Pooled Samples Research Articles

Genetic Variation in Jamaican Populations of the Coffee Berry Borer, Hypothenemus hampei.

The coffee berry borer (CBB) Hypothenemus hampei was first described in Africa in 1867 and has spread to all major coffee-producing regions worldwide, including Jamaica. Using long-read sequencing, we produced a new high-quality reference genome (172.7 Mb) for the Jamaican strain of the CBB, with 93% of the genome assembled into 14 scaffolds. Whole genome sequencing of pooled samples from different populations across Jamaica showed that the CBB harbors low levels of genetic diversity alongside an excess of low-frequency alleles, indicative of a recent genetic bottleneck. The analyses also showed a recent surge in the activity of transposable elements (TEs), particularly LINE/R1 and LTR/Gypsy elements, within CBB populations. Our findings offer first insights into the evolutionary genomics of CBB populations in Jamaica, highlighting the potential role of TEs in shaping the genome of this important pest species.

Exploring the hemp virome and assessing hemp germplasm for resistance to an emerging pathogen

Hemp (Cannabis sativa L., <0.3% tetrahydrocannabidiol, THC) as a crop has been widely adopted throughout the United States. However, there is little support or guidance on disease identification and management for growers. This study aimed to describe the diversity and distribution of viruses infecting hemp in Colorado and determine if there is genetic resistance to pathogens in hemp. Throughout 2021 and 2022, leaf tissues from symptomatic and asymptomatic plants were sampled during three phenological stages (early vegetative, late vegetative, and mature flowering) in four regions of Colorado. High Throughput Sequencing (HTS) revealed a total of seven viruses across both years from 48 pooled samples: alfalfa mosaic virus, beet curly top virus (BCTV), cannabis cryptic virus, cannabis sativa mitovirus 1, grapevine line pattern virus, opuntia umbra-like virus, and tomato bushy stunt virus. These viruses had >97% nucleotide identity to their nearest GenBank accessions. As the growing season progressed, viral incidence and the number of viral species increased. We observed similar and unique viromes between individual cultivars from the same field. Given the prevalence of BCTV in the virome and its prevalence across the western United States, 13 genotypes of hemp were screened for resistance to this pathogen. Two genotypes (4587 and 4710) had a lower BCTV copy number and disease index than others. Our study provides initial evidence of the diversity of viral communities in hemp across Colorado and provides impetus for developing accurate detection methods and screening for host resistance.

Trends of Benzotriazoles and Benzothiazoles in Australian Pooled Urine Samples from 2012 to 2023.

Benzotriazoles (BZTs) and benzothiazoles (BTs) are high-production-volume chemicals utilized in many different commercial products and industrial processes, such as metal corrosion inhibitors, vulcanization accelerators, plastic-associated UV stabilizers, and pharmaceutical precursors. This study assessed age, gender, and temporal trends of BZTs and BTs in deidentified surplus pathology urine samples, pooled and stratified by age, gender, and sample collection year from a general Australian population (168 pools representing 16,800 individuals). Tolyltriazole (TTri), 5,6-dimethyl-1H-benzotriazole (DMBZT), 1,3-benzothiazole (BTH), 2-hydroxybenzothiazole (2-OH-BTH), and 2-aminobenzothiazole (2-amino-BTH) were detected in >50% of the pools. TTri was frequently detected in pooled samples representing ≤45-year-olds (both genders). Concentrations of DMBZT, BTH (females), 2-OH-BTH, and 2-amino-BTH (females) increased with age significantly, with adults (>15 years old) showing higher levels than children (≤15 years old). Gender differences in DMBZT concentrations (females > males) were observed across all sampling years and only in some for TTri (males > females: >45 years old), BTH (females > males), and 2-amino-BTH (males > females). A temporal increase in BTH, 2-OH-BTH, and 2-amino-BTH levels within the studied period (2012-2023) has been observed. Our findings suggest ongoing exposure of the Australian general population to BZTs and BTs, highlighting age, gender, and temporal trends of these compounds as measured via their urinary concentrations.

Human-swine interface: is the hepatitis E virus a real risk for humans?

