Phylogenetic Differences Research Articles

Root microbiome of Panax ginseng in comparison with three other medicinal plants in the families of Araliaceae and Apiaceae

The intricate interplay between endophytic microorganisms and plants in the upkeep of biodiversity, the stability of communities, and the operation of ecosystems needs to be more adequately extensive. Although root-associated microbial communities of plants have been revealed for the last decade, the understanding of bacterial and fungal communities associated with the roots of medicinal plants remains elusive. To highlight the importance of Panax ginseng Meyer (PG) in our research, we investigated the root endophytic bacterial and fungal communities of Panax ginseng Meyer (PG), alongside Aralia cordata (AC), Angelica gigas (AG), and Peucedanum japonicum (PJ), utilizing amplicon-based community profiling and advanced bioinformatic methodologies. The study aimed to investigate the root-endophytic microbiota of ginseng and three other medicinal plants and identify similarities in microbiome composition across different plant species and families. Results revealed that root-endophytic bacterial and fungal communities were influenced by plant species and phylogenetic differences at the family level. Differential abundance tests and random forest models showed microbial features within the same plant family. PG had a distinctive microbial profile with significant B1653_o_Enterobacterales and F8_o_Helotiales. PG had a core microbiome, B10_Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, and a more evenly distributed microbial network compared to AG, PJ, and AC. Our research reveals the intricate endophytic microbial communities within the roots of medicinal plants, pinpointing specific taxa that may be pivotal to their medicinal qualities and overall plant health. These insights carry notable implications for future studies, particularly those focused on the endophytes of PG and their secondary metabolites, as they deepen our understanding of plant-microbe interactions and their role in enhancing the plants’ therapeutic potential.

Two in one: A case study of two rhizocephalan species invading the nervous tissue of one host

AbstractCertain parasites can manipulate their hosts to enhance their own fitness and transmission success. Rhizocephalan barnacles are a notable example, inducing significant changes in their crustacean host's morphology, physiology, and behaviour. Until recently, it was believed that the spider crab Scyra aff. ferox is parasitized by a single species Sacculina pilosella in the Sea of Japan. However, previous molecular studies have revealed a complex of unrelated species, Sacculina pugettiae (fam. Sacculinidae) and Parasacculina pilosella (fam. Polyascidae). These rhizocephalans can even parasitize one host specimen simultaneously. Here, we investigated the interaction of S. pugettiae and P. pilosella with the nervous system of their common host. Species were identified based on receptacle morphology, with further validation through 18S gene phylogenetic analysis. The parasites interacted differently with the host nervous system: S. pugettiae had goblet‐shaped organs in the ganglion periphery, while P. pilosella lacked these structures, instead possessing numerous neuropil rootlets. In case of simultaneous infection, both goblet‐shaped organs and neuropil rootlets were present. Histochemistry revealed the presence of muscular rosettes in the rootlets of both species, suggesting a similar organization of the muscular system despite phylogenetic differences. Scanning electron microscopy confirmed the presence of host cell projections enveloping the rootlets. This study provides insights into the morphological features of rhizocephalan‐decapod interaction and highlights differences in their interaction with host nervous tissue between families. Our results also confirmed the loss of the goblet‐shaped organs in Polyascidae.

Development of a seroepidemiological tool for bat-borne and shrew-borne hantaviruses and its application using samples from Zambia.

