Microplastics pollution in the Surma River, Bangladesh: A rising hazard to upstream water quality and aquatic life.

The ecological health of freshwater rivers is deteriorating globally due to careless human activities, for instance, the emission of plastic garbage into the river. The current research was the first assessment of microplastics (MPs) pollution in water, sediment, and representative organisms (fish, crustacean, and bivalve) from the Surma River. Water, sediment, and organisms were sampled from six river sites (Site 1: Charkhai; Site 2: Golapganj; Site 3: Alampur; Site 4: Kazir Bazar; Site 5: Kanishail and Site 6: Lamakazi), and major water quality parameters were recorded during sampling. Thereafter, MPs in water, sediment, and organism samples were extracted, and then microscopically examined to categorize selected MPs types. The abundance of MPs, as well as size, and color distribution, were estimated. Polymer types were analyzed by ATR-FTIR, the color loss of MPs was recorded, the Pollution Load Index (PLI) was calculated, and the relationship between MPs and water quality parameters was analyzed. Sites 4 and 5 had comparatively poorer water quality than other sites. Microplastic fibers, fragments, and microbeads were consistently observed in water, sediment, and organisms. A substantial range of MPs in water, sediment, and organisms (37.33-686.67 items/L, 0.89-15.12 items/g, and 0.66-48.93 items/g, respectively) was recorded. There was a diverse color range, and MPs of <200 µm were prevalent in sampling areas. Six polymer types were identified by ATR-FTIR, namely Polyethylene (PE), Polyamide (PA), Polypropylene (PP), Cellulose acetate (CA), Polyethylene terephthalate (PET), and Polystyrene (PS), where PE (41%) was recognized as highly abundant. The highest PLI was documented in Site 4 followed by Site 5 both in water and sediment. Likewise, Sites 4 and 5 were substantially different from other study areas according to PCA. Overall, the pervasiveness of MPs was evident in the Surma River, which requires further attention and prompt actions.

Subtractive genomics study for the identification of therapeutic targets against Cronobacter sakazakii: A threat to infants.

Cronobacter sakazakii is an opportunistic pathogen that has been associated with severe infection in neonates such as necrotizing enterocolitis (NEC), neonatal meningitis, and bacteremia. This pathogen can survive in a relatively dry environment, especially in powdered infant formula (PIF). Unfortunately, conventional drugs that were once effective against C. sakazakii are gradually losing their efficacy due to rising antibiotic resistance. In this study, a subtractive genomic approach was followed in order to identify potential therapeutic targets in the pathogen. The whole proteome of the pathogen was filtered through a step-by-step process, which involved removing paralogous proteins, human homologs, sequences that are less essential for survival, proteins with shared metabolic pathways, and proteins that are located in cells other than the cytoplasmic membrane. As a result, nine novel drug targets were identified. Further, the analysis also unveiled that the FDA-approved drug Terbinafine can be repurposed against the Glutathione/l-cysteine transport system ATP-binding/permease protein CydC of C. sakazakii. Moreover, molecular docking and dynamics studies of Terbinafine and CydC suggested that this drug can be used to treat C. sakazakii infection in neonates. However, for clinical purposes further in vitro and in vivo studies are necessary.

Exploring CDKN1A Upregulation Mechanisms: Insights into Cell Cycle Arrest Induced by NC2603 Curcumin Analog in MCF-7 Breast Cancer Cells.

Breast cancer stands out as one of the most prevalent malignancies worldwide, necessitating a nuanced understanding of its molecular underpinnings for effective treatment. Hormone receptors in breast cancer cells substantially influence treatment strategies, dictating therapeutic approaches in clinical settings, serving as a guide for drug development, and aiming to enhance treatment specificity and efficacy. Natural compounds, such as curcumin, offer a diverse array of chemical structures with promising therapeutic potential. Despite curcumin's benefits, challenges like poor solubility and rapid metabolism have spurred the exploration of analogs. Here, we evaluated the efficacy of the curcumin analog NC2603 to induce cell cycle arrest in MCF-7 breast cancer cells and explored its molecular mechanisms. Our findings reveal potent inhibition of cell viability (IC50 = 5.6 µM) and greater specificity than doxorubicin toward MCF-7 vs. non-cancer HaCaT cells. Transcriptome analysis identified 12,055 modulated genes, most notably upregulation of GADD45A and downregulation of ESR1, implicating CDKN1A-mediated regulation of proliferation and cell cycle genes. We hypothesize that the curcumin analog by inducing GADD45A expression and repressing ESR1, triggers the expression of CDKN1A, which in turn downregulates the expression of many important genes of proliferation and the cell cycle. These insights advance our understanding of curcumin analogs' therapeutic potential, highlighting not just their role in treatment, but also the molecular pathways involved in their activity toward breast cancer cells.

