Analysis Of Molecular Data Research Articles

Species Delimitation in Sciadocladus (Pterobryellaceae, Bryophyta)

Sciadocladus is a distinctive genus of large dendroid mosses restricted to New Zealand, New Caledonia and the Solomon Islands. Of the two extant species, S. kerrii is endemic to New Zealand, while S. menziesii is found in New Zealand, New Caledonia and the Solomon Islands. Populations of S. menziesii from New Caledonia and the Solomons have been recognised as subspecies splendidum, distinct from the New Zealand populations. Given the geographical isolation of the two subspecies of S. menziesii, we hypothesised that the endemic S. kerrii could have arisen in situ in New Zealand through speciation from S. menziesii subsp. menziesii. This would make these two taxa more closely related to each other than S. menziesii subsp. menziesii is to S. menziesii subsp. splendidum, challenging the species concept of S. menziesii. We tested this hypothesis by conducting a phylogenetic analysis of molecular data from multiple exemplars of Sciadocladus, including material from both New Zealand and New Caledonia. The results show all specimens of S. menziesii strongly supported as monophyletic, sister to a clade comprising S. kerrii specimens, thus rejecting the hypothesis and corroborating the established taxonomy. Implications for interpretation of the phylogeographic history of the genus are discussed.

Epigenetic perspective on atherosclerotic cardiovascular diseases: The holistic principle of systems biology and epigenetic reasoning

Atherosclerosis and coronary artery disease are the main causes of impairment and cardiac death, placing a significant burden on our health-care system. This review focuses on elucidating the involvement of various epigenetic mechanisms in the genesis and progression of cardiovascular diseases (CVDs), particularly chronic CVDs. The deregulation of epigenetic mechanisms plays a crucial role in the progression of CVDs, prompting exploration into novel preventive approaches. Advancements in molecular procedures, network-based approaches, and data analysis have identified new targets in CVDs, permitting the utilization of individualized epigenetic factors for personalized diagnosis and treatment. While promising for improving diagnostic and prognostic assessments, the clinical implementation of epigenetic biomarkers lags behind. Multicenter clinical documentation in a large sample population is crucial to confidently ascertain the clinical utility of specific epigenetic biomarkers. Of particular interest is the interplay between epigenetics and the conflict between the gene-based reductionist theory and the holistic principle of systems biology (SB). The holistic principle analyzes the structural organization and regulation of biological networks, influencing the genesis and progression of complex cardiac diseases like CVDs. This review emphasizes the complexity of CVDs, elucidates the interrelationship between disease networks and epigenetic mechanisms, and highlights the importance of the holistic principle of SB, coupled with artificial intelligence, in clarifying this interrelationship. The constant and uninterrupted epigenetic impact holds immense potential for advancing our understanding of disease progression and treatment across cells and tissues. Despite these advancements, the full integration of the epigenetic impact into medical practice remains incomplete, with limited utilization in clinical applications. Nevertheless, it is likely that in the near future, the epigenetic regulation of gene expression, with its lifelong and extended effects on health, will become an integral part of everyday clinical practice.

The pine processionary moth Thaumetopoea pityocampa (Notodontidae) species complex: a phylogeny-based revision

The pine processionary moth, Thaumetopoea pityocampa, is an iconic insect in the Mediterranean culture because of its economic and medical importance and the unique traits of the life history, namely the winter feeding and the construction of conspicuous silk tents by the larvae. Its taxonomic status, however, is unclear because the type material is not available and there is confusion among the several species and subspecies described in the last centuries. In the present study, a metadata analysis of morphological and molecular data of the species in the T. pityocampa complex were considered for species delimitation, using more than 400 individuals from more than 120 geographic locations. A reconstruction of the origin of the material used for the first formal description has allowed to identify the type locality and to design a neotype. In addition, as Denis and Schiffermüller were referring to the work of Réaumur for details about the species, the description provided by Réaumur was reviewed. The results indicate that the barcode region of mitochondrial DNA is a reliable trait to separate species in most cases whereas morphological traits are not. Hybridization among taxa makes it difficult to delimit species in contact zones when mating barriers are not present. In other cases, such as the populations of Crete Island, the lack of gene flow with the mainland population may support species delimitation even when morphological traits are not conclusive. Thus, the new species Thaumetopoea cretensis is described here based on the evidence obtained from a previous study. Species delimitation based on both mitochondrial and nuclear markers allowed maintenance of three species of the complex (T. cretensis, T. pityocampa, and T. wilkinsoni) while more data are needed to determine the status of two recently described species: T. hellenica and T. mediterranea.

