Haplotype determination of the Bombyx mori nucleopolyhedrovirus by Nanopore sequencing and linkage of single nucleotide variants.

Naturally occurring isolates of baculoviruses, such as the Bombyx mori nucleopolyhedrovirus (BmNPV), usually consist of numerous genetically different haplotypes. Deciphering the different haplotypes of such isolates is hampered by the large size of the dsDNA genome, as well as the short read length of next generation sequencing (NGS) techniques that are widely applied for baculovirus isolate characterization. In this study, we addressed this challenge by combining the accuracy of NGS to determine single nucleotide variants (SNVs) as genetic markers with the long read length of Nanopore sequencing technique. This hybrid approach allowed the comprehensive analysis of genetically homogeneous and heterogeneous isolates of BmNPV. Specifically, this allowed the identification of two putative major haplotypes in the heterogeneous isolate BmNPV-Ja by SNV position linkage. SNV positions, which were determined based on NGS data, were linked by the long Nanopore reads in a Position Weight Matrix. Using a modified Expectation-Maximization algorithm, the Nanopore reads were assigned according to the occurrence of variable SNV positions by machine learning. The cohorts of reads were de novo assembled, which led to the identification of BmNPV haplotypes. The method demonstrated the strength of the combined approach of short- and long-read sequencing techniques to decipher the genetic diversity of baculovirus isolates.

Metamagnetic multiband Hall effect in Ising antiferromagnet ErGa2.

Frustrated rare-earth-based intermetallics provide a promising platform for emergent magnetotransport properties through exchange coupling between conduction electrons and localized rare-earth magnetic moments. Metamagnetism, the abrupt change of magnetization under an external magnetic field, is a signature of first-order magnetic phase transitions; recently, metamagnetic transitions in frustrated rare earth intermetallics have attracted interest for their accompanying nontrivial spin structures (e.g., skyrmions) and associated nonlinear and topological Hall effects (THE). Here, we present metamagnetism-induced Hall anomalies in single-crystalline ErGa2, which recalls features arising from the THE but wherein the strong Ising-type anisotropy of Er moments prohibits noncoplanar spin structures. We show that the observed anomalies are neither due to anomalous Hall effect nor THE; instead, can be accounted for via 4f-5d interactions which produce a band-dependent mobility modulation. This leads to a pronounced multiband Hall response across the magnetization process-a metamagnetic multiband Hall effect that resembles a topological-Hall-like response but without nontrivial origins. The present findings may be of general relevance in itinerant metamagnetic systems regardless of coplanar/noncoplanar nature of spins and are important for the accurate identification of Hall signals due to emergent magnetic fields.

Advancing pathogen surveillance by nanopore sequencing and genotype characterization of Acheta domesticus densovirus in mass-reared house crickets.

Rapid and reliable detection of pathogens is crucial to complement the growing industry of mass-reared insects, in order to safeguard the insect colonies from outbreak of diseases, which may cause significant economic loss. Current diagnostic methods are mainly based on conventional PCR and microscopic examination, requiring prior knowledge of disease symptoms and are limited to identifying known pathogens. Here, we present a rapid nanopore-based metagenomics approach for detecting entomopathogens from the European house cricket (Acheta domesticus). In this study, the Acheta domesticus densovirus (AdDV) was detected from diseased individuals using solely Nanopore sequencing. Virus reads and genome assemblies were obtained within twenty-four hours after sequencing. Subsequently, due to the length of the Nanopore reads, it was possible to reconstruct significantly large parts or even the entire AdDV genome to conduct studies for genotype identification. Variant analysis indicated the presence of three AdDV genotypes within the same house cricket population, with association to the vital status of the diseased crickets. This contrast provided compelling evidence for the existence of non-lethal AdDV genotypes. These findings demonstrated nanopore-based metagenomics sequencing as a powerful addition to the diagnostic tool kit for routine pathogen surveillance and diagnosis in the insect rearing industry.

Three-dimensional flat bands in pyrochlore metal CaNi2.