Awareness of HPV vaccine and its socio-demographic determinants among the parents of eligible daughters in Bangladesh: A nationwide study.

Background: Vaccination against Human papillomavirus (HPV) is recommended to avoid HPV infections and its associated diseases, including cervical cancer. However, there is no awareness study among Bangladeshi population. Hence, this nationwide study was conducted to explore HPV vaccine awareness and its determinants among parents of eligible adolescent girls. Methods: This study was conducted among the parents of daughters aged 9-15 years from 42 out of 64 randomly selected districts of Bangladesh between June 28 to August 2, 2023. A multistage sampling method was used to enroll 2151 study participants from all eight divisions of Bangladesh. A semi-structured questionnaire was used for face-to-face interviews in this study. The statistical software Stata (Version 17) was used for statistical analyses. Results: The average age of the participants was 38.18 (±5.86) years. Only 22.32 % of the participants were aware of the HPV vaccine. Every additional year of age increased the likelihood of being aware of the HPV vaccine by 3 % (AOR: 1.03; 95%CI: 1.00-1.06). Participants residing in the urban area had 3.56 times higher odds of awareness than rural and semi-urban people. Businessmen and housewives had 60 % (AOR: 0.40; 95 % CI: 0.22-0.69) and 77 % (AOR: 0.23; 95 % CI: 0.16-0.33) lower odds in comparison to job holders. The lower-income group exhibited significantly higher odds of awareness (AOR: 0.25, 95%CI: 0.16-0.39) compared to the middle and the higher-income group. Participants who never went through routine health check-ups had 77 % lower odds of being aware than those who availed of regular routine check-ups (AOR: 0.23; 95%CI: 0.16-0.34). Conclusion: Awareness of the HPV vaccine among the general population of Bangladesh is very low. Age, residence, occupation, monthly income, and routine medical check-ups were associated with HPV vaccine awareness. A nationwide awareness campaign would increase this awareness level among the Bangladeshi population, especially among the parents of daughters.

Self-assembly of Ni(II) with a chiral ligand pair vs. mixture of the chiral ligand pair: structural features and recognition ability of Ni2L4 cages.

The self-assembly of NiCl2 with a chiral bidentate ligand pair, (1R,2S)-(+)- and (1S,2R)-(-)-1-(nicotinamido)-2,3-dihydro-1H-inden-2-yl nicotinate (r,s-L and s,r-L) in a mixture of ethanol and dioxane, gives rise to stable crystals consisting of [2Cl@Ni2Cl2(s,r-L)4(H2O)2]·4C4H8O2·EtOH and [2Cl@Ni2Cl2(r,s-L)4(H2O)2]·4C4H8O2·EtOH chiral cages, respectively, with two encapsulated chloride anions in the cavities. The most interesting feature is that the self-assembly of NiCl2 with the mixture of r,s-L and s,r-L (1 : 1-1 : 4) produces crystals of thermodynamically stable achiral cages, [2Cl·2H2O@Ni2Cl2(s,r-L)2(r,s-L)2(H2O)2]·7C4H8O2, in the molar ratio range. Furthermore, the [2Cl@Ni2Cl2(s,r-L)4(H2O)2]·4C4H8O2·EtOH and [2Cl@Ni2Cl2(r,s-L)4(H2O)2]·4C4H8O2·EtOH chiral crystals can recognize the pairs of L-,D-tryptophan and L-,D-cysteine via cyclic voltammetry (CV) signals, in contrast to the [2Cl·2H2O@Ni2Cl2(s,r-L)2(r,s-L)2(H2O)2]·7C4H8O2 achiral crystal.

Final phase I substudy results of ivosidenib in patients with mutant IDH1 relapsed/refractory myelodysplastic syndrome.