Phylomitogenomics bolsters the high-level classification of Demospongiae (phylum Porifera).

Class Demospongiae is the largest in the phylum Porifera (Sponges) and encompasses nearly 8,000 accepted species in three subclasses: Keratosa, Verongimorpha, and Heteroscleromorpha. Subclass Heteroscleromorpha contains ∼90% of demosponge species and is subdivided into 17 orders. The higher level classification of demosponges underwent major revision as the result of nearly three decades of molecular studies. However, because most of the previous molecular work only utilized partial data from a small number of nuclear and mitochondrial (mt) genes, this classification scheme needs to be tested by larger datasets. Here we compiled a mt dataset for 136 demosponge species-including 64 complete or nearly complete and six partial mt-genome sequences determined or assembled for this study-and used it to test phylogenetic relationships among Demospongiae in general and Heteroscleromorpha in particular. We also investigated the phylogenetic position of Myceliospongia araneosa, a highly unusual demosponge without spicules and spongin fibers, currently classified as Demospongiae incertae sedis, for which molecular data were not available. Our results support the previously inferred sister-group relationship between Heteroscleromorpha and Keratosa + Verongimorpha and suggest five main clades within Heteroscleromorpha: Clade C0 composed of order Haplosclerida; Clade C1 composed of Scopalinida, Sphaerocladina, and Spongillida; Clade C2 composed of Axinellida, Biemnida, Bubarida; Clade C3 composed of Tetractinellida; and Clade C4 composed of Agelasida, Clionaida, Desmacellida, Merliida, Suberitida, Poecilosclerida, Polymastiida, and Tethyida. The inferred relationships among these clades were (C0(C1(C2(C3+C4)))). Analysis of molecular data from M. araneosa placed it in the C3 clade as a sister taxon to the highly skeletonized tetractinellids Microscleroderma sp. and Leiodermatium sp. Molecular clock analysis dated divergences among the major clades in Heteroscleromorpha from the Cambrian to the Early Silurian, the origins of most heteroscleromorph orders in the middle Paleozoic, and the most basal splits within these orders around the Paleozoic to Mesozoic transition. Overall, the results of this study are mostly congruent with the accepted classification of Heteroscleromorpha, but add temporal perspective and new resolution to phylogenetic relationships within this subclass.

The description of Myxobolus meijiangensis n. sp. (Myxozoa: Myxobolidae) and its pathogenicity to the gills of goldfish.

Myxobolus Bütschli, 1882 is the most speciose myxozoan genus, although some species have only been described according to the morphological characteristics of spores. In the present study, a new Myxobolus species infecting the gill lamellae of goldfish from Chongqing, China, was described using a comprehensive analysis of morphological, molecular, and histological data. Mature spores were flat-pear in valvular view with tapering anterior and rounded posterior ends, measuring 11.0±0.4 (10.4-11.6) μm in length and 10.3±0.3 (9.6-11.0) μm in width. Two equal-sized elongate pyriform polar capsules were 5.6±0.6 (4.5-6.4) μm long and 3.5±0.5 (2.4-4.1) μm wide. Polar tubules were coiled with 8 or 9 turns. The small-subunit ribosomal DNA gene sequence length of the present species was 1951nt, and the highest similarity was 97.99% with M. pyramidis. Comparative analysis of the morphological and molecular data revealed that the present species was distinct from other known myxosporeans. Plasmodia were located at the interlamellar troughs nearing the top of the primary gills. Infection by the present species destroyed the original structure of gill lamellae and caused an inflammatory response, eventually leading to fish dyspnea. The morphological, molecular, and pathological data from the present study can be used for aquaculture since they provide guidance for easy detection and future control of this myxosporidiosis.

