Membraneless Organelles and Condensates Orchestrate Innate Immunity Against Viruses

The cellular defense against viruses involves the assembly of oligomers, granules and membraneless organelles (MLOs) that govern the activation of several arms of the innate immune response. Upon interaction with specific pathogen-derived ligands, a number of pattern recognition receptors (PRRs) undergo phase-separation thus triggering downstream signaling pathways. Among other relevant condensates, inflammasomes, apoptosis-associated speck-like protein containing a caspase-recruitment domain (ASC) specks, cyclic GMP-AMP synthase (cGAS) foci, protein kinase R (PKR) clusters, ribonuclease L-induced bodies (RLBs), stress granules (SGs), processing bodies (PBs) and promyelocytic leukemia protein nuclear bodies (PML NBs) play different roles in the immune response. In turn, viruses have evolved diverse strategies to evade the host defense. Viral DNA or RNA, as well as viral proteases or proteins carrying intrinsically disordered regions may interfere with condensate formation and function in multiple ways. In this review we discuss current and hypothetical mechanisms of viral escape that involve the disassembly, repurposing, or inactivation of membraneless condensates that govern innate immunity. We summarize emerging interconnections between these diverse condensates that ultimately determine the cellular outcome.

Whānau Māori and Pacific peoples' knowledge, perceptions, expectations and solutions regarding antibiotic treatment of upper respiratory tract infections: a qualitative study

INTRODUCTION

The rate of community antibiotic use is high in Aotearoa New Zealand (NZ) when compared to other nations, and in NZ, as in most other nations, antibiotics are very commonly prescribed for self-limiting upper respiratory tract infections (URTIs). Resources that build knowledge, perceptions and understanding can potentially reduce unnecessary antibiotic consumption.

METHODS

To inform the content of educational resources, we conducted an in-depth qualitative study with 47 participants via 6 focus groups of the knowledge, attitudes, and expectations of whānau Māori and Pacific peoples about antibiotics and URTIs.

RESULTS

Focus groups with 47 participants identified four themes: Knowledge that might influence expectations to receive antibiotics for URTIs; Perceptions - the factors that influence when and why to seek medical care for URTI; Expectations - the features of successful medical care for URTI; Solutions - how to build community knowledge about URTI and their treatment and prevention. Knowledge that might reduce expectations to receive antibiotics for URTI included confidence in the use of alternative remedies, knowledge that URTI are usually caused by viruses, and concerns about antibiotic adverse effects. Participants commonly reported that they would confidently accept their doctor's recommendation that an antibiotic was not necessary for an URTI, provided that a thorough assessment had been performed and that treatment decisions were clearly communicated.

CONCLUSION

These findings suggest that building patients' knowledge and skills about when antibiotics are necessary, and increasing doctors' confidence and willingness not to prescribe an antibiotic for patients with an URTI, could significantly reduce inappropriate antibiotic prescribing in NZ.

Smaug1 membrane-less organelles respond to AMPK/mTOR and affect mitochondrial function‡

Smaug is a conserved translational regulator that binds numerous mRNAs, including nuclear transcripts that encode mitochondrial enzymes. Smaug orthologs form cytosolic membrane-less organelles (MLOs) in several organisms and cell types. We have performed single-molecule FISH assays that revealed that SDHB and UQCRC1 mRNAs associate with Smaug1 bodies in U2OS cells. Loss of function of Smaug1 and Smaug2 affected both mitochondrial respiration and morphology of the mitochondrial network. Phenotype rescue by Smaug1 transfection depends on the presence of its RNA binding domain. Moreover, we identified specific Smaug1 domains involved in MLO formation, and found that impaired Smaug1 MLO condensation correlates with mitochondrial defects. Mitochondrial Complex I inhibition by rotenone -but not strong mitochondrial uncoupling by CCCP- rapidly induced Smaug1 MLOs dissolution. Metformin and rapamycin elicited similar effects, which were blocked by pharmacological inhibition of AMPK. Finally, we found that Smaug1 MLO dissolution weakens the interaction with target mRNAs, thus enabling their release. We propose that mitochondrial respiration and the AMPK/mTOR balance controls the condensation and dissolution of Smaug1 MLOs, thus regulating nuclear mRNAs that encode key mitochondrial proteins.

Factors associated with advanced colorectal cancer differ between young and older adults in England: a population-based cohort study

AIM

Advanced stage presentation of colorectal cancer is associated with poorer survival outcomes, particularly among young adults. This study aimed to determine whether demographic risk factors for advanced stage presentation differed between young and older adults.

METHOD

Individual-level data on all incident colorectal cancers in people aged 20 years and above were extracted from the National Cancer Registration and Analysis Service database for the years 2012 to 2015. Patients were divided into two cohorts: young-onset colorectal cancer (YOCC) if aged 20-49 years and older-onset colorectal cancer (OOCC) if aged 50 years and above. Logistic regression was used to identify risk factors for advanced stage presentation, defined as TNM Stage III or IV, in each cohort.

RESULTS

There were 7075 (5.2%) patients in the YOCC cohort and 128 345 (94.8%) patients in the OOCC cohort. Tumours in the YOCC cohort were more likely to be at an advanced stage (67.2% vs 55.3%, P < 0.001) and located distally (63.7% vs 55.4%, P < 0.001). No demographic factor was consistently associated with advanced stage presentation in the YOCC cohort. Among the OOCC cohort, increased social deprivation [OR (Index of Multiple Deprivation quintile 5 vs 1) = 1.11 (95% CI 1.07-1.16), P < 0.001], Black/Black British ethnicity [OR (baseline White) = 1.25 (95% CI 1.11-1.40), P < 0.001] and residence in the East Midlands [OR (baseline London) = 1.11 (95% CI 1.04-1.17), P = 0.001] were associated with advanced stage presentation.

CONCLUSION

Demographic factors associated with advanced disease were influenced by age. The effects of social deprivation and ethnicity were only observed in older adults and mirror trends in screening uptake. Targeted interventions for high-risk groups are warranted.

Demographic trends in the incidence of young-onset colorectal cancer: a population-based study

Background

Evidence is emerging that the incidence of colorectal cancer is increasing in young adults, but the descriptive epidemiology required to better understand these trends is currently lacking.

Methods

A population‐based cohort study was carried out including all adults aged 20–49 years diagnosed with colorectal cancer in England between 1974 and 2015. Data were extracted from the National Cancer Registration and Analysis Service database using ICD‐9/10 codes for colorectal cancer. Temporal trends in age‐specific incidence rates according to sex, anatomical subsite, index of multiple deprivation quintile and geographical region were analysed using Joinpoint regression.

Results

A total of 56 134 new diagnoses of colorectal cancer were analysed. The most sustained increase in incidence rate was in the group aged 20–29 years, which was mainly driven by a rise in distal tumours. The magnitude of incident rate increases was similar in both sexes and across Index of Multiple Deprivation quintiles, although the most pronounced increases in incidence occurred in the southern regions of England.

Conclusion

Colorectal cancer should no longer be considered a disease of older people. Changes in incidence rates should be used to inform future screening policy, preventative strategies and research agendas, as well as increasing public understanding that younger people need to be aware of the symptoms of colorectal cancer.

Dynamics of genomic architecture during composite breed development in cattle

Some livestock breeds face the challenge of reduced genetic variation, increased inbreeding depression owing to genetic drift and selection. Hybridization can reverse these processes and increase levels of productivity and adaptation to various environmental stressors. Samples from American Brangus were used to evaluate the indicine/taurine composition through nine generations (~45 years) after the hybridization process was completed. The purpose was to determine how hybridization alters allelic combinations of a breed over time when genetic factors such as selection and drift are operating. Furthermore, we explored genomic regions with deviations from the expected composition from the progenitor breeds and related these regions to traits under selection. The Brangus composition deviated from the theoretical expectation, defined by the breed association, of 62.5% taurine, showing taurine composition to be 70.4 ± 0.6%. Taurine and indicine proportion were not consistent across chromosomes. Furthermore, these non‐uniform areas were found to be associated with traits that were probably under selection such as intermuscular fat and average daily gain. Interestingly, the sex chromosomes were predominantly taurine, which could be due to the composite being formed particularly in the final cross that resulted in progeny designated as purebred Brangus. This work demonstrated the process of new breed formation on a genomic level. It suggests that factors like genetic drift, selection and complementarity shift the genetic architecture into a uniquely different population. These findings are important to better understand how hybridization and crossbreeding systems shape the genetic architecture of composite populations.

