Microbiome analyses of poultry feeds: Part II. Comparison of different poultry feeds.

Within the realm of poultry feed mill operations, the persistent concern over microbial feed quality necessitates the establishment of a robust baseline for enhancing and sustaining the standards of commercial feeds. This dual-phase investigation, comprising Parts I, was previously published, and the current study presented here as Part II aimed to illuminate this baseline using 16S rRNA gene sequencing. In Part II, nine distinct commercial poultry feeds formulated as starters, growers, starter/growers, or supplements, the selected feeds underwent genomic DNA extraction, amplification with custom dual-indexed primers, and subsequent Illumina MiSeq sequencing. Through data analysis in QIIME2-2021.4 and R Studio, the study unveils alpha (Kruskal-Wallis) and beta (ANOSIM) diversity, taxonomic differences (ANCOM), and core microbiomes (core_members), deeming main and pairwise effects statistically significant at p < 0.05 and Q < 0.05. Notably, the investigation identified 30% common core microbial members across the nine feed types, shedding light on potential foodborne poultry pathogens such as Helicobacter and Campylobacter. Probiotic-associated feeds exhibited distinct microbial communities, emphasizing the need to explore their impact on the early poultry gastrointestinal tract (GIT) further.

Microbiome analyses of poultry feeds: Part I. Comparison of five different DNA extraction methods.

Given extensive variability in feed composition, the absence of a dedicated DNA extraction kit for poultry feed underscores the need for an optimized extraction technique for reliable downstream sequencing analyses. This study investigates the impact of five DNA extraction techniques: Qiagen QIAamp DNA Stool Mini Kit (Qiagen), modified Qiagen with Lysing Matrix B (MQ), modified Qiagen with celite purification (MQC), polyethylene glycol (PEG), and 1-Day Direct. Genomic DNA amplification and Illumina MiSeq sequencing were conducted. QIIME2-2021.4 facilitated data analysis, revealing significant diversity and compositional differences influenced by extraction methods. Qiagen exhibited lower evenness and richness compared to other methods. 1-Day Direct and PEG enhanced bacterial diversities by employing bead beating and lysozyme. Despite similar taxonomic resolution, the Qiagen kit provides a rapid, consistent method for assessing poultry feed microbiomes. Modified techniques (MQ and MQC) improve DNA purification, reducing bias in commercial poultry feed samples. PEG and 1-Day Direct methods were effective but may require standardization. Overall, this study underscores the importance of optimized extraction techniques in poultry feed analysis, with potential implications for future standardization of effective methods.

Rotating night shift work and menopausal age.

