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Science (New York, N.Y.) May 2021We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type...
We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. In this state, centromeres cluster together at nucleoli, and heterochromatin domains merge. We propose a physical model in which lengthwise compaction of chromosomes by condensin II during mitosis determines chromosome-scale genome architecture, with effects that are retained during the subsequent interphase. This mechanism likely has been conserved since the last common ancestor of all eukaryotes.
Topics: Adenosine Triphosphatases; Algorithms; Animals; Biological Evolution; Cell Nucleolus; Cell Nucleus; Centromere; Chromosomes; Chromosomes, Human; DNA-Binding Proteins; Eukaryota; Genome; Genome, Human; Genomics; Heterochromatin; Humans; Interphase; Mitosis; Models, Biological; Multiprotein Complexes; Telomere
PubMed: 34045355
DOI: 10.1126/science.abe2218 -
Poultry Science Sep 2018The digestive system of a chicken is simple, short, and extremely efficient. In the upper gastro-intestinal tract (GIT) or foregut, in particular when feed is not... (Review)
Review
The digestive system of a chicken is simple, short, and extremely efficient. In the upper gastro-intestinal tract (GIT) or foregut, in particular when feed is not continuously available, moistening of feed occurs in the crop followed by chemical and physical digestion in the proventriculus and gizzard, respectively, as a preparation for nutrient absorption which occurs in the distal portions of the GIT-duodenum, jejunum, ileum, and to a lower extent in the ceca and colon. Broiler husbandry practices in the past have focused on achieving high intakes of readily digestible nutrients and largely failed to consider the ancestral purpose of the foregut. Besides holding important digestive functions, the rich bacterial communities in both the crop and the gizzard transform these organs in barriers preventing the invasion of the GIT by pathogens. However, the amount of time feed spends in the foregut-and therefore the environment in this gut segment-is extremely variable and can be manipulated by different feeding practices, such as feed structure and composition, frequency of feeding, and/or light regimes.With further progress in terms of performance and health of broiler chickens being sought, and following decades of research focusing on distal GIT segments, it is about time to explore how the foregut can contribute to achieve these goals. This review revisits morphological, physiological, and microbiological characteristics of the foregut; explores the importance of this GIT portion as feed intake regulator; and discusses how husbandry and feeding practices such as lighting regimes and feed structure may be adapted to activate the crop and the gizzard, which results in performance and health improvements. Finally, interactions of these feeding practices with exogenous enzymes are discussed and suggestions for further research are made.
Topics: Animal Feed; Animal Husbandry; Animals; Chickens; Gizzard, Avian; Proventriculus
PubMed: 29893913
DOI: 10.3382/ps/pey191 -
Frontiers in Plant Science 2015Bacillus thuringiensis (Bt) microbial pesticides have a 50-year history of safety in agriculture. Cry proteins are among the active insecticidal ingredients in these... (Review)
Review
Bacillus thuringiensis (Bt) microbial pesticides have a 50-year history of safety in agriculture. Cry proteins are among the active insecticidal ingredients in these pesticides, and genes coding for Cry proteins have been introduced into agricultural crops using modern biotechnology. The Cry gene sequences are often modified to enable effective expression in planta and several Cry proteins have been modified to increase biological activity against the target pest(s). Additionally, the domains of different but structurally conserved Cry proteins can be combined to produce chimeric proteins with enhanced insecticidal properties. Environmental studies are performed and include invertebrates, mammals, and avian species. Mammalian studies used to support the food and feed safety assessment are also used to support the wild mammal assessment. In addition to the NTO assessment, the environmental assessment includes a comparative assessment between the Bt crop and the appropriate conventional control that is genetically similar but lacks the introduced trait to address unintended effects. Specific phenotypic, agronomic, and ecological characteristics are measured in the Bt crop and the conventional control to evaluate whether the introduction of the insect resistance has resulted in any changes that might cause ecological harm in terms of altered weed characteristics, susceptibility to pests, or adverse environmental impact. Additionally, environmental interaction data are collected in field experiments for Bt crop to evaluate potential adverse effects. Further to the agronomic and phenotypic evaluation, potential movement of transgenes from a genetically modified crop plants into wild relatives is assessed for a new pest resistance gene in a new crop. This review summarizes the evidence for safety of crops containing Cry proteins for humans, livestock, and other non-target organisms.