Abstract Background Hepatitis E virus (HEV) is the agent of hepatitis E, an emerging public-health infection with an increasing incidence in Europe. Due to the apparent lack of species barriers, HEV is considered a zoonotic agent, with swine as the main reservoir. This study investigated HEV prevalence in humans and domestic pigs in Northern Italy, a highly anthropic area with the highest pig farm density, to gain insights into the risk of HEV transmission from swine to humans. Methods A total of 508 blood samples were collected from blood donors (341 males and 167 females; from 18 to 66 years old) and from 1619 pigs in 40 different farms. Serological analyses were performed with ELISA to detect anti-HEV antibodies. In addition, 120 faecal pool samples collected from the pig farms with the highest seroprevalence and 69 salami produced in the same area were analysed to detect viral genome by Real-time PCR. Results In humans, HEV seroprevalence was 4.9% (CI95% 0.03-0.07); positive donors were mainly males, with seroprevalence increasing up to 12% (CI95% 0.09-0.15) in the 46-55 age group. Seroprevalence in swine was 53.00% (CI95% 0.50-0.55), with HEV detected in only 1% (CI95% 0.001-0.045) faeces. All food samples tested negative. Conclusions Even if the seroprevalence in pigs highlighted that HEV was actively circulating in the farms, the low seroprevalence in humans, the scarce HEV detection in swine faeces, and the absence in food products suggested that HEV transmission via faecal-oral or foodborne routes is unlikely, probably due to the implementation of severe biosecurity measures and high standards of hygiene in swine farms, and the continuous assessment of the critical points in the pig supply chain (from farm to fork). The serological surveillance of humans and the monitoring of farmed animals are needed to support the competent authorities in timely managing public health issues, improving human health and veterinary safety from a One Health perspective. Key messages • In the human-swine interface is important to monitor HEV presence. • The One Health approach is essential to control zoonotic diseases.

Current-use pesticide exposures in remote Inuit communities

ABSTRACT The global use of pesticides is increasing; however, few studies have examined the exposure of current-use pesticide exposure in Inuit populations. Some current use pesticides are also capable of long-range transport, potentially increasing exposures to northern populations. The study aim was to analyse pesticide (chlorophenoxy, organophosphates, and pyrethroid pesticide) biomarker levels in pooled samples from an Inuit population in Nunavik, Quebec. Thirty pooled samples from the Qanuilirpitaa? 2017 survey (Q2017) from individuals aged 16–80 years were included. Creatinine-adjusted arithmetic (AM) were compared by sex, age, and region sub-groups, and geometric mean concentrations (GM) were compared to those in the Canadian Health Measures Survey (CHMS). Most analysed pesticide biomarkers were detected, and PNP (a metabolite of methyl and ethyl parathion), trans-DCCA (a metabolite of pyrethroids), and 3,5,6-TCP (a metabolite of chlorpyrifos) had the highest concentrations. Concentrations in Q2017 were largely similar to or less than CHMS concentrations. Although not significant, there was a general increase in 2,4-D (a chlorophenoxy biomarker), 3,5,6-TCP, 3-PBA (a metabolite of pyrethroids), and trans-DCCA with increasing age. Concentrations were also somewhat higher in females versus males, but these were not significant. Environmental exposures to current use pesticides were detected in Nunavik and concentrations were similar to or less than those in the general Canadian population. Regular monitoring of current use pesticide exposures is recommended given the increasing global use of pesticides.

Determining diagnostic sensitivity loss limits for sample pooling in duplex rtPCR surveillance testing: Theileria orientalis and Anaplasma marginale.

To expand surveillance testing capacity through sample pooling, a thorough understanding is needed of how sample dilution through pooling affects the sensitivity of candidate assays. We validated a robust and representative framework for assessing the dilution effect of sample pooling using duplex rtPCR surveillance of Theileria orientalis and Anaplasma marginale, both of which are causative agents of severe anemia in cattle and a serious threat to the cattle industry in Virginia and many other states. We used 200 known-positive samples with Ct values representative of typical surveillance results in a series of pools in which we re-tested each sample individually, followed by each sample diluted in equal volumes with negative samples to make pools of 2, 4, 6, 8, and 10 total samples. We compared the Ct values of the individual positives with the Ct values of each pool size to determine if Ct values increase past the limit of detection in the 45-cycle assay. We observed a maximum of 2% sensitivity loss (no more than 2 of 100 samples returned a false-negative result) for both T. orientalis and A. marginale during the pooling series, with lower-than-expected average Ct increase and sensitivity loss. We conclude that pooling up to 10 samples would be acceptable for regional surveillance of T. orientalis and A. marginale using our rtPCR assay. The described strategy is applicable to validate pooling for a wide range of single and duplex rtPCR assays, which could expand efficient disease surveillance.

