A new snake eel species of the genus Ophichthus (Anguilliformes: Ophichthidae) from the southeast coast of India, Bay of Bengal, with the taxonomic account of Ophichthus chilkensis

A new species of the ophichthid eel of the family Ophichthidae is described based on five specimens collected from the Mudasalodai fish landing center, off Cuddalore coast, southeast coast of India, Bay of Bengal. Ophichthus naevius sp. nov. is distinguished from its congeners by having a unique color pattern: dorsal body with numerous dense dark spots or patches, ventral body pale yellowish green, dorsal-fin origin just before pectoral-fin tip, vertebral formula: 12-14/52-53/134-138, and teeth on jaw uniserial and pointed. The study also reports the range extension and molecular evidence of Ophichthus chilkensis from South India. Molecular analyses were performed for both species, and their phylogenetic relationship suggests that the new species exhibits 10.2% genetic divergence with its congener Ophichthus sangjuensis, followed by Ophichthus brevicaudatus (10.4%), and Ophichthus sp. 1 (11.8%) also forms the closest clade in both Bayesian inference and maximum likelihood (ML) tree. Similarly, according to the topology of the ML tree, the species O. chilkensis forms a clade with Ophichthus sp. 5, Ophichthus remiger, Ophichthus frontalis, Ophichthus sp. 6, and Ophichthus rex, suggesting that it would be the genetically closest congener.

A new species of the genus Achalinus (Squamata, Xenodermatidae) from southwest Hunan Province, China

A new species of xenodermid snake, Achalinusnanshanensis H. Li, L.-Q. Zhu, Z.-Q. Zhang & X.-Y. Mo, sp. nov., is described based on three specimens collected from Nanshan National Park and Tongdao County of southwest Hunan Province. This new species is genetically distinct amongst its congeners with the mitochondrial COI uncorrected p-distance ranging from 4.4% (in A.yangdatongi) to 17.7% (in A.meiguensis). In addition, this new species can be distinguished from its congeners by a combination of the following morphological characters: (1) dorsal scales with 23 or 25 rows throughout and strongly keeled; (2) tail relatively longer so that TaL/ToL = 0.215-0.248; (3) length of suture between internasals significantly longer than that between prefrontals, LSBI/LSBP = 1.66-1.84; (4) single loreal scale present; (5) SPL 6 in number, with the fourth and fifth contacting eye; (6) IFL 6 in number, with the first three touching the first pair of chin shields; (7) TMP is 2-2-4/2-2(3)-4, with the anterior pair elongated and in contact with the eye; (8) ventrals 2 + 147-158; (9) subcaudals 64-77, unpaired; (10) dorsal body brownish black, with a bright yellow neck collar extending to the head and abdomen in the occipital region. The recognition of the new species increases the number of described Achalinus species to 28, of which 21 are found in China.

From Dormant Collections to Repositories for the Study of Habitat Changes: The Importance of Herbaria in Modern Life Sciences

In recent decades, the advent of new technologies for massive and automatized digitization, together with the availability of new methods for DNA sequencing, strongly increased the interest and relevance of herbarium collections for the study of plant biodiversity and evolution. These new approaches prompted new projects aimed at the creation of a large dataset of molecular and phenological data. This review discusses new challenges and opportunities for herbaria in the context of the numerous national projects that are currently ongoing, prompting the study of herbarium specimens for the understanding of biodiversity loss and habitat shifts as a consequence of climate changes and habitat destruction due to human activities. With regard to this, the National Biodiversity Future Center (active in Italy since 2022) started a large-scale digitization project of the Herbarium Centrale Italicum in Florence (Italy), which is the most important Italian botanical collection, consisting of more than 4 million samples at present.

A new species of the genus Leptobrachella Smith 1925 (Amphibia, Anura, Megophryidae) from Guangxi, China

A new species of Leptobrachella, L.wumingensissp. nov., was described from the Damingshan National Nature Reserve, Wuming District, Nanning City, Guangxi, China based on morphological, molecular and bioacoustic data. Phylogenetic analysis of 16S mtDNA fragments revealed that the new species is closely related to L.damingshanensis. Uncorrected p-distances between the new species and all homologous DNA sequences available for the 16S gene of Leptobrachella are greater than 7.1%. Morphologically, L.wumingensissp. nov. differs from its congeners in several ways, including a medium body size (SVL 26.0-26.7 mm in males, 30.6-34.8 mm in females), lack of toe webbing and lateral fringes, shagreened and granular dorsal surface, pale brown dorsum with darker brown markings, iris bicolored, with the upper half copper and fading to silver in the lower half, and the presence of small irregular black spots and tangerine tubercles on the flanks. Furthermore, we found the new species to have two types of advertisement calls and relatively high dominant frequencies, making it distinct from its congeners.

Integrated Approach to Highlighting the Molecular Bases of a Deep Vein Thrombosis Event in an Elite Basketball Athlete

Acute or intense exercise can result in metabolic imbalances, muscle injuries, or reveal hidden disorders. Laboratory medicine in sports is playing an increasingly crucial role in monitoring athletes' health conditions. In this study, we designed an integrated approach to explore the causes of a deep venous thrombosis event in an elite basketball player. Since the complete blood count revealed a marked platelet count (838 × 103 µL), and thrombophilia screening tests did not reveal any significant alteration, we evaluated the thrombin generation, which highlights a state of hypercoagulability. First-level haemostasis exams showed only a slight prolongation of the activated Partial Thromboplastin Time (aPTT). Thus, screening tests for von Willebrand Disease showed a reduction in vWF parameters. Therefore, we directed our hypothesis towards a diagnosis of acquired von Willebrand disease secondary to Essential Thrombocythemia (ET). To confirm this hypothesis and highlight the molecular mechanism underlying the observed phenotype, molecular tests were performed to evaluate the presence of the most common mutations associated with ET, revealing a 52-bp deletion in the coding region of CALR exon 9. This case report highlights the importance of an integrated approach to monitoring the athletes' health status to personalise training and treatments, thus avoiding the appearance of diseases and injuries that, if underestimated, can undermine the athlete's life.