Electronic flat-band materials host quantum states characterized by a quenched kinetic energy. These flat bands are often conducive to enhanced electron correlation effects and emergent quantum phases of matter1. Long studied in theoretical models2-4, these systems have received renewed interest after their experimental realization in van der Waals heterostructures5,6 and quasi-two-dimensional (2D) crystalline materials7,8. An outstanding experimental question is if such flat bands can be realized in three-dimensional (3D) networks, potentially enabling new materials platforms9,10 and phenomena11-13. Here we investigate the C15 Laves phase metal CaNi2, which contains a nickel pyrochlore lattice predicted at a model network level to host a doubly-degenerate, topological flat band arising from 3D destructive interference of electronic hopping14,15. Using angle-resolved photoemission spectroscopy, we observe a band with vanishing dispersion across the full 3D Brillouin zone that we identify with the pyrochlore flat band as well as two additional flat bands that we show arise from multi-orbital interference of Ni d-electrons. Furthermore, we demonstrate chemical tuning of the flat-band manifold to the Fermi level that coincides with enhanced electronic correlations and the appearance of superconductivity. Extending the notion of intrinsic band flatness from 2D to 3D, this provides a potential pathway to correlated behaviour predicted for higher-dimensional flat-band systems ranging from tunable topological15 to fractionalized phases16.

Intrinsic 1[Formula: see text] phase induced in atomically thin 2H-MoTe2 by a single terahertz pulse.

The polymorphic transition from 2H to 1[Formula: see text]-MoTe2, which was thought to be induced by high-energy photon irradiation among many other means, has been intensely studied for its technological relevance in nanoscale transistors due to the remarkable improvement in electrical performance. However, it remains controversial whether a crystalline 1[Formula: see text] phase is produced because optical signatures of this putative transition are found to be associated with the formation of tellurium clusters instead. Here we demonstrate the creation of an intrinsic 1[Formula: see text] lattice after irradiating a mono- or few-layer 2H-MoTe2 with a single field-enhanced terahertz pulse. Unlike optical pulses, the low terahertz photon energy limits possible structural damages. We further develop a single-shot terahertz-pump-second-harmonic-probe technique and reveal a transition out of the 2H-phase within 10 ns after photoexcitation. Our results not only provide important insights to resolve the long-standing debate over the light-induced polymorphic transition in MoTe2 but also highlight the unique capability of strong-field terahertz pulses in manipulating quantum materials.

Molecular Surveillance for Vector-Borne Bacteria in Rodents and Tree Shrews of Peninsular Malaysia Oil Palm Plantations.

Many human clinical cases attributed to vector-borne pathogens are underreported in Malaysia, especially in rural localities where healthcare infrastructures are lacking. Here, 217 small mammals, consisting of rodents and tree shrews, were trapped in oil palm plantations in the Peninsular Malaysia states of Johor and Perak. Species identification was performed using morphological and DNA barcoding analyses, and 203 small mammals were included in the detection of selected vector-borne bacteria. The DNA extracted from the spleens was examined for Orientia tsutsugamushi, Borrelia spp., Bartonella spp. and Rickettsia spp. using established PCR assays. The small mammals collected in this study included Rattus tanezumi R3 mitotype (n = 113), Rattus argentiventer (n = 24), Rattus tiomanicus (n = 22), Rattus exulans (n = 17), Rattus tanezumi sensu stricto (n = 1) and Tupaia glis (n = 40). Orientia tsutsugamushi, Borrelia spp. and Bartonella phoceensis were detected in the small mammals with the respective detection rates of 12.3%, 5.9% and 4.9%. Rickettsia spp., however, was not detected. This study encountered the presence of both Lyme disease and relapsing fever-related borreliae in small mammals collected from the oil palm plantation study sites. All three microorganisms (Orientia tsutsugamushi, Borrelia spp. and Bartonella phoceensis) were detected in the R. tanezumi R3 mitotype, suggesting that the species is a competent host for multiple microorganisms. Further investigations are warranted to elucidate the relationships between the ectoparasites, the small mammals and the respective pathogens.

Charge order landscape and competition with superconductivity in kagome metals.

In the kagome metals AV3Sb5 (A = K, Rb, Cs), three-dimensional charge order is the primary instability that sets the stage for other collective orders to emerge, including unidirectional stripe order, orbital flux order, electronic nematicity and superconductivity. Here, we use high-resolution angle-resolved photoemission spectroscopy to determine the microscopic structure of three-dimensional charge order in AV3Sb5 and its interplay with superconductivity. Our approach is based on identifying an unusual splitting of kagome bands induced by three-dimensional charge order, which provides a sensitive way to refine the spatial charge patterns in neighbouring kagome planes. We found a marked dependence of the three-dimensional charge order structure on composition and doping. The observed difference between CsV3Sb5 and the other compounds potentially underpins the double-dome superconductivity in CsV3(Sb,Sn)5 and the suppression of Tc in KV3Sb5 and RbV3Sb5. Our results provide fresh insights into the rich phase diagram of AV3Sb5.

