Computational approach for identifying immunogenic epitopes and optimizing peptide vaccine through in-silico cloning against Mycoplasma genitalium.

Mycoplasma genitalium is a pathogenic microorganism linked to a variety of severe health conditions including ovarian cancer, prostate cancer, HIV transmission, and sexually transmitted diseases. A more effective approach to address the challenges posed by this pathogen, given its high antibiotic resistance rates, could be the development of a peptide vaccine. In this study, we used experimentally validated 13 membrane proteins and their immunogenicity to identify suitable vaccine candidates. Thus, based on immunogenic properties and high conservation among other Mycoplasma genitalium sub-strains, the P110 surface protein is considered for further investigation. Later on, we identified T-cell epitopes and B-cell epitopes from the P110 protein to construct a multiepitope-based vaccine. As a result, the 'NIAPISFSFTPFTAA' T-cell epitope and 'KVKYESSGSNNISFDS' B-cell epitope have shown 99.53% and 87.50% population coverage along with 100% conservancy among the subspecies, and both epitopes were found to be non-allergenic. Furthermore, focusing on molecular docking analysis showed the lowest binding energy for MHC-I (-137.5 kcal/mol) and MHC-II (-183.3 kcal/mol), leading to a satisfactory binding strength between the T-cell epitopes and the MHC molecules. However, the constructed multiepitope vaccine (MEV) consisting of 54 amino acids demonstrates favorable characteristics for a vaccine candidate, including a theoretical pI of 4.25 with a scaled solubility of 0.812 and high antigenicity probabilities. Additionally, structural analyses reveal that the MEV displays substantial alpha helices and extended strands, vital for its immunogenicity. Molecular docking with the human Toll-like receptors TLR1/2 heterodimer shows strong binding affinity, reinforcing its potential to elicit an immune response. Our immune simulation analysis demonstrates immune memory development and robust immunity, while codon adaptation suggests optimal expression in E. coli using the pET-28a(+) vector. These findings collectively highlight the MEV's potential as a valuable vaccine candidate against M. genitalium.

Radiometal chelators for infection diagnostics.

Infection of native tissues or implanted devices is common, but clinical diagnosis is frequently difficult and currently available noninvasive tests perform poorly. Immunocompromised individuals (for example transplant recipients, or those with cancer) are at increased risk. No imaging test in clinical use can specifically identify infection, or accurately differentiate bacterial from fungal infections. Commonly used [18F]fluorodeoxyglucose (18FDG) positron emission computed tomography (PET/CT) is sensitive for infection, but limited by poor specificity because increased glucose uptake may also indicate inflammation or malignancy. Furthermore, this tracer provides no indication of the type of infective agent (bacterial, fungal, or parasitic). Imaging tools that directly and specifically target microbial pathogens are highly desirable to improve noninvasive infection diagnosis and localization. A growing field of research is exploring the utility of radiometals and their chelators (siderophores), which are small molecules that bind radiometals and form a stable complex allowing sequestration by microbes. This radiometal-chelator complex can be directed to a specific microbial target in vivo, facilitating anatomical localization by PET or single photon emission computed tomography. Additionally, bifunctional chelators can further conjugate therapeutic molecules (e.g., peptides, antibiotics, antibodies) while still bound to desired radiometals, combining specific imaging with highly targeted antimicrobial therapy. These novel therapeutics may prove a useful complement to the armamentarium in the global fight against antimicrobial resistance. This review will highlight current state of infection imaging diagnostics and their limitations, strategies to develop infection-specific diagnostics, recent advances in radiometal-based chelators for microbial infection imaging, challenges, and future directions to improve targeted diagnostics and/or therapeutics.

Insomnia and job stressors among healthcare workers who served COVID-19 patients in Bangladesh.