Ivosidenib is a first-in-class mutant isocitrate dehydrogenase 1 (mIDH1) inhibitor and has shown efficacy and tolerability in patients with advanced mIDH1 hematologic malignancies, leading to approval in front-line and relapsed/refractory (R/R) mIDH1 AML populations. We report final data from a phase I single-arm substudy (NCT02074839) of patients with R/R mIDH1 MDS following failure of standard-of-care therapies. Oral ivosidenib was taken once daily on days 1-28 in 28-day cycles. Primary objectives were to determine safety, tolerability, and clinical activity. The primary efficacy endpoint was the complete remission + partial remission (CR+PR) rate. Nineteen patients were enrolled; 18 were included in the efficacy analysis. Treatment-related adverse events occurred in eight (42.1%) patients, including a grade 1 QT interval prolongation in one (5.3%) patient and grade 2 differentiation syndrome in two (10.5%) patients. Rates of CR+PR and objective response (CR +PR+marrow CR) were 38.9% (95% confidence interval [CI]: 17.3, 64.3) and 83.3% (95% CI: 58.6, 96.4), respectively. Kaplan-Meier estimates showed a 68.6% probability of patients in CR achieving a remission duration of >=5 years, and a median OS of 35.7 months. Of note, 71.4% and 75.0% baseline red blood cell (RBC) and platelet transfusion-dependent patients, respectively, became transfusion independent (TI; no transfusion >=56 days); 81.8% and 100% of baseline RBC and platelet TI patients, respectively, remained TI. One (5.3%) patient proceeded to a hematopoietic stem cell transplant by data cut-off. In conclusion, ivosidenib is clinically active, with durable remissions and a manageable safety profile observed in patients with mIDH1 R/R MDS.

Alocasia macrorrhiza rhizome lectin inhibits growth of pathogenic bacteria and human lung cancer cell in vitro and Ehrlich ascites carcinoma cell in vivo in mice.

Cancer and antibiotic resistance represent significant global challenges, affecting public health and healthcare systems worldwide. Lectin, a carbohydrate-binding protein, displays various biological properties, including antimicrobial and anticancer activities. This study focused on anticancer and antibacterial properties of Alocasia macrorrhiza lectin (AML). AML, with a molecular weight of 11.0 ± 1.0 kDa was purified using Ion-exchange chromatography, and the homotetrameric form was detected by gel-filtration chromatography. It agglutinates mouse erythrocytes, that was inhibited by 4-Nitrophenyl-α-d-mannopyranoside. Maximum hemagglutination activity was observed below 60 °C and within a pH range from 8 to 11. Additionally, it exhibited moderate toxicity against brine shrimp nauplii with LD50 values of 321 µg/ml and showed antibacterial activity against Escherichia coli and Shigella dysenteriae. In vitro experiments demonstrated that AML suppressed the proliferation of mice Ehrlich ascites carcinoma (EAC) cells by 35 % and human lung cancer (A549) cells by 40 % at 512 µg/ml concentration. In vivo experiments involved intraperitoneal injection of AML in EAC-bearing mice for five consecutive days at doses of 2.5 and 5.0 mg/kg/day, and the results indicated that AML inhibited EAC cell growth by 37 % and 54 %, respectively. Finally, it can be concluded that AML can be used for further anticancer and antibacterial studies.

The impact of comorbidity on the quality of life of people who recovered from COVID-19 in Bangladesh.

Objectives: COVID-19 affects the quality of life (QoL) in a reverse way after recovery, which might be multiplied by the comorbid non-communicable diseases. This study explored the relationship between comorbidities and the QoL of people who recovered from COVID-19 in Bangladesh. Methods: The cross-sectional study was conducted among 3244 participants between June 2020 and November 2020 using a pre-tested questionnaire through over-the-phone interviews. The WHOQOL-BREF was used to explore the QoL among the study participants. A multivariable linear regression model was conducted to identify the effects of the number of comorbidities on QoL scores of all four domains. Results: Of 3244 patients who recovered from COVID-19, over one-third (39.4%) had one or more chronic diseases, such as hypertension, diabetes mellitus, ischemic heart disease, bronchial asthma/chronic obstructive pulmonary disease, chronic kidney disease, and cancer. Around 46.85% of the participants aged above 40 years presented with one to two chronic diseases, and 16.33% had three or more chronic diseases. Among all comorbidities, the participants with cancer and chronic kidney disease were found to have relatively lower scores in all four domains than other comorbidities. The lowest QoL scores were observed in the psychological domain. Those with three or more simultaneous chronic comorbidities had the lowest QoL score in all four domains: physical, psychological, social relationship, and environmental. Conclusions: Persons who recovered from COVID-19 with comorbidities undergo a lower QoL. Therefore, special attention is required to these vulnerable groups to ensure their smooth recuperation.

Risk Assessment and Sources Apportionment of Toxic Metals in Two Commonly Consumed Fishes from a Subtropical Estuarine Wetland System.