Habitat and Season Drive Chigger Mite Diversity and Abundance on Small Mammals in Peninsular Malaysia.

Chigger mites are vectors of the bacterial disease scrub typhus, caused by Orientia spp. The bacterium is vertically transmitted in the vector and horizontally transmitted to terrestrial vertebrates (primarily wild small mammals), with humans as incidental hosts. Previous studies have shown that the size of the chigger populations is correlated with the density of small mammals in scrub typhus-endemic regions. Here, we explore interactions between the small mammals and chiggers in two oil palm plantations located in the Perak and Johor states of Peninsular Malaysia. The location in Perak also contained an aboriginal (Orang Asli) settlement. A ~5% sub-sample from 40,736 chigger specimens was identified from five species of small mammals (n = 217), revealing 14 chigger species, including two new records for Malaysia. The abundance and species richness of chiggers were significantly affected by habitat type (highest in forest border), state (highest in Perak), and season (highest in dry). The overall prevalence of Orientia tsutsugamushi DNA in small-mammal tissues was 11.7% and was not significantly affected by host or habitat characteristics, but in Johor, was positively associated with infestation by Leptotrombidium arenicola. These findings highlight the risk of contracting scrub typhus in oil palm plantations and associated human settlements.

Molecular evidence of rat bocavirus among rodents in Peninsular Malaysia.

Rat bocavirus (RBoV) and rodent bocavirus (RoBoV) have previously been detected in Rattus norvegicus; however, these viruses have not been reported in rodent populations in Malaysia. We investigated the presence of RBoV and RoBoV in archived rodent specimens. DNA barcoding of the rodent cytochrome c oxidase gene identified five different species: Rattus tanezumi R3 mitotype, Rattus tiomanicus, Rattus exulans, Rattus argentiventer, and Rattus tanezumi sensu stricto. Three spleens were positive for RBoV (1.84%; 3/163), but no RoBoV was detected. Phylogenetic analyzes of the partial non-structural protein 1 gene grouped Malaysian RBoV strains with RBoV strains from China. Further studies among rats from different geographical locations are warranted for this relatively new virus.

Mapping 1D Confined Electromagnetic Edge States in 2D Monolayer Semiconducting MoS2 Using 4D-STEM.

Four-dimensional (4D) scanning transmission electron microscopy is used to study the electric fields at the edges of 2D semiconducting monolayer MoS2. Sub-nanometer 1D features in the 2D electric field maps are observed at the outermost region along zigzag edges and also along nanowire MoS-terminated MoS2 edges. Atomic-scale oscillations are detected in the magnitude of the 1D electromagnetic edge state, with spatial variations that depend on the specific periodic edge reconstructions. Electric field reconstructions, along with integrated differential phase contrast reconstructions, reveal the presence of low Z number atoms terminating many of the uniform edges, which are difficult to detect by annular dark field scanning transmission electron microscopy due to its limited dynamic range. Density functional theory calculations support the formation of periodic 1D edge states and also show that enhancement of the electric field magnitude can occur for some edge terminations. The experimentally observed electric fields at the edges are attributed to the absence of an opposing electric field from a nearest neighbor atom when the electron beam propagates through the 2D monolayer and interacts. These results show the potential of 4D-STEM to map the atomic scale structure and fluctuations of electric fields around edge atoms with different bonding states than bulk atoms in 2D materials, beyond conventional imaging.

Evidence of two-dimensional flat band at the surface of antiferromagnetic kagome metal FeSn.

The kagome lattice has long been regarded as a theoretical framework that connects lattice geometry to unusual singularities in electronic structure. Transition metal kagome compounds have been recently identified as a promising material platform to investigate the long-sought electronic flat band. Here we report the signature of a two-dimensional flat band at the surface of antiferromagnetic kagome metal FeSn by means of planar tunneling spectroscopy. Employing a Schottky heterointerface of FeSn and an n-type semiconductor Nb-doped SrTiO3, we observe an anomalous enhancement in tunneling conductance within a finite energy range of FeSn. Our first-principles calculations show this is consistent with a spin-polarized flat band localized at the ferromagnetic kagome layer at the Schottky interface. The spectroscopic capability to characterize the electronic structure of a kagome compound at a thin film heterointerface will provide a unique opportunity to probe flat band induced phenomena in an energy-resolved fashion with simultaneous electrical tuning of its properties. Furthermore, the exotic surface state discussed herein is expected to manifest as peculiar spin-orbit torque signals in heterostructure-based spintronic devices.

