Individual Specimens Research Articles

Human biting mosquitoes and implications for West Nile virus transmission

BackgroundWest Nile virus (WNV), primarily vectored by mosquitoes of the genus Culex, is the most important mosquito-borne pathogen in North America, having infected thousands of humans and countless wildlife since its arrival in the USA in 1999. In locations with dedicated mosquito control programs, surveillance methods often rely on frequent testing of mosquitoes collected in a network of gravid traps (GTs) and CO2-baited light traps (LTs). Traps specifically targeting oviposition-seeking (e.g. GTs) and host-seeking (e.g. LTs) mosquitoes are vulnerable to trap bias, and captured specimens are often damaged, making morphological identification difficult.MethodsThis study leverages an alternative mosquito collection method, the human landing catch (HLC), as a means to compare sampling of potential WNV vectors to traditional trapping methods. Human collectors exposed one limb for 15 min at crepuscular periods (5:00–8:30 am and 6:00–9:30 pm daily, the time when Culex species are most actively host-seeking) at each of 55 study sites in suburban Chicago, Illinois, for two summers (2018 and 2019).ResultsA total of 223 human-seeking mosquitoes were caught by HLC, of which 46 (20.6%) were mosquitoes of genus Culex. Of these 46 collected Culex specimens, 34 (73.9%) were Cx. salinarius, a potential WNV vector species not thought to be highly abundant in upper Midwest USA. Per trapping effort, GTs and LTs collected > 7.5-fold the number of individual Culex specimens than HLC efforts.ConclusionsThe less commonly used HLC method provides important insight into the complement of human-biting mosquitoes in a region with consistent WNV epidemics. This study underscores the value of the HLC collection method as a complementary tool for surveillance to aid in WNV vector species characterization. However, given the added risk to the collector, novel mitigation methods or alternative approaches must be explored to incorporate HLC collections safely and strategically into control programs.Graphical

Recuperação de amostras dessecadas da Coleção Helmintológica do Instituto Oswaldo Cruz (CHIOC)/Fiocruz por meio da técnica de reidratação de espécimes

The Helminthological Collection of the Oswaldo Cruz Institute is the biggest in Latin America and it is among the largest collections at worldwide reference level, with around 40,000 sets of specimens and approximately one million individual specimens. It contains helminths parasites of vertebrate and invertebrate animals that form part of the fauna of Brazil and other countries. The samples comprise holotypes, paratypes and representative specimens of Platyhelminthes, Acanthocephala, Nematoda and other non-helminth phyla, such as Annelida and Arthropoda. Some of the samples preserved in liquid media were found to have dried out. This made it impossible to analyze these samples morphologically for taxonomic purposes. The aim of this study was to test techniques used for rehydration of the tegument of specimens that had been found to have dried out and present protocols for such techniques. A total of 528 specimens that either no longer were immersed in preservatives or had already dried out were analyzed: 96 digenetic trematodes, 45 cestodes, 22 acanthocephalans, 357 nematodes, four hirudineans and four pentastomid crustaceans. The technique of rehydration using only distilled water on the specimens proved to be efficient for recovering tegument malleability, for all samples analyzed in this present study.

Nested singletons in molecular trees: Utility of adding morphological and geographical data from digitized herbarium specimens to test taxon concepts at species level in the case of Casearia (Salicaceae).

