Revisiting the role of behavior-mediated structuring in the survival of populations in hostile environments.

Increasing the population density of target species is a major goal of ecosystem and agricultural management. This task is especially challenging in hazardous environments with a high abundance of natural enemies such as parasites and predators. Safe locations with lower mortality have been long considered a beneficial factor in enhancing population survival, being a promising tool in commercial fish farming and restoration of threatened species. Here we challenge this opinion and revisit the role of behavior structuring in a hostile environment in shaping the population density. We build a mathematical model, where individuals are structured according to their defensive tactics against natural enemies. The model predicts that although each safe zone enhances the survival of an individual, for an insufficient number of such zones, the entire population experiences a greater overall mortality. This is a result of the interplay of emergent dynamical behavioral structuring and strong intraspecific competition for safe zones. Non-plastic structuring in individuals' boldness reduces the mentioned negative effects. We demonstrate emergence of non-plastic behavioral structuring: the evolutionary branching of a monomorphic population into a dimorphic one with bold/shy strains. We apply our modelling approach to explore fish farming of salmonids in an environment infected by trematode parasites.

Influence of polarized light, disruptive visual patterns, and chemical cues on oviposition in the aquatic midge, Chironomus riparius (Diptera: Chironomidae).

Chironomid nonbiting midges are common in many waterbodies, occurring at high densities in sediment and also when flying adults emerge. Although important for food webs and ecosystem processes, the mass emergences of chironomid adults make some species nuisance pests. As part of an effort to develop "push-pull" strategies for managing midge populations, we investigated the importance of visual and chemical cues used by gravid females when selecting sites for oviposition. Field and laboratory oviposition choice tests with Chironomus riparius (Meigen) were used to assess the attractiveness of dark container colors and polarized light for females seeking water for egg laying. Females were not sensitive to increased intensity of polarized light, but they laid fewer eggs in containers with white color above the water's edge but black below the surface. A disruptive pattern of vertical black and white stripes at the water's edge reduced egg laying to a similar degree as white. To investigate the importance of olfactory or gustatory cues in oviposition decisions, we tested 3 potential chemical repellents (damaged larvae simulating predator presence, azadiractin, and picaridin) and 5 potential attractants (a tannin-molasses mixture, leaf detritus, live Hydrilla plants, periphyton, and fermented alfalfa infusions used to bait mosquito oviposition traps). Chemical cues appeared to play a weak role, if any, in oviposition choices. Onlyazadiractin (0.02 and 0.11 ppm) reduced the number of egg ropes deposited, but the mechanism may have been from mechanical trapping and drowning, not deterrence.

Bispecific G-quadruplexes as inhibitors of cancer cells growth.

A therapeutic system with the ability to target more than one protein is an important aim of cancer therapy since tumor growth is accompanied by dysregulation of many biological pathways. G-quadruplexes (G4s) are non-canonical structures formed by guanine-rich DNA or RNA oligonucleotides, with the ability to bind to different targets. In this study, we constructed ten novel bispecific G-quadruplex conjugates based on AT11, TBA, T40214 and T40231 aptamer structures, with the ability to bind two different targets at once in cancer cells. We analyzed the physicochemical aspects and the anticancer properties of novel molecules relating them with the single G-quadruplex unit and attempted to comprehend the correlation between the structures of bispecific G-quadruplexes with their biological activity. Our studies uncovered conjugates with considerable antiproliferative potential in HeLa and MCF-7 cancer cell lines, however with relatively low thermal stability or low nuclease resistance. Three conjugates among all studied oligonucleotides possess improved antiproliferative activity in MCF-7 cell line in comparison to their single G-quadruplex units leading to up to 90% inhibition of cancer cells growth, but their inhibitory potential is rather comparable to the effect observed for mix of two separate G-quadruplex units. Importantly, the conjugation enhances oligonucleotides enzymatic stability leading to the improvement of their therapeutic profile. The comprehensive studies presented herein indicate new approach for possibly effective cancer therapy and for the design of G4-based drugs.