The widespread occurrence of heavy metals in aquatic environments, resulting in their bioaccumulation within aquatic organisms like fish, presents potential hazards to human health. This study investigates the concentrations of five toxic heavy metals (Pb, Hg, Zn, Cu, and Cr) and their potential health implications in two economically important fish species (Otolithoides pama and Labeo bata) from a subtropical estuarine wetland system (Feni estuary, Bangladesh). Muscle and gill samples from 36 individual fish were analyzed using energy dispersive X-ray fluorescence (EDXRF). The results revealed that the average quantities of heavy metals in both fishes' muscle followed the declining order of Zn (109.41-119.93 mg/kg) > Cu (45.52-65.43 mg/kg) > Hg (1.25-1.39 mg/kg) > Pb (0.68-1.12 mg/kg) > Cr (0.31-5.82 mg/kg). Furthermore, Zn was found to be present in the highest concentration within the gills of both species. While the levels of Cu, Zn, and Cr in the fish muscle were deemed acceptable for human consumption, the concentrations of Pb and Hg exceeded the permissible limits (>0.5 mg/kg) for human consumption. Different risk indices, including estimated daily intake (EDI), target hazard quotient (THQ), hazard index (HI), and carcinogenic or target risk (TR), revealed mixed and varying degrees of potential threat to human health. According to the EDI values, individuals consuming these fish may face health risks as the levels of Zn, Cu, and Cr in the muscle are either very close to or exceed the maximum tolerable daily intake (MTDI) threshold. Nevertheless, the THQ and HI values suggested that both species remained suitable for human consumption, as indicated by THQ (<1) and HI (<1) values. Carcinogenic risk values for Pb, Cr, and Zn all remained within permissible limits, with TR values falling below the range of (10-6 to 10-4), except for Zn, which exceeded it (>10-4). The correlation matrix and multivariate principal component analysis (PCA) findings revealed that Pb and Cr primarily stemmed from natural geological backgrounds, whereas Zn, Cu, and Hg were attributed to human-induced sources such as agricultural chemicals, silver nanoparticles, antimicrobial substances, and metallic plating. Given the significance of fish as a crucial and nutritious element of a balanced diet, it is essential to maintain consistent monitoring and regulation of the levels and origins of heavy metals found within it.

Discovery of a cell-active chikungunya virus nsP2 protease inhibitor using a covalent fragment-based screening approach.

Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that has been responsible for numerous large-scale outbreaks in the last twenty years. Currently, there are no FDA-approved therapeutics for any alphavirus infection. CHIKV non-structural protein 2 (nsP2), which contains a cysteine protease domain, is essential for viral replication, making it an attractive target for a drug discovery campaign. Here, we optimized a CHIKV nsP2 protease (nsP2pro) biochemical assay for the screening of a 6,120-compound cysteine-directed covalent fragment library. Using a 50% inhibition threshold, we identified 153 hits (2.5% hit rate). In dose-response follow up, RA-0002034, a covalent fragment that contains a vinyl sulfone warhead, inhibited CHIKV nsP2pro with an IC 50 of 58 ± 17 nM, and further analysis with time-dependent inhibition studies yielded a k inact /K I of 6.4 x 10 3 M -1 s -1 . LC-MS/MS analysis determined that RA-0002034 covalently modified the catalytic cysteine in a site-specific manner. Additionally, RA-0002034 showed no significant off-target reactivity against a panel of cysteine proteases. In addition to the potent biochemical inhibition of CHIKV nsP2pro activity and exceptional selectivity, RA-0002034 was tested in cellular models of alphavirus infection and effectively inhibited viral replication of both CHIKV and related alphaviruses. This study highlights the discovery and characterization of the chemical probe RA-0002034 as a promising hit compound from covalent fragment-based screening for development toward a CHIKV or pan-alphavirus therapeutic. Significance Statement: Chikungunya virus is one of the most prominent and widespread alphaviruses and has caused explosive outbreaks of arthritic disease. Currently, there are no FDA-approved drugs to treat disease caused by chikungunya virus or any other alphavirus-caused infection. Here, we report the discovery of a covalent small molecule inhibitor of chikungunya virus nsP2 protease activity and viral replication of four diverse alphaviruses. This finding highlights the utility of covalent fragment screening for inhibitor discovery and represents a starting point towards the development of alphavirus therapeutics targeting nsP2 protease.

The Transcriptome of BT-20 Breast Cancer Cells Exposed to Curcumin Analog NC2603 Reveals a Relationship between EGR3 Gene Modulation and Cell Migration Inhibition.