Rodent-borne orthohantaviruses are the causative agents of hemorrhagic fever with renal syndrome and hantavirus pulmonary syndrome. Apart from the classic rodent-borne hantaviruses, numerous species of hantaviruses have been identified in shrews and bats; however, their antigenicity and pathogenicity are unknown. This study focused on developing a serological method to detect antibodies against bat- and shrew-borne hantaviruses. Five bat-borne (Brno, Dakrong, Quezon, Robina, and Xuan Song) and 6 shrew-borne (Asama, Altai, Cao Bang, Nova, Seewis, and Thottapalayam) viruses were selected based on the phylogenetic differences in their N proteins. The recombinant N (rN) proteins of these viruses were expressed as antigens in Vero E6 and 293T cell lines using the pCAGGS/MCS vector. Antisera against the Nus-tagged rN fusion proteins of these viruses (mouse anti-Brno, Dakrong, Quezon, Robina, Xuan Song, Asama, Cao Bang, and Nova, while rabbit anti-Altai, Seewis and Thottapalayam) were also generated. Antigenic cross-reactivity was examined in antisera and rN-expressing Vero E6 cells. The rN proteins of almost all the tested viruses, except for the Quezon and Robina viruses, showed independent antigenicity. For serological screening of bat samples, 5 rNs of the bat-borne viruses were expressed together in a single transfection protocol. Similarly, 6 rNs of shrew-borne viruses were expressed. Reactivities of the mixed antigen system were also examined across the singly transfected Vero cell lines to ensure that all antigens were expressed. Using these antigens, bat serum samples collected from Zambia were screened using the indirect immunofluorescence antibody test (IFAT). Selected positive samples were individually tested for the respective antigens by IFAT and western blot assays using rN-expressing 293T cell lysates. Of the 1,764 bat serum samples tested, 11.4% and 17.4% were positive for bat and shrew mixed antigens, respectively. These samples showed positive reactions to the Brno, Dakrong, Quezon, Xuan Son, Robina, Asama, Altai, Cao Bang, or Thottapalayam virus antigens. These observations suggest that the mixed-antigen screening system is useful for serological screening For Orthohantavirus infections and that bats in Zambia are likely exposed to not only bat-borne hantaviruses but also to shrew-borne hantaviruses.

Parasalinivibrio latis gen. nov., sp. nov., isolated from the distal gut of healthy farmed Asian Seabass (Lates calcarifer).

Asian Seabass (Lates calcarifer) is widely farmed as a sustainable source of protein for countries in the tropical Indo-West Pacific region. However, microbial species of the gut microbiome of healthy Asian Seabass remain largely uncharacterized and uncultured. Here, we analysed the microbial composition along the gastrointestinal tract of a farmed healthy Asian Seabass. We used different cultivation approaches to obtain isolates from the seabass intestinal tract and describe the isolation and characterization of a novel strain, TLL-SE01T. Analysis of the strain's 16S rRNA gene indicates that the strain belongs to the family Vibrionaceae with Photobacterium damselae as its closest relative, albeit sharing only 94.8% (aligned region 1553bp) nucleotide identity. Comparative genomic analysis with all validly published Vibrionaceae species with available genomes revealed average nucleotide identity (ANI) and DNA-DNA hybridisation (DDH) values of around 70% and 24% respectively to strain TLL-SE01T, which are well below proposed thresholds for species delineation (ANI, 95-96%; DDH, 70%). The alignment fraction and ANI genus demarcation boundaries for all genera in the Vibrionaceae family were determined for which strain TLL-SE01T is well below the calculated values, indicating that it belongs to a novel genus. Single- and core-gene phylogenetic analysis places strain TLL-SE01T in a monophyletic clade, further supporting its designation to a novel genus. Phenotypic comparison between strain TLL-SE01T and its close relatives indicated additional differences, such as growth response at different salt concentrations and different metabolic capabilities. Based on genotypic, phylogenetic and phenotypic differences to other Vibrionaceae species, we propose a novel species in a new genus, Parasalinivibrio latis gen. nov. sp. nov. and strain TLL-SE01T (= BCRC 81435T = JCM 36283T) as the type strain.

