Grazing management for soil carbon in Australia: A review.

The livestock industry accounts for a considerable proportion of agricultural greenhouse gas emissions, and in response, the Australian red meat industry has committed to an aspirational target of net-zero emissions by 2030. Increasing soil carbon storage in grazing lands has been identified as one method to help achieve this, while also potentially improving production and provision of other ecosystem services. This review examined the effects of grazing management on soil carbon and factors that drive soil carbon sequestration in Australia. A systematic literature search and meta-analysis was used to compare effects of stocking intensity (stocking rate or utilisation) and stocking method (i.e, continuous, rotational or seasonal grazing systems) on soil organic carbon, pasture herbage mass, plant growth and ground cover. Impacts on below ground biomass, soil nitrogen and soil structure are also discussed. Overall, no significant impact of stocking intensity or method on soil carbon sequestration in Australia was found, although lower stocking intensity and incorporating periods of rest into grazing systems (rotational grazing) had positive effects on herbage mass and ground cover compared with higher stocking intensity or continuous grazing. Minimal impact of grazing management on pasture growth rate and below-ground biomass has been reported in Australia. However, these factors improved with grazing intensity or rotational grazing in some circumstances. While there is a lack of evidence in Australia that grazing management directly increases soil carbon, this meta-analysis indicated that grazing management practices have potential to benefit the drivers of soil carbon sequestration by increasing above and below-ground plant production, maintaining a higher residual biomass, and promoting productive perennial pasture species. Specific recommendations for future research and management are provided in the paper.

SARS-CoV-2 antibody responses associate with sex, age and disease severity in previously uninfected people admitted to hospital with COVID-19: An ISARIC4C prospective study.

The SARS-CoV-2 pandemic enables the analysis of immune responses induced against a novel coronavirus infecting immunologically naïve individuals. This provides an opportunity for analysis of immune responses and associations with age, sex and disease severity. Here we measured an array of solid-phase binding antibody and viral neutralising Ab (nAb) responses in participants (n=337) of the ISARIC4C cohort and characterised their correlation with peak disease severity during acute infection and early convalescence. Overall, the responses in a Double Antigen Binding Assay (DABA) for antibody to the receptor binding domain (anti-RBD) correlated well with IgM as well as IgG responses against viral spike, S1 and nucleocapsid protein (NP) antigens. DABA reactivity also correlated with nAb. As we and others reported previously, there is greater risk of severe disease and death in older men, whilst the sex ratio was found to be equal within each severity grouping in younger people. In older males with severe disease (mean age 68 years), peak antibody levels were found to be delayed by one to two weeks compared with women, and nAb responses were delayed further. Additionally, we demonstrated that solid-phase binding antibody responses reached higher levels in males as measured via DABA and IgM binding against Spike, NP and S1 antigens. In contrast, this was not observed for nAb responses. When measuring SARS-CoV-2 RNA transcripts (as a surrogate for viral shedding) in nasal swabs at recruitment, we saw no significant differences by sex or disease severity status. However, we have shown higher antibody levels associated with low nasal viral RNA indicating a role of antibody responses in controlling viral replication and shedding in the upper airway. In this study, we have shown discernible differences in the humoral immune responses between males and females and these differences associate with age as well as with resultant disease severity.

Defective Mitochondrial Dynamics and Protein Degradation Pathways Underlie Cadmium-Induced Neurotoxicity and Cell Death in Huntington's Disease Striatal Cells.

