Full Sequence Research Articles

Fluid paths to the cabinet in federal presidential systems: Argentina 1983–2020

ABSTRACT The study of political careers has focused mainly on highly institutionalized systems. This article examines the extent to which the findings from this research agenda apply to more fluid settings, looking at trajectories to the national cabinet in a regime combining presidentialism and federalism: Argentina from 1983 to 2020. We propose an operationalization of political career that integrates five definitional dimensions, looks at full sequences of single occupational positions, and tests six expectations derived from the literature. When only political jobs are taken into account, we found that careers show significant movement from the subnational level and predominance of executive experience. However, when all occupational jobs are considered, political positions are pulled into second place behind the private sector. Most unexpectedly, in a significant percentage of cases, a ministerial position does not appear to be the last step of a political career but rather an initial springboard thereof.

Distribution, inducibility, and characterisation of prophages in Latilactobacillus sakei

BackgroundLactic acid bacteria (LAB) are used as starters in a wide variety of food fermentations. While the number of reports of phages infecting other LAB steadily increased over the years, information about phage associated with Latilactobacillus sakei, a frequently used meat starter, remains scarce.ResultsIn this study, a predictive genomic analysis of 43 Latilactobacillus sakei genomes revealed the presence of 26 intact, eleven questionable and 52 incomplete prophage sequences across all analysed genomes with a range of one to five predicted prophage sequences per strain. Screening 24 sakei strains for inducible prophages by utilising UV light or mitomycin C, we identified seven lysogenic strains showing lysis after induction during subsequent growth monitoring.Electron microscopic analysis revealed fully assembled virions in the purified lysates of four samples, thus confirming successful prophage induction. All virions featured icosahedral, isomeric heads and long, most likely non-contractile tails indicating siphoviruses. By performing phylogenetic analyses with various marker genes as well as full prophage sequences, we displayed a remarkably high diversity of prophages, that share a similar gene module organisation and six different chromosomal integration sites were identified. By sequencing viral DNA purified from lysates of Latilactobacillus sakei TMW 1.46, we demonstrate that simultaneous induction of multiple prophages is possible.ConclusionsWith this work, we not only provide data about the incidence of prophages harboured by the meat starter Latilactobacillus sakei, we also demonstrated their potential to impact growth of their host after induction, as well as forming seemingly fully assembled virions.

Forensic Analysis of Novel SARS2r-CoV Identified in Game Animal Datasets in China Shows Evolutionary Relationship to Pangolin GX CoV Clade and Apparent Genetic Experimentation

Pangolins are the only animals other than bats proposed to have been infected with SARS-CoV-2 related coronaviruses (SARS2r-CoVs) prior to the COVID-19 pandemic. Here, we examine the novel SARS2r-CoV we previously identified in game animal metatranscriptomic datasets sequenced by the Nanjing Agricultural University in 2022, and find that sections of the partial genome phylogenetically group with Guangxi pangolin CoVs (GX PCoVs), while the full RdRp sequence groups with bat-SL-CoVZC45. While the novel SARS2r-CoV is found in 6 pangolin datasets, it is also found in 10 additional NGS datasets from 5 separate mammalian species and is likely related to contamination by a laboratory researched virus. Absence of bat mitochondrial sequences from the datasets, the fragmentary nature of the virus sequence and the presence of a partial sequence of a cloning vector attached to a SARS2r-CoV read suggests that it has been cloned. We find that NGS datasets containing the novel SARS2r-CoV are contaminated with significant Homo sapiens genetic material, and numerous viruses not associated with the host animals sampled. We further identify the dominant human haplogroup of the contaminating H. sapiens genetic material to be F1c1a1, which is of East Asian provenance. The association of this novel SARS2r-CoV with both bat CoV and the GX PCoV clades is an important step towards identifying the origin of the GX PCoVs.