A new species of the conger eel genus Macrocephenchelys from deep waters of the Arabian Sea

A new species of the genus Macrocephenchelys is described herein based on a single specimen collected from the deep-sea trawl landing at Kalamukku fish landing centre, Kerala coast, Arabian Sea. The new species is distinguished by having a dorsal-fin origin behind the middle of pectoral fin, a larger head, shorter trunk, larger gill opening, dorsal surface of body with dark-brown colour and ventral surface of head and belly with numerous patches of melanophores before anus, vertebrae 14-30-151. The new species shares most of the characteristics with Macrocephenchelys brevirostris but differs from it by having a more anterior dorsal-fin origin (vs. over the tip or slightly behind the pectoral-fin tip), larger head [15.3% total length (TL) vs. 10.5%-13.9% TL, 53.2% pre-anal length (PAL) vs. 35.8%-47.6% PAL], shorter trunk length (13.6% TL vs. 14.4%-20.6% TL, 47.3% PAL vs. 52.4%-66.2% PAL); further it shows 7.9%-8.1% genetic divergence from the sequences of M. brevirostris.

A new deep-water conger eel of the genus Rhynchoconger (Anguilliformes: Congridae) from the south-west coast of India, Arabian Sea

A new species of deep-water conger eel, Rhynchoconger bicoloratus sp. nov., is described herein based on three specimens collected from the deep-sea trawlers landing at Kalamukku fishing harbour, off Kochi, Arabian Sea, from a depth beyond 200 m. The new species is distinguished from its congeners by having the following combination of characters: head larger than trunk, rictus at posterior margin of pupil, dorsal fin origin slightly before the pectoral fin insertion, eye diameter 1.7-1.9 times in snout length, ethmovomerine teeth patch broader than long with 41-44 recurved pointed teeth in six or seven rows, vomerine teeth patch pentagonal shaped with single tooth on posterior end, 35 pre-anal vertebrae, body bicoloured, peritoneum and stomach black. Genetically, the new species differs from its congeners with a divergence of 12.9%-20.1% in the mitochondrial COI gene.

Description of a new montane freshwater crab (Arthropoda, Malacostraca, Decapoda, Potamonautidae) from the Eastern Cape, South Africa

A new species of freshwater crab, Potamonautesamatholesp. nov., is described from the Winterberg-Amathole mountain range in the Eastern Cape Province, South Africa. Morphologically, P.amathole Peer & Gouws, sp. nov. most closely resembles P.tuerkayi but can be distinguished by key morphological characters including the variation in the shape of the subterminal segment of gonopod 2 between both species. Genetically, P.amathole Peer & Gouws, sp. nov. is placed within the clade of small-bodied, mountain-dwelling crabs including P.parvispina, P.parvicorpus, P.brincki, P.tuerkayi, P.baziya, and P.depressus. The new species is found in slow-moving mountain streams and pools at high altitudes. The continued discovery and description of new freshwater crab species reinforces the need for ongoing research, especially in under-sampled regions.

Characterization of Five Psychrotolerant Alcanivorax spp. Strains Isolated from Antarctica

Five psychrotolerant Alcanivorax spp. strains were isolated from Antarctic coastal waters. Strains were screened for molecular and physiological properties and analyzed regarding their growth capacity. Partial 16S rDNA, alk-B1, and P450 gene sequencing was performed. Biolog EcoPlates and the API 20E test were used to evaluate metabolic and biochemical profiles. Bacterial growth in sodium acetate was determined at 4, 15, 20, and 25 °C to evaluate the optimal temperature. Furthermore, the ability of each strain to grow in a hydrocarbon mixture at 4 and 25 °C was assayed. Biosurfactant production tests (drop-collapse and oil spreading) and emulsification activity tests (E₂₄) were also performed. Concerning results of partial gene sequencing (16S rDNA, alk-B1, and P450), a high similarity of the isolates with the same genes isolated from other Alcanivorax spp. strains was observed. The metabolic profiles obtained by Biolog assays showed no significant differences in the isolates compared to the Alcanivorax borkumensis wild type. The results of biodegradative tests showed their capability to grow at different temperatures. All strains showed biosurfactant production and emulsification activity. Our findings underline the importance to proceed in the isolation and characterization of Antarctic hydrocarbon-degrading bacterial strains since their biotechnological and environmental applications could be useful even for pollution remediation in polar areas.

Combination of Biochemical, Molecular, and Synchrotron-Radiation-Based Techniques to Study the Effects of Silicon in Tomato (Solanum Lycopersicum L.)

The work focused on the analysis of two cultivars of tomato (Solanum lycopersicum L.), Aragon and Gladis, under two different treatments of silicon, Low, 2 L of 0.1 mM CaSiO3, and High, 0.5 mM CaSiO3, weekly, for 8 weeks, under stress-free conditions. We subsequently analyzed the morphology, chemical composition, and elemental distribution using synchrotron-based µ-XRF techniques, physiological, and molecular aspects of the response of the two cultivars. The scope of the study was to highlight any significant response of the plants to the Si treatments, in comparison with any response to Si of plants under stress. The results demonstrated that the response was mainly cultivar-dependent, also at the level of mitochondrial-dependent oxidative stress, and that it did not differ from the two conditions of treatments. With Si deposited mainly in the cell walls of the cells of fruits, leaves, and roots, the treatments did not elicit many significant changes from the point of view of the total elemental content, the physiological parameters that measured the oxidative stress, and the transcriptomic analyses focalized on genes related to the response to Si. We observed a priming effect of the treatment on the most responsive cultivar, Aragon, in respect to future stress, while in Gladis the Si treatment did not significantly change the measured parameters.