Concepts and principles for new rapid simple liquid chromatography method for quantification of antioxidants resveratrol, vitamin E, and coenzyme Q10 in capsules with high-performance liquid chromatography with a photo-diode array detector.

Principles and problems in the development of simultaneous liquid chromatography (LC) analytical methods for potent antioxidative molecules resveratrol, tocopherol, and coenzyme Q10 in capsules, have been investigated and systematically compared and summarized. For these purposes, experiments within the full polarity spectrum of LC techniques. were tested and recorded. The whole range of polarities included: Alkyl C18 bonded reversed phase, phenyl, cyanopropyl, diol, and the most polar base silica-filled column matrixes have been used. The summarized results concluded that all mentioned LC techniques could be used for the determination of the mentioned group of the three analytes with different run characteristics and efficiency. These successes could be achieved after careful analyses of molecular physicochemical data of analytes. They are especially organic solubilities. The ultraviolet spectral absorption characteristics of each analyte and the mobile phase constituents for appropriate separation were very important to be known. The ultimate targets were the development method with the isocratic mode of separation yielding symmetrical peak shapes for the best sensitivity and accuracy, with the shortest run time and best reproducibility. From an analytical point of view important for LC, the three analytes have quite distinct characteristics that contribute to successful method development. These features are their organic solvent and water solubility, molecular polarities, and ultraviolet-absorption characteristics, like spectra and absorptivities. All these mentioned parameters were taken into account for solving complications appearing in the development of rapid LC methods for the simultaneous determination of three antioxidant molecules.

Granger causality based on vector time series and quaternion algebra with possible applications to molecular dynamics data analysis.

Causal analysis plays a significant role in physics, chemistry, and biology. Dynamics of complex (bio)molecular and nanosystems, from the microscopic to the macroscopic scale, are characterized by time-dependent vectors such as positions, forces, momenta, angular momenta, or torques. Identification and analysis of causal relationships between these time-dependent signals is an important problem in the multidimensional time-series analysis and is of great practical importance in describing the properties of such dynamical systems, and to understanding their functionality. For linear stochastic systems characterized by multidimensional scalar signals, Granger proposed a simple procedure to detect causal relationships, called Granger causality. In this study we extended this formalism to vector signals representing physical vector quantities. For this purpose, we used quaternion algebra, where vector signals are treated as time-dependent quaternions. The developed analytical model is based on the autoregressive formalism. This formalism (Q-MVAR) and its numerical implementation were validated using two simple dynamic models: a rigid body model represented by a benzenelike molecular fragment, interacting with a short-range harmonic potential with a wall, as well as a system of three model atomic balls moving inside a soft spherical surface and interacting with long range electrostatic forces. Although the motivation to these studies was the analysis of classical motions in complex (bio)molecular systems, described with a mechanical model and based on molecular dynamics (MD) simulations, in particular coarse-grained ones, it should be noted that the developed extended formalism can be applied to any system composed of many rigid elements that interact with arbitrary potentials and are characterized by complex internal motions. A description of the detailed procedure for calculating causality measures is provided in the Appendicesof the Supplemental Material. This formalism and the prototype of its numerical implementation can be further developed and applied in many different fields of physical, natural, and engineering sciences.