A systematic review of local excision followed by adjuvant therapy in early rectal cancer: are pT1 tumours the limit?

AIM

Total mesorectal excision remains the cornerstone of treatment for rectal cancer. Significant morbidity means local excision may be more appropriate in selected patients. Adjuvant therapy reduces local recurrence and improves survival; however, there is a paucity of data on its impact following local excision, which this systematic review aims to address.

METHODS

A systematic search of the MEDLINE, Embase and Cochrane databases using validated terms for rectal cancer, adjuvant therapy and local excision was performed. Included studies focused on local excision with adjuvant therapy for adenocarcinoma of the rectum. Primary outcome measures were local recurrence, survival and morbidity. Studies providing neoadjuvant therapy or local excision alone were excluded.

RESULTS

Twenty-two studies described 804 patients. Indications for local excision included favourable histology, patient choice and comorbidities. T1, T2 and T3 tumours accounted for 35.1%, 58.0% and 6.9% of cases, respectively. The most frequent local excision technique was transanal excision (77.7%). Adjuvant therapy included long-course chemoradiation or radiotherapy. Median follow-up was 51 months (range 1-165). The pooled local recurrence was 5.8% (95% CI 3.0-9.5) for pT1, 13.8% (95% CI 10.1-17.9) for pT2 and 33.7% (95% CI 19.2-50.1) for pT3 tumours. The overall median disease-free survival was 88% (range 50%-100%) with a pooled overall morbidity of 15.1% (95% CI 11.0-18.7).

CONCLUSIONS

This area remains highly relevant to modern clinical practice. The data suggest that local excision followed by adjuvant therapy can achieve acceptable long-term outcomes in high-risk pT1 tumours, but not in T2 tumours and above in whom radical surgery should be offered.

Pre- and post-puberty expression of genes and proteins in the uterus of Bos indicus heifers: the luteal phase effect post-puberty

Progesterone signaling and uterine function are crucial in terms of pregnancy establishment. To investigate how the uterine tissue and its secretion changes in relation to puberty, we sampled tissue and uterine fluid from six pre- and six post-pubertal Brahman heifers. Post-pubertal heifers were sampled in the luteal phase. Gene expression of the uterine tissue was investigated with RNA-sequencing, whereas the uterine fluid was used for protein profiling with mass spectrometry. A total of 4034 genes were differentially expressed (DE) at a nominal P-value of 0.05, and 26 genes were significantly DE after Bonferroni correction (P < 3.1 × 10^-6 ). We also identified 79 proteins (out of 230 proteins) that were DE (P < 1 × 10^-5 ) in the uterine fluid. When we compared proteomics and transcriptome results, four DE proteins were identified as being encoded by DE genes: OVGP1, GRP, CAP1 and HBA. Except for CAP1, the other three had lower expression post-puberty. The function of these four genes hypothetically related to preparation of the uterus for a potential pregnancy is discussed in the context of puberty. All DE genes and proteins were also used in pathway and ontology enrichment analyses to investigate overall function. The DE genes were enriched for terms related to ribosomal activity. Transcription factors that were deemed key regulators of DE genes are also reported. Transcription factors ZNF567, ZNF775, RELA, PIAS2, LHX4, SOX2, MEF2C, ZNF354C, HMG20A, TCF7L2, ZNF420, HIC1, GTF3A and two novel genes had the highest regulatory impact factor scores. These data can help to understand how puberty influences uterine function.

Genome-wide association study of Stayability and Heifer Pregnancy in Red Angus cattle

Reproductive performance is the most important component of cattle production from the standpoint of economic sustainability of commercial beef enterprises. Heifer Pregnancy (HPG) and Stayability (STAY) genetic predictions are 2 selection tools published by the Red Angus Association of America (RAAA) to assist with improvements in reproductive performance. Given the importance of HPG and STAY to the profitability of commercial beef enterprises, the objective of this study was to identify QTL associated with both HPG and STAY in Red Angus cattle. A genome-wide association study (GWAS) was performed using deregressed HPG and STAY EBV, calculated using a single-trait animal model and a 3-generation pedigree with data from the Spring 2015 RAAA National Cattle Evaluation. Each individual animal possessed 74,659 SNP genotypes. Individual animals with a deregressed EBV reliability > 0.05 were merged with the genotype file and marker quality control was performed. Criteria for sifting genotypes consisted of removing those markers where any of the following were found: average call rate less than 0.85, minor allele frequency < 0.01, lack of Hardy-Weinberg equilibrium (P < 0.0001), or extreme linkage disequilibrium (r2 > 0.99). These criteria resulted in 2,664 animals with 62,807 SNP available for GWAS. Association studies were performed using a Bayes Cπ model in the BOLT software package. Marker significance was calculated as the posterior probability of inclusion (PPI), or the number of instances a specific marker was sampled divided by the total number of samples retained from the Markov chain Monte Carlo chains. Nine markers, with a PPI ≥ 3% were identified as QTL associated with HPG on BTA 1, 11, 13, 23, and 29. Twelve markers, with a PPI ≥ 75% were identified as QTL associated with STAY on BTA 6, 8, 9, 12, 15, 18, 22, and 23.

Antibacterials dispensed in the community comprise 85%-95% of total human antibacterial consumption

WHAT IS KNOWN AND OBJECTIVE

Interventions intended to slow the emergence and spread of antibacterial resistance through enhanced antimicrobial stewardship will be more effective if informed by an accurate knowledge of current patterns of antibacterial consumption. For example, knowledge of the relative magnitude of community antibacterial consumption in relation to hospital antibacterial consumption within each nation or region should help guide decisions about the relative importance of community and hospital antimicrobial stewardship programmes. It is commonly stated that community antibacterial consumption comprises approximately 80% of total national antibacterial consumption. We aimed to determine this proportion across a large range of nations.

METHODS

We measured community and hospital antibacterial consumption in New Zealand during 2015, from both reimbursement and purchase data, and compared the New Zealand data with those reported from a large range of other nations during similar time periods.

RESULTS AND DISCUSSION

Community antibacterial consumption comprised approximately 85%-95% of total antibacterial consumption in all nations for which data were available, and in New Zealand comprised a higher proportion than in any other nation. The proportion of total antibacterial consumption comprised by community consumption was significantly higher in countries with relatively high levels of total antibacterial consumption than in countries with relatively low levels of total antibacterial consumption.

WHAT IS NEW AND CONCLUSION

The high proportion of total antibacterial consumption comprised by community antibacterial consumption suggests devoting particular attention to improved community antimicrobial stewardship. These results suggest that improving antimicrobial stewardship in the community may provide greater overall benefits in combating antibacterial resistance than improving antimicrobial stewardship in hospitals.

Potentiating the effects of radiotherapy in rectal cancer: the role of aspirin, statins and metformin as adjuncts to therapy

BACKGROUND

Complete tumour response (pCR) to neo-adjuvant chemo-radiotherapy for rectal cancer is associated with a reduction in local recurrence and improved disease-free and overall survival, but is achieved in only 20-30% of patients. Drug repurposing for anti-cancer treatments is gaining momentum, but the potential of such drugs as adjuncts, to increase tumour response to chemo-radiotherapy in rectal cancer, is only just beginning to be recognised.

METHODS

A systematic literature search was conducted and all studies investigating the use of drugs to enhance response to neo-adjuvant radiation in rectal cancer were included. 2137 studies were identified and following review 12 studies were extracted for full text review, 9 studies were included in the final analysis.

RESULTS

The use of statins or aspirin during neo-adjuvant therapy was associated with a significantly higher rate of tumour downstaging. Statins were identified as a significant predictor of pCR and aspirin users had a greater 5-year progression-free survival and overall survival. Metformin use was associated with a significantly higher overall and disease-free survival, in a subset of diabetic patients.

CONCLUSIONS

Aspirin, metformin and statins are associated with increased downstaging of rectal tumours and thus may have a role as adjuncts to neoadjuvant treatment, highlighting a clear need for prospective randomised controlled trials to determine their true impact on tumour response and overall survival.

