Rapid Identifications Research Articles

A promoted MALDI-TOF-MS platform towards rapid and accurate identifications of bacteria

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) is emerging as the most powerful tool for the identification of bacteria. Herein, we demonstrated that the capability of MALDI-TOF-MS towards the discrimination of clinical bacteria can be further dramatically improved. A cooperative matrix consisting of (E)-propyl α-cyano-4-hydroxylcinnamylate (CHCA-C3) and α-cyano-4-hydroxycinnamic acid (CHCA) was used to replace the commonly used matrix CHCA. As a result, 1.4–3.8 times more fingerprint peaks have been identified by the cooperative matrix in comparison with CHCA when six different bacteria were studied. The peaks distribute in the wider m/z range, and the spectral quality has also been significantly improved. As an example of practical applications, the direct and more reliable discrimination between Escherichia coli (E. coli) and Shigella sonnei (S. sonnei) was achieved based on their protein fingerprints, which was previously claimed to be impossible by CHCA. Thus, a promoted MALDI-TOF-MS platform towards bacterial identification has been established by utilizing the new cooperative matrix, which will exhibit great potential for many applications.

Chromatograms and Mass Spectra of High-Mannose and Paucimannose N-Glycans for Rapid Isomeric Identifications.

N-Linked glycosylation is one of the most essential post-translational modifications of proteins. However, N-glycan structural determination remains challenging because of the small differences in structures between isomers. In this study, we constructed a database containing collision-induced dissociation MSn mass spectra and chromatograms of high-performance liquid chromatography for the rapid identification of high-mannose and paucimannose N-glycan isomers. These N-glycans include isomers by breaking of arbitrary numbers of glycosidic bonds at arbitrary positions of canonical Man9GlcNAc2 N-glycans. In addition, some GlcMannGlcNAc2 N-glycan isomers were included in the database. This database is particularly useful for the identification of the N-glycans not in conventional N-glycan standards. This study demonstrated the application of the database to structural assignment for high-mannose N-glycans extracted from bovine whey proteins, soybean proteins, human mammary epithelial cells, and human breast carcinoma cells. We found many N-glycans that are not expected to be generated by conventional biosynthetic pathways of multicellular eukaryotes.

Comparative study between gold standard real-time RT-PCR assay and rapid antigen test for detection of COVID-19 in Sylhet CMH

Background: The notorious pandemic coronavirus disease 2019 (COVID-19) has been spread all over the world. Its third pandemic wave has been completed and now a fourth wave is running over many countries. Almost 60 million people have been infected and more than 5.7 million people have died. Till now almost 1.2 million people have been infected and about 30000 people have died in Bangladesh from Covid-19. It has not only taken away human lives but also has put a tremendous impact on our society and economy. So early detection of this virus and isolating the patients have a significant role to control the disease. Henceforth there is an urgent need for simple, accurate and rapid identifications of C0VID -19. Rapid antigen tests can provide timely results, which is of particular importance in a primary setting. So, Performance of the Rapid antigen detection test (RAT) should be evaluated and compared with gold standard real-time reverse transcription-polymerase chain reaction (RT-PCR) test for diagnosis of COVID-19. Methods: Specimens were collected from both naso and oropharyngeal region from 1000 patients who reported to the flu centre in CMH Sylhet with the complaints of fever, cough & headache for detection of COVID virus-2 RNA by rapid antigen (RAT) and RT-PCR test. We used real time RT-PCR kit (Sansure, Biotech china, gene RdRP & N) and COVID-19 Ag Kit (Wondfo, Republic of China) for detection of COVID-19 RNA. Results: Out of 1000 samples 158 were positive and 842 were negative by real-time RT-PCR assay where 154 samples were positive, and 846 cases were negative by rapid antigen test for severe acute respiratory syndrome (SARS) CoV-2. The duration from the onset of symptoms to laboratory test in all suspected cases ranged from 0 to 02 days (with a median of 01 days). The rapid SARS-CoV-2 antigen detection tests sensitivity and specificity were 97.29% (95% CI, 90.06–99.89%) and 97.94% (95% CI, 97.26–98.57%), respectively. Seven samples were found negative in RAT but were found positive in RT-PCR, other three samples were found positive in RAT while they were found negative in RT-PCR. Conclusions: It is observed that most rapid antigen tests for COVID-19 are significantly comparable with RT-PCR tests and had enough sensitivity and specificity for 158 individuals, infected with severe acute respiratory syndrome-CoV-2.