STUDY QUESTION: How are rotating night shift schedules associated with age at menopause among a large, national cohort of shift working nurses? SUMMARY ANSWER: Our findings suggest that working rotating night shifts with sufficient frequency may modestly accelerate reproductive senescence among women who may already be predisposed to earlier menopause. WHAT IS KNOWN ALREADY: Younger age at menopause has been associated with increased risk of adverse health outcomes, particularly those linked to reproduction. Night work has been associated with reproductive dysfunction, including disruption of menstrual cycle patterns. STUDY DESIGN, SIZE, DURATION: This cohort study was conducted among 80 840 women of the Nurses' Health Study 2 (NHS2), with prospective follow-up from 1991 through 2013. Loss-to-follow-up of the NHS2 is estimated to be <10%. PARTICIPANTS/MATERIALS, SETTING, METHODS: We assessed the association between cumulative and current rotating night shift work and age at natural menopause over 22 years of follow-up (1991-2013). Cox proportional hazards models were used to estimate hazard ratios (HR) for menopause, adjusted for age, smoking status, body mass index, physical activity, alcohol consumption, reproductive factors and exogenous hormone use. MAIN RESULTS AND THE ROLE OF CHANCE: Over follow-up, 27 456 women (34%) reached natural menopause. Women who worked 20 or more months of rotating night shifts in the prior 2-year had an increased risk of earlier menopause (multivariable-adjusted (MV)-HR = 1.09, 95% CI: 1.02-1.16) compared to women without rotating night shift work. This risk was stronger among women undergoing menopause or otherwise censored under age 45 years (MV-HR = 1.25, 95% CI: 1.08-1.46), than it was for those continuing in the study when >45 years old (MV-HR = 1.05, 95% CI: 0.99-1.13). Working 10 or more years of cumulative rotating night work was also associated with higher risk of menopause among women reaching menopause under age 45 (MV-HR10-19 years = 1.22, 95% CI: 1.03-1.44; MV-HR≥20 years = 1.73, 95% CI: 0.90-3.35), though not over the age of 45 years (MV-HR10-19 years = 1.04, 95% CI: 0.99-1.10; MV-HR≥20 years = 1.01, 95% CI: 0.89-1.15). LIMITATIONS, REASONS FOR CAUTION: The degree to which observed effects of rotating night shifts on age at natural menopause are due to circadian disruption, rather than fatigue and stress associated with working more demanding schedules, is uncertain due to potential residual confounding by these factors. WIDER IMPLICATIONS OF THE FINDINGS: This is the first study to assess the effects of night work on menopausal timing among a larger national cohort of shift working women. Women already prone to earlier menopause may further truncate their reproductive lifetime by working schedules comprising day as well as night shifts. STUDY FUNDING/COMPETING INTEREST(S): This study was supported by Center for Disease Control and Prevention/The National Institute for Occupational Safety and Health Grant 5R01OH009803 (PI: Schernhammer E), as well as UM1 CA176726 from the National Institute of Health. The funding sources had no role in the design and conduct of the study; collection, management, analysis and interpretation of the data; preparation, review or approval of the article; and decision to submit the article for publication. The authors have no conflicts of interest.

Multiple Structural Transitions in Langmuir Monolayers of Charged Soft-Shell Nanoparticles.

We have investigated the morphologies of Langmuir layers of charged, polymeric hard-core/interlayer/soft-shell nanoparticles spread at the air-water interface. Depending on various mutual interactions, which are correlated to the areal densities of the deposited nanoparticles, we observed ordered patterns of nondense and closed-packed arrangements of core/interlayer/shell (CIS) nanoparticle ordering. At low areal densities, we found an almost regular distribution of the charged CIS nanoparticles on the water surface, which resulted from long-range repulsive electrostatic interactions between them. At higher areal densities, domains of more closely packed and ordered nanoparticles were formed, coexisting with regions of randomly and sparsely distributed nanoparticles. We relate these domains to the interplay of electrostatic repulsion and capillary attraction caused by the dipolar character of like-charged particles at the interface, allowing for a characteristic separation distance between nanoparticles of about 3-4 times the nanoparticle diameter. At relatively high areal densities, attractive van der Waals forces were finally capable of making nanoparticles to come in contact with each other, leading to densely packed patches of hexagonally ordered nanoparticles coexisting with regions of rather well-ordered nanoparticles separated by about 1 µm and regions of randomly and sparsely distributed nanoparticles. Intriguingly, upon re-expansion of the area available per nanoparticle, these densely packed patches disappeared, indicating that steric repulsion due to the presence of soft shells as well as long-range electrostatic repulsive forces were strong enough to assure reversibility of the morphological behavior.

A centrally generated primary care physician audit report does not improve colonoscopy uptake after a positive result on a fecal occult blood test in Ontario's ColonCancerCheck program.

BACKGROUND: Timely follow-up of fecal occult blood screening with colonoscopy is essential for achieving colorectal cancer mortality reduction. In the present study, we evaluated the effectiveness of centrally generated, physician-targeted audit and feedback to improve colonoscopy uptake after a positive fecal occult blood test (fobt) result within Ontario's population-wide ColonCancerCheck Program. METHODS: This prospective cohort study used data sets from Ontario's ColonCancerCheck Program (2008-2011) that were linked to provincial administrative health databases. Cox proportional hazards regression was used to estimate the effect of centralized, physician-targeted audit and feedback on colonoscopy uptake in an Ontario-wide fobt-positive cohort. RESULTS: A mailed physician audit and feedback report identifying individuals outstanding for colonoscopy for 3 or more months after a positive fobt result did not increase the likelihood of colonoscopy uptake (hazard ratio: 0.95; 95% confidence interval: 0.79 to 1.13). Duration of positive fobt status was strongly inversely associated with the hazard of follow-up colonoscopy (p for linear trend: <0.001). CONCLUSIONS: In a large population-wide setting, centralized tracking in the form of physician-targeted mailed audit and feedback reports does not improve colonoscopy uptake for screening participants with a positive fobt result outstanding for 3 or more months. Mailed physician-targeted screening audit and feedback reports alone are unlikely to improve compliance with follow-up colonoscopy in Ontario. Other interventions such as physician audits or automatic referrals, demonstrated to be effective in other jurisdictions, might be warranted.