Heritabilities and genetic correlations of pulmonary arterial pressure and performance traits in Angus cattle at high altitude

Pulmonary arterial pressure (PAP) is an indicator trait for pulmonary hypertension and for the risk of developing high-altitude disease (HAD) in cattle. Pulmonary arterial pressures provide a tool for selection of breeding cattle for tolerance to high altitude in mountainous regions of the United States. The objective of this study was to evaluate relationships between growth performance traits and yearling PAP (42.4 ± 9.9 mmHg; = 5,776; elevation 2,150 m) using data from 1993 to 2014 in the John E. Rouse Colorado State University Beef Improvement Center (CSU-BIC) Angus herd. The breeding program used sires ( = 299) from both low- and high-elevation environments. We hypothesized that little to no genetic relationship exists between PAP and birth weight (BWT; direct and maternal), weaning weight (WW; direct and maternal), yearling weight (YW; direct and maternal), and postweaning gain (PWG). Historic selection of natural service sires from within the herd required a PAP of ≤ 42 mmHg. Outside AI sires ( = 156) used in this breeding program were not PAP tested and therefore were used with little knowledge of these sires' high-altitude adaptability. Performance traits (± SD) routinely recorded included BWT (36.2 ± 5.1 kg; = 8,695), WW (213.5 ± 31.8 kg; = 8,010), YW (345.6 ± 83.8 kg; = 5,580), and PWG (122.0 ± 63.7 kg; = 5,449), where PWG represented the total weight gained from weaning to yearling age. Four-trait analyses using REML were conducted with an animal model. The heritability estimates (± SE) for PAP (0.26 ± 0.03), BWT direct (0.42 ± 0.04) and maternal (0.14 ± 0.02), WW direct (0.29 ± 0.04) and maternal (0.19 ± 0.03), YW direct (0.45 ± 0.04) and maternal (0.23 ± 0.03), and PWG (0.14 ± 0.02) were in the range of those reported in previous literature. Estimates of genetic correlations (± SE) revealed weak relationships between PAP and direct and maternal BWT, direct and maternal WW, direct and maternal YW, and PWG of 0.15 ± 0.09, 0.14 ± 0.10, 0.23 ± 0.09, -0.01 ± 0.10, 0.12 ± 0.08, 0.00 ± 0.09, and -0.10 ± 0.10, respectively. The results of this study suggest that selection for lower PAP measures should have minimal influence on the growth performance of yearling Angus bulls and heifers at the CSU-BIC, supporting our hypothesis.

Transcriptome analyses identify five transcription factors differentially expressed in the hypothalamus of post- versus prepubertal Brahman heifers

Puberty onset is a developmental process influenced by genetic determinants, environment, and nutrition. Mutations and regulatory gene networks constitute the molecular basis for the genetic determinants of puberty onset. The emerging knowledge of these genetic determinants presents opportunities for innovation in the breeding of early pubertal cattle. This paper presents new data on hypothalamic gene expression related to puberty in (Brahman) in age- and weight-matched heifers. Six postpubertal heifers were compared with 6 prepubertal heifers using whole-genome RNA sequencing methodology for quantification of global gene expression in the hypothalamus. Five transcription factors (TF) with potential regulatory roles in the hypothalamus were identified in this experiment: , , , , and . These TF genes were significantly differentially expressed in the hypothalamus of postpubertal versus prepubertal heifers and were also identified as significant according to the applied regulatory impact factor metric ( < 0.05). Two of these 5 TF, and , were zinc fingers, belonging to a gene family previously reported to have a central regulatory role in mammalian puberty. The gene belongs to the family of homologues of Drosophila sine oculis () genes implicated in transcriptional regulation of gonadotrope gene expression. Tumor-related genes such as and are known to affect basic cellular processes that are relevant in both cancer and developmental processes. Mutations in were associated with puberty in humans. Mutations in these TF, together with other genetic determinants previously discovered, could be used in genomic selection to predict the genetic merit of cattle (i.e., the likelihood of the offspring presenting earlier than average puberty for Brahman). Knowledge of key mutations involved in genetic traits is an advantage for genomic prediction because it can increase its accuracy.

SNP detection using RNA-sequences of candidate genes associated with puberty in cattle

Fertility traits, such as heifer pregnancy, are economically important in cattle production systems, and are therefore, used in genetic selection programs. The aim of this study was to identify single nucleotide polymorphisms (SNPs) using RNA-sequencing (RNA-Seq) data from ovary, uterus, endometrium, pituitary gland, hypothalamus, liver, longissimus dorsi muscle, and adipose tissue in 62 candidate genes associated with heifer puberty in cattle. RNA-Seq reads were assembled to the bovine reference genome (UMD 3.1.1) and analyzed in five cattle breeds; Brangus, Brahman, Nellore, Angus, and Holstein. Two approaches used the Brangus data for SNP discovery 1) pooling all samples, and 2) within each individual sample. These approaches revealed 1157 SNPs. These were compared with those identified in the pooled samples of the other breeds. Overall, 172 SNPs within 13 genes (CPNE5, FAM19A4, FOXN4, KLF1, LOC777593, MGC157266, NEBL, NRXN3, PEPT-1, PPP3CA, SCG5, TSG101, and TSHR) were concordant in the five breeds. Using Ensembl's Variant Effector Predictor, we determined that 12% of SNPs were in exons (71% synonymous, 29% nonsynonymous), 1% were in untranslated regions (UTRs), 86% were in introns, and 1% were in intergenic regions. Since these SNPs were discovered in RNA, the variants were predicted to be within exons or UTRs. Overall, 160 novel transcripts in 42 candidate genes and five novel genes overlapping five candidate genes were observed. In conclusion, 1157 SNPs were identified in 62 candidate genes associated with puberty in Brangus cattle, of which, 172 were concordant in the five cattle breeds. Novel transcripts and genes were also identified.

Diagnostic accuracy of faecal biomarkers in detecting colorectal cancer and adenoma in symptomatic patients

BACKGROUND

The diagnosis of colorectal cancer (CRC) can be difficult as symptoms are variable with poor specificity. Thus, there is a quest for simple, non-invasive testing that can help streamline those with significant colonic pathology.

AIM

To assess using faecal immunochemical test for haemoglobin (FIT) or faecal calprotectin (FCP) to detect CRC and adenoma in symptomatic patients referred from primary care.

METHODS

A total of 799 referred for urgent lower gastrointestinal investigations were prospectively recruited. Of these, 430 completed colonic investigations and returned stool samples, and were included in the final statistical analysis. Faecal immunochemical test for haemoglobin was performed on HM-JACKarc analyser (Kyowa Medex, Tokyo, Japan), and FCP by the EliA Calprotectin immunoassay (Thermo Fisher Scientific, Waltham, United States).

RESULTS

The negative predictive value (NPV) using FIT alone or both markers (FIT and FCP) in combination was similar at 99% for CRC, with a sensitivity and specificity of 84% and 93%, respectively. FIT measurements were significantly higher in left-sided colonic lesions compared with the right side; 713 vs. 94; P = 0.0203). For adenoma, the NPV using FIT alone, or both markers (FIT and FCP) in combination, was similar at 94% with a sensitivity and specificity of 69% and 56%, respectively.

CONCLUSIONS

Undetectable faecal immunochemical test for haemoglobin is sufficiently sensitive to exclude colorectal cancer, with higher values in left-sided lesions. FCP in combination does not appear to provide additional diagnostic information. Further studies to determine the health economic benefits of implementing faecal immunochemical test for haemoglobin in primary care are required.

Mean pulmonary arterial pressures in Angus steers increase from cow-calf to feedlot-finishing phases

Pulmonary arterial hypertension due to hypoxia-induced pulmonary vascular remodeling is the predominant cause of right-sided congestive heart failure (CHF) in cattle. Historically, heart failure was problematic only at altitudes over 2,134 m. However, anecdotal reports suggest that the incidence of heart failure is increasing in feedlot cattle at moderate altitude (800 to 1,600 m), with late-fed, or fat, cattle at greatest risk. The goal of this study was to evaluate pulmonary arterial pressures (PAP) in a cohort of male Angus calves from suckling to finishing to better understand why heart failure is particularly problematic in fat cattle. It was hypothesized that mean PAP would increase through the feeding period and that the calves with the greatest pressures at high altitude would have the greatest pressures as fat cattle. A total of 362 PAP measurements were obtained from 153 calves. Calves were tested at altitudes of 2,170 (4 and 6 mo old), 1,560 (13 mo old), and 1,300 m (13 and 18 mo old). Mean PAP were greater in 18-mo-old steers than any other age group (mean = 50.3 mm Hg; 95% confidence interval 48.2 to 52.4; < 0.05). Calves that had the greatest mean pressure at 6 mo of age tended to have the greatest mean pressures at 18 mo of age ( = 0.45, < 0.001). The increase in mean PAP with increasing age and adiposity likely predisposed the steers to an increased risk of CHF during the finishing phase.