First Description of Loreto Virus in Three Culicidae Species from the Atlantic Forest, Bahia, Brazil

Loreto virus (LORV) is an insect-specific virus classified into the proposed taxon Negevirus. It was originally described in Iquitos, Peru, in 1977. Here, we describe three novel LORV genomes obtained from the isolates of three pooled samples of Trichoprosopon digitatum, Aedes (Ochlerotatus) fulvus, and Limatus durhamii collected in Ilhéus—Bahia, 2014. Samples were submitted to RNA sequencing on the Illumina platform to recover the LORV genome. The genomes presented, on average, 81.5% nucleotide identity and 92.6% global amino acid identity with the LORV reference genome (NC_034158). Subsequently, phylogenetic analysis was performed based on a multiple sequence alignment of the concatenated amino acid sequences predicted for the three ORFs of the Negevirus genomes, and the target sequences were clustered within the LORV clade. The taxon Negevirus is in constant expansion of its species content and host range. New data about insect specific negeviruses are important for virus evolution studies, along with those approaching interactions with the hosts and their influence in the transmission of arboviruses. Also, the assessment of these data may allow the development of biologic control strategies for arboviral vectors. This is the original report of the identification of LORV in Brazil, infecting three Culicidae species hosts native to the Atlantic Forest biome.

Evaluation of Fecal Sample Pooling for Real-Time RT-PCR Testing SARS-CoV-2 in Animals

During the COVID-19 pandemic, veterinary diagnostic laboratories tested both human and animal samples and needed to ensure that they could accurately perform large numbers of diagnostic tests in a timely manner. Sample pooling, a methodology used effectively for over 80 years as a surveillance tool for screening large numbers of potentially infected individuals, was employed. Given its sensitivity, real-time polymerase chain reaction (PCR) is more suitable for employing this strategy, as compared to other less sensitive testing methods. In this study, we evaluated the capability of detecting SARS-CoV-2 in both 5-sample and 10-sample pools of feces using real-time reverse transcriptase polymerase chain reaction (rRT-PCR) as well as determined the level of sensitivity. A blinded method test (BMT) by an independent laboratory was conducted to assess the five-sample fecal pool. To complement detection capability, the stability of the genome within a PBS fecal suspension was measured under various time and temperature conditions across a 28-day period. Our results showed that the limit of detection for 5-sample and 10-sample fecal pools is 12.8 and 6.4 genome copies in a 25 µL PCR, respectively. The 5-sample and 10-sample pooling resulted in a cycle threshold (Ct) value loss of 2.35 and 3.45, as compared to Ct values of known positive individual samples, but consistent detection was still achieved in pools containing positive samples with an original Ct below 36 and 34, respectively. The simulation of clinical five-sample pooling showed that all positive samples could be detected regardless of the number (1–3) of positive samples in each pool. The BMT results demonstrated excellent sensitivity (100 copies/reaction) in five-sample pools for the detection of SARS-CoV-2 RNA even though a fecal matrix effect was observed. Finally, our results show that the SARS-CoV-2 genome remains stable over a wide range of time and temperature variations. Overall, our findings provide solid data to scale up SARS-CoV-2 testing capacity in veterinary diagnostic laboratories.

A spatial matrix factorization method to characterize ecological assemblages as a mixture of unobserved sources: An application to fish eDNA surveys