Exposure to heavy metals, including cadmium (Cd), can induce neurotoxicity and cell death. Cd is abundant in the environment and accumulates in the striatum, the primary brain region selectively affected by Huntington's disease (HD). We have previously reported that mutant huntingtin protein (mHTT) combined with chronic Cd exposure induces oxidative stress and promotes metal dyshomeostasis, resulting in cell death in a striatal cell model of HD. To understand the effect of acute Cd exposure on mitochondrial health and protein degradation pathways, we hypothesized that expression of mHTT coupled with acute Cd exposure would cooperatively alter mitochondrial bioenergetics and protein degradation mechanisms in striatal STHdh cells to reveal novel pathways that augment Cd cytotoxicity and HD pathogenicity. We report that mHTT cells are significantly more susceptible to acute Cd-induced cell death as early as 6 h after 40 µM CdCl2 exposure compared with wild-type (WT). Confocal microscopy, biochemical assays, and immunoblotting analysis revealed that mHTT and acute Cd exposure synergistically impair mitochondrial bioenergetics by reducing mitochondrial potential and cellular ATP levels and down-regulating the essential pro-fusion proteins MFN1 and MFN2. These pathogenic effects triggered cell death. Furthermore, Cd exposure increases the expression of autophagic markers, such as p62, LC3, and ATG5, and reduces the activity of the ubiquitin-proteasome system to promote neurodegeneration in HD striatal cells. Overall, these results reveal a novel mechanism to further establish Cd as a pathogenic neuromodulator in striatal HD cells via Cd-triggered neurotoxicity and cell death mediated by an impairment in mitochondrial bioenergetics and autophagy with subsequent alteration in protein degradation pathways.

Adeno-associated virus 2 infection in children with non-A-E hepatitis.

An outbreak of acute hepatitis of unknown aetiology in children was reported in Scotland1 in April 2022 and has now been identified in 35 countries2. Several recent studies have suggested an association with human adenovirus with this outbreak, a virus not commonly associated with hepatitis. Here we report a detailed case-control investigation and find an association between adeno-associated virus 2 (AAV2) infection and host genetics in disease susceptibility. Using next-generation sequencing, PCR with reverse transcription, serology and in situ hybridization, we detected recent infection with AAV2 in plasma and liver samples in 26 out of 32 (81%) cases of hepatitis compared with 5 out of 74 (7%) of samples from unaffected individuals. Furthermore, AAV2 was detected within ballooned hepatocytes alongside a prominent T cell infiltrate in liver biopsy samples. In keeping with a CD4+ T-cell-mediated immune pathology, the human leukocyte antigen (HLA) class II HLA-DRB1*04:01 allele was identified in 25 out of 27 cases (93%) compared with a background frequency of 10 out of 64 (16%; P = 5.49 × 10-12). In summary, we report an outbreak of acute paediatric hepatitis associated with AAV2 infection (most likely acquired as a co-infection with human adenovirus that is usually required as a 'helper virus' to support AAV2 replication) and disease susceptibility related to HLA class II status.

Viral Coinfections in Hospitalized Coronavirus Disease 2019 Patients Recruited to the International Severe Acute Respiratory and Emerging Infections Consortium WHO Clinical Characterisation Protocol UK Study.

Background: We conducted this study to assess the prevalence of viral coinfection in a well characterized cohort of hospitalized coronavirus disease 2019 (COVID-19) patients and to investigate the impact of coinfection on disease severity. Methods: Multiplex real-time polymerase chain reaction testing for endemic respiratory viruses was performed on upper respiratory tract samples from 1002 patients with COVID-19, aged <1 year to 102 years old, recruited to the International Severe Acute Respiratory and Emerging Infections Consortium WHO Clinical Characterisation Protocol UK study. Comprehensive demographic, clinical, and outcome data were collected prospectively up to 28 days post discharge. Results: A coinfecting virus was detected in 20 (2.0%) participants. Multivariable analysis revealed no significant risk factors for coinfection, although this may be due to rarity of coinfection. Likewise, ordinal logistic regression analysis did not demonstrate a significant association between coinfection and increased disease severity. Conclusions: Viral coinfection was rare among hospitalized COVID-19 patients in the United Kingdom during the first 18 months of the pandemic. With unbiased prospective sampling, we found no evidence of an association between viral coinfection and disease severity. Public health interventions disrupted normal seasonal transmission of respiratory viruses; relaxation of these measures mean it will be important to monitor the prevalence and impact of respiratory viral coinfections going forward.

Climate change and Australia's primary industries: factors hampering an effective and coordinated response.