The Ca∗Cl/P Ratio: A Novel and More Appropriate Screening Tool for Normocalcaemic or Overt Primary Hyperparathyroidism

ObjectiveThe main purpose of this study was to explore the diagnostic performance of the Ca∗Cl/P ratio for primary hyperparathyroidism (PHPT), especially normocalcaemic PHPT (NPHPT), to assist health care providers in making reliable and rapid clinical identifications. MethodsFrom January 1, 2013, to March 31, 2023, 230 PHPT patients, including 65 with NPHPT and 230 sex- and age-matched controls, were enrolled in this retrospective study. Differences between hypercalcaemic PHPT (HPHPT) and NPHPT and between them and their respective controls were analyzed. The diagnostic accuracy of the Ca∗Cl/P ratio, Ca/P ratio, Cl/P ratio and albumin-corrected calcium was assessed by the area under the receiver operating characteristic curve. ResultsCompared with corresponding controls, NPHPT and HPHPT patients both had significantly higher Ca ∗ Cl/P ratios (271.64 ± 51.74 vs 192.71 ± 26; 419.91 ± 139.11 vs 199.14 ± 36.75, P < .001). In the overall cohort, the ROC-AUC of the Ca∗Cl/P ratio (0.964, 95% CI = 0.943-0.979) for diagnosis of PHPT patients was superior to albumin-corrected calcium (0.959, 95% CI = 0.934-0.973), the Ca/P ratio (0.956, 95% CI = 0.934-0.973), and the Cl/P ratio (0.923, 95% CI = 0.895-0.946). A Ca ∗ Cl/P ratio above 239.17 mmol/L, with sensitivity (0.952), specificity (0.922), PPV (0.924), NPV (0.951) and accuracy (0.937), can distinguish PHPT patients from healthy individuals. Furthermore, the Ca ∗ Cl/P ratio yielded a sensitivity of 0.831, specificity of 0.938, PPV of 0.931, NPV of 0.847 and accuracy of 0.885 for NPHPT. ConclusionThe Ca∗Cl/P ratio provides excellent diagnostic power for diagnosis of PHPT, especially NPHPT.

Development of a handheld mass spectrometer driven by the sinusoidal frequency scanning technique

The rapid chemical identifications are critical when treating poisoning patients in hospitals. Conventional liquid chromatography-MS techniques would consume hours of valuable rescue time, even without considering sample transfer time. A diagnostic device readily available in emergency room would help doctors make quick treatment plan and greatly save rescue time. Over the past two decades, several key technologies have been developed for mass spectrometer miniaturization. As a first attempt, three complementary technologies (discontinuous atmospheric pressure interface, sinusoidal frequency scanning ion trap driving and Faraday detection) were integrated together, which enables the construction of a handheld mass spectrometer. The whole device weights 5.2 kg and could work for 2 h on battery. It has dimensions of 21 by 21.6 by 12.3 cm, which is able to be held by one hand. Different types of ionization sources could be coupled with the mass spectrometer to facilitate different sample analysis. This MS device has mass resolution: up to 900; limit of detection: 0.1 μg/mL. With acceptable analytical performances, this device could potentially be used in field or conventional hospitals for emergency management of poisonings. The capability of detecting drug of abuse and warfare agents/simulants were demonstrated.

Molormer: a lightweight self-attention-based method focused on spatial structure of molecular graph for drug-drug interactions prediction.

