Genome-Wide Mining of Selaginella moellendorffii for Hevein-like Lectins and Their Potential Molecular Mimicry with SARS-CoV-2 Spike Glycoprotein.

Multidisciplinary research efforts on potential COVID-19 vaccine and therapeutic candidates have increased since the pandemic outbreak of SARS-CoV-2 in 2019. This search has become imperative due to the increasing emergences and limited widely available medicines. The presence of bioactive anti-SARS-CoV-2 molecules was examined from various plant sources. Among them is a group of proteins called lectins that can bind carbohydrate moieties. In this article, we present ten novel, chitin-specific Hevein-like lectins that were derived from Selaginella moellendorffii v1.0's genome. The capacity of these lectin homologs to bind with the spike protein of SARS-CoV-2 was examined. Using the HDOCK server, 3D-modeled Hevein-domains were docked to the spike protein's receptor binding domain (RBD). The Smo446851, Smo125663, and Smo99732 interacted with Asn343-located complex N-glycan and RBD residues, respectively, with binding free energies of -17.5, -13.0, and -26.5 Kcal/mol. The molecular dynamics simulation using Desmond and the normal-state analyses via torsional coordinate association for the Smo99732-RBD complex using iMODS is characterized by overall higher stability and minimum deformity than the other lectin complexes. The three lectins interacting with carbohydrates were docked against five individual mutations that frequently occur in major SARS-CoV-2 variants. These were in the spike protein's receptor-binding motif (RBM), while Smo125663 and Smo99732 only interacted with the spike glycoprotein in a protein-protein manner. The precursors for the Hevein-like homologs underwent additional characterization, and their expressional profile in different tissues was studied. These in silico findings offered potential lectin candidates targeting key N-glycan sites crucial to the virus's virulence and infection.

Choice of specimen's extraction site affects wound morbidity in laparoscopic colorectal cancer surgery.

BACKGROUND: The choice for an ideal site of specimen extraction following laparoscopic colorectal surgery remains debatable. However, midline incision (MI) is usually employed for right and left-sided colonic resections while left iliac fossa or suprapubic transverse incision (STI) were reserved for sigmoid and rectal cancer resections. OBJECTIVE: To compare the incidence of surgical site infection (SSI) and incisional hernia (IH) in elective laparoscopic colorectal surgery for cancer and specimen extraction via MI or STI. METHOD: Prospectively collected data of elective laparoscopic colorectal cancer resections between January 2017 and December 2019 were retrospectively reviewed. MI was employed for right and left-sided colonic resections while STI was used for sigmoid and rectal resections. SSI is defined according to the US CDC criteria. IH was diagnosed clinically and confirmed by CT scan at 1 year. RESULTS: A total of 168 patients underwent elective laparoscopic colorectal resections. MI was used in 90 patients while 78 patients had STI as an extraction site. Demographic and preoperative data is similar for two groups. The rate of IH was 13.3% for MI and 0% in the STI (p = 0.001). SSI was seen in 16.7% of MI vs 11.5% of STI (p = 0.34). Univariate and multivariate analysis showed that the choice of extraction site is associated with statistically significant higher incisional hernia rate. CONCLUSION: MI for specimen extraction is associated with higher incidence of both SSI and IH. The choice of incision for extraction site is an independent predicative factor for significantly higher IH and increased SSI rates.

Comparative analysis of transposable elements provides insights into genome evolution in the genus Camelus.

BACKGROUND: Transposable elements (TEs) are common features in eukaryotic genomes that are known to affect genome evolution critically and to play roles in gene regulation. Vertebrate genomes are dominated by TEs, which can reach copy numbers in the hundreds of thousands. To date, details regarding the presence and characteristics of TEs in camelid genomes have not been made available. RESULTS: We conducted a genome-wide comparative analysis of camelid TEs, focusing on the identification of TEs and elucidation of transposition histories in four species: Camelus dromedarius, C. bactrianus, C. ferus, and Vicugna pacos. Our TE library was created using both de novo structure-based and homology-based searching strategies ( https://github.com/kacst-bioinfo-lab/TE_ideintification_pipeline ). Annotation results indicated a similar proportion of each genomes comprising TEs (35-36%). Class I LTR retrotransposons comprised 16-20% of genomes, and mostly consisted of the endogenous retroviruses (ERVs) groups ERVL, ERVL-MaLR, ERV_classI, and ERV_classII. Non-LTR elements comprised about 12% of genomes and consisted of SINEs (MIRs) and the LINE superfamilies LINE1, LINE2, L3/CR1, and RTE clades. Least represented were the Class II DNA transposons (2%), consisting of hAT-Charlie, TcMar-Tigger, and Helitron elements and comprising about 1-2% of each genome. CONCLUSIONS: The findings of the present study revealed that the distribution of transposable elements across camelid genomes is approximately similar. This investigation presents a characterization of TE content in four camelid to contribute to developing a better understanding of camelid genome architecture and evolution.

