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The herbivorous mud skipper, Boleophthalmus pectinirostris and carnivorous eel goby, Odontamblyopus lacepedii are important species in the mudflat ecosystem of the Ariake Sea (Japan). To gain basic knowledge of the ecological and fishery applications of the Ariake tidal flat, an important wetland area, the microbiota of the mudflat and gut contents of B. pectinirostris and O. lacepedii were analysed using 16S rDNA amplicon sequencing. The amplicon sequence variant numbers in the mud and gut of B. pectinirostris and O. lacepedii were 1200, 110, and 140, respectively. The Shannon and Simpson alpha diversity indices of the fish contents were several-fold lower than those of the mud. In mud, Exiguobacteraceae (20%), followed by Anaerolineae (13%), were identified as the predominant bacterial families. In B. pectinirostris gut, Mycoplasmoidaceae (45%) were predominant, followed by Vibrionaceae (28%). In O. lacepedii gut, Desulfovibrionaceae (17%), Brevinemataceae (Spirochaetota) (15%), Vibrionaceae (14%), and Ruminococcaceae (10%) were dominant. These results suggest that, among the wide variety of bacteria in a mud environment, only compatible bacteria can settle in the fish gut. The differences between the two fish species may be due to differences in feeding habitat. The roles of Mycoplasmoidaceae and Brevinemataceae in their hosts are subjects of future research. [ABSTRACT FROM AUTHOR]

Introduction: Classical Muscovy duck reovirus (C-MDRV) and goose-origin Muscovy duck reovirus (Go-MDRV) infections cause "Liver white-spots disease" in Muscovy duckling and gosling. It is difficult to differentiate the infections caused by C-MDRV and Go-MDRV using conventional serological methods. Methods: Specific primers were designed and synthesized according to σNS and λA nucleotide sequences of C-MDRV and Go-MDRV, respectively. The PCR amplified products were cloned into the pMD-18-T vector. The recombinant plasmid DNA was used to establish an SYBR Green І based duplex real-time PCR assay for the simultaneous detection and differentiation of C-MDRV and Go-MDRV using high-resolution melting (HRM) analysis. The specificity, sensitivity, and repeatability of the methodology were examined based on the optimization of the reaction system and amplification conditions. Results: C-MDRV and Go-MDRV were identified by their distinctive melting temperatures with 84.50 ± 0.25°C for C-MDRV and 87.50 ± 0.20°C for Go-MDRV, respectively. The amplifications were specific, and other non-targeted waterfowl viruses employed in this study did not show normalized melting peaks. The intra- and inter-assay coefficients of variations were between 0.05 and 1.83%, demonstrating good repeatability. The detection limits of this assay were 51.4 copies·μl−1 for C-MDRV and 61.8 copies·μl−1 for Go-MDRV, respectively. A total of 45 clinical samples were tested by RT-qPCR, with positive rates of 15.56% for C-MDRV and 22.22% for Go-MDRV, without co-infections. Discussion: These results suggest that this duplex RT-qPCR method is highly sensitive, specific, and reproducible. The HRM assay established in this study provides a powerful tool for the differential detection and epidemiological investigation of C-MDRV and Go-MDRV. [ABSTRACT FROM AUTHOR]

The resting spore stage of Cerataulina bicornis has been reported sporadically from the Indian Sundarbans, with one sediment core record that dates back to ∼2000 yrs. BP, but its vegetative stage has remained elusive during this entire period. The present report of its vegetative stage is a new record from this estuarine system. A comprehensive morphometric description along with molecular data of rbcL and 18s rDNA of the vegetative stage of C. bicornis is presented. The morphological and morphometric characters observed in the light microscope (LM) and scanning electron microscope (SEM) studies, along with a detailed description of the copulae, establish its distinction from other Cerataulina spp. described from different parts of the world. [ABSTRACT FROM AUTHOR]

This is the sixth contribution in a series devoted to the phylogeny and taxonomy of powdery mildews. This part includes our third treatment of the species of the genus Erysiphe. It continues the previous contribution on the phylogenetic-taxonomic assessment of the species belonging to the “Microsphaera lineage.” Since this is a large lineage, we have split the treatment of the “Microsphaera lineage” into two parts. Phylogenetic trees based on rDNA are supplemented by sequences of additional markers (CAM, GAPDH, GS, RPB2, and TUB). The “Erysiphe trifoliorum complex” is a challenging group that belongs to the “Microsphaera lineage.” Adequate clarification of this complex will be possible when additional worldwide multilocus sequence analyses are performed. The new species Erysiphe acetosae, E. acmisponis, E. lathyrina, E. salmoniana, and E. santalicola are described, and the new combinations E. biuncinata and E. pavoniae are introduced. Specimens of several species have been sequenced for the first time, particularly North American species, such as Erysiphe caryae, E. ceanothi, E. juglandis-nigrae, and E. ravenelii. Erysiphe syringae is lectotypified and 15 species names are epitypified in order to provide ex-epitype reference sequences. For other species, non-ex-type reference sequences are proposed for phylogenetic-taxonomic purposes. Ex-type sequences for Erysiphe baptisiicola, E. sesbaniae, Microsphaera sydowiana, M. umbilici, and Oidium pavoniae have been retrieved. [ABSTRACT FROM AUTHOR]

SUMMARY: Cultivar Williams 82 has served as the reference genome for the soybean research community since 2008, but is known to have areas of genomic heterogeneity among different sub‐lines. This work provides an updated assembly (version Wm82.a6) derived from a specific sub‐line known as Wm82‐ISU‐01 (seeds available under USDA accession PI 704477). The genome was assembled using Pacific BioSciences HiFi reads and integrated into chromosomes using HiC. The 20 soybean chromosomes assembled into a genome of 1.01Gb, consisting of 36 contigs. The genome annotation identified 48 387 gene models, named in accordance with previous assembly versions Wm82.a2 and Wm82.a4. Comparisons of Wm82.a6 with other near‐gapless assemblies of Williams 82 reveal large regions of genomic heterogeneity, including regions of differential introgression from the cultivar Kingwa within approximately 30 Mb and 25 Mb segments on chromosomes 03 and 07, respectively. Additionally, our analysis revealed a previously unknown large (>20 Mb) heterogeneous region in the pericentromeric region of chromosome 12, where Wm82.a6 matches the 'Williams' haplotype while the other two near‐gapless assemblies do not match the haplotype of either parent of Williams 82. In addition to the Wm82.a6 assembly, we also assembled the genome of 'Fiskeby III,' a rich resource for abiotic stress resistance genes. A genome comparison of Wm82.a6 with Fiskeby III revealed the nucleotide and structural polymorphisms between the two genomes within a QTL region for iron deficiency chlorosis resistance. The Wm82.a6 and Fiskeby III genomes described here will enhance comparative and functional genomics capacities and applications in the soybean community. Significance Statement: This study provides new genomic resources for two soybean genotypes, including a near‐gapless assembly of the community reference cultivar Williams 82. A comparison of three different Williams 82 genomes reveals large and distinct haplotypes across three of the 20 chromosomes, traceable to the original parents of Williams 82. This work reveals how introgression and recombination mechanics generated genetic heterogeneity in this cultivar and its implications for using this key genetic and genomic resource. [ABSTRACT FROM AUTHOR]

'Carteria' is a genus of quadriflagellate chlamydomonadalean green algae, however this genus is not thought to be a monophyletic group. In this study, we investigated nine strains of 'Carteria' newly isolated from China by morphological comparisons and molecular phylogeny of 18S rDNA and rbcL genes. Five strains could be identified as existing 'Carteria' species. Four strains with clearly different morphology and independent phylogenetic positions compared with the described 'Carteria' species were identified as three new species. Since the original type species, Carteria cordiformis, has been recognized as a prasinophyte alga, the generic name Carteria cannot be applied to other species previously assigned to 'Carteria'. Six 'Carteria' species (including three new species) and one Pseudocarteria species of Carteria-Clade I were transferred to the genus Corbierea, and the description of this genus was emended. A new genus, Staurocarteria gen. nov. was proposed for Carteria-Clade II. Highlights: Three new species of Carteria are described. Two correct generic names are proposed for several 'Carteria' species. This article contributes to the taxonomic revision of 'Carteria'. [ABSTRACT FROM AUTHOR]