BACKGROUND: The global outbreak of COVID-19 has created unprecedented havoc among health care workers, resulting in significant psychological strains like insomnia. This study aimed to analyze insomnia prevalence and job stressors among Bangladeshi health care workers in COVID-19 units. METHODOLOGY: We conducted this cross-sectional study to assess insomnia severity from January to March 2021 among 454 health care workers working in multiple hospitals in Dhaka city with active COVID-dedicated units. We selected 25 hospitals conveniently. We used a structured questionnaire for face-to-face interviews containing sociodemographic variables and job stressors. The severity of insomnia was measured by the Insomnia Severity Scale (ISS). The scale has seven items to evaluate the rate of insomnia, which was categorized as the absence of Insomnia (0-7); sub-threshold Insomnia (8-14); moderate clinical Insomnia (15-21); and severe clinical Insomnia (22-28). To identify clinical insomnia, a cut-off value of 15 was decided primarily. A cut-off score of 15 was initially proposed for identifying clinical insomnia. We performed a chi-square test and adjusted logistic regression to explore the association of different independent variables with clinically significant insomnia using the software SPSS version 25.0. RESULTS: 61.5% of our study participants were females. 44.9% were doctors, 33.9% were nurses, and 21.1% were other health care workers. Insomnia was more dominant among doctors and nurses (16.2% and 13.6%, respectively) than others (4.2%). We found clinically significant insomnia was associated with several job stressors (p < 0.05). In binary logistic regression, having sick leave (OR = 0.248, 95% CI = 0.116, 0.532) and being entitled to risk allowance (OR = 0.367, 95% CI = 0.124.1.081) showed lower odds of developing Insomnia. Previously diagnosed with COVID-19-positive health care workers had an OR of 2.596 (95% CI = 1.248, 5.399), pointing at negative experiences influencing insomnia. In addition, we observed that any training on risk and hazard increased the chances of suffering from Insomnia (OR = 1.923, 95% CI = 0.934, 3.958). CONCLUSION: It is evident from the findings that the volatile existence and ambiguity of COVID-19 have induced significant adverse psychological effects and subsequently directed our HCWs toward disturbed sleep and insomnia. The study recommends the imperativeness to formulate and implement collaborative interventions to help HCWs cope with this crisis and mitigate the mental stresses they experience during the pandemic.

Bacterial profile, antimicrobial resistance, and molecular detection of ESBL and quinolone resistance gene of uropathogens causing urinary tract infection in the southeastern part of Bangladesh.

Humans frequently contract urinary tract infections (UTIs), which can be brought on by uropathogens (UPs) that are multi-drug resistant. Treatment for UTIs brought on by pathogenic UPs that produce extended-spectrum lactamases (ESBLs) is more costly and potentially fatal. As a result, the objective of this study was to use culture, biochemical, and 16S rRNA sequencing to identify and characterize UPs isolated from outpatients in Noakhali, Bangladesh, who had symptoms of UTIs. ESBL gene identification and quinolone resistance gene typing were then performed on the isolates using polymerase chain reaction (PCR). Throughout the trial's 8-month duration, 152 (76%) of 200 urine samples were positive for the presence of UPs. The overall number of UPs recovered was 210, with 39 individuals having multiple UPs present in their samples. Among all of the isolates, Escherichia coli (45.24%, 95/210; 95% confidence interval (CI): 35.15-57.60%), Enterobacter spp. (24.76%, 52/210; CI: 19.15-35.77%), Klebsiella spp. (20.95%; 44/210; CI: 15.15-30.20%), and Providencia spp. (9.05%; 19/210; CI: 4.95-19.25%) were the four most prevalent bacteria found in the isolates. The UPs displayed a very high level of resistance to piperacillin 96.92% (126/130), ampicillin 90% (117/130), nalidixic acid 77.69% (101/130), cefazolin 70% (91/130), amoxicillin 50% (55/130), cefazolin 42.31% (55/130), nitrofurantoin 43.08% (56/130), and ciprofloxacin 33.08% (43/130), whereas resistance to netilmicin (3.85%), amikacin (4.62%), and imipenem (9.23%) was low. Individually, every species of E. coli and Providencia spp. showed greater ampicillin, amikacin, cefazolin, cefazolin, and nalidixic acid resistance than the others. The bivariate results indicate several antibiotic pairings, and isolates had meaningful associations. All MDR isolates were subjected to PCR, which revealed that blaCTX-M-15 genes predominated among the isolates, followed by the blaTEM class (37%). Isolates also had the qnrS, aac-6´-Ib-cr, and gyrA genes. The findings provide worrying indications of a major expansion of MDR isolates in the study locations, particularly the epidemiological balCTX-M 15, with the potential for the transmission of multi-drug-resistant UP strains in the population.

