Biology

In 1990s, the European spiny lobster Palinurus elephas, one of the most commercially important species in the Mediterranean, exhibited a population decline. For this reason, fully protected areas (FPAs) appeared effective in re-establishing natural populations and supporting fishery-management objectives. Here, the reproductive parameters of P. elephas populations in two different FPAs (Su Pallosu and Buggerru, central-western Mediterranean), where a restocking programme was carried out, and in their surrounding commercial zones, were investigated from quantitative and qualitative perspectives. The comparison of fecundity between females collected inside and outside FPAs did not show statistical differences as well as the vitellogenin concentration, which did not vary among eggs of different size classes of females caught inside and outside the FPAs, indicating the same reproductive potential. The study demonstrated a benefit of overexploited populations in terms of enhancement of egg production overtime (15 years for Su Pallosu and 6 years for Buggerru) with a mean egg production 4.25–5.5 times higher at the end of the study than that observed at the beginning of the study. The main driver of eggs production appeared to be size, with larger lobsters more present inside the FPAs than outside. Given these results, the dominant contribution of the two studied FPAs to the regional lobster reproduction is remarkable. Full article

Although an individual’s mix of MHC immune genes determines its resistance, finding MHC-dependent mate choice occurred by accident in inbred mice. Inbred mice prefer MHC dissimilar mates, even when the choice was restricted to urine. It took decades to find the info-chemicals, which have to be as polymorphic as the MHC. Microbiota were suggested repeatedly as the origin of the odor signal though germ-free mice maintained normal preference. Different versions of the ‘carrier hypothesis’ suggested MHC molecules carry volatiles after the bound peptide is released. Theory predicted an optimal individual MHC diversity to maximize resistance. The optimally complementary mate should be and is preferred as several studies show. Thus, the odor signal needs to transmit the exact information of the sender’s MHC alleles, as do MHC ligand peptides but not microbiota. The ‘MHC peptide hypothesis’ assumes that olfactory perception of the peptide ligand provides information about the MHC protein in a key-lock fashion. Olfactory neurons react only to the anchors of synthesized MHC peptides, which reflect the binding MHC molecule’s identity. Synthesized peptides supplemented to a male’s signal affect choice in the predicted way, however, not when anchors are mutated. Also, the human brain detects smelled synthesized self-peptides as such. After mate choice, the lottery of meiosis of randomly paired oocyte and sperm haplotypes would often produce MHC non-optimal offspring. In sticklebacks, eggs select MHC-compatible sperm, thus prefer the best combination close to the population optimum. Full article

Drought is a critical and increasingly common abiotic factor that has impacts on plant structures and functioning and is a challenge for the successful management of forest ecosystems. Here, we test the shifts in leaf morpho-anatomical or hydraulic traits and plant growth above ground caused by drought. A factorial experiment was conducted with two gymnosperms (Larix gmelinii and Pinus koraiensis) and two angiosperms (Fraxinus mandshurica and Tilia amurensis), tree species grown under three varying drought intensities in NE China. Considering all the species studied, the plant height (PH), root collar diameter (RCD), and plant biomass (PB) were significantly decreased by drought. The leaf thickness (LT) increased, while the leaf area (LA) decreased with drought intensity. In the gymnosperms, the mesophyll thickness (MT) increased, and the resin duct decreased, while in the angiosperms the palisade mesophyll thickness (PMT), the spongy mesophyll thickness (SMT), and the abaxial (ABE) and adaxial epidermis (ADE) thickness were increased by drought. The correlation analysis revealed that P. koraiensis and F. mandshurica had the higher RMF and total plant biomass, but the least LMF, suggesting drought tolerance. In contrast, the L. gmelinii had the least RMF and higher LMF, suggesting vulnerability to drought. Similarly, T. amurensis had the higher leaf size, which increased the evaporative demand and depleted the soil water quickly relative to the other species. The interrelation among the morpho-anatomical leaf traits was equally affected by drought across all the studied species, suggesting that there is no clear evidence to differentiate the taxa based on drought resistance vs. drought tolerance. Thus, we have identified some easily measurable traits (i.e., LMF, RMF, and PB) which evidenced the seedling’s ability to cope with drought and which therefore could be used as proxies in the selection of drought tolerant species for reforestation in the temperate forest. Full article