The Trebouxiophyceae is a widespread and species-rich green algal class encompassing mostly coccoid algae with a simple spherical, ovoid or ellipsoidal outline. However, some poorly sampled lineages have evolved more elaborate shapes or even complex thalli, adding to the morphological diversity of the class. By investigating new and previously established strains, this study expands the range of morphologies exhibited by the class members by uncovering a clade of croissant-like trebouxiophytes. Phylogenetic analyses inferred from nuclear 18S rDNA and chloroplast rbcL sequences confirmed the monophyly of the 'microcroissant' clade, which we propose to be classified as a new family, Ragelichloridaceae. This family includes two novel genera, Ragelichloris and Navichloris, and the previously described Thorsmoerkia. The position of Ragelichloridaceae within Trebouxiophyceae stayed unresolved but chloroplast phylogenomics showed that the family belongs to the broader incertae sedis group that also includes Xylochloris and Leptosira. In addition, our study showed that the similar morphotype-bearing genus Chlorolobion, previously classified within Chlorophyceae, is a genuine trebouxiophyte, potentially related to Ragelichloridaceae. Highlights: A new family-level clade uncovered within the Trebouxiophyceae. Two new genera, Ragelichloris and Navichloris, are described. The genus Chlorolobion is shown to be a trebouxiophyte. [ABSTRACT FROM AUTHOR]

During a survey of plant-parasitic nematodes in South Africa's Limpopo Province, two species of Helicotylenchus were identified, namely H. dihystera and H. pseudorobustus. The morphological and molecular characteristics of these species were found to be consistent with those of the known species. A phylogenetic analysis of Helicotylenchus populations based on 28S rDNA was conducted, and it was found that the H. dihystera identified in this study belonged to the same group as other H. dihystera specimens with a 1.00 posterior probability support. Moreover, phylogenetic analysis of H. pseudorobustus based on 18S rDNA placed the test population close to other H. pseudorobustus specimens with 0.97 posterior probability. Scanning electron microscopy (SEM) for Helicotylenchus species also revealed noticeable dissimilarities in the labial disc and lateral field of the tail region between the two species from the present study, including H. pseudorobustus, and H. dihystera. The redundancy analysis (RDA) showed that H. pseudorobustus had a correlation with pH and clay of the soil. In conclusion, despite the challenges associated with identifying Helicotylenchus species, SEM and rDNA markers can be considered as highly effective tools to distinguish the species correctly and accurately. [ABSTRACT FROM AUTHOR]

LL-37 is an antimicrobial protein expressed by the CAMP gene in humans. This protein has various antibacterial, antiviral and anticancer effects. Expressing LL-37 as a heterologous protein in E. coli cells has its challenges. LL-37 is a peptide that is so small that it must be engineered with a fusion protein to increase its size solubility and prevent proteolysis of the target protein in cells. Factor Xa is the protease chosen to cleave LL-37 from its fusion protein in this research due to leucine binding factor Xa quite strongly. The aim of this study is, therefore, to express LL-37 as a fusion protein with Histaq_SUMO at the N-terminus linked to LL-37 at the C-terminus through Factor Xa cleavage site. Then, the fusion protein was cleaved by Factor Xa to obtain pure LL-37. In this study, LL-37 was produced by recombinant DNA technology, starting with the construction, expression, purification and cleavage of the fusion protein. The constructed genes consisted of 6xHis, SUMO, the factor X cleavage site, and LL-37, a total of 450 bp inserted in the pD451-SR vector plasmid. The results of this study yielded a SUMO_LL-37 protein with a molecular weight of approximately 17.34 kDa, which could be purified by Ni-NTA under native purification conditions. Based on ImageJ SUMO_LL-37 quantification, it was 1.65 µg/µL. LL-37 can be cleaved by factor Xa from SUMO with an enzyme-to-substrate ratio of 1:12.5 at 37°C with a 24-hour incubation time and results as much as 0.144 µg/µL. [ABSTRACT FROM AUTHOR]

Establishing a highly efficient photoactivatable Cre recombinase PA‐Cre3.0 can allow spatiotemporal control of Cre recombinase activity. This technique may help to elucidate cell lineages, as well as facilitate gene and cell function analysis during development. This study examined the blue light‐mediated optical regulation of Cre‐loxP recombination using PA‐Cre3.0 transgenic early mouse pre‐implantation embryos. We found that inducing PA‐Cre3.0 expression in the heterozygous state did not show detectable recombination activation with blue light. Conversely, in homozygous embryos, DNA recombination by PA‐Cre3.0 was successfully induced by blue light and resulted in the activation of the red fluorescent protein reporter gene, while almost no leaks of Cre recombination activity were detected in embryos without light illumination. Thus, we characterize the conditions under which the PA‐Cre3.0 system functions efficiently in early mouse embryos. These results are expected to provide a new optogenetic tool for certain biological studies, such as developmental process analysis and lineage tracing in early mouse embryos. [ABSTRACT FROM AUTHOR]

Background: Aside from the canonical role of PDL1 as a tumour surface-expressed immune checkpoint molecule, tumour-intrinsic PDL1 signals regulate non-canonical immunopathological pathways mediating treatment resistance whose significance, mechanisms, and therapeutic targeting remain incompletely understood. Recent reports implicate tumour-intrinsic PDL1 signals in the DNA damage response (DDR), including promoting homologous recombination DNA damage repair and mRNA stability of DDR proteins, but many mechanistic details remain undefined. Methods: We genetically depleted PDL1 from transplantable mouse and human cancer cell lines to understand consequences of tumour-intrinsic PDL1 signals in the DNA damage response. We complemented this work with studies of primary human tumours and inducible mouse tumours. We developed novel approaches to show tumour-intrinsic PDL1 signals in specific subcellular locations. We pharmacologically depleted tumour PDL1 in vivo in mouse models with repurposed FDA-approved drugs for proof-of-concept clinical translation studies. Results: We show that tumour-intrinsic PDL1 promotes the checkpoint kinase-2 (Chk2)-mediated DNA damage response. Intracellular but not surface-expressed PDL1 controlled Chk2 protein content post-translationally and independently of PD1 by antagonising PIRH2 E3 ligase-mediated Chk2 polyubiquitination and protein degradation. Genetic tumour PDL1 depletion specifically reduced tumour Chk2 content but not ATM, ATR, or Chk1 DDR proteins, enhanced Chk1 inhibitor (Chk1i) synthetic lethality in vitro in diverse human and murine tumour models, and improved Chk1i efficacy in vivo. Pharmacologic tumour PDL1 depletion with cefepime or ceftazidime replicated genetic tumour PDL1 depletion by reducing tumour Chk2, inducing Chk1i synthetic lethality in a tumour PDL1-dependent manner, and reducing in vivo tumour growth when combined with Chk1i. Conclusions: Our data challenge the prevailing surface PDL1 paradigm, elucidate important and previously unappreciated roles for tumour-intrinsic PDL1 in regulating the ATM/Chk2 DNA damage response axis and E3 ligase-mediated protein degradation, suggest tumour PDL1 as a biomarker for Chk1i efficacy, and support the rapid clinical potential of pharmacologic tumour PDL1 depletion to treat selected cancers. [ABSTRACT FROM AUTHOR]

