Objective To investigate the metabolic characteristics of follicular fluid (FF) from human ovarian follicles of different developmental stages, and whether there are metabolic predictors of follicular development (FD) with clinical implications. Design A population-based study. Setting A two-stage study from a reproductive medicine center in Nanjing, China between 2019 and 2020. Population A total of 226 infertile women, with tubal complications or unexplained sterility, experiencing their first in vitro fertilization cycle. Methods and main outcome measures The FF from both large follicles (LFs) and matched-small follicles (SFs) was analyzed with the wide range of targeted metabolome technique. The metabolic signatures were described by multi-omics integration technology including our metabolomic data and published transcriptomic data. The potential biomarkers of FD were next verified using enzyme-linked immunoassay with FF and blood serum from an independent 200 participants. Results Overall, 116 differential metabolites were found in 26 LFs and 26 SFs. The combination of pathway analysis and network analysis revealed the importance of lysophosphatidylcholine (LPC) metabolism in FF during FD. Moreover, differential metabolites and mRNAs were connected into a network. Upon linking metabolites with clinical information, followed by an independent population verification, we found that LPC was able to predict FD and ovarian sensitivity parameters both in FF and blood serum. Conclusions We described the FF metabolic signatures from ovarian follicles of different developmental stages, and LPC can be used as a biomarker of FD and ovarian sensitivity, offering potential detection and therapeutic targets for enhancing follicle and oocyte health in humans.

Shigella flexneri 2a is one of the leading bacterial agents of diarrhoeal mortality in humans. Recently, multi-drug resistance strains have posed severe challenges. The present study was conducted to identify potential drug-target using gene interaction network (GIN) approach in order to understand the molecular mechanisms of both antimicrobial resistance (AMR) and virulence posed by the bacteria. Differential gene expression (DGE) and structural analysis were incorporated to validate our findings. Functional enrichments and topological matrices revealed evgS, ybjZ, tolC, gyrA, parC and their direct interactors to be associated with diverse AMR mechanisms. Since the druggability of TolC, GyrA, and ParC has already been exploited, the current study explored EvgS as a potential alternate drug-target candidate due to its highest prevalence in both GINs interconnecting several genes of two component system (TCS). DGE patterns in ΔPhoPQ (deleted regulatory PhoP and sensor PhoQ) led to the upregulation of TCS comprising EvgSA thereby validating EvgS as a promising therapeutic biomarker. Druggability and structural stability of EvgS was assessed through thermal shifts, backbone stability and coarse dynamics refinement. Structure-function relationship was established revealing the C-terminal extracellular domain as the drug binding site which was further validated through molecular dynamics simulation. Our findings would be pivotal for experimental biologists in designing effective lead molecules against EvgS for establishing successful therapeutic remedies against shigellosis.

Aim: Studies show that although the presence of women in the medical field has risen, there is lesser representation of women within editorial boards of journals. In our study, we aimed to investigate whether gender disparity exists within the editors and editorial board members of medical journals, especially in those related to emergency medicine. Methods: In the present cross-sectional study, we searched medical journals using the Scimago Journal/Country Rank journal system for comparison. The web sites of the journals included in the study were searched, and gender data of the editor and editorial board, associate editors, consultant editors, and section editors for each journal were obtained. Results: The total number of journals examined in this study was 276. Ten journals from each of the different branches of medicine were included. There were 26 journals from Emergency Medicine journals. The median percentage of female editorial board members (20.8%; 50–100) was lower in emergency medicine journals compared to other branches of medicine (31%; 0–100) (p<0.001). The median percentage of female editorial board members and editors was also lower in emergency medicine field (20.6%; 0–50) (p<0.001) than other branches of medicine. The percentage of female editorial board members of emergency medicine journals was 19.5% with the third lowest ranking among 26 branches. When both the editors and editorial board members were considered, the highest female percentage was found in pediatrics (50.7%) followed by geriatric medicine (43.4%). Conclusion: There is a significant gender disparity within editors and editorial board members in emergency medicine journals. The proportion of women within the editorial board was found to be lower in emergency medicine journals among all the journals included in the study.