Spectroscopic Signatures of Interlayer Coupling in Janus MoSSe/MoS2 Heterostructures.

The interlayer coupling in van der Waals heterostructures governs a variety of optical and electronic properties. The intrinsic dipole moment of Janus transition metal dichalcogenides (TMDs) offers a simple and versatile approach to tune the interlayer interactions. In this work, we demonstrate how the van der Waals interlayer coupling and charge transfer of Janus MoSSe/MoS2 heterobilayers can be tuned by the twist angle and interface composition. Specifically, the Janus heterostructures with a sulfur/sulfur (S/S) interface display stronger interlayer coupling than the heterostructures with a selenium/sulfur (Se/S) interface as shown by the low-frequency Raman modes. The differences in interlayer interactions are explained by the interlayer distance computed by density-functional theory (DFT). More intriguingly, the built-in electric field contributed by the charge density redistribution and interlayer coupling also play important roles in the interfacial charge transfer. Namely, the S/S and Se/S interfaces exhibit different levels of photoluminescence (PL) quenching of MoS2 A exciton, suggesting enhanced and reduced charge transfer at the S/S and Se/S interface, respectively. Our work demonstrates how the asymmetry of Janus TMDs can be used to tailor the interfacial interactions in van der Waals heterostructures.

Isolation of Streptococcus cuniculi from corneal lesion in laboratory-raised mice.

Corneal lesions appearing as white mass beneath intact epithelium, with ocular discharge in one mouse, was observed in a batch of laboratory-raised BALB/c mice (n=9 of 56). The affected mice remained active, well-groomed and had normal appetite. Isolates recovered from swab cultures of the external and internal contents of the eye had partial 16S rRNA gene sequence of 99.1% similarity to Streptococcus cuniculi. No previous report of S. cuniculi infection in laboratory rodents has been presented. The isolate was susceptible to all antibiotics tested. We suggest S. cuniculi is an opportunistic bacteria in laboratory mice but are uncertain of its source. Our findings revealed that S. cuniculi is able to colonize laboratory mice and should be considered when mice present with eye lesion or ocular discharge.

Molecular detection of pathogens from ectoparasites recovered from peri-domestic animals, and the first description of a Candidatus Midichloria sp. from Haemaphysalis wellingtoni from rural communities in Malaysia.

Rural communities in Malaysia have been shown to be exposed to Coxiella, Borrelia and rickettsial infections in previous seroprevalence studies. Further research is necessary to identify the actual causative agents and the potential vectors of these infections. The arthropods parasitizing peri-domestic animals in these communities may serve as the vector in transmitting arthropod-borne and zoonotic agents to the humans. Molecular screening of bacterial and zoonotic pathogens from ticks and fleas collected from dogs, cats and chickens from six rural communities in Malaysia was undertaken. These communities were made up of mainly the indigenous people of Malaysia, known as the Orang Asli, as well as settlers in oil palm plantations. The presence of Coxiella burnetii, Borrelia, and rickettsial agents, including Rickettsia and Anaplasma, was investigated by performing polymerase chain reaction (PCR) and DNA sequencing. Candidatus Rickettsia senegalensis was detected in one out of eight pools of Ctenocephalides felis fleas. A relapsing fever group Borrelia sp. was identified from one of seven Haemaphysalis hystricis ticks tested. The results from the PCR screening for Anaplasma unexpectedly revealed the presence of Candidatus Midichloria sp., a potential tick endosymbiont, in two out of fourteen Haemaphysalis wellingtoni ticks tested. C. burnetii was not detected in any of the samples tested. The findings here provide evidence for the presence of potentially novel strains of rickettsial and borrelial agents in which their impact on public health risks among the rural communities in Malaysia merit further investigation. The detection of a potential endosymbiont of ticks also suggest that the presence of tick endosymbionts in the region is not fully explored.

Magnetic Weyl Semimetallic Phase in Thin Films of Eu_{2}Ir_{2}O_{7}.