In the present study, the DNA barcoding of the nematode parasite infecting Ompok bimaculatus and Nemacheilus anguilla fish species was carried out in Barvi Reservoir, Maharashtra. To ascertain the taxonomic status of these nematode parasites, an 18S gene marker was used. Accurate identification of fish parasites is essential to formulate preventive strategies and to study host–environment relations. The present study did barcoding of the nematode parasites of the fishes caught from the Barvi Reservoir using the nuclear 18S rDNA (SSU) sequence. The nuclear 18S rDNA (SSU) was amplified into two overlapping amplicons and sequenced to identify the species based on the sequence similarity with the NCBI GenBank database. The present study sequences (both fragments) showed 98% similarity with the species of Eustrongylides. The average genetic distance value between the present study sample and species of Eustrongylides was 0.003. In the phylogenetic tree also, the sequence was clustered with the species of Eustrongylides with significant bootstrap values. The present study identified the nematode parasite of the fish caught from the Barvi Reservoir, as species of Eustrongylides. The species‐level identification could not be possible due to the insufficient/lack of reference sequences in the database. It indicates the knowledge gap concerning the species‐specific molecular markers for nematode parasites of the fish. [ABSTRACT FROM AUTHOR]

During development, most cells experience a progressive restriction of fate that ultimately results in a fully differentiated mature state. Understanding more about the gene expression patterns that underlie developmental programs can inform engineering efforts for new or optimized forms. Here, we present a four-state integrase-based recorder of gene expression history and demonstrate its use in tracking gene expression events in Arabidopsis thaliana in two developmental contexts: lateral root initiation and stomatal differentiation. The recorder uses two serine integrases to mediate sequential DNA recombination events, resulting in step-wise, history-dependent switching between expression of fluorescent reporters. By using promoters that express at different times along each of the two differentiation pathways to drive integrase expression, we tie fluorescent status to an ordered progression of gene expression along the developmental trajectory. In one snapshot of a mature tissue, our recorder is able to reveal past gene expression with single cell resolution. In this way, we are able to capture heterogeneity in stomatal development, confirming the existence of two alternate paths of differentiation. Understanding gene expression patterns that underlie developmental programs can inform engineering efforts for new or optimized forms. Here, the authors engineer a four-state history-dependent integrase-based recorder of gene expression in Arabidopsis and show its application in two developmental programs. [ABSTRACT FROM AUTHOR]

Homologous recombination during meiosis is critical for chromosome segregation and also gives rise to genetic diversity. Genetic exchange between homologous chromosomes during meiosis is mediated by the recombinase Dmc1, which is capable of recombining DNA sequences with mismatches. The Hop2-Mnd1 complex mediates Dmc1 activity. Here, we reveal a regulatory role for Hop2-Mnd1 in restricting substrate selection. Specifically, Hop2-Mnd1 upregulates Dmc1 activity with DNA substrates that are either fully homologous or contain DNA mismatches, and it also acts against DNA strand exchange between substrates solely harboring microhomology. By isolating and examining salient Hop2-Mnd1 separation-of-function variants, we show that suppressing illegitimate DNA recombination requires the Dmc1 filament interaction attributable to Hop2-Mnd1 but not its DNA binding activity. Our study provides mechanistic insights into how Hop2-Mnd1 helps maintain meiotic recombination fidelity. Homologous recombination ensures chromosome segregation and genetic diversity. Here, the authors reveal a role for the Hop2-Mnd1 complex in maintaining Dmc1-mediated recombination fidelity by preventing illegitimate DNA exchanges. [ABSTRACT FROM AUTHOR]

AbstractGenus Calvatia belongs to a gasteroid fungi which are commonly known as a puffball mushrooms including around 47 species worldwide. Approximately 25 species of the genus Calvatia have been reported previously in India from various forest regions; however, only 15 species of these are accepted on their current taxonomic status because several of them are synonymized with other genera or species. The present study reports the distribution of Calvatia holothurioides which was collected from Jambughoda Wildlife Sanctuary in Gujarat state, India. The identification was carried out based on the morphological characteristics as well as molecular phylogenetic analysis using nuclear rDNA Internal Transcribed Spacer (ITS) and rDNA LSU gene sequences data. Nucleotide sequences of different gene loci (ITS and LSU) were submitted into the BOLD data system for DNA barcoding. Additionally, this study also provides a literature-based checklist for the present status of Calvatia species reported in India so far. [ABSTRACT FROM AUTHOR]

Asterostroma roseoalbum sp. nov. was found in Yunnan Province, China, is described here as a new species based on its morphology and phylogeny. Asterostroma roseoalbum is characterised by its felted-membranous to pellicular, fimbriate basidiomata with a smooth hymenophore and a dimitic hyphal system bearing generative hyphae with simple-septate and echinulate, subglobose to globose basidiospores measuring as 8–9.5 × 7–9 µm. Phylogenetic analyses of the new species were based on the internal transcribed spacer (ITS) and large subunit (nrLSU) of ribosomal DNA (rDNA) sequences. The phylogenetic analysis indicated that the new species belongs to the genus Asterostroma, and is closely related to two species A. macrosporum and A. muscicola. A full description, illustrations and phylogenetic analysis results of the new species are provided. Furthermore, a key to the genus Asterostroma in China is provided. [ABSTRACT FROM AUTHOR]

Background: Evidence shows that full mycoheterotrophs and holoparasites often have reduced plastid genomes with rampant gene loss, elevated substitution rates, and deeply altered to conventional evolution in mitochondrial genomes, but mechanisms of cytonuclear evolution is unknown. Endoparasitic Sapria himalayana and mycoheterotrophic Gastrodia and Platanthera guangdongensis represent different heterotrophic types, providing a basis to illustrate cytonuclear evolution. Here, we focused on nuclear-encoded plastid / mitochondrial (N-pt / mt) -targeting protein complexes, including caseinolytic protease (ClpP), ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCo), oxidative phosphorylation system (OXPHOS), DNA recombination, replication, and repair (DNA-RRR) system, and pentatricopeptide repeat (PPR) proteins, to identify evolutionary drivers for cytonuclear interaction. Results: The severity of gene loss of N-pt PPR and pt-RRR genes was positively associated with increased degree of heterotrophy in full mycoheterotrophs and S. himalayana, while N-mt PPR and mt-RRR genes were retained. Substitution rates of organellar and nuclear genes encoding N-pt/mt subunits in protein complexes were evaluated, cytonuclear coevolution was identified in S. himalayana, whereas disproportionate rates of evolution were observed in the OXPHOS complex in full mycoheterotrophs, only slight accelerations in substitution rates were identified in N-mt genes of full mycoheterotrophs. Conclusions: Nuclear compensatory evolution was identified in protein complexes encoded by plastid and N-pt genes. Selection shaping codon preferences, functional constraint, mt-RRR gene regulation, and post-transcriptional regulation of PPR genes all facilitate mito-nuclear evolution. Our study enriches our understanding of genomic coevolution scenarios in fully heterotrophic plants. [ABSTRACT FROM AUTHOR]

PML, a multifunctional protein, is crucial for forming PML- nuclear bodies involved in stress responses. Under specific conditions, PML associates with nucleolar caps formed after RNA polymerase I (RNAPI) inhibition, leading to PML- nucleolar associations (PNAs). This study investigates PNAs- inducing stimuli by exposing cells to various genotoxic stresses. We found that the most potent inducers of PNAs introduced topological stress and inhibited RNAPI. Doxorubicin, the most effective compound, induced double- strand breaks (DSBs) in the rDNA locus. PNAs co- localized with damaged rDNA, segregating it from active nucleoli. Cleaving the rDNA locus with I- PpoI confirmed rDNA damage as a genuine stimulus for PNAs. Inhibition of ATM, ATR kinases, and RAD51 reduced I- PpoI- induced PNAs, highlighting the importance of ATM/ATR- dependent nucleolar cap formation and homologous recombination (HR) in their triggering. I- PpoI- induced PNAs co- localized with rDNA DSBs positive for RPA32- pS33 but deficient in RAD51, indicating resected DNA unable to complete HR repair. Our findings suggest that PNAs form in response to persistent rDNA damage within the nucleolar cap, highlighting the interplay between PML/PNAs and rDNA alterations due to topological stress, RNAPI inhibition, and rDNA DSBs destined for HR. Cells with persistent PNAs undergo senescence, suggesting PNAs help avoid rDNA instability, with implications for tumorigenesis and aging. [ABSTRACT FROM AUTHOR]

