Search

The flat bark beetle fauna (Coleoptera: Cucujidae) has not been intensively studied in the Korean Peninsula; a few records of this insect family are known from the literature from this region. Based on the data collected from the iNaturalist citizen science database, local entomological fora and websites, as well as Facebook social media, new distributional data for Cucujidae are provided from the Korean Peninsula, including the first records of Cucujus haematodes haematodes from South Gyeongsang and North Chungcheong provinces and Pediacus japonicus from North Gyeongsang and South Jeolla provinces, all in South Korea. Moreover, critical analysis of the literature suggests excluding one species, Cucujus coccinatus, from the fauna of the entire Korean Peninsula as it was recorded based on misidentification with C. h. haematodes. The citizen scientific data made 74% of all known records of Cucujidae in the studied area, which clearly proves the importance of citizen science in studies focused on insect biodiversity, especially in the case of species characterized by at least medium body size. A country-level and province-level checklist and a diagnosis of Cucujidae species currently known from the Korean Peninsula are provided.

HNO (nitroxyl, IUPAC name azanone) is an electrophilic reactive nitrogen species of growing pharmacological and biological significance. Here, we present data on the pH-dependent kinetics of azanone reactions with the low molecular thiols glutathione and N-acetylcysteine, as well as with important serum proteins: bovine serum albumin and human serum albumin. The competition kinetics method used is based on two parallel HNO reactions: with RSH/RS− or with O2. The results provide evidence that the reaction of azanone with the anionic form of thiols (RS−) is favored over reactions with the protonated form (RSH). The data are supported with quantum mechanical calculations. A comprehensive discussion of the HNO reaction with thiolates is provided.

The flat bark beetles (Coleoptera: Cucujidae) is a small insect family with only about 70 species. Most of the species are distributed in Holarctic, Oriental and/or Australasian realms, while in South America, only six species have been recorded, including a single one known from Peru.Two cucujid beetle species,Palaestes abruptusSharp, 1899 andP. nicaraguaeSharp, 1899, are recorded from South America for the first time. The species are recorded from the Pasco (P. abruptus) and Cusco and Junín (P. nicaraguae) Regions of Peru, based, in part, on data collected through the iNaturalist citizen science database. Habitats of both species are presented in photographs for the first time. A country-level checklist to Cucujidae species currently known from South America is provided.

To document a relation between abundance of arboreal, predatory tiger beetles, their ant prey, and extrafloral nectaries attracting the ants, we gathered data from more than 10 species of native and introduced trees and large, tree‐like perennial plants in Lanao del Sur Province, Mindanao, Philippines. All specimens of tiger beetles (two Tricondyla and two Neocollyris species, all endemic to the country) were noted on five tree species characterized by presence of extrafloral nectaries, including three alien/invasive and two native ones. Invasive Spathodea campanulata and native Hibiscus tiliaceus were the most inhabited ones (respectively, 56% and 19% of beetles). Presence of tiger beetles on these trees most probably depends on high abundance of ants, which are typical prey for arboreal Cicindelidae, while occurrence of ants can result from presence of extrafloral nectaries on different parts of the plants. This suggests a new mutualistic insect–plant interaction between native and invasive species., Arboreal tiger beetle species used invasive and native trees having extrafloral nectaries as preferred place for hunting on ants, the insects which are attracted to these trees because of presence of sweet substances produced in these elements. Based on these observations, we suggest a new mutualistic insect–plant interaction between native and invasive species. In our opinion, this is the first case of such interactions noted between tiger beetles and invasive trees both in the Philippines and in the entire area of the southeastern Asia.

The phenomenon of multiphasic survival curves found in drosophila is confirmed in experiments on daphnids. Mathematical modeling showed that the multiphasic nature of daphnids survival curves reflected abrupt changes in the death rate of objects during phase transition. The phase of a sharp increase in mortality observed at an early age in intact drosophila occurs in daphnids only as reaction to a negative impact. The induction of reactive changes by weak external signals resulted in decreased survival for young daphnids. A logical conclusion was made about the reaction readiness for each experimental individual. It is proven that the predisposition to reaction in daphnia persists for an indefinitely large number of generations. It is postulated that this reaction has an epigenetic nature. Earlier experimental materials suggest that a reaction of this type is widespread in natural surroundings.

Development of cervical cancer is directly associated with integration of human papillomavirus (HPV) genomes into host chromosomes and subsequent modulation of HPV oncogene expression, which correlates with multi-layered epigenetic changes at the integrated HPV genomes. However, the process of integration itself and dysregulation of host gene expression at sites of integration in our model of HPV16 integrant clone natural selection has remained enigmatic. We now show, using a state-of-the-art ‘HPV integrated site capture’ (HISC) technique, that integration likely occurs through microhomology-mediated repair (MHMR) mechanisms via either a direct process, resulting in host sequence deletion (in our case, partially homozygously) or via a ‘looping’ mechanism by which flanking host regions become amplified. Furthermore, using our ‘HPV16-specific Region Capture Hi-C’ technique, we have determined that chromatin interactions between the integrated virus genome and host chromosomes, both at short- (500 kbp), appear to drive local host gene dysregulation through the disruption of host:host interactions within (but not exceeding) host structures known as topologically associating domains (TADs). This mechanism of HPV-induced host gene expression modulation indicates that integration of virus genomes near to or within a ‘cancer-causing gene’ is not essential to influence their expression and that these modifications to genome interactions could have a major role in selection of HPV integrants at the early stage of cervical neoplastic progression., Author summary The integration of human papillomaviruses (HPVs) into host chromosomes is a major feature of HPV-associated cancers, however the process by which this occurs and subsequently drives carcinogenesis is incompletely understood. Here, we devised a state-of-the-art HPV16 genome-specific DNA capture technology to precisely determine the host integration sites at a nucleotide resolution, such that we confirm the mechanism of microhomology-mediated repair (MHMR) during both ‘direct’ and ‘looping’ integration of HPV16 genomes into the host. Furthermore, our technology detects both short- and long-range interactions between HPV16 and host chromatin after virus integration, which correlates with dysregulation of host gene expression at distances up to 500kbp from the integration site. This means that HPV16 genomes can directly affect host gene expression much further away on host chromosomes than initially thought, which may lead to competitive growth advantages for certain integrated clones. Therefore, our study provides further insight into the mechanisms by which papillomaviruses are able to initiate and drive cervical carcinogenesis at an early stage after HPV integration.

The beetle family Cucujidae is recorded from the area of Vietnam for the first time based on three specimens of Cucujus mniszechi collected in Kon Tum and Yen Bai Provinces. A key to Cucujidae spec...