Reversal of MYB-dependent suppression of MAFB expression overrides leukaemia phenotype in MLL-rearranged AML

The transcription factor MYB plays a pivotal role in haematopoietic homoeostasis and its aberrant expression is involved in the genesis and maintenance of acute myeloid leukaemia (AML). We have previously demonstrated that not all AML subtypes display the same dependency on MYB expression and that such variability is dictated by the nature of the driver mutation. However, whether this difference in MYB dependency is a general trend in AML remains to be further elucidated. Here, we investigate the role of MYB in human leukaemia by performing siRNA-mediated knock-down in cell line models of AML with different driver lesions. We show that the characteristic reduction in proliferation and the concomitant induction of myeloid differentiation that is observed in MLL-rearranged and t(8;21) leukaemias upon MYB suppression is not seen in AML cells with a complex karyotype. Transcriptome analyses revealed that MYB ablation produces consensual increase of MAFB expression in MYB-dependent cells and, interestingly, the ectopic expression of MAFB could phenocopy the effect of MYB suppression. Accordingly, in silico stratification analyses of molecular data from AML patients revealed a reciprocal relationship between MYB and MAFB expression, highlighting a novel biological interconnection between these two factors in AML and supporting new rationales of MAFB targeting in MLL-rearranged leukaemias.

The emergence and diversification of a zoonotic pathogen from within the microbiota of intensively farmed pigs.

The expansion and intensification of livestock production is predicted to promote the emergence of pathogens. As pathogens sometimes jump between species, this can affect the health of humans as well as livestock. Here, we investigate how livestock microbiota can act as a source of these emerging pathogens through analysis of Streptococcus suis, a ubiquitous component of the respiratory microbiota of pigs that is also a major cause of disease on pig farms and an important zoonotic pathogen. Combining molecular dating, phylogeography, and comparative genomic analyses of a large collection of isolates, we find that several pathogenic lineages of S. suis emerged in the 19th and 20th centuries, during an early period of growth in pig farming. These lineages have since spread between countries and continents, mirroring trade in live pigs. They are distinguished by the presence of three genomic islands with putative roles in metabolism and cell adhesion, and an ongoing reduction in genome size, which may reflect their recent shift to a more pathogenic ecology. Reconstructions of the evolutionary histories of these islands reveal constraints on pathogen emergence that could inform control strategies, with pathogenic lineages consistently emerging from one subpopulation of S. suis and acquiring genes through horizontal transfer from other pathogenic lineages. These results shed light on the capacity of the microbiota to rapidly evolve to exploit changes in their host population and suggest that the impact of changes in farming on the pathogenicity and zoonotic potential of S. suis is yet to be fully realized.

CRISPR–Cas9-based functional interrogation of unconventional translatome reveals human cancer dependency on cryptic non-canonical open reading frames

Emerging evidence suggests that cryptic translation beyond the annotated translatome produces proteins with developmental or physiological functions. However, functions of cryptic non-canonical open reading frames (ORFs) in cancer remain largely unknown. To fill this gap and systematically identify colorectal cancer (CRC) dependency on non-canonical ORFs, we apply an integrative multiomic strategy, combining ribosome profiling and a CRISPR–Cas9 knockout screen with large-scale analysis of molecular and clinical data. Many such ORFs are upregulated in CRC compared to normal tissues and are associated with clinically relevant molecular subtypes. We confirm the in vivo tumor-promoting function of the microprotein SMIMP, encoded by a primate-specific, long noncoding RNA, the expression of which is associated with poor prognosis in CRC, is low in normal tissues and is specifically elevated in CRC and several other cancer types. Mechanistically, SMIMP interacts with the ATPase-forming domains of SMC1A, the core subunit of the cohesin complex, and facilitates SMC1A binding to cis-regulatory elements to promote epigenetic repression of the tumor-suppressive cell cycle regulators encoded by CDKN1A and CDKN2B. Thus, our study reveals a cryptic microprotein as an important component of cohesin-mediated gene regulation and suggests that the ‘dark’ proteome, encoded by cryptic non-canonical ORFs, may contain potential therapeutic or diagnostic targets.

Neurodevelopmental and other phenotypes recurrently associated with heterozygous BAZ2B loss-of-function variants.