The planktonic dinoflagellate genus Centrodinium has been understudied, with the type species C. elongatum remaining undocumented since the original description. Here, we report C. elongatum isolated from Mazatlán, Mexican Pacific. In the chains, the posterior daughter cell with an incomplete apical horn shows the morphology of C. elongatum, while the anterior daughter cell with complete epitheca corresponds to C. pulchrum. For the first time, a species of Centrodinium sensu stricto (highly laterally flattened species with horns) was cultured. An unarmored life stage, known as Murrayella ovalis, derived from the spheroplast after ecdysis. In the rDNA molecular phylogenies, C. elongatum (=C. pulchrum) nested as basal to morphologically similar species (C. eminens and C. intermedium) and as a sister group of a former Murrayella species, C. punctatum. C. elongatum differs from C. eminens and C. intermedium in the chain formation, second apical (2′) plate not being divided, horns with coarse poroid ornamentation, and missing prominent distal spinules. The taxonomy of Centrodinium sensu stricto is revised, with a discussion in the identities of C. complanatum, C. eminens, and C. maximum. The name C. deflexum is restored as a senior synonym of C. intermedium and C. ovale. [ABSTRACT FROM AUTHOR]

Mesopsammic polyclad members in the family Boniniidae have attracted attention in terms of their evolutionary shifts of microhabitat and their unique morphology such as a pair of pointed tentacles extending from the anterolateral margins and prostatoid organs harbouring stylets. Here, we establish a new species of this family as Boninia panamensis sp. nov. from the Pacific coasts of Panama, based on its morphological characteristics of (i) four cerebral and 61–80 marginal eyespots, (ii) two prostatoid organs located anterior and posterior to the penis papilla, and (iii) two uterine canals departing from the anterior part of the Lang's vesicle. We also report Boninia cf. uru from Hawai'i, USA, based on its morphological identity with B. uru from Okinawa, Japan, along with their genetic distances for the partial cytochrome c oxidase subunit I (COI) sequences, which were beyond the range of intraspecific differences observed in congeners in this study. Boninia oaxaquensis is also reported from Panama as a new locality for the species. Involving the above-mentioned three species sequenced herein, we reconstructed molecular phylogenetic trees of Boninia based on the four gene markers (18S rDNA, 28S rDNA, 16S rDNA and COI). Our phylogenetic trees indicated the synapomorphy within the genus Boninia of the small numbers of stylets (2–4) and the connection route of the uterine canals to the Lang's vesicle. The results also showed a characteristic distribution pattern in which pairs of species in distinct lineages occurred sympatrically with different microhabitats, as observed in Boninia uru and Boninia yambarensis in Okinawa and B. panamensis sp. nov. and B. oaxaquensis in Panama. In addition, we discuss possible speciation pathways in this genus based on the tree topology. ZooBank: Boniniidae is a family of marine polyclad flatworms harbouring nine named species distributed worldwide. We describe a new boniniid species, Boninia panamensis from the Pacific coasts of Panama based on morphological and molecular data. We also report Boninia cf. uru from Hawai'i and Boninia oaxaquensis from Panama along with morphological descriptions. In addition, we discuss synapomorphic traits and possible speciation pathways in this genus based on the reconstructed molecular phylogenetic results using 18S rDNA, 28S rDNA, 16S rDNA and COI. (Photograph by Marco Curini-Galletti.) [ABSTRACT FROM AUTHOR]

The cestode family Gymnorhynchidae (Trypanorhyncha) comprises three genera and six valid species that, as adults, are all intestinal parasites of large pelagic sharks. Their life cycle has not been elucidated yet, but it has been proposed that copepods serve as first, pelagic euphausiids or schooling fish as second, and larger predatory fishes as third intermediate hosts. Molidae fish have been proposed as intermediate hosts for at least two gymnorhynchid species (i.e., Molicola horridus and M. uncinatus). During a parasitological survey of fish from the coast of Kerala (India), some individuals of a gymnorhynchid species were found in a sharptail mola Masturus lanceolatus. Parasites were located on the subcapsular tissue of liver showing a serpiginous route. Based on 28S rDNA molecular and phylogenetic analysis, parasites were identified as Gymnorhynchus isuri, which resulted genetically identical to G. isuri obtained from the liver of a sun fish Mola mola in the Mediterranean Sea. [ABSTRACT FROM AUTHOR]

In an extensive fungal investigation conducted in southern China, a large number of fungal strains were isolated by collecting and treating diseased and decayed leaves. Using internal transcribed spacer regions (ITSs) sequence data for a BLAST search to screen for suspected strains of Daldinia, followed by phylogenetic analysis using internal transcribed spacer regions, partial sequences of the large subunit of the rDNA (LSU), RNA polymerase II (rpb2), and beta tubulin (tub2) sequence data, combined with morphological characteristics of anamorphic species, ninety-four strains of Daldinia were identified. Furthermore, their geographical distribution and host specificity of the genus were thoroughly analyzed and summarized. Additionally, seven new anamorphic species of the genus Daldinia were also detected, Daldinia ehretiae sp. nov., D. jianfengensis sp. nov., D. ledongensis sp. nov., D. menghaiensis sp. nov., D. rhododendri sp. nov., D. spatholobi sp. nov., and D. thunbergiae sp. nov. [ABSTRACT FROM AUTHOR]

Diatoms are among the most important primary producers in alpine and polar freshwaters. Although temperate diatoms are sensitive to freezing, polar diatoms often exhibit more resistance. This is particularly true for members of the (predominantly terrestrial) Pinnularia borealis species complex. However, it remains unclear to what extent this resistance applies to other representatives of the genus. Here, we compare the freezing‐stress tolerance of 11 freshwater, benthic strains representing different species of Pinnularia (including Caloneis) from polar, alpine, and temperate habitats. As vegetative cells, strains were exposed to freezing temperatures of −4, −10, −20, −40, −80, and −196°C. Survival was assessed by light microscopy and photosynthetic measurements. We observed vegetative cells to be sensitive to low freezing temperatures; only "mild" freezing was survived by all tested strains, and most tested strains did not survive treatments ≤−10°C. However, individual strain sensitivities appeared related to their original habitats. For example, polar and alpine strains better withstood "mild" and "moderate" freezing (−4 and −10°C, respectively); although temperate strains were significantly affected by the "mild" freezing treatment, polar and alpine strains were not. The −10°C treatment was survived exclusively by polar strains, and only P. catenaborealis survived all treatments. Interestingly, this species exhibited the lowest survival in the −10°C treatment, potentially implying some metabolic activity even at freezing temperatures. Thus, despite more extensive sampling throughout the genus and finer temperature scaling compared to previous studies, the remarkable freezing‐stress tolerance of the P. borealis species complex remains unique within the genus. [ABSTRACT FROM AUTHOR]

Intracellular parasites of the genus Glugea Thélohan, 1891 (Microsporidia) comprise about 34 putative species capable of causing high morbidity and mortality in freshwater and marine teleost fishes. In this study, we report on the first mass mortality event associated with Glugea sp. infecting free‐ranging round sardinella Sardinella aurita in the southern Tyrrhenian Sea (Italy). Here, we describe the ultrastructure of mature spores of this microsporidian and characterize it molecularly, as well as report its phylogenetic position. Most of the affected fish showed an irregular swelling of its abdomen. At necropsy, a variable number of xenomas, spherical to ellipsoidal in shape, were found in the peritoneal cavity strongly attached to the viscera of all fish. Histological analysis revealed varying severity of chronic inflammation along with occasional necrosis in visceral organs associated with multiple xenoma proliferation. These pathological findings were considered the main cause of this mass mortality event. Morphologically, the present material was closely related to G. sardinellesis and G. thunni. The phylogenetically closest taxa to the newly SSU rDNA sequence were G. thunni and an erroneusly identified G. plecoglossi, which were very closely related to each other, also suggesting that all these sequences might belong to the same species. [ABSTRACT FROM AUTHOR]

