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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 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 -
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 -
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 -
Animals : An Open Access Journal From... Jun 2022The present study aimed to investigate the quality of newly hatched broiler chicks delivered to Hong Kong (imported or local), and to develop tailored recommendations to...
The present study aimed to investigate the quality of newly hatched broiler chicks delivered to Hong Kong (imported or local), and to develop tailored recommendations to improve their management. During 2019-2021, 70 batches (34 imported from mainland China and 36 local) of one/three day old chicks on 11 broiler farms were studied. From each batch, 23 or 24 chicks (1647 in total) were assessed for abnormalities in appearance, navel, crop filling, dehydration, body weight, and length uniformity. Chicks were sacrificed, and yolk sac residues in three day old chicks were measured. Maternally derived antibody levels against Newcastle disease virus (NDV), infectious bursal disease virus (IBDV), and avian reovirus (ARV) were measured in all chicks using an enzyme-linked immunosorbent assay (ELISA). The proportion of abnormal navel in most batches is high (median: 59%), ranging between 0 and 100%. The average length of chicks within batches ranges between 16.3 and 20.7 cm, and their average weights are 31-38.5 g upon delivery to the farms. On average, imported batches have a higher body weight and length than their local counterparts. The average yolk-free weight varies between 45 and 55 g, which is significantly lower in local batches (33-43 g). The mean antibody titers against NDV and ARV are higher in imported batches than in the local ones. In contrast, the mean antibody titer against IBDV is significantly lower in the imported batches. Concerning the overall lower quality of local chicks compared to the imported batches, establishing a well-managed broiler breeder farm and a hatchery in Hong Kong is highly recommended to enhance the health and productivity of the local broiler chicken industry.
PubMed: 35739857
DOI: 10.3390/ani12121520 -
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 -
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 -
Scientific Reports Jan 2022The composition of gut bacterial communities is strongly influenced by the host diet in many animal taxa. For birds, the effect of diet on the microbiomes has been...
The composition of gut bacterial communities is strongly influenced by the host diet in many animal taxa. For birds, the effect of diet on the microbiomes has been documented through diet manipulation studies. However, for wild birds, most studies have drawn on literature-based information to decipher the dietary effects, thereby, overlooking individual variation in dietary intake. Here we examine how naturally consumed diets influence the composition of the crop and cloacal microbiomes of twenty-one tropical bird species, using visual and metabarcoding-based identification of consumed diets and bacterial 16S rRNA microbiome sequencing. We show that diet intakes vary markedly between individuals of the same species and that literature-based dietary guilds grossly underestimate intraspecific diet variability. Furthermore, despite an effect of literature-based dietary guild assignment of host taxa, the composition of natural diets does not align with crop and cloacal microbiome similarity. However, host-taxon specific gut bacterial lineages are positively correlated with specific diet items, indicating that certain microbes associate with different diet components in specific avian hosts. Consequently, microbiome composition is not congruent with the overall consumed diet composition of species, but specific components of a consumed diet lead to host-specific effects on gut bacterial taxa.
Topics: Animals; Birds; Diet; Eating; Gastrointestinal Microbiome; Microbiota; Tropical Climate
PubMed: 35027664
DOI: 10.1038/s41598-022-04808-9 -
BioMed Research International 2020Defensins are a class of antimicrobial peptides in vertebrates that function as the first line of innate immunity with potent antimicrobial and immunomodulatory...
Defensins are a class of antimicrobial peptides in vertebrates that function as the first line of innate immunity with potent antimicrobial and immunomodulatory activities. Fourteen defensins, namely, avian -defensin 1 to 14 (-14), have been identified in chickens. Before characterizing the role of s in innate immunity during the early development of chickens, we collected tissue segments from the liver, spleen, and gastrointestinal (GI) tract including the esophagus, crop, proventriculus, gizzard, duodenum, jejunum, ileum, cecum, and colon from broilers at days 1, 3, 7, 14, and 28. After RNA isolation and reverse transcription, we determined the expression levels of the 14 genes in these tissues during the first 28 days after hatching by real-time PCR. The results suggested the s were widely expressed in the chicken liver, spleen, and gastrointestinal (GI) tract. Interestingly, we did not detect expressed in the GI tract, even in the liver and spleen. Additionally, s were differentially expressed in the chicken GI tract. and were expressed most abundantly in the proximal GI tract, especially the esophagus and crop. Moreover, , , , and were expressed in an inverted-V pattern with the peak being the observed expression at days 3, 7, or 14 in the chicken spleen, esophagus, duodenum, and cecum. Other s presented biphasic or inverted-V expression patterns in different tissues. The expression levels of all detected s were strengthened after hatching rather than decreasing steadily. Therefore, s were found to be expressed widely in the chicken liver, spleen, and GI tract and their expression levels were primarily up regulated during the early development of chicken, implying the potential essential roles of s in early innate defense and infection resistance of chickens.
Topics: Aging; Animals; Chickens; Digestive System; Organ Specificity; Real-Time Polymerase Chain Reaction; Spleen; beta-Defensins
PubMed: 33490238
DOI: 10.1155/2020/2567861