Two new Botryosphaeria (Botryosphaeriales, Botryosphaeriaceae) species in China

Five ascomycetous strains were isolated from dead branches and leaves of Salix (Salicaceae) and Osmanthusfragrans (Oleaceae), respectively. BLAST searches with ITS sequences in GenBank suggested a high degree of similarity to Botryosphaeriadothidea. To accurately identify these strains, we further analysed their morphological characteristics of asci, ascospores, all conidiophore cells and conidia. Phylogenetic relationships, based on ITS, rpb2, tef1 and tub2 gene sequences, confirmed our strains represented two novel species, which are introduced here as B.salicicola and B.osmanthuse spp. nov.

Raman Spectroscopy of Oral Candida Species: Molecular-Scale Analyses, Chemometrics, and Barcode Identification

Oral candidiasis, a common opportunistic infection of the oral cavity, is mainly caused by the following four Candida species (in decreasing incidence rate): Candida albicans, Candida glabrata, Candida tropicalis, and Candida krusei. This study offers in-depth Raman spectroscopy analyses of these species and proposes procedures for an accurate and rapid identification of oral yeast species. We first obtained average spectra for different Candida species and systematically analyzed them in order to decode structural differences among species at the molecular scale. Then, we searched for a statistical validation through a chemometric method based on principal component analysis (PCA). This method was found only partially capable to mechanistically distinguish among Candida species. We thus proposed a new Raman barcoding approach based on an algorithm that converts spectrally deconvoluted Raman sub-bands into barcodes. Barcode-assisted Raman analyses could enable on-site identification in nearly real-time, thus implementing preventive oral control, enabling prompt selection of the most effective drug, and increasing the probability to interrupt disease transmission.

Fresh tissue procurement and preparation for multicompartment and multimodal analysis of the prostate tumor microenvironment

BACKGROUND

Prostatic cancers include a diverse microenvironment of tumor cells, cancer-associated fibroblasts, and immune components. This tumor microenvironment (TME) is a known driving force of tumor survival after treatment, but the standard-of-care tissue freezing or fixation in pathology practice limit the use of available approaches/tools to study the TME's functionality in tumor resistance. Thus, there is a need for approaches that satisfy both clinical and laboratory endpoints for TME study. Here we present methods for clinical case identification, tissue processing, and analytical workflow that are compatible with standard histopathology while enabling molecular and functional interrogation of prostate TME components.

METHODS

We first performed a small retrospective review to identify cases where submission of alternate prostate tissue slices and a parallel live tissue processing protocol complement traditional histopathology and enable viable multicompartment analysis of the TME. Then, we tested its compatibility with commonly employed methods to study the microenvironment including quantification of components both in situ and after tissue dissociation. We also evaluated tissue digestion conditions and cell isolation techniques to aid various molecular and functional endpoints.

RESULTS

We identified Gleason Grade Group 3+ clinical cases where tumor volume was sufficient to allow slicing of unfixed tissue and distribution of alternating tissue slices to standard-of-care histopathology and viable multi-modal TME analyses. No single method was found that preserved cellular sub-types for all downstream readouts; instead, tissues were further divided so techniques could be catered to each endpoint. For instance, we show that incorporating the protease dispase into tissue dissociation improves viability for culture and functional analyses but hinders immune cell analysis by flow cytometry. We also found that flow activated cell sorting provides highly pure cell populations for quantitative reverse-transcription polymerase chain reaction and RNA-seq while isolation using antibody-labeled paramagnetic particles facilitated functional coculture experiments.

CONCLUSIONS

The identification of candidate cases and use of these techniques enable translational research and the development of molecular and functional assays to facilitate prostate TME study without compromising standard-of-care histopathological diagnosis. This allows bridging clinical histopathology and further interrogation of the prostate TME and promises to advance our understanding of tumor biology and unveil new predictive and prognostic markers of prostate cancer progression.

Infratentorial Stereotactic Biopsy of Brainstem and Cerebellar Lesions

Stereotactic biopsy of posterior fossa lesions is often regarded as hazardous due to the critical structures in that area. Therefore, the aim of the study was to evaluate the diagnostic accuracy and safety of infratentorial stereotactic biopsy of brainstem or cerebellar lesions and its associations with other clinical, laboratory, and radiological parameters. From January 2000 to May 2021, 190 infratentorial stereotactic biopsies of posterior fossa tumors, including 108 biopsies of brainstem lesions, were performed. Moreover, 63 supratentorial biopsies of cerebral peduncle lesions were analyzed to compare the safety and efficacy of both approaches. Additionally, the presence of antibodies against Toxoplasma gondii and Epstein–Barr Virus (EBV) were documented in 67 and 66 patients, respectively, and magnetic resonance imaging (MRI) scans were evaluated in 114 patients. Only 4% of patients had minor complications and 1.5% had major complications, including one patient who died from intracranial bleeding. Nine (4.7%) biopsies were non-diagnostic. Isocitrate dehydrogenase 1 (IDH1) mutation, 1p/19q codeletion, and O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation status were assessed in 29 patients, and were non-diagnostic in only 3 (10.3%) cases. Patients with high-grade gliomas (HGG) were more frequently seropositive for T. gondii than individuals with low-grade gliomas (LGG; p < 0.001). A total of 27% of HGG and 41% of LGG were non-enhancing on MRI. The infratentorial approach is generally safe and reliable for biopsy of brainstem and cerebellar lesions. In our study, the safety and efficacy of supratentorial biopsy of the cerebral peduncle and infratentorial biopsy of lesions below the cerebral peduncle were comparably high. Moreover, patients with HGG were more frequently seropositive for T. gondii than patients with LGG, and the relationship between toxoplasmosis and gliomagenesis requires further investigation.