Abstract Understanding how ecological assemblages vary in space and time is essential for advancing our knowledge of biodiversity dynamics and ecosystem functioning. Metabarcoding of environmental DNA (eDNA) is an efficient method for documenting biodiversity changes in both marine and terrestrial ecosystems. However, current methods fail to detect and display the biodiversity structure within and between eDNA samples limiting ecological and biogeographical interpretations. We present a spatial matrix factorization method that identifies optimal eDNA sample assemblages—called pools—assuming that taxonomic unit composition is based on a fixed number of unknown sources. These sources, in turn, represent taxonomic units sharing similar habitat properties or characteristics. The method aims to reduce the multi‐taxa composition structure into a low number of dimensions defined by these sources. This method is inspired by admixture analysis in population genetics. Using a marine fish eDNA survey on 263 sampling stations detecting 2888 molecular operational taxonomic units (MOTUs), we apply this method to analyse the biogeography and mixing patterns of fish assemblages at regional and large scales. At large scale, our analysis reveals six primary pools of fish samples characterized by distinct biogeographic patterns, with some mixtures between these pools. We identify pools composed of unique sources, corresponding to distinct and more isolated regions such as the Mediterranean and Scotia Seas. We also identify pools composed of a greater mix of sources, corresponding to geographically connected areas, such as tropical regions. Additionally, we identify the taxa underpinning the formation of each pool. In the regional analysis of Mediterranean eDNA samples, our method successfully identifies different pools, allowing the detection of not only geographic gradients but also human‐induced gradients corresponding to protection levels. Spatial matrix factorization adds a new method in community ecology, where each sample is considered as a mixture of K unobserved sources, to assess the dissimilarity of ecological assemblages revealing environmental and human‐induced gradients. Beyond the study of fish eDNA samples, this method has the potential to shed new light on any biodiversity survey and provide new bioindicators of global change.

Novel goose parvovirus in naturally infected ducks suffering from locomotor disorders: Molecular Detection, Histopathological examination, Immunohistochemical signals, and Full genome sequencing

In this study, we investigated the pathological effect of novel goose parvovirus (NGPV) infection on the skeletal muscle, brain, and intestine of naturally affected ducks suffering from locomotor dysfunction as a new approach for deeper understanding of such clinical form. For this purpose, a total of 97 diseased ducks, representing 24 flocks of different duck breeds (14-75 days old), were clinically examined. 72 tissue pools of intestine, brain, and skeletal muscle samples were submitted for molecular identification. Typical clinical signs among the examined ducks suggested the parvovirus infection. Regarding postmortem examination, all examined ducks showed muscle emaciation (100%) either accompanied by congestion (34%) or paleness (66%). Slight congestion, either in the brain (82.5%) or intestine (75.25%), was predominantly detected. Based on molecular identification, the intestine had the highest percentage of positive detection (91.7%), followed by the skeletal muscle (70.8%), and the brain (20.8%). The main histopathological alterations were myofiber atrophy and degeneration, marked enteritis accompanied by lymphocytic infiltration in the lamina propria and submucosa, while the affected brains showed vasculitis, diffuse gliosis, and Purkinje cell degeneration in the cerebellum. Next generation sequencing further confirmed the presence of a variant strain of goose parvovirus (vGPV) that is globally known as NGPV and closely related to Chinese NGPV isolates. Using immunohistochemistry, the NGPV antigen was positively detected in the muscle fibres, enterocytes, and Purkinje cells in the cerebellum. These findings provided proof of the involvement of virus replication in the locomotor disorders linked to NGPV infection in ducks.

Internal validation of the Precision ID GlobalFiler NGS STR panel v2 kit with locus-specific analytical threshold, and with special regard to mixtures and low template DNA detection

We performed an internal laboratory validation of the Precision ID GlobalFiler NGS STR panel v2 kit to assist the introduction of the technology into the routine forensic casework practice. The study was designed and evaluated based not only on the key validation standards like sensitivity, stability, reproducibility, repeatability, mixture, and concordance, but we also tested the effect of reduced input DNA, we measured and applied locus-specific analytical threshold values, tested two different PCR cycle conditions, sequence artifacts and stutters were also analysed. During the study we also tested the new method on real casework samples. The sensitivity study confirmed that adding 500 pg template DNA for library preparation can be optimal at base PCR cycle number (that was 24), because the measured average heterozygote balance was not lower than 0.82, and each allele was detected above the analytical threshold. However, contrary to previous communications, increasing the PCR cycle numbers up to 28 has not resulted the significant elevation of the heterozygote imbalance. According to our results, raised PCR cycle condition (i.e. 28) is appropriate at or below 150 pg total input DNA. For most loci, the calculated AT was lower than the manufacturer’s recommended. Applying the newly established ATs with raised PCR cycle conditions the allele detection sensitivity and reliability increased. We observed allele dropouts only at the 15 pg template DNA experiments with 5 % frequency, that is better to previously published studies. This result indicates that this low amount of DNA (i.e. 15 pg) could be a minimum limit of template input for a potentially successful analysis. In the mixture study the minor contributor could be detected up to 1:19 mixture ratio. We detected minor alleles in all measurements and concentrations above the threshold if the template DNA were fixed and only SNP differences were observed between the same alleles of the contributors. To test concordance between the new method and traditional STR genotyping we analysed 58 Hungarian individual samples in parallel. Nearby the detected 248 different length-based alleles on the 31 loci in the sample pool we revealed additional 75 sequence variant alleles, that represent an approximately 23 % increase in the total number of observed alleles. The casework study confirmed that the Precision ID GlobalFiler NGS STR panel v2 kit is effective even in genotyping degraded samples with extremely low levels of DNA, if we apply elevated cycle number for library preparation and use locus-specific analytical thresholds.