Barriers of access and utilization of reproductive health services by adolescents-Khartoum state-Sudan-2020: study protocol.

BACKGROUND: Adolescence is widely defined as the time in life when the developing individual attains the skills and attributes necessary to become a productive and reproductive adult. Most adolescents are healthy, but there is still substantial premature death, illness, and injury among adolescents. Illnesses can hinder their ability to grow and develop to their full potential. Alcohol or tobacco use, lack of physical activity, unprotected sex and/or exposure to violence can jeopardize not only their current health, but also their health as adults or even health of their future children. METHOD: Community and institutional-based cross sectional study will be conducted in Khartoum State the seven localities will be included. This state is the national capital of Sudan, which has an area of 22,122 km2. The sample size of participant is estimated using the population formula (n = N/1+ (n*d2)). The sample will be drawn using multistage cluster sampling. Also the concerned bodies involved in the delivery of reproductive health services for adolescents included in this study. Data will be collected using interviews with key informants and administered pre-coded, pretested closed ended questionnaire with community participants. Data will be managed and analyzed using Statistical Package for Social Sciences version 21. Analysis is mostly univariate descriptive and bi-variate with Chi Square & Fischer Exact test analysis to find associations between variables of interest. DISCUSSION: The census of adolescents mounted to 25% of the population and thus it is important to care for such significant portion of the population to document their reproductive health problems and their access to health care services. The study is expected to generate base-line indicators about barriers of access to reproductive health services by adolescents that can be used for better planning, monitoring and evaluation of the delivered services. The research about barriers of access to reproductive health services by adolescents in Sudan is still limited and the information is scanty and scattered. Thus, it is necessary to conduct such study to enrich the current database.

Molecular detection of exosomal miRNAs of blood serum for prognosis of colorectal cancer.

Colorectal cancer (CRC) is the third most common cancer affecting people. The discovery of new, non-invasive, specific, and sensitive molecular biomarkers for CRC may assist in the diagnosis and support therapeutic decision making. Exosomal miRNAs have been demonstrated in carcinogenesis and CRC development, which makes these miRNAs strong biomarkers for CRC. Deep sequencing allows a robust high-throughput informatics investigation of the types and abundance of exosomal miRNAs. Thus, exosomal miRNAs can be efficiently examined as diagnostic biomarkers for disease screening. In the present study, a number of 660 mature miRNAs were detected in patients diagnosed with CRC at different stages. Of which, 29 miRNAs were differentially expressed in CRC patients compared with healthy controls. Twenty-nine miRNAs with high abundance levels were further selected for subsequent analysis. These miRNAs were either highly up-regulated (e.g., let-7a-5p, let-7c-5p, let-7f-5p, let-7d-3p, miR-423-5p, miR-3184-5p, and miR-584) or down-regulated (e.g., miR-30a-5p, miR-99-5p, miR-150-5p, miR-26-5p and miR-204-5p). These miRNAs influence critical genes in CRC, leading to either tumor growth or suppression. Most of the reported diagnostic exosomal miRNAs were shown to be circulating in blood serum. The latter is a novel miRNA that was found in exosomal profile of blood serum. Some of the predicted target genes of highly expressed miRNAs participate in several cancer pathways, including CRC pathway. These target genes include tumor suppressor genes, oncogenes and DNA repair genes. Main focus was given to multiple critical signaling cross-talking pathways including transforming growth factor ß (TGFß) signaling pathways that are directly linked to CRC. In conclusion, we recommend further analysis in order to experimentally confirm exact relationships between selected differentially expressed miRNAs and their predicted target genes and downstream functional consequences.

Moderately Low Effectiveness of the Influenza Quadrivalent Vaccine: Potential Mismatch between Circulating Strains and Vaccine Strains.