The modern era of analytical and quantitative palaeobiology has only just begun, integrating methods such as morphological and molecular phylogenetics and divergence time estimation, as well as phenotypic and molecular rates of evolution. Calibrating the tree of life to geological time is at the nexus of many disparate disciplines, from palaeontology to molecular systematics and from geochronology to comparative genomics. Creating an evolutionary time scale of the major events that shaped biodiversity is key to all of these fields and draws from each of them. Different methodological approaches and data employed in various disciplines have traditionally made collaborative research efforts difficult among these disciplines. However, the development of new methods is bridging the historical gap between fields, providing a holistic perspective on organismal evolutionary history, integrating all of the available evidence from living and fossil species. Because phylogenies with only extant taxa do not contain enough information to either calibrate the tree of life or fully infer macroevolutionary dynamics, phylogenies should preferably include both extant and extinct taxa, which can only be achieved through the inclusion of phenotypic data. This integrative phylogenetic approach provides ample and novel opportunities for evolutionary biologists to benefit from palaeontological data to help establish an evolutionary time scale and to test core macroevolutionary hypotheses about the drivers of biological diversification across various dimensions of organisms. Full article

Proteomics methods can identify amino acid sequences in fossil proteins, thus making it possible to determine the ascription or proximity of a fossil to other species. Before mass spectrometry was used to study fossil proteins, earlier studies used antibodies to recognize their sequences. Lowenstein and colleagues, at the University of San Francisco, pioneered the identification of fossil proteins with immunological methods. His group, together with Olivares’s group at the University of Granada, studied the immunological reactions of proteins from the controversial Orce skull fragment (VM-0), a 1.3-million-year-old fossil found at the Venta Micena site in Orce (Granada province, southern Spain) and initially assigned to a hominin. However, discrepancies regarding the morphological features of the internal face of the fossil raised doubts about this ascription. In this article, we review the immunological analysis of the proteins extracted from VM-0 and other Venta Micena fossils assigned to hominins and to other mammals, and explain how these methods helped to determine the species specificity of these fossils and resolve paleontological controversies. Full article

Paratuberculosis is a disease caused by Mycobacterium avium subsp. paratuberculosis (MAP). It is of great interest to better understand the proteins involved in the pathogenicity of this organism in order to be able to identify potential therapeutic targets and design new vaccines. The protein of interest–MAP3773c–was investigated, and molecular modeling in silico, docking, cloning, expression, purification, and partial characterization of the recombinant protein were achieved. In the in silico study, it was shown that MAP3773c of MAP has 34% sequence similarity with Mycobacterium tuberculosis (MTB) FurB, which is a zinc uptake regulator (Zur) protein. The docking data showed that MAP3773c exhibits two metal-binding sites. The presence of structural Zn²⁺ in the purified protein was confirmed by SDS-PAGE PAR staining. The purification showed one band that corresponded to a monomer, which was confirmed by liquid chromatography–mass spectrometry (LC-MS). The presence of a monomer was verified by analyzing the native protein structure through BN-SDS-PAGE (Native Blue (BN) Two-Dimensional Electrophoresis) and BN–Western blotting. The MAP3773c protein contains structural zinc. In conclusion, our results show that MAP3773c displays the features of a Fur-type protein with two metal-binding sites, one of them coordinating structural Zn²⁺. Full article