Variability in the Clinical Course of COVID-19 in a Retrospective Analysis of a Large Real-World Database.

The COVID-19 pandemic proceeds in waves, with variable characteristics of the clinical picture resulting from the evolution of the SARS-CoV-2 virus. This study aimed to compare the epidemiological characteristics, symptomatology, and outcomes of the disease in patients hospitalized for COVID-19 during periods of different variants dominance. Comparing the periods of dominance of variants preceding the Delta variant, the Delta period was characterized by a higher share of hospitalized females, less frequent comorbidities among patients, and a different age distribution. The lowest need for oxygen therapy and mechanical ventilation was observed under Omicron dominance. The triad of classic COVID-19 symptoms, cough, fever, dyspnoea, and fatigue, were most prevalent during the Delta period, and significantly less common under the Omicron dominance. During the Omicron period, nearly twice as many patients as in the previous periods could be discharged from the hospital within 7 days; the overall 28-day mortality was significantly lower compared to that of the Delta period. It also did not differ between periods that were dominated by the BA.1 and BA.2 subvariants. The study indicates that the Omicron SARS-CoV-2 variant that dominated between January and June 2022 caused a disease which resembled the common cold, and was caused by seasonal alpha and beta-coronaviruses with a low pathogenicity for humans. However, one should note that this effect may not only have been related to biological features of the Omicron lineage, but may additionally have been driven by the increased levels of immunization through natural infections and vaccinations, for which we could not account for due to a lack of sufficient data.

Differences between the course of SARS-CoV-2 infections in the periods of the Delta and Omicron variant dominance in Poland.

INTRODUCTION: Up to now, COVID­19 caused more than 6 million deaths worldwide. So far, 5 variants of concerns have been identified, with Delta and Omicron being the subject of our analysis. OBJECTIVES: We aimed to compare baseline characteristics and outcomes of patients hospitalized during the Delta and Omicron predominance in Poland. PATIENTS AND METHODS: The study population consisted of 2225 patients divided into 2 groups depending on the variant with which they were infected during the corresponding period of the pandemic. RESULTS: During the Delta wave, the median age of patients was significantly lower (65 vs 73 years; P <0.001), and the cohort was significantly less burdened with comorbidities than during the Omicron surge. The Omicron­infected patients presented significantly less often in an unstable symptomatic state with SpO2 equal to or below 90% on admission (49.9% for Delta vs 29.9% for Omicron; P <0.001). Regardless of the pandemic period, the 2 most common early symptoms of COVID­19 were fever and cough. In­hospital treatment consisted of antiviral drugs, more frequently used in the Omicron wave, and immunomodulatory drugs, more frequently used during the Delta wave. The risk of mechanical ventilation was significantly lower in the patients infected with the Omicron variant (7.2% for Delta vs 3.1% for Omicron; P <0.001). For the age group above 80 years old, the risk of death was significantly higher during the Delta wave than during the Omicron wave. The risk of death was significantly lower in the patients treated with antiviral drugs regardless of the pandemic wave. CONCLUSIONS: The Delta variant is associated with a more severe clinical course of the disease and a higher risk of death than the Omicron variant.

Physicochemical and antiproliferative characteristics of RNA and DNA sequence-related G-quadruplexes.

In this article the physicochemical and biological properties of sequence-related G-quadruplex forming oligonucleotides in RNA and DNA series are analyzed and compared. The intermolecular G-quadruplexes vary in loop length, number of G-tetrads and homogeneity of the core. Our studies show that even slight variations in sequence initiate certain changes of G-quadruplex properties. DNA G-quadruplexes are less thermally stable than their RNA counterparts, more topologically diversified and are better candidates as inhibitors of cancer cells proliferation. The most efficient antiproliferative activity within the studied group of molecules was observed for two DNA G-quadruplexes with unperturbed core and lower content of thymidine residues within the loops leading to reduction of cells viability up to 65% and 33% for HeLa and MCF-7 cell lines, respectively.