Using the genus Casearia, we assessed the status of nested singletons: individual specimens corresponding to accepted species but in molecular trees appearing nested within clades of closely related species. Normally, such cases would be left undecided, while on the other hand, timely taxonomic decisions are required. We argue that morphological, chorological, and ecological data can be informative to illuminate patterns of speciation. Their use can provide a first step in testing taxon concepts at species level. We focused on five cases of nested singletons in trees of the genus Casearia. We employed PCA and cluster analysis to assess phenotypic differentiation. Using geocoordinates, we calculated niche space differentiation based on 19 bioclim variables, by means of PCA and niche equivalency and similarity tests and generated dot maps. We found that the singletons were morphologically distinctive in two of the five cases (Casearia selloana and C.manausensis), relatively distinctive in two other cases (C.zizyphoides and C.mariquitensis), and partially overlapping in the last case (C.grandiflora). For two cases (C.mariquitensis and C.selloana), ecological niche space was broadly overlapping, in two cases it was found broadly nested (C.grandiflora and C.zizyphoides), and in one case narrowly nested (C.manausensis), but in no case niche differentiation was observed. Niche overlap, similarity and equivalency showed corresponding patterns. Given these data, one would interpret C.selloana and C.manausensis as presumably well-distinguished taxa, their narrow distribution ranges suggesting recently emerging lineages. The other three cases are not clearcut. Morphological data would suggest particularly C.grandiflora conspecific with C.arborea, but differences in the distribution are intriguing. Our approach would reject the notion of potential synonymy based on nested phylogenetic placement for at least two of the five cases. The other case also shows no complete lack of differentiation which would support synonymy.

Структура Растительного покрова Амутской котловины (Джергинский заповедник, Республика Бурятия)

Large-scale vegetation mapping makes it possible to assess the spatial structure of communities at the local level. The Amut Basin is one of the small intermountain basins of the Baikal rift zone. The basin was formed in a complex orographic junction of the Barguzinsky, Severo-Muysky, Yuzhno-Muysky and Ikatsky ridges. The basin is a part of the Dzherginsky Nature Reserve. It was organized to protect the natural complexes of the sources of the Barguzin River. Despite the simplicity of the vegetation structure, there is an interpenetration of elements of different phratries of formations — the Ural-Siberian, Angarid and Berengian. This indicates a complex history of the development of the vegetation cover of the territory. A large-scale geobotanical map makes it possible to create the basis for a balanced protection of the natural complexes of the reserve and contributes to identifying the local structure of the vegetation cover of the Baikal rift zone. Analysis of the resulting map shows the relative simplicity of the communities diversity in the basin. 12 groups of indigenous associations and 3 categories of derived communities have been identified. The main coenogenetic groups were not identified due to the insignificant participation of elements of the Ural-Siberian and Berengia phratries of formations. The dominant formations in the basin belong to the Angarid phratry. They are represented by Dahurian larch communities. The Berengian element of cenoses, Pinus pumila, dominates in limitedly widespread cenoses, but as an undergrowth it is found everywhere in larch forests. Pure dark coniferous forests of the Ural-Siberian phratry of cedar (Pinus sibirica) and fir (Abies sibirica) were not recorded on the territory of the basin; however, cedar undergrowth and individual cedar specimens are found regularly on the territory. Spot growth of an element of the South Siberian formations of the Ural-Siberian phratry — Caragana jubata — in coastal shrub and forest cenoses should be noted. The overall disturbance of the area’s vegetation cover is low. Traces of fires in the basin are sporadic, and burnt areas distribution is limited. Regeneration processes are actively taking place in burnt areas. The main role in the preservation of the natural complexes of the Amut Basin is played by the fact that the basin with adjacent territories is the part of the Dzherginsky Nature Reserve. The reserve was founded on the basis of a complex zakaznik (protected area) that existed here since 1974. The created map can serve as the basis for conducting monitoring observations of succession processes in the territory, identifying widespread and less widespread cenoses in the reserve, and also for zoning the territory for environmental purposes. Currently, it is planned to create a large-scale vegetation map for the entire territory of the Dzherginsky Nature Reserve.

Experimental Formability and Finite Element Studies on AISI310 Austenitic Stainless Steel

Stainless steel, an alloy comprising chromium, iron and occasionally nickel and other metals, demonstrates exceptional corrosion resistance. The transformation of metal into thin, flat components is achieved through the industrial process known as sheet metal fabrication. The utilization of metal sheets is widespread, contributing to the creation of numerous everyday items. This study aims to investigate the formability of 310 austenitic stainless steel under varying temperatures (623K, 723K, and 823K). The evaluation was executed utilizing the Nakazima test method within the context of the stretch forming procedure. Prior to delving into the assessment of formability, an exhaustive examination of the mechanical properties of the high-strength stainless steel AISI 310 was conducted. This involved subjecting the material to tensile tests at varying temperatures - specifically, 623K, 723K, and 823K - each performed at a consistent strain rate of 0.1/s. The resultant data encompassed an array of failure modes and stress-strain curves for the individual test specimens, all of which were meticulously obtained and subjected to thorough analysis.Forming limit diagrams were subsequently constructed based on the gleaned results, affording a visual representation of the material’s formability under the specific conditions studied. Moreover, these experiments were replicated through simulations employing the LS-DYNA software, with a subsequent comparative examination conducted against the tangible outcomes derived from practical experimentation.