Australia's primary production sector operates in one of the world's most variable climates with future climate change posing a challenge to its ongoing sustainability. Recognising this, Australia has invested in understanding climate change risks to primary production with a substantial amount of research produced. Recently, focus on this research space has broadened, with interests from the financial sector and expanded scopes of works from government and industry. These expanded needs require sector- and country-wide assessments to assist with the implementation of climate strategies. We considered the applicability of the current research body for these needs by reviewing 188 peer-reviewed studies that considered the quantitative impacts of climate change on Australia's primary industries. Our broad review includes cropping, livestock, horticulture, forestry and fisheries and biosecurity threats. This is the first such review for Australia, and no other similar country-wide review was found. We reviewed the studies through three lenses, industry diversity, geographic coverage and study comparability. Our results show that all three areas are lacking for sector- and country-wide assessments. Industry diversity was skewed towards cropping and biosecurity threats (64% of all studies) with wheat in particular a major focus (25% of all studies). Geographic coverage at a state level appeared to be evenly distributed across the country; however, when considered in conjunction with industry focus, gaps emerged. Study comparability was found to be very limited due to the use of different historical baseline periods and different impact models. We make several recommendations to assist with future research directions, being (1) co-development of a standard set of method guidelines for impact assessments, (2) filling industry and geographic knowledge gaps, and (3) improving transparency in study method descriptions. Uptake of these recommendations will improve study application and transparency enabling and enhancing responses to climate change in Australia's primary industries.

Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units - A high risk community-hospital interface.

OBJECTIVES: Patients requiring haemodialysis are at increased risk of serious illness with SARS-CoV-2 infection. To improve the understanding of transmission risks in six Scottish renal dialysis units, we utilised the rapid whole-genome sequencing data generated by the COG-UK consortium. METHODS: We combined geographical, temporal and genomic sequence data from the community and hospital to estimate the probability of infection originating from within the dialysis unit, the hospital or the community using Bayesian statistical modelling and compared these results to the details of epidemiological investigations. RESULTS: Of 671 patients, 60 (8.9%) became infected with SARS-CoV-2, of whom 16 (27%) died. Within-unit and community transmission were both evident and an instance of transmission from the wider hospital setting was also demonstrated. CONCLUSIONS: Near-real-time SARS-CoV-2 sequencing data can facilitate tailored infection prevention and control measures, which can be targeted at reducing risk in these settings.

Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland.

Coronavirus disease 2019 (COVID-19) was first diagnosed in Scotland on 1 March 2020. During the first month of the outbreak, 2,641 cases of COVID-19 led to 1,832 hospital admissions, 207 intensive care admissions and 126 deaths. We aimed to identify the source and number of introductions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into Scotland using a combined phylogenetic and epidemiological approach. Sequencing of 1,314 SARS-CoV-2 viral genomes from available patient samples enabled us to estimate that SARS-CoV-2 was introduced to Scotland on at least 283 occasions during February and March 2020. Epidemiological analysis confirmed that early introductions of SARS-CoV-2 originated from mainland Europe (the majority from Italy and Spain). We identified subsequent early outbreaks in the community, within healthcare facilities and at an international conference. Community transmission occurred after 2 March, 3 weeks before control measures were introduced. Earlier travel restrictions or quarantine measures, both locally and internationally, would have reduced the number of COVID-19 cases in Scotland. The risk of multiple reintroduction events in future waves of infection remains high in the absence of population immunity.

Characterization of the temporal and spatial expression of a disintegrin and metalloprotease 17 in the human endometrium and fallopian tube.

Metalloproteinases are thought to mediate shedding of mucins from the endometrium surface, exposing oligosaccharide ligands involved in implantation. We hypothesized that a disintegrin and metalloprotease 17 (ADAM17) is upregulated during the "window of implantation" in human endometrium but not in fallopian tube (FT) where implantation is pathological. Endometrial and FT expression of ADAM17 throughout the menstrual cycle was determined using quantitative reverse-transcription polymerase chain reaction and immunohistochemistry. The ADAM17 transcription was significantly downregulated (P < .01) during the early-midsecretory phase in the endometrium but not in the FT. The ADAM17 was localized to the surface of epithelial cells and was also detected in the endometrial stroma during the late luteal and proliferative phase of the cycle. Physiological levels of estradiol significantly (P < .05) upregulated ADAM17 transcription in vitro. Our observations do not support the role of ADAM17 in shedding of mucins during the window of implantation. The precise role of ADAM17 in the female reproductive tract requires further investigation.