Water stress and nitrogen supply affect floral traits and pollination of the white mustard, Sinapis alba (Brassicaceae).

Changes in environmental conditions are likely to have a complex effect on the growth of plants, their phenology, plant-pollinator interactions, and reproductive success. The current world is facing an ongoing climate change along with other human-induced environmental changes. Most research has focused on the impact of increasing temperature as a major driving force for climate change, but other factors may have important impacts on plant traits and pollination too and these effects may vary from season to season. In addition, it is likely that the effects of multiple environmental factors, such as increasing temperature, water availability, and nitrogen enrichment are not independent. Therefore, we tested the impact of two key factors-water, and nitrogen supply-on plant traits, pollination, and seed production in Sinapis alba (Brassicaceae) in three seasons defined as three temperature conditions with two levels of water and nitrogen supply in a factorial design. We collected data on multiple vegetative and floral traits and assessed the response of pollinators in the field. Additionally, we evaluated the effect of growing conditions on seed set in plants exposed to pollinators and in hand-pollinated plants. Our results show that water stress impaired vegetative growth, decreased flower production, and reduced visitation by pollinators and seed set, while high amount of nitrogen increased nectar production under low water availability in plants grown in the spring. Temperature modulated the effect of water and nitrogen availability on vegetative and floral traits and strongly affected flowering phenology and flower production. We demonstrated that changes in water and nitrogen availability alter plant vegetative and floral traits, which impacts flower visitation and consequently plant reproduction. We conclude that ongoing environmental changes such as increasing temperature, altered precipitation regimes and nitrogen enrichment may thus affect plant-pollinator interactions with negative consequences for the reproduction of wild plants and insect-pollinated crops.

Assessment of contamination level, pollution risk and source apportionment of heavy metals in the Halda River water, Bangladesh.

This study demonstrates the level of heavy metal pollution in the Halda River, the only natural breeding source of carps in Bangladesh. Water was collected from 12 different sampling points along the Halda River. Water at various locations was found satisfactory in terms of the assessed physicochemical parameters (pH, electrical conductivity, and total dissolved solids). The presence of various cations and anions was also studied using ion chromatography. Atomic absorption spectroscopy was used to identify and quantify various heavy metals in the collected water samples. Among the heavy metals, Cd, Cr, Fe, Pb, Cu, and As concentration exceeded the safe limit suggested by WHO. The calculated heavy metal pollution index and metal index were found higher than the critical index value. The single-factor assessment (P i ) and Nemerow's multi-factor index (P N ) of heavy metals was calculated to find out the degree of pollution in the Halda River. The maximum values of P i (Cd), P i (Pb), P i (As), P i (Cu), and P i (Cr) were determined to be 26.67, 260.00, 17.00, 208.76 and 2.80 respectively. The maximum value of P N was found to be 289.04. The discharge of effluents from various large and small industries near the Halda River is considered to be the major source of the identified heavy metals. Multivariate statistical analysis such as principal component analysis, Pearson correlation matrix and cluster analysis revealed that most of the heavy metals originated from different anthropogenic sources. Multivariate analysis also showed that Co, Mn, Cu, Cr, Pb, Cd, NH4 +, NO3 - mainly came from artificial sources whereas Fe, Ca, As mainly originated from natural sources. Arsenic (As) also came from artificial sources with Cu.

Correction: Foraging strategies are maintained despite workforce reduction: A multidisciplinary survey on the pollen collected by a social pollinator.

[This corrects the article DOI: 10.1371/journal.pone.0224037.].