The bromodomain adjacent to zinc finger 2B (BAZ2B) gene encodes a chromatin remodeling protein that has been shown to perform a variety of regulatory functions. It has been proposed that loss of BAZ2B function is associated with neurodevelopmental phenotypes, and some recurrent structural birth defects and dysmorphic features have been documented among individuals carrying heterozygous loss-of-function BAZ2B variants. However, additional evidence is needed to confirm that these phenotypes are attributable to BAZ2B deficiency. Here, we report 10 unrelated individuals with heterozygous deletions, stop-gain, frameshift, missense, splice junction, indel, and start-loss variants affecting BAZ2B. These included a paternal intragenic deletion and a maternal frameshift variant that were inherited from mildly affected or asymptomatic parents. The analysis of molecular and clinical data from this cohort, and that of individuals previously reported, suggests that BAZ2B haploinsufficiency causes an autosomal dominant neurodevelopmental syndrome that is incompletely penetrant. The phenotypes most commonly seen in association with loss of BAZ2B function include developmental delay, intellectual disability, autism spectrum disorder, speech delay-with some affected individuals being non-verbal-behavioral abnormalities, seizures, vision-related issues, congenital heart defects, poor fetal growth, and an indistinct pattern of dysmorphic features in which epicanthal folds and small ears are particularly common.

Comparative and phylogenetic analyses of the chloroplast genomes of Filipendula species (Rosoideae, Rosaceae)

Genus Filipendula (Rosoideae, Rosaceae) comprises about 15 species and mainly distributed in Northern Hemisphere. The phylogenetic relationships based on the nrITS marker are not consistent with the traditional taxonomic systems of the genus. Here, we first analysed the complete chloroplast (cp) genomes of seven Filipendula species (including two varieties of F. palmate). Our results indicated that the cp genomes of Filipendula species had few changes in size, ranging from 154,205 bp to 154,633 bp and the average of 36.63% GC content. A total of 126 annotated genes had the identical order and orientation, implying that the cp genome structure of Filipendula species was rather conserved. However, the cp genomes of Filipendula species exhibited structural differences, including gene loss, transposition and inversion when compared to those of other genera of Rosoideae. Moreover, SSRs with the different number were observed in the cp genome of each Filipendula species and sequence divergence mainly occurred in noncoding regions, in which four mutational hotspots were identified. In contrast, only two positive selection genes (matK and rps8) were found. Phylogenetic and molecular-dating analysis indicated that Filipendula species were divergent from other genera of Rosoideae at about 82.88 Ma. Additionally, Filipendula species from East Asia were split at about 9.64 Ma into two major clades. These results provide a basis for further studying the infrageneric classification of Filipendula.

A Description of Echinochasmus pseudobeleocephalus n. sp. (Echinochasmidae) Based on Morphological and Molecular Data.

Adult individuals of Echinochasmus pseudobeleocephalus n. sp. were obtained during an experimental study on trematodes' life cycle. An analysis of the morphometric characteristics of the developmental stages and involvement of first intermediate hosts, snails of the genus Boreoelona, in their life cycle, revealed the identity of the obtained trematodes to the European species Echinochasmus beleocephalus previously discovered in the south of the Russian Far East. However, an analysis of molecular data, in particular sequences of the 28S rRNA gene, showed that the Far Eastern trematodes examined do not belong to European E. beleocephalus despite their morphological similarities. An analysis of phylogenetic relationships within the family Echinochasmidae supported the status of E. pseudobeleocephalus n. sp. as an independent species. Our new data confirmed that the individuals attributed to Echinochasmus can be subdivided into two groups on the basis of the number of head-collar spines and the tail length in cercariae on an intergeneric level.