County-level surveillance for the lone star tick, Amblyomma americanum, and its associated pathogen, Ehrlichia chaffeensis, in Kentucky.

Kentucky experiences some of the highest incidence rates for ehrlichiosis nationwide. Ehrlichiosis is a bacterial infection caused primarily by the pathogen Ehrlichia chaffeensis and can be transmitted to humans through the bite of an infected tick, notably Amblyomma americanum. Amblyomma americanum, the lone star tick, is common to Kentucky and much of the southeast, but has expanded farther north in recent years. As an abundant and aggressive nondiscriminatory biter, this species is of major public health concern for transmission of pathogens to humans. As this vector's range expands, surveillance remains a necessary tool providing data that allows researchers to track this expansion over time. The historical information on tick distribution in Kentucky is variable with very little data on a statewide scale. From January 2019 to December 2020, we conducted surveillance for A. americanum in Kentucky through field collections and the establishment of a statewide tick submission program with the help of the Kentucky Department for Public Health and screened for E. chaffeensis on a county-level throughout the state. We collected 5,726 A. americanum ticks in 77 counties and detected E. chaffeensis in 32 counties. The minimum infection rate was 1.8%. With the expansion of A. americanum and increasing cases of tick-borne diseases, future surveillance is needed to monitor this important tick vector over time.

The Course of COVID-19 in Patients with Systemic Autoimmune Rheumatic Diseases.

Patients with systemic autoimmune rheumatic disease (SARD) have increased susceptibility to viral infections, including SARS-CoV-2. The aim of this study was to analyse the SARD patient population with COVID-19 (coronavirus disease 2019) in terms of baseline characteristics, severity, course and outcomes of the disease compared with the non-SARD group, and to identify factors associated with prognosis, including remdesivir therapy efficacy. Retrospective study comprised 8220 COVID-19 cases from the SARSTer database, including 185 with SARD. Length of hospitalisation, duration of oxygen therapy, mortality and the need for HFNO (high-flow nasal oxygen) and/or NIV (noninvasive ventilation) were significantly higher in the SARD versus non-SARD group. There was no difference in clinical features on admission to hospital. Patients with SARD were older and more likely to have cardiovascular, pulmonary and chronic kidney diseases. Age, the presence of cardiovascular disease, more severe conditions on admission and higher inflammatory marker values were found to be risk factors for death in the SARD group. In patients with SARD treated with remdesivir, there was a trend towards improved mortality but without statistical significance. Length of hospitalisation, 28-day mortality and the need for HFNO and/or NIV were higher in the SARD group. These patients often had other chronic diseases and were older.

Optimization of Bifunctional Antisense Oligonucleotides for Regulation of Mutually Exclusive Alternative Splicing of PKM Gene.

Oligonucleotide tools, as modulators of alternative splicing, have been extensively studied, giving a rise to new therapeutic approaches. In this article, we report detailed research on the optimization of bifunctional antisense oligonucleotides (BASOs), which are targeted towards interactions with hnRNP A1 protein. We performed a binding screening assay, Kd determination, and UV melting experiments to select sequences that can be used as a high potency binding platform for hnRNP A1. Newly designed BASOs were applied to regulate the mutually exclusive alternative splicing of the PKM gene. Our studies demonstrate that at least three repetitions of regulatory sequence are necessary to increase expression of the PKM1 isoform. On the other hand, PKM2 expression can be inhibited by a lower number of regulatory sequences. Importantly, a novel branched type of BASOs was developed, which significantly increased the efficiency of splicing modulation. Herein, we provide new insights into BASOs design and show, for the first time, the possibility to regulate mutually exclusive alternative splicing via BASOs.