Cyclic GMP–AMP synthase (cGAS) is an innate immune sensor for cytosolic microbial DNA1. After binding DNA, cGAS synthesizes the messenger 2′3′-cyclic GMP–AMP (cGAMP)2–4, which triggers cell-autonomous defence and the production of type I interferons and pro-inflammatory cytokines via the activation of STING5. In addition to responding to cytosolic microbial DNA, cGAS also recognizes mislocalized cytosolic self-DNA and has been implicated in autoimmunity and sterile inflammation6,7. Specificity towards pathogen- or damage-associated DNA was thought to be caused by cytosolic confinement. However, recent findings place cGAS robustly in the nucleus8–10, where tight tethering of chromatin is important to prevent autoreactivity to self-DNA8. Here we show how cGAS is sequestered and inhibited by chromatin. We provide a cryo-electron microscopy structure of the cGAS catalytic domain bound to a nucleosome, which shows that cGAS does not interact with the nucleosomal DNA, but instead interacts with histone 2A–histone 2B, and is tightly anchored to the ‘acidic patch’. The interaction buries the cGAS DNA-binding site B, and blocks the formation of active cGAS dimers. The acidic patch robustly outcompetes agonistic DNA for binding to cGAS, which suggests that nucleosome sequestration can efficiently inhibit cGAS, even when accessible DNA is nearby, such as in actively transcribed genomic regions. Our results show how nuclear cGAS is sequestered by chromatin and provides a mechanism for preventing autoreactivity to nuclear self-DNA. Biochemical and structural analyses show how tethering of the nucleotidyltransferase cGAS to chromatin prevents autoimmune recognition of nuclear DNA.

Wolbachia is a genus containing obligate, intracellular endosymbionts with arthropod and nematode hosts. Numerous studies have identified differentially expressed transcripts in Wolbachia endosymbionts that potentially inform the biological interplay between these endosymbionts and their hosts, albeit with discordant results. Here, we re-analyze previously published Wolbachia RNA-Seq transcriptomics data sets using a single workflow consisting of the most up-to-date algorithms and techniques, with the aim of identifying trends or patterns in the pan-Wolbachia transcriptional response. We find that data from one of the early studies in filarial nematodes did not allow for robust conclusions about Wolbachia differential expression with these methods, suggesting the original interpretations should be reconsidered. Across datasets analyzed with this unified workflow, there is a general lack of global gene regulation with the exception of a weak transcriptional response resulting in the upregulation of ribosomal proteins in early larval stages. This weak response is observed across diverse Wolbachia strains from both nematode and insect hosts suggesting a potential pan-Wolbachia transcriptional response during host development that diverged more than 700 million years ago.

Strawberry culture is of extreme economic importance, especially for small producers, as it has the capacity to add value to small family farms, in addition to absorbing family labor. Principal component analysis (PCA) is a multivariate technique for modeling covariance structure, where a basic idea is to find latent variables that represent linear combinations of a group of variables under study, which in turn are related between itself. In this way, the objective of the work was estimated, through the analysis of main components (PCA), as relationships between development variables, products and fruit quality in different strawberry cultivars. The design used was a randomized block with 11 treatments, consisting of strawberry cultivars of Italian and American origins, with four replications. During the culture cycle, the following variables were evaluated: phyllochron, number of commercial (FC) and non-commercial (FNC) fruits, mass of commercial (MFC) and non-commercial (MFNC) fruits, total titratable acidity (AT), total soluble quantities (SST) and total soluble ratio, titratable acidity (SST / AT). The relationships between the variables were evaluated by the PCA analysis and the results were plotted on the Biplot graph. From the analysis, it was possible to identify the relationships between the variables that show how to cultivate the same photoperiod and the same characteristic origin. Growing short photoperiods are more productive, for example, as the neutral photoperiod has less phyllochron and less acidity. The increase in soluble solids can cause a reduction in acidity, which is one of the characteristics that add flavor to the fruit.

We investigated clinical associations of ficolins and mannose-binding lectin (MBL) in 157 patients suffering from acute myeloid leukaemia (AML). Concentrations of ficolin-1, ficolin-2, ficolin-3 and MBL (before chemotherapy) in serum were determined as were selected polymorphisms of the corresponding genes (FCN1, FCN2, FCN3 and MBL2). The control group (C) consisted of 267 healthy unrelated individuals. Median level of ficolin-1 in patients was lower (p p p p = 0.0016, respectively) compared with controls. These findings were generally associated with AML itself, however the highest MBL levels predicted higher risk of severe hospital infections (accompanied with bacteremia and/or fungaemia) (p = 0.012) while the lowest ficolin-1 concentrations tended to be associated with prolonged (> 7 days) fever (p = 0.026). Genotyping indicated an association of G/G homozygosity (corresponding to FCN1 gene − 542 G > A polymorphism) with malignancy [p = 0.004, OR = 2.95, 95% CI (1.41–6.16)]. Based on ROC analysis, ficolin-1, -2 and -3 may be considered candidate supplementary biomarkers of AML. Their high potential to differentiate between patients from non-malignant controls but also from persons suffering from other haematological cancers (multiple myeloma and lymphoma) was demonstrated.

Rift Valley fever virus (RVFV) causes Rift Valley fever (RVF), resulting in morbidity and mortality in humans and ruminants. Evidence of transboundary outbreaks means that RVFV remains a threat to human health and livestock industries in countries that are free from the disease. To enhance surveillance capability, methods for detection of RVFV are required. The generation of reagents suitable for the detection of RVFV antigen in formalin-fixed, paraffin-embedded tissues from infected animals have been developed and are described herein. Recombinant nucleoprotein (rNP) was expressed in Escherichia coli and purified using immobilized metal ion affinity chromatography. Purified rNP was used as an immunogen to produce anti-NP polyclonal antisera in rabbits for use in detection of RVFV NP in experimentally infected animals by immunohistochemistry. Antisera raised in rabbits against rNP were able to recognize viral NP antigen in fixed infected Vero cell pellets and sheep liver. Therefore, the methods and reagents described herein are useful in assays for detection of RVFV infections in animals, for research and surveillance purposes.

Substrate type determines nesting success and fitness in turtles and is a critical consideration for nesting area protection and restoration. Here, we evaluated the effect of substrate on nest removal by humans in the eastern Brazilian Amazon. We analyzed substrate composition and fate of 216 P. unifilis nests along 88 km of rivers. River segment and substrate type were the most important predictors of nest removal by humans. We found up to 36% lower removal of nests in fine sand and experimental results support the hypothesis that wind more often obscures tracks of nesting females in substrates with more (>66%) fine sand. Our findings are useful for informing the restoration of artificial nesting areas across the Amazon, as nesting area substrates should be selected not only to maintain hatchling sex ratios, but also to minimize nest removal by humans.

Soybeans are species of legume that has become one of the most widely consumed food in the world, because they are easy to cultivate and very beneficial for human health. The quality of the cultivated plants, including the content of toxic heavy metals depends to a large extent on the contaminants present in the soils in which they are grown and the method of fertilization. Through this research we aim to highlight the degree of accumulation of cadmium, chromium, cobalt, copper, nickel, lead and zinc in relation with the cultivated soybean genotype and fertilization. Three soy varieties (Cristina, Felix and Onix) were cultivated in an experimental field located at Cojocna Experimental Didactic Center of the University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca. The above-mentioned heavy metals were determined from the harvested mature soybean seeds using inductively coupled plasma-optical emission spectrometry, using an Avio 200 instrument. The obtained results demonstrated that the accumulation of heavy metals in soybean seeds is influenced by the cultivated genotype and fertilization; the Onix variety is more prone to the accumulation of heavy metals, while the highest values of the above listed metals were recorded in the case of fertilizing with „Fertitel”.