In silico Rationalization for Leads from Oldenlandia umbellata L. to Inhibit Multiple Molecular Targets Regulating Osteoporosis

Background Osteoporosis is a chronic metabolic bone disease caused due to the dysregulation in the functioning of osteoblast and osteoclast cells leading to increased bone resorption predominantly in postmenopausal women and the elderly, thereby affecting a significant global population. Purpose The present study aims to computationally screen the phytochemical constituents of Oldenlandia umbellata Linn against the unique molecular therapeutic targets of osteoporosis and validate the results using Molecular Dynamics (MD) Simulation. Materials and Methods The molecular docking analysis of the selected phytoconstituents against the molecular targets were performed using AutoDock 4.2.6 – AutoDock Tools 1.5.6. In addition, the drug likeliness, ADME, bioactivity, and toxicity were predicted using Molinspiration ADMELAB2.0, ProTox-II and Orisis DataWarrior online tools. Molecular Dynamic Simulation studies were performed using WebGRO macromolecular simulation server. Results Molecular docking results and data analysis revealed that deacetylasperuloside possesses good drug-likeness, ADME properties, and bioactive scores and did not indicate any toxicity compared to other phytochemicals exhibiting binding energies below –8.00 Kcal/mol against the targets. Together, the study emphasized that deacetylasperuloside could bind with the molecular targets of osteoporosis, and the lead is a potential therapeutic candidate for osteoporosis treatment. Further, molecular dynamic simulation analysis for 100 ns revealed that the ligand–protein complexes, including glycogen synthase kinase 3β (GSK3β)-deacetylasperuloside and cathepsin K (CTSK)-deacetylasperuloside complexes, were stable and highly compact assessed from their trajectories. Hence, it can be emphasized that deacetylasperuloside could be a potential therapeutic molecule that could inhibit the targets, including GSK3β and CTSK. Conclusion Oldenlandia umbellata L. is a potential candidate for identifying therapeutic leads for osteoporosis treatment. Further, in vitro and in vivo studies are needed as an output of this research to evaluate its therapeutic efficacy.

Phylogenetic reconstruction of Corydioidea (Dictyoptera: Blattodea) provides new insights on the placement of Latindiinae and supports the proposal of the new subfamily Ctenoneurinae

AbstractRepresentatives of the cockroach superfamily Corydioidea are less sampled than members of the two other cockroach superfamilies (Blaberoidea and Blattoidea) due to the difficulty of collecting them in the field, accentuated by a general lack of knowledge on their biology. Their evolutionary relationships have not yet been investigated with a relevant sampling and are therefore poorly known. Here, we assess the phylogenetic relationships of 35 Corydioidea species with mitochondrial genomes and two nuclear gene fragments. Our sampling for Corydiidae comprises Corydiinae and Euthyrrhaphinae representatives, whereas our sampling for the remaining Corydioidea includes species belonging to genera Beybienkonus Qiu, Wang and Che, Compsodes Hebard, Ctenoneura Hanitsch and Nocticola Bolívar. We further infer their divergence times with molecular dating analyses relying on five fossil calibrations. We also carry out reconstructions of ancestral character states for 11 phenotypic and one biological traits. Our results recover two major Corydioidea clades, one consisting solely of Corydiidae (except Latindiinae) and the other of all remaining Corydioidea taxa. Based on the results of phylogenetic analyses, an updated classification of extant Corydioidea is proposed, where Latindiinae Handlirsch stat.rev. and Ctenoneurinae Qiu and Che, subfam.nov. are assigned to the family Nocticolidae Bolívar sensu nov. A new genus Pseudoeupolyphaga Qiu and Che, gen.nov. is also established within Corydiinae. Both the origin of crown Corydioidea and the divergence of the two major lineages are estimated to have occurred during the Triassic–Jurassic boundary. Ancestral character state reconstruction analyses also suggest an adaptive relationship between phenotypic characteristics and habitat preferences.