A Note on Experimental Gigantic Eisenia and Dendrobaena Earthworms

Earthworms are iteroparous organisms with indeterminate growth, i.e. they continue to increase in size throughout their life and after completion of sexual development. Terrestrial oligochaetes vary greatly in size. Depending on the species, adult earthworms can reach between 10 mm and 3 m in length and between <1 mm and >25 mm in width, with most being of length 5-15 cm. Among the more than 7000 species described to date, very few (~20) reach lengths greater than 1 m. The longest earthworm on record is Amynthas mekongianus, which is found in the mud banks of the Mekong River in Southeast Asia and which reaches almost 3 m in length. It is about the same size as Megascolides australis, the ‘Giant Gippsland Earthworm’. These atypically giant earthworm species remain a scientific curiosity in terms of their biology, but they cannot be considered cases of gigantism. Gigantism occurs when organisms are much larger than normal or exhibit excessive growth. The biology, life cycle and growth and reproduction rates of Eisenia fetida (Savigny 1826) and Eisenia andrei (Bouché 1972), the earthworm species most commonly used in vermicomposting and vermiculture, have been widely reported. Here we present details of the enormous growth of individual specimens of Eisenia andrei and Dendrobaena hortensis reared under particular culture conditions and fed a special diet. Individuals almost 20 times the average weight of individuals of the species have been obtained. Possible explanations for this interesting phenomenon are discussed.

Article: EU Species Protection Law and Wind Energy: Current Challenges and Danish Experiences

This article highlights certain challenges as regards the reconciliation between concerns of climate change, energy security and biodiversity protection, drawing on case law of the Court of Justice of the European Union (CJEU) and the Danish experiences regarding onshore wind energy installations. The EU species protection rules are by many perceived as an obstacle to wind energy development as also reflected in the 2022 Commission proposal to amend the Renewable Energy Directive. However, it is not evident that the proposal will solve the challenges of accommodating the strict direct species protection of, in particular, Annex IV species and birds against deliberate killing or disturbance as determined by the CJEU. The article suggests that rather than setting aside the general environmental impact assessment (EIA) and appropriate assessment requirements for Natura 2000 sites, there is a need to revisit the Birds and Habitats Directives, in particular as regards ‘deliberate killing or disturbance’ caused by non-intentional activities with a view to the population level as opposed to the individual specimen level. European Union, Species protection, Biodiversity, Renewables, Wind energy

Spit or Swab? The Diagnostic Accuracy of Saliva-Based Testing as a Sars-Cov-2 Surveillance Tool

