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Codon usage bias (CUB), the uneven usage of synonymous codons encoding the same amino acid, differs among genes within and across bacteria genomes. CUB is known to be influenced by gene expression and accordingly, CUB differs between the high-expression and low-expression genes in several bacteria. In this article, we have extended codon usage study considering gene essentiality as a feature. Using machine learning (ML) based approaches, we have analysed Relative Synonymous Codon Usage (RSCU) values between essential and non-essential genes in Escherichia coli and thirty-four other bacterial genomes whose gene essentiality features were available in public databases. We observed significant differences in codon usage patterns between essential and non-essential genes for majority of the bacterial genomes and accordingly, ML based classifiers achieved high area under curve (AUC) scores, with a minimum score of 70.0 across twenty-eight organisms. Further, importance of the codons towards classifying genes found to differ among the codons in each genome. Arg codon CGT and Gly codon GGT were observed to be the most preferred codons among essential genes in Escherichia coli. Interestingly, some of the codons like CGT, ATA, GGT and GGG observed to be contributing consistently towards classifying essential genes across thirty-five bacteria genomes studied. In other hand, codons TGY and CAY encoding amino acids Cys and His respectively were among the least contributing codons towards classification among all these bacteria. This study demonstrates the gene essentiality based differences in synonymous codon usage in bacteria genomes and presents a common codon usage pattern across bacteria. [ABSTRACT FROM AUTHOR]

In our study, we compared synonymous polymorphism in co-transcribed gene pairs within five well-known Escherichia coli operons (rpoB/C, lacZ/Y, kdpA/B, araB/A and bcsA/B). Interestingly, the transition to transversion ratio between gene pairs were different due to their compositional differences of two-fold and four-fold degenerate codons. The differences in polymorphism spectra were more pronounced in four-fold and six-fold codons compared to two-fold degenerate codons. Notably, rpoB and rpoC showed significant distinctions in UCC, GUA, CCG, GCU, GGC and CGC codons. Similar trends were observed in other gene pairs, particularly in higher degenerate codons. Notably, two-fold degenerate codons primarily exhibited synonymous polymorphisms through transitions, while higher degenerate codons encompassed both transition and transversion events. This underscores the intriguing role of degenerate codons in molecular evolution. [ABSTRACT FROM AUTHOR]

The temporary exposure of single-stranded regions in the genome during the process of replication and transcription makes the region vulnerable to cytosine deamination resulting in a higher rate of C→T transition. Intraoperon intergenic regions undergo transcription along with adjacent co-transcribed genes in an operon, whereas interoperon intergenic regions are usually devoid of transcription. Hence these two types of intergenic regions (IGRs) can be compared to find out the contribution of replication-associated mutations (RAM) and transcription-associated mutations (TrAM) towards bringing variation in genomes. In our work, we performed a polymorphism spectra comparison between intraoperon IGRs and interoperon IGRs in genomes of two well-known closely related bacteria such as Escherichia coli and Salmonella enterica. In general, the size of intraoperon IGRs was smaller than that of interoperon IGRs in E. coli and S. enterica. Interestingly, the polymorphism frequency at intraoperon IGRs was 2.5-fold lesser than that in the interoperon IGRs in E. coli genome. Similarly, the polymorphism frequency at intraoperon IGRs was 2.8-fold lesser than that in the inter-operon IGRs in S. enterica genome. Therefore, the intraoperon IGRs were often observed to be more conserved. In the case of interoperon IGRs, the T→C transition frequency was a minimum of two times more frequent than T→A transversion frequency whereas in the case of intraoperon IGRs, T→C transition frequency was similar to that of T→A transversion frequency. The polymorphism was purine-biased and keto-biased more in intraoperon IGRs than the inter-operon IGRs. In E. coli, the transition/transversion ratio was observed as 1.639 and 1.338 in inter-operon and in intraoperon IGRs, respectively. In S. enterica, the transition/transversion ratio was observed as 2.134 and 2.780 in inter-operon and in intraoperon IGRs, respectively. The observation in this study indicates that transcribable IGRs might not always have higher polymorphism frequency than nontranscribable IGRs. The lower polymorphism frequency at intraoperon IGRs might be attributed to different events such as the transcription-coupled DNA repair, sequences facilitating translation initiation and avoidance of Rho-dependent transcription termination. [ABSTRACT FROM AUTHOR]