The evaluation of muscle mass in athletes correlates with sports performance directly. Bioimpedance vector analysis is a growing method of assessing body composition in athletes because it is independent of predictive formulas containing variables such as body weight, ethnicity, age, and sex. The study aims to propose a new parameter (Levi’s Muscle Index, LMI) that evaluates muscle mass through raw bioelectrical data. A total of 664 male footballers underwent bioimpedance assessment during the regular season. LMI was correlated with body cell mass (BCM) and phase angle (PA) to establish efficacy. The footballers were 24.5 ± 5.8 years old, 180.7 ± 5.9 cm tall and weighed 76.3 ± 7.1 kg. The relationships were: LMI-BMI: r = 0.908, r² = 0.824, p < 0.001; LMI-PA: r = 0.704, r² = 0.495, p = 0.009 and PA-BCM: r = 0.491, r² = 0.241, p < 0.001. The results obtained confirm that LMI could be considered a new parameter that provides reliable information to evaluate the muscle mass of athletes. Furthermore, the higher LMI-BCM relationship than PA-BCM demonstrates specificity for muscle mass evaluation in athletes regardless of body weight, ethnicity, age, and sex. Full article

Bacterial community is a key factor affecting aerobic composting, and understanding bacterial community succession is important to revealing the mechanism of organic matter degradation. In this study, the succession and metabolic characteristics of bacterial communities were explored in 45 days composting of sheep manure and wheat straw by using high-throughput sequencing technology and bioinformatics tools, respectively. Results showed that the alpha diversity of bacterial community significantly decreased in the thermophilic (T2) phase and then recovered gradually in the bio-oxidative (T3) and the maturation (T4) phases. Bacterial communities varied at different stages, but there were 158 genera in common bacterial species. Unclassified_f_Bacillaceae, Oceanobacillus, Bacillus, Pseudogracilibacillus, and Nocardiopsis were identified as keystone bacterial genera. Eleven genera were significantly correlated (p < 0.05), or even extremely significantly correlated (p < 0.001), with the physicochemical factors. Redundancy analysis (RDA) showed that changes of bacterial community diversity correlated with physicochemical factors. The highest relative abundances were amino acid and carbohydrate metabolism among the metabolic groups in the compost. These results will provide theoretical support for further optimizing sheep manure composting conditions and improving the quality of organic fertilizers. Full article

Shiga toxin-producing E. coli (STEC) is considered a worldwide public health and food safety problem. Despite the implementation of various different approaches to control food safety, outbreaks persist. The aim of study is to evaluate the applicability of phages, isolated against STEC O157:H7, as prospective food bio-preservatives. Considering the relatively wide host range and greatest protein diversity, two phages (STEC P2 and P4) from four were furtherly characterized. Complete genome analysis confirmed the absence of toxins and virulence factors—encoding genes. The results confirmed the close relation of STEC P2 to phages of Myoviridae, and STEC P4 to the Podoviridae family. The phages retained higher lytic competence of 90.4 and 92.68% for STEC P2 and P4, respectively with the HTST pasteurization. The strong acidic (pH 1) and alkaline (pH 13) conditions had influential effect on the surviving counts of the two phages. The lowest survivability of 63.37 and 86.36% in STEC P2 and P4 lysate, respectively appeared in 2% bile salt solution after 3 h. The results confirmed the strong effect of simulated gastric fluid (SGF) on the survivability of the two phages comparing with simulated intestinal fluid (SIF). Therefore, the two phages could be applied as a natural alternative for food preservation. Full article

Species occurring in sympatry and relying on similar and limited resources may partition resource use to avoid overlap and interspecific competition. Aotearoa, New Zealand hosts an extraordinarily rich marine megafauna, including 50% of the world’s cetacean species. In this study, we used carbon and nitrogen stable isotopes as ecological tracers to investigate isotopic niche overlap between 21 odontocete (toothed whale) species inhabiting neritic, mesopelagic, and bathypelagic waters. Results showed a clear niche separation for the bathypelagic Gray’s beaked whales (Mesoplodon grayi) and sperm whales (Physeter macrocephalus), but high isotopic niche overlap and potential interspecific competition for neritic and mesopelagic species. For these species, competition could be reduced via temporal or finer-scale spatial segregation or differences in foraging behaviour. This study represents the first insights into the coexistence of odontocetes in a biodiverse hotspot. The data presented here provide a critical baseline to a system already ongoing ecosystem change via ocean warming and subsequent effects on prey abundance and distributions. Full article