Background. Nasopharyngeal swab/oropharyngeal swab (NPS/OPS) qRT-PCR is the gold standard for detecting SARS-CoV-2. However, it has its own limitations including cost and invasiveness. As an alternative, individual qRT-PCR testing of saliva samples was validated and shown to be comparable in sensitivity and specificity with NP-OP qRT-PCR. To further maximize its utility, the researchers wish to explore antigen and pooled testing methods. Objective. The study aimed to evaluate the diagnostic accuracy of detecting SARS-CoV-2 infection using saliva-based pooled qRT-PCR and rapid antigen test compared with individual saliva qRT-PCR. Methodology. In this retrospective cross-sectional study, saliva specimen from individuals aged 18 years old and above from the outpatient specimen collection station at the Philippine Children’s Medical Center were tested individually using qRT-PCR (Mag-bind RNA Extraction Kit/MACURA, Allsheng Extraction Machine, Sansure PCR kit, and MA-600 Sansure Biotech). Non-probability convenience sampling was utilized. Based on the individual results, pools of five (5) individual specimens, which includes one (1) positive sample were tested with qRT-PCR for sensitivity. DNK-2150-1S Dynamiker SARS-CoV-2 Ag Rapid Test (Dynamiker Biotechnology Co., Ltd., Tianjin, China) was also used to test individual saliva specimens. . Out of 196 individual saliva specimens, 73 were detected to have SARS-COV-2 by qRT-PCR, while the remaining 123 were negative. Compared with the individual saliva qRT-PCR, rapid antigen tests done showed sensitivity of 46.58% (95% CI 35.13%, 58.02%), specificity of 86.18% (95% CI 80.08%, 92.28%), positive and negative predictive value of 66.67% (95% CI 53.71%, 79.60%) and 73.10% (95% CI 65.89%, 80.32%) respectively. Based on the results of individual saliva-based qRT-PCR, 62 pools were tested and showed sensitivity of 98.39% (95% CI 91.34%, 99.96%). Conclusion and Recommendation. Pooled saliva-based testing for SARS-CoV-2 is comparable with individual saliva-based rapid antigen testing. The use of rapid antigen testing is less sensitive and less specific compared with qRT-PCR consistent with prior reports. Additional studies are recommended to determine optimal conditions for testing.

UNIVERSAL CODING SYSTEM FOR PALEONTOLOGICAL COLLECTIONS AS AN EFFECTIVE BASIS FOR CREATING A UNIFIED ELECTRONIC COLLECTIONS CATALOG AT THE INSTITUTE OF GEOLOGICAL SCIENCES OF THE NAS OF UKRAINE

A method of universal coding of paleontological collections is proposed. It is aimed to organize a uniform electronic catalog of various geological collections of the Institute of Geological Sciences of the National Academy of Sciences of Ukraine (IGS NAS of Ukraine). The problems of arranging the data of the natural scientific collections in Ukraine and the peculiarities of the arrangement of paleontological collections of IGS NAS of Ukraine were considered. The absence of a unified template for labeling of paleontological collections of IGS NAS of Ukraine has been stated. This encourages us to elaborate of a convenient universal coding system for the systematization of existing and newly created paleontological collections. The proposed coding of paleontological collections is based on the unified principle of using universal abbreviations in Latin letters. The coding system consists of a full code, a short code, and a universal label. The full code is intended for coding the collection’s general characteristics and subsequent use in compiling the universal electronic catalog. The short code is needed for marking an individual specimen within any collection. The universal collection label is a necessary component in the design and storage of a collection, as it carries basic information. It also has an additional reference about the collection and contains information that is also used when compiling electronic catalogs of collections. The developed coding system is universal and maximally effective in ensuring the uniformity of the code of any collections of a certain scientific institution. It enables the researcher to code collections independently, protects against duplication of the existing code, and is a simple and convenient way of transferring information to the electronic catalog of collections. Our method greatly facilitates the distribution of information during the direct creation (code writing) of the electronic catalog and is the basis of the search system and sorting information into certain categories. This, in turn, makes it possible to have a multidisciplinary electronic catalog, by which one can find information about existing collections of a certain region, stratigraphic age, a certain paleontological group, or certain geological objects (such as samples from boreholes or outcrops). The adoption of the unified Catalogue strategy will ensure the reliable functioning of the paleontological collections of the IGS NAS of Ukraine, as well as become the basis for documenting new collections in accordance with established methodology. Finally, registering all collections is a small but important step in the direction of Open Science, namely, providing open access to information for the scientific community.