An orthomyxo-like virus was first isolated in 1998 as an incidental discovery from pilchards Sardinops sagax collected from waters off the South Australian coast. In the following 2 decades, orthomyxo-like viruses have been isolated from healthy pilchards in South Australia and Tasmania. In 2006, an orthomyxo-like virus was also isolated from farmed Atlantic salmon Salmo salar in Tasmania during routine surveillance and, again, from 2012 onwards from diseased Atlantic salmon. Using transmission electron microscopy, these viruses were identified as belonging to the family Orthomyxoviridae. To further characterise the viruses, the genomes of 11 viral isolates were sequenced. The open reading frames (ORFs) that encode 10 putative proteins from 8 viral genome segments were assembled from Illumina MiSeq next generation sequencing (NGS) data. The complete genome of a 2014 isolate was also assembled from NGS, RNA-sequencing (RNA-seq) data, that included conserved motifs that shared commonalities with infectious salmon anaemia virus, rainbow trout orthomyxovirus and Influenzavirus A. The presence of 8 viral proteins translated from genome segments was confirmed by mass spectrometric analysis including 2 novel proteins with no known orthologs. Sequence analysis of the ORFs, non-coding regions and proteins indicated that the viruses had minimal diversity and hence were named pilchard orthomyxovirus (POMV), based on the fish host species of its first isolation. The low homology of POMV proteins with previously characterised orthomyxoviruses suggests that POMV is the first virus to be characterised from a new genus within the Orthomyxoviridae. To facilitate more rapid detection and subsequent diagnostic confirmation of POMV infections, TaqMan and conventional nested PCRs were designed.

BACKGROUND Two popular physeal-sparing procedures used in the management of anterior cruciate ligament (ACL) injuries in skeletally immature patients are the iliotibial band (ITB) ACL reconstruction (ACLR) and the all-epiphyseal (AE) ACLR. Although there has been concern for overconstraint of the lateral compartment of the knee with the ITB ACLR technique, rotational stability, as provided by the anterolateral ligament (ALL) and ACL, has not been assessed in the setting of pediatric ACLR techniques. Our hypothesis is that the ITB ACLR and AE ACLR with ALL reconstruction (ALLR) will best replicate the biomechanical profile of the intact ACL that is lost with transection of the ACL and ALL. METHODS Eight cadaveric legs were statically loaded with an anterior drawer force and varus, valgus, internal and external rotational moments at 0, 30, 60, and 90 degrees of flexion. Displacement and rotation were recorded in the following conditions: intact ACL/intact ALL, ACL-deficient/intact ALL, ITB ACLR/intact ALL, ITB ACLR/ALL-deficient, ACL-deficient/ALL-deficient, AE ACLR/ALL-deficient, AE ACLR/ALLR. RESULTS Both ACLR techniques reduced anterior tibial translation from the ACL-deficient state, but neither restored it to the intact state (P

Background Less than 5% of medulloblastoma (MB) patients survive following failure of contemporary radiation-based therapies. Understanding the molecular drivers of medulloblastoma relapse (rMB) will be essential to improve outcomes. Initial genome-wide investigations have suggested significant genetic divergence of the relapsed disease. Methods We undertook large-scale integrated characterization of the molecular features of rMB—molecular subgroup, novel subtypes, copy number variation (CNV), and driver gene mutation. 119 rMBs were assessed in comparison with their paired diagnostic samples (n = 107), alongside an independent reference cohort sampled at diagnosis (n = 282). rMB events were investigated for association with outcome post-relapse in clinically annotated patients (n = 54). Results Significant genetic evolution occurred over disease-course; 40% of putative rMB drivers emerged at relapse and differed significantly between molecular subgroups. Non-infant MBSHH displayed significantly more chromosomal CNVs at relapse (TP53 mutation-associated). Relapsed MBGroup4 demonstrated the greatest genetic divergence, enriched for targetable (eg, CDK amplifications) and novel (eg, USH2A mutations) events. Importantly, many hallmark features of MB were stable over time; novel subtypes (>90% of tumors) and established genetic drivers (eg, SHH/WNT/P53 mutations; 60% of rMB events) were maintained from diagnosis. Critically, acquired and maintained rMB events converged on targetable pathways which were significantly enriched at relapse (eg, DNA damage signaling) and specific events (eg, 3p loss) predicted survival post-relapse. Conclusions rMB is characterised by the emergence of novel events and pathways, in concert with selective maintenance of established genetic drivers. Together, these define the actionable genetic landscape of rMB and provide a basis for improved clinical management and development of stratified therapeutics, across disease-course.

Background & Aims Oncogenic KrasG12D induces neoplastic transformation of pancreatic acinar cells through acinar-to-ductal metaplasia (ADM), an actin-based morphogenetic process, and drives pancreatic ductal adenocarcinoma (PDAC). mTOR (mechanistic target of rapamycin kinase) complex 1 (mTORC1) and 2 (mTORC2) contain Rptor and Rictor, respectively, and are activated downstream of KrasG12D, thereby contributing to PDAC. Yet, whether and how mTORC1 and mTORC2 impact on ADM and the identity of the actin nucleator(s) mediating such actin rearrangements remain unknown. Methods A mouse model of inflammation-accelerated KrasG12D-driven early pancreatic carcinogenesis was used. Rptor, Rictor, and Arpc4 (actin-related protein 2/3 complex subunit 4) were conditionally ablated in acinar cells to deactivate the function of mTORC1, mTORC2 and the actin-related protein (Arp) 2/3 complex, respectively. Results We found that mTORC1 and mTORC2 are markedly activated in human and mouse ADM lesions, and cooperate to promote KrasG12D-driven ADM in mice and in vitro. They use the Arp2/3 complex as a common downstream effector to induce the remodeling the actin cytoskeleton leading to ADM. In particular, mTORC1 regulates the translation of Rac1 (Rac family small GTPase 1) and the Arp2/3-complex subunit Arp3, whereas mTORC2 activates the Arp2/3 complex by promoting Akt/Rac1 signaling. Consistently, genetic ablation of the Arp2/3 complex prevents KrasG12D-driven ADM in vivo. In acinar cells, the Arp2/3 complex and its actin-nucleation activity mediated the formation of a basolateral actin cortex, which is indispensable for ADM and pre-neoplastic transformation. Conclusions Here, we show that mTORC1 and mTORC2 attain a dual, yet nonredundant regulatory role in ADM and early pancreatic carcinogenesis by promoting Arp2/3 complex function. The role of Arp2/3 complex as a common effector of mTORC1 and mTORC2 fills the gap between oncogenic signals and actin dynamics underlying PDAC initiation.