Background: Optimal management of intracranial infections relies on microbiological diagnosis and antimicrobial choice, but conventional culture-based testing is limited by pathogen viability and pre-sampling antimicrobial exposure. Broad-range 16S rRNA gene sequencing has been reported in the management of culture-negative infections but its utility in intracranial infection is not well-described. We studied the efficacy of 16S rRNA gene sequencing to inform microbiological diagnosis and antimicrobial choice in intracranial infections. Methods: This was a retrospective study of all intraoperative neurosurgical specimens sent for 16S rRNA gene sequencing over an 8-year period at a regional neurosurgical centre in the UK. Specimen selection was performed using multidisciplinary approach, combining neurosurgical and infection specialist discussion. Results: Twenty-five intraoperative specimens taken during neurosurgery from 24 patients were included in the study period. The most common reason for referral was pre-sampling antimicrobial exposure (68%). Bacterial rDNA was detected in 60% of specimens. 16S rRNA gene sequencing contributed to microbiological diagnosis in 15 patients and informed antimicrobial management in 10 of 24 patients with intracranial infection. These included targeted antibiotics after detection of a clinically-significant pathogen that had not been identified through other microbiological testing (3 cases), detection of commensal organisms in neurosurgical infection which justified continued broad cover (2 cases) and negative results from intracranial lesions with low clinical suspicion of bacterial infection which justified avoidance or cessation of antibiotics (5 cases). Conclusion: Overall, 16S rRNA gene sequencing represented an incremental improvement in diagnostic testing and was most appropriately used to complement, rather than replace, conventional culture-based testing for intracranial infection. [ABSTRACT FROM AUTHOR]

This study determined the effects of administering a glycoprotein with equine chorionic gonadotropin (eCG)-like activity (eCG-like) on corpus luteum (CL) area, serum progesterone concentrations, incidence of multiple ovulations (MOV), estrus expression rate (EER), and pregnancy to timed AI (P/TAI) in Angus cattle synchronized with a 5-d Co-Synch protocol. On Day −8, cattle were body condition scored (BCS), and received a 1.0 g progesterone intravaginal device (IVD) and 100 μg GnRH. On Day −3, the IVDs were removed and 500 μg cloprostenol was administered intramuscularly (i.m.). Cattle were randomly assigned into one of two groups: eCG-like (heifers, n = 232, primiparous, n = 148, and multiparous cows = 485; 300 IU (heifers) and 400 IU (cows) eCG-like i.m. on Day −3), or Control (heifers, n = 240, primiparous, n = 151, and multiparous cows, n = 478; no eCG-like). On Day −2, cattle received a second dose of 500 μg cloprostenol, and on Day 0, 100 μg GnRH was given concurrently with TAI. Estrus expression rate was assessed by observing the tail paint rubbed off in a subset of heifers (n = 372) and all cows on Day 0. Transrectal ultrasonography was used to evaluate the presence of CL on Day −8 and to diagnose P/TAI on Day 30–35. In a subset of cattle (heifers = 194 and multiparous cows = 87), CL area, serum progesterone concentrations, and incidence of MOV were evaluated on Day 7. Heifers, primiparous, and multiparous cows were analyzed separately. Treatment with eCG-like did not affect (P > 0.1) EER in heifers. Estrus expression rate was increased (P ≤ 0.03) in primiparous (68.9 % vs 45.0 %) and multiparous (75.5 % vs. 68.8 %) cows treated with eCG-like compared with Controls. Pregnancy/TAI was increased (P < 0.01) in heifers (65.2 % vs 48.3 %) and primiparous cows (48.3 % vs. 35.1 %) treated with eCG-like than Controls. In multiparous cows with a BCS ≤4 P/TAI was increased (P = 0.03) in the eCG-like group (47.7 %) than the Control group (34.8 %) but was similar (P > 0.1) between treatment groups in multiparous cows with a BCS ≥4.5. The eCG-like treatment increased (P < 0.05) CL area in heifers and multiparous cows and tended (P = 0.10) to elevate serum progesterone concentrations only in heifers. However, it did not affect (P > 0.1) the incidence of MOV in heifers and multiparous cows. Glycoprotein eCG-like administration increased fertility in heifers and primiparous cows, but in multiparous the effect of eCG-like on fertility was associated with BCS. eCG-like treatment in a 5-day Co-Synch synchronization protocol: • Increases estrus expression rate in primiparous and multiparous cows. • Increases P/TAI in heifers, primiparous cows, and multiparous cows with a BCS ≤ 4. • Increases CL area in heifers and multiparous cows. • Does not affect the incidence of multiple ovulations in heifers and multiparous cows. [ABSTRACT FROM AUTHOR]

True morels (Morchella spp.) are highly valuable and medicinal mushrooms. Saprophytic morels have been cultivated, especially in China and some Western countries, over the last few decades. Türkiye has a rich potential in terms of wild morel diversity, with nearly 40 Morchella species in its genetic pool, though only 22 of these have been identified molecularly. It has high economic value worldwide, and Türkiye exports morels worth approximately 2 million $ annually. There is also significant interest in morel mushroom cultivation in Türkiye. In this study, 40 Morchella strains were collected and isolated from different regions of Türkiye and analyzed based on the Internal Transcribed Spacer (ITS) of the nuclear ribosomal DNA (rDNA) region. A phylogenetic dendrogram was drawn. The isolates of M. importuna, M. exima, M. exuberans, M. dunali, M. tridentina, M. crassipes, and M. esculenta were identified based on the ITS rDNA region. However, the identification of isolates 849-Kg027 and 966-Kg142 could not be determined clearly, and the isolates of M. vulgarius and M. spongiola were not distinct based on the ITS analysis. The macro-morphological features of the mycelia were investigated. Mycelia colors ranged from off-white to pale gray in the juvenile stage, orange to pale brown during early pigmentation, and pale brown to dark brown in the senescence stage. M. crassipes, M. exuberans, and 966-Kg142 formed lighter-colored mycelia, whereas M. dunali and M. vulgarius exhibited the darkest mycelial pigments. Sclerotia formation was compact, pale yellow to yellow, and abundant. In conclusion, molecular identification of Turkish morel cultures was performed, and cultural characteristics along with morphological differences were examined. The cultures have been deposited for further study in the Mushroom Gene Bank at the Atatürk Central Horticultural Research Institute. [ABSTRACT FROM AUTHOR]

In developing B cells, V(D)J gene recombination is initiated by the RAG1/2 endonuclease complex, introducing double‐stranded DNA breaks (DSBs) in V, D, and J genes and resulting in the formation of the hypervariable parts of immunoglobulins (Ig). Persistent or aberrant RAG1/2 targeting is a potential threat to genome integrity. While RAG1 and RAG2 have been shown to bind various regions genome‐wide, the in vivo off‐target DNA damage instigated by RAG1/2 endonuclease remains less well understood. In the current study, we identified regions containing RAG1/2‐induced DNA breaks in mouse pre‐B cells on a genome‐wide scale using a global DNA DSB detection strategy. We detected 1489 putative RAG1/2‐dependent DSBs, most of which were located outside the Ig loci. DNA sequence motif analysis showed a specific enrichment of RAG1/2‐induced DNA DSBs at GA‐ and CA‐repeats and GC‐rich motifs. These findings provide further insights into RAG1/2 off‐target activity. The ability of RAG1/2 to introduce DSBs on the non‐Ig loci during the endogenous V(D)J recombination emphasizes its genotoxic potential in developing lymphocytes. [ABSTRACT FROM AUTHOR]