To characterize the clinical features of chronic kidney disease in dogs with serological evidence of Leptospira spp. from an endemic region, thirty-three dogs with chronic kidney disease were clinically evaluated from March 2019 to March 2020, all dogs were also serologically tested for Ehrlichia canis and Anaplasma phagocytophilum. Seroprevalence for Leptospira spp. was 39.4%. The most frequent serovars found were Pyrogenes, Canicola, Bratislava and Australis with serological titters between 1:100 and 1:800. The most frequent clinical signs detected were fever, depression, decreased body condition, vomiting, and hematuria. Significant laboratory findings (p <0.05) were anemia, leukocytosis, thrombocytopenia, increased liver enzymes, urea and creatinine, hyperbilirubinemia, and hyperphosphatemia. All leptospira seronegative dogs were positive at one or both monitored homoparasites (i.e. E. canis and A. phagocytophilum); only 3 leptospira seroposive dogs were positive to one or both hemoparasite. Leptospirosis in dogs may be involved in the development of kidney disease, so it should be considered within the battery of clinical analysis, particularly in endemic areas. However, further studies are still required to determine the specific role of the various serovars associated with CKD. Findings suggests that endemic hemoparasites of dogs should be monitored in dogs with a kidney condition for a better diagnostic and therapeutic approach.

In this article, a stochastic SIR epidemic model with saturated treatment function, non-monotone incidence rate and logistic growth is studied. Firstly, we prove that the stochastic model has a unique global positive solution. Next, by constructing a suitable Lyapunov function, we can show that the random SIR model exists an ergodic stationary distribution. Then, we show that a sufficient condition can make the disease tend to extinction. Finally, some numerical simulations were used to prove our analytical result.

Background Brain injury is the main cause of high mortality and disability after successful cardiopulmonary resuscitation (CPR) from sudden cardiac arrest (CA). Transient receptor potential M4 (TRPM4) channel is a novel target for ameliorating blood-brain barrier (BBB) disruption and neuroinflammation. Herein, we tested whether flufenamic acid (FFA), which is reported to block TRPM4 with high potency, confers neuroprotection against brain injury secondary to CA/CPR and whether the action is exerted by blocking the TRPM4 channel. Methods Wild-type (WT) and Trpm4 knockout (Trpm4−/−) mice subjected to 10-min CA/CPR were randomized to receive FFA or vehicle once daily. Post-CA/CPR brain injuries including neurological deficits, survival rate, histological damages, edema formation, BBB destabilization and neuroinflammation were assessed. Results In WT mice subjected to CA/CPR, FFA was effective in improving survival and neurologic outcome, reducing neuropathological injuries, attenuating brain edema, lessening leakage of IgG, restoring tight junction protein expression as well as promoting microglia/macrophages from the pro-inflammatory subtype towards the anti-inflammatory one. In comparison to WT mice, Trpm4−/− mice exhibited less neurologic deficiency, lighter histological impairment, more integrity of BBB and more anti-inflammatory microglia/macrophages polarization. As expected, FFA did not provide a benefit of superposition compared with vehicle in the Trpm4−/− mice after CA/CPR. Conclusions FFA mitigates BBB breach and modifies the functional status of microglia/macrophages, thereby improving survival and neurological deficits following CA/CPR. The neuroprotective effects are at least partially through interfering with the TRPM4 channel. These results provide significant clinical potentials to improve the prognosis for CA victims with successful resuscitation.

Most children and adolescents with SARS-CoV-2 infection shows asymptomatically or with mild symptoms. There are few reported cases of extracorporeal membrane oxygenation (ECMO) in pediatric patients with coronavirus disease 2019 (COVID-19). We present a previously healthy 13-year-old male, diagnosed with metastatic Ewing’s sarcoma at the same time as catastrophic acute respiratory distress syndrome due to COVID-19, which was successfully supported by veno-venous ECMO, while he received the corresponding chemotherapy protocol. ECMO can be used as salvage therapy in oncology pediatric patients with respiratory failure secondary to COVID-19. In addition, successful chemotherapy can be administered while patients are supported on ECMO.