Ectopic pregnancy as a model to identify endometrial genes and signaling pathways important in decidualization and regulated by local trophoblast.

The endometrium in early pregnancy undergoes decidualization and functional changes induced by local trophoblast, which are not fully understood. We hypothesized that endometrium from tubal ectopic pregnancy (EP) could be interrogated to identify novel genes and pathways involved in these processes. Gestation-matched endometrium was collected from women with EP (n = 11) and intrauterine pregnancies (IUP) (n = 13). RNA was extracted from the tissue. In addition, tissues were prepared for histological analysis for degree of decidualization. We compared a) the samples from EP that were decidualized (n = 6) with non-decidualized samples (n = 5), and b) the decidualized EP (n = 6) with decidualization-matched IUP (n = 6) samples using an Affymetrix gene array platform, with Ingenuity Pathway Analysis, combined with quantitative RT-PCR. Expression of PRL and IGFBP1 was used to confirm the degree of decidualization in each group. There were no differences in PRL or IGFBP1 expression in the decidualization-matched samples but a marked reduction (P<0.001) in the non-decidualized samples. Decidualization was associated with increased expression of 428 genes including SCARA5 (181-fold), DKK1 (71-fold) and PROK1 (32-fold), and decreased expression of 230 genes including MMP-7 (35-fold) and SFRP4 (21-fold). The top canonical pathways associated with these differentially expressed genes were Natural Killer Cell and Wnt/b-Catenin signaling. Local trophoblast was associated with much less alteration of endometrial gene expression with an increase in 56 genes, including CSH1 (8-fold), and a reduction in 29 genes including CRISP3 (8-fold). The top associated canonical pathway was Antigen Presentation. The study of endometrium from tubal EP may promote novel insights into genes involved in decidualization and those influenced by factors from neighboring trophoblast. This has afforded unique information not highlighted by previous studies and adds to our understanding of the endometrium in early pregnancy.

Placental growth factor: a promising diagnostic biomarker for tubal ectopic pregnancy.

CONTEXT: Tubal ectopic pregnancy is common, but accurate diagnosis is difficult and costly. There is currently no serum test to differentiate tubal from intrauterine implantation, and an effective biomarker of ectopic pregnancy would be a major clinical advance. OBJECTIVE: A key feature of successful intrauterine implantation is the establishment of a supportive vascular network, and this has been associated with the activity of placental growth factor (PIGF). We hypothesized that the local decidual environment facilitates PIGF-dependent angiogenesis and that this pathway is not active in tubal implantation. We aimed to determine whether tubal implantation is manifest by an attenuation of the normal trophoblast PIGF response and whether serum PIGF levels are different in ectopic compared with intrauterine pregnancy. DESIGN AND SETTING: Tissue and serum analysis was done at a large United Kingdom teaching hospital. PATIENTS: Tissue and sera were collected from gestation-matched pregnant women undergoing surgical termination of pregnancy (viable intrauterine) (n = 15), evacuation of uterus for embryonic missed miscarriage (nonviable intrauterine) (n = 10) and surgery for tubal ectopic pregnancy (n = 15). INTERVENTIONS: Trophoblast was examined by immunohistochemistry and quantitative RT-PCR, and serum was analyzed by ELISA. RESULTS: PIGF was localized to the cytotrophoblast cells. Expression of PIGF mRNA was reduced in trophoblast isolated from women with ectopic compared with intrauterine pregnancies (P < 0.05). Serum PIGF was undetectable in women with tubal ectopic pregnancies and reduced, or undetectable, in miscarriage compared with viable intrauterine pregnancies (P < 0.01). CONCLUSIONS: Serum PIGF is a promising novel diagnostic biomarker for early pregnancy location and outcome, and large-scale studies are now required to determine its clinical utility.

Attenuated sex steroid receptor expression in fallopian tube of women with ectopic pregnancy.