Bayesian evidence for the neural dissociation between finger and hand imitation skills

Abstract For limb apraxia ‒ a heterogeneous disorder of higher motor cognition following stroke ‒ an enduring debate has arisen regarding the existence of dissociating neural correlates for finger and hand gestures in the left hemisphere. We re-assessed this question asking whether previous attempts analysing pooled samples of patients with deficits in only one and patients with deficits in both imitation types might have led to systematically biased results. We conducted frequentist and Bayesian, voxelwise, and regionwise lesion symptom mappings on (i) the full sample (N=96) in which all patients with hand and/or finger imitation apraxia as well as without apraxia were included and (ii) three sub-samples, which excluded those patients from the full sample showing isolated hand imitation deficits, isolated finger imitation deficits or shared (finger and hand) imitation deficits. Anatomical analyses revealed a cortical dissociation of finger imitation deficits (located more anteriorly) and of hand imitation deficits (located more posteriorly). The presence of patients with shared deficits did indeed dilute associations that appeared stronger in the respective isolated samples. Also, brain regions truly associated with hand imitation deficits showed a positive bias for finger imitation deficits, when the sample contained patients with shared deficits. In addition, our frequentist parameters uncovered that some of our Bayesian evidence supported reverse associations (damage protecting from rather than increasing the deficit). Anatomo-behavioral analyses that analyse patients with shared (hand and finger) and isolated (hand or finger) imitation deficits together in one sample do indeed lead to undesirable biases. This explains why some earlier studies failed to detect the apparent neural dissociation between hand and finger imitation deficits.

Human Schistosomiasis due to Schistosoma bovis in Nigeria.

Schistosomiasis is a global public health challenge, especially in sub-Saharan Africa, where Nigeria has the highest burden of disease. Schistosoma hybrids have been discovered in various countries, including Nigeria, where livestock and human beings share common water resources. This study, carried out in three communities, two of which are endemic for urinary schistosomiasis, aimed to identify the urinary schistosomiasis causative agent by using a species-specific molecular technique and their evolutionary relationship. Polymerase chain reaction using primers specific for a partial DNA sequence of the mitochondrial cox1 gene of Schistosoma haematobium was carried out on pooled urine sediments preserved in 70% ethanol. DNA from the high-intensity pooled samples from Onye-Uku camp amplified, and a BLAST search identified the pooled samples as Schistosoma bovis, whereas S. haematobium DNA did not amplify. The phylogenetic relationship of the sequence showed that it clustered with an S. bovis hybrid obtained from a human host in Côte d'Ivoire and had close ancestry with isolates from cattle in Cameroon. This finding revealed the prevalence of S. bovis among some inhabitants in a zone in Nigeria where schistosomiasis is endemic.

Occurrence and Fate of Fluoroalkyl Sulfonamide-Based Copolymers in Earthworms-Bioavailability, Transformation, and Potential Impact of Sludge Application.