Evolution of cellular structures during Ge 1-x Si x single-crystal growth by means of a modified phase-field method.

We have studied the evolution of cellular structures in Ge 1-x Si x single-crystal growth as a function of process parameters. Because these structures are much larger than those occurring during the solidification of metals, we developed a modified phase-field method, which is able to handle these structure within reasonable computer times using the real material parameters. The model has been tested for computing equilibrium shapes of crystals, dendritic growth, and cellular growth of Ni x Cu 1-x. We also performed classical molecular dynamics calculations in order to compute the diffusion coefficients of Si and Ge in melts of various compositions.

Expression of Dlx genes during the development of the zebrafish pharyngeal dentition: evolutionary implications.

In order to investigate similarities and differences in genetic control of development among teeth within and between species, we determined the expression pattern of all eight Dlx genes of the zebrafish during development of the pharyngeal dentition and compared these data with that reported for mouse molar tooth development. We found that (i) dlx1a and dlx6a are not expressed in teeth, in contrast to their murine orthologs, Dlx1 and Dlx6; (ii) the expression of the six other zebrafish Dlx genes overlaps in time and space, particularly during early morphogenesis; (iii) teeth in different locations and generations within the zebrafish dentition differ in the number of genes expressed; (iv) expression similarities and differences between zebrafish Dlx genes do not clearly follow phylogenetic and linkage relationships; and (v) similarities and differences exist in the expression of zebrafish and mouse Dlx orthologs. Taken together, these results indicate that the Dlx gene family, despite having been involved in vertebrate tooth development for over 400 million years, has undergone extensive diversification of expression of individual genes both within and between dentitions. The latter type of difference may reflect the highly specialized dentition of the mouse relative to that of the zebrafish, and/or genome duplication in the zebrafish lineage facilitating a redistribution of Dlx gene function during odontogenesis.

Peroxisome proliferator-activated receptor and farnesoid X receptor ligands differentially regulate sebaceous differentiation in human sebaceous gland organ cultures in vitro.

BACKGROUND: Nuclear hormone receptors are important in the regulation of epidermal differentiation and have been implicated in lipid metabolism. In particular, there is evidence suggesting that the activation of peroxisome proliferator-activated receptors (PPARs) is an important factor in the regulation of sebocyte lipogenesis. OBJECTIVES: To determine the role of PPARs, farnesoid X receptor (FXR) and other orphan nuclear hormone receptors in sebaceous gland function in vitro by investigating the biochemical effects of appropriate ligands, and by establishing the RNA and protein expression patterns of a number of nuclear receptors in sebaceous glands ex vivo. METHODS: Human chest sebaceous glands were maintained in vitro as freshly isolated and as 7-day cultured whole organs. We then studied the effects of appropriate ligands on the glandular rates of lipogenesis and DNA synthesis, as well as determining the mRNA (reverse transcription-polymerase chain reaction) and protein expression patterns (immunohistochemistry/immunoblotting) of the nuclear hormone receptors of interest. RESULTS: PPAR ligands, but not FXR ligands, inhibited sebaceous lipogenesis, in particular the PPARalpha ligands LY 171883 and WY 14643, and the PPARgamma ligands BRL 49653 and 15-deoxy-Delta-12,14-prostaglandin J(2). We detected RNA expression of PPARalpha, PPARbeta, PPARgamma, retinoid X receptor alpha, liver X receptor alpha (LXRalpha) and pregnane X receptor but not FXR in freshly isolated and 7-day maintained sebaceous glands. PPARalpha, PPARbeta, PPARgamma and LXRalpha protein were detected in nuclear extracts of sebaceous glands. CONCLUSIONS: We conclude that activation of nuclear hormone receptors, in particular activation of PPARalpha and PPARgamma, can regulate lipogenesis in human sebaceous glands. As suppression of sebum secretion is associated with reduced acne activity, the nuclear hormone receptors involved may open new avenues in the development of novel acne treatments.

