requirements of two applications, i.e., (1) the removal of humic acid (HA) from water and (2) separation of oil-in-water emulsions. It was revealed that the hydrophobic buckypapers showed high separation performance for Shell oil-in-water emulsions filtration, with up to 98% through the accumulation of oil droplets onto the membrane surface. The absorption capacity of buckypaper membranes for various organic liquids (oil, chloroform and toluene) was evaluated over 10 absorption cycles to investigate their recyclability and robustness. Moreover, surface modification was introduced to the pristine CNTs to increase their surface hydrophilicity and improve the pure water permeability of buckypapers. These modified buckypapers showed high flux for HA solutions and excellent HA rejection efficiency up to 95%via size exclusion and electrostatic repulsion mechanisms.

Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data.

Gene model annotations are important community resources that ensure comparability and reproducibility of analyses and are typically the first step for functional annotation of genomic regions. Without up-to-date genome annotations, genome sequences cannot be used to maximum advantage. It is therefore essential to regularly update gene annotations by integrating the latest information to guarantee that reference annotations can remain a common basis for various types of analyses. Here, we report an improvement of the Arabidopsis lyrata gene annotation using extensive RNA-seq data. This new annotation consists of 31,132 protein coding gene models in addition to 2,089 genes with high similarity to transposable elements. Overall, ~87% of the gene models are corroborated by evidence of expression and 2,235 of these models feature multiple transcripts. Our updated gene annotation corrects hundreds of incorrectly split or merged gene models in the original annotation, and as a result the identification of alternative splicing events and differential isoform usage are vastly improved.

Hidden genetic nature of epigenetic natural variation in plants.

Transcriptional gene silencing (TGS) is an epigenetic mechanism that suppresses the activity of repetitive DNA elements via accumulation of repressive chromatin marks. We discuss natural variation in TGS, with a particular focus on cases that affect the function of protein-coding genes and lead to developmental or physiological changes. Comparison of the examples described has revealed that most natural variation is associated with genetic determinants, such as gene rearrangements, inverted repeats, and transposon insertions that triggered TGS. Recent technical advances have enabled the study of epigenetic natural variation at a whole-genome scale and revealed patterns of inter- and intraspecific epigenetic variation. Future studies exploring non-model species may reveal species-specific evolutionary adaptations at the level of chromatin configuration.