To date, considerable knowledge and data gaps regarding the occurrence, environmental levels, and fate of polymeric perfluoroalkyl and polyfluoroalkyl substances (PFAS) exist. In the present study availability, accumulation, and transformation of C4- and C8-fluoroalkylsulfonamide (FASA)-based copolymers were assessed in laboratory-grown earthworms (Eisenia fetida, triplicate of exposure tests and control). Further, a field study on earthworms (18 pooled samples) in sludge-amended soil was conducted to assess the environmental impact of sludge-amended soil with regard to the FASA-based copolymers, together with the applied sludge (n = 3), and the field soils during the period (n = 4). In the laboratory study, the FASA-based copolymers were taken up by the earthworms in concentrations between 19 and 33 ng/g of dw for the C8- and between 767 and 1735 ng/g of dw for the C4-FASA-based copolymer. Higher biota soil accumulation factors (BAFs) were observed for the copolymer with a longer perfluorinated side-chain length (C8, average BAF value of 0.7) compared to the copolymer with a shorter side-chain length (C4, average BAF value of 0.02). Perfluorooctane sulfonamidoacetates (FOSAAs) and perfluorooctane sulfonamide (FOSA), including both branched and linear isomers, were detected after exposure to the C8-FASA-based copolymer. Two metabolites were detected in the earthworms exposed to the C4-FASA-based copolymer: perfluorobutanesulfonamide (FBSA) and perfluorobutanesulfonic acid (PFBS). Although the presence of other monomers or impurities in the copolymer formulation cannot be ruled out, the present laboratory study suggests that the FASA-based copolymers may be an indirect source of lower molecular weight PFAS in the environment through transformation. Elevated levels of C8-FASA-based copolymer were found in the field sludge-amended soil compared to nontreated soil (32 versus 11 ng/g d.w.), and higher concentrations of PFAS in earthworms living in sludge-amended soil compared to nontreated soil (566 versus 103 ng/g d.w.) were observed. These findings imply that the application of sludge is a potential pathway of PFAS to the environment.

Application of a new highly multiplexed amplicon sequencing tool to evaluate Plasmodium falciparum antimalarial resistance and relatedness in individual and pooled samples from Dschang, Cameroon.

Resistance to antimalarial drugs remains a major obstacle to malaria elimination. Multiplexed, targeted amplicon sequencing is being adopted for surveilling resistance and dissecting the genetics of complex malaria infections. Moreover, genotyping of parasites and detection of molecular markers drug resistance in resource-limited regions requires open-source protocols for processing samples, using accessible reagents, and rapid methods for processing numerous samples including pooled sequencing. P lasmodium falciparum S treamlined M ultiplex A ntimalarial R esistance and R elatedness T esting ( Pf -SMARRT) is a PCR-based amplicon panel consisting of 15 amplicons targeting antimalarial resistance mutations and 9 amplicons targeting hypervariable regions. This assay uses oligonucleotide primers in two pools and a non-proprietary library and barcoding approach. We evaluated Pf -SMARRT using control mocked dried blood spots (DBS) at varying levels of parasitemia and a mixture of 3D7 and Dd2 strains at known frequencies, showing the ability to genotype at low parasite density and recall within-sample allele frequencies. We then piloted Pf -SMARRT to genotype 100 parasite isolates collected from uncomplicated malaria cases at three health facilities in Dschang, Western Cameroon. Antimalarial resistance genotyping showed high levels of sulfadoxine-pyrimethamine resistance mutations, including 31% prevalence of the DHPS A613S mutation. No K13 candidate or validated artemisinin partial resistance mutations were detected, but one low-level non-synonymous change was observed. Pf -SMARRT's hypervariable targets, used to assess complexity of infections and parasite diversity and relatedness, showed similar levels and patterns compared to molecular inversion probe (MIP) sequencing. While there was strong concordance of antimalarial resistance mutations between individual samples and pools, low-frequency variants in the pooled samples were often missed. Overall, Pf -SMARRT is a robust tool for assessing parasite relatedness and antimalarial drug resistance markers from both individual and pooled samples. Control samples support that accurate genotyping as low as 1 parasite per microliter is routinely possible. Malaria remains a critical global public health problem. Antimalarial drug resistance has repeatedly undermined control and the emergence of artemisinin partial resistance in Africa is the latest major challenge. Malaria molecular surveillance (MMS) has emerged as a powerful tool to monitor molecular markers of resistance and changes in the parasite population. Streamlined methods are needed that can be readily adopted in endemic countries. We developed P lasmodium falciparum S treamlined M ultiplex A ntimalarial R esistance and R elatedness T esting ( Pf -SMARRT), a multiplex amplicon deep sequencing approach that uses easily accessible products without proprietary steps and can be sequenced on any Illumina sequencer. We validated this tool using controls, including mocked dried blood spots, and then implemented it to evaluate resistance and parasite relatedness among 100 samples from Cameroon. The assay was able to reliably assess the within-sample allele frequency of antimalarial resistance markers and discriminate strains within and between individuals. We also evaluated a more cost-effective surveillance approach for antimalarial resistance polymorphisms using pooled samples. While within-pool frequencies of mutations were accurate in pools with higher numbers of samples, this resulted in the loss of the ability to detect variants uncommon in the pool. Overall Pf- SMARRT provides a new protocol for conducting MMS that is easily implementable in Africa.