Multi-drug combinations for the treatment of complex diseases are gradually becoming an important treatment, and this type of treatment can take advantage of the synergistic effects among drugs. However, drug-drug interactions (DDIs) are not just all beneficial. Accurate and rapid identifications of the DDIs are essential to enhance the effectiveness of combination therapy and avoid unintended side effects. Traditional DDIs prediction methods use only drug sequence information or drug graph information, which ignores information about the position of atoms and edges in the spatial structure. In this paper, we propose Molormer, a method based on a lightweight attention mechanism for DDIs prediction. Molormer takes the two-dimension (2D) structures of drugs as input and encodes the molecular graph with spatial information. Besides, Molormer uses lightweight-based attention mechanism and self-attention distilling to process spatially the encoded molecular graph, which not only retains the multi-headed attention mechanism but also reduces the computational and storage costs. Finally, we use the Siamese network architecture to serve as the architecture of Molormer, which can make full use of the limited data to train the model for better performance and also limit the differences to some extent between networks dealing with drug features. Experiments show that our proposed method outperforms state-of-the-art methods in Accuracy, Precision, Recall and F1 on multi-label DDIs dataset. In the case study section, we used Molormer to make predictions of new interactions for the drugs Aliskiren, Selexipag and Vorapaxar and validated parts of the predictions. Code and models are available at https://github.com/IsXudongZhang/Molormer.

Identification of Antibiotic Resistance Proteins via MiCId's Augmented Workflow. A Mass Spectrometry-Based Proteomics Approach.

Fast and accurate identifications of pathogenic bacteria along with their associated antibiotic resistance proteins are of paramount importance for patient treatments and public health. To meet this goal from the mass spectrometry aspect, we have augmented the previously published Microorganism Classification and Identification (MiCId) workflow for this capability. To evaluate the performance of this augmented workflow, we have used MS/MS datafiles from samples of 10 antibiotic resistance bacterial strains belonging to three different species: Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. The evaluation shows that MiCId’s workflow has a sensitivity value around 85% (with a lower bound at about 72%) and a precision greater than 95% in identifying antibiotic resistance proteins. In addition to having high sensitivity and precision, MiCId’s workflow is fast and portable, making it a valuable tool for rapid identifications of bacteria as well as detection of their antibiotic resistance proteins. It performs microorganismal identifications, protein identifications, sample biomass estimates, and antibiotic resistance protein identifications in 6–17 min per MS/MS sample using computing resources that are available in most desktop and laptop computers. We have also demonstrated other use of MiCId’s workflow. Using MS/MS data sets from samples of two bacterial clonal isolates, one being antibiotic-sensitive while the other being multidrug-resistant, we applied MiCId’s workflow to investigate possible mechanisms of antibiotic resistance in these pathogenic bacteria; the results showed that MiCId’s conclusions agree with the published study. The new version of MiCId (v.07.01.2021) is freely available for download at https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads.html.

Revision of the species of Mythimna Ochsenheimer, 1816 (Pseudaletia) (Lepidoptera: Noctuidae: Noctuinae: Leucaniini) occurring in Brazil

The genus Mythimna Ochsenheimer, 1816 groups aproximatelly 270 species worldwide. This genus is subdivided into many subgenera and species-groups, with those species occurring in the Neotropical region included in the subgenus Mythimna (Pseudaletia) Franclemont, 1951. Species of this subgenus frequently reach high population levels, causing economic damage to Poaceae cultivars. Hence, it is crucial a well-defined taxonomy allowing rapid and precise identifications. However, the species of this subgenus are cryptic, their recognition requires molecular analyses and in-depth morphological studies, which has often resulted in misidentifications. In Brazil, the occurrence of the following species had been mentioned: Mythimna (P.) adultera (Schaus, 1894), Mythimna (P.) roraimae Franclemont, 1951, Mythimna (P.) sequax Franclemont, 1951, and Mythimna (P.) unipuncta (Haworth, 1809). Yet, until now, we lack a broader knowledge about the geographic distribution and taxonomy of these species. Thus, this study aims to revise the taxonomy of those species based on morphological and molecular (COI) data to provide an updated comprehension of this group in the country. The analysis of 1,664 specimens allowed us to confirm the presence of three species in the country: Mythimna (P.) adultera, Mythimna (P.) sequax, and Mythimna (P.) unipuncta. A lectotype for Mythimna (P.) adultera is designated; a new synonym is proposed: Pseudaletia roraimae syn. nov. of Mythimna (P.) unipuncta; and a new species, Mythimna (P.) celiae sp. nov. is described from Bagé, Rio Grande do Sul, Brazil.