The implications of subspecialisation on the management and outcome of surgery for rectal carcinoma.

BACKGROUND: The management of rectal carcinoma has changed significantly over the last decade. We studied the changing trends in the management of rectal carcinoma over a 7-year period in a district general hospital. METHODS: A retrospective analysis of all patients with histologically proven rectal adenocarcinoma who underwent operative treatment between January 1991 and December 1997 was performed. The type of operative procedure, local recurrence rate and completeness of pathology reporting was documented. RESULTS: There were 200 operative procedures: 102 anterior resections (AR), and 98 abdominoperineal resections (APR). This included 17 palliative resections because of metastatic disease (n = 8) or extensive local invasion (n = 7) or both (n = 2). The APR rate steadily declined from 72% in 1991 to 19% in 1997 (p < 0.005). Subspecialist 'colorectal' surgeons performed only 24% of the operations in 1991 but the figure for 1997 was 85% (p < 0.01). No circumferential resection margin was reported in 1991 but was reported in 85% of the cases in 1997 (p < 0.001). There was a steady increase in stapled anastomoses from 43% in 1991 to 93% in 1997 (p < 0.03). There were 15 local recurrences following 'curative' resection; 7 following APR and 8 following AR (n.s.). CONCLUSION: There was a significant increase in the rate of restorative resection of rectal cancer with a concomitant reduction in permanent stoma formation; this may be attributed to an increase in subspecialisation. Despite this, a low rate of local recurrence was maintained throughout the study period.

Electromyography and computed tomography scan-guided fine needle aspiration biopsy of discrete extraocular muscle metastases.

Discrete or isolated metastasis to the extraocular muscles without an accompanying intraconal or extraconal mass is rare. Although it is estimated that 5% of orbital metastasis involves extraocular muscles only, to our knowledge there are no reports of discrete extraocular muscle involvement from renal cell carcinoma. With discrete extraocular muscle involvement, accurate localization within the infiltrated region of the muscle is of paramount importance in achieving a safe and positive biopsy. We describe a case with discrete extraocular muscle metastasis from a renal cell carcinoma, where a novel technique of FNAB (fine needle aspiration biopsy) of the medial rectus was undertaken, with EMG (electromyography) control and CT (computerized tomography) scan guidance.

The genetic basis of modularity in the development and evolution of the vertebrate dentition.

The construction of organisms from units that develop under semi-autonomous genetic control (modules) has been proposed to be an important component of their ability to undergo adaptive phenotypic evolution. The organization of the vertebrate dentition as a system of repeated parts provides an opportunity to study the extent to which phenotypic modules, identified by their evolutionary independence from other such units, are related to modularity in the genetic control of development. The evolutionary history of vertebrates provides numerous examples of both correlated and independent evolution of groups of teeth. The dentition itself appears to be a module of the dermal exoskeleton, from which it has long been under independent genetic control. Region-specific tooth loss has been a common trend in vertebrate evolution. Novel deployment of teeth and reacquisition of lost teeth have also occurred, although less frequently. Tooth shape differences within the dentition may be discontinuous (referred to as heterodonty) or graded. The occurrence of homeotic changes in tooth shape provides evidence for the decoupling of tooth shape and location in the course of evolution. Potential mechanisms for region-specific evolutionary tooth loss are suggested by a number of mouse gene knockouts and human genetic dental anomalies, as well as a comparison between fully-developed and rudimentary teeth in the dentition of rodents. These mechanisms include loss of a tooth-type-specific initiation signal, alterations of the relative strength of inductive and inhibitory signals acting at the time of tooth initiation and the overall reduction in levels of proteins required for the development of all teeth. Ectopic expression of tooth initiation signals provides a potential mechanism for the novel deployment or reacquisition of teeth; a single instance is known of a gene whose ectopic expression in transgenic mice can lead to ectopic teeth. Differences in shape between incisor and molar teeth in the mouse have been proposed to be controlled by the region-specific expression of signalling molecules in the oral epithelium. These molecules induce the expression of transcription factors in the underlying jaw mesenchyme that may act as selectors of tooth type. It is speculated that shifts in the expression domains of the epithelial signalling molecules might be responsible for homeotic changes in tooth shape. The observation that these molecules are regionally restricted in the chicken, whose ancestors were not heterodont, suggests that mammalian heterodonty may have evolved through the use of patterning mechanisms already acting on skeletal elements of the jaws. In general, genetic and morphological approaches identify similar types of modules in the dentition, but the data are not yet sufficient to identify exact correspondences. It is speculated that modularity may be achieved by gene expression differences between teeth or by differences in the time of their development, causing mutations to have cumulative effects on later-developing teeth. The mammalian dentition, for which virtually all of the available developmental genetic data have been collected, represents a small subset of the dental diversity present in vertebrates as a whole. In particular, teleost fishes may have a much more extensive dentition. Extension of research on the genetic control of tooth development to this and other vertebrate groups has great potential to further the understanding of modularity in the dentition.