The interplay between electronic interactions and strong spin-orbit coupling is expected to create a plethora of fascinating correlated topological states of quantum matter. Of particular interest are magnetic Weyl semimetals originally proposed in the pyrochlore iridates, which are only expected to reveal their topological nature in thin film form. To date, however, direct experimental demonstrations of these exotic phases remain elusive, due to the lack of usable single crystals and the insufficient quality of available films. Here, we report on the discovery of signatures for the long-sought magnetic Weyl semimetallic phase in (111)-oriented Eu_{2}Ir_{2}O_{7} high-quality epitaxial thin films. We observed an intrinsic anomalous Hall effect with colossal coercivity but vanishing net magnetization, which emerges right below the onset of a peculiar magnetic phase with all-in-all-out (AIAO) antiferromagnetic ordering. The anomalous Hall conductivity obtained experimentally is consistent with the theoretical prediction, likely arising from the nonzero Berry curvature emanated by Weyl node pairs near the Fermi level that act as sources and sinks of Berry flux, activated by broken cubic crystal symmetry at the top and bottom terminations of the thin film.

Enhancement of van der Waals Interlayer Coupling through Polar Janus MoSSe.

Interlayer coupling plays essential roles in the quantum transport, polaritonic, and electrochemical properties of stacked van der Waals (vdW) materials. In this work, we report the unconventional interlayer coupling in vdW heterostructures (HSs) by utilizing an emerging 2D material, Janus transition metal dichalcogenides (TMDs). In contrast to conventional TMDs, monolayer Janus TMDs have two different chalcogen layers sandwiching the transition metal and thus exhibit broken mirror symmetry and an intrinsic vertical dipole moment. Such a broken symmetry is found to strongly enhance the vdW interlayer coupling by as much as 13.2% when forming MoSSe/MoS2 HS as compared to the pristine MoS2 counterparts. Our noncontact ultralow-frequency Raman probe, linear chain model, and density functional theory calculations confirm the enhancement and reveal the origins as charge redistribution in Janus MoSSe and reduced interlayer distance. Our results uncover the potential of tuning interlayer coupling strength through Janus heterostacking.

Topological flat bands in frustrated kagome lattice CoSn.

Electronic flat bands in momentum space, arising from strong localization of electrons in real space, are an ideal stage to realize strongly-correlated phenomena. Theoretically, the flat bands can naturally arise in certain geometrically frustrated lattices, often with nontrivial topology if combined with spin-orbit coupling. Here, we report the observation of topological flat bands in frustrated kagome metal CoSn, using angle-resolved photoemission spectroscopy and band structure calculations. Throughout the entire Brillouin zone, the bandwidth of the flat band is suppressed by an order of magnitude compared to the Dirac bands originating from the same orbitals. The frustration-driven nature of the flat band is directly confirmed by the chiral d-orbital texture of the corresponding real-space Wannier functions. Spin-orbit coupling opens a large gap of 80 meV at the quadratic touching point between the Dirac and flat bands, endowing a nonzero Z2 invariant to the flat band. These findings demonstrate that kagome-derived flat bands are a promising platform for novel emergent phases of matter at the confluence of strong correlation and topology.

Isolation and Propagation of Laboratory Strains and a Novel Flea-Derived Field Strain of Wolbachia in Tick Cell Lines.

Wolbachia are intracellular endosymbionts of several invertebrate taxa, including insects and nematodes. Although Wolbachia DNA has been detected in ticks, its presence is generally associated with parasitism by insects. To determine whether or not Wolbachia can infect and grow in tick cells, cell lines from three tick species, Ixodes scapularis, Ixodes ricinus and Rhipicephalus microplus, were inoculated with Wolbachia strains wStri and wAlbB isolated from mosquito cell lines. Homogenates prepared from fleas collected from cats in Malaysia were inoculated into an I. scapularis cell line. Bacterial growth and identity were monitored by microscopy and PCR amplification and sequencing of fragments of Wolbachia genes. The wStri strain infected Ixodes spp. cells and was maintained through 29 passages. The wAlbB strain successfully infected Ixodes spp. and R. microplus cells and was maintained through 2-5 passages. A novel strain of Wolbachia belonging to the supergroup F, designated wCfeF, was isolated in I. scapularis cells from a pool of Ctenocephalides sp. cat fleas and maintained in vitro through two passages over nine months. This is the first confirmed isolation of a Wolbachia strain from a flea and the first isolation of any Wolbachia strain outside the "pandemic" A and B supergroups. The study demonstrates that tick cells can host multiple Wolbachia strains, and can be added to panels of insect cell lines to improve success rates in isolation of field strains of Wolbachia.