Objective To explore the differences in auditory speech effects and quality of family life of pre-lingual deaf children with different hearing aid models within one year afrer postoperative, and analyze the relationship between them. Design A prospective cohort study Setting and Participants Fifty-eight cases of children with prelingual deafness who underwent cochlear implantion at the First Affiliated Hospital of Anhui Medical University from March to July 2020 were selected. Main Outcome Measures According to the hearing aid mode, Children with prelingual deafness were divided into 21 cases in the unilateral cochlear implant group (CI), 8 cases in the bimodal group (CI+HA), and 29 cases in the bilateral cochlear implant group (BCI). The speech,spatial and qualities of hearing scale-parent’s version(SSQ-P) and children using hearing implants quality of life (CuHI QoL) were used to measure auditory speech ability and family quality of life in three groups. Results At one year postoperatively, the speech perception, spatial hearing, hearing sound quality and SSQ-P scores of the BCI group were significantly higher than those of the CI+HA group, and the CI+HA group was superior to the CI group. Especially in spatial hearing and hearing sound quality, the BCI group was more advantageous than the other two groups (P<0.05). At 6 months postoperatively, the BCI group had the highest quality of family life scores. while at 1 year postoperatively, there was no differences in quality of family life between the three groups (P>0.05). Overall, their quality of family life and SSQ-P scores showed a gradual increase with the postoperative time. Auditory speech effects were positively correlated with quality of family life (r=0.312, P<0.01). Conclusions BCI can effectively improve children’s spatial hearing and hearing quality. The better the postoperative auditory speech effects, the higher the quality of family life.

● Laisk method uses truncated A/Ci curves (demand function, DF) to estimate Ci* and Rd. In Laisk dataset, the Ca-Ci relationship reflects the supply function (SF), and points (Ci, A) for the same Ca can be fitted to a regression line (referred to Supply and Demand Function, DSF). ● The application of DSF to estimating Ci* and Rd by Laisk method and the relationship between DSF slope (dsf) and gs, and photosynthetic parameters were investigated in this study. ● Results showed that dsf was not affected by Laisk measurement conditions (PAR or Ca), while, it was inversely related to gs, apparent carboxylation efficiency (ACE) and apparent quantum yield (AQY). The dsf was essentially the slope of a light response curve (△A/△Ci-lrc) at low Ci. We devised an auxiliary line vertical to DSF and used it to improve the stability of Ci* and Rd estimates from Laisk data set for. ● We found that DSF slope was species-specific and independent of PAR and Ca. The dsf related CO2 diffusion to biochemical characteristics and represents the coordination between the two when Rubisco and RuBP regeneration co-limit photosynthesis. In conclusion, dsf can be used to describe the intrinsic characteristics of photosynthesis.

The market demand for biopharmaceuticals, the leading drugs in the pharmaceutical industry, has promoted the development of various protein expression hosts and bioprocessing technologies. While advances in the field of recombinant protein production have changed the previous situation, resulting in increased production and reduced costs, industrialized production helped in the treatment of a variety of diseases. Since mammalian cells have the unique advantages of being able to direct the correct folding of proteins and provide post-translational processing such as complex glycosylation the recombinant protein drugs produced by them currently account for approximately 80% of the approved marketed protein drugs, while Chinese hamster ovary (CHO) cells are currently the preferred host cells for the production of recombinant protein drugs. Obtaining recombinant protein drugs involves the synthesis, processing, transport, and secretion of proteins, and the secretion of proteins greatly limits the manufacturing of recombinant protein drugs. Here, we review the current research status of CHO cells as an important engineering tool for recombinant protein drug expression systems, focus on the recombinant protein secretion process of CHO cells and its influencing factors, and discuss the optimization strategy for recombinant protein secretion and expression in CHO cells.