First Report of Blood Fluke Pathogens with Potential Risk for Emerging Yellowtail Kingfish (Seriola lalandi) Aquaculture on the Chilean Coast, with Descriptions of Two New Species of Paradeontacylix (Aporocotylidae)

Blood flukes are digeneans that infect wild and farmed fish that can cause a severe and potentially lethal disease in farmed fish. These parasites are undetectable in the larval stage based on macroscopic observations in the definitive host with the infection becoming evident when eggs accumulate in the branchial vessels. There are nine known species of the genus Paradeontacylix and seven exclusively parasitize Seriola spp. from several geographical areas. Seriola lalandi aquaculture farms are emerging at various localities in northern Chile. Here, we report, for the first time, two blood fluke species parasitizing S. lalandi in the Southeastern Pacific (Chile). In the laboratory, the gills and heart of fish were removed. The retained blood flukes were separated according to the infection site, fixed in 70% or 95% ethanol for taxonomic and molecular analysis, respectively. Morphometrical differences among the fluke species were evaluated with a principal component analysis (PCA) using proportional body measurements. Phylogenetic trees were constructed based on 28S rDNA, cox1 mDNA using Bayesian inference (BI), and maximum likelihood (ML). Based on morphology, morphometry, and molecular analyses, two new species are proposed: P. humboldti n. sp. from the gills and P. olivai n. sp. from the heart of S. lalandi. Both were clearly distinguished from other species of Paradeontacylix by a combination of morphologic features (posterior tegumental spines, testes arrangement, body size). The genetic distance (based on cox1) among species was >10%. P. humboldti n. sp. and P. olivai n. sp. are sister species (with a common ancestor) independent of P. godfreyi from S. lalandi in Australia. The newly identified parasites may pose a risk to farmed S. lalandi as aporocotylids have been the cause of diseases in farmed fish from other geographical areas. In addition, some cages of S. lalandi are currently maintained in an open circulating system, which could favor the transmission of these parasites (if involved hosts are present in the environment).

Aspergillus niger Environmental Isolates and Their Specific Diversity Through Metabolite Profiling

We present a biological profile of 16 Aspergillus niger environmental isolates from different types of soils and solid substrates across a pH range, from an ultra-acidic (<3.5) to a very strongly alkaline (>9.0) environment. The soils and solid substrates also differ in varying degrees of anthropic pollution, which in most cases is caused by several centuries of mining activity at old mining sites, sludge beds, ore deposits, stream sediments, and coal dust. The values of toxic elements (As, Sb, Zn, Cu, Pb) very often exceed the limit values. The isolates possess different macro- and micromorphological features. All the identifications of Aspergillus niger isolates were confirmed by molecular PCR analysis and their similarity was expressed by RAMP analysis. The biochemical profile of isolates based on FF-MicroPlate tests from the Biolog system showed identical biochemical reactions in 50 tests, while in 46 tests the utilisation reactions differed. The highest similarity of strains isolated from substrates with the same pH, as well as the most suitable biochemical tests for analysis of the phenotypic similarity of isolated strains, were confirmed when evaluating the biochemical profile using multicriterial analysis in the Canoco program. The isolates were screened for mycotoxin production by thin-layer chromatography (TLC), as well. Two of them were able to synthesise ochratoxin A, while none produced fumonisins under experimental conditions. Presence of toxic compounds in contaminated sites may affect environmental microscopic fungi and cause the genome alteration, which may result in changes of their physiology, including the production of different (secondary) metabolites, such as mycotoxins.

Perinatal Exposure to Diesel Exhaust-Origin Secondary Organic Aerosol Induces Autism-Like Behavior in Rats

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by impaired social communication, poor social interactions, and repetitive behaviors. We aimed to examine autism-like behaviors and related gene expressions in rats exposed to diesel exhaust (DE)-origin secondary organic aerosol (DE-SOA) perinatally. Sprague–Dawley pregnant rats were exposed to clean air (control), DE, and DE-SOA in the exposure chamber from gestational day 14 to postnatal day 21. Behavioral phenotypes of ASD were investigated in 10~13-week-old offspring using a three-chambered social behavior test, social dominance tube test, and marble burying test. Prefrontal cortex was collected to examine molecular analyses including neurological and immunological markers and glutamate concentration, using RT-PCR and ELISA methods. DE-SOA-exposed male and female rats showed poor sociability and social novelty preference, socially dominant behavior, and increased repetitive behavior. Serotonin receptor (5-HT(5B)) and brain-derived neurotrophic factor (BDNF) mRNAs were downregulated whereas interleukin 1 β (IL-β) and heme oxygenase 1 (HO-1) mRNAs were upregulated in the prefrontal cortex of male and female rats exposed to DE-SOA. Glutamate concentration was also increased significantly in DE-SOA-exposed male and female rats. Our results indicate that perinatal exposure to DE-SOA may induce autism-like behavior by modulating molecules such as neurological and immunological markers in rats.

Acrogenospora (Acrogenosporaceae, Minutisphaerales) Appears to Be a Very Diverse Genus

During a study of diversity and taxonomy of lignicolous freshwater fungi in China, nine species of Acrogenospora were collected. Seven of these were new species and they are described and illustrated. With morphology, additional evidence to support establishment of new species is provided by phylogeny derived from DNA sequence analyses of a combined LSU, SSU, TEF1α, and RPB2 sequence dataset. Acrogenospora subprolata and A. verrucispora were re-collected and sequenced for the first time. The genus Acrogenospora is far more species rich than originally thought, with nine species found in a small area of Yunnan Province, China.

Antibiotic susceptibility and molecular analyses of clinical Enterobacter cloacae isolates in Eastern Heilongjiang Province, China

BACKGROUND

Enterobacter cloacae is an emerging opportunistic pathogen. We retrospectively conducted a study to assess antimicrobial susceptibility and investigated the Molecular characteristics of carbapenem-resistant Enterobacter cloacae (CREL) isolates.