Unequal usage of synonymous codons is known as codon usage bias (CUB), which is generally different between the high‐expression genes (HEG) and low‐expression genes (LEG) in organisms is not yet adequately reported across different bacteria. In this study, a machine learning‐based approach was implemented initially to find out codons that are significantly different between the HEG and LEG in Escherichia coli. It identified Cys codons such as UGU and UGC, Lys codons such as AAA and AAG that were least influenced by gene expression. Codons such as UCU (Ser), CUG (Leu), GGG (Gly), CGG (Arg) etc. were identified to be influenced maximum by the gene expression. The study was extended to analyze codon usage in 683 other bacterial species. Cys (UGU/UGC) and Ser (AGU/AGC) codons were identified being the least different between the two groups of genes across these bacterial species. Codons such as CGA, CUG, GGG, GCC, ACC, AUA, and AUC were identified to be influenced by the gene expression across majority of these species. This study supports the role of CUB on gene expression across bacteria and demonstrates a commonality among bacteria regarding behavior of certain codons with regard to gene expression. [ABSTRACT FROM AUTHOR]

Transversion and transition mutations have variable effects on the stability of RNA secondary structure considering that the former destabilizes the double helix geometry to a greater extent by introducing purine:purine (R:R) or pyrimidine:pyrimidine (Y:Y) base pairs. Therefore, transversion frequency is likely to be lower than that of transition in the secondary structure regions of RNA genes. Here, we performed an analysis of transition and transversion frequencies in tRNA genes defined well with secondary structure and compared with the intergenic regions in five bacterial species namely Escherichia coli, Klebsiella pneumoniae, Salmonella enterica, Staphylococcus aureus and Streptococcus pneumoniae using a large genome sequence data set. In general, the transversion frequency was observed to be lower than that of transition in both tRNA genes and intergenic regions. The transition to transversion ratio was observed to be greater in tRNA genes than that in the intergenic regions in all the five bacteria that we studied. Interestingly, the intraspecies base substitution analysis in tRNA genes revealed that non-compensatory substitutions were more frequent than compensatory substitutions in the stem region. Further, transition to transversion ratio in the loop region was observed to be significantly lesser than that among the non-compensatory substitutions in the stem region. This indicated that the transversion is more deleterious than transition in the stem regions. In addition, substitutions from amino bases (A/C) to keto bases (G/T) were also observed to be more than the reverse substitutions in the stem region. Substitution from amino bases to keto bases are likely to facilitate the stable G:U pairing unlike the reverse substitution that facilitates the unstable A:C pairing in the stem region of tRNA. This work provides additional support that the secondary structure of tRNA molecule is what drives the different substitutions in its gene sequence. [ABSTRACT FROM AUTHOR]