Millennial-scale drivers of small mammal isotopic niche dynamics in southern California

Quantifying the niche of contemporary and fossil organisms is key to identifying the primary factors driving species and community dynamics through time, in particular teasing apart abiotic and biotic drivers of change. However, niche quantification can be difficult due to short time spans (for contemporary systems), time averaging (for fossil systems), and incomplete information on different aspects of ecology and environment (for both contemporary and fossil systems). Here, we use stable isotope analyses coupled with specimen-level radiocarbon dating from the Rancho La Brea Tar Pits in Los Angeles, California to examine niche dynamics over the last >55,000 years. We sampled over 100 specimens of small and mid-sized mammals, mostly sciurids (squirrels) and leporids (rabbits), from Rancho La Brea to quantify their isotopic niche, track niche changes through time, and identify probable cause(s) of those changes. Individual specimens were radiocarbon dated and niches were quantified from stable carbon (δ13C) and nitrogen (δ15N) isotope analysis of fossil collagen to track individual isotopic niches at precise points in time. Overall, sciurids and leporids exhibit different isotopic signals, suggesting niche variation among taxa. Comparison of animals during the Pleistocene versus the Holocene reveals overall greater δ13C values and greater δ13C and δ15N isotopic niche breadth among Holocene individuals, suggesting that small mammal resource use changed from the last glacial to current interglacial period. Evaluating the isotopic data continuously through time against a high-resolution regional paleoclimate record shows that climate contributed to small mammal niche variation over the last 55,000 years in the Los Angeles Basin. These findings reveal the complexity of long-term abiotic and biotic forcings on organismal niches and emphasize the importance of scale and data resolution when quantifying and interpreting (paleo)ecological patterns and processes.

Comparison of linear and nonlinear stepwise μFE displacement predictions to digital volume correlation measurements of trabecular bone biopsies

Digital volume correlation (DVC) enables to evaluate the ability of μFE models in predicting experimental results on the mesoscale. In this study predicted displacement fields of three different linear and materially nonlinear μFE simulation methods were compared to DVC measured displacement fields at specific load steps in the elastic regime (StepEl) and after yield (StepUlt). Five human trabecular bone biopsies from a previous study were compressed in several displacement steps until failure. At every compression step, μCT images (resolution: 36 μm) were recorded. A global DVC algorithm was applied to compute the displacement fields at all loading steps. The unloaded 3D images were then used to generate homogeneous, isotropic, linear and materially nonlinear μFE models. Three different μFE simulation methods were used: linear (L), nonlinear (NL), and nonlinear stepwise (NLS). Regarding L and NL, the boundary conditions were derived from the interpolated displacement fields at StepEl and StepUlt, while for the NLS method nonlinear changes of the boundary conditions of the experiments were captured using the DVC displacement field of every available load step until StepEl and StepUlt. The predicted displacement fields of all μFE simulation methods were in good agreement with the DVC measured displacement fields (individual specimens: R2>0.83 at StepEl and R2>0.59 at StepUlt; pooled data: R2>0.97 at StepEl and R2>0.92 at StepUlt). At StepEl, all three simulation methods showed similar intercepts, slopes, and coefficients of determination while the nonlinear μFE models improved the prediction of the displacement fields slightly in all Cartesian directions at StepUlt (individual specimens: L: R2>0.59 and NL, NLS: R2>0.68; pooled data: L: R2>0.92 and NL, NLS: R2>0.94). Damaged/overstrained elements in L, NL, and NLS occurred at similar locations but the number of overstrained elements was overestimated when using the L simulation method. Considering the increased solving time of the nonlinear μFE models as well as the acceptable performance in displacement prediction of the linear μFE models, one can conclude that for similar use cases linear μFE models represent the best compromise between computational effort and accuracy of the displacement field predictions.

Getting Your Laboratory on Track With Neurotrophic Receptor Tyrosine Kinase.

Neurotrophic receptor tyrosine kinase (NTRK) fusion testing has both diagnostic and therapeutic implications for patient care. With 2 tumor-agnostic US Food and Drug Administration-approved tropomyosin receptor kinase (TRK) inhibitors, testing is increasingly used for therapeutic decision making. However, the testing landscape for NTRK fusions is complex, and optimal testing depends on the clinicopathologic scenario. To compare different NTRK testing methods to help pathologists understand test features and performance characteristics and make appropriate selections for NTRK fusion detection for their laboratory and individual patient specimens. A literature search for NTRK gene fusions and TRK protein was performed, including papers that discussed treatment, testing methodology, and detection or prevalence of fusion-positive cases. As standard of care in some tumor types, next-generation sequencing (NGS) panel testing is a cost effective and reliable way to detect a broad range of NTRK fusions. The design of the panel and use of DNA or RNA will affect performance characteristics. Pan-TRK immunohistochemistry may be used as a rapid, less expensive screen in cases that will not undergo routine NGS testing, or on specimens unsuitable for NGS testing. Fluorescence in situ hybridization may be appropriate for low-tumor-content specimens that are unsuitable for NGS testing. Quantitative reverse transcription polymerase chain reaction is best suited for monitoring low-level disease of a specific, previously identified target. This information should help laboratories develop a laboratory-specific NTRK testing algorithm that best suits their practice setting and patients' needs.