Changes in physicochemical and anticancer properties modulated by chemically modified sugar moieties within sequence-related G-quadruplex structures.

We systematically investigated the influence of locked nucleic acid (LNA), unlock nucleic acid (UNA), and 2'-O-methyl-RNA (2'-O-Me-RNA) residues on the thermal stability, structure folding topology, biological activity and enzymatic resistance of three sequence-related DNA G-quadruplexes. In order to better understand the mechanism of action of the studied modifications, a single-position substitution in the loops or G-tetrads was performed and their influence was analyzed for a total of twenty-seven modified G-quadruplex variants. The studies show that the influence of each modification on the physicochemical properties of G-quadruplexes is position-dependent, due to mutual interactions between G-tetrads, loops, and additional guanosine at 5' or 3' end. Nevertheless, the anticancer activity of the modified G-quadruplexes is determined by their structure, thus also by the local changes of chemical character of sugar moieties, what might influence the specific interactions with therapeutic targets. In general, UNA modifications are efficient modulators of the G-quadruplex thermodynamic stability, however they are poor tools to improve the anticancer properties. In contrast, LNA and 2'-O-Me-RNA modified G-quadruplexes demonstrated certain antiproliferative potential and might be used as molecular tools for designing novel G-quadruplex-based therapeutics.

Evaluation of Gene Expression Knock-Down by Chemically and Structurally Modified Gapmer Antisense Oligonucleotides.

We analyzed the effect of modified nucleotides within gapmer antisense oligonucleotides on RNase H mediated gene silencing. Additionally, short hairpins were introduced into antisense oligonucleotides as structural motifs, and their influence on biological and physicochemical properties of pre-structured gapmers was investigated for the first time. The results indicate that two LNA residues in specified positions of the gap flanking regions are sufficient and favorable for efficient knock-down of the ß-actin gene. Furthermore, the introduction of other modified nucleotides, i. e. glycyl-amino-LNA-T, 2'-O-propagyluridine, polyamine functionalized uridine, and UNA, in specified positions, also increases the inhibition of ß-actin expression. Importantly, the presence of hairpins within the gapmers improves their silencing properties.

A Structural Potential of Rare Trinucleotide Repeat Tracts in RNA.

Among types of trinucleotide repeats, there is some disproportion in the frequency of their occurrence in the human exome. This research presents new data describing the folding and thermodynamic stability of short, tandem RNA repeats of 23 types, focusing on the rare, yet poorly analyzed ones. UV-melting experiments included the presence of PEG or potassium and magnesium ions to determine their effect on the stability of RNA repeats structures. Rare repeats predominantly stayed single-stranded but had the potential for base pairing with other partially complementary repeat tracts. A coexistence of suitably complementary repeat types in a single RNA creates opportunities for interaction in the context of the secondary structure of RNA. We searched the human transcriptome for model RNAs in which different, particularly rare trinucleotide repeats coexist and selected the GABRA4 and CHIC1 RNAs to study intramolecular interactions between the repeat tracts that they contain. In vitro secondary structure probing results showed that the UAA and UUG repeat tracts, present in GABRA4 3' UTR, form a double helix, which separates one of its structural domains. For the RNA CHIC1 ORF fragment containing four short AGG repeat tracts and the CGU tract, we proved the formation of quadruplexes that blocked reverse transcription.

Allee effect in a manipulative parasite within poikilothermic host under temperature change.

Temperature and intraspecific competition are important factors influencing the growth of all organisms, including parasites. The temperature increase is suggested to stimulate the development of parasites within poikilothermic hosts. However, at high parasite densities, this effect could be diminished, due to stronger intraspecific competition. Our study, for the first time, addressed the joint effects of warming and parasite abundances on parasite growth in poikilothermic hosts. The growth of the common fish parasite larvae (trematode Diplostomum pseudospathaceum) within the rainbow trout at different infection intensities and temperatures (15°C and 18°C) was experimentally investigated. The results showed that temperature was positively correlated with both parasite infection success and growth rates. The growth rates increased much more compared to those in many free-living poikilothermic animals. Atypically for a majority of parasites, D. pseudospathaceum larvae grow faster when abundant (Allee effect). The possible causes for this phenomenon (manipulation cost sharing, etc.) are discussed in this study. Importantly, limited evidence of the interaction between temperature and population density was found. It is likely that temperature did not change the magnitude of the Allee effect but affected its timing. The impact of these effects is supposed to become more pronounced in freshwater ecosystems under current climate changes.