Background Reliable testing for SARS-CoV-2 is key for the management of the COVID-19 pandemic. Aim We estimate diagnostic accuracy for nucleic acid and antibody tests 5 months into the COVID-19 pandemic, and compare with manufacturer-reported accuracy. Methods We reviewed the clinical performance of SARS-CoV-2 nucleic acid and antibody tests based on 93,757 test results from 151 published studies and 20,205 new test results from 12 countries in the European Union and European Economic Area (EU/EEA). Results Pooling the results and considering only results with 95% confidence interval width ≤ 5%, we found four nucleic acid tests, including one point-of-care test and three antibody tests, with a clinical sensitivity ≥ 95% for at least one target population (hospitalised, mild or asymptomatic, or unknown). Nine nucleic acid tests and 25 antibody tests, 12 of them point-of-care tests, had a clinical specificity of ≥ 98%. Three antibody tests achieved both thresholds. Evidence for nucleic acid point-of-care tests remains scarce at present, and sensitivity varied substantially. Study heterogeneity was low for eight of 14 sensitivity and 68 of 84 specificity results with confidence interval width ≤ 5%, and lower for nucleic acid tests than antibody tests. Manufacturer-reported clinical performance was significantly higher than independently assessed in 11 of 32 and four of 34 cases, respectively, for sensitivity and specificity, indicating a need for improvement in this area. Conclusion Continuous monitoring of clinical performance within more clearly defined target populations is needed.

The importance of statins in cancer has been discussed in many studies. They are known for their anticancer properties against solid tumors of the liver or lung, as well as diffuse cancers, such as multiple myeloma or leukemia. Currently, the most commonly used statins are simvastatin, rosuvastatin and atorvastatin. The anti-tumor activity of statins is largely related to their ability to induce apoptosis by targeting cancer cells with high selectivity. Statins are also involved in the regulation of the histone acetylation level, the disturbance of which can lead to abnormal activity of genes involved in the regulation of proliferation, differentiation and apoptosis. As a result, tumor growth and its invasion may be promoted, which is associated with a poor prognosis. High levels of histone deacetylases are observed in many cancers; therefore, one of the therapeutic strategies is to use their inhibitors. Combining statins with histone deacetylase inhibitors can induce a synergistic anticancer effect.

Ficolin-2 is regarded as an important innate immunity factor endowed with both lectin (carbohydrate recognition) qualities and ability to induce complement activation. The aim of this study was to investigate the association of the FCN2 3’-untranslated region (3’UTR) polymorphisms with ficolin-2 expression and perinatal complications in preterm neonates. The sequencing analysis allowed us to identify six 3’UTR polymorphisms with minor allele frequency (MAF) >1%: rs4521835, rs73664188, rs11103564, rs11103565, rs6537958 and rs6537959. Except for rs4521835, all adhered to Hardy-Weinberg expectations. Moreover, rs6537958 and rs6537959 were shown to be in perfect linkage disequilibrium (LD) with nine other genetic polymorphisms: rs7040372, rs7046516, rs747422, rs7847431, rs6537957, rs6537960, rs6537962, rs11462298 and rs7860507 together stretched on a distance of 1242 bp and very high LD with rs11103565. The 3’UTR region was shown to bind nuclear extract proteins. The polymorphisms at rs4521835 and rs73664188 were found to influence serum ficolin-2 concentration significantly. All polymorphisms identified create (together with exon 8 polymorphism, rs7851696) two haplotype blocks. Among 49 diplotypes (D1-D49) created from rs7851696 (G>T), rs4521835 (T>G), rs73664188 (T>C), rs11103564 (T>C), rs11103565 (G>A) and rs6537959 (T>A), twenty two occurred with frequency >1%. Two diplotypes: D13 (GTTTGT/GGTCGT) and D10 (GTTTGT/GGTCGA), were significantly more frequent among preterm neonates with early onset of infection and pneumonia, compared with newborns with no infectious complications (OR 2.69 and 2.81, respectively; both p

The sequence diversity of natural and laboratory populations of Brugia pahangi and Brugia malayi was assessed with Illumina resequencing followed by mapping in order to identify single nucleotide variants and insertions/deletions. In natural and laboratory Brugia populations, there is a lack of sequence diversity on chromosome X relative to the autosomes (πX/πA = 0.2), which is lower than the expected (πX/πA = 0.75). A reduction in diversity is also observed in other filarial nematodes with neo-X chromosome fusions in the genera Onchocerca and Wuchereria, but not those without neo-X chromosome fusions in the genera Loa and Dirofilaria. In the species with neo-X chromosome fusions, chromosome X is abnormally large, containing a third of the genetic material such that a sizable portion of the genome is lacking sequence diversity. Such profound differences in genetic diversity can be consequential, having been associated with drug resistance and adaptability, with the potential to affect filarial eradication., Author summary Almost a billion people receive >7.7 billion doses of treatment aimed at eliminating lymphatic filariasis, which is caused by three filarial nematodes: Wuchereria bancrofti, Brugia malayi, and Brugia timori. Drug resistance and adaptation are both associated with pathogen success as well as higher levels of genetic diversity. In an examination of genetic diversity in Brugia malayi and Brugia pahangi, we observed a lack of genetic diversity over a third of the genome that is found on chromosome X. These species have neo-X chromosomes where a chromosome X fused with an autosome. Using publicly-available published data, the other filarial nematodes of greatest human significance are also found to have a similar lack of genetic diversity on their neo-X chromosomes. The two filarial nematodes with publicly-available data that lack neo-X chromosomes did not have this lack of genetic diversity. This lack of sequence diversity in B. malayi, W. bancrofti, and O. volvulus could have profound effects on all traits encoded on chromosome X.

The fungus Microdochium albescens can interfere in the germination of seeds and in the death of rice seedlings; however, there is not technical indication for its control by seed treatment. This research evaluated the efficiency of fungicides in the treatment of pre-germinated and dryland rice seeds in the control of M. albescens. Seeds of the cultivars, Epagri 109, SCS116 Satoru, SCS121 CL and SCS122 Miura were treated with the following fungicides (g a.i./100 kg of seeds): fluazinam + thiophanate methyl (9.45 + 63), pyraclostrobin + thiophanate methyl (5 + 45), carboxin + thiram (60 + 60), metalaxyl-M + thiabendazole + fludioxonil (3 + 22.5 + 3.75), carbendazim + thiram (45 + 105), carbendazim (45). Seeds without fungicide treatment constituted the control. The treated seeds were sown in potato-sucrose-agar (PSA) culture medium and incubated at 25 ± 2 °C and photoperiod of 12 hours for 14 days. Treated seeds were also submitted to the germination test. Fluazinam + thiophanate methyl and metalaxyl-M + thiabendazole + fludioxonil showed greater control of M. albescens, not differing statistically between them, in the five cultivars and in the two cultivation systems. The tested fungicides provided seed germination above 90% in the four cultivars. RESUMO: O fungo Microdochium albescens pode interferir na germinação de sementes e na emergência de plântulas de arroz, porém não há indicação técnica para seu controle via tratamento de semente. Este trabalho teve como objetivo avaliar a eficiência de fungicidas em tratamento de sementes de arroz pré-germinado e sequeiro no controle de M. albescens. Sementes das cultivares Epagri 109, SCS116 Satoru, SCS121 CL e SCS122 Miura foram tratadas com os seguintes fungicidas (g i.a./100 kg de sementes): fluazinam + tiofanato metílico (9,45 + 63), piraclostrobina + tiofanato metílico (5 + 45), carboxina + tiram (60 + 60), metalaxil-M + tiabendazol + fludioxonil (3 + 22,5 + 3,75), carbendazim + tiram (45 + 105), carbendazim (45). Sementes sem tratamento com fungicida constituíram a testemunha. As sementes tratadas foram semeadas em meio de cultura de batata-sacarose-ágar (BSA) e incubadas a 25 ± 2°C e fotoperíodo de 12 horas por 14 dias. Sementes tratadas também foram submetidas ao teste de germinação. Fluazinam + tiofanato metílico e metalaxil-M + tiabendazol + fludioxonil apresentaram maior controle de M. albescens, não diferindo estatisticamente entre si, nas cinco cultivares e nos dois sistemas de cultivo. Contudo, os fungicidas testados proporcionaram germinação das sementes superior a 90% nas quatro cultivares.