CURRENT PERSPECTIVES OF DNA BARCODING IN BOSNIA AND HERZEGOVINA THROUGH BOLD DATABASE

UDK: 577.212:574]:007.5(497.6)&#x0D; DNA barcoding is a method designed to provide rapid and precise species identifications by using one or more of short gene sequences called barcodes. In most plant and fungi studies, the standard barcodes of choice are three plastid (rbcL, matK and trnH-psbA) and one nuclear (ITS) gene regions. The relatively high, but comparatively conserved rate of sequence evolution of mtDNA has made COI the marker of choice in animals. BOLD is a freely available cloud-based data storage and analysis platform developed with the aim to advance biodiversity science through DNA barcoding species identification. To date, over 6 million barcodes have been deposited in BOLD with 196,000 animal species, 68,000 plant species and 22,000 species of fungi and other organism entries. In this database, there are currently 447 entries for organisms from Bosnia and Herzegovina, which makes 0.0067% of the total number of BOLD entries. According to BOLD statistics, only 1.11% of all organism entries from B&amp;H were submitted by B&amp;H institutions.&#x0D; Despite the fact that Bosnia and Herzegovina has valuable natural resources with a high percentage of endemic and autochthonous species, BOLD statistics elucidated the lack of coordinated and systematic DNA barcoding research so far. It is necessary to establish continuous progress of molecular-genetic characterization of these resources in the future. It is up to B&amp;H institutions to decide if they want to continue the practice of submitting the data sporadically or if they will animate the research community to actively participate in this global project.

DNA barcoding of tropical black flies (Diptera: Simuliidae) in Thailand: One decade of progress

Black flies (Diptera: Simuliidae) are important blood sucking insects because they are the vectors of disease agents transmitted to human and other animals. Rapid and correct species identifications are necessary for all aspects of the study of black flies. DNA barcodes based on mitochondrial cytochrome c oxidase I (COI) have been effectively used for the determination of black fly species. However, the success of this method requires a large and reliable COI sequence library. In this study, 171 DNA barcoding sequences from 17 black fly species were added to NCBI GenBank database, six of these species were reported for the first time. Efficacy of DNA barcodes for species identification was examined using 1,286 sequences representing 89 nominal species of black flies in Thailand. A considerable level of success (90%) was achieved but efficiency of COI sequences for species identification was very low in the following species-groups; Simulium asakoae, S. feuerborni, S. multistriatum and S. striatum. Incomplete lineage sorting or inadequate variation of this genetic marker for differentiation of recently diverged species are the more likely explanations, and thus, more variable genetic markers are needed. Other reasons for unsuccessful DNA barcoding are imperfect taxonomy and the misidentification of sources of reference sequences. Because many new black fly species in Thailand were described recently, a reassessment of the COI sequences reported previously is necessary.

Hidden diversity of Ctenophora revealed by new mitochondrial COI primers and sequences.

The mitochondrial gene cytochrome‐c‐oxidase subunit 1 (COI) is useful in many taxa for phylogenetics, population genetics, metabarcoding, and rapid species identifications. However, the phylum Ctenophora (comb jellies) has historically been difficult to study due to divergent mitochondrial sequences and the corresponding inability to amplify COI with degenerate and standard COI “barcoding” primers. As a result, there are very few COI sequences available for ctenophores, despite over 200 described species in the phylum. Here, we designed new primers and amplified the COI fragment from members of all major groups of ctenophores, including many undescribed species. Phylogenetic analyses of the resulting COI sequences revealed high diversity within many groups that was not evident from more conserved 18S rDNA sequences, in particular among the Lobata (Ctenophora; Tentaculata; Lobata). The COI phylogenetic results also revealed unexpected community structure within the genus Bolinopsis, suggested new species within the genus Bathocyroe, and supported the ecological and morphological differences of some species such as Lampocteis cruentiventer and similar undescribed lobates (Lampocteis sp. “V” stratified by depth, and “A” differentiated by colour). The newly designed primers reported herein provide important tools to enable researchers to illuminate the diversity of ctenophores worldwide via quick molecular identifications, improve the ability to analyse environmental DNA by improving reference libraries and amplifications, and enable a new breadth of population genetic studies.