(1) Background: Accurate localization of the epileptogenic zone and understanding the related functional connectivity (FC) alterations are critical for the prediction of clinical prognosis in patients with temporal lobe epilepsy (TLE). We aim to localize the hypometabolic region in TLE patients, compare the differences in FC alterations based on hypometabolic region and structural lesion, respectively, and explore their relationships with clinical prognosis. (2) Methods: Thirty-two TLE patients and 26 controls were recruited. Patients underwent ¹⁸F-FDG PET/MR scan, surgical treatment, and a 2–3-year follow-up. Visual assessment and voxel-wise analyses were performed to identify hypometabolic regions. ROI-based FC analyses were performed. Relationships between clinical prognosis and FC values were performed by using Pearson correlation analyses and receiver operating characteristic (ROC) analysis. (3) Results: Hypometabolic regions in TLE patients were found in the ipsilateral hippocampus, parahippocampal gyrus, and temporal lobe (p < 0.001). Functional alterations based on hypometabolic regions showed a more extensive whole-brain FC reduction. FC values of these regions negatively correlated with epilepsy duration (p < 0.05), and the ROC curve of them showed significant accuracy in predicting postsurgical outcome. (4) Conclusions: In TLE patients, FC related with hypometabolic region obtained by PET/fMRI may provide value in the prediction of disease progression and seizure-free outcome. Full article

Recent recoveries of peptide sequences from two Cretaceous dinosaur bones require paleontologists to rethink traditional notions about how fossilization occurs. As part of this shifting paradigm, several research groups have recently begun attempting to characterize biomolecular decay and stabilization pathways in diverse paleoenvironmental and diagenetic settings. To advance these efforts, we assessed the taphonomic and geochemical history of Brachylophosaurus canadensis specimen MOR 2598, the left femur of which was previously found to retain endogenous cells, tissues, and structural proteins. Combined stratigraphic and trace element data show that after brief fluvial transport, this articulated hind limb was buried in a sandy, likely-brackish, estuarine channel. During early diagenesis, percolating groundwaters stagnated within the bones, forming reducing internal microenvironments. Recent exposure and weathering also caused the surficial leaching of trace elements from the specimen. Despite these shifting redox regimes, proteins within the bones were able to survive through diagenesis, attesting to their remarkable resiliency over geologic time. Synthesizing our findings with other recent studies reveals that oxidizing conditions in the initial ~48 h postmortem likely promote molecular stabilization reactions and that the retention of early-diagenetic trace element signatures may be a useful proxy for molecular recovery potential. Full article

The treatment of pig manure is a major environmental issue, and photobioreactors containing consortia of microalgae and bacteria have proven to be a promising and sustainable treatment alternative. This work studies the effect of Cu, Zn and As, three toxic elements frequently present in piggery wastewater, on the performance and microbiome of photobioreactors. After dopage with Zn (100 mg/L), Cu (100 mg/L), and As (500 µg/L), the high biomass uptake of Zn (69–81%) and Cu (81–83%) decreased the carbon removal in the photobioreactors, inhibited the growth of Chlorella sp., and affected heterotrophic bacterial populations. The biomass As uptake result was low (19%) and actually promoted microalgae growth. The presence of Cu and As decreased nitrogen removal, reducing the abundance of denitrifying bacterial populations. The results showed that metal(loid)s significantly affected 24 bacterial genera and that they did not recover after exposure. Therefore, this study makes an important contribution on the impact of the presence of metal(loid)s in piggery wastewater that compromises the overall performance of PBRs, and so, the environmental and health impact of treated effluents. Full article