Breast cancer represents a critical global health issue, accounting for a substantial portion of cancer-related deaths worldwide. Metastasis, the spread of cancer cells to distant organs, is the primary cause of approximately 90% of breast cancer-related fatalities. Despite advances in cancer treatment, conventional chemotherapeutic drugs often encounter resistance and demonstrate limited efficacy against metastasis. Natural products have emerged as promising sources for innovative cancer therapies, with curcumin being one such example. However, despite its therapeutic potential, curcumin exhibits several limitations. Analogous compounds possessing enhanced bioavailability, potency, or specificity offer a promising avenue for overcoming these challenges and demonstrate potent anti-tumor activities. Our study investigates the antimetastatic potential of the curcumin analog NC2603 in breast cancer cells, utilizing BT-20 cells known for their migratory properties. Cell viability assessments were performed using the MTT reduction method, while migration inhibition was evaluated through scratch and Transwell migration assays. Transcriptome analysis via next-generation sequencing was employed to elucidate gene modulation and compound mechanisms, with subsequent validation using RT-qPCR. The IC50 of NC2603 was determined to be 3.5 µM, indicating potent inhibition of cell viability, and it exhibited greater specificity for BT-20 cells compared with non-cancerous HaCaT cells, surpassing the efficacy of doxorubicin. Notably, NC2603 demonstrated superior inhibition of cell migration in both scratch and Transwell assays compared with curcumin. Transcriptome analysis identified 10,620 modulated genes. We validated the expression of six: EGR3, ATF3, EMP1, SOCS3, ZFP36, and GADD45B, due to their association with migration inhibition properties. We hypothesize that the curcumin analog induces EGR3 expression, which subsequently triggers the expression of ATF3, EMP1, SOCS3, ZFP36, and GADD45B. In summary, this study significantly advances our comprehension of the intricate molecular pathways involved in cancer metastasis, while also examining the mechanisms of analog NC2603 and underscoring its considerable potential as a promising candidate for adjuvant therapy.

Assessment of dietary polyvinylchloride, polypropylene and polyethylene terephthalate exposure in Nile tilapia, Oreochromis niloticus: Bioaccumulation, and effects on behaviour, growth, hematology and histology.

Microplastics (MPs) have been recognized as emerging aquatic pollutants receiving major concern due to their detrimental effects on aquatic life. Nile Tilapia, Oreochromis niloticus is a model species considered in toxicological studies to address the effects of pollutants in freshwater animals. However, comprehensive knowledge comparing the impacts on fish across various MPs polymers is scarce. Therefore, the overarching aim of the current study was to examine the bioconcentration of MPs polymers: polyvinylchloride (PVC), polypropylene (PP), and polyethylene terephthalate (PET), and their toxic effects on growth, and behavioral responses, hematology, and histology of gills, liver, and intestine in O. niloticus. Fishes were subjected to a 21-day dietary exposure to MPs by assigning them into six treatment groups: T1 (4% of PVC), T2 (4% of PP), T3 (4% of PET), T4 (8% of PVC), T5 (8% of PP), T6 (8% of PET), and control (0% of MPs), to assess the effects on fish across the polymers and dosage. Results showed several abnormalities in anatomical and behavioral parameters, lower growth, and high mortality in MPs-exposed fish, indicating a dose-dependent relationship. The elevated dosage of polymers raised the bioavailability of PVC, PP, and PET in gills and gut tissues. Noteworthy erythrocyte degeneration referred to cytotoxicity and stress imposed by MPs, whereas the alterations in hematological parameters were possibly due to blood cell damage, also indicating mechanisms of defense against MPs toxicity. Histopathological changes in the gills, liver, and intestine confirmed the degree of toxicity and associated dysfunctions in fish. A higher sensitivity of O. niloticus to PET-MPs compared to other polymers is likely due to its chemical properties and species-specific morphological and physiological characteristics. Overall, the present study reveals valuable insights into the emerging threat of MPs toxicity in freshwater species, which could be supportive of future toxicological research.

Pharmacokinetics/pharmacodynamics of ivosidenib in advanced IDH1-mutant cholangiocarcinoma: findings from the phase III ClarIDHy study.