Smaug variants in neural and non-neuronal cells

Mammalian Smaug1/Samd4a is an mRNA regulator involved in synapse plasticity and additional non-neuronal functions. Here we analyzed the expression of Smaug1/Samd4a variants and Smaug2/Samd4b in primary hippocampal neurons and non-neuronal cell lines. We found that multiple Smaug proteins are present in several mammalian cell lines, including a canonical full length Smaug1, a Smaug1 variant that lacks the third exon, termed ΔEIII, and Smaug2, the product of a highly homologous gene. These three major isoforms are expressed differentially along neuron development and form cytosolic bodies when transfected in cell lines. By using luciferase reporters, we found that the ΔEIII isoform, which lacks 10 amino acids in the sterile α motif involved in RNA binding, shows a RNA-binding capacity and repressor activity comparable to that of the full length Smaug1. These observations are an important groundwork for molecular studies of the Smaug post-transcriptional pathway, which is relevant to neuron development, mitochondrial function and muscle physiology in health and disease.

Novel mRNA-silencing bodies at the synapse: A never-ending story

Several cellular responses depend on translational regulation and in most cases, this involves the formation of cytoplasmic granules that contain repressed mRNAs. In neurons, numerous mRNAs travel along dendrites to be locally regulated upon synapse activity and we have recently shown that the exoribonuclease XRN1 forms dynamic aggregates at the post synapse that respond to specific stimuli.¹ These foci were termed SX-bodies and are distinct from stress granules (SGs), processing bodies (PBs) and other RNA granules previously described. Together with Smaug1-foci and FMRP-granules, the SX-bodies contribute to dynamically shape the transcriptome available for translation at the post-synapse.

The altitude at which a calf is born and raised influences the rate at which mean pulmonary arterial pressure increases with age

Right heart failure secondary to pulmonary hypertension is a leading cause of mortality among suckling beef calves in the Rocky Mountain region. The objective of this study was to track changes in pulmonary arterial pressures (PAP) in healthy calves born and raised at altitudes ranging from 1,470 to 2,730 m. It was hypothesized that calves located at higher altitudes would show a greater increase in mean PAP (mPAP) with age than would be experienced by calves located at lower altitudes. The rationale is that high altitude hypobaric hypoxia causes a greater rate of vascular remodeling and, consequently, greater resistance to blood flow than calves located at lower altitudes. A prospective study was conducted on 5 cohorts of suckling calves from 4 herds located at altitudes of 1,470, 2,010, 2,170, and 2,730 m. In total, 470 PAP measurements were obtained from 258 calves. As hypothesized, calves located at altitudes ≥2,170 m showed a significant increase in mPAP with age ( ≤ 0.002) whereas calves at 1,470 m did not ( = 0.16). Except for calves at 2,170 m ( < 0.001), systolic PAP did not increase with age ( ≥ 0.16). Diastolic PAP increased with age at altitudes ≥ 2,170 m ( ≤ 0.09) but did not change in calves at 1,470 m ( = 0.20). In summary, mPAP and the rate at which mPAP increases with age are positively associated with the altitude at which calves are born and raised.

A dynamic framework for the study of optimal birth intervals reveals the importance of sibling competition and mortality risks

Human reproductive patterns have been well studied, but the mechanisms by which physiology, ecology and existing kin interact to affect the life history need quantification. Here, we create a model to investigate how age-specific interbirth intervals adapt to environmental and intrinsic mortality, and how birth patterns can be shaped by competition and help between siblings. The model provides a flexible framework for studying the processes underlying human reproductive scheduling. We developed a state-based optimality model to determine age-dependent and family-dependent sets of reproductive strategies, including the state of the mother and her offspring. We parameterized the model with realistic mortality curves derived from five human populations. Overall, optimal birth intervals increase until the age of 30 after which they remain relatively constant until the end of the reproductive lifespan. Offspring helping each other does not have much effect on birth intervals. Increasing infant and senescent mortality in different populations decreases interbirth intervals. We show that sibling competition and infant mortality interact to lengthen interbirth intervals. In lower-mortality populations, intense sibling competition pushes births further apart. Varying the adult risk of mortality alone has no effect on birth intervals between populations; competition between offspring drives the differences in birth intervals only when infant mortality is low. These results are relevant to understanding the demographic transition, because our model predicts that sibling competition becomes an important determinant of optimal interbirth intervals only when mortality is low, as in post-transition societies. We do not predict that these effects alone can select for menopause.

Genomewide association study of reproductive efficiency in female cattle

Reproductive efficiency is of economic importance in commercial beef cattle production, as failure to achieve pregnancy reduces the number of calves marketed per cow exposed. Identification of genetic markers with predictive merit for reproductive success would facilitate early selection of sires with daughters having improved reproductive rate without increasing generation intervals. To identify regions of the genome harboring variation affecting reproductive success, we applied a genomewide association study (GWAS) approach based on the >700,000 SNP marker assay, using a procedure based on genotyping multianimal pools of DNA to increase the number of animals that could be genotyped with available resources. Cows from several populations were classified according to reproductive efficiency, and DNA was pooled within population and phenotype prior to genotyping. Populations evaluated included a research population at the U.S. Meat Animal Research Center, 2 large commercial ranch populations, and a number of smaller populations (<100 head) across the United States. We detected 2 SNP with significant genomewide association (P ≤ 1.49 × 10(-7)), on BTA21 and BTA29, 3 SNP with suggestive associations (P ≤ 2.91 × 10(-6)) on BTA5, and 1 SNP with suggestive association each on BTA1 and BTA25. In addition to our novel findings, we confirmed previously published associations for SNP on BTA-X and all autosomes except 3 (BTA21, BTA22, and BTA28) encompassing substantial breed diversity including Bos indicus and Bos taurus breeds. The study identified regions of the genome associated with reproductive efficiency, which are being targeted for further analysis to develop robust marker systems, and demonstrated that DNA pooling can be used to substantially reduce the cost of GWAS in cattle.

Synaptic control of mRNA translation by reversible assembly of XRN1 bodies

Repression of mRNA translation is linked to the formation of specific cytosolic foci such as Stress Granules (SGs) and Processing Bodies (PBs), which store or degrade mRNAs. In neurons, synaptic activity regulates translation at the postsynapse and this is important for plasticity. NMDA receptor stimulation downregulates translation and we speculate that this is linked to the formation of unknown mRNA-silencing foci. Here we show that the 5′-3′ exoribonuclease XRN1 forms discrete clusters associated to the postsynapse that are different from PBs or SGs, and we named them Synaptic XRN1-bodies (SX-bodies). Using primary neurons, we found that the SX-bodies respond to synapse stimulation and that their formation correlates inversely with the local translation rate. SX-bodies enlarge in size and number upon NMDA stimulation, and metabotropic glutamate receptor activation provokes SX-body dissolution, along with increased translation. The response is specific and the previously described Smaug1-foci and FMRP granules show a different response. Finally, XRN1 knockdown impairs the translational repression triggered by NMDA. Collectively, these observations support a role for the SX-bodies in the reversible masking and silencing of mRNAs at the synapse.

A systematic review of outcome reporting in colorectal cancer surgery

AIM

Evaluation of surgery for colorectal cancer (CRC) is necessary to inform clinical decision-making and healthcare policy. The standards of outcome reporting after CRC surgery have not previously been considered.

METHOD

Systematic literature searches identified randomized and nonrandomized prospective studies reporting clinical outcomes of CRC surgery. Outcomes were listed verbatim, categorized into broad groups (outcome domains) and examined for a definition (an appropriate textual explanation or a supporting citation). Outcome reporting was considered inconsistent if results of the outcome specified in the methods were not reported. Outcome reporting was compared between randomized and nonrandomized studies.

RESULTS

Of 5644 abstracts, 194 articles (34 randomized and 160 nonrandomized studies) were included reporting 766 different clinical outcomes, categorized into seven domains. A mean of 14 ± 8 individual outcomes were reported per study. 'Anastomotic leak', 'overall survival' and 'wound infection' were the three most frequently reported outcomes in 72, 60 and 44 (37.1%, 30.9% and 22.7%) studies, respectively, and no single outcome was reported in every publication. Outcome definitions were significantly more often provided in randomized studies than in nonrandomized studies (19.0% vs 14.9%, P = 0.015). One-hundred and twenty-seven (65.5%) papers reported results of all outcomes specified in the methods (randomized studies, n = 21, 61.5%; nonrandomized studies, n = 106, 66.2%; P = 0.617).