Foraging strategies are maintained despite workforce reduction: A multidisciplinary survey on the pollen collected by a social pollinator.

The way pollinators gather resources may play a key role for buffering their population declines. Social pollinators like bumblebees could adjust their foraging after significant workforce reductions to keep provisions to the colony optimal, especially in terms of pollen diversity and quantity. To test what effects a workforce reduction causes on the foraging for pollen, commercially-acquired colonies of the bumblebee Bombus terrestris were allowed to forage in the field and they were experimentally manipulated by removing half the number of workers. For each bumblebee, the pollen pellets were taxonomically identified with DNA metabarcoding of the ITS2 region followed by a statistical filtering based on ROC curves to filter out underrepresented OTUs. Video cameras and network analyses were employed to investigate changes in foraging strategies and behaviour. After filtering out the false-positives, HTS metabarcoding yielded a high plant diversity in the pollen pellets; for plant identity and pollen quantity traits no differences emerged between samples from treated and from control colonies, suggesting that plant choice was influenced mainly by external factors such as the plant phenology. The colonies responded to the removal of 50% of their workers by increasing the foraging activity of the remaining workers, while only negligible changes were found in diet breadth and indices describing the structure of the pollen transport network. Therefore, a consistency in the bumblebees' feeding strategies emerges in the short term despite the lowered workforce.

Prophages and satellite prophages are widespread in Streptococcus and may play a role in pneumococcal pathogenesis.

Prophages (viral genomes integrated within a host bacterial genome) can confer various phenotypic traits to their hosts, such as enhanced pathogenicity. Here we analyse >1300 genomes of 70 different Streptococcus species and identify nearly 800 prophages and satellite prophages (prophages that do not encode their own structural components but rely on the bacterial host and another helper prophage for survival). We show that prophages and satellite prophages are widely distributed among streptococci in a structured manner, and constitute two distinct entities with little effective genetic exchange between them. Cross-species transmission of prophages is not uncommon. Furthermore, a satellite prophage is associated with virulence in a mouse model of Streptococcus pneumoniae infection. Our findings highlight the potential importance of prophages in streptococcal biology and pathogenesis.

Experimental loss of generalist plants reveals alterations in plant-pollinator interactions and a constrained flexibility of foraging.

Species extinctions undermine ecosystem functioning, with the loss of a small subset of functionally important species having a disproportionate impact. However, little is known about the effects of species loss on plant-pollinator interactions. We addressed this issue in a field experiment by removing the plant species with the highest visitation frequency, then measuring the impact of plant removal on flower visitation, pollinator effectiveness and insect foraging in several sites. Our results show that total visitation decreased exponentially after removing 1-4 most visited plants, suggesting that these plants could benefit co-occurring ones by maintaining high flower visitor abundances. Although we found large variation among plant species, the redistribution of the pollinator guild affected mostly the other plants with high visitor richness. Also, the plant traits mediated the effect of removal on flower visitation; while visitation of plants which had smaller inflorescences and more sugar per flower increased after removal, flower visitors did not switch between flower shapes and visitation decreased mostly in plants visited by many morpho-species of flower visitors. Together, these results suggest that the potential adaptive foraging was constrained by flower traits. Moreover, pollinator effectiveness fluctuated but was not directly linked to changes of flower visitation. In conclusion, it seems that the loss of generalist plants alters plant-pollinator interactions by decreasing pollinator abundance with implications for pollination and insect foraging. Therefore, generalist plants have high conservation value because they sustain the complex pattern of plant-pollinator interactions.

Flower visitation by hoverflies (Diptera: Syrphidae) in a temperate plant-pollinator network.