The molecular classification of Acanthamoeba is currently based on the analysis of 18S rDNA sequences, delimiting around twenty genotypes (T1–T23). In some cases, however, the resolution of 18S is limited, and other genetic markers could be useful for unravelling poorly resolved lineages. In this study, the partial large subunit (LSU) of rDNA and ITS were used to re-examine the Acanthamoeba palestinensis group (T2/T6 lineage), which consists of various poorly defined lineages, including the T2 and T6 genotypes. New sequences overlapping 18S, ITS, and LSU were recovered. The analysis placed previously identified partial ITS-LSU sequences as T2/T6 and further confirmed the separation of the OX1 lineage from T2. In addition, analysis of the second internal transcribed spacer (ITS-2) suggests that multiple species may be present within the T6 and OX1 lineages. The results obtained from the T2/T6 lineage analysis confirm the utility of partial LSU and ITS for the study of Acanthamoeba, suggesting their advantage for disentangling complex lineages. [ABSTRACT FROM AUTHOR]

Vaccine manufacturing fosters the prevention, control, and eradication of infectious diseases. Recombinant DNA and in vitro (IVT) mRNA vaccine manufacturing technologies were enforced to combat the recent pandemic. Despite the impact of these technologies, there exists no scientific announcement that compares them. Digital Shadows are employed in this study to simulate each technology, investigating root cause deviations, technical merits, and liabilities, evaluating cost scenarios. Under this lens we provide an unbiased, advanced comparative technoeconomic study, one that determines which of these manufacturing platforms are suited for the two types of vaccines considered (monoclonal antibodies or antigens). We find recombinant DNA technology to exhibit higher Profitability Index due to lower capital and starting material requirements, pertaining to lower Minimum Selling Price per Dose values, delivering products of established quality. However, the potency of the mRNA, the streamlined and scalable synthetic processes involved and the raw material availability, facilitate faster market penetration and product flexibility, constituting these vaccines preferable whenever short product development cycles become a necessity. [ABSTRACT FROM AUTHOR]

Background: iPSC reprogramming technology exhibits significant promise in the realms of clinical therapeutics, disease modeling, pharmaceutical drug discovery, and various other applications. However, the extensive utilization of this technology has encountered impediments in the form of inefficiency, prolonged procedures, and ambiguous biological processes. Consequently, in order to improve this technology, it is of great significance to delve into the underlying mechanisms involved in iPSC reprogramming. The BET protein BRD4 plays a crucial role in the late stage of reprogramming; however, its precise function in the early stage remains unclear. Results: Our study aims to investigate BRD4's role in the early stages of iPSC reprogramming. Our investigation reveals that early inhibition of BRD4 substantially enhances iPSC reprogramming, whereas its implementation during the middle-late stage impedes the process. During the reprogramming, ribosome DNA expression initially increases before decreasing and then gradually recovers. Early inhibition of BRD4 improved the decline and restoration of rDNA expression in the early and middle-late stages, respectively. Additionally, we uncovered the mechanism of BRD4's regulation of rDNA transcription throughout reprogramming. Specifically, BRD4 interacts with UBF and co-localizes to both the rDNA promoter and enhancer regions. Ultimately, BRD4 facilitates rDNA transcription by promoting the enrichment of histone H3 lysine 27 acetylation in the surrounding chromatin. Moreover, we also discovered that early inhibition of BRD4 facilitates cells' transition out of the somatic cell state and activate pluripotent genes. Conclusions: In conclusion, our results demonstrate that early inhibition of BRD4 promotes sequential dynamic expression of rDNA, which improves iPSC reprogramming efficiency. [ABSTRACT FROM AUTHOR]

Escherichia coli has shouldered a massive workload with the discovery of recombinant DNA technology. A new era began in the biopharmaceutical industry with the production of insulin, the first recombinant protein, in E. coli and its use in treating diabetes. After insulin, many biopharmaceuticals produced from E. coli have been approved by the US Food and Drug Administration and the European Medicines Agency to treat various human diseases. Although E. coli has some disadvantages, such as lack of post‐translational modifications and toxicity, it is an important host with advantages such as being a well‐known bacterium in recombinant protein production, cheap, simple production system, and high yield. This study examined biopharmaceuticals produced and approved in E. coli under the headings of peptides, hormones, enzymes, fusion proteins, antibody fragments, vaccines, and other pharmaceuticals. The topics on which these biopharmaceuticals were approved for treating human diseases, when and by which company they were produced, and their use and development in the field are included. [ABSTRACT FROM AUTHOR]

Ribosomal DNA (rDNA) encodes the ribosomal RNA genes and represents an intrinsically unstable genomic region. However, the underlying mechanisms and implications for genome integrity remain elusive. Here, we use Bloom syndrome (BS), a rare genetic disease characterized by DNA repair defects and hyper-unstable rDNA, as a model to investigate the mechanisms leading to rDNA instability. We find that in Bloom helicase (BLM) proficient cells, the homologous recombination (HR) pathway in rDNA resembles that in nuclear chromatin; it is initiated by resection, replication protein A (RPA) loading and BRCA2-dependent RAD51 filament formation. However, BLM deficiency compromises RPA-loading and BRCA1/2 recruitment to rDNA, but not RAD51 accumulation. RAD51 accumulates at rDNA despite depletion of long-range resection nucleases and rDNA damage results in micronuclei when BLM is absent. In summary, our findings indicate that rDNA is permissive to RAD51 accumulation in the absence of BLM, leading to micronucleation and potentially global genomic instability. Ribosomal DNA is an unstable genomic region with the underlying mechanisms remaining elusive. Here the authors find that rDNA hyper recombination in Bloom Syndrome cells arises from RAD51 accumulation in the absence of long-range resection and cause genome instability through micronuclei formation. [ABSTRACT FROM AUTHOR]

A study of corticioid fungi collections from Costa Rica, Panama, Colombia, and Ecuador has resulted in the identification of 26 morphospecies of Lyomyces. These distinctions were made based on characters such as basidiospore size and shape, cystidia morphology, basidioma texture, and hymenial surface configuration. Sequences of rDNA ITS were obtained for 12 of these species, and their relationships to previously known taxa were illustrated using Bayesian and Maximum Likelihood reconstructions of the phylogeny. Protologues are given for 10 new species of Lyomyces: L. boquetensis (found in Panama, belonging to L. sambuci group), L. granulosus (from Costa Rica and Panama, related to L. fimbriatus), L. napoensis (from Ecuador, related to L. elaeidicola), L. neocrustosus (from Panama, L. crustosus group), L. oleifer (from Ecuador, L. crustosus group), L. pantropicus (from Panama and Ecuador, related to L. microfasciculatus), L. orarius (from Ecuador, L. sambuci group), L. parvus (from Costa Rica and Ecuador, L. crustosus group), L. sceptrifer (from Ecuador, related to L. gatesiae), and L. subcylindricus (from Panama, L. crustosus group). Macro- and micro-morphology illustrations are provided for these new species. Additionally, the range of L. organensis is extended to Ecuador. Scanning electron microscopy of crystalline deposits in basidiomata has shown the differences in crystal size and aggregation manner between species. [ABSTRACT FROM AUTHOR]

The increase in the use of molecular methodologies in systematics has driven the necessity for a comprehensive understanding of the limitations of different genetic markers. Not every marker is optimal for all species, which has led to multiple approaches in the study of the taxonomy and phylogeny of polyclad flatworms. The present study evaluates base-substitution rates of nuclear ribosomal (18S rDNA and 28S rDNA), mitochondrial ribosomal (16S rDNA), and protein-codifying (cytb , cox1) markers for this taxonomic group, with the main objective of assessing the robustness of these different markers for phylogenetic studies. Mutation rates and Ti/Tv ratios of the other markers were assessed for the first time. We estimated substitution rates and found cytb to be the most variable, while 18S rDNA was the least variable among them. On the other hand, the transition to transversion (Ti/Tv) ratio of the different genes revealed differences between the markers, with a higher number of transitions in the nuclear gene 28S and a higher number of transversions in the mitochondrial genes. Lastly, we identified that the third codon position of the studied protein-codifying genes was highly variable and that this position was saturated in the cox1 marker but not in cytb. We conclude that it is important to assess the markers employed for different phylogenetic levels for future studies, particularly in the order Polycladida. We encourage the use of mitochondrial genes cytb and 16S for phylogenetic studies at suborder, superfamily, and family levels and species delimitation in polyclads, in addition to the well-known 28S and cox1. [ABSTRACT FROM AUTHOR]