Isometric activity can be used as a strategy to improve health, fitness, and functional performance in the elderly population, but differences in fatigability may occur. This study aimed to understand fatigability behavior during an upper limb isometric task (ULIT) and the role of health status and physical activity in the fatigability of elderly participants. Thirty-two (32) elderly participants (72.5 ± 5.18 years) were instructed to perform ULIT. The Borg CR10 scale and task failure point (TTF) were used to measure perceived and performance fatigability. Self-reported measures were used to assess the quality of life and physical activity level. A significant relationship between perceived and performance fatigability was found only in the final phase of activity (p < 0.01). Significant correlations were found between perceived fatigability and the social functioning dimension (p < 0.05), and between performance fatigability (TTF) and BMI (p < 0.01), physical functioning (p < 0.01), and role functioning/physical (p < 0.05) dimensions. In conclusion, ULIT produces changes in fatigability of elderly people, which are positively related in the final stage of the activity. Changes in fatigability are negatively related to BMI. It is also negatively related to health, social functioning, physical functioning and role functioning/physical quality of life dimensions. Full article

Hepatocellular carcinoma (HCC) is at the forefront of the global cancer burden, and biomarkers for HCC are constantly being sought. Interestingly, RGS (Regulators of G protein signaling) proteins, which negatively regulate GPCR signaling, have been associated with various cancers, with some members of the RGS family being associated with liver cancer as well. Considering this, we investigated the role of RGS20 as a potential prognostic marker in 28 different cancer types with special emphasis on HCC. By using the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) data, our analysis revealed that (a) RGS20 was strongly upregulated in tumor tissue compared with adjacent normal tissue of HCC patients; (b) RGS20 was strongly associated with some important clinical parameters such as alpha-fetoprotein and tumor grade in the HCC patients; (c) besides HCC (p < 0.001), RGS20 was found to be an important factor for survival in four other cancers (clear renal cell carcinoma: p < 0.001, lung adenocarcinoma: p = 0.004, mesothelioma: p = 0.039, ovarian serous cystadenocarcinoma: p = 0.048); (d) RGS20 was found to be significantly associated with some tumor-related signaling pathways and long intergenic non-coding RNAs (lincRNAs: LINC00511, PVT1, MIR4435-2HG, BCYRN1, and MAPKAPK5-AS1) that exhibit oncogenic potential. Taken together, we showed that RGS20 correlates with a few HCC-associated lincRNAs harboring oncogenic potential and is markedly upregulated in HCC patients. Our analysis further supports the putative function of RGS proteins, particularly RGS20, in cancer. Full article

Pot trials were performed to explore the impacts of seed priming (SPr) plus leaf treatment (LTr) with trans-zeatin-type cytokinin (tZck; 0.05 mM) and silymarin (Sim; 0.5 mM) on growth, yield, physio-biochemical responses, and antioxidant defense systems in Cd-stressed wheat. tZck + Sim applied as SPr + LTr was more effective than individual treatments, and the impacts were more pronounced under stress conditions. Cd stress (0.6 mM) severely declined growth and yield traits, and photosynthesis efficiency (pigment contents, instantaneous carboxylation efficiency, and photochemical activity) compared to the control. These negative impacts coincided with increased levels of Cd²⁺, O₂^•− (superoxide), H₂O₂ (hydrogen peroxide), MDA (malondialdehyde), and EL (electrolyte leakage). Non-enzymatic and enzymatic antioxidant activities, and tZck and Sim contents were also increased. However, tZck + Sim increased photosynthesis efficiency, and further boosted antioxidant activities, and contents of tZck and Sim, while minimizing Cd²⁺ levels in roots, leaves, and grains. The levels of O₂^•−, H₂O₂, MDA, and EL were also minimized, reflecting positively on growth and productivity. tZck + Sim applied as SPr + LTr was highly effective in promoting antioxidants and photosynthesis machineries, minimizing oxidative stress biomarkers and Cd²⁺ levels, boosting tolerance to Cd stress, and improving wheat productivity under Cd stress. Full article