PubMed: 25972882
DOI: 10.3389/fpls.2015.00283 -
Frontiers in Physiology 2020There are marked differences between the physiology of birds and mammals. These reflect the evolutionary distance between the two classes with the last common ancestor... (Review)
Review
There are marked differences between the physiology of birds and mammals. These reflect the evolutionary distance between the two classes with the last common ancestor estimated as existing 318 million years ago. There are analogous organ systems in birds and mammals. However, marked differences exist. For instance, in the avian gastro-intestinal tract, there is a crop at the lower end of the esophagus. This functions both to store feed and for microbial action. The avian immune system lacks lymph nodes and has a distinct organ producing B-lymphocytes, namely the bursa . The important of spleen has been largely dismissed until recently. However, its importance in both innate and specific immunity is increasingly recognized. There is a major difference between birds and mammals is the female reproductive system as birds produce large yolk filled eggs. The precursors of the yolk are synthesized by the liver. Another difference is that there is a single ovary and oviduct in birds.
PubMed: 33240094
DOI: 10.3389/fphys.2020.542466 -
Revue Scientifique Et Technique... Aug 2008This paper discusses impacts of climate change on the ecology of avian influenza viruses (AI viruses), which presumably co-evolved with migratory water birds, with virus... (Review)
Review
This paper discusses impacts of climate change on the ecology of avian influenza viruses (AI viruses), which presumably co-evolved with migratory water birds, with virus also persisting outside the host in subarctic water bodies. Climate change would almost certainly alter bird migration, influence the AI virus transmission cycle and directly affect virus survival outside the host. The joint, net effects of these changes are rather unpredictable, but it is likely that AI virus circulation in water bird populations will continue with endless adaptation and evolution. In domestic poultry, too little is known about the direct effect of environmental factors on highly pathogenic avian influenza transmission and persistence to allow inference about the possible effect of climate change. However, possible indirect links through changes in the distribution of duck-crop farming are discussed.
Topics: Adaptation, Physiological; Animal Migration; Animals; Animals, Domestic; Animals, Wild; Birds; Greenhouse Effect; Influenza A virus; Influenza in Birds
PubMed: 18819672
DOI: No ID Found -
General and Comparative Endocrinology Jan 2022During breeding, multiple circulating hormones, including prolactin, facilitate reproductive transitions in species that exhibit parental care. Prolactin underlies...
During breeding, multiple circulating hormones, including prolactin, facilitate reproductive transitions in species that exhibit parental care. Prolactin underlies parental behaviors and related physiological changes across many vertebrates, including birds and mammals. While circulating prolactin levels often fluctuate across breeding, less is known about how relevant target tissues vary in their prolactin responsiveness via prolactin receptor (PRLR) expression. Recent studies have also investigated prolactin (PRL) gene expression outside of the pituitary (i.e., extra-pituitary PRL), but how PRL gene expression varies during parental care in non-pituitary tissue (e.g., hypothalamus, gonads) remains largely unknown. Further, it is unclear if and how tissue-specific PRL and PRLR vary between the sexes during biparental care. To address this, we measured PRL and PRLR gene expression in tissues relevant to parental care, the endocrine reproductive hypothalamic-pituitary- gonadal (HPG) axis and the crop (a tissue with a similar function as the mammalian mammary gland), across various reproductive stages in both sexes of a biparental bird, the rock dove (Columba livia). We also assessed how these genes responded to changes in offspring presence by adding chicks mid-incubation, simulating an early hatch when prolactin levels were still moderately low. We found that pituitary PRL expression showed similar increases as plasma prolactin levels, and detected extra-pituitary PRL in the hypothalamus, gonads and crop. Hypothalamic and gonadal PRLR expression also changed as birds began incubation. Crop PRLR expression correlated with plasma prolactin, peaking when chicks hatched. In response to replacing eggs with a novel chick mid-incubation, hypothalamic and gonadal PRL and PRLR gene expression differed significantly compared to mid-incubation controls, even when plasma prolactin levels did not differ. We also found sex differences in PRL and PRLR that suggest gene expression may allow males to compensate for lower levels in prolactin by upregulating PRLR in all tissues. Overall, this study advances our understanding of how tissue-specific changes in responsiveness to parental hormones may differ across key reproductive transitions, in response to offspring cues, and between the sexes.