Phylogenetic evaluation and haplotype mapping of phytoplasma disease in sesame: insights into leafhopper-mediated disease transmission through molecular investigation

The predominance of leafhopper species like Orosius albicinctus, Hishimonus phycitis, and Amrasca biguttula biguttula indeed poses a significant threat to sesame production in India and globally. This disease is a major challenge for sesame farming, as it can lead to yield reductions of up to 95%. The current study examined phytoplasma and leafhoppers in sesame and analyzed the phylogenetic differences in the phyllody phytoplasma. The identification of both 16Sr group I and group II phytoplasma isolates, along with the discovery of the 16SrI-B group reported for the first time in Tamil Nadu, represents a significant advancement in our understanding of phytoplasma diversity in the region. The utilization of virtual RFLP analysis in sequencing the sesame phyllody phytoplasma highlights the importance of molecular techniques in characterizing the phytoplasma. Leafhoppers in sesame were a co-occurring species complex of O. albicinctus, H. phycitis, and A. bigutulla bigutulla. The leafhoppers were identified using species-specific taxonomical traits, and a mtCOI gene-based genetic study confirmed the species. In disease transmission efficiency studies in the greenhouse, O. albicinctus transmitted phyllody at a rate ranging from 7.8% to 84%, while H. phycitis transmitted phyllody at a rate of 5.2% to 74%. Both of these species showed the highest transmission efficiency in the combination of three insects per plant with five days of acquisition feeding and one day of inoculation feeding. A comprehensive understanding of leafhopper-phytoplasma interactions through molecular studies supports effective monitoring, early detection, and the development of integrated pest management strategies.

A shift in substrate requirement might cause speciation of the lichenized fungi, Varicellaria hemisphaerica and V. lactea (Pertusariales, Ascomycota)

Proper species recognition is required to correctly estimate species preferences and their vulnerability or for eco-evolutionary inference. Varicellaria hemisphaerica and Varicellaria lactea are almost completely morphologically homogeneous species with unclear identification features. To evaluate the importance of morphological, chemical, and ecological characteristics used in recognition of these species, we tested 670 specimens, of which 42 were analyzed phylogenetically using nucITS rDNA, SSU rDNA, and LSU rDNA markers. This integrated taxonomical approach showed that V. hemisphaerica is distinct from V. lactea, and that substrate requirements, together with phylogenetic differences and the size of soredia, differentiate these species. The chemical composition of secondary lichen metabolites in both analyzed species showed similar variation and, therefore, this feature is not diagnostic in species recognition, although suggested by previous studies. The potential speciation of the two species seems to be caused by the shift in the substrate requirements.

Microbial source tracking and identification of fecal contamination patterns in saltwater estuaries between base- and storm-flow events using dual genome-based approaches

Fecal contamination from natural and anthropogenic sources poses significant threats to saltwater estuaries, particularly after storms or heavy rainfall. Monitoring fecal contamination is essential for protecting these vulnerable ecosystems having important ecological and economic values. In this study, we investigated the abundance, sources, and potential causes of fecal contamination at three marine and seven freshwater stations across Vaughn Bay (WA, USA), a shellfish growing district, during base- and storm-flow events. Additionally, we evaluated the performance of fecal indicator bacteria (FIB) quantification, optical brightener assessment, and qPCR analysis for fecal contamination quantification. We compared the effectiveness of qPCR-based microbial source tracking (MST), which targeted a broad range of hosts including, such as humans, birds, cows, horses, ruminants, dogs, and pigs, with sequencing-based MST in identifying fecal contamination sources. Both MST analysis approaches identified birds and humans as the primary sources of fecal contamination. For marine water stations, freshwater creeks VBU001, VBU002, and VB047, along with drain VB007, were identified as the main sources of human-derived fecal contamination in Vaughn Bay, based on Kendall's tau analysis (τ: 0.58–0.97). This information indicates that the septic systems in the catchment areas of these creeks and drains require further investigation to achieve effective fecal contamination control. Optical brightener, FIB enumeration and qPCR quantification results were generally higher during storm-flow events, although they showed poor correlation with each other (Pearson r < 0.40), likely due to physiological and phylogenetic differences among the target organisms of these methods. However, the sequencing-based method faces challenges in precise quantitative identification of differences in fecal contamination between base- and storm-flow events. Due to its high-throughput and cost-effectiveness, we recommend using sequencing-based analysis for large-scale identification of the primary sources of fecal contamination in water environments, followed by targeted qPCR quantification of MST markers for more precise assessments.