Bacterial soft rot, caused by Pectobacterium brasiliense, can infect several economically important horticultural crops. However, the management strategies available to control this disease are limited. Plant-growth-promoting rhizobacteria (PGPR) have been considered to be promising biocontrol agents. With the aim of obtaining a strain suitable for agricultural applications, 161 strains were isolated from the rhizosphere soil of healthy cucumber plants and screened through plate bioassays and greenhouse tests. Paenibacillus peoriae ZF390 exhibited an eminent control effect against soft rot disease and a broad antagonistic activity spectrum in vitro. Moreover, ZF390 showed good activities of cellulase, protease, and phosphatase and a tolerance of heavy metal. Whole-genome sequencing was performed and annotated to explore the underlying biocontrol mechanisms. Strain ZF390 consists of one 6,193,667 bp circular chromosome and three plasmids. Comparative genome analysis revealed that ZF390 involves ten gene clusters responsible for secondary metabolite antibiotic synthesis, matching its excellent biocontrol activity. Plenty of genes related to plant growth promotion, biofilm formation, and induced systemic resistance were mined to reveal the biocontrol mechanisms that might consist in strain ZF390. Overall, these findings suggest that strain ZF390 could be a potential biocontrol agent in bacterial-soft-rot management, as well as a source of antimicrobial mechanisms for further exploitation. Full article

Bacterial pigments (e.g., melanin and carotenoids) are considered to be among the most important secondary metabolites due to their various pharmacological activities against cancer and microbial resistance. Different pigmented bacterial strains were isolated from soil samples from El Mahmoudiyah governance and screened for their antimicrobial activity. The most promising pigment producer was identified as Micrococcus lylae MW407006; furthermore, the produced pigment was identified as echinenone (β-carotene pigment). The pigment production was optimized through a central composite statistical design to maximize the biomass production, pigment concentration, and the antimicrobial activity. It was revealed that the most significant fermentation parameters were the glucose (as a carbon source) and asparagine (as a nitrogen source) concentrations. Nano-echinenone was synthesized using the ball milling technique, characterized, and finally assessed for potential antimicrobial, antioxidant, and antitumor activities. The data revealed that the synthesized nano-echinenone had higher antimicrobial activity than the crude pigment. The cytotoxic potency of echinenone and nano-echinenone was investigated in different cell lines (normal and cancer cells). The inhibition of cell proliferation and induction of cell death was observed in Caco-2 and Hep-G2 cells. The data proved that nano-echinenone is a suitable candidate for use as a safe antimicrobial and anti-hepatocellular-carcinoma agent. Full article

The environmental bacterium Pseudomonas mosselii produces antagonistic secondary metabolites with inhibitory effects on multiple plant pathogens, including Ralstonia solanacearum, the causal agent of bacterial wilt. In this study, an engineered P. mosselii strain was generated to express R. solanacearum ripAA, which determines the incompatible interactions with tobacco plants. The ripAA gene, together with its native promoter, was integrated into the P. mosselii chromosome. The resulting strain showed no difference in antimicrobial activity against R. solanacearum. Promoter-LacZ fusion and RT-PCR experiments demonstrated that the ripAA gene was transcribed in culture media. Compared with that of the wild type, the engineered strain reduced the disease index by 9.1% for bacterial wilt on tobacco plants. A transcriptome analysis was performed to identify differentially expressed genes in tobacco plants, and the results revealed that ethylene- and jasmonate-dependent defense signaling pathways were induced. These data demonstrates that the engineered P. mosselii expressing ripAA can improve biological control against tobacco bacterial wilt by the activation of host defense responses. Full article