Accuracy of pooling specimens from different individuals in the detection of genital Chlamydia trachomatis infection: a Meta analysis

Objective: To determine the accuracy of pooled specimens from multiple individuals for detection of infection with Chlamydia trachomatis. Methods: By April 2022, PubMed and Embase searched relevant studies published in peer-reviewed journals. The QUADAS-2 scale of a quality assessment tool was used to assess the quality of the studies. A curve of summary receiver operating characteristic was applied as a comprehensive assessment of diagnosed accuracy. A bivariate mixed-effects model was used for overall value merging in sensitivity and specificity. In addition, the subgroup analyses regarding sample type, testing method, and the number of samples per pool were performed. Results: A total of 14 846 subjects were included in the analysis. Three studies were from the United States, three from Canada, three from Denmark, two from Lithuania, two from India, two from the Netherlands, and one from Australia, Russia, and Singapore. Compared with the individual specimens, the pooled specimens of multiple individuals had an overall sensitivity of 0.98 (95%CI: 0.97-0.99) and specificity of 1.00 (95%CI: 1.00-1.00) for the detection of Chlamydia trachomatis. Results from the subgroup showed that the overall sensitivity of ligase chain reaction was significantly higher than that of PCR in the diagnosis of pooled samples. Conclusion: It is concluded from the published studies that the pooled specimens were substantially consistent with the single specimens in detecting infection with Chlamydia trachomatis.

Comparative genomics of Campylobacter jejuni from clinical campylobacteriosis stool specimens

BackgroundCampylobacter jejuni is a pervasive pathogen of major public health concern with a complex ecology requiring accurate and informative approaches to define pathogen diversity during outbreak investigations. Source attribution analysis may be confounded if the genetic diversity of a C. jejuni population is not adequately captured in a single specimen. The aim of this study was to determine the genomic diversity of C. jejuni within individual stool specimens from four campylobacteriosis patients. Direct plating and pre-culture filtration of one stool specimen per patient was used to culture multiple isolates per stool specimen. Whole genome sequencing and pangenome level analysis were used to investigate genomic diversity of C. jejuni within a patient.ResultsA total 92 C. jejuni isolates were recovered from four patients presenting with gastroenteritis. The number of isolates ranged from 13 to 30 per patient stool. Three patients yielded a single C. jejuni multilocus sequence type: ST-21 (n = 26, patient 4), ST-61 (n = 30, patient 1) and ST-2066 (n = 23, patient 2). Patient 3 was infected with two different sequence types [ST-51 (n = 12) and ST-354 (n = 1)]. Isolates belonging to the same sequence type from the same patient specimen shared 12–43 core non-recombinant SNPs and 0–20 frameshifts with each other, and the pangenomes of each sequence type consisted of 1406–1491 core genes and 231–264 accessory genes. However, neither the mutation nor the accessory genes were connected to a specific functional gene category.ConclusionsOur findings show that the C. jejuni population recovered from an individual patient’s stool are genetically diverse even within the same ST and may have shared common ancestors before specimens were obtained. The population is unlikely to have evolved from a single isolate at the time point of initial patient infection, leading us to conclude that patients were likely infected with a heterogeneous C. jejuni population. The diversity of the C. jejuni population found within individual stool specimens can inform future methodological approaches to attribution and outbreak investigations.