Cryptic species complex shows population-dependent, rather than lineage-dependent tolerance to a neonicotinoid

Cryptic species are rarely considered in ecotoxicology, resulting in misleading outcomes when using a single morphospecies that encompasses multiple cryptic species. This oversight contributes to the lack of reproducibility in ecotoxicological experiments and promotes unreliable extrapolations. The important question of ecological differentiation and the sensitivity of cryptic species is rarely tackled, leaving a substantial knowledge gap regarding the vulnerability of individual cryptic species within species complexes. In times of agricultural intensification and the frequent use of pesticides, there is an urgent need for a better understanding of the vulnerability of species complexes and possible differences in adaptive processes. We used the cryptic species complex of the aquatic amphipod Gammarus roeselii, which comprises at least 13 genetic mtDNA lineages and spans from small-scale endemic lineages in Greece to a large-scale widely distributed lineage in central Europe. We exposed eleven populations belonging to four lineages to the neonicotinoid thiacloprid in an acute toxicity assay. We recorded various environmental variables in each habitat to assess the potential pre-exposure of the populations to contaminants. Our results showed that the populations differed up to 4-fold in their tolerances. The lineage identity had a rather minor influence, suggesting that the cryptic species complex G. roeselii does not differ significantly in tolerance to the neonicotinoid thiacloprid. However, the observed population differentiation implies that recent pre-exposure to thiacloprid (or similar substances) or general habitat contamination has triggered adaptive processes. Though, the extent to which these mechanisms are equally triggered in all lineages needs to be addressed in the future. Our study provides two key findings: Firstly, it shows that observed phylogenetic differences within the G. roeselii species complex did not reveal differences in thiacloprid tolerance. Second, it confirms that differentiation occurs at the population level, highlighting that susceptibility to toxicants is population-dependent. The population-specific differences were within the range of accepted intraspecific variability from a regulatory standpoint. From an evolutionary-ecological perspective, it remains intriguing to observe how persistent stresses will continue to influence tolerance and whether different populations are on distinct pathways of adaptation. Given that the potential selection process has only lasted a relatively short number of generations, it is crucial to monitor these populations in the future, as even brief exposure periods significantly impact evolutionary responses.

Genomic Analyses of Methicillin-Susceptible and Methicillin-Resistant Staphylococcus pseudintermedius Strains Involved in Canine Infections: A Comprehensive Genotypic Characterization.

Staphylococcus pseudintermedius is frequently associated with several bacterial infections in dogs, highlighting a One Health concern due to the zoonotic potential. Given the clinical significance of this pathogen, we performed comprehensive genomic analyses of 28 S. pseudintermedius strains isolated from canine infections throughout whole-genome sequencing using Illumina HiSeq, and compared the genetic features between S. pseudintermedius methicillin-resistant (MRSP) and methicillin-susceptible (MSSP) strains. Our analyses determined that MRSP genomes are larger than MSSP strains, with significant changes in antimicrobial resistance genes and virulent markers, suggesting differences in the pathogenicity of MRSP and MSSP strains. In addition, the pangenome analysis of S. pseudintermedius from canine and human origins identified core and accessory genomes with 1847 and 3037 genes, respectively, which indicates that most of the S. pseudintermedius genome is highly variable. Furthermore, phylogenomic analysis clearly separated MRSP from MSSP strains, despite their infection sites, showing phylogenetic differences according to methicillin susceptibility. Altogether our findings underscore the importance of studying the evolutionary dynamics of S. pseudintermedius, which is crucial for the development of effective prevention and control strategies of resistant S. pseudintermedius infections.

Development and validation of systems for genetic manipulation of the Old World tick-borne relapsing fever spirochete, Borrelia duttonii.