Analysis of Deaths among HIV-Infected Patients Hospitalized in 2009-2018 in Main Centre of Infectious Disease in Region of Lower Silesia in Poland, Detailing Lesions in the Central Nervous System.

Background and Objectives: Patients living with HIV (PLWH), especially those diagnosed too late or not receiving treatment with antiretroviral drugs in the stage of advanced immunodeficiency AIDS for various reasons, develop additional opportunistic infections or AIDS-defining diseases that may contribute directly to the death of these patients. Material and Methods: In this work, we focused on disorders of the central nervous system (CNS) by retrospectively analyzing the symptoms, clinical and autopsy diagnoses of patients diagnosed with HIV infection who died in the provincial specialist hospital in the Lower Silesia region in Poland. Results: The autopsy was performed in 27.4% cases. The cause of death was determined to be HIV-related/AIDS-associated in 78% patients. The most common AIDS-defining CNS diseases in our cohort were toxoplasmosis and cryptococcosis. Conslusions: The presented results of the most common causes of changes in the central nervous system among deceased HIV-infected patients are comparable to the results of studies by other scientists cited in the publication.

Application of a Web-based Self-assessment Triage Tool During the COVID-19 Pandemic: Descriptive Study.

BACKGROUND: The COVID-19 pandemic has sped up the implementation of telehealth solutions in medicine. A few symptom checkers dedicated for COVID-19 have been described, but it remains unclear whether and how they can affect patients and health systems. OBJECTIVE: This paper demonstrates our experiences with the COVID-19 risk assessment (CRA) tool. We tried to determine who the user of the web-based COVID-19 triage app is and compare this group with patients in the infectious diseases ward's admission room to evaluate who could benefit from implementing the COVID-19 online symptom checker as a remote triage solution. METHODS: We analyzed the answers of 248,862 people interacting with an online World Health Organization-based triage tool for assessing the probability of SARS-CoV-2 infection. These users filled in an online questionnaire between April 7 and August 6, 2020. Based on the presented symptoms, risk factors, and demographics, the tool assessed whether the user's answers were suggestive of COVID-19 and recommended appropriate action. Subsequently, we compared the sociodemographic and clinical characteristics of tool users with patients admitted to the Infectious Diseases Admission Room of J. Gromkowski Hospital in Wroclaw. RESULTS: The CRA tool tended to be used by asymptomatic or oligosymptomatic individuals (171,226 [68.80%] of all users). Most users were young (162,432 [65.27%] were below 40 years of age) and without comorbidities. Only 77,645 (31.20%) of the self-assessment app users were suspected of COVID-19 based on their reported symptoms. On the contrary, most admission room patients were symptomatic-symptoms such as fever, cough, and dyspnea were prevalent in both COVID-19-positive and COVID-19-negative patients. COVID-19-suspected patients in the CRA tool group presented similar COVID-19 symptoms as those who presented to the admission room. These were cough (25,062/40,007 [62.64%] in the CRA tool group vs 138/232 [59.48%] in the admission room group), fever (23,123/40,007 [57.80%] in the CRA tool group vs 146/232 [62.93%] in the admission room group), and shortness of breath (15,157/40,007 [37.89%] in the CRA tool group vs 87/232 [37.50%] in the admission room group). CONCLUSIONS: The comparison between the symptomatology of the users interacting with the CRA tool and those visiting the admission room revealed 2 major patient groups who could have benefited from the implementation of the self-assessment app in preclinical triage settings. The primary users of the CRA tool were young, oligosymptomatic individuals looking for screening for COVID-19 and reassurance early in the COVID-19 pandemic. The other group were users presenting the typical symptoms suggestive of COVID-19 at that time. The CRA tool recognized these individuals as potentially COVID-19 positive and directed them to the proper level of care. These use cases fulfil the idea of preclinical triage; however, the accuracy and influence on health care must be examined in the clinical setting.