PURPOSE: Report pharmacokinetic (PK)/pharmacodynamic (PD) findings from the phase III ClarIDHy study and any association between PK/PD parameters and treatment outcomes in this population. METHODS: Patients with mutant isocitrate dehydrogenase 1 (mIDH1) advanced cholangiocarcinoma were randomized at a 2:1 ratio to receive ivosidenib or matched placebo. Crossover from placebo to ivosidenib was permitted at radiographic disease progression. Blood samples for PK/PD analyses, a secondary endpoint, were collected pre-dose and up to 4 h post-dose on day (D) 1 of cycles (C) 1 - 2, pre-dose and 2 h post-dose on D15 of C1 - 2, and pre-dose on D1 from C3 onwards. Plasma ivosidenib and D-2-hydroxyglutarate (2-HG) were measured using liquid chromatography-tandem mass spectrometry. All clinical responses were centrally reviewed previously. RESULTS: PK/PD analysis was available for samples from 156 ivosidenib-treated patients. Ivosidenib was absorbed rapidly following single and multiple oral doses (time of maximum observed plasma concentration [Tmax] of 2.63 and 2.07 h, respectively). Ivosidenib exposure was higher at C2D1 than after a single dose, with low accumulation. In ivosidenib-treated patients, mean plasma 2-HG concentration was reduced from 1108 ng/mL at baseline to 97.7 ng/mL at C2D1, close to levels previously observed in healthy individuals. An average 2-HG inhibition of 75.0% was observed at steady state. No plasma 2-HG decreases were seen with placebo. Plasma 2-HG reductions were observed in ivosidenib-treated patients irrespective of best overall response (progressive disease, or partial response and stable disease). CONCLUSION: Once-daily ivosidenib 500 mg has a favorable PK/PD profile, attesting the 2-HG reduction mechanism of action and, thus, positive outcomes in treated patients with advanced mIDH1 cholangiocarcinoma. CLINICAL TRIAL REGISTRATION: NCT02989857 Registered February 20, 2017.

Dimeric 3,5-Bis(benzylidene)-4-piperidones: Tumor-Selective Cytotoxicity and Structure-Activity Relationships.

Background: The objective of this study is to find novel antineoplastic agents that display greater toxicity to malignant cells than to neoplasms. In addition, the mechanisms of action of representative compounds are sought. This report describes the cytotoxicity of a number of dimers of 3,5-bis(benzylidene)-4-piperidones against human malignant cells (promyelocytic leukemia HL-60 and squamous cell carcinoma HSC-2, HSC-3, and HSC-4). Methods: Tumor specificity was evaluated by the selectivity index (SI), that is the ratio of the mean CC50 for human non-malignant oral cells (gingival fibroblasts, pulp cells, periodontal ligament fibroblasts) to that for malignant cells. Results: The compounds were highly toxic to human malignant cells. On the other hand, these molecules were less toxic to human non-malignant cells. In particular, a potent lead molecule, 3b, was identified. A QSAR study revealed that the placement of electron-releasing and hydrophilic substituents into the aryl rings led to increases in cytotoxic potencies. The modes of action of a lead compound discovered in this study designated 3b were the activation of caspases-3 and -7, as well as causing PARP1 cleavage and G2 arrest, followed by sub-G1 accumulation in the cell cycle. This compound also depolarized the mitochondrial membrane and generated reactive oxygen species in human colon carcinoma HCT116 cells. In conclusion, this study has revealed that, in general, the compounds described in this report are tumor-selective cytotoxins.

Gene silencing of Helicobacter pylori through newly designed siRNA convenes the treatment of gastric cancer.

BACKGROUND: Helicobacter pylori is a gastric pathogen that is responsible for causing chronic inflammation and increasing the risk of gastric cancer development. It is capable of persisting for decades in the harsh gastric environment because of the inability of the host to eradicate the infection. Several treatment strategies have been developed against this bacterium using different antibiotics. But the effectiveness of treating H. pylori has significantly decreased due to widespread antibiotic resistance, including an increased risk of gastric cancer. The small interfering RNAs (siRNA), which is capable of sequence-specific gene-silencing can be used as a new therapeutic approach for the treatment of a variety of such malignancies. In the current study, we rationally designed two siRNA molecules to silence the cytotoxin-associated gene A (CagA) and vacuolating cytotoxin A (VacA) genes of H. pylori for their significant involvement in developing cancer. METHODS: We selected a common region of all the available transcripts from different countries of CagA and VacA to design the siRNA molecules. The final siRNA candidate was selected based on the results from machine learning algorithms, off-target similarity, and various thermodynamic properties. RESULT: Further, we utilized molecular docking and all atom molecular dynamics (MD) simulations to assess the binding interactions of the designed siRNAs with the major components of the RNA-induced silencing complex (RISC) and results revealed the ability of the designed siRNAs to interact with the proteins of RISC complex in comparable to those of the experimentally reported siRNAs. CONCLUSION: These designed siRNAs should effectively silence the CagA and VacA genes of H. pylori during siRNA mediated treatment in gastric cancer.