Relapsing fever (RF), a vector-borne disease caused by Borrelia spp., is characterized by recurring febrile episodes due to repeated bouts of bacteremia. RF spirochetes can be geographically and phylogenetically divided into two distinct groups; Old World RF Borrelia (found in Africa, Asia, and Europe) and New World RF Borrelia (found in the Americas). While RF is a rarely reported disease in the Americas, RF is prevalent in endemic parts of Africa. Despite phylogenetic differences between Old World and New World RF Borrelia and higher incidence of disease associated with Old World RF spirochete infection, genetic manipulation has only been described in New World RF bacteria. Herein, we report the generation of genetic tools for use in the Old World RF spirochete, Borrelia duttonii. We describe methods for transformation and establish shuttle vector- and integration-based approaches for genetic complementation, creating green fluorescent protein (gfp)-expressing B. duttonii strains as a proof of principle. Allelic exchange mutagenesis was also used to inactivate a homolog of the Borrelia burgdorferi p66 gene, which encodes an important virulence factor, in B. duttonii and demonstrate that this mutant was attenuated in a murine model of RF. Finally, the B. duttonii p66 mutant was complemented using shuttle vector- and cis integration-based approaches. As expected, complemented p66 mutant strains were fully infectious, confirming that P66 is required for optimal mammalian infection. The genetic tools and techniques reported herein represent an important advancement in the study of RF Borrelia that allows for future characterization of virulence determinants and colonization factors important for the enzootic cycle of Old World RF spirochetes.

Comparative analysis of optional hunting behavior in Cricetinae hamsters using the data compression approach

Research into the hunting behavior in members of the Cricetidae family offers an opportunity to reveal what changes in the predatory behavioral sequences occur when a rodent species shifts from an omnivorous to a predatory lifestyle. The study tests the following hypotheses: are there phylogenetic differences in the divergence of species’ predatory lifestyles in hamsters or do ecological factors lead to shaping their hunting behavior? We applied the data compression approach for performing comparative analysis of hunting patterns as biological “texts.” The study presents a comparative analysis of hunting behaviors in five Cricetinae species, focusing on the new data obtained for the desert hamster Phodopus roborovskii whose behavior has never been studied before. The hunting behavior of P. roborovskii appeared to be the most variable one. In contrast, behavioral sequences in P. campbelli and Allocricetulus curtatus display more significant order and predictability of behavior during hunting. Optional hunting behavior in the most ancient species P. roborovskii displayed similarities with obligate patterns in “young” Allocricetulus species. It thus turned out to be the most advanced hunter among members of the Phodopus genus. Differences in hunting sequences among Phodopus representatives suggest that the hunting behavior of these species, despite its optional mode, was subject to selection during species splitting within the genus. These results did not reveal the role played by phylogenetic differences in the divergence of species’ predatory lifestyles. They suggested that ecological conditions are the main factors in speciation of the hunting behavior in hamsters.

Global Phylogeography and Microdiversity of the Marine Diazotrophic Cyanobacteria Trichodesmium and UCYN-A.

Cyanobacterial diazotrophs, specifically the genera Trichodesmium and UCYN-A, play a pivotal role in marine nitrogen cycling through their capacity for nitrogen fixation. Despite their global distribution, the microdiversity and environmental drivers of these diazotrophs remain underexplored. This study provides a comprehensive analysis of the global diversity and distribution of Trichodesmium and UCYN-A using the nitrogenase gene ( nifH ) as a genetic marker. We sequenced 954 samples from the Pacific, Atlantic, and Indian Oceans as part of the Bio-GO-SHIP project. Our results reveal significant phylogenetic and biogeographic differences between and within the two genera. Trichodesmium exhibited greater microdiversity compared to UCYN-A, with clades showing region-specific distribution. Trichodesmium clades were primarily influenced by temperature and nutrient availability, and particularly frequent in regions of phosphorus stress. In contrast UCYN-A was found in regions of iron stress. UCYN-A clades demonstrated a more homogeneous distributions, with a single sequencing variant within the UCYN-A1 clade dominating across varied environments. The biogeographic patterns and environmental correlations of Trichodesmium and UCYN-A highlight the role of microdiversity in their ecological adaptation and reflect their different ecological strategies. This study underscores the importance of characterizing the global patterns of fine-scale genetic diversity to better understand the functional roles and distribution of marine nitrogen-fixing cyanobacteria.

Variation in near-surface soil temperature drives plant assemblage differentiation across aspect.