Independent origins or single dispersal? Phylogenetic study supports early Cenozoic origin of three endemic Indo‐Sri Lankan Lygosomine skink genera

AbstractThe Western Ghats‐Sri Lanka biodiversity hotspot is home to three endemic Lygosomine (Reptilia, Scincidae) skink genera—Kaestlea, Ristella and Lankascincus. Phylogenetic reconstructions in the past have suggested a sister relationship between the Western Ghats endemic Ristella and the Sri Lankan endemic Lankascincus, while the placement of Kaestlea has been uncertain. We reconstruct a global, genus‐level, multi‐locus phylogeny of the sub‐family Lygosominae to ask if these endemic genera share an immediate common ancestor, that is, did they arise from a single dispersal event? Furthermore, to understand the possible centres of origin and dispersal routes of these three genera of Indo‐Sri Lankan skinks, we construct a time‐calibrated phylogeny and perform ancestral range evolution. We find that Kaestlea does not share an immediate ancestor with Ristella + Lankascincus. Therefore, their presence in the Indian subcontinent results from two independent colonization events. Both these dispersal events likely occurred during the late Palaeocene‐early Eocene from the Asian landmass. Our molecular dating and ancestral range evolution analyses add further evidence of probable transoceanic dispersal in skinks and early land connections between the Indian subcontinent and Asia. It also reveals that these skinks were some of the earliest lizards to disperse into the Indian subcontinent.

On the conservation of white-clawed crayfish in the Iberian Peninsula: Unraveling its genetic diversity and structure, and origin.

European crayfish species are a clear example of the drastic decline that freshwater species are experiencing. In particular, the native species of the Iberian Peninsula, the white clawed-crayfish (WCC) Austropotamobius pallipes, is listed as "endangered" by the IUCN and included in Annex II of the EU Habitat Directive and requires especially attention. Currently, implemented conservation management strategies require a better understanding of the genetic diversity and phylogeographic patterns, as well as of its evolutionary history. For this purpose, we have generated the largest datasets of two informative ribosomal mitochondrial DNA regions, i.e., cytochrome oxidase subunit I and 16S, from selected populations of the WCC covering its geographical distribution. These datasets allowed us to analyze in detail the (i) genetic diversity and structure of WCC populations, and (ii) divergence times for Iberian populations by testing three evolutionary scenarios with different mtDNA substitution rates (low, intermediate, and high rates). The results indicate high levels of haplotype diversity and a complex geographical structure for WCC in the Iberian Peninsula. The diversity found includes new unique haplotypes from the Iberian Peninsula and reveals that most of the WCC genetic variability is concentrated in the northern and central-eastern regions. Despite the fact that molecular dating analyses provided divergence times that were not statistically supported, the proposed scenarios were congruent with previous studies, which related the origin of these populations with paleogeographic events during the Pleistocene, which suggests an Iberian origin for these WCC. All results generated in this study, indicate that the alternative hypothesis of an introduced origin of the Iberian WCC is highly improbable. The result of this study, therefore, has allowed us to better understand of the genetic diversity, structure patterns, and evolutionary history of the WCC in the Iberian Peninsula, which is crucial for the management and conservation needs of this endangered species.

Molecular Profiling and Data Analysis of Lung Adenocarcinoma

Abstract: Lung adenocarcinoma, a major cause of cancer-related deaths globally, was examined through a comprehensive analysis of 230 resected tumors. This study integrated various sequencing techniques to profile messenger RNA, microRNA, and DNA, along with evaluating copy number variations, methylation patterns, and proteomic data. The findings revealed a notable rate of somatic mutations (average of 8.9 mutations per megabase). Among the 18 significantly mutated genes were RIT1 activating mutations and newly identified MGA loss-of-function mutations, which were mutually exclusive with MYC amplification. Gender-based differences were observed, with EGFR mutations being more common in females and RBM10 mutations in males. Genetic abnormalities in NF1, MET, ERBB2, and RIT1 were detected in 13% of cases, often in tumors lacking other activated oncogenes, suggesting their potential driver roles. Splicing alterations were driven by somatic genomic changes, as evidenced by DNA and mRNA sequencing from the same tumor, including MET mRNA exon 14 skipping in 4% of cases. While MAPK and PI(3)K pathway activity was explained by known mutations in some cases, unexplained mechanisms appeared to activate the pathways in others. These findings lay the groundwork for understanding lung adenocarcinoma’s molecular basis and offer insights for classification and further investigations. Molecular profiling is crucial for identifying actionable mutations, guiding treatment choices in advanced adenocarcinoma and acquired resistance to tyrosine kinase inhibitors. Circulating tumor DNA sequencing gains importance in NSCLC diagnostics due to its accessibility, allowing longitudinal disease monitoring. Notably, the overall cancer death rate dropped by 27% between 1991 and 2016, resulting in around 2,629,200 fewer expected cancer deaths compared to peak death rates.