CONCLUSION

Outcome reporting in CRC surgery lacks consistency and method. Improved standards of outcome measurement are recommended to permit data synthesis and transparent cross-study comparisons.

Synaptic control of local translation: the plot thickens with new characters

The production of proteins from mRNAs localized at the synapse ultimately controls the strength of synaptic transmission, thereby affecting behavior and cognitive functions. The regulated transcription, processing, and transport of mRNAs provide dynamic control of the dendritic transcriptome, which includes thousands of messengers encoding multiple cellular functions. Translation is locally modulated by synaptic activity through a complex network of RNA-binding proteins (RBPs) and various types of non-coding RNAs (ncRNAs) including BC-RNAs, microRNAs, piwi-interacting RNAs, and small interference RNAs. The RBPs FMRP and CPEB play a well-established role in synaptic translation, and additional regulatory factors are emerging. The mRNA repressors Smaug, Nanos, and Pumilio define a novel pathway for local translational control that affects dendritic branching and spines in both flies and mammals. Recent findings support a role for processing bodies and related synaptic mRNA-silencing foci (SyAS-foci) in the modulation of synaptic plasticity and memory formation. The SyAS-foci respond to different stimuli with changes in their integrity thus enabling regulated mRNA release followed by translation. CPEB, Pumilio, TDP-43, and FUS/TLS form multimers through low-complexity regions related to prion domains or polyQ expansions. The oligomerization of these repressor RBPs is mechanistically linked to the aggregation of abnormal proteins commonly associated with neurodegeneration. Here, we summarize the current knowledge on how specificity in mRNA translation is achieved through the concerted action of multiple pathways that involve regulatory ncRNAs and RBPs, the modification of translation factors, and mRNA-silencing foci dynamics.

Deletion on chromosome 5 associated with decreased reproductive efficiency in female cattle

Reproductive efficiency is arguably the most economically important trait in commercial beef cattle production, as failure to achieve pregnancy reduces the number of calves marketed per cow exposed to breeding. Identification of variation in the genome with predictive merit for reproductive success would facilitate accurate prediction of daughter pregnancy rate in sires enabling effective selection of bulls producing daughters with improved fertility. Copy number variation (CNV) is one form of structural variation that results in abnormal copies of DNA in the genome. Our lab previously reported a region between 25 and 70 Mb on chromosome 5 associated with reproductive efficiency. To further evaluate this region for genomic variations such as CNV, we initially applied a genomewide association approach based on the >700,000 SNP marker assay and PennCNV analysis to 68 Bos indicus cross females from a large commercial ranch in central Florida. A genomic segment located on chromosome 5, spanning the region of approximately 58.37 to 58.44 Mb (Bovine UMD3.1 assembly) was identified as containing a deletion associated with decreased reproductive efficiency. To verify this deletion, a quantitative real-time PCR test was developed to evaluate additional females in the central Florida and U.S. Meat Animal Research Center (USMARC) populations. The frequency of the homozygous deletion was 7% (23/319) in the central Florida population (Bos indicus cross) for females with 2 consecutive failed breeding seasons and 0% in the USMARC population (predominantly Bos taurus) of low reproductive females. To date, we have not identified the deletion in Bos taurus cattle, suggesting that the deletion is specific to Bos indicus cattle. From these data, we have identified a deletion on chromosome 5 associated with reproductive efficiency in Bos indicus-influenced cattle.

Nicotinamide N-methyltransferase expression in SH-SY5Y neuroblastoma and N27 mesencephalic neurones induces changes in cell morphology via ephrin-B2 and Akt signalling

Nicotinamide N-methyltransferase (NNMT, E.C. 2.1.1.1) N-methylates nicotinamide to produce 1-methylnicotinamide (MeN). We have previously shown that NNMT expression protected against neurotoxin-mediated cell death by increasing Complex I (CxI) activity, resulting in increased ATP synthesis. This was mediated via protection of the NDUFS3 subunit of CxI from degradation by increased MeN production. In the present study, we have investigated the effects of NNMT expression on neurone morphology and differentiation. Expression of NNMT in SH-SY5Y human neuroblastoma and N27 rat mesencephalic dopaminergic neurones increased neurite branching, synaptophysin expression and dopamine accumulation and release. siRNA gene silencing of ephrin B2 (EFNB2), and inhibition of Akt phosphorylation using LY294002, demonstrated that their sequential activation was responsible for the increases observed. Incubation of SH-SY5Y with increasing concentrations of MeN also increased neurite branching, suggesting that the effects of NNMT may be mediated by MeN. NNMT had no significant effect on the expression of phenotypic and post-mitotic markers, suggesting that NNMT is not involved in determining phenotypic fate or differentiation status. These results demonstrate that NNMT expression regulates neurone morphology in vitro via the sequential activation of the EFNB2 and Akt cellular signalling pathways.

Bayesian genome-wide association analysis of growth and yearling ultrasound measures of carcass traits in Brangus heifers

Data from developing Brangus heifers (3/8 Brahman-Bos indicus × 5/8 Angus-Bos taurus; n ≈ 802 from 67 sires) registered with International Brangus Breeders Association were analyzed to detect QTL associated with growth traits and ultrasound measures of carcass traits. Genotypes were from BovineSNP50 (Infinium BeadChip, Illumina, San Diego, CA; 53,692 SNP). Phenotypes included BW collected at birth and ∼205 and 365 d of age, and yearling ultrasound assessment of LM area, percent intramuscular fat, and depth of rib fat. Simultaneous association of SNP windows with phenotype were undertaken with Bayes C analyses, using GenSel software. The SNP windows were ≈ 5 SNP in length. Analyses fitted a mixture model that treated SNP effects as random, with an assumed fraction pi = 0.999 having no effect on phenotype. Bootstrap analyses were used to obtain significance values for the SNP windows with the greatest contribution to observed variation. The SNP windows with P < 0.01 were considered as QTL associated with a trait in which case their location was queried from dbSNP and the presence of a previously reported QTL in that location was checked in CattleQTLdb. For 9 traits, QTL were mapped to 139 regions on 25 chromosomes. Forty-one of these QTL were already described in CattleQTLdb, so 98 are new additions. The SNP windows on chromosomes 1, 3, and 6 were associated with multiple traits (i.e., 205- and 365- d BW, and ADG from birth to 205 and 365 d of age). Several chromosomes harbored regions associated with multiple traits; however, the SNP that comprised the window often varied among traits (i.e., chromosomes 1, 3, 4, 5, 6, 7, 9, 10, 11, 13, 14, 15, 16, 20, 21, 22, 24, 28, and 29). Results from whole genome association of SNP with growth and ultrasound carcass traits in developing Brangus heifers confirmed several published QTL and detected several new QTL.

BUHO: a MATLAB script for the study of stress granules and processing bodies by high-throughput image analysis

The spontaneous and reversible formation of foci and filaments that contain proteins involved in different metabolic processes is common in both the nucleus and the cytoplasm. Stress granules (SGs) and processing bodies (PBs) belong to a novel family of cellular structures collectively known as mRNA silencing foci that harbour repressed mRNAs and their associated proteins. SGs and PBs are highly dynamic and they form upon stress and dissolve thus releasing the repressed mRNAs according to changes in cell physiology. In addition, aggregates containing abnormal proteins are frequent in neurodegenerative disorders. In spite of the growing relevance of these supramolecular aggregates to diverse cellular functions a reliable automated tool for their systematic analysis is lacking. Here we report a MATLAB Script termed BUHO for the high-throughput image analysis of cellular foci. We used BUHO to assess the number, size and distribution of distinct objects with minimal deviation from manually obtained parameters. BUHO successfully addressed the induction of both SGs and PBs in mammalian and insect cells exposed to different stress stimuli. We also used BUHO to assess the dynamics of specific mRNA-silencing foci termed Smaug 1 foci (S-foci) in primary neurons upon synaptic stimulation. Finally, we used BUHO to analyze the role of candidate genes on SG formation in an RNAi-based experiment. We found that FAK56D, GCN2 and PP1 govern SG formation. The role of PP1 is conserved in mammalian cells as judged by the effect of the PP1 inhibitor salubrinal, and involves dephosphorylation of the translation factor eIF2α. All these experiments were analyzed manually and by BUHO and the results differed in less than 5% of the average value. The automated analysis by this user-friendly method will allow high-throughput image processing in short times by providing a robust, flexible and reliable alternative to the laborious and sometimes unfeasible visual scrutiny.