Full-Length Transcriptome Profile of Apis cerana Revealed by Nanopore Sequencing

The Asian honey bee (Apis cerana) plays a crucial role in providing abundant bee products and in maintaining ecological balance. Despite the availability of the genomic sequence of the Asian honey bee, its transcriptomic information remains largely incomplete. To address this issue, here we constructed three pooled RNA samples from the queen, drone, and worker bees of A. cerana and performed full-length RNA sequencing using Nanopore single-molecule sequencing technology. Ultimately, we obtained 160,811 full-length transcript sequences from 19,859 genes, with 141,189 being novel transcripts, of which 130,367 were functionally annotated. We detected 520, 324, and 1823 specifically expressed transcripts in the queen, worker, and drone bees, respectively. Furthermore, we identified 38,799 alternative splicing (AS) events from 5710 genes, 44,243 alternative polyadenylation (APA) sites from 1649 gene loci, 88,187 simple sequence repeats (SSRs), and 17,387 long noncoding RNAs (lncRNAs). Leveraging these transcripts as references, we identified 6672, 7795, and 6804 differentially expressed transcripts (DETs) in comparisons of queen ovaries vs drone testes, worker ovaries vs drone testes, and worker ovaries vs queen ovaries, respectively. Our research results provide a comprehensive set of reference transcript datasets for Apis cerana, offering important sequence information for further exploration of its gene functions.

Molecular epidemiology of avian influenza viruses and avian coronaviruses in environmental samples from migratory bird inhabitants in Bangladesh.

Migratory birds are a natural reservoir for major respiratory viruses such as the avian influenza virus (AIV) and the avian coronavirus (AvCoV). Transmission of these viruses from migratory birds to domestic birds increases the prevalence of those diseases that cause severe economic and public health concerns in Bangladesh. The study focused on active surveillance of major respiratory viral pathogens in migratory birds, molecular identification of the viruses, and their phylogenetic origin. To conduct this study, 850 environmental samples (830 fecal samples, 10 soil samples, and 10 water samples) were collected during three consecutive winter seasons from three divisions (Dhaka, Sylhet, and Mymensingh) and pooled according to the year of collection and locations, resulting in a total of 184 tested samples. Using gene-specific primers and probes in TaqMan-and SYBR Green-based RT-qPCR assays, the samples were screened for AIV and AvCoV, respectively. Out of the 184 pooled samples, 37 were found to be positive for these respiratory pathogens. Furthermore, out of the 37 (20.11%) positive respiratory pathogens, 11.96% were AIV (n = 22) and 8.15% were AvCoV (n = 15). For the first time in Bangladesh, AIV H4N2, H4N6, and AvCoVs have been found in fecal samples from migratory birds through surveillance. Phylogenetic analyses of the HA and NA genes of AIV and the polymerase gene (Orf 1) of AvCoV revealed that these strains share a close phylogenetic relationship with the isolates from wild birds in Europe and Asia. The Bangladeshi strains with Eurasian ancestry might pose a significant threat to migratory birds flying through the Asian flyways. They might also be a potential source of virus introduction and spread to poultry raised on land. These findings emphasize the significance of ongoing AIV and AvCoV surveillance in migratory birds in Bangladesh.