Optimum arrangement of rubber layout for stretch bending method to improve the shape accuracy

In bending process of sheet materials, a springback is remarkable due to the residual stress generated inside of the material, which greatly affects the product accuracy. In order to suppress the springback, the rubber-assisted stretch bending method, which bending process is performed with applying a tensile force in the longitudinal direction of a sheet material has been proposed. We propose the optimum arrangement of the two kinds of rubbers for the “rubber-assisted stretch bending method” for the uniform bending with a constant curvature radius. The optimum tensile stress is realized by each frictional force between the individual rubber and specimen. And since the rubber is partially affixed to the dies, the bending deformation is carried out by the metal surface of the die material, improvement of shape accuracy can be expected. The upper and lower dies are divided into three division on the surface, and the two elastic rubbers are placed on each part on the bending surface of the die. The springback was decreased to 17% in comparison with simple bending using ordinary metal dies by the optimum arrangement of rubber layout.

Phospho-heavy-labeled-spiketide FAIMS stepped-CV DDA (pHASED) provides real-time phosphoproteomics data to aid in cancer drug selection

Global high-throughput phosphoproteomic profiling is increasingly being applied to cancer specimens to identify the oncogenic signaling cascades responsible for promoting disease initiation and disease progression; pathways that are often invisible to genomics analysis. Hence, phosphoproteomic profiling has enormous potential to inform and improve individualized anti-cancer treatment strategies. However, to achieve the adequate phosphoproteomic depth and coverage necessary to identify the activated, and hence, targetable kinases responsible for driving oncogenic signaling pathways, affinity phosphopeptide enrichment techniques are required and often coupled with offline high-pressure liquid chromatographic (HPLC) separation prior to nanoflow liquid chromatography–tandem mass spectrometry (nLC-MS/MS). These complex and time-consuming procedures, limit the utility of phosphoproteomics for the analysis of individual cancer patient specimens in real-time, and restrict phosphoproteomics to specialized laboratories often outside of the clinical setting. To address these limitations, here we have optimized a new protocol, phospho-heavy-labeled-spiketide FAIMS stepped-CV DDA (pHASED), that employs online phosphoproteome deconvolution using high-field asymmetric waveform ion mobility spectrometry (FAIMS) and internal phosphopeptide standards to provide accurate label-free quantitation (LFQ) data in real-time. Compared with traditional single-shot LFQ phosphoproteomics workflows, pHASED provided increased phosphoproteomic depth and coverage (phosphopeptides = 4617 pHASED, 2789 LFQ), whilst eliminating the variability associated with offline prefractionation. pHASED was optimized using tyrosine kinase inhibitor (sorafenib) resistant isogenic FLT3-mutant acute myeloid leukemia (AML) cell line models. Bioinformatic analysis identified differential activation of the serine/threonine protein kinase ataxia-telangiectasia mutated (ATM) pathway, responsible for sensing and repairing DNA damage in sorafenib-resistant AML cell line models, thereby uncovering a potential therapeutic opportunity. Herein, we have optimized a rapid, reproducible, and flexible protocol for the characterization of complex cancer phosphoproteomes in real-time, a step towards the implementation of phosphoproteomics in the clinic to aid in the selection of anti-cancer therapies for patients.

Drained Shear Strength Parameters Of Saprock From A Weathering Profile Over Porphyritic Biotite Granite At Km 31 Of The Kuala Lumpur - Karak Highway, Peninsular Malaysia