Quantifying assemblage variation across environmental gradients provides insight into the ecological and evolutionary mechanisms that differentiate assemblages locally within a larger climate regime. We assessed how vascular plant functional composition and diversity varied across microenvironment to identify ecological differences in assemblages in a mountainous fieldsite in northeastern Utah, USA. Then, we looked at how life-history strategies and information about phylogenetic differences affect the relationship between functional metrics and environment. We found less functionally dispersed assemblages that were shorter and more resource-conservative on south-facing slopes where intra-annual soil temperature was hotter and more variable. In contrast, we found more functionally dispersed assemblages, that were taller and more resource-acquisitive on north-facing slopes where intra-annual temperature was cooler and less variable. Herbaceous and woody perennials drove these trends. Additionally, including information about phylogenetic differences in a dispersion metric indicated that phylogeny accounts for traits we did not measure. At this fieldsite, soil temperature acts as an environmental filter across aspect. If soil temperature increases and becomes more variable, intra-annually, the function of north- versus south-facing assemblages may be at risk for contrasting reasons. On south-facing slopes, assemblages may not have the variance in functional diversity needed to respond to more intense, stressful conditions. Conversely, assemblages on north-facing slopes may not have the resource-conservative strategies needed to persist if temperatures become hotter and more variable intra-annually. Given these results, we advocate for the inclusion of aspect differentiation in studies seeking to understand species and assemblage shifts in response to changing climate conditions.

Utilizing whole genome sequencing to delineate relapse and reinfection tuberculosis on the Canadian prairies

RATIONALE Recurrent tuberculosis (TB) accounts for 5% of the Canadian TB burden. Recurrence can occur from relapse or reinfection. Identifying reinfection has implications for developing control policies. OBJECTIVE The objectives of this study were to quantify reinfection in recurrent TB using whole genome phylogenetic and single nucleotide polymorphism (SNP) and compare with epidemiological and clinical parameters from the Canadian prairies. METHODS DNA sequences of Mycobacterium tuberculosis isolates from recurrent TB cases along with epidemiological and clinical parameters were collected from Alberta and Saskatchewan. Inclusion criteria were two or more culture positive notifications age ≥17 years. SNP and phylogenetic tree scale differences (TIP) were used to determine the relapse and reinfection categories. RESULTS Of 7,627 notifications of TB disease, 533 were recurrent. 93 pairs (180 cases) were culture positive from which 26 (50 cases) were available for sequencing. 19 cases with SNP and TIP values ≤25 and ≤.001 were classified relapse. Seven SNP and TIP values >160 and >.001 were classified reinfection. Five of seven reinfections were Indigenous cases from high TB incidence areas. The non-sequenced and sequenced pairs differed only in age. CONCLUSIONS Recurrent culture positive TB is uncommon on the Canadian prairies and is more likely to be relapse. Reinfection is more likely in Indigenous persons living in high TB incidence communities. A limitation was the risk of selection bias since only 28% of eligible cases were sequenced. Since we did not know the non-sequenced reinfection risk, we could only conclude that the non-sequenced and sequenced categories were similar.

Partitioning purification, biochemical characterization, and milk coagulation efficiency of protease from a newly Streptomyces sp. isolate.

An actinobacteria strain was isolated from an olive waste mill and tested for protease production on skimmed milk media. The strain identification was achieved through both 16S rDNA sequencing and phenotypic characterization. The enzyme was purified using the ammonium sulfate/t-butanol three-phase partitioning (TPP) method, followed by characterization to investigate the effect of pH, temperature, and various chemical agents. Subsequently, the enzyme was assessed for its milk coagulation activity. The strain belonging to the Streptomyces genera, exhibits significant phylogenetic and phenotypic differences from the aligned species, suggesting its novelty as a new strain. The enzyme was best separated in the TPP aqueous phase with a 5.35 fold and 56.25% yield. Optimal activity was observed at pH 9.0 and 60°C, with more than half of the activity retained within the pH range of 7-10 over one hour. The protease demonstrated complete stability between 30 and 60°C. While metallic ions enhanced enzyme activity, EDTA acted as an inhibitor. The enzyme displayed resistance to H2O2, SDS, Tween 80, and Triton X-100. Notably, it was activated in organic solvents (ethyl acetate, petroleum ether, and xylene), maintaining > 75% of its original activity in butanol, ethanol, and methanol. Additionally, the enzyme yielded high milk coagulant activity of 11,478 SU/mL. The new Streptomyces sp. protease revealed high activity and stability under a wide range of biochemical conditions. Its use in the dairy industry appears particularly promising. Further industrial process investigations will be valuable in determining potential uses for this enzyme.