Mapping distributions of the Lyme disease vector, Ixodes scapularis, and spirochete, Borrelia burgdorferi, in Kentucky using passive and active surveillance.

Lyme disease is the most common tick-borne illness in the United States and is becoming more prevalent each year. It is transmitted to humans and animals through the bites of Ixodes scapularis ticks infected with Borrelia burgdorferi in the eastern United States, I. pacificus in the western U.S, and I. ricinus in Europe and Asia. In Kentucky, where Lyme disease is non-endemic, the number of reported human cases in 2010 totaled five. In 2019, that number had increased by over 300%. Identifying the distribution of I. scapularis populations infected with B. burgdorferi is important data for effective prevention strategies and an important first step in monitoring disease spread. In collaboration with the Kentucky Department for Public Health, we performed surveillance for I. scapularis throughout the state of Kentucky using both active and passive surveillance methods. Diagnostic testing for the identification of B. burgdorferi (sensu stricto) was also conducted. We identified 457 I. scapularis ticks from March 2019 to December 2020 from 32 counties in Kentucky. B. burgdorferi was detected in I. scapularis populations collected from 14 different counties. These results add to the little data that exists in Kentucky on I. scapularis and B. burgdorferi distribution.

A Comprehensive Analysis of the Thrombin Binding Aptamer Containing Functionalized Pyrrolo-2'-deoxycytidines.

Aptamers constitute an answer for the growing need for targeted therapy development. One of the most well-known representatives of this group of compounds is thrombin binding aptamers (TBA) targeted towards thrombin. The TBA inhibitory activity is determined by its spatial arrangement, which consists of two G-tetrads linked by two shorter TT loops and one longer TGT loop and folds into a unimolecular, antiparallel G-quadruplex structure. Interesting properties of the aptamer can be further improved via the introduction of a number of chemical modifications. Herein, a comprehensive analysis of the influence of pyrrolo-2'-deoxycytidine (Py-dC) and its derivatives on TBA physicochemical and biological properties has been presented. The studies have shown that the presence of modified residues at the T7 position of the TGT loop has only minor effects on TBA thermodynamic stability without affecting its folding topology. All analyzed oligomers exhibit anticoagulant properties, but only aptamer modified with a decyl derivative of Py-dC was able to inhibit thrombin activity more efficiently than unmodified, parental compounds. Importantly, the same compound also possessed the potential to effectively restrain HeLa cell line growth.

Beyond G-Quadruplexes-The Effect of Junction with Additional Structural Motifs on Aptamers Properties.

G-quadruplexes constitute an important type of nucleic acid structure, which can be found in living cells and applied by cell machinery as pivotal regulatory elements. Importantly, robust development of SELEX technology and modern, nucleic acid-based therapeutic strategies targeted towards various molecules have also revealed a large group of potent aptamers whose structures are grounded in G-quadruplexes. In this review, we analyze further extension of tetraplexes by additional structural elements and investigate whether G-quadruplex junctions with duplex, hairpin, triplex, or second G-quadruplex motifs are favorable for aptamers stability and biological activity. Furthermore, we indicate the specific and pivotal role of the G-quadruplex domain and the additional structural elements in interactions with target molecules. Finally, we consider the potency of G-quadruplex junctions in future applications and indicate the emerging research area that is still waiting for development to obtain highly specific and effective nucleic acid-based molecular tools.