Three broad zones can be differentiated at the weathering profile; an upper, 9.4 m thick, pedological soil (zone I), an intermediate, 31.7 m thick, saprock (zone II) and the bottom bedrock (zone III). The saprock (zone II) comprises gravelly silty sands that distinctly preserve the minerals, textures and structures of the original bedrock and can be separated into sub-zones II A, II B, II C and II D based on differences in preservation of relict structures and content of litho-relicts (core-boulders). To characterize the drained strength of saprock, samples were collected from sub-zones II B, II C and II D, and their physical and soil index properties determined before consolidated, drained triaxial tests were carried out on remolded specimens. Three individual specimens from each sub-zone were consolidated for 24 hours and compressed at a rate of 0.152 mm/min under confining pressures of 138 kPa, 207 kPa and 276 kPa. The tests yielded effective cohesions (c’) of 30.6 kPa, 9.5 kPa, and 20.2 kPa, and friction angles of 33.2o, 31.4o and 34.4o, for the samples from sub-zones II B, II C and II D, respectively. Regression analyses show effective cohesions (c’) to increase with increasing moisture contents retained at 4.19 pF (1,500 kPa) suction; a feature indicating the influence of negative pore water pressures (matric suction). Regression analyses also show effective friction angles to increase with increasing sand, and sand and gravel, contents; a feature indicating increased inter-locking and resistance to displacement of coarse particles during shear. It is concluded that the saprock is characterized by an average effective cohesion of 14.5 kPa, and friction angle of 34.3o; these parameters influenced by the moisture content retained at 1,500 kPa suction, and the sand and gravel contents.

Metabarcoding of zooplankton to derive indicators of pelagic ecosystem status

Zooplankton play a key role in marine food webs and carbon cycling and are useful indicators of climaterelated changes and ocean health in pelagic ecosystems. Zooplankton are traditionally identified to species through microscopy, but new molecular techniques have enabled the identification of individual specimens (DNA barcoding) or multiple species in the same sample (DNA metabarcoding). Metabarcoding has been tested and refined using zooplankton collected in South African waters for the first time. Challenges to the implementation of DNA-based methods to measure zooplankton biodiversity easily and routinely include an incomplete DNA barcode reference library, logistical complexity and uptake of the new technology by environmental management agencies. These challenges call for a national effort to intensify zooplankton barcoding initiatives and to effectively engage stakeholders in developing a roadmap towards application of DNA-based methods in marine environmental management. Significance: Metabarcoding has been successfully applied to marine zooplankton for the first time in South Africa, demonstrating its potential as a tool to generate ecosystem indicators during routine ocean observations. National barcoding efforts must be intensified to provide a comprehensive reference library of zooplankton DNA. Effective engagement with stakeholders is required to overcome logistical and policy challenges, and to provide a roadmap towards application of DNA-based methods in marine environmental management.

Color change of glass ceramic restorations cemented by four types of dual-cured resin luting agents with different initiator systems.

This study aimed to comprehensively evaluate the effect of dual-cured resin luting agents with different initiator systems on the color stability of glass ceramic restorations by simulating various clinical glass ceramic restorations. Three commonly used shades from each of the two dual-cured resin luting agents with an amine-initiation system or without it were studied. The individual specimens had different translucency and thickness and were artificially aged using a xenon light aging machine. The color was measured before and after aging using a digital spectrophotometer with the difference calculated and analyzed statistically. As results, the amine-free dual-cured resin luting agents were more color stable than those using amine-initiation systems for both uncovered and bonding groups. The translucency and thickness of the ceramic, and shade and type of the resin luting agent significantly affected the color stability of glass ceramic restorations.

Cultivation and Imaging of S. latissima Embryo Monolayered Cell Sheets Inside Microfluidic Devices.

The culturing and investigation of individual marine specimens in lab environments is crucial to further our understanding of this highly complex ecosystem. However, the obtained results and their relevance are often limited by a lack of suitable experimental setups enabling controlled specimen growth in a natural environment while allowing for precise monitoring and in-depth observations. In this work, we explore the viability of a microfluidic device for the investigation of the growth of the alga Saccharina latissima to enable high-resolution imaging by confining the samples, which usually grow in 3D, to a single 2D plane. We evaluate the specimen's health based on various factors such as its growth rate, cell shape, and major developmental steps with regard to the device's operating parameters and flow conditions before demonstrating its compatibility with state-of-the-art microscopy imaging technologies such as the skeletonisation of the specimen through calcofluor white-based vital staining of its cell contours as well as the immunolocalisation of the specimen's cell wall. Furthermore, by making use of the on-chip characterisation capabilities, we investigate the influence of altered environmental illuminations on the embryonic development using blue and red light. Finally, live tracking of fluorescent microspheres deposited on the surface of the embryo permits the quantitative characterisation of growth at various locations of the organism.