This study compares thirteen rice-based cropping systems in the coastal part of West Bengal, India in terms of productivity, profitability, energetics, and emissions. Information on the crop management practices of these systems was collected on 60 farms through a questionnaire survey. Rice-bitter gourd system was observed to have the highest system yield (49.88 ± 4.34 tha−1yr−1) followed by rice-potato-ridge gourd (37.78 ± 2.77 tha−1yr−1) and rice-potato-pumpkin (36.84 ± 2.04 tha−1yr−1) systems. The rice-bitter gourd system also recorded the highest benefit:cost ratio (3.92 ± 0.061). The lowest system yield and economics were recorded in the rice-fallow-fallow system. Rice-sunflower system recorded highest specific energy (2.54 ± 0.102 MJkg−1), followed by rice-rice (2.14 ± 0.174 MJkg−1) and rice-fallow-fallow (1.91 ± 0.327 MJkg−1) systems, lowest being observed in the rice-bitter gourd (0.52 ± 0.290 MJkg−1) and rice-pointed gourd (0.52 ± 0.373 MJkg−1) systems. Yield-scaled GHGs (YSGHG) emission was highest (1.265 ± 0.29 t CO2eqt−1 system yield) for rice-fallow-fallow system and was lowest for rice-vegetable systems. To estimate the uncertainty of the YSGHG across different systems under study, Monte-Carlo Simulation was performed. It was observed that there was a 5% probability of recording YSGHG emission > 1.15 t CO2eqt−1 system yield from different cropping systems in the present experiment. Multiple system properties such as productivity, economics, energy, and emission from all rice-based systems taken together, the rice-vegetable system performed consistently well across parameters and may be practised for higher economic returns with judicious and sustainable utilization of resources in the coastal saline tracts of the region. [ABSTRACT FROM AUTHOR]

This study aimed to determine the relation of best corrected visual acuity (BCVA) and low luminance visual acuity (LLVA) in proliferative diabetic retinopathy (PDR) following treatment with either aflibercept or pan-retinal photocoagulation (PRP). The study was conducted as a post-hoc analysis of the CLARITY trial in which naïve and PRP treated PDR patients were randomised to receive either aflibercept or PRP. BCVA and LLVA were assessed at baseline and at week 52. Our analyses showed that the BCVA and LLVA correlate well in treatment naïve PDR with an average low luminance deficit of 11.79 Early Treatment Diabetic Retinopathy Score (ETDRS) letters. However, LLVA at lower levels of BCVA showed more variance. Post aflibercept therapy, the mean change in BCVA and LLVA at 52 weeks after aflibercept was +2.1 (SD 6.05) letters and +0.39 (SD 5.6) letters, respectively. Similarly, after PRP, it was −2.5 (SD 4.9) letters and −1.9 (SD 8.7) letters, respectively. When comparing treatment arms, BCVA change was found to be statistically significant (p < 0.001) whereas LLVA was not (p = 0.11). These findings show that LLVA does not respond as well as BCVA following any treatment for PDR, even though BCVA and LLVA both test foveal function. [ABSTRACT FROM AUTHOR]

Reliable outcome measures are required for clinical trials investigating novel agents for preventing progression of capillary non-perfusion (CNP) in retinal vascular diseases. Currently, accurate quantification of topographical distribution of CNP on ultrawide field fluorescein angiography (UWF-FA) by retinal experts is subjective and lack standardisation. A U-net style network was trained to extract a dense segmentation of CNP from a newly created dataset of 75 UWF-FA images. A subset of 20 images was also segmented by a second expert grader for inter-grader reliability evaluation. Further, a circular grid centred on the FAZ was used to provide standardised CNP distribution analysis. The model for dense segmentation was five-fold cross-validated achieving area under the receiving operating characteristic of 0.82 (0.03) and area under precision-recall curve 0.73 (0.05). Inter-grader assessment on the 20 image subset achieves: precision 59.34 (10.92), recall 76.99 (12.5), and dice similarity coefficient (DSC) 65.51 (4.91), and the centred operating point of the automated model reached: precision 64.41 (13.66), recall 70.02 (16.2), and DSC 66.09 (13.32). Agreement of CNP grid assessment reached: Kappa 0.55 (0.03), perfused intraclass correlation (ICC) 0.89 (0.77, 0.93), non-perfused ICC 0.86 (0.73, 0.92), inter-grader agreement of CNP grid assessment values are Kappa 0.43 (0.03), perfused ICC 0.70 (0.48, 0.83), non-perfused ICC 0.71 (0.48, 0.83). Automated dense segmentation of CNP in UWF-FA images achieves performance levels comparable to inter-grader agreement values. A grid placed on the deep learning-based automatic segmentation of CNP generates a reliable and quantifiable method of measurement of CNP, to overcome the subjectivity of human graders. [ABSTRACT FROM AUTHOR]