Study on the association between pregnancy-associated plasma protein-A and acute cerebral infarction.

Objective: We aimed to study the correlation between pregnancy-associated plasma protein-A (PAPP-A) and acute cerebral infarction (ACI). Methods: Patients who had the symptoms of paralysis, aphasia, or sudden neurological impairment from June 2020 to October 2021 were chosen. There were 159 patients diagnosed with ACI as the experimental group and 102 patients without ACI as the control group. We collected clinical data and observed whether they have a certain impact on plasma PAPP-A levels. The ACI group was divided into two groups: mild neurological deficit group (NIHSS score < 3) and moderate and severe neurological deficit group (NIHSS score > 3). The ACI group was divided into the atherosclerotic-type group and the arteriolar occlusion-type group according to the TOAST classification. The ACI group was divided into a good prognosis group (mRS ≤ 2 points) and a poor prognosis group (mRS > 2 points) using the Modified Rankin Scale (mRS) for 90 days of follow-up. Plasma PAPP-A levels were compared between those groups. Results: (1) The plasma PAPP-A level in patients with ACI (1.840 ± 0.281) was significantly higher than that in the control group (1.690 ± 0.260). Smoking history, leukocyte count, cystatin C, homocysteine, and plasma PAPP-A levels were independently correlated with ACI. (2) The level of PAPP-A in patients with moderate and severe neurological impairment was lower than that in patients with mild neurological impairment. (3) The level of PAPP-A in patients in the arteriolar occlusion-type group was higher than that in patients in the atherosclerosis-type group. (4) The PAPP-A levels in the group with elevated low-density lipoprotein are higher than those in the group with normal low-density lipoprotein. (5) Plasma PAPP-A level was not correlated with infarction location, infarction volume, or prognosis at the 90-day follow-up. Conclusion: (1) The level of plasma PAPP-A could be the independent risk factor of ACI. It is positively correlated with triglyceride and cholesterol content. (2) PAPP-A level is positively correlated with low-density lipoprotein. (3) PAPP-A levels between different disease severities have a significant difference. (4) The level of plasma PAPP-A in the arteriolar occlusion-type group was higher than that in the atherosclerotic-type group.

In silico based analysis to explore genetic linkage between atherosclerosis and its potential risk factors.

Atherosclerosis (ATH) is a chronic cardiovascular disease characterized by plaque formation in arteries, and it is a major cause of illness and death. Although therapeutic advances have significantly improved the prognosis of ATH, missing therapeutic targets pose a significant residual threat. This research used a systems biology approach to identify the molecular biomarkers involved in the onset and progression of ATH, analysing microarray gene expression datasets from ATH and tissues impacted by risk factors such as high cholesterol, adipose tissue, smoking, obesity, sedentary lifestyle, stress, alcohol consumption, hypertension, hyperlipidaemia, high fat, diabetes to find the differentially expressed genes (DEGs). Bioinformatic analyses of Protein-Protein Interaction (PPI), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) were conducted on differentially expressed genes, revealing metabolic and signaling pathways (the chemokine signaling pathway, cytokine-cytokine receptor interaction, the cytosolic DNA-sensing pathway, the peroxisome proliferator-activated receptors signaling pathway, and the nuclear factor-kappa B signaling pathway), ten hubs proteins (CCL5, CCR1, TLR1, CCR2, FCGR2A, IL1B, CD163, AIF1, CXCL-1 and TNF), five transcription factors (YY1, FOXL1, FOXC1, SRF, and GATA2), and five miRNAs (mir-27a-3p, mir-124-3p, mir-16-5p, mir-129-2-3p, mir-1-3p). These findings identify potential biomarkers that may increase knowledge of the mechanisms underlying ATH and their connection to risk factors, aiding in the development of new therapies.

Bone marrow stem cells incubated with ellipticine regenerate articular cartilage by attenuating inflammation and cartilage degradation in rabbit model.