Next-Generation Breeding Strategies for Climate-Ready Crops.

Climate change is a threat to global food security due to the reduction of crop productivity around the globe. Food security is a matter of concern for stakeholders and policymakers as the global population is predicted to bypass 10 billion in the coming years. Crop improvement via modern breeding techniques along with efficient agronomic practices innovations in microbiome applications, and exploiting the natural variations in underutilized crops is an excellent way forward to fulfill future food requirements. In this review, we describe the next-generation breeding tools that can be used to increase crop production by developing climate-resilient superior genotypes to cope with the future challenges of global food security. Recent innovations in genomic-assisted breeding (GAB) strategies allow the construction of highly annotated crop pan-genomes to give a snapshot of the full landscape of genetic diversity (GD) and recapture the lost gene repertoire of a species. Pan-genomes provide new platforms to exploit these unique genes or genetic variation for optimizing breeding programs. The advent of next-generation clustered regularly interspaced short palindromic repeat/CRISPR-associated (CRISPR/Cas) systems, such as prime editing, base editing, and de nova domestication, has institutionalized the idea that genome editing is revamped for crop improvement. Also, the availability of versatile Cas orthologs, including Cas9, Cas12, Cas13, and Cas14, improved the editing efficiency. Now, the CRISPR/Cas systems have numerous applications in crop research and successfully edit the major crop to develop resistance against abiotic and biotic stress. By adopting high-throughput phenotyping approaches and big data analytics tools like artificial intelligence (AI) and machine learning (ML), agriculture is heading toward automation or digitalization. The integration of speed breeding with genomic and phenomic tools can allow rapid gene identifications and ultimately accelerate crop improvement programs. In addition, the integration of next-generation multidisciplinary breeding platforms can open exciting avenues to develop climate-ready crops toward global food security.

Integrative Description of Cryptic Tigriopus Species From Korea Using MALDI-TOF MS and DNA Barcoding

MALDI Time-of-Flight Mass Spectrometry (MALDI-TOF MS) provides a fast and reliable alternative method for species-level identification of pathogens and various metazoans. Compared to the commonly used mitochondrial cytochrome c oxidase subunit I (mtCOI) barcoding, advantages of MALDI-TOF MS are rapid species identifications and low costs. In this study, we used MALDI-TOF MS to determine whether spectra patterns of different species can be used for species identification. We obtained a total of 138 spectra from individual specimens of Tigriopus, which were subsequently used for various cluster analyses. Our findings revealed these spectra form three clear clusters with high AU value support. This study validates the viability of MALDI-TOF MS as a methodology for higher-resolution species identification, allowing detection of cryptic species of harpacticoida. In addition, we propose a new species, Tigriopus koreanus sp. nov. by utilizing integrative methods such as morphological comparison, mtCOI barcoding, and MALDI-TOF MS.

A DNA barcode-based survey of wild urban bees in the Loire Valley, France

The current decline of wild bees puts important ecosystem services such as pollination at risk. Both inventory and monitoring programs are needed to understand the causes of wild bee decline. Effective insect monitoring relies on both mass-trapping methods coupled with rapid and accurate identifications. Identifying wild bees using only morphology can be challenging, in particular, specimens from mass-trapped samples which are often in poor condition. We generated DNA barcodes for 2931 specimens representing 157 species (156 named and one unnamed species) and 28 genera. Automated cluster delineation reveals 172 BINs (Barcodes Index Numbers). A total of 36 species (22.93%) were found in highly urbanized areas. The majority of specimens, representing 96.17% of the species barcoded form reciprocally exclusive groups, allowing their unambiguous identification. This includes several closely related species notoriously difficult to identify. A total of 137 species (87.26%) show a “one-to-one” match between a named species and the BIN assignment. Fourteen species (8.92%) show deep conspecific lineages with no apparent morphological differentiation. Only two species pairs shared the same BIN making their identification with DNA barcodes alone uncertain. Therefore, our DNA barcoding reference library allows reliable identification by non-experts for the vast majority of wild bee species in the Loire Valley.