Hoverflies (Diptera: Syrphidae) are among the most important pollinators, although they attract less attention than bees. They are usually thought to be rather opportunistic flower visitors, although previous studied demonstrated that they show colour preferences and their nectar feeding is affected by morphological constraints related to flower morphology. Despite the growing appreciation of hoverflies and other non-bee insects as pollinators, there is a lack of community-wide studies of flower visitation by syrphids. The aim of this paper is to provide a detailed analysis of flower visitation patterns in a species rich community of syrphids in a Central European grassland and to evaluate how species traits shape the structure of the plant-hoverfly flower visitation network. We found that different species varied in the level of specialisation, and while some species visited a similar spectre of flowers, others partitioned resources more strongly. There was a consistent difference in both specialisation and flower preferences between three syrphid subfamilies. Eristalinae and Pipizinae were more specialised than Syrphinae. Trait-based analyses showed that relative flower visitation (i) increased with plant height, but most strongly in Eristalinae; (ii) increased with inflorescence size in small species from all three subfamilies, but was independent of inflorescence size in large species of Eristalinae and Syrphinae; and (iii) depended on flower colour, but in a subfamily-specific way. Eristalinae showed the strongest flower colour preferences for white flowers, Pipizinae visited mostly white and yellow flowers, while Syrphinae were less affected by flower colour. Exploration of the structure of the plant-hoverfly flower visitation network showed that the network was both modular and nested. We also found that there were almost no differences in specialisation and relative visitation frequency between males and females. Overall, we showed that flower visitation in syrphids was affected by phylogenetic relatedness, body size of syrphids and several plant traits.

Effects of small-scale clustering of flowers on pollinator foraging behaviour and flower visitation rate.

Plants often grow in clusters of various sizes and have a variable number of flowers per inflorescence. This small-scale spatial clustering affects insect foraging strategies and plant reproductive success. In our study, we aimed to determine how visitation rate and foraging behaviour of pollinators depend on the number of flowers per plant and on the size of clusters of multiple plants using Dracocephalum moldavica (Lamiaceae) as a target species. We measured flower visitation rate by observations of insects visiting single plants and clusters of plants with different numbers of flowers. Detailed data on foraging behaviour within clusters of different sizes were gathered for honeybees, Apis mellifera, the most abundant visitor of Dracocephalum in the experiments. We found that the total number of flower visitors increased with the increasing number of flowers on individual plants and in larger clusters, but less then proportionally. Although individual honeybees visited more flowers in larger clusters, they visited a smaller proportion of flowers, as has been previously observed. Consequently, visitation rate per flower and unit time peaked in clusters with an intermediate number of flowers. These patterns do not conform to expectations based on optimal foraging theory and the ideal free distribution model. We attribute this discrepancy to incomplete information about the distribution of resources. Detailed observations and video recordings of individual honeybees also showed that the number of flowers had no effect on handling time of flowers by honeybees. We evaluated the implications of these patterns for insect foraging biology and plant reproduction.

Novel toxicity of Bacillus thuringiensis strains against the melon fruit fly, Bactrocera cucurbitae (Diptera: Tephritidae).

Bactrocera cucurbitae (melon fruit fly) is one of the most detrimental vegetable-damaging pests in Bangladesh. The toxicity of Bacillus thuringiensis (Bt) has been reported against a few genera of Bactrocera in addition to numerous other insect species. Bt strains, harbouring cry1A-type genes were, therefore, assayed in vivo against the 3(rd) instar larvae of B. cucurbitae in this study. The biotype-based prevalence of cry1 and cry1A genes was calculated to be 30.8% and 11.16%, respectively, of the test strains (n=224) while their prevalence was greatest in biotype kurstaki. Though three indigenous Bt strains from biotype kurstaki with close genetic relationship exhibited higher toxicity, maximum mortalities were recorded for Btk HD-73 (96%) and the indigenous Bt JSc1 (93%). LC50 and LC99 values were determined to be 6.81 and 8.32 for Bt JSc1, 7.30 and 7.92 for Bt SSc2, and 6.99 and 7.67 for Btk HD-73, respectively. The cause of toxicity and its variation among the strains was found to be correlated with the synergistic toxic effects of cry1, cry2, cry3 and cry9 gene products, i.e. relevant Cry proteins. The novel toxicity of the B. thuringiensis strains against B. cucurbitae revealed in the present study thus will help in developing efficient and eco-friendly control measures such as Bt biopesticides and transgenic Bt cucurbits.