METHODS

Three hundred forty-two isolates of Enterobacter cloacae were collected from January 2014 to December 2018. Ten strains of CREL were collected for further research. The species identifications and minimum inhibitory concentrations (MICs) of all antibiotics tested were analyzed using the Vitek 2 Compact system (BioMerieux, France) and supplemented by the disk diffusion method. Polymerase chain reaction (PCR) was performed to detect extended-spectrum β-lactamase (ESBL) and carbapenemase resistance genes.

RESULTS

The results showed that most of the isolates remained susceptible to tested antibiotics; however, the resistance rate of Cefepime has been increasing in recent years. One strain co-producing New Delhi Metallo-β-lactamase NDM-1 and Imipenem hydrolase IMP-4. NDM-1 and IMP-4-producing isolates highlight that active surveillance is necessary to prevent the further spread of the bacteria. Multilocus sequence typing (MLST) showed that two KPC-producing isolates assigned to ST93, two isolates carrying NDM-1 assigned to ST1120. Moreover, the MEGA analysis showed that ST93, ST256, and ST1120 have homology, showing that CREL in our area has a potential spread risk.

CONCLUSIONS

These findings indicating that CREL clonal dissemination may occurred in this region and should be taken seriously concern. Our study highlights an urgent need to monitor these isolates to prevent their further spread.

Morphological, Molecular, and Pathological Appraisal of Hymenolepis nana (Hymenolepididae) Infecting Laboratory Mice (Mus musculus)

Hymenolepis nana, typically a parasite found in conventionally established mouse colonies, has zoonotic potential characterized by autoinfection and direct life cycle. The objective of this study was to determine the rate of parasite infection in laboratory mice. The hymenolepidide cestode infected 40% of the 50 mice sampled. The rate of infection in males (52%) was higher than in females (28%). Morphological studies on the cestode parasite showed that worms had a globular scolex with four suckers, a retractable rostellum with 20-30 hooks, and a short unsegmented neck. In addition, the remaining strobila consisted of immature, mature, and gravid proglottids, irregularly alternating genital pores, lobulated ovaries, postovarian vitelline glands, and uteri with up to 200 eggs in their gravid proglottids. The parasite taxonomy was confirmed by using molecular characterization based on the sequence analysis of the mitochondrial cytochrome c oxidase subunit 1 (mtCOX1) gene. The parasite recovered was up to 80% identical to other species in GenBank. High blast scores and low divergence were noted between the isolated parasite and previously described H. nana (gb| AP017666.1). The phylogenetic analysis using the COX1 sequence places this hymenolepidid species of the order Cyclophyllidea.

LOXL2 Expression Status Is Correlated With Molecular Characterizations of Cervical Carcinoma and Associated With Poor Cancer Survival via Epithelial-Mesenchymal Transition (EMT) Phenotype

As molecular analyses based on high-throughput sequencing have developed, the molecular classification of cancer has facilitated clinical work. The aim of the present study was to identify a new potential therapeutic target for cervical carcinoma by molecular analyses. We firstly tested the LOXL2 expression pattern in 50 paired normal cervix and cervical carcinoma via qPCR and immunohistochemistry, and the LOXL2 expression pattern was found to be in accordance with public datasets from Gene Expression Omnibus (GEO). Then, we comprehensively rewired the 176 cervical carcinoma samples from The Cancer Genome Atlas (TCGA), subsequently clustered the samples into two groups corresponding to LOXL2 expression to determined the associations between LOXL2 expression status and molecular characterizations of cervical carcinoma. In vitro assays for further verifying the correlations in SiHa-shLOXL2 and HeLa-shLOXL2 cell lines. In this study, we found that LOXL2 highly expressed in carcinoma tissue, with 14 CpG islands of LOXL2 promoter that were significantly and negatively associated with its expression in cervical carcinoma. And there were notable correlations among LOXL2 expression status and molecular characterizations of cervical carcinoma, including diagnostic age, HPV A7 types, mRNA molecular clusters, miRNA molecular clusters, and DNA methylation molecular clusters et al. In addition, high LOXL2 expression was negatively correlated with lower tumor mutation density, especially in EP300, ERBB2, EGFR and NOTCH2, and was negatively correlated with lower expression of APOBEC3 family genes, such as APOBEC3A, APOBEC3B, APOBEC3D, and APOBEC3G. Furthermore, high LOXL2 expression was associated with poor overall (OS) and poor disease-free survival (DFS) in cervical carcinoma, and was associated with higher epithelial-mesenchymal transition (EMT) score, enrichment of extracellular matrix (ECM) signaling, the phenotype that was found to be associated with poor prognosis in cervical carcinoma from TCGA. Conversely, the ability of cell proliferation and cell migration were reversed in LOXL2 knock-down cervical cell lines via regulating the genes' expression of EMT phenotype in vitro. Overall, we demonstrated the correlation between LOXL2 expression status and cancer molecular characterizations of cervical carcinoma, and identified LOXL2 may serve as a therapeutic target for such carcinoma.

Morphophylogenetic analyses revealed that Podosphaera tridactyla constitutes a species complex

Podosphaera tridactyla (s. lat.) is a powdery mildew species occurring on a wide range of Prunus spp. almost worldwide. We have investigated the phylogeny of the Po. tridactyla complex, with special emphasis on potential aspects of cryptic speciation. The results suggested that Po. tridactyla represents a species complex consisting of at least 12 different species. Based on detailed morphological examinations and molecular sequence analyses, we propose dividing Po. tridactyla s. lat. into 10 species, encompassing 7 new species (Po. ampla, Po. pruni-avium, Po. pruni-cerasoidis, Po. prunigena, Po. pruni-lusitanicae, Po. prunina, and Po. pruni-japonicae) and 3 known species (Po. longiseta, Po. salatai, and Po. tridactyla s. str.). Oidium passerinii on Pr. laurocerasus is confirmed as a synonym of Po. tridactyla s. str. Epitypes are designated for Po. tridactyla and Oidium passerinii.