Phylogenetic differences in the morphology and shape of the central sulcus in great apes and humans: implications for the evolution of motor functions.

The central sulcus divides the primary motor and somatosensory cortices in many anthropoid primate brains. Differences exist in the surface area and depth of the central sulcus along the dorso-ventral plane in great apes and humans compared to other primate species. Within hominid species, there are variations in the depth and aspect of their hand motor area, or knob, within the precentral gyrus. In this study, we used post-image analyses on magnetic resonance images to characterize the central sulcus shape of humans, chimpanzees (Pan troglodytes), gorillas (Gorilla gorilla), and orangutans (Pongo pygmaeus and Pongo abelii). Using these data, we examined the morphological variability of central sulcus in hominids, focusing on the hand region, a significant change in human evolution. We show that the central sulcus shape differs between great ape species, but all show similar variations in the location of their hand knob. However, the prevalence of the knob location along the dorso-ventral plane and lateralization differs between species and the presence of a second ventral motor knob seems to be unique to humans. Humans and orangutans exhibit the most similar and complex central sulcus shapes. However, their similarities may reflect divergent evolutionary processes related to selection for different positional and habitual locomotor functions.

Microbiota recovery in a chronosquences of impoverished Cerrado soils with biosolids applications

Mining activities put the Brazilian savannas, a global biodiversity hotspot, in danger of species and soil carbon losses. Experiments employing biosolids have been applied to rejuvenate this degraded ecosystem, but a lingering question yet to be answered is whether the microbiota that inhabits these impoverished soils can be recovered towards its initial steady state after vegetation recovery. Here, we selected an 18-year-old restoration chronosequence of biosolids-treated, untreated mining and native soils to investigate the soil microbiota recovery based on composition, phylogeny, and diversity, as well as the potential factors responsible for ecosystem recovery. Our results revealed that the soil microbiota holds a considerable recovery potential in the degraded Cerrado biome. Biosolids application not only improved soil health, but also led to 41.7 % recovery of the whole microbial community, featuring significantly higher microbiota diversity and enriched groups (e.g., Firmicutes) that benefit carbon storage compared to untreated mining and native soils. The recovered community showed significant compositional distinctions from the untreated mining or native soils, rather than phylogenetic differences, with physiochemical properties explaining 55 % of the overall community changes. This study advances our understanding of soil microbiota dynamics in response to disturbance and restoration by shedding light on its recovery associated with biosolid application in a degraded biodiverse ecosystem.

Acclimation capacity to global warming of amphibians and freshwater fishes: Drivers, patterns, and data limitations.