The annual seasonal influenza vaccination is the most effective way of preventing influenza illness and hospitalization. However, the effectiveness of influenza vaccines has always been controversial. Therefore, we investigated the ability of the quadrivalent influenza vaccine to induce effective protection. Here we report strain-specific influenza vaccine effectiveness (VE) against laboratory-confirmed influenza cases during the 2019/2020 season, characterized by the co-circulation of four different influenza strains. During 2019-2020, 778 influenza-like illness (ILI) samples were collected from 302 (39%) vaccinated ILI patients and 476 (61%) unvaccinated ILI patients in Riyadh, Saudi Arabia. VE was found to be 28% and 22% for influenza A and B, respectively. VE for preventing A(H3N2) and A(H1N1)pdm09 illness was 37.4% (95% CI: 43.7-54.3) and 39.2% (95% CI: 21.1-28.9), respectively. The VE for preventing influenza B Victoria lineage illness was 71.7% (95% CI: -0.9-3), while the VE for the Yamagata lineage could not be estimated due to the limited number of positive cases. The overall vaccine effectiveness was moderately low at 39.7%. Phylogenetic analysis revealed that most of the Flu A genotypes in our dataset clustered together, indicating their close genetic relatedness. In the post-COVID-19 pandemic, flu B-positive cases have reached three-quarters of the total number of influenza-positive cases, indicating a nationwide flu B surge. The reasons for this phenomenon, if related to the quadrivalent flu VE, need to be explored. Annual monitoring and genetic characterization of circulating influenza viruses are important to support Influenza surveillance systems and to improve influenza vaccine effectiveness.

Offspring sex ratios among male tobacco smokers in Khartoum, Sudan.

OBJECTIVES: To explore any association between paternal tobacco smoking and the offspring secondary sex ratio, as well as the effect of duration and intensity of smoking on gender ratio. METHODS: The cross-sectional study was conducted around major public areas within Khartoum, Sudan, between August and September 2008 and involved 458 married Sudanese males with offsprings. The sample consisted of 111 (24.2%) smokers and 347 (75.8%) non-smokers who were evaluated using a questionnaire on their offspring gender. Data on duration and intensity of smoking was also collected from the smokers' group. SPSS 16 was used for statistical purposes. Chi-square test was used to test for significance of associations between variables. Analysis of variance (ANOVA) was used to test for significance between ratios. RESULTS: The number of cigarettes smoked in males increases the likelihood of having a male offspring. The gender ratio in non-smokers was 1.11, while it was 1.15 in smokers. CONCLUSION: Paternal smoking increases the offspring sex ratio.

Outcomes of a Short Course in Improving Eye Healthcare Knowledge and Skills Among Final-Year Medical Students.

Background: Globally, at least, more than 2 billion people are either blind or visually impaired, the majority of whom live in low-income settings. Visually impaired people experience limitations in their daily activities in addition to the negative psychological impact. Ophthalmology is not a major focus in medical curricula, including in Sudan. The purpose of this study was to evaluate the effects of a short course in improving eye healthcare knowledge and skills among final-year medical students in a public university in Khartoum State, Sudan. Methods: A mixed-methods interventional study was conducted among 25 final-year medical students in Sudan. A short ophthalmology course was designed and conducted aiming to strengthen the knowledge and ability of the medical students to deal with common eye disorders, eye emergencies, prevention of blindness, and promotion for eye health. Data were collected using a closed-ended questionnaire at the start and 1 month after completion of the course. The quantitative data were analyzed using Excel, and the Fisher exact test was performed using Statistical Package for the Social Sciences (version 21.0) to examine any association between variables of interest. A p value of less than 0.05 was considered statistically significant. The quantitative data was supplemented by one focus group discussion that was conducted at the end of the course. Results: The average ophthalmology knowledge of participants improved from 52.6 to 86.6% (p < 0.001). Diagnostic skills improved from 57.3 to 93.6% (p < 0.001), and knowledge regarding the needed interventional actions improved from 58.6% to 94% (p < 0.001). Participants both enjoyed and learnt from this short course. Participants felt more confident and able to distinguish between simple, complicated, and urgent conditions. The majority of course content was new to them, but they suggested replacing some content with actual clinical work. Conclusion: A well-designed short ophthalmology course significantly improves the levels of medical students' knowledge and skills towards eye health. Implementing such a course as a standard component in the national medical curriculum has the potential to contribute towards the reduction of blindness in the long term.

Risk factors of ocular morbidity among under-five years old children in Khartoum State- Sudan- 2020.