Cancer Targeted Therapy Strategy: The Pathologist's Perspectives

The effectiveness of new personalized treatment procedures in oncology is based on the fact that certain tumors exhibit specific molecular features. More in detail, neoplastic tissues of patients should display a specific biomarker, most often a specific genetic alteration and/or under/overexpression of a definite protein, that could be the target of its respective drug. Immunohistochemical and molecular analyses, which usually include examination of nucleic acids from either tissues or fluids, are common tests to define the status of a tumor. This review focuses on the pathologist's role in carefully controlling pre- analytic procedures and standard operating procedures that are a crucial prerequisite to reach reliable and reproducible results. Six paradigmatic applications of targeted therapy, for which pathological diagnosis plays a fundamental role, are summarized. Traditional and next-generation sequencing are also addressed from the pathologist's perspective as well as the importance pathologists have in this shift to more accurate definition of disease risk and prognostication of therapy response in the personalized medicine era.

Dermoscopic similarity is an independent predictor of BRAF mutational concordance in multiple melanomas

BACKGROUND

The association of clinical and dermoscopic features with BRAF mutational status has been poorly analysed in multiple primary melanomas (MPM).

OBJECTIVE

To investigate whether concordance of BRAF mutational status is associated with dermoscopic similarity in multiple melanomas of the same patient.

METHODS

Dermoscopic images and corresponding tissue sections of 124 melanomas from 62 patients with MPM were selected at four Italian Dermatology Departments. Similarity of dermoscopic appearance between multiple melanomas was evaluated according to the presence of the same prevalent dermoscopic feature. The BRAF^V600 mutational status was analysed with allele-specific TaqMan^TM assays or pyrosequencing. Spearman's correlation and univariate and multivariate regression analysis were used for statistical analysis.

RESULTS

A similar dermoscopic appearance was identified in 38.7% (24/62) of patients with MPM and was correlated with older age at first diagnosis (rho: 0.26; P: 0.042) and occurrence on sun-damaged skin (rho: 0.27; P: 0.037). The BRAF^V600 mutation was detected in 39.5% (49/124) of the tumors and a concordant BRAF mutational status between melanomas in 33/62 (53.2%) MPM patients. Dermoscopically similar melanomas showed 5.7-fold higher odds to be concordant for BRAF mutational status compared to dissimilar lesions (OR: 5.7; 95% CI 1.7-19.5; P: 0.005).

CONCLUSION

Dermoscopic similarity of multiple melanomas represents an independent clinical predictor of a concordant BRAF mutational status in MPM patients.

The evolution and molecular characteristics of H9N2 avian influenza viruses in Jiangxi of China

To understand the evolution and molecular characteristics of Jiangxi H9N2 viruses, we isolated 17 viruses in 2011 and analyzed their characteristics. Phylogenetic analyses revealed that their hemagglutinin genes originate from JS/1/00-like sublineage, neuraminidase genes originate from BJ/94-like sublineage, PB1, PA, NP, and NS genes all come from SH/F/98-like sublineage, PB2 genes originate from ST/163/04-like sublineage, while M genes come from G1-like sublineage. Genotype analysis showed that our isolates were classified as genotype 57. Molecular analyses indicated that our strains contained specific sites characteristic of low-pathogenic viruses. The current study once again highlights the necessity for continued surveillance of novel H9N2 viruses.

Diversity of Cryptosporidium in common voles and description of Cryptosporidium alticolis sp. n. and Cryptosporidium microti sp. n. (Apicomplexa: Cryptosporidiidae)

Fecal samples from wild-caught common voles (n = 328) from 16 locations in the Czech Republic were screened for Cryptosporidium by microscopy and PCR/sequencing at loci coding small-subunit rRNA, Cryptosporidium oocyst wall protein, actin and 70 kDa heat shock protein. Cryptosporidium infections were detected in 74 voles (22.6%). Rates of infection did not differ between males and females nor between juveniles and adults. Phylogenetic analysis revealed the presence of eight Cryptosporidium species/genotypes including two new species, C. alticolis and C. microti. These species from wild-caught common voles were able to infect common and meadow voles under experimental conditions, with a prepatent period of 3-5 days post-infection (DPI), but they were not infectious for various other rodents or chickens. Meadow voles lost infection earlier than common voles (11-14 vs 13-16 DPI) and had significantly lower infection intensity. Cryptosporidium alticolis infects the anterior small intestine and has larger oocysts (5.4 × 4.9 µm), whereas C. microti infects the large intestine and has smaller oocysts (4.3 × 4.1 µm). None of the rodents developed clinical signs of infection. Genetic and biological data support the establishment of C. alticolis and C. microti as separate species of the genus Cryptosporidium.

Immunohistochemical and molecular profile of salivary gland cancer in children

BACKGROUND

Pediatric salivary gland carcinomas (SGCs) are very rare. They differ from the adult SGCs in terms of epidemiologic and clinical behavior, being generally limited only to selected histotypes (e.g. low-grade mucoepidermoid [LG-MEC] and acinic cell cancer [AcCC]) and characterized by very good outcome. Our aim was to investigate therapeutic targets on a series of pediatric SGCs by immunohistochemical and molecular analysis.

METHODS

A retrospective analysis was performed to search for cases of pediatric SGCs in the database of the Pediatric Oncology Unit at the Istituto Nazionale Tumori and in the Pathology database at the Gerhard-Seifert-Reference-Centre. The expressions of the most common tyrosine-kinase receptors (TKRs) reported in adult SGCs as EGFR, HER2, KIT and hormonal receptors (HRs) (estrogen α and β, progesterone as well as androgen receptors) were investigated. CRTC1/MAML2 and MYB/NFIB were also analyzed in MEC and adenoid cystic carcinoma cases, respectively.