Pseudomonas Species Diversity Along the Danube River Assessed by rpoD Gene Sequence and MALDI-TOF MS Analyses of Cultivated Strains.

A collection of 611 Pseudomonas isolated from 14 sampling sites along the Danube River were identified previously by MALDI-TOF MS with the VITEK MS system and were grouped in 53 clusters by their main protein profiles. The strains were identified in the present study at the phylospecies level by rpoD gene sequencing. Partial sequences of the rpoD gene of 190 isolates representatives of all clusters were analyzed. Strains in the same MALDI-TOF cluster were grouped in the same phylospecies when they shared a minimum 95% similarity in their rpoD sequences. The sequenced strains were assigned to 34 known species (108 strains) and to 32 possible new species (82 strains). The 611 strains were identified at the phylospecies level combining both methods. Most strains were assigned to phylospecies in the Pseudomonas putida phylogenetic group of species. Special attention was given to 14 multidrug resistant strains that could not be assigned to any known Pseudomonas species and were considered environmental reservoir of antibiotic resistance genes. Coverage indices and rarefaction curves demonstrated that at least 50% of the Pseudomonas species in the Danube River able to grow in the isolation conditions have been identified at the species level. Main objectives were the confirmation of the correlation between the protein profile clusters detected by MALDI-TOF MS and the phylogeny of Pseudomonas strains based on the rpoD gene sequence, the assessment of the higher species discriminative power of the rpoD gene sequence, as well as the estimation of the high diversity of Pseudomonas ssp. along the Danube river. This study highlights the Pseudomonas species diversity in freshwater ecosystems and the usefulness of the combination of MALDI-TOF mass spectrometry for the dereplication of large sets of strains and the rpoD gene sequences for rapid and accurate identifications at the species level.

Performance of a multiplex polymerase chain reaction panel for identifying bacterial pathogens causing pneumonia in critically ill patients with COVID-19

The FilmArray® Pneumonia Plus (FA-PP) panel can provide rapid identifications and semiquantitative results for many pathogens. We performed a prospective single-center study in 43 critically ill patients with coronavirus disease 2019 (COVID-19) in which we performed 96 FA-PP tests and cultures of blind bronchoalveolar lavage (BBAL). FA-PP detected 1 or more pathogens in 32% (31/96 of samples), whereas culture methods detected at least 1 pathogen in 35% (34/96 of samples). The most prevalent bacteria detected were Pseudomonas aeruginosa (n = 14) and Staphylococcus aureus (n = 11) on both FA-PP and culture. The FA-PP results from BBAL in critically ill patients with COVID-19 were consistent with bacterial culture findings for bacteria present in the FA-PP panel, showing sensitivity, specificity, and positive and negative predictive value of 95%, 99%, 82%, and 100%, respectively. Median turnaround time for FA-PP was 5.5 h, which was significantly shorter than for standard culture (26 h) and antimicrobial susceptibility testing results (57 h).

Phase flicker optimisation in digital liquid crystal on silicon devices.

Phase flickers in the digital liquid crystal on silicon (LCOS) devices employing the pulse width modulation (PWM) driving scheme have a detrimental effect on optical performances, especially in the non-display applications. This paper investigated the relationship between the PWM waveform and the corresponding phase flicker in digital LCOS devices. It has been identified that the magnitude of the phase flicker depends on the pulse patterns in the driving waveform as well as the dynamic response of the liquid crystal molecules at different tilting angles. A simple but generic method has been developed based on these findings, which is able to accurately predict the temporal phase response of the liquid crystal to any PWM waveforms. This method is further used for rapid identifications of low-flicker PWM waveforms, without the need for increasing the complexity of the driving circuitry. The peak-to-peak phase flicker in the LCOS device under our investigation has been reduced by >80% from ∼0.16pi to ∼0.03pi when operating at 30°C.