CONTEXT: Sex steroid hormone receptor (SHR) dynamics are well-documented in human endometrium but have not been comprehensively studied in Fallopian tube (FT). OBJECTIVE: The aim of the study was to compare expression patterns and hormonal regulation of SHR in FT with that described in endometrium and to determine whether SHR expression is altered in FT of women with ectopic pregnancy (EP). DESIGN: Tissue was analyzed and cultured. PATIENTS OR OTHER PARTICIPANTS: Women undergoing surgery for benign gynecological conditions (n = 14) and EP (n = 6) participated in the study. INTERVENTIONS: Quantitative RT-PCR and immunohistochemistry were used to determine SHR mRNA expression and protein localization, respectively. SHR levels were measured in tubal explant cultures stimulated with estrogen and progestogen. RESULTS: ERalpha and ERbeta mRNAs were constitutively expressed in FT during the menstrual cycle. PR-AB and PR-B mRNAs were decreased in midluteal phase compared to follicular phase. ERalpha, PR-AB, and PR-B mRNAs were down-regulated in human FT in vitro by treatment with progestogen. ERalpha, ERbeta1, ERbeta2, PR, and AR proteins localized to cell nuclei of epithelium, stroma, and smooth muscle of nonpregnant FT. In FT from women with EP, PR-B mRNA was decreased when compared to midluteal FT, and ERalpha protein was not detected. CONCLUSIONS: SHR expression in FT is different from that observed in endometrium recovered at similar stages of the menstrual cycle, and expression in FT from women with EP is also altered compared with normal FT. These data are an important benchmark for furthering the understanding of normal human FT physiology, changes in expression of SHR in FT in response to progesterone, and disorders of FT function, such as EP.

Expression of secretory leukocyte protease inhibitor and elafin in human fallopian tube and in an in-vitro model of Chlamydia trachomatis infection.

BACKGROUND: Secretory leukocyte protease inhibitor (SLPI) and elafin are anti-protease and anti-microbial molecules with a role in innate immune defence. They have been demonstrated at multiple mucosal surfaces including those of the female reproductive tract. METHODS AND RESULTS: This study details their expression in human Fallopian tubes (ampullary region) throughout the menstrual cycle (n = 18) and from women with ectopic pregnancy (n = 6), and examined their regulation by infection with Chlamydia trachomatis in an in-vitro model. Quantitative real-time PCR analysis showed that SLPI and elafin were constitutively expressed in the Fallopian tube during the menstrual cycle but were increased in ectopic pregnancy (P < 0.05 versus early-mid luteal phase, P < 0.01 versus all phases, respectively). SLPI and elafin were immunolocalised to the Fallopian tube epithelium in biopsies from non-pregnant women and those with ectopic pregnancy. An in-vitro culture model of C. trachomatis infection of the OE-E6/E7 oviductal epithelial cell line showed that elafin mRNA expression was upregulated in response to chlamydial infection. CONCLUSION: These data suggest that SLPI and elafin have a role in the innate immune defence of the Fallopian tube in infection and ectopic pregnancy. Their role is likely to include regulation of protease activity, wound healing and tissue remodelling.

CB1 expression is attenuated in Fallopian tube and decidua of women with ectopic pregnancy.