The rotary mechanism of ATP synthase.

Since the chemiosmotic theory was proposed by Peter Mitchell in the 1960s, a major objective has been to elucidate the mechanism of coupling of the transmembrane proton motive force, created by respiration or photosynthesis, to the synthesis of ATP from ADP and inorganic phosphate. Recently, significant progress has been made towards establishing the complete structure of ATP synthase and revealing its mechanism. The X-ray structure of the F(1) catalytic domain has been completed and an electron density map of the F(1)-c(10) subcomplex has provided a glimpse of the motor in the membrane domain. Direct microscopic observation of rotation has been extended to F(1)-ATPase and F(1)F(o)-ATPase complexes.

Consistency in the observation of features used to classify duct carcinoma in situ (DCIS) of the breast.

AIM: To determine interobserver and intra-observer agreement in the assessment of cytological grade and intraduct necrosis in pure duct carcinoma in situ (DCIS) of the breast. METHODS: Sixty unselected cases with illustrated diagnostic criteria were circulated to 19 practising histopathologists. RESULTS: Overall agreement was moderate for cytological grade in three categories: 71% agreement; weighted kappa (kappa w), 0.36; intraduct necrosis in three categories (absent, present, extensive): 76% agreement; kappa w, 0.57; and the Van Nuys classification system: 73% agreement; kappa w, 0.48. Agreement was no better among observers participating in the National External Quality Assurance Programme. Intra-observer agreement for cytological assessment (69.6% agreement; kappa w, 0.52) and intraduct necrosis (68.3% agreement; kappa w, 0.48) was moderate, suggesting that individual variation rather than precision of criteria contributes to the lack of agreement. CONCLUSIONS: Moderate agreement on observations can be achieved by non-specialist pathologists, with better agreement on necrosis than cytological grade. There was evidence of consistent individual bias towards over or under scoring cytological grade, which could be corrected with adequate and prompt feedback.

In vitro resistance profile of the human immunodeficiency virus type 1 protease inhibitor BMS-232632.

BMS-232632 is an azapeptide human immunodeficiency virus (HIV) type 1 (HIV-1) protease inhibitor that displays potent anti-HIV-1 activity (50% effective concentration [EC(50)], 2.6 to 5.3 nM; EC(90), 9 to 15 nM). In vitro passage of HIV-1 RF in the presence of inhibitors showed that BMS-232632 selected for resistant variants more slowly than nelfinavir or ritonavir did. Genotypic and phenotypic analysis of three different HIV strains resistant to BMS-232632 indicated that an N88S substitution in the viral protease appeared first during the selection process in two of the three strains. An I84V change appeared to be an important substitution in the third strain used. Mutations were also observed at the protease cleavage sites following drug selection. The evolution to resistance seemed distinct for each of the three strains used, suggesting multiple pathways to resistance and the importance of the viral genetic background. A cross-resistance study involving five other protease inhibitors indicated that BMS-232632-resistant virus remained sensitive to saquinavir, while it showed various levels (0. 1- to 71-fold decrease in sensitivity)-of cross-resistance to nelfinavir, indinavir, ritonavir, and amprenavir. In reciprocal experiments, the BMS-232632 susceptibility of HIV-1 variants selected in the presence of each of the other HIV-1 protease inhibitors showed that the nelfinavir-, saquinavir-, and amprenavir-resistant strains of HIV-1 remained sensitive to BMS-232632, while indinavir- and ritonavir-resistant viruses displayed six- to ninefold changes in BMS-232632 sensitivity. Taken together, our data suggest that BMS-232632 may be a valuable protease inhibitor for use in combination therapy.