Annotating Nontargeted LC-HRMS/MS Data with Two Complementary Tandem Mass Spectral Libraries.

Tandem mass spectral databases are indispensable for fast and reliable compound identification in nontargeted analysis with liquid chromatography–high resolution tandem mass spectrometry (LC-HRMS/MS), which is applied to a wide range of scientific fields. While many articles now review and compare spectral libraries, in this manuscript we investigate two high-quality and specialized collections from our respective institutes, recorded on different instruments (quadrupole time-of-flight or QqTOF vs. Orbitrap). The optimal range of collision energies for spectral comparison was evaluated using 233 overlapping compounds between the two libraries, revealing that spectra in the range of CE 20–50 eV on the QqTOF and 30–60 nominal collision energy units on the Orbitrap provided optimal matching results for these libraries. Applications to complex samples from the respective institutes revealed that the libraries, combined with a simple data mining approach to retrieve all spectra with precursor and fragment information, could confirm many validated target identifications and yield several new Level 2a (spectral match) identifications. While the results presented are not surprising in many ways, this article adds new results to the debate on the comparability of Orbitrap and QqTOF data and the application of spectral libraries to yield rapid and high-confidence tentative identifications in complex human and environmental samples.

Method for Mueller matrix acquisition based on a division-of-aperture simultaneous polarimetric imaging technique

The Mueller matrix is an important parameter in the field of polarization optics, and how to measure it efficiently and accurately becomes considerably significant for its practical applications. In this paper, for the first time to our knowledge, we propose a new method for Mueller matrix acquisition based on a division-of-aperture simultaneous polarimetric imaging technique. Different from the traditional method where, for obtaining the 16 elements of the Mueller matrix, a 16-times-measurement must be conducted by jointly changing the states of polarization (SOPs) of the input and output lights, while in our method it is enough by just changing the SOPs of the input light 4 times. This time-saving and easy-calculating feature is owing to our specific polarimetric camera, where a full-Stokes vector is obtained easily since 3 linear SOPs (0°, 45°, 90°) and 1 circular SOP can be recorded simultaneously by spatially sharing the same detector. To simply verify the effectiveness of our method, a specific polarization device patched by 8 sub-polarizers is chosen as the sample to be measured. Experimental results show that they are consistent with the theoretical results, both in the Mueller matrix and the corresponding images. We predict that this method for Mueller matrix acquisition can get wide potential applications for rapid identifications in biomedicine and material science.

DNA Barcoding Highlights Cryptic Diversity in the New Zealand Psylloidea (Hemiptera: Sternorrhyncha)

The insect superfamily Psylloidea (Hemiptera) includes economically important biocontrol agents, pests and plant pathogen vectors, for which a rapid and accurate identification is fundamental for international biosecurity. Australasia is a hot spot for psyllid diversity, but previous species assessments in the region were largely based on morphology and host plant association. Morphological identification of psyllids remains challenging for a wide number of species and for juvenile insects, while a robust molecular framework for identification is not available. Consequently, knowledge of psyllid biology is compromised. Here, incorporating morphological evidence and host plant associations, insects collected from almost 600 primarily New Zealand locations were linked to 67 previously described species. By applying species delimitation methods including GYMC (General Mixed Yule–Coalescent method), PTP (Poisson Tree Processes), mPTP (multi–rate Poisson Tree Processes) and ABGD (Automatic Barcode Gap Discovery) to a dataset composed of 425 cytochrome oxidase I (COI) DNA barcode sequences, further cryptic diversity was revealed among the psyllid collection; more than 20 undescribed taxa are reported here for the first time, resulting in a total of 90 taxa across 21 genera and six families included in this study. Our improved understanding of psyllid diversity in New Zealand revealed new plant host-psyllid associations and geographical variation. The DNA barcode resource will enable future studies of psyllid ecology and more accurate, rapid identifications of psyllids that pose biosecurity threats to Australasia.