Analytical Formulation and Field-Theoretic Simulation of Sequence-Specific Phase Separation of Protein-Like Heteropolymers with Short- and Long-Spatial-Range Interactions.

A theory for sequence-dependent liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs) in the study of biomolecular condensates is formulated by extending the random phase approximation (RPA) and field-theoretic simulation (FTS) of heteropolymers with spatially long-range Coulomb interactions to include the fundamental effects of short-range, hydrophobic-like interactions between amino acid residues. To this end, short-range effects are modeled by Yukawa interactions between multiple nonelectrostatic charges derived from an eigenvalue decomposition of pairwise residue-residue contact energies. Chain excluded volume is afforded by incompressibility constraints. A mean-field approximation leads to an effective Flory-Huggins χ parameter, which, in conjunction with RPA, accounts for the contact-interaction effects of amino acid composition and the sequence-pattern effects of long-range electrostatics in IDP LLPS, whereas FTS based on the formulation provides full sequence dependence for both short- and long-range interactions. This general approach is illustrated here by applications to variants of a natural IDP in the context of several different amino-acid interaction schemes as well as a set of different model hydrophobic-polar sequences sharing the same composition. Effectiveness of the methodology is verified by coarse-grained explicit-chain molecular dynamics simulations.

DECCAN VOLCANIC OF MALWA, STRATIGRAPHY AND CORRELATION OF BASALTIC LAVA FLOWS USING MEGACRYST BEARING HORIZON AS TOOL, PARTS OF WESTERN M.P. INDIA

A review of earlier studies of the Deccan Trap occurrences of parts of Ratlam, Mandsaur, Jhabua, Dhar, Khargone, Indore, Ujjain and Shajapur districts of Madhya Pradesh, India was carried out of the area falling between latitudes 220 0000 to 2400000N and longitudes 7400000 to 7600000 in Survey of India Quadrangle sheet Nos. 46I, 46J, 46M and 46N.The main objectives of the study were to synthesize the data on the Deccan Trap basaltic lava flows , their types ,their diagnostic characteristics with special emphasis on delineating and identifying the various megacryst horizons , their levels with specific elevation above m.s.l. to build up the litho-stratigraphy for regional correlation. Broadly the area exhibits the Proterozoic Aravalli Supergroup, the Cretaceous, Bagh and Lameta Groups and the Deccan basaltic lava flows with intruded dykes and sills. The Aravalli Supergroup is represented by the Udaipur, Lunavada and Champaner Groups. The Udaipur Group consists mainly of hornblende gneiss, marble and calc-silicate, carbonaceous phyllites and chlorite schist. The Lunavada Group comprises dolomitic limestone (Phosphate bearing), quartzite, muscovite quartzite, quartz muscovite schist, feldspathised quartzite, gneissic feldspathic rock and biotitic gneiss. The Champaner Group is represented by dolomite, phyllite, slates and basic intrusives. The Aravalli Super group of rocks is also intruded by serpentinite, pyroxinite, granite and basic rocks. The Aravalli Supergroup of rocks is unconformably overlain by Cretaceous marine sedimentary deposits of Bagh Group. It includes Lower arenaceous and Upper calcareous units and occurs as discontinuous outcrops. These are almost horizontally to sub horizontally disposed. The Bagh Group is represented by three units / Formations i.e. Nimar sandstone overlain by nodular limestone and subsequently by coralline limestone. The Lameta Group of rocks is noticed in the area east and South East of Bagh exposures, overlying the Nimar sandstones. These rocks predominantly consist of limestone, gritty sandstone and conglomerate and generally exhibit hummocky topography and sometimes display solution channels. These are mostly horizontally to sub-horizontally disposed with an average thickness of 5- 6 m. The Deccan Trap has occupied a very long stretch of area which consists of a sequence of 121 basaltic lava flows with a cumulative thickness of about 610 m. These flows represent a sequence of cyclic lava eruptions with fine to medium grained a aphyric to sparsely / moderately / highly / mega porphyritic lava. About two third of the total flows exhibit Aa characters and the rest are compound and simple Pahoehoe. Some of these flows consist of megacryst units containing feldspar laths varying in size round two to five cm. These megacryst horizons have been identified at different elevations in Quadrangles 46I, J, M, N and on the basis of these horizons, various flows have been grouped into to six Formations which have specific nomenclatures and stratigraphic status. These formations are in the order of antiquity 1) Mandleshwar formation, 2) Choral formation,3) Dhar formations 4) Indore Formation 5) Bargonda Formation and 6) Singarchori Formation. Full sequence is exposed only in quadrangle 46N whereas the Quadrangles 46I, J, M do not exhibit Bargonda and Singarchori Formations. An attempt has been made to correlate the various Formations in degree sheets 46 I, J, M, N with the surroundings Geological Quadrangles. The Megacryst bearing lava- flows act as marker horizons for this purpose. A large number of dykes and dyke swamps of basaltic as well as doleritic compositions have been marked around the Narmada River. The intensity of the dykes is more in the oldest Mandleshwar Formations and it gradually decreases in increasing order of antiquity towards the younger Bargonda and Singarchori Formations. The general trend of these dykes varies from East North East – West South West to E-W running sub parallel to the Narmada lineament, besides a few dykes also cut across this lineament trend and oriented along NNW-SSE to N-S direction. The Length of these dykes varies from about 200 m to 20 Km with width varying from a few meters to as much as 200 m. The possibility exists that these dykes may have been actually feeders through which periodic eruptions of tholiitic basaltic lava took place resulting in formation of such a thick pile of lava flows. Besides as many as seven Intertrapean fossiliferous sedimentary horizons have been recognized within the basal part of the flows. These demonstrate episodic nature of volcanic activity, long periods of quiescence and resilience. The overall study of various lava flow s and their interrelations their relative dispositions thinning /swelling and pinching nature. Their relative elevations, occurrence of marker megacryst units, change in lava characters, overall gradient of lava flows and their relation to preexisting topography and slope elements reveals that the sources of lava eruptions of Older Formations are situated somewhere in the west and south west whereas those of Younger Formations are located in the Eastern part of Mhow of the area studied.