BACKGROUND: Ellipticine (Ellip.) was recently reported to have beneficial effects on the differentiation of adipose-derived stem cells into mature chondrocyte-like cells. On the other hand, no practical results have been derived from the transplantation of bone marrow stem cells (BMSCs) in a rabbit osteoarthritis (OA) model. OBJECTIVES: This study examined whether autologous BMSCs incubated with ellipticine (Ellip.+BMSCs) could regenerate articular cartilage in rabbit OA, a model similar to degenerative arthritis in human beings. METHODS: A portion of rabbit articular cartilage was surgically removed, and Ellip.+BMSCs were transplanted into the lesion area. After two and four weeks of treatment, the serum levels of proinflammatory cytokines, i.e., tumor necrosis factor α (TNF-α) and prostaglandin E2 (PGE2), were analyzed, while macroscopic and micro-computed tomography (CT) evaluations were conducted to determine the intensity of cartilage degeneration. Furthermore, immuno-blotting was performed to evaluate the mitogen-activated protein kinases, PI3K/Akt, and nuclear factor-κB (NF-κB) signaling in rabbit OA models. Histological staining was used to confirm the change in the pattern of collagen and proteoglycan in the articular cartilage matrix. RESULTS: The transplantation of Ellip.+BMSCs elicited a chondroprotective effect by reducing the inflammatory factors (TNF-α, PGE2) in a time-dependent manner. Macroscopic observations, micro-CT, and histological staining revealed articular cartilage regeneration with the downregulation of matrix-metallo proteinases (MMPs), preventing articular cartilage degradation. Furthermore, histological observations confirmed a significant boost in the production of chondrocytes, collagen, and proteoglycan compared to the control group. Western blotting data revealed the downregulation of the p38, PI3K-Akt, and NF-κB inflammatory pathways to attenuate inflammation. CONCLUSIONS: The transplantation of Ellip.+BMSCs normalized the OA condition by boosting the recovery of degenerated articular cartilage and inhibiting the catabolic signaling pathway.

SGC-CLK-1: A chemical probe for the Cdc2-like kinases CLK1, CLK2, and CLK4.

Small molecule modulators are important tools to study both basic biology and the complex signaling of protein kinases. The cdc2-like kinases (CLK) are a family of four kinases that have garnered recent interest for their involvement in a diverse set of diseases such as neurodegeneration, autoimmunity, and many cancers. Targeted medicinal chemistry around a CLK inhibitor hit identified through screening of a kinase inhibitor set against a large panel of kinases allowed us to identify a potent and selective inhibitor of CLK1, 2, and 4. Here, we present the synthesis, selectivity, and preliminary biological characterization of this compound - SGC-CLK-1 (CAF-170). We further show CLK2 has the highest binding affinity, and high CLK2 expression correlates with a lower IC50 in a screen of multiple cancer cell lines. Finally, we show that SGC-CLK-1 not only reduces serine arginine-rich (SR) protein phosphorylation but also alters SR protein and CLK2 subcellular localization in a reversible way. Therefore, we anticipate that this compound will be a valuable tool for increasing our understanding of CLKs and their targets, SR proteins, at the level of phosphorylation and subcellular localization.

Investigation of pathogenic germline variants in gastric cancer and development of "GasCanBase" database.

BACKGROUND: Gastric cancer, which is also known as stomach cancer, can be influenced by both germline and somatic mutations. Non-synonymous Single Nucleotide Polymorphisms (nsSNPs) in germline have long been reported to play a pivotal role in cancer progression. AIM: The aim of this study is to examine the nsSNP in GC-associated genes. The study also aims to develop a database with extensive information regarding the nsSNPs in the GC-associated genes and their impacts. METHODS AND RESULTS: A total of 34,588 nsSNPs from 1,493,460 SNPs of the 40 genes were extracted from the available SNP database. Drug binding and energy minimization were examined by molecular docking and YASARA. To validate the existence of the germline CDH1 gene mutation (rs34466743) in the isolated blood DNA of gastric cancer (GC) patients, polymerase chain reaction (PCR) and DNA sequencing were performed. According to the results of the gene network analysis, 17 genes may interact with other types of cancer. A total of 11,363 nsSNPs were detected within the 40 GC genes. Among these, 474 nsSNPs were predicted to be damaging and 40 to be the most damaging. The SNPs in domain regions were thought to be strong candidates that alter protein functions. Our findings proposed that most of the selected nsSNPs were within the domains or motif regions. Free Energy Deviation calculation of protein structure pointed toward noteworthy changes in the structure of each protein that can demolish its natural function. Subsequently, drug binding confirmed the structural variation and the ineffectiveness of the drug against the mutant model in individuals with these germline variants. Furthermore, in vitro analysis of the rs34466743 germline variant from the CDH1 gene confirmed the strength and robustness of the pipeline that could expand the somatic alteration for causing cancer. In addition, a comprehensive gastric cancer polymorphism database named "GasCanBase" was developed to make data available to researchers. CONCLUSION: The findings of this study and the "GasCanBase" database may greatly contribute to our understanding of molecular epidemiology and the development of precise therapeutics for gastric cancer. GasCanBase is available at: https://www.gascanbase.com/.