International audience; The cerebral vasculature is a dense network of arteries, capillaries, and veins. Quantifying variations of the vascular organization across individuals, brain regions, or disease models is challenging. We used immunolabeling and tissue clearing to image the vascular network of adult mouse brains and developed a pipeline to segment terabyte-sized multichannel images from light sheet microscopy, enabling the construction, analysis, and visualization of vascular graphs composed of over 100 million vessel segments. We generated datasets from over 20 mouse brains, with labeled arteries, veins, and capillaries according to their anatomical regions. We characterized the organization of the vascular network across brain regions, highlighting local adaptations and functional correlates. We propose a classification of cortical regions based on the vascular topology. Finally, we analysed brain-wide rearrangements of the vasculature in animal models of congenital deafness and ischemic stroke, revealing that vascular plasticity and remodeling adopt diverging rules in different models.

Funder: Arcadia Fund; FundRef: https://doi.org/10.13039/100012088, Funder: Coordenação de Aperfeiçoamento de Pessoal de Nível Superior; FundRef: https://doi.org/10.13039/501100002322, Funder: The David and Claudia Harding Foundation, Funder: MAVA Foundation; FundRef: https://doi.org/10.13039/100013324, Background and Research Aims Dams impact freshwater ecosystems and biodiversity. Freshwater turtles are at direct and indirect risk due to changes caused by damming including the loss of terrestrial and aquatic nesting habitats, changes to food availability, and blocking movement. Effective management of these impacts requires robust evidence in order to gain an understanding of conservation solutions that work. Methods We reviewed the global scientific literature that evaluated the impact of dams on freshwater turtles, and carried out additional searches of literature published in seventeen languages for studies evaluating actions to mitigate dam impacts. Results The search produced 47 published articles documenting dam impacts on 30 freshwater turtle species from seven families (Chelidae, Chelydridae, Emydidae, Geoemydidae, Kinosternidae, Podocnemididae, and Trionychidae) in 13 countries. Few studies were found from Europe and Asia and none from Africa. Most studies were from temperate latitudes, where studies focused more on adults and less threatened species compared with tropical latitudes. More than half of the studies (57%, n = 27) suggested actions to help mitigate dam impacts. Yet, only five studies (three temperate and two tropical) documented the effect of interventions (dam removal, flow management, artificial pond maintenance and community-based action). Conclusion These findings demonstrate a serious lack of documented evidence evaluating mitigation actions for dam impacts on freshwater turtles. Implications for Conservation This lack of evidence reinforces the importance of strengthening and maintaining robust long-term studies needed to develop effective and adaptive conservation actions for this group of threatened vertebrates particularly in tropical regions.

A preliminary study of 2-amino-4-aryl-3,5-dicarbonitrile-6-thiopyridines as new potential antimicrobial drugs was performed. Special emphasis was placed on the selection of the structure of target pyridine derivatives with the highest biological activity against different types of Gram-stained bacteria by lipopolysaccharide (LPS). Herein, Escherichia coli model strains K12 (without LPS in its structure) and R2–R4 (with different lengths of LPS in its structure) were used. Studied target compounds were provided with yields ranging from 53% to 91% by the lipase-catalyzed one pot multicomponent reaction of various aromatic aldehydes with malononitrile, and thiols. The presented work showed that the antibacterial activity of the studied pyridines depends on their structure and affects the LPS of bacteria. Moreover, the influence of the pyridines on bacteria possessing smooth and rough LPS and oxidative damage to plasmid DNA caused by investigated compounds was indicated. Additionally, the modification of the bacterial DNA with the tested compounds was performed to detect new potential oxidative damages, which are recognized by the Fpg protein. The obtained damage modification values of the analyzed compounds were compared with the modifications after antibiotics were used in this type of research. The presented studies demonstrate that 2-amino-4-aryl-3,5-dicarbonitrile-6-thiopyridines can be used as substitutes for known antibiotics. The observed results are especially important in the case of the increasing resistance of bacteria to various drugs and antibiotics.

Helicobacter pylori (H. pylori) is most known to cause a wide spectrum of gastrointestinal impairments; however, an increasing number of studies indicates that H. pylori infection might be involved in numerous extragastric diseases such as neurological, dermatological, hematologic, ocular, cardiovascular, metabolic, hepatobiliary, or even allergic diseases. In this review, we focused on the nervous system and aimed to summarize the findings regarding H. pylori infection and its involvement in the induction/progression of neurological disorders. Neurological impairments induced by H. pylori infection are primarily due to impairments in the gut–brain axis (GBA) and to an altered gut microbiota facilitated by H. pylori colonization. Currently, regarding a potential relationship between Helicobacter infection and neurological disorders, most of the studies are mainly focused on H. pylori.

Construction of hydropower dams is associated with negative impacts on biodiversity, yet there remains a lack of robust scientific evidence documenting the magnitude of these impacts particularly across highly biodiverse tropical waterways. Hydropower expansion is an increasing threat to the Endangered yellow-spotted river turtle (Podocnemis unifilis) across its tropical South American range.Yellow-spotted river turtle nesting areas were monitored as an indicator of dry season river level changes following run-of-river dam reservoir filling. A Before-After-Control-Impact (BACI) study design was used with multi-year field campaigns monitoring turtle nesting areas upstream of the dam.The cause and extent of changes in nesting areas were established using Generalized Additive Models. Nesting area density was evaluated in relation to: time (before versus after), treatment (control versus impact), time treatment interaction (BACI), distance to the dam and precipitation. The extent of changes was examined by comparing the proportion of nesting areas remaining during four years after reservoir filling.Dam construction generated an immediate and apparently permanent dry season river level rise that extended more than 20 km beyond impact assessment limits. On average the density of nesting areas declined 69% (from 0.48 to 0.15 per km) across 33 km of river directly impacted by the dam. This loss was reflected in a significant BACI interaction. Nesting area density was not explained by seasonal precipitation.Standardized monitoring of freshwater turtle nesting areas provided an effective means to quantify impacts of hydropower developments across biodiverse yet rapidly changing waterways. The negative impacts documented in this study should be preventable by mitigation actions including habitat creation and dry season flow regulation. Such measures would also likely benefit multiple species elsewhere in tropical rivers increasingly impacted by run-of-river dams.