Taming the Selection of Optimal Substitution Models in Phylogenomics by Site Subsampling and Upsampling.

The selection of the optimal substitution model of molecular evolution imposes a high computational burden for long sequence alignments in phylogenomics. We discovered that the analysis of multiple tiny subsamples of site patterns from a full sequence alignment recovers the correct optimal substitution model when sites in the subsample are upsampled to match the total number of sites in the full alignment. The computational costs of maximum-likelihood analyses are reduced by orders of magnitude in the subsample-upsample (SU) approach because the upsampled alignment contains only a small fraction of all site patterns. We present an adaptive protocol, ModelTamer, that implements the new SU approach and automatically selects subsamples to estimate optimal models reliably. ModelTamer selects models hundreds to thousands of times faster than the full data analysis while needing megabytes rather than gigabytes of computer memory.

Online Assortment Optimization for Two-Sided Matching Platforms

Motivated by online labor markets, we consider the online assortment optimization problem faced by a two-sided matching platform that hosts a set of suppliers waiting to match with a customer. Arriving customers are shown an assortment of suppliers and may choose to issue a match request to one of them. After spending some time on the platform, each supplier reviews all the match requests she has received and, based on her preferences, she chooses whether to match with a customer or to leave unmatched. We study how platforms should design online assortment algorithms to maximize the expected number of matches in such two-sided settings. We establish that a simple greedy algorithm is 1/2-competitive against an optimal clairvoyant algorithm that knows in advance the full sequence of customers’ arrivals. However, unlike related online assortment problems, no randomized algorithm can achieve a better competitive ratio, even in asymptotic regimes. To advance beyond this general impossibility, we consider structured settings where suppliers’ preferences are described by the multinomial logit and nested logit choice models. We develop new forms of balancing algorithms, which we call preference-aware, that leverage structural information about suppliers’ choice models to design the associated discount function. In certain settings, these algorithms attain competitive ratios provably larger than the standard “barrier” of [Formula: see text] in the adversarial arrival model. Our results suggest that the shape and timing of suppliers’ choices play critical roles in designing online assortment algorithms for two-sided matching platforms. This paper was accepted by Omar Besbes, revenue management and market analytics. Supplemental Material: The data files and online appendices are available at https://doi.org/10.1287/mnsc.2022.4464 .