RESULTS

Twenty-nine cases were identified: 22 MECs, 4 AcCCs, 1 adenoid cystic carcinoma (ACC), 1 adenocarcinoma not otherwise specified and 1 sialoblastoma. EGFR was the most expressed TKR, whilst HRs were negative in all cases except for ER-β in four cases of MEC. CRTC1/MAML2 was present in 15 out of 17 evaluable MEC cases and MYB/NFIB was identified in the ACC case.

CONCLUSIONS

The immunohistochemical and molecular profiles of pediatric SGCs analyzed in our series are similar to that observed in adults, especially for MEC, supporting a common biological background.

[New developments in molecularbiological diagnostic]

Today, we have access to excellent and advanced molecular methods that are already widely used. This requires rules to control the quality of the methods as well as the laboratory. Both aspects will be discussed in the article. Following the isolation of nucleic acids they are used for genotyping which allows to address several questions: diagnosis of inherited diseases, inherited predispositions, forensic analyses, identification and typing of bacteria or viruses, elucidation of evolutionary aspects. Importantly, it has to be realized that the type and heterogeneity of phenotypically relevant mutations determines the method used for testing. Today, most laboratories use either PCR analyses or Sanger sequencing for diagnostic applications. However, increasingly next generation sequencing (NGS) is applied. The clinical use of NGS is still very challenging, but we can expect that the switch to regular application of this method will be coming in the very near future. The price for NGS has gone down to approx. USD 1000,- which makes the routine diagnostic use feasible. Nevertheless, several challenges have yet to be solved, such as the processing of the large data volume as well as storage of the data. Supporting data bases exist already and some will be discussed in the article. The understanding of the clinical relevance of many polymorphisms is another issue that has yet to be solved, particularly as in the context of personalized medicine polymorphisms have become increasingly important.

Prognostic indicators for papillary thyroid carcinoma

Differentiated thyroid cancer (DTC) includes more than 90% of all thyroid carcinoma and its incidence is growing, mainly due to an increase in the incidence of papillary thyroid cancer (PTC) for the widespread use of neck ultrasonography. Areas covered: Several prognostic factors should be considered during the management of PTC in order to provide the most effective treatment. The most important prognostic factors in PTC include personal and pathological features such as patient's age, gender, hystotype, tumor size, extrathyroidal extension, lymph node involvement, presence of local or distant metastases and molecular analyses. We performed a search in the PubMed database for studies published in English since 1960 using the terms: 'thyroid cancer', 'prognostic factors', 'age', 'gender', 'hystotype', 'tumor size', 'extrathyroidal extension', 'lymph node', 'metastases' and 'molecular analyses'. Expert commentary: Prognostic factors can guide clinicians during the treatment and follow-up of DTC patients, but it is now evident that the risk of recurrence or death must be evaluated periodically, on the basis of individual risk, according to the response to initial therapy or the subsequent therapy required during follow-up.

Human induced pluripotent stem cells generated neural cells behaving like brain and spinal cord cells: An insight into the involvement of retinoic acid and sonic hedgehog proteins

OBJECTIVES

The previous studies generated neural progenitor cells (NPCs) from human induced pluripotent stem cells (hiPSCs) using different protocols. However, the nature of the temporal or regional specificity of NPCs derived using these protocols is not well defined. Therefore, this study aimed to generate age- and region-specific NPCs from hiPSCs, which mimic in vivo fetal brain (FNPC-B) or spinal cord (FNPC-SC) tissues, in the absence or presence of retinoic acid (RA) and sonic hedgehog (SHH).

MATERIALS AND METHODS

Ventral, caudal and posterior neural cells were generated from hiPSCs with morphogens (RA and SHH), or dorsal, rostral, and anterior neural cells by the withdrawal of these morphogens from the NPC-media. NPCs generated from hiPSCs were compared to FNPC-B or FNPC-SC using immunocytochemical staining assays and global microarray for the evaluations of general and region-specific neural cells markers of neural induction, differentiation, and maturation. Microarray profiling results were analyzed using quantitative unpaired t-test (P < 0.05).

RESULTS

Immunocytochemical analyzes showed that generated NPCs expressed general neural cells markers (PAX6 and MUSASHI-2). Furthermore, FNPC-B and anterior NPCs were characterized with marked expression of cortical neural cells marker (SOX1) when compared to FNPC-SC and posterior NPCs. Microarray profiling results showed the up-regulation of brain cells markers (EMX2 and PAX6) in FNPC-B and anterior NPCs. Similarly, spinal cord cells markers (COL5A2, HOXB5, HOXB7, HOXB8, HOXC4, and HOXD4) were up-regulated in FNPC-SC and posterior NPCs.

CONCLUSION

NPCs that mimic in vivo brain and spinal cord cells can be generated from hiPSCs in the absence or presence of RA and SHH.

Unexpected diversity and a new species of Epizoanthus (Anthozoa, Hexacorallia) attached to eunicid worm tubes from the Pacific Ocean

Epizoanthus species are generally found in association with other marine invertebrates such as hermit crabs and gastropods. Although Epizoanthus spp. are relatively common, there is limited information about their diversity and ecology due to their habitats or hosts, often being below the depths of SCUBA diving (>~50 m). In particular, the Epizoanthus fauna of the Indo-Pacific Ocean remains poorly understood. In this study, the diversity of Epizoanthus species associated with eunicid worm tubes from shallow waters in the Pacific Ocean we investigated using molecular analyses (mitochondrial cytochrome oxidase subunit 1 = COI, mitochondrial 16S ribosomal DNA = mt 16S-rDNA, nuclear internal transcribed spacer region of ribosomal DNA = ITS-rDNA) combined with morphological and ecological data. The combined data set leads us to describe two new species; Epizoanthus inazuma sp. n. and Epizoanthus beriber sp. n. Both new species are found in low-light environments: Epizoanthus inazuma sp. n. on mesophotic coral reef slopes and reef floors, or on the sides of overhangs; Epizoanthus beriber sp. n. has only been found in caves. Morphological characteristics of these two new species are very similar to Epizoanthus illoricatus Tischbierek, 1930 but the two new species are genetically distinct. Mesentery numbers and coloration of polyps may be useful diagnostic characteristics among eunicid-associated Epizoanthus species. These results demonstrate that there is high potential for other potentially undescribed zoantharian species, particularly in underwater cave habitats.