Ralstonia solanacearum causes a lethal bacterial wilt disease in many plants by colonizing the vascular tissues of the hosts. Upon inoculation of tomato seedlings through either leaf or root, the wilting symptoms occur first at the apical region and then proceed downward along the shoot. The systemic order of the disease initiation and progression in the host, independent of the site of pathogen inoculation, is yet to be investigated. To understand the disease progression more clearly, we have carried out a systematic study of the pathogen localization by GUS staining of inoculated tomato seedlings, at 24‐hour intervals from 0 days post‐inoculation (dpi) to 5 dpi. In both inoculation methods, pathogen colonization was observed at 1 dpi at the apical meristem as well as the cotyledon leaves, where the disease initiates. As the disease progressed, colonization by the pathogen towards the lower region of the shoot was observed. Disease consistency and pathogenicity magnitude were observed to be higher using the leaf inoculation method than the root inoculation method. Several R. solanacearum transposon‐induced mutants that were reduced in virulence by root inoculation but virulent by leaf inoculation were obtained. Using GUS staining, it was observed that these mutants were unable to localize in the shoot region when inoculated in the root. Our study indicates that the apical meristem and the cotyledon leaves are the first regions to be colonized in inoculated tomato seedlings, which might explain the disease initiation from this region. [ABSTRACT FROM AUTHOR]

The thresholds of macular microvasculature parameters associated with mild visual impairment in diabetic macular ischemia (DMI) patients are unclear. Therefore, this prospective observational study is aimed at demonstrating the optical coherence tomography angiography parameters that best correlate with mild visual impairment (<70 Early Treatment Diabetic Retinopathy Study (ETDRS) letters, Snellen equivalent 20/40) in DMI. The study was completed at the Moorfields Eye Hospital from December 2019 to August 2021. A total of 123 eyes of 87 patients with stable-treated proliferative diabetic retinopathy following panretinal photocoagulation were recruited. DMI was defined as an irregular foveal avascular zone (FAZ) area ≥ 0.5 mm2 or a smaller FAZ area with parafoveal capillary dropout in at least one quadrant. The analysis showed that the whole image deep vascular complex vessel density (DVC VD) in the 3 × 3 mm area had the best discriminatory ability to identify participants with mild visual impairment at 41.9% (area under the curve = 0.77, sensitivity 94%, specificity 54%, likelihood ratio [LR] = 2.04), and the FAZ area had the greatest post-test LR = 4.21 at 0.64 mm2. The 3 × 3 mm whole image DVC VD and FAZ area cutoffs are useful for screening vision-threatening DMI, but DVC VD has low specificity. [ABSTRACT FROM AUTHOR]

Diabetic macular ischemia (DMI) is a common complication of diabetic retinopathy that can lead to progressive and irreversible visual loss. Despite substantial clinical burden, there are no treatments for DMI, no validated clinical trial endpoints, and few clinical trials focusing on DMI. Therefore, generating consensus on validated endpoints that can be used in DMI for the development of effective interventions is vital. In this review, we discuss potential endpoints appropriate for use in clinical trials of DMI, and consider the data required to establish acceptable and meaningful endpoints. A combination of anatomical, functional, and patient-reported outcome measures will provide the most complete picture of changes that occur during the progression of DMI. Potential endpoint measures include change in size of the foveal avascular zone measured by optical coherence tomography angiography and change over time in best-corrected visual acuity. However, these endpoints must be supported by further research. We also recommend studies to investigate the natural history and progression of DMI. In addition to improving understanding of how patient demographics and comorbidities such as diabetic macular edema affect clinical trial endpoints, these studies would help to build the consensus definition of DMI that is currently missing from clinical practice and research. [ABSTRACT FROM AUTHOR]