Genomic Characterisation of Canis Familiaris Papillomavirus Type 24, a Novel Papillomavirus Associated with Extensive Pigmented Plaque Formation in a Pug Dog.

Numerous large dark plaques developed over the ventrum, legs and head of a 9-year-old pug dog over a 4-year-period. Histology confirmed a diagnosis of viral pigmented plaque and a short section of a novel papillomavirus (PV) type was amplified using consensus PCR primers. Taking advantage of the circular nature of PV DNA, 'outward facing' PCR primers allowed amplification of the full sequence. As this is the 24th PV known to infect dogs, the novel PV was designated canine papillomavirus (CPV) type 24. The CPV24 genome contained putative coding regions for 5 early proteins and 2 late ones. The CPV24 open reading frame L1 showed the highest (78.2%) similarity to CPV4 and phylogenetic analysis showed that CPV24 clustered with CPV4 and CPV16 suggesting CPV24 is the third species 2 Chipapillomavirus type identified in dogs. This is the third report of extensive pigmented plaques covering a high proportion of the skin. Both previous cases were caused CPV4 and, considering the high genetic similarity between CPV4 and CP24, infection by these CPV types may predispose to more severe clinical disease. In addition, as plaques caused by CPV16 appear more likely to progress to neoplasia, the detection of a species 2 Chipapillomavirus within a pigmented plaque may indicate the potential for more severe disease.

Splicing factor BUD31 promotes ovarian cancer progression through sustaining the expression of anti-apoptotic BCL2L12

Dysregulated expression of splicing factors has important roles in cancer development and progression. However, it remains a challenge to identify the cancer-specific splicing variants. Here we demonstrate that spliceosome component BUD31 is increased in ovarian cancer, and its higher expression predicts worse prognosis. We characterize the BUD31-binding motif and find that BUD31 preferentially binds exon-intron regions near splicing sites. Further analysis reveals that BUD31 inhibition results in extensive exon skipping and a reduced production of long isoforms containing full coding sequence. In particular, we identify BCL2L12, an anti-apoptotic BCL2 family member, as one of the functional splicing targets of BUD31. BUD31 stimulates the inclusion of exon 3 to generate full-length BCL2L12 and promotes ovarian cancer progression. Knockdown of BUD31 or splice-switching antisense oligonucleotide treatment promotes exon 3 skipping and results in a truncated isoform of BCL2L12 that undergoes nonsense-mediated mRNA decay, and the cells subsequently undergo apoptosis. Our findings reveal BUD31-regulated exon inclusion as a critical factor for ovarian cancer cell survival and cancer progression.

Isotope-edited vibrational circular dichroism study reveals a flexible N-terminal structure of islet amyloid peptide (NFGAIL) in amyloid fibril form: A site-specific local structural analysis