Characterization of DNA Methylation in Circulating Tumor Cells

Epigenetics contributes to molecular mechanisms leading to tumor cell transformation and systemic progression of cancer. However, the dynamics of epigenetic remodeling during metastasis remains unexplored. In this context, circulating tumor cells (CTCs) might enable a direct insight into epigenetic mechanisms relevant for metastasis by providing direct access to systemic cancer. CTCs can be used as prognostic markers in cancer patients and are regarded as potential metastatic precursor cells. However, despite substantial technical progress, the detection and molecular characterization of CTCs remain challenging, in particular the analysis of DNA methylation. As recent studies have started to address the epigenetic state of CTCs, we discuss here the potential of such investigations to elucidate mechanisms of metastasis and to develop tumor biomarkers.

Utility of Classical α-Taxonomy for Biodiversity of Aquatic Nematodes

"Classical α-taxonomy" has different interpretations. Therefore, within the framework of an integrated taxonomic approach it is not relevant to divide taxonomy in different components, each being allocated a different weight of importance. Preferably, taxonomy should be seen in a holistic way, including the act of delimiting and describing taxa, based on different features and available methods, and taxonomy can not be interpreted without looking at evolutionary relationships. The concept of diversity itself is quite diverse as is the measure of diversity. Taxonomic descriptions of free-living aquatic nematodes are very valuable as they provide basic phenotypic information that is necessary for the functional ecological, behavioral, and evolutionary interpretation of data gathered from molecular analyses and of the organism as a whole. In general, molecular taxonomic analyses have the advantage of being much faster and of being able to deal with a larger number of specimens but also possess the important advantage of dealing with a huge amount of features compared to the morphology-based approach. However, just as morphological studies, molecular analyses deal only with partial of an organism.

Classical Biological Control of Invasive Legacy Crop Pests: New Technologies Offer Opportunities to Revisit Old Pest Problems in Perennial Tree Crops

Advances in scientific disciplines that support classical biological control have provided "new tools" that could have important applications for biocontrol programs for some long-established invasive arthropod pests. We suggest that these previously unavailable tools should be used in biological control programs targeting "legacy pests", even if they have been targets of previously unsuccessful biocontrol projects. Examples of "new tools" include molecular analyses to verify species identities and likely geographic area of origin, climate matching and ecological niche modeling, preservation of natural enemy genetic diversity in quarantine, the use of theory from invasion biology to maximize establishment likelihoods for natural enemies, and improved understanding of the interactions between natural enemy and target pest microbiomes. This review suggests that opportunities exist for revisiting old pest problems and funding research programs using "new tools" for developing biological control programs for "legacy pests" could provide permanent suppression of some seemingly intractable pest problems. As a case study, we use citricola scale, Coccus pseudomagnoliarum, an invasive legacy pest of California citrus, to demonstrate the potential of new tools to support a new classical biological control program targeting this insect.

A TAXONOMIC STUDY OF THE GENUS PADINA (DICTYOTALES, PHAEOPHYCEAE) INCLUDING THE DESCRIPTIONS OF FOUR NEW SPECIES FROM JAPAN, HAWAII, AND THE ANDAMAN SEA(1)

A taxonomic study of the genus Padina from Japan, Southeast Asia, and Hawaii based on morphology and gene sequence data (rbcL and cox3) resulted in the recognition of four new species, that is, Padina macrophylla and Padina ishigakiensis from Ryukyu Islands, Japan; Padina maroensis from Hawaii; and Padina usoehtunii from Myanmar and Thailand. All species are bistratose and morphologically different from one another as well as from any known taxa by a combination of characters relating to degree of calcification; the structure, position, and arrangement of hairlines (HLs) and reproductive sori; and the presence or absence of rhizoid-like groups of hairs and an indusium. Molecular phylogenetic analyses demonstrated a close relationship between P. ishigakiensis, P. macrophylla, P. maroensis, and Padina australis Hauck. The position of P. usoehtunii, however, was not fully resolved, being either sister to a clade comprising the other three new species and P. australis in the rbcL tree or more closely related to a clade comprising several other recently described species in the cox3 tree. The finding of the four new species demonstrates high species diversity particularly in southern Japan. The following characters were first recognized here to be useful for species delimitation: the presence or absence of small rhizoid-like groups of hairs on the thallus surface, structure and arrangement of HLs on both surfaces either alternate or irregular, and arrangement of the alternating HLs between both surfaces in equal or unequal distance. The evolutionary trajectory of these and six other morphological characters used in species delineation was traced on the phylogenetic tree.

Epstein-Barr virus-associated gastric carcinoma 33 years after kidney transplantation

Epstein-Barr virus-associated gastric carcinoma (EBVaGC) is a unique type of gastric cancer, defined as the presence of EBV in gastric tumour cells, usually identified by in situ hybridization. A poorly differentiated gastric adenocarcinoma was detected in a kidney recipient 33 years after transplantation. Neoplastic epithelial cells were EBV positive by in situ hybridization. Gene sequencing confirmed the amplicon specificity, and real-time polymerase chain reaction quantified 2 600 000 genomes/μL DNA in neoplastic tissue. No cases of EBVaGC have been reported in solid organ transplants, thus this is the first case of de novo EBVaGC arising in a 65-year-old renal transplant recipient.