Several mortality events involving barn swallows (Hirundo rustica) and cliff swallows (Petrochelidon pyrrhonota) were reported in the Upper Midwestern states in 2017 and 2018. Barn swallow mortality followed unseasonal cold snaps, with the primary cause of death being emaciation with concurrent air sac nematodiasis. Lesions in cliff swallows were consistent with blunt force trauma from suspected car impacts. Examination of air sac nematodes from both bird species revealed morphological characters consistent with Diplotriaena obtusa. Sequence analysis of the partial 18S rRNA gene indicated the samples clustered with other species in the genus Diplotriaena. These nematodes provide a link between morphological specimens and DNA sequence data for D. obtusa.

Hematopoietic cell lineages support organismal needs by responding to positional and systemic signals that balance proliferative and differentiation events. Drosophila provides an excellent genetic model to dissect these signals, where the activity of cues in the hemolymph or substrate can be traced to determination and differentiation events of well characterized hemocyte types. Plasmatocytes in third instar larvae increase in number in response to infection and in anticipation of metamorphosis. Here we characterize hemocyte clustering, proliferation and transdifferentiation on the heart or dorsal vessel. Hemocytes accumulate on the inner foldings of the heart basement membrane, where they move with heart contraction, and are in proximity to the heart ostia and pericardial nephrocytes. The numbers of hemocytes vary, but increase transiently before pupariation, and decrease by 4 h before pupa formation. During their accumulation at the heart, plasmatocytes can proliferate and can transdifferentiate into crystal cells. Serrate expressing cells as well as lamellocyte-like, Atilla expressing ensheathing cells are associated with some, but not all hemocyte clusters. Hemocyte aggregation is enhanced by the presence of a heart specific Collagen, Pericardin, but not the associated pericardial cells. The varied and transient number of hemocytes in the pericardial compartment suggests that this is not a hematopoietic hub, but a niche supporting differentiation and rapid dispersal in response to systemic signals.

The freshwater amphipod species Gammarus pulex (Linnaeus, 1758) is widespread across Europe and Asia and is able to live in a broad range of environmental conditions. Yet, it is of great interest to which degree it is able to tolerate and adapt to the current rapid anthropogenic environmental changes affecting its habitat, such as pollution, changes in river morphology, and invasions of alien gammarid species. Microsatellite primers for genetic population studies with G. pulex have been developed but due to the existence of several genetically different lineages within the species, the application of these primers is not always successful. In order to investigate the impacts of anthropogenic environmental changes on the spatio-genetic patterns of G. pulex lineage E in streams in the Saale river catchment in Germany, we designed eleven novel polymorphic microsatellites for this lineage using a high-throughput sequencing approach. These microsatellites enabled highly specific characterization of three closely related populations. The results show genetically distinct populations reflected by both a principal coordinates analysis and an analysis of molecular variance. Several of the newly designed microsatellite primers also enabled successful cross-amplification of the respective microsatellites in specimens of G. pulex lineage C, while only two microsatellites were amplified successfully and showed polymorphisms for all of the analyzed specimens of G. fossarum Koch, 1836. The microsatellites identified here are suitable for future assessments of micro-evolutionary dynamics of G. pulex from central Germany.

Plant diversity loss can alter higher trophic -level communities via non -random species interactions, which in turn may cascade to affect key ecosystem func-tions. These non -random linkages might be best captured by patterns of phyloge-netic diversity, which take into account co -evolutionary dependencies. However,lack of adequate phylogenetic data of higher trophic levels hampers our mecha-nistic understanding of biodiversity relationships in species-rich ecosystems.2. We used DNA barcoding to generate data on the phylogenetic diversity of lepi-dopteran caterpillars in a large- scale forest biodiversity experiment in subtropicalChina. We analysed how different metrics of lepidopteran phylogenetic diversity(Faith's PD, MPD, MNTD) and taxonomic diversity were influenced by multiple components of tree diversity (taxonomic, functional, phylogenetic).3. Our data from six sampling periods represent 7,204 mitochondrial cytochrome c oxidase subunit I (COI) sequences of lepidopteran larvae, clustered into 461 mo-lecular operational taxonomic units. Lepidopteran abundance, the effective num-ber of species (irrespective of the focus on rare or common species) and Faith's PD and MPD (reflecting basal evolutionary splits), but not MNTD (reflecting re-cent evolutionary splits), significantly increased with experimentally manipulated ree species richness. Lepidopteran MNTD decreased with increasing tree MNTD. Path analyses showed that tree phylogenetic and functional diversity explained part, but not all of the effects of tree species richness on lepidopteran diversity. Importantly, tree diversity effects on lepidopteran diversity were to a large extent indirect, operating via changes in lepidopteran abundance. 4. Synthesis. Our study shows that evolutionary dependencies determine the response of herbivore communities to changes in host plant diversity. Incorporating a wider range of diversity metrics both at the level of producers and consumers can thus help to develop a more comprehensive understanding of the functional consequences of biodiversity change across trophic levels. Moreover, the dependence of trophic linkages on herbivore abundances underlines the need to address the consequences of current declines in insect abundances for ecosystem structure and functioning. peerReviewed

OBJECTIVE The objective of this study was to determine the effects of age and gender (bull vs steer) on feeding behavior parameters in young beef cattle fed grass silage. METHODS The study was conducted on 180 young beef cattle at 7 to 18 mo of age. The experimental materials comprised 90 bulls produced by commercial crossing of Polish Holstein-Friesian cows with Charolais, Limousin and Hereford bulls (30 animals of each breed) and 90 steers of the same genotypes. The animals had ad libitum access to grass silage; the concentrate was fed separately, in feed stations. They received 28 g dry matter of concentrate per kg of metabolic body weight per day. Bunk visit data and silage intake for all experimental animals were recorded individually using the Roughage Intake Control system (5 feed bunks per 15 animals). RESULTS Age and gender (bull vs steer) exerted significant effects on the feeding behavior of young beef cattle. The frequency of bunk visits and meal frequency decreased, whereas the feeding rate of silage, and the average duration and size of a single meal increased with age (p

Experimental stroke studies yielded insights into single reactions of the neurovascular unit (NVU) and associated extracellular matrix (ECM). However, the extent of simultaneous processes caused by ischemia and their underlying transcriptional changes are still poorly understood. Strictly following the NVU and ECM concept, this study explored transcriptional responses of cellular and non-cellular components as well as their morphological characteristics following ischemia. Mice were subjected to 4 or 24 h of unilateral middle cerebral artery occlusion. In the neocortex and the striatum, cytoskeletal and glial elements as well as blood-brain barrier and ECM components were analyzed using real-time PCR. Western blot analyses allowed characterization of protein levels and multiple immunofluorescence labeling enabled morphological assessment. Out of 37 genes analyzed, the majority exhibited decreased mRNA levels in ischemic areas, while changes occurred as early as 4 h after ischemia. Down-regulated mRNA levels were predominantly localized in the neocortex, such as the structural elements α-catenin 2, N-cadherin, β-catenin 1, and βIII-tubulin, consistently decreasing 4 and 24 h after ischemia. However, a few genes, e.g., claudin-5 and Pcam1, exhibited increased mRNA levels after ischemia. For several components such as βIII-tubulin, N-cadherin, and β-catenin 1, matching transcriptional and immunofluorescence signals were obtained, whereas a few markers including neurofilaments exhibited opposite directions. In conclusion, the variety in gene regulation emphasizes the complexity of interactions within the ischemia-affected NVU and ECM. These data might help to focus future research on a set of highly sensitive elements, which might prospectively facilitate neuroprotective strategies beyond the traditional single target perspective.