The short peptide fragment NFGAIL (IAPf) is a well-known amyloidogenic peptide (22–27), derived from human islet amyloid polypeptide(hIAPP), whose fibrillar structure is often used to better understand the wild-type hIAPP amyloid fibrils, associated with type II diabetes. Despite an extensive study, the fibrillar structure of IAPf at the amino acid residue level is still unclear. Herein, the vibrational circular dichroism(VCD) spectroscopic technique coupled with isotope labelling strategy has been used to study the site-specific local structure of IAPf amyloid fibrils. Two 13C labeled IAPfs were designed and used along with unlabelled IAPf to achieve this. The 13C labelled (on -C=O) glycine(IAPf-G) and phenylalanine (IAPf-F) residues were introduced into the IAPf sequence separately by replacing natural glycine (residue 24) and phenylalanine (residue 23), respectively. VCD spectral analysis on IAPf-G suggests that IAPf fibrils adopt parallel β-sheet conformation with glycine residues are part of β-sheet and in-register. Unlike IAPf-G, VCD analysis on IAPf-F reveals that phenylalanine residues exist in the turn/hairpin conformation rather than β-sheet region. Both VCD results thus suggest that IAPf amyloid fibril consists of a mixture of β-sheet as a major conformation involving GAIL and turn/hairpin as a minor conformation involving NF rather than an idealized β-sheet involving all the amino acids. While previous studies speculated that the full NFGAIL sequence could participate in the β-sheet formation, the present site-specific structural analysis of IAPf amyloid fibrils at residue level using isotope-edited VCD has gained significant attention. Such residue level information has important implications for understanding the role of NFGAIL sequence in the amyloid fibrillation of hIAPP.

K- and L-shell theoretical fluorescence yields for the Fe isonuclear sequence

In this work, we present K- and L- shell fluorescence yield values of the full isonuclear sequence of Fe ions, using a state-of-the-art multiconfiguration Dirac–Fock approach. These results may be of importance for spectral fitting and plasma modeling, both in laboratory and astrophysical studies, where Fe is an important benchmark element. The K-shell fluorescence yields were found to be very similar up to the removal of 14 electrons.

Effects of Charged Polyelectrolytes on Amyloid Fibril Formation of a Tau Fragment.

The microtubule-associated protein tau is involved in more than 20 different neurological disorders characterized by aberrant intracellular aggregation of tau in the brain. Here, we investigated the aggregation of a novel 20-residue model peptide, tau298-317, which is derived from the key microtubule binding domain of the full sequence tau. Our results show that tau298-317 highly mimics the physical and aggregation properties of tau. Under normal physiological conditions, the peptide maintains a disordered random coil without aggregation. The presence of polyanionic heparin (Hep) significantly promotes the aggregation of this peptide to form amyloid fibrils. The Hep-induced aggregation is sensitive to the ionic strength of the solution and the introduction of the negatively charged phosphate group on a serine (Ser305) residue in the sequence, suggesting an important role of electrostatic interactions in the mechanism of Hep-mediated aggregation. In addition, two positively charged polysaccharides, chitosan (CHT) and its quaternary derivative N-trimethyl chitosan (TMC), were found to effectively inhibit Hep-induced aggregation of tau298-317 in a concentration-dependent manner. Attractive electrostatic interactions between the positively charged moieties in CHT/TMC and the negatively charged residues of Hep play a critical role in inhibiting Hep-peptide interactions and suppressing peptide aggregation. Our results suggest that positively charged polyelectrolytes with optimized charged groups and charge distribution patterns can serve as effective molecular candidates to block tau-Hep interactions and prevent aggregation of tau induced by Hep and other polyanions.

Identification of a novel polyomavirus from a marsupial host.

We report the identification and analysis of a full sequence of a novel polyomavirus from a brushtail possum (Trichosurus vulpecula) termed possum polyomavirus (PPyV). The sequence was obtained from the next-generation sequencing assembly during an investigation into the aetiological agent for a neurological disease of possums termed wobbly possum disease (WPD), but the virus was not aetiologically involved in WPD. The PPyV genome was 5,224 nt long with the organisation typical for polyomaviruses, including early (large and small T antigens) and late (Viral Protein 1 (VP1), VP2, and VP3) coding regions separated by the non-coding control region of 465 nt. PPyV clustered with betapolyomaviruses in the WUKI clade but showed less than 60 per cent identity to any of the members of this clade. We propose that PPyV is classified within a new species in the genus Betapolyomavirus. These data add to our limited knowledge of marsupial viruses and their evolution.