Zymomonas mobilis ZM4 is an attractive host for the development of microbial cell factories to synthesize high-value compounds, including prebiotics. In this study, a straightforward process to produce fructooligosaccharides (FOS) from sucrose was established. To control the relative FOS composition, recombinant Z. mobilis strains secreting a native levansucrase (encoded by sacB) or a mutated β-fructofuranosidase (Ffase-Leu196) from Schwanniomyces occidentalis were constructed. Both strains were able to produce a FOS mixture with high concentration of 6-kestose. The best results were obtained with Z. mobilis ZM4 pB1-sacB, that was able to produce 73.4 ± 1.6 g L−1 of FOS, with a productivity of 1.53 ± 0.03 g L-1 h-1 and a yield of 0.31 ± 0.03 gFOS gsucrose-1. This is the first report on the FOS production using a mutant Z. mobilis ZM4 strain in a one-step process.

Background: While the coronavirus disease 2019 (COVID-19) is most commonly associated with the respiratory system, disorders in other organ systems, such as the cardiovascular, neurologic, or renal, can also contribute to disease fatality. This study aimed to evaluate the relation of comorbidities to COVID-19 short-term mortality. Method: This was a single-center observational study with a historical cohort method at Bethesda Hospital Yogyakarta, Indonesia. COVID-19 diagnosis was made by utilizing reverse transcriptase-polymerase chain reaction (RT-PCR) on nasopharyngeal swabs. Patient data were retrieved from electronic medical records and used for Charlson Comorbidity Index assessments. In-hospital mortality was monitored throughout their hospital stay. Results: This study enrolled 333 patients. According to the total number of comorbidities in Charlson, 11.7% (n=39) of patients had no comorbidities; 30.9% (n=103) of patients had one comorbidity; 20.1% (n=67) of patients had two comorbidities; and 37.2% (n=124) of patients had more than three comorbidities. In multivariate analysis, these variables were significantly related to short-term mortality in COVID-19 patients: older age (odds ratio [OR] per year 1.64; 95% confidence interval [CI] 1.23-2.19; p 0.001), myocardial infarction (OR 3.57 ; 95% CI 1.49-8.56; p: 0.004), diabetes mellitus (OR 2.41; 95 CI 1.17-4.97; p: 0.017), renal disease (OR 5.18 ; 95% CI 2.07-12.97; p <0.001), and longer duration of stay (OR 1.20; 95% CI 1.08-1.32; p <0.001). Conclusion: Our study revealed multiple risk factors for mortality in patients with COVID-19. The coexistence of cardiovascular disease, diabetes, and renal problem are significant predictors of short-term mortality in COVID-19 patients.

Study Objective: The purpose of this study was to determine the effects of self-prone positioning on oxygenation in COVID-19 positive patients utilizing supplemental oxygen and incidence of intubation. Method: A one-year observational cohort pilot study at a major inner-city hospital to evaluate self-proning on independent COVID-19 positive patients. Qualified patients 18 years of age or older were recruited based on inclusion and exclusion criteria. Data collection included vital signs and timing for body position changes, and results were analyzed using descriptive and inferential statistics. Results: Between April 2020 and May 2021, 93 COVID-19 enrolled patients engaged in stomach or lateral self-prone positioning. Eighty-four percent (n=78) of the population did not require intubation, whereas 16% (n=15) were intubated during their hospital stay. SpO2 means were determined for each population and prone position: Non-intubated (stomach) - before proning 93% (IQR 4) and during proning 95% (IQR 3); (lateral) before proning 92% (IQR 4) and during proning 93% (IQR 4). Intubated (stomach) - before proning 90% (IQR 7) and during proning 95% (IQR 4); (lateral) before proning 92% (IQR 5) and during proning 95% (IQR 5). Stomach proning significantly increased oxygenation in the non-intubated (p <0.001) and intubated (p 0.017) populations. Lateral proning significantly improved oxygenation in the intubated population (p 0.002). Conclusion: Self-proning in the independent COVID-19 positive patient on supplemental oxygen was effective in improving SpO2 levels short-term. Further controlled trial studies will elucidate the duration of proning effects and reinforce its use as a noninvasive rescue intervention to prevent intubation.