Sustainable use as a mechanism for the conservation and recovery of exploited wildlife populations remains intensely debated, including for freshwater turtles, a diverse and imperilled group of aquatic reptiles that are an important food source for many residents of tropical regions. Here we evaluated the geographical extent of recovery options for a heavily exploited tropical freshwater turtle fauna across 8.86 M km2 of South American river catchments under Business-as-Usual (BAU), Protection (Pr) and Community-Based-Management (CBM) scenarios. For the widespread indicator species, Podocnemis unifilis, demographic analysis showed that populations subject moderate levels of female harvest (≤10%) can recover over broad areas if concurrent headstarting of hatchlings is practiced more widely. With regional strengthening of the protected area network unlikely, CBM developed with harvest frameworks derived from demographic rates appropriate to tropical species could catalyse a rapid continental scale recovery of Amazonian freshwater turtles within a few decades.

Background and aimsBesides well-defined genetic alterations, the dedifferentiation of mature acinar cells is an important prerequisite for pancreatic carcinogenesis. Acinar-specific genes controlling cell homeostasis are extensively downregulated during cancer development; however, the underlying mechanisms are poorly understood. Now, we devised a novel in vitro strategy to determine genome-wide dynamics in the epigenetic landscape in pancreatic carcinogenesis.DesignWith our in vitro carcinogenic sequence, we performed global gene expression analysis and ChIP sequencing for the histone modifications H3K4me3, H3K27me3 and H2AK119ub. Followed by a comprehensive bioinformatic approach, we captured gene clusters with extensive epigenetic and transcriptional remodelling. Relevance of Ring1b-catalysed H2AK119ub in acinar cell reprogramming was studied in an inducible Ring1b knockout mouse model. CRISPR/Cas9-mediated Ring1b ablation as well as drug-induced Ring1b inhibition were functionally characterised in pancreatic cancer cells.ResultsThe epigenome is vigorously modified during pancreatic carcinogenesis, defining cellular identity. Particularly, regulatory acinar cell transcription factors are epigenetically silenced by the Ring1b-catalysed histone modification H2AK119ub in acinar-to-ductal metaplasia and pancreatic cancer cells. Ring1b knockout mice showed greatly impaired acinar cell dedifferentiation and pancreatic tumour formation due to a retained expression of acinar differentiation genes. Depletion or drug-induced inhibition of Ring1b promoted tumour cell reprogramming towards a less aggressive phenotype.ConclusionsOur data provide substantial evidence that the epigenetic silencing of acinar cell fate genes is a mandatory event in the development and progression of pancreatic cancer. Targeting the epigenetic repressor Ring1b could offer new therapeutic options.

Summary Mute swans (Cygnus olor) of the Anatidae family are common in wetlands of Europe. They winter in Africa, Asia and some parts of Europe. The species is exposed to many pathogens in its places of residence, including parasites possibly introduced from tropical countries by other species of birds that take long wanderings and occupy a similar ecological niche. One such case is the infection of the Sarconema eurycerca, nematode belonging to the Filarioidea family. It invades the bird’s myocardium and, according to some authors, this nematode may be one of the main causes of swans’ deaths. The material for the present study was an approximately 2 year old female mute swan, which during the flight fell suddenly to the ground in Pomorskie Voivodeship (Poland, 53°50′18″N 18°12′54″E) in November. During the examination and medical observation, weakness, diarrhea and infestation with lice were found. The cause of its eventual death was attributed to a failure of the circulatory system. Post mortem, two abscesses with diameters of 2-3 cm were found in its liver parenchyma. Three nematodes were visible in the epicardium and many more in myocardium. Upon cutting open the heart, small yellowish foci, about 1 mm in diameter were scattered over valves. On the basis of morphological features, infection by Sarconema eurycerca was concluded. As far as we are aware, in Poland there were no earlier reports of this parasite infecting a swan.

Background. The somatic features of the athletes’ bodies partially determine their sporting level and are conditioned to a large extent by the state of nutrition. Objective. The aim of this paper is to present nutritional status and its correlation with the somatic determinants of training athletes and physical education students. Material and methods. This study involved 12 weightlifting players (subgroup-WL), 15 soccer players (subgroup-SP), 12 table tennis players (subgroup-TT) and 12 female students of physical education (subgroup-C). In all subjects, the age and somatic variables were recorded and the daily intake of energy, water, proteins, fats and carbohydrates was determined by 24-h dietary recalls. Results. Although the analysis of variance did not show significant differences in somatic variables and nutrition data, post hoc analysis showed significant differences between some subgroups in terms of age, BMI, fat content (BF), fat-free mass (FFM) and the amount of water, protein and carbohydrates consumed during the day. It was also shown that somatic variables correlated with relatively expressed amounts of energy, proteins and carbohydrates consumed in individual subgroups, as well as in the whole group formed from all subgroups of studied women. In addition, there were significant correlations between somatic variables and the total amount of water consumed in the whole group and the total amount of protein consumed in subgroup C (p

There are six described pathotypes of Escherichia coli that cause significant clinical illness in humans. Enteroinvasive E. coli (EIEC) strains have been shown to be separated into three phylogenomic clades. To add to a limited body of EIEC genomic data, we report two high-quality draft genomes representing different EIEC phylogenomic clades.

OBJECTIVES: Dietary synthetic emulsifiers have recently been shown to promote metabolic syndrome and alter gut microbiota. The effects of natural emulsifiers, such as vegetable lecithin, remain, however, poorly described. Our objective was to evaluate, in mice, the impact of soy and rapeseed lecithin, both rich in essential α-linolenic acid (ALA), when incorporated in high-fat (HF) Western diets on the bioavailability of ALA, as well as on HF-induced adiposity, inflammation and gut microbiota. METHODS: For 13 weeks, male Swiss mice (n = 72) were fed either a standard Chow diet, a control semi-synthetic HF-diet (25 wt% lipids) poor in ALA (HFC), or different ALA-enriched (4.7% of total fatty acids) HF-diets containing 0% lecithin (HFA-L0), a nutritional dose of soy or rapeseed lecithin (10 wt% of lipids; HFA-SL10, HFA-RL10), or a 20 wt% supplemental dose of RL (HFA-RL20). Histomorphology of the epididymal adipose tissue (EAT) was analysed; hepatic lipid composition was determined by GC-FID, gene expression by RT-PCR, and faecal microbiota composition by 16S sequencing. RESULTS: Within ALA-rich HF diets, the hepatic bioavailability of ALA was similar whether ALA was vectorised as lecithin (HFA-RL10, HFA-RL20, HFA-SL10) or as oil only (HFA-L0) (yet, all higher than HFC). Similarly to HFC, HFA-SL10 and HFA-RL20, but not HFA-RL10, increased body weight gain (P