This work provides new molecular data on seven species representing three genera (Protoancylodiscoides, Schilbetrema and Synodontella) in the order Dactylogyridea. The results help to explain the origin of Synodontella spp. and to elucidate the phylogenetic position of Synodontella in relation to the other genera. The findings also highlight the importance of the haptoral elements in determing phylogenetic relationships between and within Dactylogyridea taxa, which are monogenean parasites of mostly cyprinid fishes in fresh water. A total of 36 catfish specimens representing five species in three genera (Synodontis, Schilbe and Chrysichthys) were collected from two rivers in Cameroon: the Sanaga River (at Edéa and Nachtigal, in the Littoral and Cental regions, respectively) and Boumba River (at Mang-kaka, East Region), and examined for gill parasites. The novel 28S rDNA sequences of seven species belonging to Dactylogyridea were obtained and their phylogenetic relationships inferred. Synodontella resulted as a monophyletic lineage; the samples obtained from the catfish in Cameroon were well-differentiated into two groups. Synodontella appears to be more closely related to Schilbetrema than to the other Dactylogyridea species investigated here. The shape of the ventral bar should be considered an important feature for distinguishing among Dactylogyridea genera. The existence of two or more lineages within the genus Synodontella, as suggested by previous morphological studies, is here molecularly confirmed, indicating speciation as likely an outcome of ecological influences or the phylogenetic relationships among parasites and/or hosts. [ABSTRACT FROM AUTHOR]

The genus Xanthoparmelia includes several subcrustose, squamulose, small foliose, and small subfruticose species, primarily in the Southern Hemisphere. Here, we report on the first small foliose species lacking usnic acid in the genus occurring in the Holarctic. The species has been previously known as Lecanora olivascens Nyl., but subsequent studies of the morphology, secondary chemistry, and molecular data of the nuITS rDNA indicate that this species instead belongs to Xanthoparmelia. Consequently, the new combination Xanthoparmelia olivascens (Nyl.) V.J. Rico and G. Amo is proposed, and an epitype is designated here. We discuss the unique presence of a subcrustose Xanthoparmelia species lacking cortical usnic acid in the Northern Hemisphere. This species fits phylogenetically into a clade that was previously only known from the Southern Hemisphere, and hence represents another example of N-S disjunction in lichenized fungi. [ABSTRACT FROM AUTHOR]

Wastewater treatment plants are one of the major pathways for microplastics to enter the environment. In general, microplastics are contaminants of global concern that pose risks to ecosystems and human health. Here, we present a proof‐of‐concept for reduction of microplastic pollution emitted from wastewater treatment plants: delivery of recombinant DNA to bacteria in wastewater to enable degradation of polyethylene terephthalate (PET). Using a broad‐host‐range conjugative plasmid, we enabled various bacterial species from a municipal wastewater sample to express FAST‐PETase, which was released into the extracellular environment. We found that FAST‐PETase purified from some transconjugant isolates could degrade about 40% of a 0.25 mm thick commercial PET film within 4 days at 50°C. We then demonstrated partial degradation of a post‐consumer PET product over 5–7 days by exposure to conditioned media from isolates. These results have broad implications for addressing the global plastic pollution problem by enabling environmental bacteria to degrade PET. [ABSTRACT FROM AUTHOR]

Understanding how the process of gene expression can be engineered to biomanufacture proteins for medical, agricultural, and industrial applications provides an opportunity to link basic concepts of molecular biology with applications. Here we present a simple activity that uses commonly available materials to simulate the process by which the bacterium Agrobacterium tumefaciens transfers genes to plants and allows students to visualize the expressed protein of interest. The activity provides an overview of transcription and translation, and how recombinant DNA technology has revolutionized the manufacturing of biological molecules. After students work through the overview worksheet and complete the hands-on activity, they will be able to summarize the roles of transcription and translation in plant gene expression. Students will also be able to explain the process of Agrobacterium-mediated gene expression and describe applications in plant biotechnology. This simulation activity is accessible to a wide range of students, easily adaptable to different proficiency levels, and provides a straightforward approach for students to explore the practical applications of biotechnology. [ABSTRACT FROM AUTHOR]

As a result of recombination, adjacent nucleotides can have different paths of genetic inheritance and therefore the genealogical trees for a sample of DNA sequences vary along the genome. The structure capturing the details of these intricately interwoven paths of inheritance is referred to as an ancestral recombination graph (ARG). Classical formalisms have focused on mapping coalescence and recombination events to the nodes in an ARG. However, this approach is out of step with some modern developments, which do not represent genetic inheritance in terms of these events or explicitly infer them. We present a simple formalism that defines an ARG in terms of specific genomes and their intervals of genetic inheritance, and show how it generalizes these classical treatments and encompasses the outputs of recent methods. We discuss nuances arising from this more general structure, and argue that it forms an appropriate basis for a software standard in this rapidly growing field. [ABSTRACT FROM AUTHOR]

Pseudohydnum, commonly known as cat's tongue mushrooms, is a monophyletic assemblage within Auriculariales, which encompasses species with gelatinous basidiomata, spathulate, flabellate, or shell-shaped pileus, hydnoid hymenophore, globose to ellipsoidal basidiospores, and longitudinally cruciate-septate basidia. According to the available literature, 16 species have been described in Pseudohydnum, mostly represented in temperate-boreal forests of the Northern Hemisphere. However, the limited morphological, molecular, and ecological information, especially from the Southern Hemisphere ecosystems, does not presently allow a reliable assessment of its taxonomic boundaries nor provide a complete picture of the species diversity in the genus. In an ongoing effort to examine specimens collected in dense and mixed ombrophilous forest fragments (Atlantic Rainforest domain) from Southeastern and Southern Brazil, additional taxa assigned to Pseudohydnum were identified. Four new species are recognized based mostly on characters of the pileus surface, stipe, hymenium, and basidiospores. Molecular phylogenetic analyses based on nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode), partial nuc rDNA 28S, and partial RNA polymerase II largest subunit (RPB1) sequences supported the description of these new taxa. Here, we propose Pseudohydnum brasiliense, P. brunneovelutinum, P. cupulisnymphae, and P. viridimontanum as new species. Morphological descriptions, line drawings, habitat photos, and comparisons with closely related taxa are provided. A dichotomous key for identification of currently known Southern Hemisphere Pseudohydnum species is presented. [ABSTRACT FROM AUTHOR]

Two new Psilocybe species (Hymenogastraceae), P. ingeli and P. maluti, are described from southern Africa. Morphology and phylogeny were used to separate the two novel fungi from their closest relatives in the genus. Psilocybe ingeli was found fruiting on bovine manure–enriched grasslands in the Kwa-Zulu Natal Province of South Africa and differs from its closest relative P. keralensis and others in the internal transcribed spacer ITS1-5.8S-ITS2, partial 28S nuc rDNA, and translation elongation factor 1-alpha regions, distribution, and having larger basidiospores. Similarly, P. maluti was collected from the Free State Province of South Africa and observed in the Kingdom of Lesotho, growing on bovine manure. A secotioid pileus, geographic distribution, and differences in the same DNA regions distinguish P. maluti from its closest relative P. chuxiongensis. Furthermore, the spore dispersal and traditional, spiritualistic use of P. maluti are discussed here. [ABSTRACT FROM AUTHOR]