BACKGROUND AND AIMS: Visual impairment in early childhood can significantly affect the development of visual, motor, and cognitive function and potentially lead to long-term adverse psychosocial consequences. This study aimed to identify the risk factors of ocular morbidity among under 5-year old children in Khartoum State, Sudan. METHODS: A cross-sectional study was conducted in three tertiary eye care hospitals in Khartoum State, Sudan. The study included 391 children under the age of 5 years. The parent(s) were interviewed using a precoded, pretested, closed-ended questionnaire that included questions regarding socio-demographic profile and possible risk factors. Data were analyzed using Statistical Package for the Social Sciences (version 21.0). A P-value of less than .05 was regarded as significant. RESULTS: There was a significant association between participants with diabetes mellitus and poor vision (P-value <.001). Two-thirds of participants (57%) with visual impairment had mothers, who reportedly attended antenatal care services regularly (P-value .001), revealing a significant statistical association. Maternal diseases, specifically diabetes, was identified as a risk factor for poor visual acuity in their offspring (P-value <.001). A significant relation was revealed between family history of eye disease and the degree of relationship to the affected participant (P-value <.001). There was an association between watching TV and current visual acuity (P-value <.001); as well as using mobile phones and current visual acuity (P-value <.001). Multilinear analysis revealed the stronger influence of TV watching rather than the use of mobile phones (P-value <.001). CONCLUSIONS: Diabetes, diabetic mothers, a family history of ocular morbidity, watching television, and using mobile phones emerged as significant risk factors of ocular morbidity among children under the age of 5 years in this study. Many of these risk factors are either modifiable or controllable ocular morbidities among under-five children can be reduced with suitable interventions.

Genome-wide comparative analysis of transposable elements in Palmae genomes.

Background: Transposable elements (TEs) are the largest component of the genetic material of most eukaryotes and can play roles in shaping genome architecture and regulating phenotypic variation; thus, understanding genome evolution is only possible if we comprehend the contributions of TEs. However, the quantitative and qualitative contributions of TEs can vary, even between closely related lineages. For palm species, in particular, the dynamics of the process through which TEs have differently shaped their genomes remains poorly understood because of a lack of comparative studies. Materials and methods: We conducted a genome-wide comparative analysis of palm TEs, focusing on identifying and classifying TEs using the draft assemblies of four palm species: Phoenix dactylifera, Cocos nucifera, Calamus simplicifolius, and Elaeis oleifera. Our TE library was generated using both de novo structure-based and homology-based methodologies. Results: The generated libraries revealed the TE component of each assembly, which varied from 41-81%. Class I retrotransposons covered 36-75% of these species' draft genome sequences and primarily consisted of LTR retroelements, while non-LTR elements covered about 0.56-2.31% of each assembly, mainly as LINEs. The least represented were Class DNA transposons, comprising 1.87-3.37%. Conclusion: The current study contributes to a detailed identification and characterization of transposable elements in Palmae draft genome assemblies.

Non-classical presentation of vitamin D deficiency: a case report.

BACKGROUND: Vitamin D is a fat-soluble vitamin; vitamin D is essential to sustain health and it protects against osteoporosis. It is crucial to the human body's physiology in terms of muscular movement and neurological signal transmission, and to the immune system in defense against invading pathogens. CASE PRESENTATION: This was a case of a 26-year-old Sudanese woman who presented with a 2-year history of anosmia, recurrent nasal polyps, back pain, and chronic fatigue. She was diagnosed as having a case of vitamin D deficiency and responded well to treatment. CONCLUSION: There is an association between vitamin D deficiency and recurrent allergic nasal conditions.

Post COVID 19 acute acalculous cholecystitis raising the possibility of underlying dysregulated immune response, a case report.

INTRODUCTION: Novel Coronavirus disease 2019 or COVID-19 has rapidly spread throughout the world and has become an unprecedented pandemic. It has a vast spectrum of clinical presentations and can affect various organs. Rarely, it has been reported to cause acalculous cholecystitis in a non ICU setting patient. CASE PRESENTATION: Here we report a rare association of COVID 19 with acalculous cholecystitis in a 40 years old healthy woman. She developed fever, malaise, generalized body weakness, and right hypochondrial pain after fourteen days of COVID 19 infection, raising the possibility of Post COVID dysregulated immune response resulting in acalculous cholecystitis. She was managed conservatively with broad spectrum antibiotics. DISCUSSION: Acalculous cholecystitis primarily occurs due to the gall bladder's hypomotility and most commonly seen in critically ill patients such as severe burns, mechanically ventilated patients, and prolonged parenteral nutrition. The management depends upon treating the underlying pathology and, in some severe cases, may need surgical intervention as well. Up to our knowledge, COVID 19, causing acalculous cholecystitis, is a rare association described only in a few critically ill patients but not in young, healthy patients. It can be attributed to the body's dysregulated immunological response against the virus resulting in systemic inflammation. CONCLUSION: Currently, there is are no clear guidelines for managing acute cholecystitis in COVID-19 patients. It depends on the patient's clinical state and disease severity. We aim to highlight the importance of early diagnosis and management in such clinical scenarios to avoid fatal complications.