Cas endonuclease-mediated genome editing provides a long-awaited molecular biological approach to the modification of predefined genomic target sequences in living organisms. Although cas9/guide (g)RNA constructs are straightforward to assemble and can be customized to target virtually any site in the plant genome, the implementation of this technology can be cumbersome, especially in species like Triticale that are difficult to transform, for which only limited genome information is available and/or which carry comparatively large genomes. To cope with these challenges, we have pre-validated cas9/gRNA constructs (1) by frameshift restitution of a reporter gene co-introduced by ballistic DNA transfer to barley epidermis cells, and (2) via transfection in Triticale protoplasts followed by either a T7E1-based cleavage assay or by deep-sequencing of target-specific PCR amplicons. For exemplification, we addressed the Triticale ABA 8’-hydroxylase 1 gene, one of the putative determinants of pre-harvest sprouting of grains. We further show that in-del induction frequency in Triticale can be increased by TREX2 nuclease activity, which holds true for both well- and poorly performing gRNAs. The presented results constitute a sound basis for the targeted induction of heritable modifications in Triticale genes.

This study was carried out in north-eastern Poland during two hunting seasons between 2018 and 2020. Ticks (Ixodes ricinus and Dermacentor reticulatus) were removed from wild cervids and boars and examined for the presence of Borrelia spirochetes and Rickettsiales members: Rickettsia spp. and Anaplasma phagocytophilum. The present study contributes to the knowledge of even-toed ungulates, which are an important reservoir of the above-mentioned pathogens and a potential source of infections for humans through ticks as vectors. Almost 40% of the collected ticks (191 out of 484) were infected with the following pathogens: 3.3% with Borrelia spp., 19.2% with A. phagocytophilum and 26.9% with Rickettsia spp. Only the ticks collected from cervids carried Borrelia. Typing of the species DNA confirmed the presence of B. afzelii, B. garinii, B. lusitaniae and B. miyamotoi. An analysis of Rickettsia spp. sequences using the GenBank data revealed the presence of R. helvetica, R. raoultii and R. monacensis. Monoinfections (79.1%) dominated over co-infections (20.9%). Among co-infections, the most frequent was A. phagocytophilum/Rickettsia spp. (70%), however co-infections, including B. afzelii/A. phagocytophilum, B. afzelii/Rickettsia spp., B. miyamotoi/A. phagocytophilum and B. afzelii/B. garinii/B. lusitaniae, were also noted. Significant differences were observed in the affinity of some pathogens to their vectors. Thus, Borrelia spp. and A. phagocytophilum were more frequently detected in I. ricinus (5.3% and 23.1%) than in D. reticulatus (1.2% and 15.3%). Infection frequency with Rickettsia spp. was similar (approximately 25–29%) in both tick species. The prevalence of A. phagocytophilum and Rickettsia spp. in ticks removed from cervids was 19.8% and 27.1%, and in ticks from wild boars it was 13.3% and 24.4%, respectively.

Development of cervical cancer is directly associated with integration of human papillomavirus (HPV) genomes into host chromosomes and subsequent modulation of HPV oncogene expression, which correlates with multi-layered epigenetic changes at the integrated HPV genomes. However, the process of integration itself and dysregulation of host gene expression at sites of integration in our model of HPV16 integrant clone natural selection has remained enigmatic. We now show, using a state-of-the-art ‘HPV integrated site capture’ (HISC) technique, that integration likely occurs through microhomology-mediated repair (MHMR) mechanisms via either a direct process, resulting in host sequence deletion (in our case, partially homozygously) or via a ‘looping’ mechanism by which flanking host regions become amplified. Furthermore, using our ‘HPV16-specific Region Capture Hi-C’ technique, we have determined that three-dimensional (3D) interactions between the integrated virus genome and host chromosomes, both at short- (500 kbp), appear to drive host gene dysregulation through the disruption of local host:host 3D interactions known as topologically associating domains (TADs). This mechanism of HPV-induced host gene expression modulation indicates that integration of virus genomes near to or within a ‘cancer-causing gene’ is not essential to influence such genes within an entire TAD and that these modifications to 3D interactions could have a major role in selection of HPV integrants at the early stage of cervical neoplastic progression.

Anthropogenic micropollutants alter chemical and ecological conditions of freshwater ecosystems and impact aquatic species that live along the pollution gradient of a river. Species sensitivity to micropollutants depends on the site-specific exposure; however, it remains unclear to what degree this sensitivity relates to the species' genetic structure. Here, we explored the relationship between the toxic sensitivity and genetic structure of the amphipod species Gammarus pulex (Linnaeus, 1758) along an organic micropollutant gradient in the Holtemme River in central Germany. We determined the river's site-specific micropollutant patterns and analyzed the genetic structure of G. pulex using nuclear and mitochondrial genetic markers. Furthermore, we examined the exposure sensitivities and bioaccumulation of the commonly detected insecticide imidacloprid in G. pulex from different sites. Our results show that throughout the Holtemme River, G. pulex forms a well-connected and homogeneous population with no observable pollution-related differences in the genetic structure. However, G. pulex from polluted sites responded more sensitively to imidacloprid; survival times for half of the amphipods were up to 54% shorter, the percentage of immobile individuals increased up to 65%, and the modeled imidacloprid depuration rate was lower in comparison to amphipods from non-polluted sites. Altogether, these results suggest that the level of sensitivity of G. pulex amphipods to micropollutants in the river depends on the degree of pollution: amphipods may thrive in food-rich but polluted habitats; yet, their sensitivity is increased when chronically exposed to organic micropollutants.

The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds of kilobases in length. Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. We used whole-genome sequencing data produced by three PacBio protocols (Sequel II CLR, Sequel II HiFi, RS II) and two ONT protocols (Rapid Sequencing and Ligation Sequencing) to compare assemblies of the bacteria Escherichia coli and the fruit fly Drosophila ananassae. In both organisms tested, Sequel II assemblies had the highest consensus accuracy, even after accounting for differences in sequencing throughput. ONT and PacBio CLR had the longest reads sequenced compared to PacBio RS II and HiFi, and genome contiguity was highest when assembling these datasets. ONT Rapid Sequencing libraries had the fewest chimeric reads in addition to superior quantification of E. coli plasmids versus ligation-based libraries. The quality of assemblies can be enhanced by adopting hybrid approaches using Illumina libraries for bacterial genome assembly or polishing eukaryotic genome assemblies, and an ONT-Illumina hybrid approach would be more cost-effective for many users. Genome-wide DNA methylation could be detected using both technologies, however ONT libraries enabled the identification of a broader range of known E. coli methyltransferase recognition motifs in addition to undocumented D. ananassae motifs. The ideal choice of long read technology may depend on several factors including the question or hypothesis under examination. No single technology outperformed others in all metrics examined.