Topics: Animals; Columbidae; Crop, Avian; Female; Gene Expression; Hypothalamo-Hypophyseal System; Male; Pituitary Gland; Pituitary-Adrenal System; Prolactin; Receptors, Prolactin
PubMed: 34756919
DOI: 10.1016/j.ygcen.2021.113940 -
A generic avian physiologically-based kinetic (PBK) model and its application in three bird species.Environment International Nov 2022Physiologically-based kinetic (PBK) models are effective tools for designing toxicological studies and conducting extrapolations to inform hazard characterization in...
Physiologically-based kinetic (PBK) models are effective tools for designing toxicological studies and conducting extrapolations to inform hazard characterization in risk assessment by filling data gaps and defining safe levels of chemicals. In the present work, a generic avian PBK model for male and female birds was developed using PK-Sim and MoBi from the Open Systems Pharmacology Suite (OSPS). The PBK model includes an ovulation model (egg development) to predict concentrations of chemicals in eggs from dietary exposure. The model was parametrized for chicken (Gallus gallus), bobwhite quail (Colinus virginianus) and mallard duck (Anas platyrhynchos) and was tested with nine chemicals for which in vivo studies were available. Time-concentration profiles of chemicals reaching tissues and egg compartment were simulated and compared to in vivo data. The overall accuracy of the PBK model predictions across the analyzed chemicals was good. Model simulations were found to be in the range of 22-79% within a 3-fold and 41-89% were within 10- fold deviation of the in vivo observed data. However, for some compounds scarcity of in-vivo data and inconsistencies between published studies allowed only a limited goodness of fit evaluation. The generic avian PBK model was developed following a "best practice" workflow describing how to build a PBK model for novel species. The credibility and reproducibility of the avian PBK models were scored by evaluation according to the available guidance documents from WHO (2010), and OECD (2021), to increase applicability, confidence and acceptance of these in silico models in chemical risk assessment.
Topics: Animals; Chickens; Computer Simulation; Ducks; Female; Kinetics; Male; Models, Biological; Reproducibility of Results
PubMed: 36179644
DOI: 10.1016/j.envint.2022.107547 -
PloS One 2019Birds are essential components of most ecosystems and provide many services valued by society. However, many populations have undergone striking declines as their...