Viruses that emerge pose challenges for treatment options as their uniqueness would not know completely. In spite of large diversity, viruses share common characteristics for infection. There are at least 12 different respiratory borne viruses that belong to different virus taxonomic families. Many of these viruses multiply and cause damage to the upper and lower respiratory tracts. The description about these viruses in comparison to each other with reference to their epidemiology, molecular characteristics, disease manifestations, diagnosis and treatment is lacking. Such information helps to diagnose, differentiate and for formulating the control measures at faster pace. The leading cause of acute illness worldwide are the acute respiratory infections (ARIs) and are being responsible for nearly 4 million deaths every year which are mostly in young children and infants. Among the above ARIs, influenza, respiratory syncytial virus (RSV), parainfluenza virus type 3 (PIV-3), Streptococcus pneumoniae, Haemophilus influenzae and corona viruses are the main infectious agents. WHO recognized respiratory syncytial virus, parainfluenza viruses, coronavirus, rhinovirus, and human metapneumovirus [non-influenza RNA respiratory viruses (NIRVs)], as considerable global health burden. Lower respiratory tract infections are the fourth most common cause of death globally, after the non-infectious chronic conditions. This review aimed at presenting the characteristics of different viruses causing the respiratory infections highlighting the uniqueness of Covid-19. We expect that this review would help in understanding the similarities and differences among the closely related viruses causing respiratory infections and hence to formulate the specific preventive or control measures.

Background: There is an urgent need to review the status of COVID-19 vaccine immunization in pregnant women globally so that the adverse outcomes may be prevented. Objective: To evaluate the probable outcome of COVID-19 vaccination in pregnant women. Search strategy: An electronic search was conducted over the period of 3 months (June 15-August 15, 2021). Selection criteria: The original studies evaluating safety concerns in pregnant women for COVID-19 vaccination were included. Data collection and analysis: Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2009 guidelines were used for the collection of the data and reporting of the findings. The inclusion and exclusion criteria for the studies were determined based on ‘PICO principle’ (Population, Intervention, Comparator, and Outcome, Study design. Risk of bias assessment was done using National Institute of Health (NIH) tool for systematic reviews. Main results: COVID-19 vaccination in pregnant women was not associated with increased adverse effects or complications to the mother as well as developing fetus or newborn compared to non-vaccinated pregnant women. Vaccinated pregnant women showed a robust immune response against COVID-19 infection. Conclusions: COVID-19 vaccination during pregnancy causes no significant health risks for the mother or developing fetus or newborn.

Background: Gender biases among patients and medical students regarding the participation of men in obstetrics and gynecology (Ob/Gyn) may affect career decisions and pathways. This systematic review collects female patients’ gender preferences and perceptions of men, as Ob/Gyns and/or medical students, examining their influence on medical education and subsequent career decisions. Search Strategy: We identified relevant research via PubMed using variations of three concepts in combination: Ob/Gyn care, gender bias or gender preference, and medical education or career. We conducted the initial review in 2018 and repeated the search after initial analysis in March 2021, restricting the review to original research from the United States between 2000-2021. Results: Fifteen studies met inclusion, categorized into three groups: (1) patient’s gender preference for Ob/Gyns, (2) gender preference for medical students during their Ob/Gyn clerkship, (3) influence of gender bias on Ob/Gyn career decisions. Patients prioritized their physician’s care attributes (e.g., technical skill, compassion, experience) over gender when choosing an Ob/Gyn; however, provider gender was prioritized with medical student care. Accordingly, male medical students more commonly reported exclusions from clinical opportunities, though objective clinical exposure was like that of female counterparts. Despite perceived gender bias, male medical students reported increased Ob/Gyn interest post- clerkship; however, interest did not translate into more residency applications. These findings are limited by the quality and heterogeneity of studies. Conclusions: The combination of real and perceived gender bias among female patients and male medical students in obstetrics and gynecology may underlie declining numbers of men entering the field.