Derived categories of skew quadric hypersurfaces

The existence of a full strong exceptional sequence in the derived category of a smooth quadric hypersurface was proved by Kapranov. In this paper, we present a skew generalization of this result. Namely, we show that if S is a standard graded (±1)-skew polynomial algebra in n variables with n ≥ 3 and f = x 21 + ⋯ + x 2n ∈ S, then the derived category Db(qgr S/(f)) of the noncommutative scheme qgr S/(f) has a full strong exceptional sequence. The length of this sequence is given by n−2+2r where r is the nullity of a certain matrix over \({\mathbb{F}_2}\). As an application, by studying the endomorphism algebra of this sequence, we obtain the classification of Db(qgr S/(f)) for n = 3, 4.

A methodological framework to study the behavior and kinetic influence of V, Mn, Co, Ni, Cu, Zn, As, Se and Mo during pyrite formation via the polysulfide pathway at ambient temperature

Pyritization links the biogeochemical cycles of Fe, S and C to those of trace elements (TE) such as As, Ni, Cu, Co, Mn, Zn, Se and Mo in reducing environments. The scavenging modes of such impurities in pyrite are parameters of importance for evaluating to which extent pyrite can immobilize TE under diverse (sub)surface conditions. Furthermore, determining the fate of TE during pyritization is a prerequisite to evaluate the ability of pyrite to record the chemical signature of surrounding waters at the time of precipitation. Here, we provide a methodological framework to study the incorporation of TE during a reaction sequence leading to pyrite formation via the polysulfide pathway. Laboratory syntheses were conducted by reacting a FeS precursor with elemental sulfur – both readily obtained by reducing FeCl3 with Na2S in solution under strict anoxia – at ambient temperature and in the presence of aqueous V, Mn, Co, Ni, Cu, Zn, As, Se and Mo in a TE/Fe molar ratio of 0.5 mol%. Within this simplified framework, our experiments aimed at reproducing the early formation of pyrite in water column aggregates/bottom sediments before the late diagenetic aging phases. Solids and liquids were sampled over time during the reaction sequence leading to pyrite formation, up to 3100 h, and further analyzed by ICP-OES, XRD, XRF and STEM-EDXS to obtain information on (1) the kinetics of pyrite formation and (2) the extent of TE incorporation in the solid phase, during and after the complete conversion of FeS to FeS2. Pyrite formation kinetic is observed to be strongly influenced by the identity of the added TE, with the delay before nucleation decreasing in the order Ni >> Mn, Co > Cu, Zn, Se > Control, V >> As, Mo. During the full reaction sequence, i.e. FeS plus S(0) conversion to FeS2, Mn remains in the liquid phase, Ni, Co, V, Cu, and Se quickly precipitate and remain sequestered overtime, Zn and Mo precipitate and are further released into solution, and As is partially incorporated in the solid. Elemental mapping at the microscale using STEM-EDXS show that, except for Mn, the TE are associated with pyrite. Moreover, while TE are homogeneously distributed at the particle scale for Co, Cu, Zn, As, and Se, Ni-pyrite exhibited an enriched core. The solid-liquid partition coefficients of each TE during our pyritization experiments in our simplified model system are calculated and ranks as follows: Cu ≥ Ni ≥ Co > Se > V > Mo >> As > Zn >> Mn. These partitions are discussed in the light of values reported in the literature from natural settings. The important differences observed exemplify the complexity to predict TE pyrite-water partition in sedimentary environments, in particular when considering additional multifactorial processes such as the local biogeochemistry of micro-environments, as well as the partial sequestration of TE by non-sulfide minerals such as authigenic clays and carbonates.