Heritability and Bayesian genome-wide association study of first service conception and pregnancy in Brangus heifers

Brangus [3/8 Brahman (Bos indicus) × 5/8 Angus (Bos taurus); n ≈ 800] heifers from 67 sires were used to estimate heritability and conduct a genome-wide association study (GWAS) for 2 binary fertility traits: first service conception (FSC) and heifer pregnancy (HPG). Genotypes were from 53,692 loci on the BovineSNP50 (Infinium Bead Chips, Illumina, San Diego, CA). Yearling heifers were estrous synchronized, bred by AI, and then exposed to natural service breeding. Reproductive ultrasound and DNA-based parentage testing were used to determine if the heifer conceived by AI or natural service, and code for FSC and HPG traits. Success rates for FSC and HPG were 53.3% and 78.0% ± 0.01%, and corresponding heritability estimates were 0.18 ± 0.07 and 0.10 ± 0.06, respectively. The models used in obtaining these heritability estimates and GWAS included fixed effects of year (i.e., 2005 to 2007), birth location, calving season, age of dam, and contemporary group. In GWAS, simultaneous associations of 1 Mb SNP windows with phenotype were undertaken with Bayes C analyses using GenSel software. The 1 Mb windows contained 21.3 ± 1.1 SNP. Analyses fitted a mixture model that treated SNP effects as random, with an assumed fraction pi = 0.9995 having no effect on phenotype. The windows that accounted for 1.0% of genetic variance were considered as QTL associated with FSC or HPG. Eighteen QTL existed on 15 chromosomes for the 2 traits. On average, each QTL accounted for 2.43% ± 0.2% of the genetic variance. Chromosome 8 harbored 2 QTL for FSC and 1 for HPG; however, these regions did not overlap. Chromosomes 3, 15, 16, 19, 24, 26, 27, 29, and X included QTL only for FSC, whereas chromosomes 2, 4, 10, 13, and 20 contained QTL only for HPG. The multitude of QTL detected for FSC and HPG in this GWAS involving Brangus heifers exemplifies the complex regulation of variation in heifer fertility traits of low heritability.

The flickering genes of the last mammoths

Woolly mammoths, Mammuthus primigenius, are arguably the most iconic of the extinct Pleistocene megafauna, and an abundance of large permafrost-embedded bone and ivory material (Fig. 1) means they were also among the first to yield credible DNA sequences (Hagelberg et al. 1994; Hoss et al. 1994). Despite mammoth remains being numerous throughout northern Eurasia and North America, both the earliest and most recent fossils are found in northeast Siberia, with the last known population being confined to Wrangel Island in the Arctic Ocean from around 10,000 years ago until their extinction around 4,000 years ago. The extent to which these Holocene mammoths were descended from the Pleistocene populations of Wrangel Island and the demographic nature of their terminal decline have, until now, remained something of a mystery. In this issue of Molecular Ecology, Nyström et al. (2012) report the first use of autosomal variation to track the decline of the last mammoths and, in doing so, take a significant step towards resolving these questions. The authors genotyped four microsatellite loci in 59 Pleistocene and Holocene mammoths from Wrangel Island and Chukotka in mainland northeastern Siberia and showed that while the Pleistocene-to-Holocene transition is associated with a significant reduction in genetic diversity, subsequent levels of variation remain constant until extinction. Such a pattern is somewhat surprising as it indicates that while the last mammoths were confined to only a few Arctic islands, their final extinction on Wrangel Island was not a gradual process resulting from loss of genetic diversity/inbreeding. Instead, it seems they maintained a viable effective population size of around 500 until near their presumably rapid extinction. While the ultimate agent of mammoth extinction remains unknown, the work of Nyström et al. (2012). suggests that we should be looking for something sudden, like a rapid change in climate/ecology or perhaps the arrival of humans.

Reconstruction of the perineum following extralevator abdominoperineal excision for carcinoma of the lower rectum: a systematic review

AIM

An improvement in oncological outcome has been reported following an extralevator approach to abdominoperineal excision (ELAPE) for low rectal carcinoma. A larger perineal defect following ELAPE and the impact of neoadjuvant radiotherapy are sources of considerable morbidity for patients. We report an evidence-based systematic review of published data on the outcome of perineal reconstruction following ELAPE for low rectal carcinoma, comparing the use of tissue flap and biological mesh techniques.

METHOD

A literature search was performed of electronic databases including the Medline, Embase and Scopus databases (1995-2011). Studies describing outcomes relating to the perineum following ELAPE were included for review.

RESULTS

Eleven small cohort studies reported the outcome relating to the perineum following ELAPE. Pooled-analysis of 255 combined patients undergoing flap repair and 85 undergoing biological mesh repair showed no significant difference in the rates of perineal wound complications or perineal hernia formation.

CONCLUSION

There is little information on the optimal technique of perineal wound closure following ELAPE. With the limited data available, there was no significant difference in complication rates between biological mesh and flap repair. There is a need for high-quality prospective trials to compare methods of reconstruction to determine the long-term results, quality of life and function.

Evaluation of gut bacterial populations using an electronic e-nose and field asymmetric ion mobility spectrometry: further insights into 'fermentonomics'

The fermentation of undigested foods in the large bowel, by its resident bacteria, results in the production of several chemicals including volatile gases. Perturbance in gut bacteria is known to influence colonic and metabolic health, but to determine this requires prolonged culture (often unsuccessful) or expensive genomic sequencing. Clearly this is not practical for daily clinical practice. Previously, we have reported our insights into fermentonomics through the detection of volatile organic compounds (VOCs) in patients with gastrointestinal and metabolic diseases, using the electronic nose. In this paper we report on the changes in the fermentone produced by patients undergoing complete versus partial bowel cleansing. Using urine samples, preliminary results from 23 individuals receiving bowel cleansing indicate the ability of the electronic nose to distinguish between the partial and complete procedures. Moreover in a subset of individuals, we have been able to track evolving bacterial recolonization over time using the e-nose and field asymmetric ion mobility spectrometry (FAIMS). Such an approach has practical application in tracking bacterial dysbiosis following perturbation.

Gene network analyses of first service conception in Brangus heifers: use of genome and trait associations, hypothalamic-transcriptome information, and transcription factors

Measures of heifer fertility are economically relevant traits for beef production systems and knowledge of candidate genes could be incorporated into future genomic selection strategies. Ten traits related to growth and fertility were measured in 890 Brangus heifers (3/8 Brahman × 5/8 Angus, from 67 sires). These traits were: BW and hip height adjusted to 205 and 365 d of age, postweaning ADG, yearling assessment of carcass traits (i.e., back fat thickness, intramuscular fat, and LM area), as well as heifer pregnancy and first service conception (FSC). These fertility traits were collected from controlled breeding seasons initiated with estrous synchronization and AI targeting heifers to calve by 24 mo of age. The BovineSNP50 BeadChip was used to ascertain 53,692 SNP genotypes for ∼802 heifers. Associations of genotypes and phenotypes were performed and SNP effects were estimated for each trait. Minimally associated SNP (P < 0.05) and their effects across the 10 traits formed the basis for an association weight matrix and its derived gene network related to FSC (57.3% success and heritability = 0.06 ± 0.05). These analyses yielded 1,555 important SNP, which inferred genes linked by 113,873 correlations within a network. Specifically, 1,386 SNP were nodes and the 5,132 strongest correlations (|r| ≥ 0.90) were edges. The network was filtered with genes queried from a transcriptome resource created from deep sequencing of RNA (i.e., RNA-Seq) from the hypothalamus of a prepubertal and a postpubertal Brangus heifer. The remaining hypothalamic-influenced network contained 978 genes connected by 2,560 edges or predicted gene interactions. This hypothalamic gene network was enriched with genes involved in axon guidance, which is a pathway known to influence pulsatile release of LHRH. There were 5 transcription factors with 21 or more connections: ZMAT3, STAT6, RFX4, PLAGL1, and NR6A1 for FSC. The SNP that identified these genes were intragenic and were on chromosomes 1, 5, 9, and 11. Chromosome 5 harbored both STAT6 and RFX4. The large number of interactions and genes observed with network analyses of multiple sources of genomic data (i.e., GWAS and RNA-Seq) support the concept of FSC being a polygenic trait.