Birds are essential components of most ecosystems and provide many services valued by society. However, many populations have undergone striking declines as their habitats have been lost or degraded by human activities. Terrestrial grasslands are vital habitat for birds in the North American Prairie Pothole Region (PPR), but grassland conversion and fragmentation from agriculture and energy-production activities have destroyed or degraded millions of hectares. Conservation grasslands can provide alternate habitat. In the United States, the Conservation Reserve Program (CRP) is the largest program maintaining conservation grasslands on agricultural lands, but conservation grasslands in the PPR have declined by over 1 million ha since the program's zenith in 2007. We used an ecosystem-services model (InVEST) parameterized for the PPR to quantify grassland-bird habitat remaining in 2014 and to assess the degradation status of the remaining grassland-bird habitat as influenced by crop and energy (i.e., oil, natural gas, and wind) production. We compared our resultant habitat-quality ratings to grassland-bird abundance data from the North American Breeding Bird Survey to confirm that ratings were related to grassland-bird abundance. Of the grassland-bird habitat remaining in 2014, about 19% was degraded by crop production that occurred within 0.1 km of grassland habitats, whereas energy production degraded an additional 16%. We further quantified the changes in availability of grassland-bird habitat under various land-cover scenarios representing incremental losses (10%, 25%, 50%, 75%, and 100%) of CRP grasslands from 2014 levels. Our model identified 1 million ha (9%) of remaining grassland-bird habitat in the PPR that would be lost or degraded if all CRP conservation grasslands were returned to crop production. Grassland regions world-wide face similar challenges in maintaining avian habitat in the face of increasing commodity and energy production to sate the food and energy needs of a growing world population. Identifying ways to model the impacts of the tradeoff between food and energy production and wildlife production is an important step in creating solutions.
Topics: Animals; Birds; Crop Production; Grassland; Humans; Models, Biological; Population Dynamics; United States
PubMed: 30625148
DOI: 10.1371/journal.pone.0198382 -
Frontiers in Physiology 2022Physiologically based kinetic (PBK) models facilitate chemical risk assessment by predicting exposure while reducing the need for animal testing. PBK models for mammals...
Physiologically based kinetic (PBK) models facilitate chemical risk assessment by predicting exposure while reducing the need for animal testing. PBK models for mammals have seen significant progress, which has yet to be achieved for avian systems. Here, we quantitatively compare physiological, metabolic and anatomical characteristics between birds and mammals, with the aim of facilitating bird PBK model development. For some characteristics, there is considerable complementarity between avian and mammalian species with identical values for the following: blood hemoglobin and hemoglobin concentrations per unit erythrocyte volume together with relative weights of the liver, heart, and lungs. There are also systematic differences for some major characteristics between avian and mammalian species including erythrocyte volume, plasma concentrations of albumin, total protein and triglyceride together with liver cell size and relative weights of the kidney, spleen, and ovary. There are also major differences between characteristics between sexually mature and sexually immature female birds. For example, the relative weights of the ovary and oviduct are greater in sexually mature females compared to immature birds as are the plasma concentrations of triglyceride and vitellogenin. Both these sets of differences reflect the genetic "blue print" inherited from ancestral archosaurs such as the production of large eggs with yolk filled oocytes surrounded by egg white proteins, membranes and a calciferous shell together with adaptions for flight in birds or ancestrally in flightless birds.
PubMed: 35450159
DOI: 10.3389/fphys.2022.858386 -
Vaccines Mar 2022Viral diseases, including avian influenza (AI) and Newcastle disease (ND), are an important cause of morbidity and mortality in poultry, resulting in significant... (Review)
Review
Viral diseases, including avian influenza (AI) and Newcastle disease (ND), are an important cause of morbidity and mortality in poultry, resulting in significant economic losses. Despite the availability of commercial vaccines for the major viral diseases of poultry, these diseases continue to pose a significant risk to global food security. There are multiple factors for this: vaccine costs may be prohibitive, cold chain storage for attenuated live-virus vaccines may not be achievable, and commercial vaccines may protect poorly against local emerging strains. The development of transient gene expression systems in plants provides a versatile and robust tool to generate a high yield of recombinant proteins with superior speed while managing to achieve cost-efficient production. Plant-derived vaccines offer good stability and safety these include both subunit and virus-like particle (VLP) vaccines. VLPs offer potential benefits compared to currently available traditional vaccines, including significant reductions in virus shedding and the ability to differentiate between infected and vaccinated birds (DIVA). This review discusses the current state of plant-based vaccines for prevention of the AI and ND in poultry, challenges in their development, and potential for expanding their use in low- and middle-income countries.
PubMed: 35335110
DOI: 10.3390/vaccines10030478