Optimization and Identification of Single Mutation in Hemoglobin Variants with 2,2,2 Trifluoroethanol Modified Digestion Method and Nano-LC Coupled MALDI MS/MS.

Background: Hemoglobin (Hb) variants arise due to point mutations in globin chains and their pathological treatments rely heavily on the identification of the nature and location of the mutation in the globin chains. Traditional methods for diagnosis such as HPLC and electrophoresis have their own limitations. Therefore, the present study aims to develop and optimize a specific method of sample processing that could lead to improved sequence coverage and analysis of Hb variants by nano LC−MALDI MS/MS. Methods: In our study, we primarily standardized various sample processing methods such as conventional digestion with trypsin followed by 10% acetonitrile treatment, digestion with multiple proteases like trypsin, Glu−C, Lys−C, and trypsin digestion subsequent to 2,2,2 trifluoroethanol (TFE) treatment. Finally, the peptides were identified by LC−MALDI MS/MS. All of these sample processing steps were primarily tested with recombinant Hb samples. After initial optimization, we found that the TFE method was the most suitable one and the efficiency of this method was applied in Hb variant identification based on high sequence coverage. Results: We developed and optimized a method using an organic solvent TFE and heat denaturation prior to digestion, resulting in 100% sequence coverage in the β−chains and 95% sequence coverage in the α−chains, which further helped in the identification of Hb mutations. A Hb variant protein sequence database was created to specify the search and reduce the search time. Conclusion: All of the mutations were identified using a bottom−up non−target approach. Therefore, a sensitive, robust and reproducible method was developed to identify single substitution mutations in the Hb variants from the sequence of the entire globin chains. Biological Significance: Over 330,000 infants are born annually with hemoglobinopathies and it is the major cause of morbidity and mortality in early childhood. Hb variants generally arise due to point mutation in the globin chains. There is high sequence homology between normal Hb and Hb variant chains. Due to this high homology between the two forms, identification of variants by mass spectrometry is very difficult and requires the full sequence coverage of α− and β−chains. As such, there is a need for a suitable method that provides 100% sequence coverage of globin chains for variant analysis by mass spectrometry. Our study provides a simple, robust, and reproducible method that is suitable for LC−MALDI and provides nearly complete sequence coverage in the globin chains. This method may be used in the near future in routine diagnosis for Hb variant analysis.

Spectrophotometric Detection of the BRCA1 Gene via Exponential Isothermal Amplification and Hybridization Chain Reaction of Surface-Bound Probes.

In this work, we demonstrated an ultrasensitive approach with a dual-amplification strategy for DNA assay based on isothermal exponential amplification (EXPAR) and the hybridization chain reaction (HCR). In the presence of target DNA, the hairpin probe DNA (HP1) recognized and partially hybridized with the target DNA to form double-stranded structures containing the full recognition sequences for nicking endonuclease and then initiated EXPAR. Under the reaction of EXPAR, a large number of single-stranded DNA (ssDNA) was produced in the circle of nicking, polymerization, and strand displacement. The resulting ssDNA can bind to the surface-bound probe on the well of the microplate and trigger the hybridization chain reaction, resulting in the production of numerous double-stranded DNA concatamers with biotin labeling. In the presence of streptavidin-conjugated horseradish peroxidase (HRP), the amplified signal can be detected by a spectrophotometer via HRP-catalyzed substrate 3,3'5,5'-tetramethylbenzidine (TMB). This proposed dual-amplification method provides a detection limit of 74.48 aM, which also exhibits good linearity ranging from 0.1 fM to 100 pM.

Identification and Molecular Characterization of a Divergent Asian-like Canine Parvovirus Type 2b (CPV-2b) Strain in Southern Italy.