A monoclonal antibody against p53 cross-reacts with processing bodies

The p53 tumor suppressor protein is an important regulator of cell proliferation and apoptosis. p53 can be found in the nucleus and in the cytosol, and the subcellular location is key to control p53 function. In this work, we found that a widely used monoclonal antibody against p53, termed Pab 1801 (Pan antibody 1801) yields a remarkable punctate signal in the cytoplasm of several cell lines of human origin. Surprisingly, these puncta were also observed in two independent p53-null cell lines. Moreover, the foci stained with the Pab 1801 were present in rat cells, although Pab 1801 recognizes an epitope that is not conserved in rodent p53. In contrast, the Pab 1801 nuclear staining corresponded to genuine p53, as it was upregulated by p53-stimulating drugs and absent in p53-null cells. We identified the Pab 1801 cytoplasmic puncta as P Bodies (PBs), which are involved in mRNA regulation. We found that, in several cell lines, including U2OS, WI38, SK-N-SH and HCT116, the Pab 1801 puncta strictly colocalize with PBs identified with specific antibodies against the PB components Hedls, Dcp1a, Xrn1 or Rck/p54. PBs are highly dynamic and accordingly, the Pab 1801 puncta vanished when PBs dissolved upon treatment with cycloheximide, a drug that causes polysome stabilization and PB disruption. In addition, the knockdown of specific PB components that affect PB integrity simultaneously caused PB dissolution and the disappearance of the Pab 1801 puncta. Our results reveal a strong cross-reactivity of the Pab 1801 with unknown PB component(s). This was observed upon distinct immunostaining protocols, thus meaning a major limitation on the use of this antibody for p53 imaging in the cytoplasm of most cell types of human or rodent origin.

Smaug1 mRNA-silencing foci respond to NMDA and modulate synapse formation

S-foci, the first reported mRNA-silencing foci specific to neurons, may control local mRNA translation in response to NMDA receptor stimulation and synaptic plasticity.

Mammalian Smaug1/Samd4A is a translational repressor. Here we show that Smaug1 forms mRNA-silencing foci located at postsynapses of hippocampal neurons. These structures, which we have named S-foci, are distinct from P-bodies, stress granules, or other neuronal RNA granules hitherto described, and are the first described mRNA-silencing foci specific to neurons. RNA binding was not required for aggregation, which indicates that S-foci formation is not a consequence of mRNA silencing. N-methyl-d-aspartic acid (NMDA) receptor stimulation provoked a rapid and reversible disassembly of S-foci, transiently releasing transcripts (the CaMKIIα mRNA among others) to allow their translation. Simultaneously, NMDA triggered global translational silencing, which suggests the specific activation of Smaug1-repressed transcripts. Smaug1 is expressed during synaptogenesis, and Smaug1 knockdown affected the number and size of synapses, and also provoked an impaired response to repetitive depolarizing stimuli, as indicated by a reduced induction of Arc/Arg3.1. Our results suggest that S-foci control local translation, specifically responding to NMDA receptor stimulation and affecting synaptic plasticity.

Physiology and Endocrinology Symposium: How single nucleotide polymorphism chips will advance our knowledge of factors controlling puberty and aid in selecting replacement beef females

The promise of genomic selection is accurate prediction of the genetic potential of animals from their genotypes. Simple DNA tests might replace low-accuracy predictions for expensive or lowly heritable measures of puberty and fertility based on performance and pedigree. Knowing with some certainty which DNA variants (e.g., SNP) affect puberty and fertility is the best way to fulfill the promise. Several SNP from the BovineSNP50 assay have tentatively been associated with reproductive traits including age at puberty, antral follicle count, and pregnancy observed on different sets of heifers. However, sample sizes are too small and SNP density is too sparse to definitively determine genomic regions harboring causal variants affecting reproductive success. Additionally, associations between individual SNP and similar phenotypes are inconsistent across data sets, and genomic predictions do not appear to be globally applicable to cattle of different breeds. Discrepancies may be a result of different QTL segregating in the sampled populations, differences in linkage disequilibrium (LD) patterns such that the same SNP are not correlated with the same QTL, and spurious correlations with phenotype. Several approaches can be used independently or in combination to improve detection of genomic factors affecting heifer puberty and fertility. Larger samples and denser SNP will increase power to detect real associations with SNP having more consistent LD with underlying QTL. Meta-analysis combining results from different studies can also be used to effectively increase sample size. High-density genotyping with heifers pooled by pregnancy status or early and late puberty can be a cost-effective means to sample large numbers. Networks of genes, implicated by associations with multiple traits correlated with puberty and fertility, could provide insight into the complex nature of these traits, especially if corroborated by functional annotation, established gene interaction pathways, and transcript expression. Example analyses are provided to demonstrate how integrating information about gene function and regulation with statistical associations from whole-genome SNP genotyping assays might enhance knowledge of genomic mechanisms affecting puberty and fertility, enabling reliable DNA tests to guide heifer selection decisions.

Coping processes and health-related quality of life in Parkinson's disease

OBJECTIVE

This study investigated the predictive value of various coping processes for the psychological and disease specific aspects of health-related quality of life (HRQoL) in Parkinson's disease (PD).

METHOD

Cross-sectional study of 85 participants with PD using the Ways of Coping Questionnaire (WCQ), Depression, Anxiety, and Stress Scale (DASS-21), quality of life (PDQ-39), and socio-demographic and clinical variables.

RESULTS

Greater use of planful problem solving coping was found to be significantly associated with better HRQoL in relation to cognitive impairment, communication and bodily discomfort. In addition to greater disease duration, greater use of escape-avoidance coping processes were identified as significant predictors of poorer HRQoL outcomes in the domains of mood and emotional well-being.

CONCLUSION

Psychological interventions such as mindfulness training, aimed at reducing the use of escape-avoidance copying, may help to improve HRQoL in PD.

Genetic analyses involving microsatellite ETH10 genotypes on bovine chromosome 5 and performance trait measures in Angus- and Brahman-influenced cattle

ETH10 is a dinucleotide microsatellite within the promoter of signal transducer and activator of transcription 6 (STAT6) gene on bovine chromosome 5. ETH10 is included in the panel of genetic markers used in parentage testing procedures of cattle breed associations. Allelic sizes of ETH10 PCR amplicons range from 199 to 225 bp. Objectives of this study were to use microsatellite data from beef cattle breed associations to investigate genetic distance and population stratification among Angus- and Brahman-influenced cattle and to use ETH10 genotypes and growth and ultrasound carcass data to investigate their statistical relationships. Three series of genotype to phenotype association analyses were conducted with 1) Angus data (n=5,094), 2) Brangus data (3/8 Brahman × 5/8 Angus; n=2,296), and 3) multibreed data (n=4,426) of Angus and Brangus cattle. Thirteen alleles and 38 genotypes were observed, but frequencies varied among breed groups. Tests of genetic identity and distance among 6 breed composition groups increasing in Brahman influence from 0 to 75% revealed that as Brahman-influence increased to ≥50%, genetic distance from Angus ranged from 18.3 to 43.5%. This was accomplished with 10 microsatellite loci. A mixed effects model involving genotype as a fixed effect and sire as a random source of variation suggested that Angus cattle with the 217/219 genotype tended to have 2.1% heavier (P=0.07) 205-d BW than other genotypes. In Brangus cattle, allele combinations were classified as small (≤215 bp) or large (≥217 bp). Brangus cattle with the small/large genotype had 2.0% heavier (P<0.05) birth weight, yet cattle with the large/large genotype had approximately 5.1% greater (P<0.05) percentage of fat within LM and more LM per BW than cattle with small/large or small/small genotypes. Genotype-to-phenotype relationships were not detected in multibreed analyses. The ETH10 locus appears to be associated with growth and carcass traits in Angus and Brangus cattle. Results from this study provide support for STAT6 as one of the candidate genes underlying cattle growth QTL on chromosome 5.

Exercise and Parkinson's: benefits for cognition and quality of life

OBJECTIVES

The benefits of physical exercise for psychological aspects of quality of life (QoL) are well established in normally ageing adults, yet potential benefits for people with Parkinson's disease (PD) have received limited attention. This study evaluated the benefits of exercise for cognitive functioning, mood and disease-specific QoL for people with PD.

METHODS

Twenty-eight individuals with PD were allocated to an exercise intervention program (EIP, n = 15) or control group (n = 13). The EIP group undertook a programme of progressive anabolic and aerobic exercise twice weekly for 12 weeks. The control group maintained their usual lifestyle.

RESULTS

Exercise was shown to have selective benefits for cognitive functioning by improving frontal lobe based executive function. No significant effects were demonstrated for mood or disease-specific QoL.