BACKGROUND: Embryo retention in the Fallopian tube (FT) is thought to lead to ectopic pregnancy (EP), a considerable cause of morbidity. In mice, genetic/pharmacological silencing of cannabinoid receptor Cnr1, encoding CB1, causes retention of embryos in the oviduct. The role of the endocannabinoids in tubal implantation in humans is not known. METHODS AND FINDINGS: Timed FT biopsies (n = 18) were collected from women undergoing gynecological procedures for benign conditions. Endometrial biopsies and whole blood were collected from women undergoing surgery for EP (n = 11); management of miscarriage (n = 6), and termination of pregnancy (n = 8). Using RT-PCR and immunohistochemistry, CB1 mRNA and protein expression levels/patterns were examined in FT and endometrial biopsies. The distribution of two polymorphisms of CNR1 was examined by TaqMan analysis of genomic DNA from the whole blood samples. In normal FT, CB1 mRNA was higher in luteal compared to follicular-phase (p<0.05). CB1 protein was located in smooth muscle of the wall and of endothelial vessels, and luminal epithelium of FT. In FT from women with EP, CB1 mRNA expression was low. CB1 mRNA expression was also significantly lower (p<0.05) in endometrium of women with EP compared to intrauterine pregnancies (IUP). Although of 1359G/A (rs1049353) polymorphisms of CNR1 gene suggests differential distribution of genotypes between the small, available cohorts of women with EP and those with IUP, results were not statistically significant. CONCLUSIONS: CB1 mRNA shows temporal variation in expression in human FT, likely regulated by progesterone. CB1 mRNA is expressed in low levels in both the FT and endometrium of women with EP. We propose that aberrant endocannabinoid-signaling in human FT leads to EP. Furthermore, our finding of reduced mRNA expression along with a possible association between polymorphism genotypes of the CNR1 gene and EP, suggests a possible genetic predisposition to EP that warrants replication in a larger sample pool.

Mid-luteal endometrial intracrinology following controlled ovarian hyperstimulation involving use of a gonadotrophin releasing hormone antagonist.

BACKGROUND: There are concerns of reduced pregnancy rates with the use of gonadotrophin-releasing hormone antagonists (GnRH antagonists) in IVF/ICSI cycles. Sex steroids and their metabolizing enzymes in the endometrium may play a vital role in embryo implantation. This study has evaluated the levels and localization of sex-steroid receptors and metabolizing enzymes, 3beta-hydroxysteroid dehydrogenases (3betaHSD) and selected 17beta-HSD (17betaHSD), in mid-luteal endometrium of women treated with GnRH antagonist (Cetrorelix) and recombinant FSH (rFSH; Gonal-F) with luteal phase progesterone supplementation. METHODS: Mid-luteal phase endometrial biopsies were obtained from oocyte donors undergoing ovarian stimulation and from control women with regular periods. Immunohistochemistry and real-time quantitative-polymerase chain reaction (QRT-PCR) were used to compare protein and mRNA expression of progesterone receptor (PR), estrogen receptor alpha (ERalpha), estrogen receptor beta (ERbeta), androgen receptor (AR), 3betaHSD1, 3betaHSD2, 17betaHSD2 and 17betaHSD5. RESULTS: Cetrorelix-rFSH treatment caused a mid-luteal suppression of PR protein expression in the endometrial stroma, surface epithelium and glands, although expression in the glands of control samples was variable. In contrast, the treatment caused an increase in PR staining in perivascular cells. No other significant differences in protein expression were observed between the two groups. mRNA levels of AR, ERalpha, 3betaHSD1 and 17betaHSD2 were significantly reduced in the treatment group. PR mRNA levels were also reduced by GnRH antagonist-rFSH treatment, but the difference was not significant. CONCLUSIONS: Changes in the expression of sex-steroid receptors and metabolizing enzymes may lead to alterations in the activity and intracellular availability of estrogens, progestogens and androgens in endometrium of women treated with Cetrorelix and rFSH. Their impact on embryo implantation merits further evaluation.

11Beta-hydroxysteroid dehydrogenases in human endometrium.

Key reproductive events, such as menstruation and implantation, are considered to be inflammatory processes and glucocorticoids act as anti-inflammatory agents. The balance of expression of types 1 and 2 11beta-hydroxysteroid dehydrogenases (11betaHSD) controls the availability of cortisol to bind to the glucocorticoid receptor (GR) and mineralocorticoid receptor (MR). Expression profiles of glucocorticoid-metabolising enzymes and their cognate receptors have been characterized in the reproductive tract. We propose that factors that peripherally promote glucocorticoid action are part of an anti-inflammatory response to tissue remodelling in human endometrium. Protein and mRNA expression in endometrium were investigated using immunohistochemistry and quantitative real-time PCR. There was up-regulated expression of 11betaHSD-1 at menstruation and in first trimester decidua. 11BetaHSD-2 and GR were expressed across the cycle. The MR expression pattern across the cycle and in decidua implies progesterone may also play a regulatory role. The precise roles and interactions of these proteins require further investigation.