Remote sensing capabilities to monitor evergreen broadleaved vegetation are limited by the low temporal variability in the greenness signal. With canopy greenness computed from digital repeat photography (PhenoCam), we investigated how canopy greenness related to seasonal changes in leaf age and traits as well as variation of trees’ water fluxes (characterized by sap flow and canopy conductance). The results showed sprouting leaves, with significantly different leaf traits compared to mature and old leaves, are mainly responsible for the rapid increase in canopy green chromatic coordinate (GCC) in spring. Thus, the temporal dynamics of canopy GCC can be explained by leaf spectral properties and leaf age. Air temperature and vapor pressure deficit (VPD) explained most of sap flow and canopy conductance variance, respectively. Besides, GCC is an important explanatory variable for variation of canopy conductance may because GCC can represent the leaf ontogeny information. We conclude that PhenoCam GCC can be used to identify the new leaf flushing for evergreen broadleaved trees, which carries important information about leaf ontogeny and traits thus can better estimate of water fluxes such as canopy conductance.

Sweet cherry, an economically important horticultural crop, has strong antioxidant activity. The fruits contain compounds potentially beneficial to human health─particularly anthocyanins, which are synthesized in cytosol and predominantly accumulated in vacuoles. Although anthocyanin levels differ among dark-red, blush, and yellow sweet cherry cultivars, the regulatory mechanism of anthocyanin transport and accumulation is not well understood in this species. In this study, we identified 53 glutathione S-transferase genes (PavGSTs) from sweet cherry and found that PavGST1 expression was well correlated with anthocyanin accumulation in cultivars with different fruit skin colors. TRV-mediated virus-induced silencing of PavGST1 decreased anthocyanin accumulation in sweet cherry fruits and downregulated the expressions of anthocyanin biosynthetic and regulatory genes. In addition, transient overexpression of PavGST1 promoted anthocyanin accumulation. Furthermore, yeast one-hybrid and dual-luciferase assays revealed that PavMYB10.1 and PavMYB75 directly bind to different MYB binding sites of the PavGST1 promoter (MBS-1 and MBS-3) to activate PavGST1 transcription. According to our results, PavGST1 plays a central role in sweet cherry fruit anthocyanin accumulation. Our findings provide novel insights into the coordinative regulatory mechanisms of PavGST1 and PavMYBs in anthocyanin accumulation in sweet cherry.

The present study reports the effect new DFT methods introduced in Gaussian 16 viz B2PLYP, B2PLYPD, DSDPBEP86 and MPW2LPLYP on spectroscopic characterization and nonlinear optical properties (NLO) of 2-Bromo-5-nitrothiozole and Nitrosodimethylamine. The obtained results have compared with the old DFT as well as MP2 and HF. The spectroscopic characterization viz. geometrical parameters, vibrational, electronic absorption spectra and HOMO to LUMO gap with their molecular orbitals have been reported. The geometrical parameters such as optimized energy, dipole moment, bond length and angles have reported for both molecules at all methods using higher basis set (6-311++G**). The first and second order hyperpolarizabilities have also been reported for both 2-Bromo-5-nitrothiozole (C3HBrN2O2S) & Nitrosodimethylamine (C2H6N2O) molecules at all methods. This study shows that these two molecules are responsive to nonlinear optical (NLO), which reflect its enhanced applicability in development of photonic devices. The finite field approach has been applied for calculating first and second hyperpolarizabilities β and ϒ respectively. The HOMO to LUMO energy gap of Nitrosodimethylamine is found to be greater than that of 2-Bromo-5-nitrothiozole. All these calculations have performed using Gaussian 16 program package.

abundantly occurring methylation process at CpG island, which has been well-known as an epigenetic modification linked to many human’s diseases. Recently, another methylation approach has been discovered to show that DNA methyltransferases (DNMTs) promote the addition of methyl group at position 3 to yield 3mC. The existence of 3mC can cause severe damages to the DNA strand, such as blocking its replication, repair, and transcription, affecting its stability, and initiating a double-strand DNA break. To gain a deeper insight into the formation of 3mC, we have performed density functional theory (DFT) modeling studies at different levels of theory to clearly map out the mechanistic details for this new methylation approach. Our computed results are in harmony with pertinent experimental observations and shed light on a crucial off-target activity of DNMTs.