Sweet cherry (Prunus avium) is a commercially important species in China, experiencing a rapid increase in production. In June 2022, a severe infection, affecting more than 8% of sweet cherry trees, was observed on the Tetian cultivar in a 2–3‐year‐old orchard in Dalian City, northern China. Initially, spindle‐shaped brown disease spots formed on the surfaces of the branches. These spots continued to spread and merge, and the middle portion of the cankers sunk inward and gradually dried. Small black particles were found on the surface of the stems. The disease spread was more prevalent during the rainy season, leading to the withering of numerous branches and the death of the whole plant. Seven isolates, named lncy1‐1, lncy4‐1, lncy5‐1, lncy6‐1, lncy7‐1, lncy8‐1 and lncy9‐1, were obtained from 24 disease samples. Phylogenetic analysis based on three loci (rDNA ITS, TEF1 and TUB2) coupled with morphological identification confirmed that these seven isolates belong to Diaporthe eres. A representative isolate, lncy1‐1, was inoculated onto sweet cherry branches in a controlled environment, and showed that the isolate lncy1‐1 was pathogenic. The fungus isolated from diseased tissues was identified as D. eres based on morphological and molecular criteria. To the best of our knowledge, this is the first report of stem canker in sweet cherry caused by D. eres in China, which will promote disease management and expand the known host range of D. eres. [ABSTRACT FROM AUTHOR]

Nematodes of the Onchocercidae family, such as Pelecitus spp., are filarial parasites of medical and veterinary importance. Although infections are widely distributed among avian species, only 2 cases of human Pelecitus ocular infection, both in South America, have been reported. We describe a 61-year-old man in northeast Thailand diagnosed with an ocular infection. Morphologic characteristics suggested the causative agent was a female Pelecitus nematode: coiled body, rounded anterior and posterior extremities, a distinct preesophageal cuticular ring, lateral alae, a postdeirid, and a protuberant vulva. Sequences of the 12S rDNA gene indicated 95%–96% identity and cox1 gene 92%–96% identity with published P. copsychi sequences. P-distance for cox1 sequences between the causative agent and P. copsychi was 6.71%. Phylogenetic trees of 12S rDNA and cox1 genes indicated the species differed from but is closely associated with P. copsychi. Healthcare providers should be aware of the threat of ocular infection from Pelecitus spp. nematodes. [ABSTRACT FROM AUTHOR]

The genus Vigna (Leguminosae) comprises about 150 species grouped into five subgenera. The present study aimed to improve the understanding of karyotype diversity and evolution in Vigna, using new and previously published data through different cytogenetic and DNA content approaches. In the Vigna subgenera, we observed a random distribution of rDNA patterns. The 35S rDNA varied in position, from terminal to proximal, and in number, ranging from one (V. aconitifolia, V. subg. Ceratotropis) to seven pairs (V. unguiculata subsp. unguiculata, V. subg. Vigna). On the other hand, the number of 5S rDNA was conserved (one or two pairs), except for V. radiata (V. subg. Ceratotropis), which had three pairs. Genome size was relatively conserved within the genus, ranging from 1C = 0.43 to 0.70 pg in V. oblongifolia and V. unguiculata subsp. unguiculata, respectively, both belonging to V. subg. Vigna. However, we observed a positive correlation between DNA content and the number of 35S rDNA sites. In addition, data from chromosome-specific BAC-FISH suggest that the ancestral 35S rDNA locus is conserved on chromosome 6 within Vigna. Considering the rapid diversification in the number and position of rDNA sites, such conservation is surprising and suggests that additional sites may have spread out from this ancestral locus. [ABSTRACT FROM AUTHOR]

The monotypic genus Prasiolopsis has been known for a long time, but is often overlooked because of difficulties in identification and the morphological variability between uniseriate filaments and cell packages forming pseudoparenchymatic thalli depending on age. We investigated a strain (SAG 84.81) originally denoted as Trichophilus welckeri, which was isolated from the hairs of the sloth Bradypus tridactylus, and compared it with other available strains of Prasiolopsis and of the sister genus Pseudomarvania. Our investigations clearly showed that this strain differed in morphology, especially of the chloroplast, from those originally described for Trichophilus. Phylogenetic analyses of the SSU and ITS rDNA sequences revealed that the strain SAG 84.81 is sister to several strains of P. ramosa within the Prasiola clade (Trebouxiophyceae). Using the ITS-2/CBC approach, we clearly demonstrated that this strain represented a new species of Prasiolopsis, which we proposed here as P. wulf-kochii. In addition, we evaluated the ITS-2/CBC approach by comparing it with the two species of Pseudomarvania. All investigated strains showed CBCs and HCBCs, which support their species delimitation. The sequencing data of Trichophilus welckeri available in GenBank were phylogenetically re-evaluated by including all representatives of the Ulotrichales (Ulvophyceae). Our analyses showed that these sequences formed their own lineage within this order. [ABSTRACT FROM AUTHOR]

Traditional vaccines can be classified into inactivated vaccines, live attenuated vaccines, and subunit vaccines given orally or via intramuscular (IM) injection or subcutaneous (SC) injection for the prevention of infectious diseases. Recently, recombinant protein vaccines, DNA vaccines, mRNA vaccines, and multiple/alternative administering route vaccines (e.g., microneedle or inhalation) have been developed to make vaccines more secure, effective, tolerable, and universal for the public. In addition to preventing infectious diseases, novel vaccines have currently been developed or are being developed to prevent or cure noninfectious diseases, including cancer. These vaccine platforms have been developed using various biotechnologies such as viral vectors, nanoparticles, mRNA, recombination DNA, subunit, novel adjuvants, and other vaccine delivery systems. In this review, we will explore the development of novel vaccines applying biotechnologies, such as vaccines based on novel administration routes, vaccines based on novel vectors, including viruses and nanoparticles, vaccines applied for cancer prevention, and therapeutic vaccines. [ABSTRACT FROM AUTHOR]

Acrobeloides nanus, belonging to the family Cephalobidae (Cephalobomorpha), are bacterivores that inhabit soil. Information on bacteria-feeding nematodes is sparse. Therefore, identifying this group of nematodes is important because they are one of the main consumers of soil bacteria. Hence, study on this group of nematodes is essential. This molecular study was conducted in 2024 at Limpopo University to identify the freeliving bacterivores nematodes from South Africa's soils, using a 28S rDNA marker. The nematode was extracted using the tray method, and then its DNA was extracted using the Chelex method. The nematode was identified as A. nanus. In addition, molecular sequence data of the D2-D3 region of 28S rDNA from this species are provided as DNA barcode sequences. The Nblast analysis based on the 28S rDNA showed that South African A. nanus has a 99% similarity (KX669640) with the population of the Republic of Korea. Phylogenetic analysis using maximum likelihood placed this species with those molecularly identified as A. nanus in the same clade with highly supported (89%) bootstrap values. In conclusion, this species was properly identified using 28S rDNA. However, other rDNA markers are recommended to better understand Acrobeloides phylogeny. [ABSTRACT FROM AUTHOR]

The Cephalobidae (Free-living nematodes) family are bacterivores that inhabit soil. Bacterial-feeding nematodes are one of the main consumers of soil bacteria. Therefore, study on this group of nematodes is essential. This molecular study was conducted in 2024 at Limpopo University to identify the free-living bacterivores nematodes from South Africa's soils, using a 28S rDNA marker. The recovered nematode was extracted using the tray method, and then its DNA was extracted using the Chelex method. The nematode was identified as Zeldia punctata. Afterwards, 28S rDNA was amplified using specific primers to identify the nematode. The Nblast analysis based on the 28S rDNA showed South African Z. punctata has 98% similarity (DQ145662) with the American population. Phylogenetic analysis using maximum likelihood placed this species with those molecularly identified as Z. punctata in the same clade with highly supported (94%) bootstrap values. In conclusion, this species was properly identified using 28S rDNA. However, other rDNA markers are recommended to better understand Zeldia phylogeny. [ABSTRACT FROM AUTHOR]