Canine parvovirus type 2 (CPV-2) is an infectious agent relevant to domestic and wild carnivorans. Recent studies documented the introduction and spread of CPV-2c strains of Asian origin in the Italian canine population. We investigated tissue samples from a puppy collected during necropsy for the presence of viral enteropathogens and all samples tested positive only for CPV-2. The full coding sequence of a CPV-2b (VP2 426Asp) strain was obtained. This virus was related to CPV-2c strains of Asian origin and unrelated to European CPV-2b strains. The sequence had genetic signatures typical of Asian strains (NS1: 60Val, 545Val, 630Pro; VP2: 5Gly, 267Tyr, 324Ile) and mutations rarely reported in Asian CPV-2b strains (NS1: 588N; VP2: 370Arg). Phylogenetic analyses placed this strain in well-supported clades, including Asian CPV-2c-like strains, but always as a basal, single-sequence long branch. No recombination was observed for this strain, and we speculate that it could have originated from an Asian CPV-2c-like strain that acquired the 426Asp mutation. This study reports the first evidence of an Asian-like CPV-2b strain in Italy, confirming the occurrence of continuous changes in the global CPV-2 spread. Since positive convergent mutations complicate data interpretation, a combination of phylogenetic and mutation pattern analyses is crucial in studying the origin and evolution of CPV-2 strains.

31 Genotype Concordance between SNP Chip and Imputed Low-Pass Whole-Genome Sequence in Beef Cattle

Abstract Genotypes generated from common single nucleotide polymorphisms (SNP) chips have been the sole source of genomic information for current beef cattle genetic evaluations. More recently, the development of low-pass whole-genome sequencing (LPS) followed by imputation to full sequence and variant calls has provided an alternative option to generate genotypes for inclusion into genetic evaluations. The objective of this study was to estimate the genotype concordance between SNP chip and LPS genotypes. Ear samples, via tissue sampling units, were obtained from 226 individuals. A subset of 109 individuals also had blood samples collected. Samples were sent to GeneSeek (Neogen company, Lincoln, NE) for genotyping (100K or 50K) and LPS and imputation was performed by Gencove. A total of 33,451 and 78,032 SNP overlapping between SNP panel and LPS for ear and blood samples, respectively, were used for further analyses. Genotype concordance was performed by counting the number of matching genotypes per SNP between (1) SNP chip vs. LPS in ear and blood samples, and (2) LPS in blood vs. LPS in ear samples. The average concordances between SNP chip vs. LPS in ear and blood samples were 0.97±0.04 and 0.98±0.06, respectively. The average concordance between LPS in blood vs. ear samples was 0.97±0.03. In conclusion, the concordance was high regardless of the tissue type, and, at least in these data, differences in resulting genetic predictions would not be expected between the use of genotypes derived from SNP chips or LPS. Additional work is warranted to determine sensitivity to relationships between target animals and the reference set used for imputation. The USDA is an equal opportunity provider and employer.

Multi-agent Intelligent Ensembles with Professional Competencies, Pattern Recognition and Decision Making

Each competence is exercised by an intellectual agent with a competent functional professional image. Intellectual agents form an ensemble with clever ethical artificial intelligence. The use of an ensemble with intelligent ethical artificial intelligence in various environments is carried out by synergistically adjusting the interaction of intelligent agents based on data from a specific environment obtained by an analytical competent intellectual agent. Modeling holographic processes of the human psyche based on artificial intelligence of machine learning with Fourier transformation using full parametric sequences of necessary and sufficient data of holograms of target objects solves the problem of their unambiguous detection in different environments and in different conditions. An ensemble of intelligent decision-making agents is a cognitive information system that makes a decision based on an objective analysis of available data in difficult situations, in an interactive mode, taking into account performance criteria and resource-time constraints. Decision-making criteria are functionalities that express preferences and allow ranking the quality of decisions. Decisions are made on the basis of rules. Decision rules are a set of logical constructs used to produce a decision based on criteria, data, and knowledge. An ensemble of intellectual agents with professional competencies, pattern recognition and decision-making fully model the abilities of the human psyche.