CONCLUSIONS

These results are consistent with previous research demonstrating selective benefits of exercise for executive function among normal ageing adults and PD.

RNA granules: the good, the bad and the ugly

Processing bodies (PBs) and Stress Granules (SGs) are the founding members of a new class of RNA granules, known as mRNA silencing foci, as they harbour transcripts circumstantially excluded from the translationally active pool. PBs and SGs are able to release mRNAs thus allowing their translation. PBs are constitutive, but respond to stimuli that affect mRNA translation and decay, whereas SGs are specifically induced upon cellular stress, which triggers a global translational silencing by several pathways, including phosphorylation of the key translation initiation factor eIF2alpha, and tRNA cleavage among others. PBs and SGs with different compositions may coexist in a single cell. These macromolecular aggregates are highly conserved through evolution, from unicellular organisms to vertebrate neurons. Their dynamics is regulated by several signaling pathways, and depends on microfilaments and microtubules, and the cognate molecular motors myosin, dynein, and kinesin. SGs share features with aggresomes and related aggregates of unfolded proteins frequently present in neurodegenerative diseases, and may play a role in the pathology. Virus infections may induce or impair SG formation. Besides being important for mRNA regulation upon stress, SGs modulate the signaling balancing apoptosis and cell survival. Finally, the formation of Nuclear Stress Bodies (nSBs), which share components with SGs, and the assembly of additional cytosolic aggregates containing RNA -the UV granules and the Ire1 foci-, all of them induced by specific cell damage factors, contribute to cell survival.

Optimising methods for communicating survival data to patients undergoing cancer surgery

BACKGROUND

Patients undergoing cancer surgery require outcome data to inform decisions, but communication of numerical risk is difficult. This study assessed patient understanding of survival data presented in different formats.

METHODS

Semi-structured interviews in which patients interpreted four presentation formats of survival data (three graphical and one narrative) were audio-recorded. The interviewer and a blinded observer (listening to the audio-recordings) scored patients' understanding of each format. Logistic regression examined associations between understanding and clinical and socio-demographic details.

RESULTS

Seventy participants with colorectal cancer were interviewed and 67 [95.7%, 95% confidence intervals (CIs) 90.9-100%] correctly interpreted a simplified Kaplan-Meier survival curve. A high proportion accurately understood data presented as a bar chart or pictograph (94.3%, 95% CIs 88.7-99.9% and 92.9%, 95% CIs 86.7-99.0% respectively). Standard narrative alone was least well understood (n = 53, 75.7%, 95% CIs 65.4-86.0%). Multivariable analyses demonstrated that older and female patients had poorer overall understanding (OR 0.93 per year, 95% CIs 0.87-0.98, p = 0.01 and OR 0.24, 95% CIs 0.07-0.86, p = 0.03).

CONCLUSION

Patient understanding of survival data was higher when presented with graphs compared to narrative alone. Further work examining understanding in the clinical context and before surgery is recommended before this can be used routinely.

Metal clusters in catalysis: Hydrocarbon reactions

A set of metal carbonyl clusters, Ru(3)(CO)(12), Os(3)(CO)(12), and Ir(4)(CO)(12), has been evaluated as catalysts for a series of hydrocarbon reactions which comprise skeletal rearrangement, metathesis, dehydrogenation, hydrogenation, isomerization, and H-D exchange. None was especially effective as a hydrogenation catalyst even for olefins. Os(3)(CO)(12) was a catalyst for H-D exchange between C(6)H(6) and D(2) at 195 degrees but the ruthenium congener was inactive at temperatures below 175 degrees , a temperature where ruthenium metal formed at an appreciable rate. Deuterium incorporation in the benzene was a single-step process. Ir(4)(CO)(12) was an effective catalyst for the conversion of cyclohexadiene to cyclohexene and benzene. A similar reaction occurred with cyclohexene but the rate was extremely low at 160 degrees . The ruthenium and osmium clusters catalyzed the isomerization of linear hexenes, with the former the more active. Relative rates for the hexenes were 1 > 2 > 3. At high temperatures, the osmium and iridium clusters catalyzed skeletal reactions of 2-hexene, as evidenced by the formation of pentenes, heptenes, heptanes, and small amounts of propane.

Dynamics of GHRH in third-ventricle cerebrospinal fluid of cattle: relationship with serum concentrations of GH and responses to appetite-regulating peptides

Objectives were to (1) characterize the relationship of third-ventricle (IIIV) cerebrospinal fluid (CSF) concentrations of growth hormone-releasing hormone (GHRH) with concentrations of GH in the peripheral circulation; and (2) assess the influence of acute administration of appetite-regulating peptides leptin (anti-orexigenic) and neuropeptide Y (NPY; orexigenic) on the release of GHRH. Six mature beef cows fitted with IIIV and jugular vein cannulae were treated intracerebroventricularly with saline, and leptin (600 microg) and NPY (500 microg) in saline, in a replicated 3x3 Latin square design. Third-ventricle CSF and blood were collected 10 min before and continued 220 min after treatments. Mean concentrations of GHRH and frequency of pulses after treatments were 2.2+/-0.13 ng/mL and 1.2+/-0.15 pulses/220 min, respectively. These measures were not influenced by treatments. Concentrations of GHRH in CSF were weakly correlated (r=0.15; P<0.03) with serum concentrations of GH; however, 58% of the GH pulses were preceded by a pulse of GHRH and 90% of the GHRH pulses occurred within 20 min preceding a pulse of GH. Leptin tended (P<0.10) to suppress GH area under the curve (AUC) compared to saline. Concomitantly, NPY tended (P<0.10) to increase GH AUC, which appeared to be a consequence of increased (P<0.05) pulse amplitude. Infusion of NPY also increased (P<0.05) AUC of GHRH relative to saline. No differences were detected among treatments in serum concentrations of insulin-like growth factor-I or its AUC. Sampling CSF from the IIIV appears to be a viable procedure for assessing hypothalamic release of GHRH coincident with anterior pituitary gland secretion of GH in cattle. These data also demonstrate the differential responsiveness of the GH axis to appetite-regulating peptides.

Obstructive endo-bronchial pseudotumour due to herpes simplex type 2 infection in an HIV-infected man

We report a 31-year-old man with an obstructive bronchial lesion due to herpes simplex type 2 infection, who responded promptly to endoscopic resection and oral treatment with acyclovir. Exophytic lesions of the respiratory tract are rare, potentially life-threatening, but readily treated complication of herpes simplex virus infection in HIV-infected individuals.

Genetic discontinuity between local hunter-gatherers and central Europe's first farmers

After the domestication of animals and crops in the Near East some 11,000 years ago, farming had reached much of central Europe by 7500 years before the present. The extent to which these early European farmers were immigrants or descendants of resident hunter-gatherers who had adopted farming has been widely debated. We compared new mitochondrial DNA (mtDNA) sequences from late European hunter-gatherer skeletons with those from early farmers and from modern Europeans. We find large genetic differences between all three groups that cannot be explained by population continuity alone. Most (82%) of the ancient hunter-gatherers share mtDNA types that are relatively rare in central Europeans today. Together, these analyses provide persuasive evidence that the first farmers were not the descendants of local hunter-gatherers but immigrated into central Europe at the onset of the Neolithic.

Mammalian Staufen 1 is recruited to stress granules and impairs their assembly

Stress granules are cytoplasmic mRNA-silencing foci that form transiently during the stress response. Stress granules harbor abortive translation initiation complexes and are in dynamic equilibrium with translating polysomes. Mammalian Staufen 1 (Stau1) is a ubiquitous double-stranded RNA-binding protein associated with polysomes. Here, we show that Stau1 is recruited to stress granules upon induction of endoplasmic reticulum or oxidative stress as well in stress granules induced by translation initiation blockers. We found that stress granules lacking Stau1 formed in cells depleted of this molecule, indicating that Stau1 is not an essential component of stress granules. Moreover, Stau1 knockdown facilitated stress granule formation upon stress induction. Conversely, transient transfection of Stau1 impaired stress granule formation upon stress or pharmacological initiation arrest. The inhibitory capacity of Stau1 mapped to the amino-terminal half of the molecule, a region known to bind to polysomes. We found that the fraction of polysomes remaining upon stress induction was enriched in Stau1, and that Stau1 overexpression stabilized polysomes against stress. We propose that Stau1 is involved in recovery from stress by stabilizing polysomes, thus helping stress granule dissolution.