Parasitic plants have been shown to affect soil-organic-matter (SOM) decomposition, but the mechanism is unknown. As arbuscular mycorrhizal fungi (AMF) can affect decomposition and compete with parasitic plants for carbon, we hypothesized that parasitic plants can indirectly regulate decomposition by suppressing AMF. We conducted two experiments in which Bidens pilosa was inoculated with AMF or not, and parasitized with Cuscuta australis or not. In hyphae-in-growth bags, we provided SOM in one experiment as 13C-/15N-labelled maize leaves and in the other as phytate P. In the presence of AMF, Parasitization increased the 13C but decreased the organic P remaining in the bags. In the absence of the parasite, AMF decreased the 13C and increased the organic P remaining in the bags. Our results demonstrate that parasitic plants can indirectly regulate the decomposition of organic materials by suppressing the effect of the extraradical AMF hyphae on decomposition.

Largemouth bass (Micropterus salmoides) has become a cosmopolitan species due to its widespread introduction as game and domesticated fish. Here a high-quality chromosome-level reference genome of a female M. salmoides was produced by combining Illumina, PacBio and Hi-C sequencing, aiming to better understand the evolution of traits such as pathogen resistance and environmental adaptations. The genome size was 844.88 Mb with a contig N50 of 15.68 Mb, and 23 chromosomes anchoring 99.9% of the genome sequences. A total of 26,370 protein-coding genes from 3415 gene families, of which 127 unique to M. salmoides. Mining of publicly available RNA-Seq sequences from healthy M salmoides identified sequences of known fish viral pathogens whose apparent tolerance could be linked to the expansion of 91 immune-related gene families providing high resistance to disease. The prevalence of such expressed viral elements captured in the M. salmoides transcriptome suggests an history of interaction between the fish and the viral environment. The high-quality genome will be a fundamental resource to understand M. salmoides traits that enable the successful colonization of novel and changing environments across the world.

The genetic underpinnings of phenotypic differentiation during animal breeding has important implications in both evolutionary biology and agriculture. However, how cis-regulatory variants influence pig phenotypes is not well understood. Here, we present a high-resolution phased chromosome-scale reference genome with contig N50 of 18.03 Mb for Luchuan pig (a representative Eastern breed), and profiled potential selective sweeps in Eastern and Western pigs by re-sequencing of 234 pigs. In these regions, multi-tissue transcriptome and chromatin accessibility analyses suggest tissue-specific selection pressure mediated through promoters and distal cis-regulatory elements. Promoter variants associated with higher LYZ expression in the small intestine might enhance pig gastrointestinal immunity and roughage tolerance. In the skeletal muscles, an enhancer-modulating SNP associated with higher TNNC1 expression might increase slow muscle fibers and affect meat quality. Our work also provides valuable resources and new perspectives to explore gene regulatory evolution in animal domestication and breeding.

Homo neanderthalensis is the closest relative to Homo sapiens in the tree of human evolution. It is estimated that the Neanderthals became extinct around 30 thousand years ago. Several hypotheses have been put forward to explain this extinction. Larger brains hence larger heads were favoured by evolution among the Hominids for over two million years but stopped being an advantage due to trade-offs between bipedal walking, larger brains and birth. Our hypothesis states that H. neanderthalensis became extinct as a result of their larger head circumference, compared with H. sapiens, leading to birth complications. We use population dynamics to demonstrate that a small difference in the rate of mortality during birth can cause extinction of one population. We simulate two populations with an Agent Based Simulation technique to show that in the case of interbreeding between two populations, unexpected results can emerge depending on random events in simulations. We demonstrate that sharing the same habitat with capacity constraints over thousands of years, with a relatively higher death rate during birth could be the main cause of the slow decline in the H. neanderthalensis population, and its eventual extinction.