Metabolic pathways engineering for drought or/and heat tolerance in cereals.

Drought (D) and heat (H) are the two major abiotic stresses hindering cereal crop growth and productivity, either singly or in combination (D/+H), by imposing various negative impacts on plant physiological and biochemical processes. Consequently, this decreases overall cereal crop production and impacts global food availability and human nutrition. To achieve global food and nutrition security vis-a-vis global climate change, deployment of new strategies for enhancing crop D/+H stress tolerance and higher nutritive value in cereals is imperative. This depends on first gaining a mechanistic understanding of the mechanisms underlying D/+H stress response. Meanwhile, functional genomics has revealed several stress-related genes that have been successfully used in target-gene approach to generate stress-tolerant cultivars and sustain crop productivity over the past decades. However, the fast-changing climate, coupled with the complexity and multigenic nature of D/+H tolerance suggest that single-gene/trait targeting may not suffice in improving such traits. Hence, in this review-cum-perspective, we advance that targeted multiple-gene or metabolic pathway manipulation could represent the most effective approach for improving D/+H stress tolerance. First, we highlight the impact of D/+H stress on cereal crops, and the elaborate plant physiological and molecular responses. We then discuss how key primary metabolism- and secondary metabolism-related metabolic pathways, including carbon metabolism, starch metabolism, phenylpropanoid biosynthesis, γ-aminobutyric acid (GABA) biosynthesis, and phytohormone biosynthesis and signaling can be modified using modern molecular biotechnology approaches such as CRISPR-Cas9 system and synthetic biology (Synbio) to enhance D/+H tolerance in cereal crops. Understandably, several bottlenecks hinder metabolic pathway modification, including those related to feedback regulation, gene functional annotation, complex crosstalk between pathways, and metabolomics data and spatiotemporal gene expressions analyses. Nonetheless, recent advances in molecular biotechnology, genome-editing, single-cell metabolomics, and data annotation and analysis approaches, when integrated, offer unprecedented opportunities for pathway engineering for enhancing crop D/+H stress tolerance and improved yield. Especially, Synbio-based strategies will accelerate the development of climate resilient and nutrient-dense cereals, critical for achieving global food security and combating malnutrition.

Connecting the dots: DNA barcoding and lectotype designation shedding light on Labrundinia longipalpis (Goetghebuer, 1921), an intriguing non-biting midge (Chironomidae, Tanypodinae).

Accurate taxonomic classification is deemed paramount for gaining an understanding of the diversity and distribution of insect species. In this study, an essential stride was made towards advancing the taxonomy of the non-biting midge Labrundinia longipalpis (Chironomidae, Tanypodinae), which serves as the type species of the genus. The distribution of L. longipalpis is particularly intriguing as it contrasts with the predominantly tropical distribution of the genus, with this species being found across the Holarctic region. The main goal of this investigation was to designate a lectotype and several paralectotypes, which was achieved through a comprehensive reexamination of the original material, alongside additional specimens obtained from the type-locality in Flanders. Furthermore, the distribution of L. longipalpis across Europe and North America was examined, and the proposed synonymization of L. maculata with the latter was challenged using the analysis of molecular data. Through the comparison of DNA barcodes, it was revealed that the North American population of L. longipalpis clustered together with the European population, which alludes to a considerable level of genetic similarity between these two populations. These results provide valuable insights into the behavior, ecological dynamics and biogeography of L. longipalpis, while also raising interesting questions about colonization and distribution patterns attributed to its adaptability and potential for long-distance dispersal.