BMS-232632, a highly potent human immunodeficiency virus protease inhibitor that can be used in combination with other available antiretroviral agents.

BMS-232632 is an azapeptide human immunodeficiency virus type 1 (HIV-1) protease (Prt) inhibitor that exhibits potent anti-HIV activity with a 50% effective concentration (EC(50)) of 2.6 to 5.3 nM and an EC(90) of 9 to 15 nM in cell culture. Proof-of-principle studies indicate that BMS-232632 blocks the cleavage of viral precursor proteins in HIV-infected cells, proving that it functions as an HIV Prt inhibitor. Comparative studies showed that BMS-232632 is generally more potent than the five currently approved HIV-1 Prt inhibitors. Furthermore, BMS-232632 is highly selective for HIV-1 Prt and exhibits cytotoxicity only at concentrations 6,500- to 23, 000-fold higher than that required for anti-HIV activity. To assess the potential of this inhibitor when used in combination with other antiretrovirals, BMS-232632 was evaluated for anti-HIV activity in two-drug combination studies. Combinations of BMS-232632 with either stavudine, didanosine, lamivudine, zidovudine, nelfinavir, indinavir, ritonavir, saquinavir, or amprenavir in HIV-infected peripheral blood mononuclear cells yielded additive to moderately synergistic antiviral effects. Importantly, combinations of drug pairs did not result in antagonistic anti-HIV activity or enhanced cytotoxic effects at the highest concentrations used for antiviral evaluation. Our results suggest that BMS-232632 may be an effective HIV-1 inhibitor that may be utilized in a variety of different drug combinations.

4-Thiazolidinones: novel inhibitors of the bacterial enzyme MurB.

4-Thiazolidinones were synthesized and evaluated for their ability to inhibit the bacterial enzyme MurB. Selected 4-thiazolidinones displayed activity against the enzyme in vitro. This activity, coupled with the design principles of the thiazolidinones, supports the postulate that 4-thiazolidinones may be recognized as diphosphate mimics by a biological selector.

Expression of Dlx genes during the development of the murine dentition.

The mammalian Dlx homeobox gene family has been shown to play multiple roles in tooth development, but a detailed comparison of the expression pattern of all members throughout tooth development has been lacking. We provide such an analysis for the six known murine Dlx genes. The expression patterns for these genes allow a refinement of previously proposed models for the role of Dlx genes in tooth type specification and raise the possibility of roles for subsets of these genes in tooth initiation, morphogenesis (enamel navel formation, enamel knot induction, cervical loop growth), and enamel formation. The relationship of Dlx gene expression to their genomic organization suggests coordinate regulation of linked genes at early stages but regulatory differences at later stages.

Molecular architecture of the rotary motor in ATP synthase.

Adenosine triphosphate (ATP) synthase contains a rotary motor involved in biological energy conversion. Its membrane-embedded F0 sector has a rotation generator fueled by the proton-motive force, which provides the energy required for the synthesis of ATP by the F1 domain. An electron density map obtained from crystals of a subcomplex of yeast mitochondrial ATP synthase shows a ring of 10 c subunits. Each c subunit forms an alpha-helical hairpin. The interhelical loops of six to seven of the c subunits are in close contact with the gamma and delta subunits of the central stalk. The extensive contact between the c ring and the stalk suggests that they may rotate as an ensemble during catalysis.