Adaptive support vector machine for time-variant failure probability function estimation

Time variant reliability analysis introduces additional complexity due to the inclusion of time. When the time-variant failure probability function (TFPF) of the structure is of interest, it inherently involves sequential evaluations of the failure probabilities of series systems varied with time in discretized space, posing a challenge to reliability analysis. An efficient approach for the evaluation of the TFPF, called ‘Time-dependent Adaptive Support Vector Machine combined with Monte Carlo Simulation’ (TASVM-MCS), is presented to reduce the corresponding computational cost. Based on the samples from Monte Carlo simulation (MCS), an iterative strategy is proposed to actively extract the most valuable sample points from the sample pool and iteratively update the support vector machine (SVM) model. In particular, an active learning function is proposed to take into account the diversity of samples and time simultaneously. In this way, the built SVM will be more suitable for the evaluation of TFPF other than a point-wise failure probability. The proposed TASVM-MCS method is relatively less sensitive to the dimensionality of the input variables, making it a powerful and promising approach for time-variant reliability computations. Four representative examples are given to demonstrate the significant effectiveness and efficiency of the proposed method.

Intergroup variability of the khakas based on non-metric cranial traits data

Introduction. The formation of the gene pool of modern Khakas people occurred through the interaction of various groups of ancient inhabitants of the Minusinsk Basin. This article is focused on the inter-group analysis of craniological series representing different Khakassian subethnic groups. Materials and Methods. The cranial series of the Kachins, Koibals, Sagais, and Beltirs was studied using the battery of 36 cranial non-metric characteristics. The obtained data was compared with data on other populations of Southern and Western Siberia: Shors, Tuvans, Telengits, Selkups, Khants, and Mansis. The analysis of the biological diversity of populations was carried out using Smith's mean measure of divergence (MMD) followed by multidimensional scaling and cluster analysis. Results. The Kachins are the most distant from the other Khakas subethnic groups, forming a cluster with the Telengits and Tuvans. The Koibals and Beltirs were positioned quite close to the Shors. The Sagais occupied a separate position in the Khakas cluster, presumably due to a greater proportion of Europoid admixture compared to other Khakas groups. The pooled Khakas sample shares similar cranial non-metric characteristics with Turkic-speaking ethnic groups of Southern Siberia: Shors, Telengits, and Tuvans. Discussion. The nature of phenetic differentiation of the Khakas sub-ethnic groups presumably reveals their complex population history. The position of the Kachins outside the Khakas cluster based on non-metric traits resulted from specificity of their phenofund, which is also supported by molecular genetic data. The similarity in the phenofund of the Khakas groups to those of the Tuvans and Telengits may result from gene flow between Khakas populations and the peoples of Southern Siberia or/and from their common episodes in their ethnogenesis. The similarity between pooled Khakassian sample and the Shors presumably suggests involvement of common genetic components in the gene pools of these peoples, which is consistent with molecular genetic data. Conclusion. The correspondence of the obtained results with genetic data suggests the possibility of using cranial non-metric traits to identify genetic relationships between ancient populations in the absence of direct genetic information.

Multiplexed chromatin immunoprecipitation sequencing for quantitative study of histone modifications and chromatin factors.

ChIP-seq is a widely used technique for studying histone post-translational modifications and DNA-binding proteins. DNA fragments associated with a specific protein or histone modification epitope are captured by using antibodies, sequenced and mapped to a reference genome. Albeit versatile and popular, performing many parallel ChIP-seq experiments to compare different conditions, replicates and epitopes is laborious, is prone to experimental variation and does not allow quantitative comparisons unless adequate spike-in chromatin is included. We present a detailed protocol for performing and analyzing a multiplexed quantitative chromatin immunoprecipitation-sequencing experiment (MINUTE-ChIP), in which multiple samples are profiled against multiple epitopes in a single workflow. Multiplexing not only dramatically increases the throughput of ChIP-seq experiments (e.g., profiling 12 samples against multiple histone modifications or DNA-binding proteins in a single experiment), but also enables accurate quantitative comparisons. The protocol consists of four parts: sample preparation (i.e., lysis, chromatin fragmentation and barcoding of native or formaldehyde-fixed material), pooling and splitting of the barcoded chromatin into parallel immunoprecipitation reactions, preparation of next-generation sequencing libraries from input and immunoprecipitated DNA and data analysis using our dedicated analysis pipeline. This pipeline autonomously generates quantitatively scaled ChIP-seq tracks for downstream analysis and visualization, alongside necessary quality control indicators. The entire workflow requires basic knowledge in molecular biology and bioinformatics and can be completed in 1 week. MINUTE-ChIP empowers biologists to perform every ChIP-seq experiment with an appropriate number of replicates and control conditions, delivering more statistically robust, exquisitely quantitative and biologically meaningful results.