Amphibians and fishes play a central role in shaping the structure and function of freshwater environments. These organisms have a limited capacity to disperse across different habitats and the thermal buffer offered by freshwater systems is small. Understanding determinants and patterns of their physiological sensitivity across life history is, therefore, imperative to predicting the impacts of climate change in freshwater systems. Based on a systematic literature review including 345 experiments with 998 estimates on 96 amphibian (Anura/Caudata) and 93 freshwater fish species (Teleostei), we conducted a quantitative synthesis to explore phylogenetic, ontogenetic, and biogeographic (thermal adaptation) patterns in upper thermal tolerance (CTmax) and thermal acclimation capacity (acclimation response ratio, ARR) as well as the influence of the methodology used to assess these thermal traits using a conditional inference tree analysis. We found globally consistent patterns in CTmax and ARR, with phylogeny (taxa/order), experimental methodology, climatic origin, and life stage as significant determinants of thermal traits. The analysis demonstrated that CTmax does not primarily depend on the climatic origin but on experimental acclimation temperature and duration, and life stage. Higher acclimation temperatures and longer acclimation times led to higher CTmax values, whereby Anuran larvae revealed a higher CTmax than older life stages. The ARR of freshwater fishes was more than twice that of amphibians. Differences in ARR between life stages were not significant. In addition to phylogenetic differences, we found that ARR also depended on acclimation duration, ramping rate, and adaptation to local temperature variability. However, the amount of data on early life stages is too small, methodologically inconsistent, and phylogenetically unbalanced to identify potential life cycle bottlenecks in thermal traits. We, therefore, propose methods to improve the robustness and comparability of CTmax/ARR data across species and life stages, which is crucial for the conservation of freshwater biodiversity under climate change.

JN.1 variant in enduring COVID-19 pandemic: is it a variety of interest (VoI) or variety of concern (VoC)?

The emergence of the SARS-CoV-2 Omicron variant, classified as a Variant of Concern (VoC) in November 2021, marked a significant shift in the COVID-19 landscape. This study investigates the subsequent development of a novel Omicron sublineage, JN.1, which displays distinctive mutations in the spike protein. The study delves into the phylogenetic differences between these variants and their potential implications. A comprehensive analysis of the genomic profiles and mutation patterns of JN.1 and BA.2.86 was conducted, utilizing SARS-CoV-2 database. The study explores the unique mutations, such as S:L455S in JN.1, associated with increased transmissibility and immune escape. Furthermore, a comparison with prevalent strains like XBB.1.5 and HV.1 highlights the substantial genetic divergence of JN.1. JN.1, first detected in August 2023, exhibits a notable spike protein mutation profile, including the reappearance of earlier variants' mutations (E484K and P681R). The variant's increased transmissibility and immune evasion potential are attributed to specific spike protein mutations like R21T, S50L, V127F, R158G, and others. The study also explores the distribution and prevalence of JN.1 globally, with a focus on the rising cases in India. JN.1 poses aunique challenge as one of the most immune-evading variants, with potential implications for COVID-19 transmission. The study emphasizes the importance of monitoring and understanding emerging variants, especially those with distinct spike protein mutations. The observed cases in India highlight the need for vigilance and prompt public health responses. As JN.1 continues to evolve, ongoing surveillance, vaccination strategies, and adherence to preventive measures are crucial to mitigating its potential impact on global public health.

Avian IgY antibodies and its immunotherapeutic applications

Antibodies, also called immunoglobulins, are specialized proteins produced by the immune system in response to the presence of pathogens or foreign substances in the body. These unique proteins are commonly used for diagnostic and therapeutic purposes because they easily bind to antigenic molecules. Polyclonal antibody production currently involves the use of laboratory animals such as rats, rabbits, sheep, goats, and horses. However, the manufacture of these antibodies generally involves practices that cause pain to animals, such as prolonged bloodletting. In recent years, isolating antibodies from egg yolk following hyperimmunization of chickens has emerged as a popular approach for producing significant amounts of antibodies. This approach combines the principles of natural passive immunity and artificial passive immunity. To ensure a continuous accumulation of antibodies in egg yolks, chickens are regularly immunized with specific antigens. Egg yolk antibodies, known as IgY, are extracted and used for immunotherapy and immunodiagnostic purposes in human and animal applications due to their promising antibacterial properties. The antibacterial properties of egg yolk antibodies have been a significant focus in IgY studies. Several reports have shown that IgY helps prevent bacterial transmission or infection in vivo. The production of IgY against mammalian antigens has a higher success rate than IgG production. This is because of the phylogenetic difference between mammals and chickens. Furthermore, these antibodies have a more comprehensive range of antigenic epitope recognition and can respond to more than one species, making them more versatile. This study compiles information on the properties, mechanisms of action, and uses of egg yolk antibodies based on existing literature on IgY technology.